bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomics revealed differential regulation of defense related genes in Brassica juncea leading to successful and unsuccessful infestation by aphid species
Authors: Duhlian Lianthanzauva , Koramutla Murali Krishna , Subramanian S. , Chamola Rohit , Bhattacharya Ramcharan 
Published: June 2020

AbstractProductivity of Indian mustard (B. juncea), a major oil yielding crop in rapeseed-mustard group is heavily inflicted by mustard aphid,L. erysimi. Mustard aphid, a specialist aphid species on rapeseed-mustard crops, rapidly multiplies and colonizes the plants leading to successful infestation. In contrary, legume specific cowpea aphid,A. craccivorawhen released onB. junceaplants fails to build up population and thus remains unsuccessful in infestation. In the present study, differential host response ofB. junceato the two aphid species, one being successful insect-pest and the other being unsuccessful on it has been studied based on transcriptome analysis. Differential feeding efficiency of the two aphid species on mustard plants was evident from the amount of secreted honeydews. Leaf-transcriptomes of healthy and infested plants, treated with the two aphid species, were generated by RNA sequencing on Illumina platform andde novoassembly of the quality reads. A comparative assessment of the differentially expressed genes due to treatments revealed a large extent of overlaps as well as distinctness with respect to the set of genes and their direction of regulation. With respect to host-genes related to transcription factors, oxidative homeostasis, defense hormones and secondary metabolites,L. erysimiled to either suppression or limited activation of the transcript levels compared toA.craccivora. Further, a comprehensive view of the DEGs suggested more potential of successful insect-pests towards transcriptional reprogramming of the host. qRT-PCR based validation of randomly selected up- and down-regulated transcripts authenticated the transcriptome data.
A Geomorphological Regionalization using the Upscaled DEM: the Beijing-Tianjin-Hebei Area, China Case Study
Authors: Zhang Bin , Fan ZeMeng , Du ZhengPing , Zheng JiLin , Luo Jun , Wang NaNa , Wang Qing 
Published: June 2020

AbstractCharacterizing geomorphological patterns based on digital elevation models (DEMs) has become a basic focus of current geomorphology. A new DEM upscaling method based on the high-accuracy surface modelling method (HASM-US method) has been developed to improve the accuracy of current models and the subjectivity of macroscopic geomorphological patterns. The topographic variables of elevation (EL), slope (SL), aspect (AS), relief amplitude (RA), surface incision (SI), surface roughness (SR), and profile curvature (PC) with a spatial resolution of 1 km × 1 km in the Beijing-Tianjin-Hebei (BTH) area of China have been obtained by using the HASM-US method combined with the principal component analysis (PCA) method in terms of the elevation data of the SRTM-4 DEM, meteorological station location information, and field measurements with a GPS receiver. A geomorphological regionalization pattern has been developed to quantitatively classify the geomorphological types in the BTH area by combining the seven topographic factors of EL, SL, AS, RA, SI, SR, and PC that have significant spatial variation. The results show that the upscaling accuracy of elevation (mean difference only −2.32 m) with the HASM-US method is higher than that with the bilinear interpolation method and nearest neighbour interpolation method. The geomorphologic distribution in the BTH area includes 11 types: low plain, low tableland, low hill, low basin, middle plain, middle hill, low mountain with low RA values, low mountain with medium RA values, middle mountain with low RA values, middle mountain with medium RA values, and middle mountain with high RA values. The low plain is the dominant geomorphological type that covers 40.58% of the whole BTH area. The geomorphological distribution shows the different significant characteristics: the elevation rapidly decreases from the Taihang Mountains to the eastern area, gradually decreases from the Yanshan Mountains to the southern area, and first increases and then decreases from the Bashang Plateau to the southeastern area in the whole BTH area.
Quantifying solvent action in oil paint using portable laser speckle imaging
Authors: Baij Lambert , Buijs Jesse , Hermans Joen J. , Raven Laura , Iedema Piet D. , Keune Katrien , Sprakel Joris 
Published: June 2020

AbstractThe exposure of oil paintings to organic solvents for varnish removal or to water for the removal of surface dirt can affect the chemical and physical properties of oil paint in an undesired way. Solvents can temporarily plasticise and swell the polymerised oil paint binding medium, enhancing both the thermal mobility and mechanical displacement of pigments embedded in this film. The enhancement of these microscopic motions can affect both the chemical and physical stability of the object as a whole. In order to minimise solvent exposure during cleaning, an analytical method that can quantitatively measure the microscopic motions induced by solvent uptake, is required first. In this study, we use Fourier Transform Laser Speckle Imaging (FT-LSI) and a newly developed portable FT-LSI setup as highly resolved motion detection instruments. We employ FT-LSI to probe pigment motion, with high spatiotemporal resolution, as a proxy for the destabilising effects of cleaning solvents. In this way, we can study solvent diffusion and evaporation rates and the total solvent retention time. In addition, qualitative spatial information on the spreading and homogeneity of the applied solvent is obtained. We study mobility in paint films caused by air humidity, spreading of solvents as a result of several cleaning methods and the protective capabilities of varnish. Our results show that FT-LSI is a powerful technique for the study of solvent penetration during oil paint cleaning and has a high potential for future use in the conservation studio.
Climate drives intraspecific differentiation in the expression of growth-defence trade-offs in a long-lived pine species
Authors: Vázquez-González Carla , Sampedro Luis , Rozas Vicente , Zas Rafael 
Published: June 2020

AbstractIntraspecific variation in plant defences is expected to be the result of adaptive and plastic responses to environmental conditions, where trade-offs between growth and defences are thought to play a key role shaping phenotypic patterns in defensive investment. Axial resin ducts are costly defensive structures that remain imprinted in the tree rings of conifers, therefore being a valuable proxy of defensive investment along the trees’ lifespan. We aimed to disentangle climate-driven adaptive clines and plastic responses to both spatial and temporal environmental variation in resin duct production, and to explore growth-defence trade-offs. To that aim, we applied dendrochronological procedures to quantify annual growth and resin duct production during a 31-year-period in a Mediterranean pine species, including trees from nine populations planted in two common gardens. Both genetic factors and plastic responses modulated annual resin duct production. However, we found no evidence of adaptive clines with climate gradients driving population differentiation. Our results revealed a marked physiological trade-off between growth and defences, where the slope of the trade-off was genetically variable and associated with climatic gradients. Our results help to enlighten the evolutionary patterns and genetic basis of defensive allocation within species, particularly revealing a key role of growth-defence trade-offs.
Small vertebrates are key elements in the frugivory networks of a hyperdiverse tropical forest
Authors: Carreira Daiane C. , Dáttilo Wesley , Bruno Dáfini L. , Percequillo Alexandre Reis , Ferraz Katia M. P. M. B. , Galetti Mauro 
Published: June 2020

AbstractThe local, global or functional extinction of species or populations of animals, known as defaunation, can erode important ecological services in tropical forests. Many mutualistic interactions, such as seed dispersal of large seeded plants, can be lost in large continuous forests due to the rarity of large-bodied mammalian frugivores. Most of studies that try to elucidate the effects of defaunation on seed dispersal focused on primates or birds, and we lack a detailed understanding on the interactions between ground-dwelling fauna and fleshy fruits. Using camera traps in forest areas with different degrees of defaunation, we described the organization of frugivory networks involving birds, mammals and plants. We recorded 375 frugivory interactions between 21 frugivores and 150 fruiting trees of 30 species of fleshy fruit plants in six sites in continuous Atlantic forest of Brazil. We found that small frugivores—particularly small rodents and birds—were responsible for 72% of the events of frugivory. Large frugivores, such as tapirs and peccaries, were responsible for less than 21% of frugivory events. Our results indicate that the interactions between flesh fruiting plants and frugivores are dominated by small frugivores, an indication of a functional loss of large frugivores in this endangered biome.
Peritumoral and intratumoral radiomic features predict survival outcomes among patients diagnosed in lung cancer screening
Authors: Pérez-Morales Jaileene , Tunali Ilke , Stringfield Olya , Eschrich Steven A. , Balagurunathan Yoganand , Gillies Robert J. , Schabath Matthew B. 
Published: June 2020

AbstractThe National Lung Screening Trial (NLST) demonstrated that screening with low-dose computed tomography (LDCT) is associated with a 20% reduction in lung cancer mortality. One potential limitation of LDCT screening is overdiagnosis of slow growing and indolent cancers. In this study, peritumoral and intratumoral radiomics was used to identify a vulnerable subset of lung patients associated with poor survival outcomes. Incident lung cancer patients from the NLST were split into training and test cohorts and an external cohort of non-screen detected adenocarcinomas was used for further validation. After removing redundant and non-reproducible radiomics features, backward elimination analyses identified a single model which was subjected to Classification and Regression Tree to stratify patients into three risk-groups based on two radiomics features (NGTDM Busyness and Statistical Root Mean Square [RMS]). The final model was validated in the test cohort and the cohort of non-screen detected adenocarcinomas. Using a radio-genomics dataset, Statistical RMS was significantly associated with FOXF2 gene by both correlation and two-group analyses. Our rigorous approach generated a novel radiomics model that identified a vulnerable high-risk group of early stage patients associated with poor outcomes. These patients may require aggressive follow-up and/or adjuvant therapy to mitigate their poor outcomes.
The shutting down of the insulin pathway: a developmental window for Wolbachia load and feminization
Authors: Herran Benjamin , Geniez Sandrine , Delaunay Carine , Raimond Maryline , Lesobre Jérôme , Bertaux Joanne , Slatko Barton , Grève Pierre 
Published: June 2020

AbstractUsing the isopodArmadillidium vulgareas a case study, we review the significance of the "bacterial dosage model", which connects the expression of the extended phenotype to the rise of theWolbachiaload. In isopods, the Insulin-like Androgenic Gland hormone (IAG) induces male differentiation:Wolbachiafeminizes males through insulin resistance, presumably through defunct insulin receptors. This should prevent an autocrine development of the androgenic glands so that females differentiate instead: feminization should translate asIAGsilencing and increasedWolbachiaload in the same developmental window. In line with the autocrine model, uninfected males expressed IAG from the first larval stage on, long before the androgenic gland primordia begin to differentiate, and exponentially throughout development. In contrast in infected males, expression fully stopped at stage 4 (juvenile), when male differentiation begins. This co-occurred with the only significant rise in theWolbachiaload throughout the life-stages. Concurrently, the raw expression of the bacterial Secretion Systems co-increased, but they were not over-expressed relative to the number of bacteria. The isopod model leads to formulate the "bacterial dosage model" throughout extended phenotypes as the conjunction between bacterial load as the mode of action, timing of multiplication (pre/post-zygotic), and site of action (soma vs. germen).
Plant palatability and trait responses to experimental warming
Authors: Dostálek Tomáš , Rokaya Maan Bahadur , Münzbergová Zuzana 
Published: June 2020

AbstractClimate warming is expected to significantly affect plant–herbivore interactions. Even though direct effects of temperature on herbivores were extensively studied, indirect effects of temperature (acting via changes in host plant quality) on herbivore performance have rarely been addressed. We conducted multiple-choice feeding experiments with generalist herbivore Schistocerca gregaria feeding on six species of genus Impatiens cultivated at three different temperatures in growth chambers and a common garden. We also studied changes in leaf morphology and chemistry. We tested effects of temperature on plant palatability and assessed whether the effects could be explained by changes in the leaf traits. The leaves of most Impatiens species experienced the highest herbivory when cultivated at the warmest temperature. Traits related to leaf morphology (specific leaf area, leaf dry matter content and leaf area), but not to leaf chemistry, partly mediated the effects of temperature on plant palatability. Herbivores preferred smaller leaves with lower specific leaf area and higher leaf dry matter content. Our study suggests that elevated temperature will lead to changes in leaf traits and increase their palatability. This might further enhance the levels of herbivory under the increased herbivore pressure, which is forecasted as a consequence of climate warming.
Mechanistic insights on the mode of action of an antiproliferative thiosemicarbazone-nickel complex revealed by an integrated chemogenomic profiling study
Authors: Baruffini Enrico , Ruotolo Roberta , Bisceglie Franco , Montalbano Serena , Ottonello Simone , Pelosi Giorgio , Buschini Annamaria , Lodi Tiziana 
Published: June 2020

AbstractThiosemicarbazones (TSC) and their metal complexes display diverse biological activities and are active against multiple pathological conditions ranging from microbial infections to abnormal cell proliferation. Ribonucleotide reductase (RNR) is considered one of the main targets of TSCs, yet, the existence of additional targets, differently responsible for the multifaceted activities of TSCs and their metal complexes has been proposed. To set the basis for a more comprehensive delineation of their mode of action, we chemogenomically profiled the cellular effects of bis(citronellalthiosemicarbazonato)nickel(II) [Ni(S-tcitr)2] using the unicellular eukaryote Saccharomyces cerevisiae as a model organism. Two complementary genomic phenotyping screens led to the identification of 269 sensitive and 56 tolerant deletion mutant strains and of 14 genes that when overexpressed make yeast cells resistant to an otherwise lethal concentration of Ni(S-tcitr)2. Chromatin remodeling, cytoskeleton organization, mitochondrial function and iron metabolism were identified as lead cellular processes responsible for Ni(S-tcitr)2 toxicity. The latter process, and particularly glutaredoxin-mediated iron loading of RNR, was found to be affected by Ni(S-tcitr)2. Given the multiple pathways regulated by glutaredoxins, targeting of these proteins by Ni(S-tcitr)2 can negatively affect various core cellular processes that may critically contribute to Ni(S-tcitr)2 cytotoxicity.
Mitochondrial DNA genomes revealed different patterns of high-altitude adaptation in high-altitude Tajiks compared with Tibetans and Sherpas
Authors: Chen Yu , Gong Liang , Liu Xinyuan , Chen Xingshu , Yang Shenghong , Luo Yongjun 
Published: June 2020

AbstractHigh-altitude Tajiks (HA-Tajiks), Tibetans and Sherpas are three groups of high-altitude native people in China. The differences in the mtDNA genome between the three populations and the role of the mtDNA genome in the high-altitude adaptation of HA-Tajiks were seldom investigated. In this study, 80 HA-Tajiks were enrolled, and their whole mtDNA genomes were sequenced. The haplogroup of each subject was determined by comparison to the revised Cambridge Reference Sequence (rCRS). Ten additional populations from East Asia and Central Asia, including Tibetans and Sherpas, were selected as references. The top haplogroup was U, followed by H, T and J. Principle component analysis and genetic distance analysis indicated that HA-Tajiks showed a close relationship with Wakhi Tajiks, Pamiri Tajiks and Sarikoli Tajiks, indicating that they should be considered one nation scattered around the Pamirs. The difference in the mtDNA genome between HA-Tajiks and Sherpas was significantly greater than that between HA-Tajiks and Tibetans. Among the 13 genes related to the OXPHOS pathway encoded by the mtDNA genome, HA-Tajiks showed more significant differences in ND3 and CYTB compared to Tibetans. Compared to Sherpas, HA-Tajiks showed more significant differences in ND1, ND2, COX1, ATP8, ATP6, ND3, ND4L, ND4, ND5 and CYTB. The associated functional changes and underlying molecular mechanisms should be explored by molecular and biochemical investigations in further studies.
Selection and identification of a novel bone-targeting peptide for biomedical imaging of bone
Authors: Bang Jinho , Park Heesun , Yoo Jihye , Lee Donghyun , Choi Won Il , Lee Jin Hyung , Lee Young-Ran , Kim Chungho , Koo Heebeom , Kim Sunghyun 
Published: June 2020

AbstractThe global burden of bone-related diseases is increasing in the aging society; thus, improved bone targeted imaging for their early identification and treatment are needed. In this study, we screened novel peptide ligands for hydroxyapatite, a major inorganic component of teeth and bones, and identified a peptide enabling in vivo bone targeting and real-time fluorescence bone detection. To isolate peptides highly specific for hydroxyapatite, we used negative and positive selection from a randomized 8-mer peptide phage library and identified hydroxyapatite-specific peptides (HA-pep2, HA-pep3, and HA-pep7). Among these three peptides, HA-pep3 showed the highest binding capacity and superior dissociation constant towards hydroxyapatite surfaces over time (~ 88.3% retained on hydroxyapatite after two weeks). Furthermore, HA-pep3 was highly specific for hydroxyapatite compared to other calcium salt-based materials. Using this superior specificity, HA-pep3 showed higher accumulation in skull, spine, and joints in comparison with scrambled control peptide during real-time whole-body imaging. Ex vivo analysis of the major organs and bone from mice demonstrated that the fluorescence intensity in bone was about 3.32 folds higher in the case of HA-pep3 than the one exhibited by the scrambled control peptide. Our study identified a novel approach for targeting ligands for bone specific imaging and can be useful for drug delivery applications.
A novel FRET peptide assay reveals efficient Helicobacter pylori HtrA inhibition through zinc and copper binding
Authors: Bernegger Sabine , Brunner Cyrill , Vizovišek Matej , Fonovic Marko , Cuciniello Gaetano , Giordano Flavia , Stanojlovic Vesna , Jarzab Miroslaw , Simister Philip , Feller Stephan M. , Obermeyer Gerhard , Posselt Gernot , Turk Boris , Cabrele Chiara , Schneider Gisbert , Wessler Silja 
Published: June 2020

AbstractHelicobacter pylori (H. pylori) secretes the chaperone and serine protease high temperature requirement A (HtrA) that cleaves gastric epithelial cell surface proteins to disrupt the epithelial integrity and barrier function. First inhibitory lead structures have demonstrated the essential role of HtrA in H. pylori physiology and pathogenesis. Comprehensive drug discovery techniques allowing high-throughput screening are now required to develop effective compounds. Here, we designed a novel fluorescence resonance energy transfer (FRET) peptide derived from a gel-based label-free proteomic approach (direct in-gel profiling of protease specificity) as a valuable substrate for H. pylori HtrA. Since serine proteases are often sensitive to metal ions, we investigated the influence of different divalent ions on the activity of HtrA. We identified Zn++ and Cu++ ions as inhibitors of H. pylori HtrA activity, as monitored by in vitro cleavage experiments using casein or E-cadherin as substrates and in the FRET peptide assay. Putative binding sites for Zn++ and Cu++ were then analyzed in thermal shift and microscale thermophoresis assays. The findings of this study will contribute to the development of novel metal ion-dependent protease inhibitors, which might help to fight bacterial infections.
The effect of rapid high-intensity light-curing on micromechanical properties of bulk-fill and conventional resin composites
Authors: Par Matej , Marovic Danijela , Attin Thomas , Tarle Zrinka , Tauböck Tobias T. 
Published: June 2020

AbstractRapid high-intensity light-curing of dental resin composites is attractive from a clinical standpoint due to the prospect of time-savings. This study compared the effect of high-intensity (3 s with 3,440 mW/cm2) and conventional (10 s with 1,340 mW/cm2) light-curing on micromechanical properties of conventional and bulk-fill resin composites, including two composites specifically designed for high-intensity curing. Composite specimens were prepared in clinically realistic layer thicknesses. Microhardness (MH) was measured on the top and bottom surfaces of composite specimens 24 h after light-curing (initial MH), and after subsequent immersion for 24 h in absolute ethanol (ethanol MH). Bottom/top ratio for initial MH was calculated as a measure of depth-dependent curing effectiveness, whereas ethanol/initial MH ratio was calculated as a measure of crosslinking density. High-intensity light-curing showed a complex material-dependent effect on micromechanical properties. Most of the sculptable composites showed no effect of the curing protocol on initial MH, whereas flowable composites showed 11–48% lower initial MH for high-intensity curing. Ethanol/initial MH ratios were improved by high-intensity curing in flowable composites (up to 30%) but diminished in sculptable composites (up to 15%). Due to its mixed effect on MH and crosslinking density in flowable composites, high-intensity curing should be used with caution in clinical work.