bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhalational Anesthetics Induce Neuronal Protein Aggregation and Affect ER Trafficking
Authors: Coghlan Matthew , Richards Elizabeth , Shaik Sadiq , Rossi Pablo , Vanama Ramesh Babu , Ahmadi Saumel , Petroz Christelle , Crawford Mark , Maynes Jason T. 
Published: March 2018

AbstractAnesthetic agents have been implicated in the causation of neurological and cognitive deficits after surgery, the exacerbation of chronic neurodegenerative disease, and were recently reported to promote the onset of the neurologic respiratory disease Congenital Central Hypoventilation Syndrome (CCHS), related to misfolding of the transcription factor Phox2B. To study how anesthetic agents could affect neuronal function through alterations to protein folding, we created neuronal cell models emulating the graded disease severity of CCHS. We found that the gas anesthetic isoflurane and the opiate morphine potentiated aggregation and mislocalization of Phox2B variants, similar to that seen in CCHS, and observed transcript and protein level changes consistent with activation of the endoplasmic reticulum (ER) unfolded protein response. Attenuation of ER stress pathways did not result in a correction of Phox2B misfolding, indicating a primary effect of isoflurane on protein structure. We also observed that isoflurane hindered the folding and activity of proteins that rely heavily on ER function, like the CFTR channel. Our results show how anesthetic drugs can alter protein folding and induce ER stress, indicating a mechanism by which these agents may affect neuronal function after surgery.
Freestanding photocatalytic materials based on 3D graphene and polyporphyrins
Authors: Ussia Martina , Bruno Elena , Spina Emanuela , Vitalini Daniele , Pellegrino Giovanna , Ruffino Francesco , Privitera Vittorio , Carroccio Sabrina C. 
Published: March 2018

AbstractA new concept in the formulation of hybrid nanostructured materials combining high quality graphene 3D supported by Nickel foam and polyporphyrins for visible light photocatalytic application is here reported. Our innovative approach involves the development of a freestanding device able to: i) offer a high surface area to bind the photosensitizers by π-π interactions, and ii) enhance stability and photocatalytic efficiency by using cyclic porphyrin polymers. For these purposes, homo- and co-polymerization reactions by using different porphyrin (free or zinc complexed) monomers were performed. The microscopic structures and morphology of graphene polymer nanocomposites were investigated by using Scanning Electron Microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and Atomic Force Microscopy (AFM). Finally, photocatalytic activity under visible light irradiation of the obtained nanocomposites was tested, by using methylene blue (MB) as organic pollutant. The obtained data suggested that hindered cyclic polymeric structures stacked on graphene surface by non-covalent interactions, restrict the formation of non photoactive aggregates and, as a consequence, induce an enhancement of photocatalytic activity. Remarkably, our systems show a degradation efficiency in the visible-light range much higher than other similar devices containing nanoporphyrin units reported in literature.
Magnetic field effect on the energy levels of an exciton in a GaAs quantum dot: Application for excitonic lasers
Authors: Jahan K. Luhluh , Boda A. , Shankar I. V. , Raju Ch. Narasimha , Chatterjee Ashok 
Published: March 2018

AbstractThe problem of an exciton trapped in a Gaussian quantum dot (QD) of GaAs is studied in both two and three dimensions in the presence of an external magnetic field using the Ritz variational method, the 1/N expansion method and the shifted 1/N expansion method. The ground state energy and the binding energy of the exciton are obtained as a function of the quantum dot size, confinement strength and the magnetic field and compared with those available in the literature. While the variational method gives the upper bound to the ground state energy, the 1/N expansion method gives the lower bound. The results obtained from the shifted 1/N expansion method are shown to match very well with those obtained from the exact diagonalization technique. The variation of the exciton size and the oscillator strength of the exciton are also studied as a function of the size of the quantum dot. The excited states of the exciton are computed using the shifted 1/N expansion method and it is suggested that a given number of stable excitonic bound states can be realized in a quantum dot by tuning the quantum dot parameters. This can open up the possibility of having quantum dot lasers using excitonic states.
Nature-Inspired Hierarchical Steels
Authors: Cao Shan Cecilia , Liu Jiabin , Zhu Linli , Li Ling , Dao Ming , Lu Jian , Ritchie Robert O. 
Published: March 2018

AbstractMaterials can be made strong, but as such they are often brittle and prone to fracture when under stress. Inspired by the exceptionally strong and ductile structure of byssal threads found in certain mussels, we have designed and manufactured a multi-hierarchical steel, based on an inexpensive austenitic stainless steel, which defeats this “conflict” by possessing both superior strength and ductility. These excellent mechanical properties are realized by structurally introducing sandwich structures at both the macro- and nano-scales, the latter via an isometric, alternating, dual-phase crystal phases comprising nano-band austenite and nano-lamellar martensite, without change in chemical composition. Our experiments (transmission and scanning electron microscopy, electron back-scattered diffraction, nano-indentation and tensile tests) and micromechanics simulation results reveal a synergy of mechanisms underlying such exceptional properties. This synergy is key to the development of vastly superior mechanical properties, and may provide a unique strategy for the future development of new super strong and tough (damage-tolerant), lightweight and inexpensive structural materials.
Predation scars may influence host susceptibility to pathogens: evaluating the role of corallivores as vectors of coral disease
Authors: Nicolet K. J. , Chong-Seng K. M. , Pratchett M. S. , Willis B. L. , Hoogenboom M. O. 
Published: March 2018

AbstractInfectious diseases not regulated by host density, such as vector-borne diseases, have the potential to drive population declines and extinctions. Here we test the vector potential of the snailDrupellasp. and butterflyfishChaetodon plebeiusfor two coral diseases, black band (BBD) and brown band (BrB) disease.Drupellatransmitted BrB to healthy corals in 40% of cases immediately following feeding on infected corals, and even in 12% of cases 12 and 24 hours following feeding. However,Drupellawas unable to transmit BBD in either transmission treatment. In a field experiment testing the vector potential of naturally-occurring fish assemblages, equivalent numbers of caged and uncaged coral fragments became infected with either BrB, BBD or skeletal eroding band, indicating that corallivorous fish were unlikely to have caused transmission. In aquaria,C.plebeiusdid not transmit either BBD or BrB, even following extended feeding on both infected and healthy nubbins. A literature review confirmed only four known coral disease vectors, all invertebrates, corroborating our conclusion that polyp-feeding fishes are unlikely to be vectors of coral diseases. This potentially because polyp-feeding fishes produce shallow lesions, not allowing pathogens to invade coral tissues. In contrast, corallivorous invertebrates that create deeper feeding scars increase pathogens transmission.
Long term potentiation, but not depression, in interlamellar hippocampus CA1
Authors: Sun Duk-gyu , Kang Hyeri , Tetteh Hannah , Su Junfeng , Lee Jihwan , Park Sung-Won , He Jufang , Jo Jihoon , Yang Sungchil , Yang Sunggu 
Published: March 2018

AbstractSynaptic plasticity in the lamellar CA3 to CA1 circuitry has been extensively studied while interlamellar CA1 to CA1 connections have not yet received much attention. One of our earlier studies demonstrated that axons of CA1 pyramidal neurons project to neighboring CA1 neurons, implicating information transfer along a longitudinal interlamellar network. Still, it remains unclear whether long-term synaptic plasticity is present within this longitudinal CA1 network. Here, we investigate long-term synaptic plasticity between CA1 pyramidal cells, using in vitro and in vivo extracellular recordings and 3D holography glutamate uncaging. We found that the CA1-CA1 network exhibits NMDA receptor-dependent long-term potentiation (LTP) without direction or layer selectivity. By contrast, we find no significant long-term depression (LTD) under various LTD induction protocols. These results implicate unique synaptic properties in the longitudinal projection suggesting that the interlamellar CA1 network could be a promising structure for hippocampus-related information processing and brain diseases.
Evaluation of a dimeric-cRGD peptide for targeted PET-CT imaging of peripheral angiogenesis in diabetic mice
Authors: Hedhli Jamila , Slania Stephanie L. L. , Płoska Agata , Czerwinski Andrzej , Konopka Christian J. , Wozniak Marcin , Banach Maciej , Dobrucki Iwona T. , Kalinowski Leszek , Dobrucki Lawrence W. 
Published: March 2018

AbstractThe α
V
β3 integrin plays an important role in many physiological functions and pathological disorders. α
V
β3 is minimally expressed in normal quiescent endothelial cells, but significantly upregulated during neovascularization. In this study, we evaluated a 64Cu-labeled dimeric cRGD tracer targeted at α
V
β3 integrin and report its applicability to assess peripheral angiogenesis in diabetes mellitus (DM). We established a murine model of type-1 DM characterized by elevated glucose, glycated serum protein (GSP), and glycated hemoglobin A1c (HbA1c). We demonstrated that our imaging probe is specific to α
V
β3 integrin under both normo- and hyperglycemic conditions. We found that the analysis of in vivo PET-CT images correlated well with gamma well counting (GWC). Both GWC and PET-CT imaging demonstrated increased uptake of 64Cu-NOTA-PEG4-cRGD2 in the ischemic hindlimb in contrast to non-ischemic control. GWC of the distal ischemic tissue from DM mice showed significantly lower probe accumulation than in non-DM mice. The immunofluorescence staining of the ischemic tissues showed a 3-fold reduction in CD31 and 4-fold reduction in the α
V
β3 expression in DM vs. non-DM animals. In conclusion, we successfully demonstrated that diabetes-associated reductions in peripheral angiogenesis can be non-invasively detected with PET-CT imaging using targeted dimeric-cRGD probe.
Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs
Authors: Kiros T. G. , Derakhshani H. , Pinloche E. , D’Inca R. , Marshall Jason , Auclair E. , Khafipour E. , Van Kessel A. 
Published: March 2018

AbstractAs an alternative to antibiotic growth promoters, live yeast supplementation has proven useful in reducing weaning stress and improving performance parameters of piglets. Here, we compared the performance and hindgut microbiota of weanling piglets subjected to different pre- and post-weaning yeast supplementation regimens using a live strain of Saccharomyces cerevisiae (Actisaf Sc 47). Average feed intake and average daily weight gain of piglets within Yeast-Control and Yeast-Yeast groups were higher than those in the Control-Control group. Yeast supplementation resulted in development of microbial communities that were phylogenetically more homogenous and less dispersed compared to the microbiota of control piglets. Key bacterial taxa overrepresented in the microbiota of yeast supplemented piglets included phylum Actinobacteria, specifically family Coriobacteriaceae, as well as Firmicutes families Ruminococcaceae, Clostridiaceae, Peptostreptococcaceae, and Peptococcaceae. Correlation network analysis revealed that yeast supplementation was associated with enrichment of positive correlations among proportions of different bacterial genera within the hindgut ecosystem. In particular, within the cecal microbiota of supplemented piglets, higher numbers of positive correlations were observed among potentially beneficial genera of the phyla Actinobacteria and Firmicutes, suggesting a mechanism by which yeast supplementation may contribute to regulation of intestinal homeostasis and improved performance of piglets.
Efficacy and safety of boosted darunavir-based antiretroviral therapy in HIV-1-positive patients: results from a meta-analysis of clinical trials
Authors: Antinori A. , Lazzarin A. , Uglietti A. , Palma M. , Mancusi D. , Termini R. 
Published: March 2018

AbstractDarunavir/ritonavir (DRV/r) is a second-generation protease inhibitor used in treatment-naïve and -experienced HIV-positive adult patients. To evaluate efficacy and safety in these patient settings, we performed a meta-analysis of randomized controlled trials. We considered eight studies involving 4240 antiretroviral treatment (ART)-naïve patients and 14 studies involving 2684 ART-experienced patients. Regarding efficacy in the ART-naive patients, the virological response rate was not significantly different between DRV/r and the comparator. For the ART-experienced failing patients, the virological response rate was significantly higher with DRV/r than with the comparator (RR 1.45, 95% CI: 1.01–2.08); conversely, no significant differences were found between the treatment-experienced and virologically controlled DRV/r and comparator groups. Regarding safety, the discontinuation rates due to adverse events (AEs) and DRV/r-related serious adverse events (SAEs) did not significantly differ from the rates in the comparator group (RR 0.84, 95% CI: 0.59–1.19 and RR 0.78, 95% CI: 0.57–1.05, respectively). Our meta-analysis indicated that DRV/r-based regimens were effective and tolerable for both types of patients, which was consistent with published data.
Operating length and velocity of human vastus lateralis muscle during walking and running
Authors: Bohm S. , Marzilger R. , Mersmann F. , Santuz A. , Arampatzis A. 
Published: March 2018

AbstractAccording to the force-length-velocity relationships, the muscle force potential during locomotion is determined by the operating fibre length and velocity. We measured fascicle and muscle-tendon unit length and velocity as well as the activity of the human vastus lateralis muscle (VL) during walking and running. Furthermore, we determined the VL force-length relationship experimentally and calculated the force-length and force-velocity potentials (i.e. fraction of maximum force according to the force-length-velocity curves) for both gaits. During the active state of the stance phase, fascicles showed significantly (p < 0.05) smaller length changes (walking: 9.2 ± 4.7% of optimal length (L0); running: 9.0 ± 8.4%L0) and lower velocities (0.46 ± 0.36 L0/s; 0.03 ± 0.83 L0/s) compared to the muscle-tendon unit (walking: 19.7 ± 5.3%L0, −0.94 ± 0.32 L0/s; running: 34.5 ± 5.8%L0, −2.59 ± 0.41 L0/s). The VL fascicles operated close to optimum length (L0 = 9.4 ± 0.11 cm) in both walking (8.6 ± 0.14 cm) and running (10.1 ± 0.19 cm), resulting in high force-length (walking: 0.92 ± 0.08; running: 0.91 ± 0.14) and force-velocity (0.91 ± 0.08; 0.97 ± 0.13) potentials. For the first time we demonstrated that, in contrast to the current general conception, the VL fascicles operate almost isometrically and close to L0 during the active state of the stance phase of walking and running. The findings further verify an important contribution of the series-elastic element to VL fascicle dynamics.
Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module
Authors: Wojciechowski Michał , Różycki Bartosz , Huy Pham Dinh Quoc , Li Mai Suan , Bayer Edward A. , Cieplak Marek 
Published: March 2018

AbstractThe assembly of the polysaccharide degradating cellulosome machinery is mediated by tight binding between cohesin and dockerin domains. We have used an empirical model known as FoldX as well as molecular mechanics methods to determine the free energy of binding between a cohesin and a dockerin from Clostridium thermocellum in two possible modes that differ by an approximately 180° rotation. Our studies suggest that the full-length wild-type complex exhibits dual binding at room temperature, i.e., the two modes of binding have comparable probabilities at equilibrium. The ability to bind in the two modes persists at elevated temperatures. However, single-point mutations or truncations of terminal segments in the dockerin result in shifting the equilibrium towards one of the binding modes. Our molecular dynamics simulations of mechanical stretching of the full-length wild-type cohesin-dockerin complex indicate that each mode of binding leads to two kinds of stretching pathways, which may be mistakenly taken as evidence of dual binding.
Metal-organic framework and Tenax-TA as optimal sorbent mixture for concurrent GC-MS analysis of C1 to C5 carbonyl compounds
Authors: Dutta Tanushree , Kim Ki-Hyun , Brown Richard J. C. , Kim Yong-Hyun , Boukhvalov Danil 
Published: March 2018

AbstractWe report a multi adsorbent-based method using combinations of metal-organic frameworks (MOFs) and a commercial sorbent Tenax-TA for sampling and thermal desorption (TD) gas chromatography-mass spectrometry (GC-MS) quantification of mixtures of six (C1 to C5) aldehydes. The feasibility of this approach was demonstrated along with the optical analytical conditions for maximum recovery. Optimal TD conditions for adsorption and desorption of aldehydes using MOF-5 (Zn-based MOF)+ Tenax-TA were determined as −25 °C and 150 °C, respectively (purge volume: 100 ml). These conditions yielded good linearity (R2 = 0.997), precision, and high sensitivity. Analysis of the aldehyde mixtures yielded slightly smaller R2 values than the analysis of single species. Additionally, the performance of MOF-5+ Tenax-TA was compared with other combinations comprising of Cu-based MOF-199 and Zr-based MOF of UiO-66 topology. The results of the theoretical modelling analyses propose simultaneous interaction of the C=O group of aldehydes with open metal sites of the studied MOFs and van der Waals interaction of hydrocarbon “tail” of aldehydes with linkers of MOFs. The combined interactions significantly increased the enthalpy (eV/molecule) of formaldehyde adsorption on MOF. Our findings unravel a potential way to extend the application of GC-based detection toward concurrent analysis of organic molecules of variable sizes.
Physical and biological roles of mesoscale eddies in Japanese eel larvae dispersal in the western North Pacific Ocean
Authors: Chang Yu-Lin K. , Miyazawa Yasumasa , Béguer-Pon Mélanie , Han Yu-San , Ohashi Kyoko , Sheng Jinyu 
Published: March 2018

AbstractThe physical and biological roles of mesoscale eddies in Japanese eel larvae dispersal are investigated using a three-dimensional (3D) particle-tracking method, with a focus on the Subtropical Counter Current eddies of the western North Pacific Ocean. Virtual eel larvae (v-larvae) movements depends on the 3D ocean currents and active swimming behavior, including vertical swimming (diel vertical migration), horizontal directional swimming toward settlement habitat, and horizontal swimming toward available food. V-larvae are able to remain in eddies passively due to mesoscale eddy nonlinearity and/or actively due to attraction to rich food supplies. Thus, both physical trapping and biological attraction to food contribute to the retention of v-larvae in eddies. Physical trapping dominates the retention of v-larvae whose swimming speeds are slower than the eddy propagation speed, whereas biological food attraction prevails in the retention of v-larvae swimming faster than eddy propagation. Food availability differs between warm (anti-cyclonic) and cold (cyclonic) eddies, with the latter providing a richer food supply. Fish larvae that are retained for longer durations in cold eddies (shorter durations in warm eddies) are able to obtain more food and potentially grow faster, which enhances survival rates.
Machine learning approaches for large scale classification of produce
Authors: Gupta Otkrist , Das Anshuman J. , Hellerstein Joshua , Raskar Ramesh 
Published: March 2018

AbstractThe analysis and identification of different attributes of produce such as taxonomy, vendor, and organic nature is vital to verifying product authenticity in a distribution network. Though a variety of analysis techniques have been studied in the past, we present a novel data-centric approach to classifying produce attributes. We employed visible and near infrared (NIR) spectroscopy on over 75,000 samples across several fruit and vegetable varieties. This yielded 0.90–0.98 and 0.98–0.99 classification accuracies for taxonomy and farmer classes, respectively. The most significant factors in the visible spectrum were variations in the produce color due to chlorophyll and anthocyanins. In the infrared spectrum, we observed that the varying water and sugar content levels were critical to obtaining high classification accuracies. High quality spectral data along with an optimal tuning of hyperparameters in the support vector machine (SVM) was also key to achieving high classification accuracies. In addition to demonstrating exceptional accuracies on test data, we explored insights behind the classifications, and identified the highest performing approaches using cross validation. We presented data collection guidelines, experimental design parameters, and machine learning optimization parameters for the replication of studies involving large sample sizes.
Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations
Authors: Tomczak Aurelie , Mortensen Jonathan M. , Winnenburg Rainer , Liu Charles , Alessi Dominique T. , Swamy Varsha , Vallania Francesco , Lofgren Shane , Haynes Winston , Shah Nigam H. , Musen Mark A. , Khatri Purvesh 
Published: March 2018

AbstractGene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high throughput molecular data and generating hypotheses about underlying biological phenomena of experiments. However, the two building blocks of this analysis — the ontology and the annotations — evolve rapidly. We used gene signatures derived from 104 disease analyses to systematically evaluate how enrichment analysis results were affected by evolution of the GO over a decade. We found low consistency between enrichment analyses results obtained with early and more recent GO versions. Furthermore, there continues to be a strong annotation bias in the GO annotations where 58% of the annotations are for 16% of the human genes. Our analysis suggests that GO evolution may have affected the interpretation and possibly reproducibility of experiments over time. Hence, researchers must exercise caution when interpreting GO enrichment analyses and should reexamine previous analyses with the most recent GO version.