bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bamboo leaf flavone changed the community of cecum microbiota and improved the immune function in broilers
Authors: Shu Gang , Kong Fanli , Xu Dan , Yin Lizi , He Changliang , Lin Juchun , Fu Hualin , Wang Kaiyu , Tian Yaofu , Zhao Xiaoling 
Published: July 2020

AbstractIt has been shown that bamboo leaf flavone (BLF) displays biological and pharmacological activities in mammals. However, the effects of BLF on broiler gut microbiota and related immune function have not been investigated. The aim of this study was to test our hypothesis that BLF can improve the health status of broilers by modulating the gut microbiota. A total of 300 one-day-old Arbor Acres (AA) broilers were used to characterize their gut microbiota and immune status after feeding diet supplemented with BLF. The V4 hypervariable region of the 16S rRNA gene from cecal bacteria was sequenced via the Illumina MiSeq platform. The Immune status and related parameters were assessed, including the immune organ index (the spleen, thymus, and bursa), serum concentrations of IL-2 and INF-γ, and spleen IL-2 and INF-γ gene expressions. The results showed the BLF diet had an Immune enhancement effect on broilers. In addition, BFL caused the changes of the gut microbial community structure, resulting in greater proportions of bacterial taxa belonging to Lactobacillus, Clostridiales, Ruminococcus, and Lachnospiraceae. These bacteria have been used as probiotics for producing short chain fatty acids in hosts. These results indicate that BLF supplement improves immune function in chicken via modulation of the gut microbiota.
Photocatalytic degradation of industrial acrylonitrile wastewater by F–S–Bi–TiO2 catalyst of ultrafine nanoparticles dispersed with SiO2 under natural sunlight
Authors: Ouyang Feng , Li Hanliang , Gong Zhengya , Pang Dandan , Qiu Lu , Wang Yun , Dai Fangwei , Cao Gang , Bharti Bandna 
Published: July 2020

AbstractHighly active photocatalyst, having certain anti-ionic interfering function, of F, S and Bi doped TiO2/SiO2 was used for the first time to degrade the organic pollutants in acrylonitrile industrial wastewater under natural sunlight. The photocatalyst were prepared and characterized by UV–Vis, XRD, TEM, EDS, Nitrogen physical adsorption and XPS technique. UV–Vis analysis revealed addition of F, S and Bi into the lattice of TiO2 led to the expansion of TiO2 response in the visible region and hence the efficient separation of charge carrier. The photocatalytic potential of as prepared catalyst to degrade acrylonitrile wastewater under simulated and natural sunlight irradiation was investigated. The extent of degradation of acrylonitrile wastewater was evaluated by chemical oxygen demand (CODCr). CODCr in wastewater decreased from 88.36 to 7.20 mgL−1 via 14 h irradiation of simulated sunlight and achieved regulation discharge by 6 h under natural sunlight, illuminating our photocatalyst effectiveness for refractory industrial wastewater treatment. From TEM results, we found that SiO2 could disperse the photocatalyst with different component distributions between the surface and the bulk phase that should also be responsible for the light absorption and excellent photocatalytic performance. The XPS analysis confirmed the presence of surface hydroxyl group, oxygen vacancies.
Transcriptome analysis of desmoplastic small round cell tumors identifies actionable therapeutic targets: a report from the Children’s Oncology Group
Authors: Hingorani Pooja , Dinu Valentin , Zhang Xiyuan , Lei Haiyan , Shern Jack F. , Park Jin , Steel Jason , Rauf Femina , Parham David , Gastier-Foster Julie , Hall David , Hawkins Douglas S. , Skapek Stephen X. , Labaer Joshua , McEachron Troy A. 
Published: July 2020

AbstractTo further understand the molecular pathogenesis of desmoplastic small round cell tumor (DSRCT), a fatal malignancy occurring primarily in adolescent/young adult males, we used next-generation RNA sequencing to investigate the gene expression profiles intrinsic to this disease. RNA from DSRCT specimens obtained from the Children’s Oncology Group was sequenced using the Illumina HiSeq 2000 system and subjected to bioinformatic analyses. Validation and functional studies included WT1 ChIP-seq, EWS-WT1 knockdown using JN-DSRCT-1 cells and immunohistochemistry. A panel of immune signature genes was also evaluated to identify possible immune therapeutic targets. Twelve of 14 tumor samples demonstrated presence of the diagnostic EWSR1-WT1 translocation and these 12 samples were used for the remainder of the analysis. RNA sequencing confirmed the lack of full-length WT1 in all fusion positive samples as well as the JN-DSRCT-1 cell line. ChIP-seq for WT1 showed significant overlap with genes found to be highly expressed, including IGF2 and FGFR4, which were both highly expressed and targets of the EWS-WT1 fusion protein. In addition, we identified CD200 and CD276 as potentially targetable immune checkpoints whose expression is independent of the EWS-WT1 fusion gene in cultured DSCRT cells. In conclusion, we identified IGF2, FGFR4, CD200, and CD276 as potential therapeutic targets with clinical relevance for patients with DSRCT.
Milk fat globule size development in the mammary epithelial cell: a potential role for ether phosphatidylethanolamine
Authors: Walter Leonie , Narayana Vinod K. , Fry Richard , Logan Amy , Tull Dedreia , Leury Brian 
Published: July 2020

AbstractMilk fat globule (MFG) size is a milk production trait characteristic to the individual animal and has important effects on the functional and nutritional properties of milk. Although the regulation of MFG size in the mammary epithelial cell is not fully understood, lipid droplet (LD) fusion prior to secretion is believed to play a role. We selected cows that consistently produced milk with predominantly small or large MFGs to compare their lipidomic profiles, with focus on the polar lipid fraction. The polar lipid composition of the monolayer surrounding the LD is believed to either promote or prevent LD fusion. Using a targeted LC–MS/MS approach we studied the relative abundance of 301 detected species and found significant differences between the studied groups. Here we show that the lipidomic profile of milk from small MFG cows is characterised by higher phosphatidylcholine to phosphatidylethanolamine ratios. In contrast, the milk from large MFG cows contained more ether-phosphatidylethanolamine species. This is the first time that a potential role for ether-phosphatidylethanolamine in MFG size development has been suggested.
Using an ontology of the human cardiovascular system to improve the classification of histological images
Authors: Mazo Claudia , Alegre Enrique , Trujillo Maria 
Published: July 2020

AbstractThe advantages of automatically recognition of fundamental tissues using computer vision techniques are well known, but one of its main limitations is that sometimes it is not possible to classify correctly an image because the visual information is insufficient or the descriptors extracted are not discriminative enough. An Ontology could solve in part this problem, because it gathers and makes possible to use the specific knowledge that allows detecting clear mistakes in the classification, occasionally simply by pointing out impossible configurations in that domain. One of the main contributions of this work is that we used a Histological Ontology to correct, and therefore improve the classification of histological images. First, we described small regions of images, denoted as blocks, using Local Binary Pattern (LBP) based descriptors and we determined which tissue of the cardiovascular system was present using a cascade Support Vector Machine (SVM). Later, we built Resource Description Framework (RDF) triples for the occurrences of each discriminant class. Based on that, we used a Histological Ontology to correct, among others, “not possible” situations, improving in this way the global accuracy in the blocks first and in tissues classification later. For the experimental validation, we used a set of 6000 blocks of $$100\times100$$100×100 pixels, obtaining F-Scores between 0.769 and 0.886. Thus, there is an improvement between 0.003 and $$0.769\%$$0.769% when compared to the approach without the histological ontology. The methodology improves the automatic classification of histological images using a histological ontology. Another advantage of our proposal is that using the Ontology, we were capable of recognising the epithelial tissue, previously not detected by any of the computer vision methods used, including a CNN proposal called HistoResNet evaluated in the experiments. Finally, we also have created and made publicly available a dataset consisting of 6000 blocks of labelled histological tissues.
Salinity and temperature increase impact groundwater crustaceans
Authors: Castaño-Sánchez Andrea , Hose Grant C. , Reboleira Ana Sofia P. S. 
Published: July 2020

AbstractAnthropogenic impacts in groundwater ecosystems remain poorly known. Climate change is omnipresent, while groundwater salinization poses serious long-term environmental problems in arid and semi-arid regions, and is exacerbated by global warming. Both are present threats to the conservation of groundwater ecosystems, which harbour highly specialized species, with peculiar traits and limited geographic distributions. We tested the temperature and salinity tolerance of groundwater-adapted invertebrates to understand the effect of global warming and salinization in groundwater ecosystems. We used species representative of groundwater-adapted crustaceans: two copepods (harpacticoid and cyclopoid) and one syncarid, endemic to Australia. Our results show that 50% of the populations died at salt concentrations between 2.84 to 7.35 g NaCl/L after 96 h, and at 6.9 °C above the ambient aquifer temperature for copepods and more than 10 °C for syncarids. Both copepods were more sensitive to temperature and NaCl than the syncarid. We calculated a salinity risk quotient of 9.7 and predicted the risk of loss of 10% of syncarid and 20% of copepod population abundances under a worst-case scenario of global warming predictions for 2070. These results highlight that both salinity and temperature increases pose a risk to the ecological integrity of groundwater ecosystems.
Specific localisation of ions in bacterial membranes unravels physical mechanism of effective bacteria killing by sanitiser
Authors: Thoma Judith , Abuillan Wasim , Furikado Ippei , Habe Taichi , Yamamoto Akihisa , Gierlich Simone , Kaufmann Stefan , Brandenburg Klaus , Gutsmann Thomas , Konovalov Oleg , Inoue Shigeto , Tanaka Motomu 
Published: July 2020

AbstractAntimicrobial resistance is a major threat to public health. Although many commercial sanitisers contain a combination of cationic surfactants and aromatic alcohols, the physical mechanisms where these two substances bind to or how they disturb bacterial membranes are still largely unknown. In this study, we designed a well-defined model of Gram-negative bacteria surfaces based on the monolayer of lipopolysaccharides with uniform saccharide head groups. Since commonly used X-ray reflectivity is sensitive to changes in the thickness, roughness and electron density but is not sensitive to elements, we employed grazing incidence X-ray fluorescence. In the absence of Ca2+, cationic surfactants can penetrate into the membrane core with no extra support by disturbing the layer of K+ coupled to negatively charged saccharide head group at z = 17 Å from the air/chain interface. On the other hand, Ca2+ confined at z = 19 Å crosslink charged saccharides and prevent the incorporation of cationic surfactants. We found that the addition of nonlethal aromatic alcohols facilitate the incorporation of cationic surfactants by the significant roughening of the chain/saccharide interface. Combination of precise localisation of ions and molecular-level structural analysis quantitatively demonstrated the synegtestic interplay of ingredients to achieve a high antibacterial activity.
$$\text {DRTOP}$$: deep learning-based radiomics for the time-to-event outcome prediction in lung cancer
Authors: Afshar Parnian , Mohammadi Arash , Tyrrell Pascal N. , Cheung Patrick , Sigiuk Ahmed , Plataniotis Konstantinos N. , Nguyen Elsie T. , Oikonomou Anastasia 
Published: July 2020

AbstractHand-crafted radiomics has been used for developing models in order to predict time-to-event clinical outcomes in patients with lung cancer. Hand-crafted features, however, are pre-defined and extracted without taking the desired target into account. Furthermore, accurate segmentation of the tumor is required for development of a reliable predictive model, which may be objective and a time-consuming task. To address these drawbacks, we propose a deep learning-based radiomics model for the time-to-event outcome prediction, referred to as DRTOP that takes raw images as inputs, and calculates the image-based risk of death or recurrence, for each patient. Our experiments on an in-house dataset of 132 lung cancer patients show that the obtained image-based risks are significant predictors of the time-to-event outcomes. Computed Tomography (CT)-based features are predictors of the overall survival (OS), with the hazard ratio (HR) of 1.35, distant control (DC), with HR of 1.06, and local control (LC), with HR of 2.66. The Positron Emission Tomography (PET)-based features are predictors of OS and recurrence free survival (RFS), with hazard ratios of 1.67 and 1.18, respectively. The concordance indices of $$68\%$$68%, $$63\%$$63%, and $$64\%$$64% for predicting the OS, DC, and RFS show that the deep learning-based radiomics model is as accurate or better in predicting predefined clinical outcomes compared to hand-crafted radiomics, with concordance indices of $$51\%$$51%, $$64\%$$64%, and $$47\%$$47%, for predicting the OS, DC, and RFS, respectively. Deep learning-based radiomics has the potential to offer complimentary predictive information in the personalized management of lung cancer patients.
Der p 1-based immunotoxin as potential tool for the treatment of dust mite respiratory allergy
Authors: Lázaro-Gorines Rodrigo , López-Rodríguez Juan Carlos , Benedé Sara , González Miguel , Mayorga Cristobalina , Vogel Lothar , Martínez-del-Pozo Álvaro , Lacadena Javier , Villalba Mayte 
Published: July 2020

AbstractImmunotoxins appear as promising therapeutic molecules, alternative to allergen-specific-immunotherapy. In this work, we achieved the development of a protein chimera able to promote specific cell death on effector cells involved in the allergic reaction. Der p 1 allergen was chosen as cell-targeting domain and the powerful ribotoxin α-sarcin as the toxic moiety. The resultant construction, named proDerp1αS, was produced and purified from the yeastPichia pastoris. Der p 1-protease activity and α-sarcin ribonucleolytic action were effectively conserved in proDerp1αS. Immunotoxin impact was assayed by using effector cells sensitized with house dust mite-allergic sera. Cell degranulation and death, triggered by proDerp1αS, was exclusively observed on Der p 1 sera sensitized-humRBL-2H3 cells, but not when treated with non-allergic sera. Most notably, equivalent IgE-binding and degranulation were observed with both proDerp1αS construct and native Der p 1 when using purified basophils from sensitized patients. However, proDerp1αS did not cause any cytotoxic effect on these cells, apparently due to its lack of internalization after their surface IgE-binding, showing the complex in vivo panorama governing allergic reactions. In conclusion, herein we present proDerp1αS as a proof of concept for a potential and alternative new designs of therapeutic tools for allergies. Development of new, and more specific, second-generation of immunotoxins following proDerp1αS, is further discussed.
A robust and miniaturized screening platform to study natural products affecting metabolism and survival in Caenorhabditis elegans
Authors: Zwirchmayr Julia , Kirchweger Benjamin , Lehner Theresa , Tahir Ammar , Pretsch Dagmar , Rollinger Judith M. 
Published: July 2020

AbstractIn this study a robust, whole organism screening based onCaenorhabditis elegansis presented for the discovery of natural products (NP) with beneficial effects against obesity and age-related diseases. Several parameters of the elaborated workflow were optimized to be adapted for probing multicomponent mixtures combining knowledge from traditional medicine and NP chemistry by generating optimized small-scale extracts considering scarcity of the natural source, solubility issues, and potential assay interferences. The established miniaturized assay protocol allows for in vivo probing of small amounts of even complex samples (~ 1 mg) to test their ability to increase the nematodes’ survival time and the suppression of fat accumulation assessed by Nile red staining as hall marks of “healthy aging”. The workflow was applied on 24 herbal and fungal materials traditionally used against symptoms of the metabolic syndrome and revealed promising results for the extracts ofGardenia jasminoidesfruits and the sclerotia fromInonotus obliquus. Tested at 100 µg/mL they were able to significantly reduce the Nile red fluorescence and extend the 50% survival rate (DT50) compared to the control groups. This phenotype-directed in vivo approach opens up new horizons for the selection of natural starting materials and the investigation of their active principles as fast drug discovery tool with predictive value for human diseases.
Epigenetic alterations in cytochrome P450 oxidoreductase (Por) in sperm of rats exposed to tetrahydrocannabinol (THC)
Authors: Acharya Kelly S. , Schrott Rose , Grenier Carole , Huang Zhiqing , Holloway Zade , Hawkey Andrew , Levin Edward D. , Murphy Susan K. 
Published: July 2020

AbstractAs marijuana legalization is increasing, research regarding possible long-term risks for users and their offspring is needed. Little data exists on effects of paternal tetrahydrocannabinol (THC) exposure prior to reproduction. This study determined if chronic THC exposure alters sperm DNA methylation (DNAm) and if such effects are intergenerationally transmitted. Adult male rats underwent oral gavage with THC or vehicle control. Differentially methylated (DM) loci in motile sperm were identified using reduced representation bisulfite sequencing (RRBS). Another cohort was injected with vehicle or THC, and sperm DNAm was analyzed. Finally, THC-exposed and control adult male rats were mated with THC-naïve females. DNAm levels of target genes in brain tissues of the offspring were determined by pyrosequencing. RRBS identified 2,940 DM CpGs mapping to 627 genes. Significant hypermethylation was confirmed (p < 0.05) following oral THC administration for cytochrome P450 oxidoreductase (Por), involved in toxin processing and disorders of sexual development. Por hypermethylation was not observed after THC injection or in the subsequent generation. These results support that THC alters DNAm in sperm and that route of exposure can have differential effects. Although we did not observe evidence of intergenerational transmission of the DNAm change, larger studies are required to definitively exclude this possibility.
Effects of nitrogen deposition and phosphorus addition on arbuscular mycorrhizal fungi of Chinese fir (Cunninghamia lanceolata)
Authors: Lin Chuyu , Wang Yaoxiong , Liu Meihua , Li Quan , Xiao Wenfa , Song Xinzhang 
Published: July 2020

AbstractNitrogen (N) deposition is a key factor that affects terrestrial biogeochemical cycles with a growing trend, especially in the southeast region of China, where shortage of available phosphorus (P) is particularly acute and P has become a major factor limiting plant growth and productivity. Arbuscular mycorrhizal fungi (AMF) establish a mutualistic symbiosis with plants, and play an important role in enhancing plant stress resistance. However, the response of AMF to the combined effects of N deposition and P additions is poorly understood. Thus, in this study, a field experiment was conducted in 10-year Chinese fir forests to estimate the effects of simulated nitrogen (N) deposition (low-N, 30 kg ha−1 year−1 and high-N, 60 kg ha−1 year−1) and phosphorus (P) addition treatments (low-P, 20 mg kg−1 and high-P, 40 mg kg−1) on AMF since April 2017, which was reflected in AMF root colonization rates and spore density of rhizosphere soil. Our results showed that N deposition significantly decreased AMF root colonization rates and spore density. In N-free plots, P addition significantly decreased AMF root colonization rates, but did not significantly alter spore density. In low-N plots, colonization rates significantly decreased under low P addition, but significantly increased under high P addition, and spore density exhibited a significant decline under high P additions. In high-N plots, colonization rates and spore density significantly increased under P additions. Interactive effects of simulated N deposition and P addition on both colonization rates and spore density were significant. Moderate N deposition or P addition can weaken the symbiotic relationship between plants and AMF, significantly reducing AMF colonization rates and inhibiting spore production. However, a moderate addition of P greatly enhances spore yield. In the case of interactive effects, the AMF colonization rates and spore density are affected by the relative content of N and P in the soil.
Label-free multiphoton microscopy as a tool to investigate alterations of cerebral aneurysms
Authors: Sehm Tina , Uckermann Ortrud , Galli Roberta , Meinhardt Matthias , Rickelt Elke , Krex Dietmar , Schackert Gabriele , Kirsch Matthias 
Published: July 2020

AbstractCerebral aneurysms are abnormal focal dilatations of arterial vessel walls with pathological vessel structure alterations. Sudden rupture can lead to a subarachnoid hemorrhage, which is associated with a high mortality. Therefore, the origin of cerebral aneurysms as well as the progression to the point of rupture needs to be further investigated. Label-free multimodal multiphoton microscopy (MPM) was performed on resected human aneurysm domes and integrated three modalities: coherent anti-Stokes Raman scattering, endogenous two-photon fluorescence and second harmonic generation. We showed that MPM is a completely label-free and real-time powerful tool to detect pathognomonic histopathological changes in aneurysms, e.g. thickening and thinning of vessel walls, intimal hyperplasia, intra-wall haemorrhage, calcification as well as atherosclerotic changes. In particular, the loss or fragmentation of elastin as well as fibromatous wall remodelling appeared very distinct. Remarkably, cholesterol and lipid deposits were clearly visible in the multiphoton images. MPM provides morphological and biochemical information that are crucial for understanding the mechanisms of aneurysm formation and progression.