bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social and Reproductive Behavior of Captive Malayan Tapirs’ (Tapirus indicus): Interactions with Maternal Experience and Environmental Conditions
Authors: Arumugam Kalai Arasi , Top Marina Mohd. , Ibrahim Wan Norhamidah Wan , Buesching Christina D. , Annavi Geetha 
Published: March 2020

AbstractMalayan tapirs are listed as endangered and are bred in captivity under governmental management. The success of captive breeding programs varies and the underlying causes are unclear. Here, we investigate how tapir reproduction is affected by previous breeding experience, enclosure type/size and visitor numbers so that appropriate steps can be taken to achieve self-sustaining captive populations. Data on social and reproductive behaviors were collected from six tapirs (three males, three females), from different breeding centers in Peninsular Malaysia for 18 weeks. Results revealed that social and reproductive behavior of both sexes was significantly influenced by social and environmental conditions. Larger enclosure size tended to increase social and reproductive behaviors, whereas high number of visitors reduced initial interaction between males and females. No specific breeding month was confirmed; however, reproductive behaviors were highest in April. Overall, this study contributes to a better understanding of the relationships between social and reproductive behaviors, and captive environments on Malayan tapirs. In future, frequency of sexual interactions should be monitored regularly to identify animals exhibiting below-average frequency and who might, therefore, be prone to reproductive difficulties.
Shared Causal Paths underlying Alzheimer’s dementia and Type 2 Diabetes
Authors: Hu Zixin , Jiao Rong , Wang Panpan , Zhu Yun , Zhao Jinying , De Jager Phil , Bennett David A. , Jin Li , Xiong Momiao 
Published: March 2020

AbstractAlthough Alzheimer’s disease (AD) is a central nervous system disease and type 2 diabetes MELLITUS (T2DM) is a metabolic disorder, an increasing number of genetic epidemiological studies show clear link between AD and T2DM. The current approach to uncovering the shared pathways between AD and T2DM involves association analysis; however such analyses lack power to discover the mechanisms of the diseases. As an alternative, we developed novel causal inference methods for genetic studies of AD and T2DM and pipelines for systematic multi-omic casual analysis to infer multilevel omics causal networks for the discovery of common paths from genetic variants to AD and T2DM. The proposed pipelines were applied to 448 individuals from the ROSMAP Project. We identified 13 shared causal genes, 16 shared causal pathways between AD and T2DM, and 754 gene expression and 101 gene methylation nodes that were connected to both AD and T2DM in multi-omics causal networks.
Classification models for Invasive Ductal Carcinoma Progression, based on gene expression data-trained supervised machine learning
Authors: Roy Shikha , Kumar Rakesh , Mittal Vaibhav , Gupta Dinesh 
Published: March 2020

AbstractEarly detection of breast cancer and its correct stage determination are important for prognosis and rendering appropriate personalized clinical treatment to breast cancer patients. However, despite considerable efforts and progress, there is a need to identify the specific genomic factors responsible for, or accompanying Invasive Ductal Carcinoma (IDC) progression stages, which can aid the determination of the correct cancer stages. We have developed two-class machine-learning classification models to differentiate the early and late stages of IDC. The prediction models are trained with RNA-seq gene expression profiles representing different IDC stages of 610 patients, obtained from The Cancer Genome Atlas (TCGA). Different supervised learning algorithms were trained and evaluated with an enriched model learning, facilitated by different feature selection methods. We also developed a machine-learning classifier trained on the same datasets with training sets reduced data corresponding to IDC driver genes. Based on these two classifiers, we have developed a web-server Duct-BRCA-CSP to predict early stage from late stages of IDC based on input RNA-seq gene expression profiles. The analysis conducted by us also enables deeper insights into the stage-dependent molecular events accompanying IDC progression. The server is publicly available at http://bioinfo.icgeb.res.in/duct-BRCA-CSP.
Backwash sediment record of the 2009 South Pacific Tsunami and 1960 Great Chilean Earthquake Tsunami
Authors: Riou Brieuc , Chaumillon Eric , Chagué Catherine , Sabatier Pierre , Schneider Jean-Luc , Walsh John-Patrick , Zawadzki Atun , Fierro Daniela 
Published: March 2020

AbstractFollowing recent tsunamis, most studies have focused on the onshore deposits, while the offshore backwash deposits, crucial for a better understanding of the hydrodynamic processes during such events and offering an opportunity for sedimentary archives of past tsunamis, have mostly been omitted. Here, we present a unique sedimentary record of the backwash from two historical tsunamis sampled in a sheltered bay in American Samoa, namely the 2009 South Pacific Tsunami and the 1960 Great Chilean Earthquake Tsunami. Although not always concomitant with a marked grain size change, backwash deposits are identified by terrestrial geochemical and mineralogical signatures, associated with basal soft sediment micro-deformations. These micro-deformations, including asymmetric flame structures, are described for the first time in historic shallow marine backwash deposits and lead us to propose an improved depositional mechanism for tsunami backflow based on hyperpycnal currents. Moreover, this study brings a potential new criterion to the proxy toolkit for identifying tsunami backwash deposits, namely the basal soft sediment micro-deformations. We suggest that further studies focus on these micro-deformations in order to test the representability of this criterion for tsunami backwash deposits. Sheltered shallow marine environments in areas repeatedly impacted by tsunamis have a higher potential for the reconstruction of paleo-tsunami catalogs and should be preferentially investigated for coastal risk assessment.
Immunization with DNA prime-subunit protein boost strategy based on influenza H9N2 virus conserved matrix protein M1 and its epitope screening
Authors: Liu Fen , Wang Xueliang , Zheng Mei , Xiong Feifei , Liu Xueying , Zhou Linting , Tan Wensong , Chen Ze 
Published: March 2020

AbstractDeveloping an effective universal influenza vaccine against influenza virus with highly conserved antigenic epitopes could induce a broad-spectrum immune response to prevent infection. The soluble protein M1 that can induce the M1 specific immune response was first confirmed in our previous study. In this study, we characterized the immune response induced by DNA prime-subunit protein boost strategy based on the relatively conserved matrix protein 1 (M1) in the BALB/c mouse model, and evaluated its protection ability against a lethal challenge of homologous H9N2 avian influenza virus (A/Chicken/Jiangsu/11/2002). The results showed that 100 μg DNA prime + 100 μg M1 subunit protein boost-strategy significantly increased antibody levels more than vaccination with M1 DNA or M1 subunit protein alone, and induced a more balanced Th1 / Th2 immune response, which not only can provide protection against the homologous virus but also can provide part of the cross-protection against the heterosubtypic PR8 H1N1 strain. In addition, we used an Elispot assay to preliminary screen the T cell epitope in M1 protein, and identified that p22 (M111–25VLSIIPSGPLKAEIA) epitope was the only immunodominant M1-specific CD4+T cell epitopes, which could be helpful in understanding the function of influenza virus T cell epitopes.
Prototyping Trastuzumab Docetaxel Immunoliposomes with a New FCM-Based Method to Quantify Optimal Antibody Density on Nanoparticles
Authors: Rodallec A. , Franco C. , Robert S. , Sicard G. , Giacometti S. , Lacarelle B. , Bouquet F. , Savina A. , Lacroix R. , Dignat-George F. , Ciccolini J. , Poncelet P. , Fanciullino R. 
Published: March 2020

AbstractDeveloping targeted nanoparticles is a rising strategy to improve drug delivery in oncology. Antibodies are the most commonly used targeting agents. However, determination of their optimal number at the surface remains a challenging issue, mainly due to the difficulties in measuring precisely surface coating levels when prototyping nanoparticles. We developed an original quantitative assay to measure the exact number of coated antibodies per nanoparticle. Using flow cytometry optimized for submicron particle analysis and beads covered with known amounts of human IgG-kappa mimicking various amounts of antibodies, this new method was tested as part of the prototyping of docetaxel liposomes coated with trastuzumab against Her2+ breast cancer. This quantification method allowed to discriminate various batches of immunoliposomes depending on their trastuzumab density on nanoparticle surface (i.e., 330 (Immunoliposome-1), 480 (Immunoliposome-2) and 690 (Immunoliposome-3), p = 0.004, One-way ANOVA). Here we showed that optimal number of grafted antibodies on nanoparticles should be finely tuned and highest density of targeting agent is not necessarily associated with highest efficacy. Overall, this new method should help to better prototype third generation nanoparticles.
Latitudinal consistency of biomass size spectra - benthic resilience despite environmental, taxonomic and functional trait variability
Authors: Mazurkiewicz Mikołaj , Górska Barbara , Renaud Paul E. , Włodarska-Kowalczuk Maria 
Published: March 2020

AbstractGlobal warming is expected to cause reductions in organism body size, a fundamental biological unit important in determining biological processes. Possible effects of increasing temperature on biomass size spectra in coastal benthic communities were investigated. We hypothesized higher proportions of smaller size classes in warmer conditions. Soft bottom infauna samples were collected in six Norwegian and Svalbard fjords, spanning wide latitudinal (60–81°N) and bottom water temperature gradients (from −2 to 8 °C). Investigated fjords differed in terms of environmental settings (e.g., pigments or organic carbon in sediments). The slopes of normalised biomass size spectra (NBSS) did not differ among the fjords, while the benthic biomass and NBSS intercepts varied and were related to chlorophyllaand δ13C in sediments. The size spectra based on both abundance and biomass remained consistent, regardless of the strong variability in macrofauna taxonomic and functional trait composition. Variable relationships between temperature and body size were noted for particular taxa. Our results indicate that while benthic biomass depends on the nutritional quality of organic matter, its partitioning among size classes is consistent and independent of environmental and biological variability. The observed size structure remains a persistent feature of studied communities and may be resilient to major climatic changes.
Social media, nature, and life satisfaction: global evidence of the biophilia hypothesis
Authors: Chang Chia-chen , Cheng Gwyneth Jia Yi , Nghiem Thi Phuong Le , Song Xiao Ping , Oh Rachel Rui Ying , Richards Daniel R. , Carrasco L. Roman 
Published: March 2020

AbstractHumans may have evolved a need to connect with nature, and nature provides substantial cultural and social values to humans. However, quantifying the connection between humans and nature at a global scale remains challenging. We lack answers to fundamental questions: how do humans experience nature in different contexts (daily routines, fun activities, weddings, honeymoons, other celebrations, and vacations) and how do nature experiences differ across countries? We answer these questions by coupling social media and artificial intelligence using 31,534 social media photographs across 185 countries. We find that nature was more likely to appear in photographs taken during a fun activity, honeymoon, or vacation compared to photographs of daily routines. More importantly, the proportion of photographs with nature taken during fun activities is associated with national life satisfaction scores. This study provides global evidence of the biophilia hypothesis by showing a connection between humans and nature that contributes to life satisfaction and highlights how nature serves as background to many of our positive memories.
A Rationale for the Use of Clotted Vertebral Bone Marrow to Aid Tissue Regeneration Following Spinal Surgery
Authors: Salamanna F. , Contartese D. , Giavaresi G. , Sicuro L. , Barbanti Brodano G. , Gasbarrini A. , Fini M. 
Published: March 2020

AbstractVertebral body bone marrow aspirate (V-BMA), easily accessible simultaneously with the preparation of the site for pedicle screw insertion during spinal procedures, is becoming an increasingly used cell therapy approach in spinal surgery. However, the main drawbacks for V-BMA use are the lack of a standardized procedure and of a structural texture with the possibility of diffusion away from the implant site. The aim of this study was to evaluate, characterize and compare the biological characteristics of MSCs from clotted V-BMA and MSCs from whole and concentrate V-BMAs. MSCs from clotted V-BMA showed the highest cell viability and growth factors expression (TGF-β, VEGF-A, FGF2), the greatest colony forming unit (CFU) potency, cellular homogeneity, ability to differentiate towards the osteogenic (COL1AI, TNFRSF11B, BGLAP) and chondrogenic phenotype (SOX9) and the lowest ability to differentiate toward the adipogenic lineage (ADIPOQ) in comparison to all the other culture conditions. Additionally, results revealed that MSCs, differently isolated, expressed different level of HOX and TALE signatures and that PBX1 and MEIS3 were down-regulated in MSCs from clotted V-BMA in comparison to concentrated one. The study demonstrated for the first time that the cellular source inside the clotted V-BMA showed the best biological properties, representing an alternative and advanced cell therapy approach for patients undergoing spinal surgery.
Cannabidiol is an effective helper compound in combination with bacitracin to kill Gram-positive bacteria
Authors: Wassmann Claes Søndergaard , Højrup Peter , Klitgaard Janne Kudsk 
Published: March 2020

AbstractThe cannabinoid cannabidiol (CBD) is characterised in this study as a helper compound against resistant bacteria. CBD potentiates the effect of bacitracin (BAC) against Gram-positive bacteria (Staphylococcus species, Listeria monocytogenes, and Enterococcus faecalis) but appears ineffective against Gram-negative bacteria. CBD reduced the MIC value of BAC by at least 64-fold and the combination yielded an FIC index of 0.5 or below in most Gram-positive bacteria tested. Morphological changes in S. aureus as a result of the combination of CBD and BAC included several septa formations during cell division along with membrane irregularities. Analysis of the muropeptide composition of treated S. aureus indicated no changes in the cell wall composition. However, CBD and BAC treated bacteria did show a decreased rate of autolysis. The bacteria further showed a decreased membrane potential upon treatment with CBD; yet, they did not show any further decrease upon combination treatment. Noticeably, expression of a major cell division regulator gene, ezrA, was reduced two-fold upon combination treatment emphasising the impact of the combination on cell division. Based on these observations, the combination of CBD and BAC is suggested to be a putative novel treatment in clinical settings for treatment of infections with antibiotic resistant Gram-positive bacteria.
Human glutaredoxin-1 can transfer copper to isolated metal binding domains of the P1B-type ATPase, ATP7B
Authors: Maghool Shadi , Fontaine Sharon La , Roberts Blaine R. , Kwan Ann H. , Maher Megan J. 
Published: March 2020

AbstractIntracellular copper (Cu) in eukaryotic organisms is regulated by homeostatic systems, which rely on the activities of soluble metallochaperones that participate in Cu exchange through highly tuned protein-protein interactions. Recently, the human enzyme glutaredoxin-1 (hGrx1) has been shown to possess Cu metallochaperone activity. The aim of this study was to ascertain whether hGrx1 can act in Cu delivery to the metal binding domains (MBDs) of the P1B-type ATPase ATP7B and to determine the thermodynamic factors that underpin this activity. hGrx1 can transfer Cu to the metallochaperone Atox1 and to the MBDs 5-6 of ATP7B (WLN5-6). This exchange is irreversible. In a mixture of the three proteins, Cu is delivered to the WLN5-6 preferentially, despite the presence of Atox1. This preferential Cu exchange appears to be driven by both the thermodynamics of the interactions between the proteins pairs and of the proteins with Cu(I). Crucially, protein-protein interactions between hGrx1, Atox1 and WLN5-6 were detected by NMR spectroscopy both in the presence and absence of Cu at a common interface. This study augments the possible activities of hGrx1 in intracellular Cu homeostasis and suggests a potential redundancy in this system, where hGrx1 has the potential to act under cellular conditions where the activity of Atox1 in Cu regulation is attenuated.
Cellular metabolic activity marker via selective turn-ON detection of transporter protein using nitrobenzoxadiazole-based fluorescent reporter
Authors: Dutta Tanoy , Pal Kaushik , Koner Apurba L. 
Published: March 2020

AbstractA nitrobenzoxadiazole-based fluoroprobe (NBD-Bu) is designed to probe cellular metabolic activity in cancer and normal cells. NBD-Bu shows a significant fluorescence enhancement upon selective binding to the transport protein serum albumin in PBS buffer at ambient conditions. Encouraged by this finding, the site- specificity of NBD-Bu has been explored through a competitive displacement assay in the presence of site-specific markers such as warfarin and ibuprofen. Notably, even at micromolar concentrations, the probe possesses the ability to displace the site marker drug ibuprofen, efficiently. Subsequently, high-resolution fluorescence imaging results consolidated the potential of NBD-Bu for detection of abnormal cellular metabolic activity.
Going Beyond Rate Changes as the Sole Indicator for Dynamic Triggering of Earthquakes
Authors: Pankow Kristine L. , Kilb Debi 
Published: March 2020

AbstractRemote earthquake triggering is a well-established phenomenon. Triggering is commonly identified from statistically significant increases in earthquake rate coincident with the passage of seismic energy. In establishing rate changes, short duration earthquake catalogs are commonly used, and triggered sequences are not typically analyzed within the context of background seismic activity. Using 500 mainshocks and four western USA 33-yearlong earthquake catalogs, we compare the ability of three different statistical methods to identify remote earthquake triggering. Counter to many prior studies, we find remote dynamic triggering is rare (conservatively, <2% of the time). For the mainshocks associated with remote rate increases, the spatial and temporal signatures of triggering differ. We find that a rate increase coincident in time with mainshock energy alone is insufficient to conclude that dynamic triggering occurred. To classify dynamically triggered sequences, we suggest moving away from strict statistical measurements and instead use a compatibility assessment that includes multiple factors, like spatial and temporal indicators.
Rapid isothermal duplex real-time recombinase polymerase amplification (RPA) assay for the diagnosis of equine piroplasmosis
Authors: Lei Rong , Wang Xinyi , Zhang Di , Liu Yize , Chen Qijun , Jiang Ning 
Published: March 2020

AbstractEquine piroplasmosis (EP) is a severe disease of horses caused by the tick-borne protozoa Theileria equi (T. equi) and Babesia caballi (B. caballi). Infectious carriers are not always symptomatic, meaning there is a risk to non-enzootic areas. Regulatory tests for EP include sero-epidemiological methods for equine babesiosis, but these lack specificity due to cross-reactivity with other Babesia species. In this study, we present a real-time quantitative recombinase polymerase amplification (qRPA) method for fast simultaneous detection of both T. equi and B. caballi. In this method, primers and probes targeting the 18S rRNA gene of both T. equi and B. caballi, the ema-1 gene of T. equi and the bc48 gene of B. caballi were designed and evaluated. The sensitivity of qRPA was evaluated using the pUC57 plasmid DNA containing the target gene. For the pUC57-bc48 gene DNA, the R2 value was 0.983 for the concentration range 0.2 ng (4.1 × 107 DNA copies) to 2.0 fg (4.1 × 101 DNA copies). For the pUC57-ema gene DNA, the R2 value was 0.993 for the concentration range 0.2 ng (5.26 × 107 DNA copies) to 2.0 fg (5.26 × 102 DNA copies). For the pUC57-Bc18S gene DNA the R2 value was 0.976 for the concentration range 2.0 ng (4.21 × 108 DNA copies) to 2.0 fg (4.21 × 102 DNA copies). For the pUC57-Te18S gene DNA, the R2 value was 0.952 (Fig. S3b) for the concentration range 2.0 ng (4.16 × 108 DNA copies) to 2.0 fg (4.16 × 102 DNA copies). Furthermore, a duplex qRPA analysis was developed and optimized and the results showed that primers and probes targeting for the bc48 gene of B. caballi and the 18S rRNA gene of T. equi is the best combination for a duplex qRPA analysis in one reaction. The developed duplex qRPA assay has good specificity, and had negative amplification for several similar parasite. For DNA extracted from real horse blood specimens, this qRPA method has comparable sensitivity to traditional qPCR, but a simpler and more rapid operating process to obtain positive amplification. The qRPA, including the duplex strategy described here, could allow fast identification of the EP-causing T. equi and B. caballi, showing great potential for on-site EP screening of horses.
Compost Soil Microbial Fuel Cell to Generate Power using Urea as Fuel
Authors: Magotra Verjesh Kumar , Kumar Sunil , Kang T. W. , Inamdar Akbar I. , Aqueel Abu Talha , Im Hyunsik , Ghodake Gajanan , Shinde Surendra , Waghmode D. P. , Jeon H. C. 
Published: March 2020

AbstractThe acute problem of eutrophication increasing in the environment is due to the increase of industrial wastewater, synthetic nitrogen, urine, and urea. This pollutes groundwater, soil and creates a danger to aquatic life. Therefore, it is advantageous to use these waste materials in the form of urea as fuel to generate power using Microbial Fuel Cell (MFC). In this work, we studied the compost soil MFC(CSMFC) unlike typical MFC with urea from the compost as fuel and graphite as a functional electrode. The electrochemical techniques such as Cyclic Voltammetry, Chronoamperometry are used to characterise CSMFC. It is observed that the CSMFC in which the compost consists of urea concertation of 0.5 g/ml produces maximum power. Moreover, IV measurement is carried out using polarization curves in order to study its sustainability and scalability. Bacterial studies were also playing a significant role in power generation. The sustainability study revealed that urea is consumed in CSMFC to generate power. This study confirmed that urea has a profound effect on the power generation from the CSMFC. Our focus is to get power from the soil processes in future by using waste like urine, industrial wastewater, which contains much amount of urea.