bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proton Gradient-Dependent Transport of p-Glucocoumaryl Alcohol in Differentiating Xylem of Woody Plants
Authors: Tsuyama Taku , Matsushita Yasuyuki , Fukushima Kazuhiko , Takabe Keiji , Yazaki Kazufumi , Kamei Ichiro 
Published: June 2019

AbstractLignin is a cell wall component of vascular plants crucial for survival in terrestrial environments. While p-hydroxyphenyl lignin is minor, it is considered to be localised in the outermost part of the cell wall providing strong adhesion between cells, which determines cell shape. Transport of the lignin precursor from the cytosol to the cell wall is critical to regulate temporal and spatial lignin deposition; however, little information on the transport step is available. Here, we report transport activity of p-glucocoumaryl alcohol, a precursor of p-hydroxyphenyl lignin, in a broad-leaved tree (hybrid poplar, Populus sieboldii × P. grandidentata) and a coniferous tree (Japanese cypress, Chamaecyparis obtusa). Membrane vesicles of both trees were prepared from differentiating xylem with vigorous lignification and used for transport assays. Several inhibition assays indicated that not ABC transporters but the proton gradient and V-ATPase are involved in p-glucocoumaryl alcohol transport depending on ATP. These results support the hypothesis that p-glucocoumaryl alcohol is loaded into the secretory vesicles and delivered to the cell wall by exocytosis. Furthermore, this transport mechanism was common in both poplar and Japanese cypress, strongly suggesting that p-glucocoumaryl alcohol transport in the differentiating xylem is conserved within woody plants.
Food-provisioning negatively affects calf survival and female reproductive success in bottlenose dolphins
Authors: Senigaglia V. , Christiansen F. , Sprogis K. R. , Symons J. , Bejder L. 
Published: June 2019

AbstractFood-provisioning of wildlife can facilitate reliable up-close encounters desirable by tourists and, consequently, tour operators. Food-provisioning can alter the natural behavior of an animal, encouraging adverse behavior (e.g. begging for food handouts), and affect the reproductive success and the viability of a population. Studies linking food-provisioning to reproductive success are limited due to the lack of long-term datasets available, especially for long-lived species such as marine mammals. In Bunbury, Western Australia, a state-licensed food-provisioning program offers fish handouts to a limited number of free-ranging bottlenose dolphins (Tursiops aduncus). Coupled with long-term historical data, this small (<200 individuals), resident dolphin population has been extensively studied for over ten years, offering an opportunity to examine the effect of food-provisioning on the reproductive success of females (ntotal = 63;nprovisioned females = 8). Female reproductive success was estimated as the number of weaned calves produced per reproductive years and calf survival at year one and three years old was investigated. The mean reproductive success of provisioned and non-provisioned females was compared using Bayes factor. We also used generalized linear models (GLMs) to examine female reproductive success in relation to the occurrence of food-provisioning, begging behavior and location (within the study area). Furthermore, we examined the influence of these variables and birth order and climatic fluctuations (e.g. El Niño Southern Oscillation) on calf survival. Bayes factor analyses (Bayes factor = 6.12) and results from the best fitting GLMs showed that female reproductive success and calf survival were negatively influenced by food-provisioning. The negative effects of food-provisioning, although only affecting a small proportion of the adult females’ population (13.2%), are of concern, especially given previous work showing that this population is declining.
Palladium/palladium oxide coated electrospun fibers for wearable sweat pH-sensors
Authors: Diculescu Victor C. , Beregoi Mihaela , Evanghelidis Alexandru , Negrea Raluca F. , Apostol Nicoleta G. , Enculescu Ionut 
Published: June 2019

AbstractThe work describes the development of a flexible, hydrogel embedded pH-sensor that can be integrated in inexpensive wearable and non-invasive devices at epidermal level for electrochemical quantification of H+ ions in sweat. Such a device can be useful for swift, real time diagnosis and for monitoring specific conditions. The sensors’ working electrodes are flexible poly(methyl methacrylate) electrospun fibers coated with a thin gold layer and electrochemically functionalized with nanostructured palladium/palladium oxide. The response to H+ ions is investigated by cyclic voltammetry and electrochemical impedance spectroscopy while open circuit potential measurements show a sensitivity of aprox. −59 mV per pH unit. The modification of the sensing interface upon basic and acid treatment is characterized by scanning and transmission electron microscopy and the chemical composition by X-ray photoelectron spectroscopy. In order to demonstrate the functionality of the pH-sensor at epidermal level, as a wearable device, the palladium/palladium oxide working electrode and silver/silver chloride reference electrode are embedded within a pad of polyacrylamide hydrogel and measurements in artificial sweat over a broad pH range were performed. Sensitivity up to −28 mV/pH unit, response time below 30 s, temperature dependence of approx. 1 mV/°C as well as the minimum volume to which the sensor responses of 250 nanoliters were obtained for this device. The proposed configuration represents a viable alternative making use of low-cost and fast fabrication processes and materials.
PolyBall: A new adsorbent for the efficient removal of endotoxin from biopharmaceuticals
Authors: Razdan Sidharth , Wang Jee-Ching , Barua Sutapa 
Published: June 2019

AbstractThe presence of endotoxin, also known as lipopolysaccharides (LPS), as a side product appears to be a major drawback for the production of certain biomolecules that are essential for research, pharmaceutical, and industrial applications. In the biotechnology industry, gram-negative bacteria (e.g., Escherichia coli) are widely used to produce recombinant products such as proteins, plasmid DNAs and vaccines. These products are contaminated with LPS, which may cause side effects when administered to animals or humans. Purification of LPS often suffers from product loss. For this reason, special attention must be paid when purifying proteins aiming a product as free as possible of LPS with high product recovery. Although there are a number of methods for removing LPS, the question about how LPS removal can be carried out in an efficient and economical way is still one of the most intriguing issues and has no satisfactory solution yet. In this work, polymeric poly-ε-caprolactone (PCL) nanoparticles (NPs) (dP = 780 ± 285 nm) were synthesized at a relatively low cost and demonstrated to possess sufficient binding sites for LPS adsorption and removal with ~100% protein recovery. The PCL NPs removed greater than 90% LPS from protein solutions suspended in water using only one milligram (mg) of NPs, which was equivalent to ~1.5 × 106 endotoxin units (EU) per mg of particle. The LPS removal efficacy increased to a higher level (~100%) when phosphate buffered saline (PBS containing 137 mM NaCl) was used as a protein suspending medium in place of water, reflecting positive effects of increasing ionic strength on LPS binding interactions and adsorption. The results further showed that the PCL NPs not only achieved 100% LPS removal but also ~100% protein recovery for a wide concentration range from 20–1000 μg/ml of protein solutions. The NPs were highly effective in different buffers and pHs. To scale up the process further, PCL NPs were incorporated into a supporting cellulose membrane which promoted LPS adsorption further up to ~100% just by running the LPS-containing water through the membrane under gravity. Its adsorption capacity was 2.8 × 106 mg of PCL NPs, approximately 2 -fold higher than that of NPs alone. This is the first demonstration of endotoxin separation with high protein recovery using polymer NPs and the NP-based portable filters, which provide strong adsorptive interactions for LPS removal from protein solutions. Additional features of these NPs and membranes are biocompatible (environment friendly) recyclable after repeated elution and adsorption with no significant changes in LPS removal efficiencies. The results indicate that PCL NPs are an effective LPS adsorbent in powder and membrane forms, which have great potential to be employed in large-scale applications.
Engineering a 3D functional human peripheral nerve in vitro using the Nerve-on-a-Chip platform
Authors: Sharma Anup D. , McCoy Laurie , Jacobs Elizabeth , Willey Hannah , Behn Jordan Q. , Nguyen Hieu , Bolon Brad , Curley J. Lowry , Moore Michael J. 
Published: June 2019

AbstractDevelopment of “organ-on-a-chip” systems for neuroscience applications are lagging due in part to the structural complexity of the nervous system and limited access of human neuronal & glial cells. In addition, rates for animal models in translating to human success are significantly lower for neurodegenerative diseases. Thus, a preclinical in vitro human cell-based model capable of providing critical clinical metrics such as nerve conduction velocity and histomorphometry are necessary to improve prediction and translation of in vitro data to successful clinical trials. To answer this challenge, we present an in vitro biomimetic model of all-human peripheral nerve tissue capable of showing robust neurite outgrowth (~5 mm), myelination of hNs by primary human Schwann cells (~5%), and evaluation of nerve conduction velocity (0.13–0.28 m/sec), previously unrealized for any human cell-based in vitro system. To the best of our knowledge, this Human Nerve-on-a-chip (HNoaC) system is the first biomimetic microphysiological system of myelinated human peripheral nerve which can be used for evaluating electrophysiological and histological metrics, the gold-standard assessment techniques previously only possible with in vivo studies.
Deep-learning-based imaging-classification identified cingulate island sign in dementia with Lewy bodies
Authors: Iizuka Tomomichi , Fukasawa Makoto , Kameyama Masashi 
Published: June 2019

AbstractThe differentiation of dementia with Lewy bodies (DLB) from Alzheimer’s disease (AD) using brain perfusion single photon emission tomography is important but is challenging because these conditions exhibit typical features. The cingulate island sign (CIS) is the most recently identified specific feature of DLB for a differential diagnosis. The current study aimed to examine the usefulness of deep-learning-based imaging classification for the diagnoses of DLB and AD. Furthermore, we investigated whether CIS was emphasized by a deep convolutional neural network (CNN) during differentiation. Brain perfusion single photon emission tomography images from 80 patients, each with DLB and AD, and 80 individuals with normal cognition (NL) were used for training and 20 each for final testing. The CNN was trained on brain surface perfusion images. Gradient-weighted class activation mapping (Grad-CAM) was applied to the CNN to visualize the features that was emphasized by the trained CNN. The binary classifications between DLB and NL, DLB and AD, and AD and NL were 93.1%, 89.3%, and 92.4% accurate, respectively. The CIS ratios closely correlated with the output scores before softmax for DLB–AD discrimination (DLB/AD scores). The Grad-CAM highlighted CIS in the DLB discrimination. Visualization of learning process by guided Grad-CAM revealed that CIS became more focused by the CNN as the training progressed. The DLB/AD score was significantly associated with the three core features of DLB. Deep-learning-based imaging classification was useful for an objective and accurate differentiation of DLB from AD and for predicting clinical features of DLB. The CIS was identified as a specific feature during DLB classification. The visualization of specific features and learning processes could be critical in deep learning to discover new imaging features.
Self-assembly of plant protein fibrils interacting with superparamagnetic iron oxide nanoparticles
Authors: Li Jing , Pylypchuk Ievgen , Johansson Daniel P. , Kessler Vadim G. , Seisenbaeva Gulaim A. , Langton Maud 
Published: June 2019

AbstractIn situ fibrillation of plant proteins in presence of the superparamagnetic iron oxide nanoparticles (NP) promoted formation of a hybrid nanocomposite. The morphology of NP-fibril composite was revealed using ex-situ atomic force microscopy (AFM) in air. The NP-fibrils were associated into extended multi-fibril structures, indicating that the addition of NPs promoted protein association via β-sheet assembly. Real-time movement of NPs attached to fibrils under an external magnetic field was visualized using in-situ AFM in liquid, revealing that composite structures were stable at low pH, and displaying dipolar property of the NPs in the composite at high pH. Changes in magnetic properties of NPs when interacting with protein fibrils were quantitatively mapped using magnetic force microscopy (MFM). The magnetic moment of the NPs in composite was increased by co-existing with protein at low pH, while their dipolar nature was maintained at high pH. Self-assembly of the protein into fibrils is accelerated with increasing NP concentration within an optimal range, which is attributed to a fibrillation-competent conformation of the peptides. The latter was explained by the formation of favorable hydrogen bonds, electrostatic interactions, and efficient surface energy transfer between NPs and proteins.
Computational analysis of single-cell transcriptomics data elucidates the stabilization of Oct4 expression in the E3.25 mouse preimplantation embryo
Authors: Gerovska Daniela , Araúzo-Bravo Marcos J. 
Published: June 2019

AbstractOur computational analysis focuses on the 32- to 64-cell mouse embryo transition, Embryonic day (E3.25), whose study in literature is concentrated mainly on the search for an early onset of the second cell-fate decision, the specification of the inner cell mass (ICM) to primitive endoderm (PE) and epiblast (EPI). We analysed single-cell (sc) microarray transcriptomics data from E3.25 using Hierarchical Optimal k-Means (HOkM) clustering, and identified two groups of ICM cells: a group of cells from embryos with less than 34 cells (E3.25-LNCs), and another group of cells from embryos with more than 33 cells (E3.25-HNCs), corresponding to two developmental stages. Although we found massive underlying heterogeneity in the ICM cells at E3.25-HNC with over 3,800 genes with transcriptomics bifurcation, many of which are PE and EPI markers, we showed that the E3.25-HNCs are neither PE nor EPI. Importantly, analysing the differently expressed genes between the E3.25-LNCs and E3.25-HNCs, we uncovered a non-autonomous mechanism, based on a minimal number of four inner-cell contacts in the ICM, which activates Oct4 in the preimplantation embryo. Oct4 is highly expressed but unstable at E3.25-LNC, and stabilizes at high level at E3.25-HNC, with Bsg highly expressed, and the chromatin remodelling program initialised to establish an early naïve pluripotent state. Our results indicate that the pluripotent state we found to exist in the ICM at E3.25-HNC is the in vivo counterpart of a new, very early pluripotent state. We compared the transcriptomics profile of this in vivo E3.25-HNC pluripotent state, together with the profiles of E3.25-LNC, E3.5 EPI and E4.5 EPI cells, with the profiles of all embryonic stem cells (ESCs) available in the GEO database from the same platform (over 600 microarrays). The shortest distance between the set of inner cells (E3.25, E3.5 and E4.5) and the ESCs is between the E3.25-HNC cells and 2i + LIF ESCs; thus, the developmental transition from 33 to 34 cells decreases dramatically the distance with the naïve ground state of the 2i + LIF ESCs. We validated the E3.25 events through analysis of scRNA-seq data from early and late 32-cell ICM cells.
Intestinal translocation of enterococci requires a threshold level of enterococcal overgrowth in the lumen
Authors: Archambaud Cristel , Derré-Bobillot Aurélie , Lapaque Nicolas , Rigottier-Gois Lionel , Serror Pascale 
Published: June 2019

AbstractEnterococci are subdominant members of the human gastrointestinal microbiota. Enterococcus faecalis is generally harmless for healthy individuals, but it can cause a diverse range of infections in immunodeficient or elderly patients with severe underlying diseases. In this study, we analysed the levels of intestinal translocation of indigenous enterococci in C57BL/6, CF-1 and CX3CR1−/− mice upon clindamycin antibiotic-induced dysbiosis. We found that C57BL/6 was the most permissive model for enterococcal translocation and that initiation of E. faecalis translocation coincided with a threshold of enterococcal colonisation in the gut lumen, which once reached, triggered E. faecalis dissemination to deeper organs. We showed that the extent to which E. faecalis clinical strain VE14821 competed with indigenous enterococci differed between the C57BL/6 and CX3CR1−/− models. Finally, using a simplified gnotobiotic model, we observed E. faecalis crossing an intact intestinal tract using intestinal epithelial cells as one route to reach the lamina propria. Our study opens new perspectives for assessing the effect of various immunodeficiencies and for investigating mechanisms underlying enterococcal translocation.
Localization of RalB signaling at endomembrane compartments and its modulation by autophagy
Authors: Singh Manish Kumar , Martin Alexandre P. J. , Joffre Carine , Zago Giulia , Camonis Jacques , Coppey Mathieu , Parrini Maria Carla 
Published: June 2019

AbstractThe monomeric GTPase RalB controls crucial physiological processes, including autophagy and invasion, but it still remains unclear how this multi-functionality is achieved. Previously, we reported that the RalGEF (Guanine nucleotide Exchange Factor) RGL2 binds and activates RalB to promote invasion. Here we show that RGL2, a major activator of RalB, is also required for autophagy. Using a novel automated image analysis method, Endomapper, we quantified the endogenous localization of the RGL2 activator and its substrate RalB at different endomembrane compartments, in an isogenic normal and Ras-transformed cell model. In both normal and Ras-transformed cells, we observed that RGL2 and RalB substantially localize at early and recycling endosomes, and to lesser extent at autophagosomes, but not at trans-Golgi. Interestingly the use of a FRET-based RalB biosensor indicated that RalB signaling is active at these endomembrane compartments at basal level in rich medium. Furthermore, induction of autophagy by nutrient starvation led to a considerable reduction of early and recycling endosomes, in contrast to the expected increase of autophagosomes, in both normal and Ras-transformed cells. However, autophagy mildly affected relative abundances of both RGL2 and RalB at early and recycling endosomes, and at autophagosomes. Interestingly, RalB activity increased at autophagosomes upon starvation in normal cells. These results suggest that the contribution of endosome membranes (carrying RGL2 and RalB molecules) increases total pool of RGL2-RalB at autophagosome forming compartments and might contribute to amplify RalB signaling to support autophagy.
Evolutionary analysis of human parechovirus type 3 and clinical outcomes of infection during the 2017–18 Australian epidemic
Authors: Chamings Anthony , Druce Julian , Caly Leon , Yoga Yano , Britton Philip N. , Macartney Kristine K. , Alexandersen Soren 
Published: June 2019

AbstractHuman parechovirus type 3 (HPeV3) can cause severe sepsis-like illness in young infants and may be associated with long term neurodevelopmental delay later in childhood. We investigated the molecular epidemiology of HPeV infection in thirty three infants requiring hospitalization before, during and after the peak of the 2017/18 HPeV epidemic wave in Australia. During the peak of the epidemic, all cases were infected with an HPeV3, while before and after the peak, HPeV1 was the predominant type detected. The predominant HPeV3 was the recombinant HPeV3 also detected in the 2013/14 and 2015/16 Australian epidemics. Sepsis-like or meningitis-like symptoms were only reported in cases infected with the recombinant HPeV3. Phylogenetic analysis of the recombinant HPeV3 revealed that the virus continued to evolve, also between the Australian outbreaks, thus indicating continued circulation, despite not being detected and reported in Australia or elsewhere in between epidemic waves. The recombinant HPeV3 continued to show a remarkable stability in its capsid amino acid sequence, further strengthening our previous argument for development of a vaccine or immunotherapeutics to reduce the severity of HPeV3 outbreaks due to this virus.
In-depth analysis of swim bladder-associated microbiota in rainbow trout (Oncorhynchus mykiss)
Authors: Villasante Alejandro , Ramírez Carolina , Rodríguez Héctor , Catalán Natalia , Díaz Osmán , Rojas Rodrigo , Opazo Rafael , Romero Jaime 
Published: June 2019

AbstractOur knowledge regarding microbiota associated with the swim bladder of physostomous, fish with the swim bladder connected to the esophagus via the pneumatic duct, remains largely unknown. The goal of this study was to conduct the first in-depth characterization of the swim bladder-associated microbiota using high-throughput sequencing of the V4 region of the 16 S rRNA gene in rainbow trout (Oncorhynchus mykiss). We observed major differences in bacterial communities composition between swim bladder-associated microbiota and distal intestine digesta microbiota in fish. Whilst bacteria genera, such as Cohnella, Lactococcus and Mycoplasma were more abundant in swim bladder-associated microbiota, Citrobacter, Rhodobacter and Clavibacter were more abundant in distal intestine digesta microbiota. The presumptive metabolic function analysis (PICRUSt) revealed several metabolic pathways to be more abundant in the swim bladder-associated microbiota, including metabolism of carbohydrates, nucleotides and lipoic acid as well as oxidative phosphorylation, cell growth, translation, replication and repair. Distal intestine digesta microbiota showed greater abundance of nitrogen metabolism, amino acid metabolism, biosynthesis of unsaturated fatty acids and bacterial secretion system. We demonstrated swim bladder harbors a unique microbiota, which composition and metabolic function differ from microbiota associated with the gut in fish.