bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved oil recovery in nanopores: NanoIOR
Authors: de Almeida James Moraes , Miranda Caetano Rodrigues 
Published: June 2016

AbstractFluid flow through minerals pores occurs in underground aquifers, oil and shale gas reservoirs. In this work, we explore water and oil flow through silica nanopores. Our objective is to model the displacement of water and oil through a nanopore to mimic the fluid infiltration on geological nanoporous media and the displacement of oil with and without previous contact with water by water flooding to emulate an improved oil recovery process at nanoscale (NanoIOR). We have observed a barrier-less infiltration of water and oil on the empty (vacuum) simulated 4 nm diameter nanopores. For the water displacement with oil, we have obtained a critical pressure of 600 atm for the oil infiltration, and after the flow was steady, a water layer was still adsorbed to the surface, thus, hindering the direct contact of the oil with the surface. In addition, oil displacement with water was assessed, with and without an adsorbed water layer (AWL). Without the AWL, the pressure needed for oil infiltration was 5000 atm, whereas, with the AWL the infiltration was observed for pressures as low as 10 atm. Hence, the infiltration is greatly affected by the AWL, significantly lowering the critical pressure for oil displacement.
Postnatal development of the electrophysiological properties of somatostatin interneurons in the anterior cingulate cortex of mice
Authors: Pan Geng , Yang Jian-Ming , Hu Xing-Yue , Li Xiao-Ming 
Published: June 2016

AbstractSomatostatin (SST)-positive interneurons in the anterior cingulate cortex (ACC) play important roles in neuronal diseases, memory and cognitive functions. However, their development in the ACC remains unclear. Using postnatal day 3 (P3) to P45 GIN mice, we found that most of the intrinsic membrane properties of SST interneurons in the ACC were developmentally mature after the second postnatal week and that the development of these neurons differed from that of parvalbumin (PV) interneurons in the prefrontal cortex. In addition, electrical coupling between SST interneurons appeared primarily between P12–14. The coupling probability plateaued at approximately P21–30, with a non-age-dependent development of coupling strength. The development of excitatory chemical afferents to SST interneurons occurred earlier than the development of inhibitory chemical afferents. Furthermore, eye closure attenuated the development of electrical coupling probability at P21–30 but had no effect on coupling strength. Eye closure also delayed the development of inhibitory chemical afferent frequency but had no effect on the excitatory chemical afferent amplitude, frequency or rise time. Our data suggest that SST interneurons in the ACC exhibit inherent developmental characteristics distinct from other interneuron subtypes, such as PV interneurons and that some of these characteristics are subject to environmental regulation.
Direct acceleration of electrons by a CO2 laser in a curved plasma waveguide
Authors: Yi Longqing , Pukhov Alexander , Shen Baifei 
Published: June 2016

AbstractLaser plasma interaction with micro-engineered targets at relativistic intensities has been greatly promoted by recent progress in the high contrast lasers and the manufacture of advanced micro- and nano-structures. This opens new possibilities for the physics of laser-matter interaction. Here we propose a novel approach that leverages the advantages of high-pressure CO2 laser, laser-waveguide interaction, as well as micro-engineered plasma structure to accelerate electrons to peak energy greater than 1 GeV with narrow slice energy spread (~1%) and high overall efficiency. The acceleration gradient is 26 GV/m for a 1.3 TW CO2 laser system. The micro-bunching of a long electron beam leads to the generation of a chain of ultrashort electron bunches with the duration roughly equal to half-laser-cycle. These results open a way for developing a compact and economic electron source for diverse applications.
Key diffusion mechanisms involved in regulating bidirectional water permeation across E. coli outer membrane lectin
Authors: Sachdeva Shivangi , Kolimi Narendar , Nair Sanjana Anilkumar , Rathinavelan Thenmalarchelvi 
Published: June 2016

AbstractCapsular polysaccharides (CPSs) are major bacterial virulent determinants that facilitate host immune evasion. E. coli group1 K30CPS is noncovalently attached to bacterial surface by Wzi, a lectin. Intriguingly, structure based phylogenetic analysis indicates that Wzi falls into porin superfamily. Molecular dynamics (MD) simulations further shed light on dual role of Wzi as it also functions as a bidirectional passive water specific porin. Such a functional role of Wzi was not realized earlier, due to the occluded pore. While five water specific entry points distributed across extracellular & periplasmic faces regulate the water diffusion involving different mechanisms, a luminal hydrophobic plug governs water permeation across the channel. Coincidently, MD observed open state structure of “YQF” triad is seen in sugar-binding site of sodium-galactose cotransporters, implicating its involvement in K30CPS surface anchorage. Importance of Loop 5 (L5) in membrane insertion is yet another highlight. Change in water diffusion pattern of periplasmic substitution mutants suggests Wzi’s role in osmoregulation by aiding in K30CPS hydration, corroborating earlier functional studies. Water molecules located inside β-barrel of Wzi crystal structure further strengthens the role of Wzi in osmoregulation. Thus, interrupting water diffusion or L5 insertion may reduce bacterial virulence.
Ultrasensitive proteomic quantitation of cellular signaling by digitized nanoparticle-protein counting
Authors: Jacob Thomas , Agarwal Anupriya , Ramunno-Johnson Damien , O’Hare Thomas , Gönen Mehmet , Tyner Jeffrey W. , Druker Brian J. , Vu Tania Q. 
Published: June 2016

AbstractMany important signaling and regulatory proteins are expressed at low abundance and are difficult to measure in single cells. We report a molecular imaging approach to quantitate protein levels by digitized, discrete counting of nanoparticle-tagged proteins. Digitized protein counting provides ultrasensitive molecular detection of proteins in single cells that surpasses conventional methods of quantitating total diffuse fluorescence, and offers a substantial improvement in protein quantitation. We implement this digitized proteomic approach in an integrated imaging platform, the single cell-quantum dot platform (SC-QDP), to execute sensitive single cell phosphoquantitation in response to multiple drug treatment conditions and using limited primary patient material. The SC-QDP: 1) identified pAKT and pERK phospho-heterogeneity and insensitivity in individual leukemia cells treated with a multi-drug panel of FDA-approved kinase inhibitors, and 2) revealed subpopulations of drug-insensitive CD34+ stem cells with high pCRKL and pSTAT5 signaling in chronic myeloid leukemia patient blood samples. This ultrasensitive digitized protein detection approach is valuable for uncovering subtle but important differences in signaling, drug insensitivity, and other key cellular processes amongst single cells.
GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide
Authors: Lima D. C. , Duarte F. T. , Medeiros V. K. S. , Carvalho P. C. , Nogueira F. C. S. , Araujo G. D. T. , Domont G. B. , Batistuzzo de Medeiros S. R. 
Published: June 2016

AbstractChromobacterium violaceumis a free-living bacillus with several genes that enables it survival under different harsh environments such as oxidative and temperature stresses. Here we performed a label-free quantitative proteomic study to unravel the molecular mechanisms that enableC. violaceumto survive oxidative stress. To achieve this, total proteins extracted from control andC. violaceumcultures exposed during two hours with 8 mM hydrogen peroxide were analyzed using GeLC-MS proteomics. Analysis revealed that under the stress condition, the bacterium expressed proteins that protected it from the damage caused by reactive oxygen condition and decreasing the abundance of proteins responsible for bacterial growth and catabolism. GeLC-MS proteomics analysis provided an overview of the metabolic pathways involved in the response ofC. violaceumto oxidative stress ultimately aggregating knowledge of the response of this organism to environmental stress. This study identified approximately 1500 proteins, generating the largest proteomic coverage ofC. violaceumso far. We also detected proteins with unknown function that we hypothesize to be part of new mechanisms related to oxidative stress defense. Finally, we identified the mechanism of clustered regularly interspaced short palindromic repeats (CRISPR), which has not yet been reported for this organism.
F1 rotary motor of ATP synthase is driven by the torsionally-asymmetric drive shaft
Authors: Kulish O. , Wright A. D. , Terentjev E. M. 
Published: June 2016

AbstractF1F0 ATP synthase (ATPase) either facilitates the synthesis of ATP in a process driven by the proton moving force (pmf), or uses the energy from ATP hydrolysis to pump protons against the concentration gradient across the membrane. ATPase is composed of two rotary motors, F0 and F1, which compete for control of their shared γ -shaft. We present a self-consistent physical model of F1 motor as a simplified two-state Brownian ratchet using the asymmetry of torsional elastic energy of the coiled-coil γ -shaft. This stochastic model unifies the physical concepts of linear and rotary motors and explains the stepped unidirectional rotary motion. Substituting the model parameters, all independently known from recent experiments, our model quantitatively reproduces the ATPase operation, e.g. the ‘no-load’ angular velocity is ca. 400 rad/s anticlockwise at 4 mM ATP. Increasing the pmf torque exerted by F0 can slow, stop and overcome the torque generated by F1, switching from ATP hydrolysis to synthesis at a very low value of ‘stall torque’. We discuss the motor efficiency, which is very low if calculated from the useful mechanical work it produces - but is quite high when the ‘useful outcome’ is measured in the number of H+ pushed against the chemical gradient.
Elucidating the contributions of multiple aldehyde/alcohol dehydrogenases to butanol and ethanol production in Clostridium acetobutylicum
Authors: Dai Zongjie , Dong Hongjun , Zhang Yanping , Li Yin 
Published: June 2016

AbstractEthanol and butanol biosynthesis in Clostridium acetobutylicum share common aldehyde/alcohol dehydrogenases. However, little is known about the relative contributions of these multiple dehydrogenases to ethanol and butanol production respectively. The contributions of six aldehyde/alcohol dehydrogenases of C. acetobutylicum on butanol and ethanol production were evaluated through inactivation of the corresponding genes respectively. For butanol production, the relative contributions from these enzymes were: AdhE1 > BdhB > BdhA ≈ YqhD > SMB_P058 > AdhE2. For ethanol production, the contributions were: AdhE1 > BdhB > YqhD > SMB_P058 > AdhE2 > BdhA. AdhE1 and BdhB are two essential enzymes for butanol and ethanol production. AdhE1 was relatively specific for butanol production over ethanol, while BdhB, YqhD, and SMB_P058 favor ethanol production over butanol. Butanol synthesis was increased in the adhE2 mutant, which had a higher butanol/ethanol ratio (8.15:1) compared with wild type strain (6.65:1). Both the SMB_P058 mutant and yqhD mutant produced less ethanol without loss of butanol formation, which led to higher butanol/ethanol ratio, 10.12:1 and 10.17:1, respectively. To engineer a more efficient butanol-producing strain, adhE1 could be overexpressed, furthermore, adhE2, SMB_P058, yqhD are promising gene inactivation targets. This work provides useful information guiding future strain improvement for butanol production.
Serum Concentrations of Ubiquitin C-Terminal Hydrolase-L1 and Glial Fibrillary Acidic Protein after Pediatric Traumatic Brain Injury
Authors: Mondello Stefania , Kobeissy Firas , Vestri Annarita , Hayes Ronald L. , Kochanek Patrick M. , Berger Rachel P. 
Published: June 2016

AbstractObjective reliable markers to assess traumatic brain injury (TBI) and predict outcome soon after injury are a highly needed tool for optimizing management of pediatric TBI. We assessed serum concentrations of Glial Fibrillary Acidic Protein (GFAP) and Ubiquitin C-Terminal Hydrolase-L1 (UCH-L1) in a cohort of 45 children with clinical diagnosis of TBI (Glasgow Coma Scale [GCS] 3–15) and 40 healthy subjects, evaluated their associations with clinical characteristics and outcomes, and compared their performance to previously published data on two well-studied blood biomarkers, S100B and MBP. We observed higher serum levels of GFAP and UCH-L1 in brain-injured children compared with controls and also demonstrated a step-wise increase of biomarker concentrations over the continuum of severity from mild to severe TBI. Furthermore, while we found that only the neuronal biomarker UCH-L1 holds potential to detect acute intracranial lesions as assessed by computed tomography (CT), both markers were substantially increased in TBI patients even with a normal CT suggesting the presence of undetected microstructural injuries. Serum UCH-L1 and GFAP concentrations also strongly predicted poor outcome and performed better than S100B and MBP. Our results point to a role of GFAP and UCH-L1 as candidate biomarkers for pediatric TBI. Further studies are warranted.
Ferromagnetic resonance induced large microwave magnetodielectric effect in cerium doped Y3Fe5O12 ferrites
Authors: Chen Fu , Wang Xian , Nie Yan , Li Qifan , Ouyang Jun , Feng Zekun , Chen Yajie , Harris Vincent G. 
Published: June 2016

AbstractIn recent years, multifunctional materials contained simultaneous ferroelectric and ferromagnetic ordering have been realized. Here, a real time room temperature adaptive materials system, which demonstrates an RF magnetodielectric (MD) response, i.e., CexY3−xFe5O12 (x = 0, 0.05, 0.1, 0.15, 0.2), is reported. The magnetic and dielectric properties of Ce-doped YIG microwave ferrites processed by a traditional ceramic route have been measured over a frequency range of 4–8 GHz (C-band). The substitution of Ce not only enhances the microwave electromagnetic properties of the YIG, but also modulates the magnetodielectric response. The maximum magnetodielectric response in Ce-doped YIG sample ranges in magnitude from approximately +5% to −5% under an applied field of 1.78 kOe. This effect was attributed to electron fluctuations on the Fe cation sites. Furthermore, the magnitude of the MD response was shown to be enhanced by the cerium content. It is believed that research of the magnetodielectric effect in YIG ferrites is of great importance to the development of next generation multifunctional adaptive microwave materials, devices and integrated circuits.
Gate Tuning of Förster Resonance Energy Transfer in a Graphene - Quantum Dot FET Photo-Detector
Authors: Li Ruifeng , Schneider Lorenz Maximilian , Heimbrodt Wolfram , Wu Huizhen , Koch Martin , Rahimi-Iman Arash 
Published: June 2016

AbstractGraphene photo-detectors functionalized by colloidal quantum dots (cQDs) have been demonstrated to show effective photo-detection. Although the transfer of charge carriers or energy from the cQDs to graphene is not sufficiently understood, it is clear that the mechanism and efficiency of the transfer depends on the morphology of the interface between cQDs and graphene, which is determined by the shell of the cQDs in combination with its ligands. Here, we present a study of a graphene field-effect transistor (FET), which is functionalized by long-ligand CdSe/ZnS core/shell cQDs. Time-resolved photo-luminescence from the cQDs as a function of the applied gate voltage has been investigated in order to probe transfer dynamics in this system. Thereby, a clear modification of the photo-luminescence lifetime has been observed, indicating a change of the decay channels. Furthermore, we provide responsivities under a Förster-like energy transfer model as a function of the gate voltage in support of our findings. The model shows that by applying a back-gate voltage to the photo-detector, the absorption can be tuned with respect to the photo-luminescence of the cQDs. This leads to a tunable energy transfer rate across the interface of the photo-detector, which offers an opportunity to optimize the photo-detection.
Predict or classify: The deceptive role of time-locking in brain signal classification
Authors: Rusconi Marco , Valleriani Angelo 
Published: June 2016

AbstractSeveral experimental studies claim to be able to predict the outcome of simple decisions from brain signals measured before subjects are aware of their decision. Often, these studies use multivariate pattern recognition methods with the underlying assumption that the ability to classify the brain signal is equivalent to predict the decision itself. Here we show instead that it is possible to correctly classify a signal even if it does not contain any predictive information about the decision. We first define a simple stochastic model that mimics the random decision process between two equivalent alternatives and generate a large number of independent trials that contain no choice-predictive information. The trials are first time-locked to the time point of the final event and then classified using standard machine-learning techniques. The resulting classification accuracy is above chance level long before the time point of time-locking. We then analyze the same trials using information theory. We demonstrate that the high classification accuracy is a consequence of time-locking and that its time behavior is simply related to the large relaxation time of the process. We conclude that when time-locking is a crucial step in the analysis of neural activity patterns, both the emergence and the timing of the classification accuracy are affected by structural properties of the network that generates the signal.
Effects of Long-term Diving Training on Cortical Gyrification
Authors: Zhang Yuanchao , Zhao Lu , Bi Wenwei , Wang Yue , Wei Gaoxia , Evans Alan , Jiang Tianzi 
Published: June 2016

AbstractDuring human brain development, cortical gyrification, which is believed to facilitate compact wiring of neural circuits, has been shown to follow an inverted U-shaped curve, coinciding with the two-stage neurodevelopmental process of initial synaptic overproduction with subsequent pruning. This trajectory allows postnatal experiences to refine the wiring, which may manifest as endophenotypic changes in cortical gyrification. Diving experts, typical elite athletes who commence intensive motor training at a very young age in their early childhood, serve ideal models for examining the gyrification changes related to long-term intensive diving training. Using local gyrification index (LGI), we compared the cortical gyrification between 12 diving experts and 12 controls. Compared with controls, diving experts showed widespread LGI reductions in regions relevant to diving performance. Negative correlations between LGIs and years of diving training were also observed in diving experts. Further exploratory network efficiency analysis of structural cortical networks, inferred from interregional correlation of LGIs, revealed comparable global and local efficiency in diving experts relative to controls. These findings suggest that gyrification reductions in diving experts may be the result of long-term diving training which could refine the neural circuitry (via synaptic pruning) and might be the anatomical substrate underlying their extraordinary diving performance.
A two-year field measurement of methane and nitrous oxide fluxes from rice paddies under contrasting climate conditions
Authors: Sun Huifeng , Zhou Sheng , Fu Zishi , Chen Guifa , Zou Guoyan , Song Xiangfu 
Published: June 2016

AbstractThe effects of three irrigation levels (traditional normal amount of irrigation [NA100%], 70%, and 30% of the normal amount [NA70% and NA30%]) and two rice varieties (Oryza sativa L. Huayou14 and Hanyou8) on CH4 and N2O emissions were investigated over two years under contrasting climate conditions (a ‘warm and dry’ season in 2013 and a normal season in 2014). Hanyou8 was developed as a drought-resistant variety. The mean seasonal air temperature in 2013 was 2.3 °C higher than in 2014, while the amount of precipitation from transplanting to the grain-filling stage in 2013 was only 36% of that in 2014. CH4 emission rose by 93–161%, but rice grain yield fell by 7–13% in 2013, compared to 2014 under the NA100% conditions. Surface standing water depths (SSWD) were higher in Hanyou8 than in Huayou14 due to the lower water demand by Hanyou8. A reduction in the amount of irrigation water applied can effectively reduce the CH4 emissions regardless of the rice variety and climate condition. However, less irrigation during the ‘warm and dry’ season greatly decreased Huayou14 grain yield, but had little impact on Hanyou8. In contrast, N2O emission depended more on fertilization and SSWD than on rice variety.
Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient
Authors: Lanzén Anders , Epelde Lur , Blanco Fernando , Martín Iker , Artetxe Unai , Garbisu Carlos 
Published: June 2016

AbstractMountain elevation gradients are invaluable sites for understanding the effects of climate change on ecosystem function, community structure and distribution. However, relatively little is known about the impact on soil microbial communities, in spite of their importance for the functioning of the soil ecosystem. Previous studies of microbial diversity along elevational gradients were often limited by confounding variables such as vegetation, pH, and nutrients. Here, we utilised a transect in the Pyrenees established to minimise variation in such parameters, to examine prokaryotic, fungal, protist and metazoan communities throughout three consecutive years. We aimed to determine the influences of climate and environmental parameters on soil microbial community structure; as well as on the relationships between those microbial communities. Further, functional diversity of heterotrophic bacteria was determined using Biolog. Prokaryotic and fungal community structure, but not alpha-diversity, correlated significantly with elevation. However, carbon-to-nitrogen ratio and pH appeared to affect prokaryotic and protist communities more strongly. Both community structure and physicochemical parameters varied considerably between years, illustrating the value of long-term monitoring of the dynamic processes controlling the soil ecosystem. Our study also illustrates both the challenges and strengths of using microbial communities as indicators of potential impacts of climate change.