bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast quantum control in dissipative systems using dissipationless solutions
Authors: Impens François , Guéry-Odelin David 
Published: March 2019

AbstractWe report on a systematic geometric procedure, built up on solutions designed in the absence of dissipation, to mitigate the effects of dissipation in the control of open quantum systems. Our method addresses a standard class of open quantum systems that encompasses non-Hermitian Hamiltonians. It provides the analytical expression of the extra magnetic field to be superimposed to the driving field in order to compensate the geometric distortion induced by dissipation for spin systems, and produces an exact geometric optimization of fast population transfer. Interestingly, it also preserves the robustness properties of protocols originally optimized against noise. Its extension to two interacting spins restores a fidelity close to unity for the fast generation of Bell state in the presence of dissipation.
Tissue-specific extracellular matrix accelerates the formation of neural networks and communities in a neuron-glia co-culture on a multi-electrode array
Authors: Lam Doris , Enright Heather A. , Cadena Jose , Peters Sandra K. G. , Sales Ana Paula , Osburn Joanne J. , Soscia David A. , Kulp Kristen S. , Wheeler Elizabeth K. , Fischer Nicholas O. 
Published: March 2019

AbstractThe brain’s extracellular matrix (ECM) is a macromolecular network composed of glycosaminoglycans, proteoglycans, glycoproteins, and fibrous proteins. In vitro studies often use purified ECM proteins for cell culture coatings, however these may not represent the molecular complexity and heterogeneity of the brain’s ECM. To address this, we compared neural network activity (over 30 days in vitro) from primary neurons co-cultured with glia grown on ECM coatings from decellularized brain tissue (bECM) or MaxGel, a non-tissue-specific ECM. Cells were grown on a multi-electrode array (MEA) to enable noninvasive long-term interrogation of neuronal networks. In general, the presence of ECM accelerated the formation of networks without affecting the inherent network properties. However, specific features of network activity were dependent on the type of ECM: bECM enhanced network activity over a greater region of the MEA whereas MaxGel increased network burst rate associated with robust synaptophysin expression. These differences in network activity were not attributable to cellular composition, glial proliferation, or astrocyte phenotypes, which remained constant across experimental conditions. Collectively, the addition of ECM to neuronal cultures represents a reliable method to accelerate the development of mature neuronal networks, providing a means to enhance throughput for routine evaluation of neurotoxins and novel therapeutics.
Effects of bowel preparation on the human gut microbiome and metabolome
Authors: Nagata Naoyoshi , Tohya Mari , Fukuda Shinji , Suda Wataru , Nishijima Suguru , Takeuchi Fumihiko , Ohsugi Mitsuru , Tsujimoto Tetsuro , Nakamura Tomoka , Shimomura Akira , Yanagisawa Naohiro , Hisada Yuya , Watanabe Kazuhiro , Imbe Koh , Akiyama Junichi , Mizokami Masashi , Miyoshi-Akiyama Tohru , Uemura Naomi , Hattori Masahira 
Published: March 2019

AbstractLarge bowel preparation may cause a substantial change in the gut microbiota and metabolites. Here, we included a bowel prep group and a no-procedure control group and evaluated the effects of bowel prep on the stability of the gut microbiome and metabolome as well as on recovery. Gut microbiota and metabolome compositions were analyzed by 16S rRNA sequencing and capillary electrophoresis time-of-flight mass spectrometry, respectively. Analysis of coefficients at the genus and species level and weighted UniFrac distance showed that, compared with controls, microbiota composition was significantly reduced immediately after the prep but not at 14 days after it. For the gut metabolome profiles, correlation coefficients between before and immediately after the prep were significantly lower than those between before and 14 days after prep and were not significantly different compared with those for between-subject differences. Thirty-two metabolites were significantly changed before and immediately after the prep, but these metabolites recovered within 14 days. In conclusion, bowel preparation has a profound effect on the gut microbiome and metabolome, but the overall composition recovers to baseline within 14 days. To properly conduct studies of the human gut microbiome and metabolome, fecal sampling should be avoided immediately after bowel prep.
Independent and combined effects of dietary iron composition and selected risk factors on the risk of NAFLD in a Chinese population
Authors: Peng Xian-E. , Xu Shang-Hua , Liu Wenjuan , Hu Zhijian , Lin Zheng , Lin Xu 
Published: March 2019

AbstractIron is an essential mineral required for most forms of life. However, very little is known in relation to the different forms of dietary iron on the development of NAFLD. The aims of this study were to investigate the effects of iron intake from different food types on risk of NAFLD and whether this effect may be modified by other factors. We conducted a hospital-based case–control study including 1,273 NAFLD cases and 1,273 gender and age-matched controls. We conducted in-person interviews while participants completed a questionnaire on food habits. We assessed animal- and plant-derived intake of iron and fat. We observed that animal-derived iron intake (>4.16 mg/day) was positively associated with augmented NAFLD risk in a Chinese population (ORadjusted = 1.66 in the highest quartile compared with the lowest, 95% confidence interval [CI] = 1.01–2.73). In contrast, a high consumption of iron (>16.87 mg/day) from plant-based foods was associated with a decreased NAFLD risk (ORadjusted = 0.61 in the highest quartile compared with the lowest; 95% CI = 0.40–0.935). In addition, high intake of fat or being overweight may exacerbate this effect. Reduced consumption of iron and fat from animal sources could reduce NAFLD risk, as would weight loss.
Spin to orbital light momentum conversion visualized by particle trajectory
Authors: Arzola Alejandro V. , Chvátal Lukáš , Jákl Petr , Zemánek Pavel 
Published: March 2019

AbstractIn a tightly focused beam of light having both spin and orbital angular momentum, the beam exhibits the spin-orbit interaction phenomenon. We demonstrate here that this interaction gives rise to series of subtle, but observable, effects on the dynamics of a dielectric microsphere trapped in such a beam. In our setup, we control the strength of spin-orbit interaction with the width, polarization and vorticity of the beam and record how these parameters influence radius and orbiting frequency of the same single orbiting particle pushed by the laser beam. Using Richard and Wolf model of the non-paraxial beam focusing, we found a very good agreement between the experimental results and the theoretical model based on calculation of the optical forces using the generalized Lorenz-Mie theory extended to a non-paraxial vortex beam. Especially the radius of the particle orbit seems to be a promising parameter characterizing the spin to orbital momentum conversion independently on the trapping beam power.
Degradation pathways in standard and inverted DBP-C70 based organic solar cells
Authors: Sherafatipour Golnaz , Benduhn Johannes , Patil Bhushan R. , Ahmadpour Mehrad , Spoltore Donato , Rubahn Horst-Günter , Vandewal Koen , Madsen Morten 
Published: March 2019

AbstractAchieving long-term stability in organic solar cells is a remaining bottleneck for the commercialization of this otherwise highly appealing technology. In this work, we study the performance and stability differences in standard and inverted DBP/C70 based organic solar cells. Differences in the charge-transfer state properties of inverted and standard configuration DBP/C70 solar cells are revealed by sensitive external quantum efficiency measurements, leading to differences in the open-circuit voltages of the devices. The degradation of standard and inverted solar cell configurations at ISOS aging test conditions (ISOS-D-3 and ISOS-T-3) was investigated and compared. The results indicate that the performance drop in the small molecule bilayer solar cells is less related to changes at the D-A interface, suggesting also a pronounced morphological stability, and instead, in the case of inverted cells, dominated by degradation at the electron transport layer (ETL) bathocuproine (BCP). Photoluminescence measurements, electron-only-device characteristics, and stability measurements show improved exciton blocking, electron transport properties and a higher stability for BCP/Ag ETL stacks, giving rise to inverted devices with enhanced performance and device stability.
Interpretable genotype-to-phenotype classifiers with performance guarantees
Authors: Drouin Alexandre , Letarte Gaël , Raymond Frédéric , Marchand Mario , Corbeil Jacques , Laviolette François 
Published: March 2019

AbstractUnderstanding the relationship between the genome of a cell and its phenotype is a central problem in precision medicine. Nonetheless, genotype-to-phenotype prediction comes with great challenges for machine learning algorithms that limit their use in this setting. The high dimensionality of the data tends to hinder generalization and challenges the scalability of most learning algorithms. Additionally, most algorithms produce models that are complex and difficult to interpret. We alleviate these limitations by proposing strong performance guarantees, based on sample compression theory, for rule-based learning algorithms that produce highly interpretable models. We show that these guarantees can be leveraged to accelerate learning and improve model interpretability. Our approach is validated through an application to the genomic prediction of antimicrobial resistance, an important public health concern. Highly accurate models were obtained for 12 species and 56 antibiotics, and their interpretation revealed known resistance mechanisms, as well as some potentially new ones. An open-source disk-based implementation that is both memory and computationally efficient is provided with this work. The implementation is turnkey, requires no prior knowledge of machine learning, and is complemented by comprehensive tutorials.
Quantitative reconstruction of time-varying 3D cell forces with traction force optical coherence microscopy
Authors: Mulligan Jeffrey A. , Feng Xinzeng , Adie Steven G. 
Published: March 2019

AbstractCellular traction forces (CTFs) play an integral role in both physiological processes and disease, and are a topic of interest in mechanobiology. Traction force microscopy (TFM) is a family of methods used to quantify CTFs in a variety of settings. State-of-the-art 3D TFM methods typically rely on confocal fluorescence microscopy, which can impose limitations on acquisition speed, volumetric coverage, and temporal sampling or coverage. In this report, we present the first quantitative implementation of a new TFM technique: traction force optical coherence microscopy (TF-OCM). TF-OCM leverages the capabilities of optical coherence microscopy and computational adaptive optics (CAO) to enable the quantitative reconstruction of 3D CTFs in scattering media with minute-scale temporal sampling. We applied TF-OCM to quantify CTFs exerted by isolated NIH-3T3 fibroblasts embedded in Matrigel, with five-minute temporal sampling, using images spanning a 500 × 500 × 500 μm3 field-of-view. Due to the reliance of TF-OCM on computational imaging methods, we have provided extensive discussion of the equations, assumptions, and failure modes of these methods. By providing high-throughput, label-free, volumetric imaging in scattering media, TF-OCM is well-suited to the study of 3D CTF dynamics, and may prove advantageous for the study of large cell collectives, such as the spheroid models prevalent in mechanobiology.
The NLRP3 inflammasome modulates glycolysis by increasing PFKFB3 in an IL-1β-dependent manner in macrophages
Authors: Finucane Orla M. , Sugrue Jamie , Rubio-Araiz Ana , Guillot-Sestier Marie-Victoire , Lynch Marina A. 
Published: March 2019

AbstractInflammation and metabolism are intricately linked during inflammatory diseases in which activation of the nucleotide-binding domain–like receptors Family Pyrin Domain Containing 3 (NLRP3) inflammasome, an innate immune sensor, is critical. Several factors can activate the NLRP3 inflammasome, but the nature of the link between NLRP3 inflammasome activation and metabolism remains to be thoroughly explored. This study investigates whether the small molecule inhibitor of the NLRP3 inflammasome, MCC950, modulates the lipopolysaccharide (LPS) -and amyloid-β (Aβ)-induced metabolic phenotype and inflammatory signature in macrophages. LPS + Aβ induced IL-1β secretion, while pre-treatment with MCC950 inhibited this. LPS + Aβ also upregulated IL-1β mRNA and supernatant concentrations of TNFα, IL-6 and IL-10, however these changes were insensitive to MCC950, confirming that MCC950 specifically targets inflammasome activation in BMDMs. LPS + Aβ increased glycolysis and the glycolytic enzyme, PFKFB3, and these effects were decreased by MCC950. These findings suggest that NLRP3 inflammasome activation may play a role in modulating glycolysis. To investigate this further, the effect of IL-1β on glycolysis was assessed. IL-1β stimulated glycolysis and PFKFB3, mimicking the effect of LPS + Aβ and adding to the evidence that inflammasome activation impacts on metabolism. This contention was supported by the finding that the LPS + Aβ-induced changes in glycolysis and PFKFB3 were attenuated in BMDMs from NLRP3-deficient and IL-1R1-deficient mice. Consistent with a key role for PFKFB3 is the finding that the PFKFB3 inhibitor, 3PO, attenuated the LPS + Aβ-induced glycolysis. The data demonstrate that activation of the NLRP3 inflammasome, and the subsequent release of IL-1β, play a key role in modulating glycolysis via PFKFB3. Reinstating metabolic homeostasis by targeting the NLRP3 inflammasome-PFKFB3 axis may provide a novel therapeutic target for treatment of acute and chronic disease.
Invasive shrub re-establishment following management has contrasting effects on biodiversity
Authors: O’Loughlin Luke S , Gooden Ben , Foster Claire N. , MacGregor Christopher I. , Catford Jane A. , Lindenmayer David B. 
Published: March 2019

AbstractEffective control of an invasive species is frequently used to infer positive outcomes for the broader ecosystem. In many situations, whether the removal of an invasive plant is of net benefit to biodiversity is poorly assessed. We undertook a 10-year study on the effects of invasive shrub management (bitou bush, Chrysanthemoides monilifera ssp. rotundata) on native flora and fauna in a eucalypt forest in south-eastern Australia. Bitou bush eradication is a management priority, yet the optimal control regime (combination of herbicide spray and fire) is difficult to implement, meaning managed sites have complex management histories that vary in effectiveness of control. Here we test the long-term response of common biodiversity indicators (species richness, abundance and diversity of native plants, birds, herpetofauna and small mammals) to both the management, and the post-management status of bitou bush (% cover). While average bitou bush cover decreased with management, bitou bush consistently occurred at around half of our managed sites despite control efforts. The relationship between biodiversity and bitou bush cover following management differed from positive, neutral or negative among species groups and indicators. Native plant cover was lower under higher levels of bitou bush cover, but the abundance of birds and small mammals were positively related to bitou bush cover. Evidence suggests that the successful control of an invader may not necessarily result in beneficial outcomes for all components of biodiversity.
Hydrogen ventilation combined with mild hypothermia improves short-term neurological outcomes in a 5-day neonatal hypoxia-ischaemia piglet model
Authors: Htun Yinmon , Nakamura Shinji , Nakao Yasuhiro , Mitsuie Tsutomu , Nakamura Makoto , Yamato Satoshi , Jinnai Wataru , Koyano Kosuke , Ohta Kenichi , Morimoto Aya , Wakabayashi Takayuki , Sugino Masashiro , Fujioka Kazumichi , Kato Ikuko , Kondo Sonoko , Yasuda Saneyuki , Miki Takanori , Ueno Masaki , Kusaka Takashi 
Published: March 2019

AbstractDespite its poor outcomes, therapeutic hypothermia (TH) is the current standard treatment for neonatal hypoxic-ischaemic encephalopathy (HIE). In this study, due to its antioxidant, anti-inflammatory, and antiapoptotic properties, the effectiveness of molecular hydrogen (H2) combined with TH was evaluated by means of neurological and histological assessments. Piglets were divided into three groups: hypoxic-ischaemic insult with normothermia (NT), insult with hypothermia (TH, 33.5 ± 0.5 °C), and insult with hypothermia with H2 ventilation (TH-H2, 2.1–2.7%). H2 ventilation and TH were administered for 24 h. After ventilator weaning, neurological assessment was performed every 6 h for 5 days. On day 5, the brains of the piglets were harvested for histopathological analysis. Regarding the neurological score, the piglets in the TH-H2 group consistently had the highest score from day 2 to 5 and showed a significantly higher neurological score from day 3 compared with the NT group. Most piglets in the TH-H2 group could walk at day 3 of recovery, whereas walking ability was delayed in the two other groups. The histological results revealed that TH-H2 tended to improve the status of cortical gray matter and subcortical white matter, with a considerable reduction in cell death. In this study, the combination of TH and H2 improved short-term neurological outcomes in neonatal hypoxic-ischaemic piglets.
Anti-bacterial activity of baicalin against APEC through inhibition of quorum sensing and inflammatory responses
Authors: Peng Lu-Yuan , Yuan Meng , Wu Zong-Mei , Song Ke , Zhang Chun-Lei , An Qiang , Xia Fang , Yu Jia-Lin , Yi Peng-Fei , Fu Ben-Dong , Shen Hai-Qing 
Published: March 2019

AbstractAvian pathogenic Escherichia coli (APEC), collectively known as causative agent of extraintestinal infections, is an important cause of morbidity and mortality in poultry. Currently, quorum sensing (QS), biofilm formation and virulence factors are considered as novel prospective targets for antimicrobial therapy to control APEC invasion. In addition, inflammatory responses are also served as the major pathological features of APEC invasion. This study was aimed to explore the effect of baicalin on APEC and APEC-induced inflammatory responses. After treatment with baicalin, we mainly examined the AI-2 secretion, biofilm formation, expression of virulence genes of APEC, and the levels of inflammatory cytokines, as well as the expression of NF-κB pathway. Our results showed that baicalin significantly inhibited the QS via decreasing the AI-2 secretion, biofilm formation, and the expression of virulence genes of APEC such as LsrB, LsrK, LuxS, pfs, H-NS, fimA, fimB, fyuA, csgA, csgB, and rpoS. Moreover, baicalin significantly attenuated the release of lactate dehydrogenase (LDH), and the adhesion of APEC to chicken type II pneumocytes to reduce cell damage. Furthermore, baicalin also inhibited the expression of pro-inflammatory cytokines and NF-κB activation. Thus, our data revealed that baicalin could interfere with the quorum sensing, biofilm formation and virulence genes expression to relieve the APEC pathogenicity. Additionally, baicalin decreased the inflammatory responses of chicken type II pneumocytes induced by APEC. Taken together, these data provide a novel potential pharmaco-therapeutic approach to chicken colibacillosis.
Control of the ductile and brittle behavior of titanium alloys in diamond cutting by applying a magnetic field
Authors: Yip W. S. , To S. 
Published: March 2019

AbstractAs a result of extensive investigations into deformation mechanisms of titanium alloys, it has been found that ductile and brittle behavior occurs during diamond cutting of the alloys. Other than implementing ductile regime machining for improving machining performances, in this study, an application of magnetic field in diamond cutting is proposed to enhance the machining performances in both ductile and brittle deformations in diamond cutting of titanium alloys. Results from the experiments showed that under the influence of a magnetic field, the cutting heat at the tool/titanium interface decreased, and surface damages induced from the brittle deformation were remarkably suppressed. The surface quality of both ductile and brittle deformation areas was enhanced in a presence of the magnetic field, which the surface profiles were less distortive with fewer cracks and defects in brittle deformation regions, and the cutting forces at the transition point became less fluctuant and much smoother. This study contributes enhancements of machining performances in ductile and brittle machining in diamond cutting of titanium alloys, increasing the precise level of machined components made with titanium alloys.
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes
Authors: Singh Nirupma , Bhatia Venugopal , Singh Shubham , Bhatnagar Sonika 
Published: March 2019

AbstractMicrobe induced cardiovascular diseases (CVDs) are less studied at present. Host-pathogen interactions (HPIs) between human proteins and microbial proteins associated with CVD can be found dispersed in existing molecular interaction databases. MorCVD database is a curated resource that combines 23,377 protein interactions between human host and 432 unique pathogens involved in CVDs in a single intuitive web application. It covers endocarditis, myocarditis, pericarditis and 16 other microbe induced CVDs. The HPI information has been compiled, curated, and presented in a freely accessible web interface (http://morcvd.sblab-nsit.net/About). Apart from organization, enrichment of the HPI data was done by adding hyperlinked protein ID, PubMed, gene ontology records. For each protein in the database, drug target and interactors (same as well as different species) information has been provided. The database can be searched by disease, protein ID, pathogen name or interaction detection method. Interactions detected by more than one method can also be listed. The information can be presented in tabular form or downloaded. A comprehensive help file has been developed to explain the various options available. Hence, MorCVD acts as a unified resource for retrieval of HPI data for researchers in CVD and microbiology.
Enzymatic origin and various curvatures of metabolic scaling in microbes
Authors: Li Liyan , Wang Genxuan 
Published: March 2019

AbstractThe famous and controversial power law is a basal metabolic scaling model mainly derived from the “surface rule” or a fractal transport network. However, this law neglects biological mechanisms in the important active state. Here, we hypothesized that the relative metabolic rate and growth rate of actively growing microbes are driven by the changeable rate of their rate-limiting enzymes and concluded that natural logarithmic microbial metabolism (lnλ) and growth (or biomass) (lnM) are both dependent on limiting resources, and then developed novel models with interdependence between lnλ and lnM. We tested the models using the data obtained from the literature. We explain how and why the scaling is usually curved with the difference between microbial metabolic and growth (or biomass’s) half-saturation constants (KM, Kλ) in the active state and agree that the linear relationship of the power law is a particular case under the given condition: KM = Kλ, which means that the enzyme dynamics may drive active and basal metabolic scaling relationships. Our interdependent model is more general than the power law, which is important for integrating the ecology and biochemical processes.