bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiomics features on radiotherapy treatment planning CT can predict patient survival in locally advanced rectal cancer patients
Authors: Wang Jiazhou , Shen Lijun , Zhong Haoyu , Zhou Zhen , Hu Panpan , Gan Jiayu , Luo Ruiyan , Hu Weigang , Zhang Zhen 
Published: October 2019

AbstractThis retrospective study was to investigate whether radiomics feature come from radiotherapy treatment planning CT can predict prognosis in locally advanced rectal cancer patients treated with neoadjuvant chemoradiation followed by surgery. Four-hundred-eleven locally advanced rectal cancer patients which were treated with neoadjuvant chemoradiation enrolled in this study. All patients’ radiotherapy treatment planning CTs were collected. Tumor was delineated on these CTs by physicians. An in-house radiomics software was used to calculate 271 radiomics features. The results of test-retest and contour-recontour studies were used to filter stable radiomics (Spearman correlation coefficient > 0.7). Twenty-one radiomics features were final enrolled. The performance of prediction model with the radiomics or clinical features were calculated. The clinical outcomes include local control, distant control, disease-free survival (DFS) and overall survival (OS). Model performance C-index was evaluated by C-index. Patients are divided into two groups by cluster results. The results of chi-square test revealed that the radiomics feature cluster is independent of clinical features. Patients have significant differences in OS (p = 0.032, log rank test) for these two groups. By supervised modeling, radiomics features can improve the prediction power of OS from 0.672 [0.617 0.728] with clinical features only to 0.730 [0.658 0.801]. In conclusion, the radiomics features from radiotherapy CT can potentially predict OS for locally advanced rectal cancer patients with neoadjuvant chemoradiation treatment.
The Evolutionary Radiation of Hominids: a Phylogenetic Comparative Study
Authors: Rocatti Guido , Perez S. Ivan 
Published: October 2019

AbstractOver the last 150 years the diversity and phylogenetic relationships of the hominoids have been one of the main focuses in biological and anthropological research. Despite this, the study of factors involved in their evolutionary radiation and the origin of the hominin clade, a key subject for the further understanding of human evolution, remained mostly unexplored. Here we quantitatively approach these events using phylogenetic comparative methods and craniofacial morphometric data from extant and fossil hominoid species. Specifically, we explore alternative evolutionary models that allow us to gain new insights into this clade diversification process. Our results show a complex and variable scenario involving different evolutionary regimes through the hominid evolutionary radiation –modeled by Ornstein-Uhlenbeck multi-selective regime and Brownian motion multi-rate scenarios–. These different evolutionary regimes might relate to distinct ecological and cultural factors previously suggested to explain hominid evolution at different evolutionary scales along the last 10 million years.
A novel metric reveals biotic resistance potential and informs predictions of invasion success
Authors: Cuthbert Ross N. , Callaghan Amanda , Dick Jaimie T. A. 
Published: October 2019

AbstractInvasive species continue to proliferate and detrimentally impact ecosystems on a global scale. Whilst impacts are well-documented for many invaders, we lack tools to predict biotic resistance and invasion success. Biotic resistance from communities may be a particularly important determinant of the success of invaders. The present study develops traditional ecological concepts to better understand and quantify biotic resistance. We quantified predation towards the highly invasive Asian tiger mosquitoAedes albopictusand a representative native mosquitoCulex pipiensby three native and widespread cyclopoid copepods, using functional response and prey switching experiments. All copepods demonstrated higher magnitude type II functional responses towards the invasive prey over the analogous native prey, aligned with higher attack and maximum feeding rates. All predators exhibited significant, frequency-independent prey preferences for the invader. With these results, we developed a novel metric for biotic resistance which integrates predator numerical response proxies, revealing differential biotic resistance potential among predators. Our results are consistent with field patterns of biotic resistance and invasion success, illustrating the predictive capacity of our methods. We thus propose the further development of traditional ecological concepts, such as functional responses, numerical responses and prey switching, in the evaluation of biotic resistance and invasion success.
Illumina-based Analysis of Endophytic Bacterial Diversity of four Allium species
Authors: Huang Yonghong 
Published: October 2019

AbstractAllium species are popular vegetables in China and possess antifungal and antibacterial activities. This study aimed to compare the endophytic bacterial community in the four crucial Allium species in China, Chinese leek (CL), garlic (GA), onion (ON,) and Welsh onion (WO), using sequences of the V3–V4 region of the bacterial 16S rRNA gene. A total of 1,036,637 high-quality sequences and 719 operational taxonomic units (OTUs) were obtained across all libraries. A total of 20 phyla, 50 classes, 80 orders, 134 families, and 234 genera were identified. Among them, 18 OTUs and 19 genera were shared among the four Allium species. Proteobacteria (42.68%) and Bacteroidetes (20.18%) were the dominant phyla in CL, while one unclassified (>70%) was the dominant phyla in the other three Allium species. The alpha-diversity analysis showed the bacterial richness and diversity in CL were significantly higher than those in the other three Allium species. Principal coordinate analysis (PCA) showed endophytic bacterial communities in GA, WO, and ON were more similar than those in CL. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed endophytic bacteria mostly enriched in Membrane Transport, Amino Acid Metabolism and Carbohydrate Metabolism pathway. 17 of the 23 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories and 159 of the 206 lower-level KEGG pathways in CL were significantly higher than those in the other three Allium species. Pearson’s correlation indicated that KEGG pathways with significant differences among the Allium species were closely related to the bacterial genera with significant differences between the Allium species. The findings of our study provided insight into the complex endophytic microbial communities in Allium species.
Effects of intramuscular and vaginal progesterone supplementation on frozen-thawed embryo transfer
Authors: Jiang Lei , Luo Zhuo-Ye , Hao Gui-Min , Gao Bu-Lang 
Published: October 2019

AbstractThis study was to investigate effects of progesterone vaginal sustained-release gel and intramuscular injection of progesterone on frozen-thawed embryos transfer in 3013 patients receiving vaginal progesterone sustained-release gel and progesterone injection in artificial cycle for frozen-thawed embryo transfer. All patients were divided into two groups: group A with progesterone intramuscular injection (60 mg/d) plus dydrogesterone (10 mg tid) and group B with progesterone vaginal sustained-release gel of progesterone (90 mg/d) plus dydrogesterone (10 mg tid). There were 1988 women in group A treated with progesterone injection and 1025 women in group B with progesterone vaginal sustained-release gel. There were no statistically (P > 0.05) significant difference between the two groups in age, years of infertility, body mass index, endometrial thickness at transfer time, the average numbers of embryo transferred, cause of infertility, number of cycles, pregnancy rate and ectopic pregnancy rate. No significant (P > 0.05) differences existed in the clinical pregnancy (52.5% vs. 56.0%) and ectopic pregnancy (2.2% vs. 3.0%) rate between groups A and B. However, group B with vaginal progesterone supplementation had significantly (P < 0.05) greater implantation (37.0% vs 34.4%), delivery (45.1% vs. 41.0%) and live birth (45.0% vs. 40.8%) rate than group A with intramuscular progesterone injection, whereas group A had significantly (P < 0.05) greater early abortion rate (19.4% vs. 15.3%) than group B. This study showed that vaginal gel progesterone supplementation has good effects on frozen-thawed embryo transfer and can significantly increase the rate of implantation, delivery and live birth but decrease the abortion rate compared with intramuscular progesterone injection.
Seasonality of climatic drivers of flood variability in the conterminous United States
Authors: Dickinson Jesse E. , Harden Tessa M. , McCabe Gregory J. 
Published: October 2019

AbstractFlood variability due to changes in climate is a major economic and social concern. Climate drivers can affect the amount and distribution of flood-generating precipitation through seasonal shifts in storm tracks. An understanding of how the drivers may change in the future is critical for identifying the regions where the magnitude of floods may change. Here we show the regions in the conterminous U.S. where seasonal changes in global-scale climate oscillations have driven a large part of the variability of flood magnitude. The regions are cohesive across multiple watershed boundaries suggesting that variability in floods is driven by regional climate influences. Correlations with climate indices indicate that floods in the western and southern U.S. are most affected by global-scale climate. The regions provide a useful approach for characterizing flood variability and for attributing climatic drivers on flood variability and magnitude.
Protection from noise-induced cochlear synaptopathy by virally mediated overexpression of NT3
Authors: Hashimoto Ken , Hickman Tyler T. , Suzuki Jun , Ji Lingchao , Kohrman David C. , Corfas Gabriel , Liberman M. Charles 
Published: October 2019

AbstractNoise exposures causing only transient threshold shifts can destroy auditory-nerve synapses without damaging hair cells. Here, we asked whether virally mediated neurotrophin3 (NT3) overexpression can repair this damage. CBA/CaJ mice at 6 wks were injected unilaterally with adeno-associated virus (AAV) containing either NT3 or GFP genes, via the posterior semicircular canal, 3 wks prior to, or 5 hrs after, noise exposure. Controls included exposed animals receiving vehicle only, and unexposed animals receiving virus. Thresholds were measured 2 wks post-exposure, just before cochleas were harvested for histological analysis. In separate virus-injected animals, unexposed cochleas were extracted for qRT-PCR. The GFP reporter showed that inner hair cells (IHCs) were transfected throughout the cochlea, and outer hair cells mainly in the apex. qRT-PCR showed 4- to 10-fold overexpression of NT3 from 1–21 days post-injection, and 1.7-fold overexpression at 40 days. AAV-NT3 delivered prior to noise exposure produced a dose-dependent reduction of synaptopathy, with nearly complete rescue at some cochlear locations. In unexposed ears, NT3 overexpression did not affect thresholds, however GFP overexpression caused IHC loss. In exposed ears, NT3 overexpression increased permanent threshold shifts. Thus, although NT3 overexpression can minimize noise-induced synaptic damage, the forced overexpression may be harmful to hair cells themselves during cochlear overstimulation.
Effect of natural ageing and heat treatments on GII.4 norovirus binding to Histo-Blood Group Antigens
Authors: Robin Maëlle , Chassaing Manon , Loutreul Julie , de Rougemont Alexis , Belliot Gaël , Majou Didier , Gantzer Christophe , Boudaud Nicolas 
Published: October 2019

AbstractHuman noroviruses (HuNoVs) are the leading cause of viral foodborne outbreaks worldwide. To date, no available methods can be routinely used to detect infectious HuNoVs in foodstuffs. HuNoVs recognize Histo-Blood Group Antigens (HBGAs) through the binding pocket (BP) of capsid protein VP1, which promotes infection in the host cell. In this context, the suitability of human HBGA-binding assays to evaluate the BP integrity of HuNoVs was studied on GII.4 virus-like particles (VLPs) and GII.4 HuNoVs during natural ageing at 20 °C and heat treatments. Our results demonstrate that this approach may reduce the over-estimation of potential infectious HuNoVs resulting from solely using the genome detection, even though some limitations have been identified. The specificity of HBGA-binding to the BP is clearly dependent on the HGBA type (as previously evidenced) and the ionic strength of the media without disturbing such interactions. This study also provides new arguments regarding the ability of VLPs to mimic HuNoV behavior during inactivation treatments. The BP stability of VLPs was at least 4.3 fold lower than that of HuNoVs at 20 °C, whereas capsids of both particles were disrupted at 72 °C. Thus, VLPs are relevant surrogates of HuNoVs for inactivation treatments inducing significant changes in the capsid structure.
The role of item size on choosing contrasted food quantities in angelfish (Pterophyllum scalare)
Authors: Gómez-Laplaza Luis M. , Romero Laura , Gerlai Robert 
Published: October 2019

AbstractComparative studies on quantity discrimination in animals are important for understanding potential evolutionary roots of numerical competence. A previous study with angelfish has shown that they discriminate numerically different sets of same-sized food items and prefer the larger set. However, variables that covary with number were not controlled and choice could have been influenced by variables such as size or density of the food items rather than numerical attributes. Here using a recently developed approach, we examined whether contour length of the food items affects choice in a spontaneous binary choice task. In Experiment 1, a contrast of 1 vs. 1 food item was presented, but the ratio between the size (diameter) of the food items was varied. In Experiment 2, numerically different food sets were equated in overall size by increasing the size (diameter) of the items in the numerically small sets. In both Experiments, subjects showed a preference for the larger sized food items with a discrimination limit. These results show that item size plays a prominent role in foraging decisions in angelfish. Experiment 3 placed numerical and size attributes of the sets in conflict by presenting one larger-sized food item in the numerically smaller set that also had smaller overall size (diameter) of food items. Angelfish showed no preference in any of the contrasts, suggesting that they could not make optimal foraging decisions when these attributes were in conflict. Maximization of energy return is central to optimal foraging. Accordingly, here item size was also found to be a key feature of the sets, although the numerical attributes of the sets also influenced the choice.
Small extracellular vesicles convey the stress-induced adaptive responses of melanoma cells
Authors: Harmati Maria , Gyukity-Sebestyen Edina , Dobra Gabriella , Janovak Laszlo , Dekany Imre , Saydam Okay , Hunyadi-Gulyas Eva , Nagy Istvan , Farkas Attila , Pankotai Tibor , Ujfaludi Zsuzsanna , Horvath Peter , Piccinini Filippo , Kovacs Maria , Biro Tamas , Buzas Krisztina 
Published: October 2019

AbstractExosomes are small extracellular vesicles (sEVs), playing a crucial role in the intercellular communication in physiological as well as pathological processes. Here, we aimed to study whether the melanoma-derived sEV-mediated communication could adapt to microenvironmental stresses. We compared B16F1 cell-derived sEVs released under normal and stress conditions, including cytostatic, heat and oxidative stress. The miRNome and proteome showed substantial differences across the sEV groups and bioinformatics analysis of the obtained data by the Ingenuity Pathway Analysis also revealed significant functional differences. The in silico predicted functional alterations of sEVs were validated by in vitro assays. For instance, melanoma-derived sEVs elicited by oxidative stress increased Ki-67 expression of mesenchymal stem cells (MSCs); cytostatic stress-resulted sEVs facilitated melanoma cell migration; all sEV groups supported microtissue generation of MSC-B16F1 co-cultures in a 3D tumour matrix model. Based on this study, we concluded that (i) molecular patterns of tumour-derived sEVs, dictated by the microenvironmental conditions, resulted in specific response patterns in the recipient cells; (ii) in silico analyses could be useful tools to predict different stress responses; (iii) alteration of the sEV-mediated communication of tumour cells might be a therapy-induced host response, with a potential influence on treatment efficacy.
Environmental fungi and bacteria facilitate lecithin decomposition and the transformation of phosphorus to apatite
Authors: Li Chunkai , Li Qisheng , Wang Zhipeng , Ji Guanning , Zhao He , Gao Fei , Su Mu , Jiao Jiaguo , Li Zhen , Li Huixin 
Published: October 2019

AbstractOrganophosphorus compounds (OP) are stable P source in nature, and can increase eutrophication risk in waterbodies. Lecithin was the most difficult OP to be broken down. In this study, two typical phosphate-solubilizing microorganisms, Aspergillus niger and Acinetobacter sp., were applied to evaluate their ability to decompose both inorganic phosphates and lecithin. A. niger and Acinetobacter sp. could solubilize calcium phosphates by secreting various organic acids, e.g., oxalic and formic acids. The fungus, A. niger, shows significantly higher ability of solubilizing these inorganic phosphates than Acinetobacter sp., primarily due to its secretion of abundant oxalic acid. However, the bacterium, Acinetobacter sp., could secrete more acid phosphatase than A. niger for lecithin decomposition, i.e., 9300 vs. 8500 μmol L−1 h−1. Moreover, after addition of CaCl2, the released P from lecithin was transformed to stable chlorapatite in the medium. To the contrast, Ca cations inclined to form calcium oxalate (rather than stable phosphate mineral) after the incubation of A. niger, as it induced relatively acidic environment after breaking down lecithin. Therefore, this work sheds light on the bright future of applying bacteria and Ca cations in OP pollutant management.
Peripheral Nerve Ligation Elicits Widespread Alterations in Cortical Sensory Evoked and Spontaneous Activity
Authors: Ashby Donovan M. , LeDue Jeffrey , Murphy Timothy H. , McGirr Alexander 
Published: October 2019

AbstractPeripheral neuropathies result in adaptation in primary sensory and other regions of cortex, and provide a framework for understanding the localized and widespread adaptations that arise from altered sensation. Mesoscale cortical imaging achieves high temporal resolution of activity using optical sensors of neuronal activity to simultaneously image across a wide expanse of cortex and capture this adaptation using sensory-evoked and spontaneous cortical activity. Saphenous nerve ligation in mouse is an animal model of peripheral neuropathy that produces hyperalgesia circumscribed to the hindlimb. We performed saphenous nerve ligation or sham, followed by mesoscale cortical imaging using voltage sensitive dye (VSD) after ten days. We utilized subcutaneous electrical stimulation at multiple stimulus intensities to characterize sensory responses after ligation or sham, and acquired spontaneous activity to characterize functional connectivity and large scale cortical network reorganization. Relative to sham animals, the primary sensory-evoked response to hindlimb stimulation in ligated animals was unaffected in magnitude at all stimulus intensities. However, we observed a diminished propagating wave of cortical activity at lower stimulus intensities in ligated animals after hindlimb, but not forelimb, sensory stimulation. We simultaneously observed a widespread decrease in cortical functional connectivity, where midline association regions appeared most affected. These results are consistent with localized and broad alterations in intracortical connections in response to a peripheral insult, with implications for novel circuit level understanding and intervention for peripheral neuropathies and other conditions affecting sensation.
Binding partner- and force-promoted changes in αE-catenin conformation probed by native cysteine labeling
Authors: Terekhova Ksenia , Pokutta Sabine , Kee Yee S. , Li Jing , Tajkhorshid Emad , Fuller Gerald , Dunn Alexander R. , Weis William I. 
Published: October 2019

AbstractAdherens Junctions (AJs) are cell-cell adhesion complexes that sense and propagate mechanical forces by coupling cadherins to the actin cytoskeleton via β-catenin and the F-actin binding protein αE-catenin. When subjected to mechanical force, the cadherin•catenin complex can tightly link to F-actin through αE-catenin, and also recruits the F-actin-binding protein vinculin. In this study, labeling of native cysteines combined with mass spectrometry revealed conformational changes in αE-catenin upon binding to the E-cadherin•β-catenin complex, vinculin and F-actin. A method to apply physiologically meaningful forces in solution revealed force-induced conformational changes in αE-catenin when bound to F-actin. Comparisons of wild-type αE-catenin and a mutant with enhanced vinculin affinity using cysteine labeling and isothermal titration calorimetry provide evidence for allosteric coupling of the N-terminal β-catenin-binding and the middle (M) vinculin-binding domain of αE-catenin. Cysteine labeling also revealed possible crosstalk between the actin-binding domain and the rest of the protein. The data provide insight into how binding partners and mechanical stress can regulate the conformation of full-length αE-catenin, and identify the M domain as a key transmitter of conformational changes.
Synthetic calcium carbonate improves the effectiveness of treatments with nanolime to contrast decay in highly porous limestone
Authors: Ševčík Radek , Viani Alberto , Machová Dita , Lanzafame Gabriele , Mancini Lucia , Appavou Marie-Sousai 
Published: October 2019

AbstractThree synthetized polymorphs of calcium carbonate have been tested in combination with the suspension of nanolime particles as potential consolidating agents for contrasting stone decay and overcome some of the limitations of nanolime agents when applied to substrates with large porosity. The modifications induced in the pore network of the Maastricht limestone were analyzed with microscopy and in a non-invasive fashion with small angle neutron scattering and synchrotron radiation micro-computed tomography. A reduction in porosity and pore accessibility at the micrometric scale was detected with the latter technique, and ascribed to the improved pore-filling capacity of the consolidation agent containing CaCO3particles. These were found to be effectively bound to the carbonated nanolime, strengthening the pore-matrix microstructure. Penetration depth and positive effect on porosity were found to depend on the particle size and shape. Absence of significant changes in the fractal nature of the pore surface at the nanoscale, was interpreted as indication of the negligible contribution of nanolime-based materials in the consolidation of stones with large porosity. However, the results indicate that in such cases, their effectiveness may be enhanced when used in combination with CaCO3particles, owing to the synergic effect of chemical/structural compatibility and particle size distribution.