bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial Heterogeneity in Particle‐Associated, Light‐Independent Superoxide Production Within Productive Coastal Waters
Authors: Sutherland Kevin M. , Grabb Kalina C. , Karolewski Jennifer S. , Plummer Sydney , Farfan Gabriela A. , Wankel Scott D. , Diaz Julia M. , Lamborg Carl H. , Hansel Colleen M. 
Published: October 2020

AbstractIn the marine environment, the reactive oxygen species (ROS) superoxide is produced through a diverse array of light‐dependent and light‐independent reactions, the latter of which is thought to be primarily controlled by microorganisms. Marine superoxide production influences organic matter remineralization, metal redox cycling, and dissolved oxygen concentrations, yet the relative contributions of different sources to total superoxide production remain poorly constrained. Here we investigate the production, steady‐state concentration, and particle‐associated nature of light‐independent superoxide in productive waters off the northeast coast of North America. We find exceptionally high levels of light‐independent superoxide in the marine water column, with concentrations ranging from 10 pM to in excess of 2,000 pM. The highest superoxide concentrations were particle associated in surface seawater and in aphotic seawater collected meters off the seafloor. Filtration of seawater overlying the continental shelf lowered the light‐independent, steady‐state superoxide concentration by an average of 84%. We identify eukaryotic phytoplankton as the dominant particle‐associated source of superoxide to these coastal waters. We contrast these measurements with those collected at an off‐shelf station, where superoxide concentrations did not exceed 100 pM, and particles account for an average of 40% of the steady‐state superoxide concentration. This study demonstrates the primary role of particles in the production of superoxide in seawater overlying the continental shelf and highlights the importance of light‐independent, dissolved‐phase reactions in marine ROS production.
Geomagnetically Induced Currents and Harmonic Distortion: High Time Resolution Case Studies
Authors: Clilverd Mark A. , Rodger Craig J. , Brundell James B. , Dalzell Michael , Martin Ian , Mac Manus Daniel H. , Thomson Neil R. 
Published: October 2020

AbstractHigh time resolution (1–5 s) magnetometer, geomagnetically induced current (GIC), and mains harmonic distortion data from the Halfway Bush substation in Dunedin, New Zealand, are analyzed. A recently developed technique using very low frequency (VLF) radio wave data provides high‐resolution measurements of mains harmonic distortion levels. Three case studies are investigated, each involving high rates of change of local geomagnetic field, but with different timescales of magnetospheric driver mechanisms, and different substation transformer configurations. Two cases of enhanced GIC during substorm events are analyzed, and one case of a storm sudden commencement. Time delays between magnetic field fluctuations and induced transformer currents are found to be ~100 s for substorm events, but only ~20 s for the storm sudden commencement containing higher‐frequency variations. Boxcar averaging of the magnetic field fluctuations using running windows of ±2 min leads to spectral power profiles similar to those of GIC profiles, with reduced power at frequencies >0.003 Hz (periods <5 min). Substantially lower mains harmonic distortion levels were observed after the removal of the single phase bank transformer, HWB T4, from the high‐voltage configuration at Halfway Bush. No systematic time delay was found between GIC variations and mains harmonic distortion levels. The power spectra of magnetic field fluctuations and GIC variations during the sudden storm commencement with no harmonic distortion showed low levels of low‐frequency power (<0.003 Hz, periods >5 min). This low‐frequency component of the magnetic field power spectrum appears necessary for mains harmonic distortion to occur.
Local and Reach‐Scale Hyporheic Flow Response From Boulder‐Induced Geomorphic Changes
Authors: Dudunake T. , Tonina D. , Reeder W. J. , Monsalve A. 
Published: October 2020

AbstractStream hydromorphology regulates in‐stream water flow and interstitial flow of water within streambed sediments, the latter known as hyporheic exchange. Whereas hyporheic flow has been studied in sand‐bedded streams with ripples and dunes and in gravel‐bedded streams with pool‐riffle morphology, little is known about its characteristics in plane bed morphology with subdued streambed undulations and sparse macroroughness elements such as boulders and cobbles. Here, we present a proof‐of‐concept investigation on the role of boulder‐induced morphological changes on hyporheic flows based on coupling large‐scale flume sediment transport experiments with computational fluid dynamics. Our results show that placement of boulders on plane beds increase the reach‐scale hyporheic median residence time, τ50, by 15% and downwelling flux, qd, by 18% from the plane bed. However, reach‐scale hyporheic exchange changes are stronger with τ50 decreasing by 20% and qd increasing by 79% once the streambed morphology reached equilibrium (with the imposed upstream sediment and flow inputs on boulders). These results suggest that hyporheic flow is sensitive to the geomorphic response from bed topography and sediment transport in gravel‐bedded streams, a process that has been overlooked in previous work.
CD44/HA signaling mediates acquired resistance to a PI3Kα inhibitor
Authors: Yang Cuixia , Sheng Yumeng , Shi Xiaoxing , Liu Yiwen , He Yiqing , Du Yan , Zhang Guoliang , Gao Feng 
Published: October 2020

AbstractMost luminal breast carcinomas (BrCas) bearing PIK3CA mutations initially respond to phosphoinositide-3-kinase (PI3K)-α inhibitors, but many eventually become resistant. The underlying mechanisms of this resistance remain obscure. In this work, we showed that a CD44high state due to aberrant isoform splicing was acquired from adaptive resistance to a PI3Kα inhibitor (BLY719) in luminal BrCas. Notably, the expression of CD44 was positively correlated with estrogen receptor (ER) activity in PIK3CA-mutant breast cancers, and ER-dependent transcription upon PI3Kα pathway inhibition was in turn mediated by CD44. Furthermore, the interaction of CD44 with the ligand hyaluronan (HA) initiated the Src-ERK signaling cascade, which subsequently maintained AKT and mTOR activity in the presence of a PI3Kα inhibitor. Activation of this pathway was prevented by disruption of the CD44/HA interaction, which in turn restored sensitivity to BLY719. Our results revealed that an ER-CD44-HA signaling circuit that mediates robust compensatory activation of the Src-ERK signaling cascade may contribute to the development of acquired resistance to PI3Kα inhibitors. This study provides new insight into the mechanism of adaptive resistance to PI3Kα inhibition therapy.
Simulations on the dual effects of flavonoids as suppressors of Aβ42 fibrillogenesis and destabilizers of mature fibrils
Authors: Gargari Sahar Andarzi , Barzegar Abolfazl 
Published: October 2020

AbstractStructural studies of the aggregation inhibition of the amyloid-β peptide (Aβ) by different natural compounds are of the utmost importance due to their great potential as neuroprotective and therapeutic agents for Alzheimer’s disease. We provided the simulation of molecular dynamics for two different states of Aβ42, including “monomeric aggregation-prone state (APS)” and “U-shaped pentamers of amyloidogenic protofilament intermediates” in the absence and presence of polyphenolic flavonoids (Flvs, myricetin and morin) in order to verify the possible mechanism of Flvs fibrillogenesis suppression. Data showed that Flvs directly bind into Aβ42 species in both states of “monomeric APS β-sheets” and “pentameric amyloidogenic intermediates”. Binding of Flvs with amyloidogenic protofilament intermediates caused the attenuation of some inter-chains H-bonds, salt bridges, van der Waals and interpeptide interaction energies without interfering with their secondary β-sheets. Therefore, Flvs redirect oligomeric amyloidogenic intermediates into unstructured aggregates by significant disruption of the "steric zipper" motif of fibrils—pairs of self-complementary β-sheets—without changing the amount of β-sheets. It is while Flvs completely destruct the disadvantageous secondary β-sheets of monomeric APS conformers by converting them into coil/helix structures. It means that Flvs suppress the fibrillogenesis process of the monomeric APS structures by converting their β-sheets into proper soluble coil/helices structures. The different actions of Flvs in contact with two different states of Aβ conformers are related to high interaction tendency of Flvs with additional H-bonds for monomeric APS β-sheet, rather than oligomeric protofilaments. Linear interaction energy (LIE) analysis confirmed the strong binding of monomeric Aβ-Flvs with more negative ∆Gbinding, rather than oligomeric Aβ-Flvs system. Therefore, atomic scale computational evaluation of Flvs actions demonstrated different dual functions of Flvs, concluded from the application of two different monomeric and pentameric Aβ42 systems. The distinct dual functions of Flvs are proposed as suppressing the aggregation by converting β-sheets of monomeric APS to proper soluble structures and disrupting the "steric zipper" fibril motifs of oligomeric intermediate by converting on-pathway into off-pathway. Taken together, our data propose that Flvs exert dual and more effective functions against monomeric APS (fibrillogenesis suppression) and remodel the Aβ aggregation pathway (fibril destabilization).
Fabrication and characteristics of highly $$\langle {110} \rangle $$-oriented nanotwinned Au films
Authors: Chiu Wei-Lan , Liu Chien-Min , Lin Han-wen , Wu John A. , Chou Y.-C. , Tu K. N. , Chen Chih 
Published: October 2020

AbstractFine grained and nanotwinned Au has many excellent properties and is widely used in electronic devices. We have fabricated $$\langle {110} \rangle $$

⟨
110
⟩

preferred-oriented Au thin films by DC plating at 5 mA/cm2. Microstructure analysis of the films show a unique fine grain structure with a twin formation. Hardness tests performed on electroplated $$\langle {110} \rangle $$

⟨
110
⟩

Au films show a hardness 47% greater than random and untwinned Au. We then achieved direct bonding between two Au $$\langle {110} \rangle $$

⟨
110
⟩

surfaces operating at 200 °C for an hour in a vacuum oven. The highly-oriented $$\langle {110} \rangle $$

⟨
110
⟩

nanotwinned Au films could be an ideal material in many gold products.
Heat transfer flow of Maxwell hybrid nanofluids due to pressure gradient into rectangular region
Authors: Chu Yu-Ming , Ali Rizwan , Asjad Muhammad Imran , Ahmadian Ali , Senu Norazak 
Published: October 2020

AbstractIn this work, influence of hybrid nanofluids (Cu and$$\mathrm{Al}_{2}\mathrm{O}_{3}$$Al2O3) on MHD Maxwell fluid due to pressure gradient are discussed. By introducing dimensionless variables the governing equations with all levied initial and boundary conditions are converted into dimensionless form. Fractional model for Maxwell fluid is established by Caputo time fractional differential operator. The dimensionless expression for concentration, temperature and velocity are found using Laplace transform. As a result, it is found that fluid properties show dual behavior for small and large time and by increasing volumetric fraction temperature increases and velocity decreases respectively. Further, we compared the Maxwell, Casson and Newtonian fluids and found that Newtonian fluid has greater velocity due to less viscosity. Draw the graphs of temperature and velocity by Mathcad software and discuss the behavior of flow parameters and the effect of fractional parameters.
Rab6 is required for rapid, cisternal-specific, intra-Golgi cargo transport
Authors: Dickson Lindsey James , Liu Shijie , Storrie Brian 
Published: October 2020

AbstractRab6, the most abundant Golgi associated small GTPase, consists of 2 equally common isoforms, Rab6A and Rab6A′, that differ in 3 amino acids and localize to trans Golgi cisternae. The two isoforms are largely redundant in function and hence are often referred to generically as Rab6. Rab6 loss-of-function inhibits retrograde Golgi trafficking, induces an increase in Golgi cisternal number in HeLa cells and delays the cell surface appearance of the anterograde cargo protein, VSVG. We hypothesized that these effects are linked and might be explained by a cisternal-specific delay in cargo transport. In pulse chase experiments using a deconvolved, confocal line scanning approach to score the distribution of the tsO45 mutant of VSVG protein in Rab6 depleted cells, we found that anterograde transport at 32 °C, permissive conditions, through the Golgi apparatus was locally delayed, almost tenfold, between medial and trans Golgi cisterna. Cis to medial transport was nearly normal as was trans Golgi to TGN transport. TGN exit was unaffected by Rab6 depletion. These effects were the same with either of two siRNAs. Similar intra-Golgi transport delays were seen at 37 °C with RUSH VSVG or a RUSH GPI-anchored construct using a biotin pulse to release the marker proteins from the ER. Using 3D-SIM, a super resolution approach, we found that RUSH VSVG transport was delayed pre-trans Golgi. These visual approaches suggest a selective slowing of anterograde transport relative to 3 different marker proteins downstream of the trans Golgi. Using a biochemical approach, we found that the onset of VSVG endoglycosidase H resistance in Rab6 depleted cells was delayed. Depletion of neither Rab6A or Rab6A′ isoforms alone had any effect on anterograde transport through the Golgi suggesting that Rab6A and Rab6A′ act coordinately. Delayed cargo transport conditions correlate strongly with a proliferation of Golgi cisternae observed in earlier electron microscopy. Our results strongly indicate that Rab6 is selectively required for rapid anterograde transport from the medial to trans Golgi. We suggest that the observed correlation with localized cisternal proliferation fits best with a cisternal progression model of Golgi function.
Using epidemic simulators for monitoring an ongoing epidemic
Authors: Raghavan Mohan , Sridharan Kousik Sarathy , Mandayam Rangayyan Yashaswini 
Published: October 2020

AbstractPrediction of infection trends, estimating the efficacy of contact tracing, testing or impact of influx of infected are of vital importance for administration during an ongoing epidemic. Most effective methods currently are empirical in nature and their relation to parameters of interest to administrators are not evident. We thus propose a modified SEIRD model that is capable of modeling effect of interventions and inward migrations on the progress of an epidemic. The tunable parameters of this model bear relevance to monitoring of an epidemic. This model was used to show that some of the commonly seen features of cumulative infections in real data can be explained by piecewise constant changes in interventions and population influx. We also show that the data of cumulative infections from twelve Indian states between mid March and mid April 2020 can be generated from the model by applying interventions according to a set of heuristic rules. Prediction for the next ten days based on this model, reproduced real data very well. In addition, our model also reproduced the time series of recoveries and deaths. Our work constitutes an important first step towards an effective dashboard for the monitoring of epidemic by the administration, especially in an Indian context.
Acoustic probing of the particle concentration in turbulent granular suspensions in air
Authors: van den Wildenberg S. , Jia X. , Roche O. 
Published: October 2020

AbstractDilute gas–particle suspensions in which the particles are carried by the fluid are found in various industrial and geophysical contexts. One fundamental issue that limits our understanding of such systems is the difficulty to obtain information on the particle concentration inside these often optically opaque suspensions. To overcome this difficulty, we develop ultrasonic spectroscopy to monitor the local particle concentration $$\phi$$
ϕ
of glass particles (with diameters $$d\sim$$

d
∼

77 $$\upmu$$
μ
m or 155 $$\upmu$$
μ
m) suspended in air. First, we determine the minimal air velocity, $$U^*$$

U
∗

, necessary to suspend the particles from the maximum decrease in the transmitted wave amplitude and velocity of ultrasound propagating through the suspension. Next, setting the air velocity at $$U^*$$

U
∗

, we increase the mass of particles and monitor acoustically the local solid volume fraction, $$\phi$$
ϕ
, by measuring the ultrasound wave attenuation coefficient and phase velocity as a function of frequency on the basis of classical scattering and hydrodynamic models. For the frequency ranges and suspensions considered here, the viscous dissipation dominates over scattering and thermal conduction losses. We show that, for a characteristic air velocity $$U^*$$

U
∗

, the locally measured $$\phi$$
ϕ
reaches a critical value, in agreement with a recent study on turbulent gas–particle mixtures. Moreover, we find that this critical $$\phi$$
ϕ
increases with the size of the particles. Finally, analysis of the temporal fluctuations of the locally measured solid volume fraction, suggests that high density regions (clusters) are present even in suspensions with concentrations below the critical concentration. This differs from the current hypothesis according to which the critical concentration coincides with the onset of cluster formation.
Circulating branched-chain amino acids and long-term risk of obesity-related cancers in women
Authors: Tobias Deirdre K. , Hazra Aditi , Lawler Patrick R. , Chandler Paulette D. , Chasman Daniel I. , Buring Julie E. , Lee I-Min , Cheng Susan , Manson JoAnn E. , Mora Samia 
Published: October 2020

AbstractObesity is a risk factor for > 13 cancer sites, although it is unknown whether there is a common mechanism across sites. Evidence suggests a role for impaired branched-chain amino acid (BCAAs; isoleucine, leucine, valine) metabolism in obesity, insulin resistance, and immunity; thus, we hypothesized circulating BCAAs may be associated with incident obesity-related cancers. We analyzed participants in the prospective Women’s Health Study without a history of cancer at baseline blood collection (N = 26,711, mean age = 54.6 years [SD = 7.1]). BCAAs were quantified via NMR spectroscopy, log-transformed, and standardized. We used Cox proportional regression models adjusted for age, race, smoking, diet, alcohol, physical activity, menopausal hormone use, Body Mass Index (BMI), diabetes, and other risk factors. The endpoint was a composite of obesity-related cancers, defined per the International Agency for Research on Cancer 2016 report, over a median 24 years follow-up. Baseline BMI ≥ 30 kg/m2 compared with BMI 18.5–25.0 kg/m2 was associated with 23% greater risk of obesity-related cancers (n = 2751 events; multivariable HR 1.23, 95% CI 1.11–1.37). However, BCAAs were not associated with obesity-related cancers (multivariable HR per SD = 1.01 [0.97–1.05]). Results for individual BCAA metabolites suggested a modest association for leucine with obesity-related cancers (1.04 [1.00–1.08]), and no association for isoleucine or valine (0.99 [0.95–1.03] and 1.00 [0.96–1.04], respectively). Exploratory analyses of BCAAs with individual sites included positive associations between leucine and postmenopausal breast cancer, and isoleucine with pancreatic cancer. Total circulating BCAAs were unrelated to obesity-related cancer incidence although an association was observed for leucine with incident obesity-related cancer.
Structural insights into rice SalTol QTL located SALT protein
Authors: Kaur Navdeep , Sagar Amin , Sharma Pankaj , Ashish  , Pati Pratap Kumar 
Published: October 2020

AbstractSalinity is one of the major stresses affecting rice production worldwide, and various strategies are being employed to increase salt tolerance. Recently, there has been resurgence of interest to characterize SalTol QTL harbouring number of critical genes involved in conferring salt stress tolerance in rice. The present study reports the structure of SALT, a SalTol QTL encoded protein by X-ray crystallography (PDB ID: 5GVY; resolution 1.66 Å). Each SALT chain was bound to one mannose via 8 hydrogen bonds. Compared to previous structure reported for similar protein, our structure showed a buried surface area of 900 Å2 compared to only 240 Å2 for previous one. Small-angle X-ray scattering (SAXS) data analysis showed that the predominant solution shape of SALT protein in solution is also dimer characterized by a radius of gyration and maximum linear dimension of 2.1 and 6.5 nm, respectively. The SAXS profiles and modelling confirmed that the dimeric association and relative positioning in solution matched better with our crystal structure instead of previously reported structure. Together, structural/biophysical data analysis uphold a tight dimeric structure for SALT protein with one mannose bound to each protein, which remains novel to date, as previous structures indicated one sugar unit sandwiched loosely between two protein chains.
Transcriptome analysis uncovers the diagnostic value of miR-192-5p/HNF1A-AS1/VIL1 panel in cervical adenocarcinoma
Authors: Xu Junfen , Zou Jian , Wu Luyao , Lu Weiguo 
Published: October 2020

AbstractDespite the fact that the incidence of cervical squamous cell carcinoma has decreased, there is an increase in the incidence of cervical adenocarcinoma. However, our knowledge on cervical adenocarcinoma is largely unclear. Transcriptome sequencing was conducted to compare 4 cervical adenocarcinoma tissue samples with 4 normal cervical tissue samples. mRNA, lncRNA, and miRNA signatures were identified to discriminate cervical adenocarcinoma from normal cervix. The expression of VIL1, HNF1A-AS1, MIR194-2HG, SSTR5-AS1, miR-192-5p, and miR-194-5p in adenocarcinoma were statistically significantly higher than that in normal control samples. The Receiver Operating Characteristic (ROC) curve analysis indicated that combination of miR-192-5p, HNF1A-AS1, and VIL1 yielded a better performance (AUC = 0.911) than any single molecule -and could serve as potential biomarkers for cervical adenocarcinoma. Of note, the combination model also gave better performance than TCT test for cervical adenocarcinoma diagnosis. However, there was no correlation between miR-192-5p or HNF1A-AS1 and HPV16/18 E6 or E7. VIL1 was weakly correlated with HPV18 E7 expression. In summary, our study has identified miR-192-5p/HNF1A-AS1/VIL1 panel that accurately discriminates adenocarcinoma from normal cervix. Detection of this panel may provide considerable clinical value in the diagnosis of cervical adenocarcinoma.