bluuebunny/crossref_metadata_2025 huggingface dataset:
Isotopic Equilibrium Between Precipitation and Water Vapor in Northern Patagonia and Its Consequences on δ18Ocellulose Estimate
Authors: Penchenat Tiphaine , Vimeux Françoise , Daux Valérie , Cattani Olivier , Viale Maximiliano , Villalba Ricardo , Srur Ana , Outrequin Clément
Published: February 2020

Modeling work of the isotopic composition of tree ring cellulose (δ18Ocell) relies on the isotopic equilibrium assumption between atmospheric water vapor and tree source water, frequently assimilated to integrated precipitation. Here, we explore the veracity of this assumption based on observations collected during a field campaign in Río Negro province (Argentina) in February–March 2017. We examine how the observed isotopic composition of water vapor deviates from equilibrium with precipitation. This deviation, named isotopic disequilibrium (Δ18Ovap_eq), is low (between −2.0‰ and 4.1‰) and a significant relationship is observed between the isotopic composition of water vapor and its expected value at equilibrium. Negative Δ18Ovap_eq can be explained by evaporation of small raindrops (from 1% to 5% of initial droplet mass). Positive Δ18Ovap_eq can result from vegetation transpiration with transpired water accounting for 14% to 29% to ambient water vapor. The low Δ18Ovap_eq at the study site may be due to the high level of relative humidity (from 70% to 96%) favoring isotopic diffusive exchanges between the two water phases and thus promoting the isotopic equilibrium. We examine the impact of the isotopic equilibrium assumption on the calculation of δ18Ocell. A perfect agreement is shown between observed and calculated δ18Ocell provided that the isotopic composition of source water is significantly higher than the expected averaged isotopic composition of precipitation over the tree growing period.
A Novel Modeling Framework for Computationally Efficient and Accurate Real‐Time Ensemble Flood Forecasting With Uncertainty Quantification
Authors: Tran Vinh Ngoc , Dwelle M. Chase , Sargsyan Khachik , Ivanov Valeriy Y. , Kim Jongho
Published: February 2020

A novel modeling framework that simultaneously improves accuracy, predictability, and computational efficiency is presented. It embraces the benefits of three modeling techniques integrated together for the first time: surrogate modeling, parameter inference, and data assimilation. The use of polynomial chaos expansion (PCE) surrogates significantly decreases computational time. Parameter inference allows for model faster convergence, reduced uncertainty, and superior accuracy of simulated results. Ensemble Kalman filters assimilate errors that occur during forecasting. To examine the applicability and effectiveness of the integrated framework, we developed 18 approaches according to how surrogate models are constructed, what type of parameter distributions are used as model inputs, and whether model parameters are updated during the data assimilation procedure. We conclude that (1) PCE must be built over various forcing and flow conditions, and in contrast to previous studies, it does not need to be rebuilt at each time step; (2) model parameter specification that relies on constrained, posterior information of parameters (so‐called Selected specification) can significantly improve forecasting performance and reduce uncertainty bounds compared to Random specification using prior information of parameters; and (3) no substantial differences in results exist between single and dual ensemble Kalman filters, but the latter better simulates flood peaks. The use of PCE effectively compensates for the computational load added by the parameter inference and data assimilation (up to ~80 times faster). Therefore, the presented approach contributes to a shift in modeling paradigm arguing that complex, high‐fidelity hydrologic and hydraulic models should be increasingly adopted for real‐time and ensemble flood forecasting.
A New Multiobjective Simulated Annealing Algorithm—MOSA‐GR: Application to the Optimal Design of Water Distribution Networks
Authors: Cunha M. , Marques J.
Published: February 2020

This paper presents a simulated annealing multiobjective algorithm developed to include novel features for promoting the convergence toward the best Pareto front that shows diversity and uniformity in the distribution of solutions. The new algorithm, MultiObjective Simulated Annealing with new Generation and Reannealing procedures (MOSA‐GR), is a trajectory‐based algorithm, where, in a first phase, diversified generation strategies are used to define candidate solutions at different stages of the search procedure. In a second phase a reannealing process starting at low temperature is implemented to intensify the search based on the last solutions of the first phase. An extensive comparison with solutions obtained by various multiobjective evolutionary algorithms (MOEAs) described in the literature is provided. Using a limited budget for the number of function evaluations, the results show that MOSA‐GR has a very good performance and gives rise to better fronts, even compared with those obtained by merging the results from different MOEAs implemented in similar conditions.
The World in 2050 Pursues Paths to a Sustainable Future
Authors: Crowell Rachel
Published: February 2020

This initiative aims to provide fact-based knowledge to help implement and achieve the United Nations’ Sustainable Development Goals.
Richard J. Walker Receives 2019 Harry H. Hess Medal
Authors:   AGU
Published: February 2020

Richard J. Walker was awarded the 2019 Harry H. Hess Medal at AGU’s Fall Meeting 2019 Honors Ceremony, held on 11 December 2019 in San Francisco, Calif. The medal is for “outstanding achievements in research on the constitution and evolution of the Earth and other planets.”
Anaerobic Activity Is a Big Contributor in Marine “Dead Zones”
Authors: Stanley Sarah
Published: February 2020

Climate models that do not account for anaerobic microbial activity may underestimate future expansion of oxygen-depleted waters.
Investigating Rates of Microbial Methane Munching in the Ocean
Authors: Stanley Sarah
Published: February 2020

Analyses of microbial activity in seawater samples help clarify the fate of methane released from the seafloor.
Scientists Say Land and Ocean Are Key to Tackling Climate Crisis
Authors: Showstack Randy
Published: February 2020

A House committee listened to experts on why ocean science is critical to understanding the changing climate and why better land use could be a major part of mitigating climate change.
Another Scorcher: 2019 Was the Second-Hottest Year on Record
Authors: Duncombe Jenessa
Published: February 2020

Heat waves, massive melts, and droughts, oh my. The past decade was our hottest yet.
Growth and Challenges for JGR: Solid Earth
Authors: ten Brink Uri
Published: February 2020

The outgoing Editor in Chief of JGR: Solid Earth reflects on his tenure and expresses appreciation to all those who contributed to the success of the journal over recent years.
Even Tardigrades Will Feel the Heat of Climate Change
Authors: Cartier Kimberly
Published: February 2020

Hardy tardigrades are much more vulnerable to heat than cold, but they show some signs that they could adapt over time.
Interstellar Visitors Could Export Terrestrial Life to Other Stars
Authors: Redd Nola
Published: February 2020

A handful of interstellar objects and long-period comets could have scooped up microorganisms from Earth and carried them to worlds around other stars.
Scientific Meetings for All
Authors: Lauer AJ , Gram Wendy , Crall Alycia , Diaz Eaton Carrie , Haacker Rebecca , Jack-Scott Emily , Pendergrass Angeline , Stack Whitney Kaitlin
Published: February 2020

Two organizations found ways to be more intentional about encouraging participation by a diverse spectrum of attendees at scientific meetings—the scientific community can learn from their experiences.
Podcast: Discovering Europe’s History Through Its Timbers
Authors: Bompey Nanci
Published: February 2020

An analysis of timber used to construct buildings in Europe hundreds of years ago is giving scientists and historians new insights into the region’s history from the 13th to 17th centuries.
How Scientists Search for Martian Methane
Authors: Wendel JoAnna
Published: February 2020

Finding subsurface reserves of methane on Mars could revolutionize human space travel, but it won’t be an easy hunt.
Europe’s Rivers Are the Most Obstructed on Earth
Authors: Kornei Katherine
Published: February 2020

By analyzing satellite imagery of rivers worldwide, researchers have pinpointed over 35,000 obstructions like dams and locks that affect an environment’s ecology, hydrology, and water resources management.
Finding Wildfire’s Fingerprint in the Atmosphere
Authors: Goss Heather
Published: February 2020

Smoke from burning landscapes is increasingly filling the air. Eos has dedicated its February 2020 issue to the increasingly important study of wildfire emissions.
Oil-Exposed Mahi-Mahi More Likely to Lose Oil-Avoidance Behavior
Authors: Crowell Rachel
Published: February 2020

Contact with oil may make it harder for the fish to avoid additional exposure, creating a vicious cycle following offshore oil spills.
Using Climate Studies to Better Predict Diarrhea Outbreaks
Authors: Crowell Rachel
Published: February 2020

Researchers have found new connections between La Ni�a climate conditions and the leading killer of children worldwide.
Japan Puts Its Mark on Geologic Time with the Chibanian Age
Authors: Hornyak Tim
Published: February 2020

The newly named period in the Pleistocene identifies a key moment in geological history: the last time Earth’s magnetic poles switched places.
Scientists Search for Deltas on Saturn’s Largest Moon
Authors: Wendel JoAnna
Published: February 2020

Saturn’s moon Titan has rivers that empty into seas...but where are the deltas?
This Week: From Rising Roads in Miami to Dead Zones in the Gulf
Authors:   AGU
Published: February 2020

What Earth and space science stories are we recommending this week?
Antarctic Ice Cores Might Be Older Than Dirt
Authors: Hendricks Jessie
Published: February 2020

Using cosmogenic nuclide dating, scientists determined a 10-meter core just below the surface to be over a million years old.
New Study Hints at Bespoke Future of Lightning Forecasting
Authors: Kelvey Jon
Published: February 2020

Researchers used machine learning to develop a model that can predict lightning strikes to within 30 minutes of their occurrence and within 30 kilometers of a weather station by using just four simple atmospheric measurements.
How to Read Atmospheric History Written in Flowstones
Authors: Thompson Elizabeth
Published: February 2020

Oxygen isotope ratios in cave deposits reflect past climates, but interpreting these data is not straightforward. A new study explores what these ratios really tell us.
Violence Increases with Climate Change
Authors: Duncombe Jenessa
Published: February 2020

Stresses from environmental triggers are leading to more gender-based violence around the world.
30 by 30: A Push to Protect U.S. Land and Water
Authors: Showstack Randy
Published: February 2020

The effort to conserve at least 30% of U.S. land and ocean by 2030 is part of an international push for conservation aiming to protect biodiversity and mitigate climate change impacts.
New Clean Water Act Rule Leaves U.S. Waters Vulnerable
Authors: Ward Adam , Walsh Riley
Published: February 2020

A revised definition of which waters can be protected from pollution by the federal government ignores established science.
Shedding Light on the Darkest Regions of the Moon
Authors: Fogerty Christian
Published: February 2020

An international team of researchers is analyzing boulder tracks to learn more about some of the most elusive regions on the Moon.
Podcast: Exhuming a Buried Piece of American History
Authors: Lipuma Lauren
Published: February 2020

Scientists are using grave soil to reconstruct the lives of enslaved Africans in colonial New York.
This Week: Creation Stories, Climate Skeptics, and Wine
Authors:   AGU
Published: February 2020

What Earth and space science stories are we recommending this week?
Submarine Canyons Breed Megawaves in Japan
Authors: Duncombe Jenessa
Published: February 2020

The canyons act like a prism, focusing waves into mammoths of destruction.
Sources and Transformation Processes of Proteinaceous Matter and Free Amino Acids in PM2.5
Authors: Zhu Ren‐guo , Xiao Hua‐Yun , Zhu Yuwen , Wen Zequn , Fang Xiaozheng , Pan Yuanyuan
Published: February 2020

Amino acids is an important organic nitrogen compound class in aerosol. Its origins and transformation in the atmosphere remain poorly understood. The concentrations of free amino acids (FAAs) and combined amino acids (CAAs) and δ15N values of free and combined Glycine (Gly) in PM2.5 and main emission sources (plant, soil, and aerosol from biomass burning) were investigated from five sampling sites in Nanchang area (Jiangxi Province, China). Our results showed that the composition profiles of CAAs and FAAs were quite different from each other in PM2.5. For CAAs, percentages of individual combined amino acids were different between biomass burning sources and plant or soil sources, and we found that the composition profiles of aerosol CAAs could reflect the contribution of the main emission sources. For FAAs, a predominance of free Gly was observed in aerosol FAAs pool because atmospheric photooxidative processes could increase free Gly and decrease other reactive FAAs. This implied that the composition of aerosol FAAs could not reflect their origins. A strong correlation between δ15NF‐Gly values in aerosols or sources and the δ15NC‐Gly values in their parent CAAs was observed, indicating that the isotope effect associated with Gly transformation in aerosols may be small. Additionally, we found more positive δ15NGly in aerosols emitted by biomass burning, which was likely due to 15N‐depleted amino‐N loss from Gly molecule. The results suggested that δ15NGly values in aerosols might be used to identify biomass burning sources.
AMPK-dependent activation of the Cyclin Y/CDK16 complex controls autophagy
Authors: Dohmen Marc , Krieg Sarah , Agalaridis Georgios , Zhu Xiaoqing , Shehata Saifeldin N. , Pfeiffenberger Elisabeth , Amelang Jan , Bütepage Mareike , Buerova Elena , Pfaff Carolina M. , Chanda Dipanjan , Geley Stephan , Preisinger Christian , Sakamoto Kei , Lüscher Bernhard , Neumann Dietbert , Vervoorts Jörg
Published: February 2020

The AMP-activated protein kinase (AMPK) is a master sensor of the cellular energy status that is crucial for the adaptive response to limited energy availability. AMPK is implicated in the regulation of many cellular processes, including autophagy. However, the precise mechanisms by which AMPK controls these processes and the identities of relevant substrates are not fully understood. Using protein microarrays, we identify Cyclin Y as an AMPK substrate that is phosphorylated at Serine 326 (S326) both in vitro and in cells. Phosphorylation of Cyclin Y at S326 promotes its interaction with the Cyclin-dependent kinase 16 (CDK16), thereby stimulating its catalytic activity. When expressed in cells, Cyclin Y/CDK16 is sufficient to promote autophagy. Moreover, Cyclin Y/CDK16 is necessary for efficient AMPK-dependent activation of autophagy. This functional interaction is mediated by AMPK phosphorylating S326 of Cyclin Y. Collectively, we define Cyclin Y/CDK16 as downstream effector of AMPK for inducing autophagy.
Uncovering near-free platinum single-atom dynamics during electrochemical hydrogen evolution reaction
Authors: Fang Shi , Zhu Xiaorong , Liu Xiaokang , Gu Jian , Liu Wei , Wang Danhao , Zhang Wei , Lin Yue , Lu Junling , Wei Shiqiang , Li Yafei , Yao Tao
Published: February 2020

Single-atom catalysts offering intriguing activity and selectivity are subject of intense investigation. Understanding the nature of single-atom active site and its dynamics under working state are crucial to improving their catalytic performances. Here, we identify at atomic level a general evolution of single atom into a near-free state under electrocatalytic hydrogen evolution condition, via operando synchrotron X-ray absorption spectroscopy. We uncover that the single Pt atom tends to dynamically release from the nitrogen-carbon substrate, with the geometric structure less coordinated to support and electronic property closer to zero valence, during the reaction. Theoretical simulations support that the Pt sites with weakened Pt–support interaction and more 5d density are the real active centers. The single-atom Pt catalyst exhibits very high hydrogen evolution activity with only 19 mV overpotential in 0.5 M H2SO4 and 46 mV in 1.0 M NaOH at 10 mA cm−2, and long-term durability in wide-pH electrolytes.
Author Correction: Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1
Authors: Minderjahn Julia , Schmidt Andreas , Fuchs Andreas , Schill Rudolf , Raithel Johanna , Babina Magda , Schmidl Christian , Gebhard Claudia , Schmidhofer Sandra , Mendes Karina , Ratermann Anna , Glatz Dagmar , Nützel Margit , Edinger Matthias , Hoffmann Petra , Spang Rainer , Längst Gernot , Imhof Axel , Rehli Michael
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Demographic characteristics of free-roaming dogs (FRD) in rural and urban India following a photographic sight-resight survey
Authors: Tiwari Harish Kumar , Robertson Ian D. , O’Dea Mark , Vanak Abi Tamim
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher Correction: mTORC1 and mTORC2 Differentially Regulate Cell Fate Programs to Coordinate Osteoblastic Differentiation in Mesenchymal Stromal Cells
Authors: Schaub Theres , Gürgen Dennis , Maus Deborah , Lange Claudia , Tarabykin Victor , Dragun Duska , Hegner Björn
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher Correction: High resolution structural and functional analysis of a hemopexin motif protein from Dolichos
Authors: Sharma Sarita Chandan , Kumar Ashish , Vashisht Sharad , Salunke Dinakar M.
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Hand posture affects brain-function measures associated with listening to speech
Authors: Tsunoda Koichi , Takazawa Mihiro , Sekimoto Sotaro , Itoh Kenji , Baer Thomas
Published: February 2020

A major difficulty in studies of the brain, from the molecular to large-scale network level, is ensuring the accuracy and reliability of results, since repeatability has been a problem in studies utilizing functional magnetic resonance imaging (f-MRI) near-infrared spectroscopy (NIRS), and positron-emission tomography (PET). More generally, an effort to replicate psychological studies has shown that the original results were unambiguously reobtained only 39% of the time. It has been suggested that researchers must undertake studies to identify factors that reduce reliability and conduct more carefully controlled studies to improve reliability. In our previous work, we examined whether changes in hand/arm posture can have a confounding effect on task-related brain activity. Here we show a solution to enhance reproducibility in a NIRS study in a hearing task. The results showed that crossed posture can lead to different results than parallel posture with respect to asymmetric functional connectivity, especially during non-resting state. Even when the only task is listening to speech stimuli, participants should be asked to place their hands on a surface and feet on the floor and keep the same stable posture to increase reproducibility of results. To achieve accurate reliability and reproductively of results, stable hand posture through the experiment is important.
Combined cardio-protective ability of syringic acid and resveratrol against isoproterenol induced cardio-toxicity in rats via attenuating NF-kB and TNF-α pathways
Authors: S. Manjunatha , Shaik Althaf Hussain , E. Maruthi Prasad , Al Omar Suliman Yousef , Mohammad Altaf , Kodidhela Lakshmi Devi
Published: February 2020

The study was conducted to evaluate the cardio-protective activity of combination (COMB) of syringic acid (SA) and resveratrol (RV) against isoproterenol (ISO) induced cardio-toxicity in rats. Rats were pre-treated orally with SA (50 mg/kg), RV (50 mg/kg) and combination of SA (25 mg/kg) and RV (25 mg/kg) along with positive control gallic acid (50 mg/kg) for 30 days. The effects of ISO on cardiac markers, lipid profile and lipid peroxidation marker, anti-oxidant enzymes and m-RNA expression of nuclear factor-kappa B (NF-kB) and tumor necrosis factor-α (TNF-α) were observed along with histopathological observations of simple and transmission electron microscopes (TEM). Serum creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH) and alkaline phosphatase were significantly increased while cardiac tissue CK-MB, LDH, superoxide dismutase and catalase were significantly decreased in ISO administered rats, which also exhibited a significant increase in total cholesterol, triglycerides, low density lipoprotein cholesterol, very low density lipoprotein cholesterol and thiobarbutyric acid reactive substances and significant decrease in high density lipoprotein cholesterol in serum and heart. The m-RNA levels of inflammatory markers NF-kB and TNF-α were significantly increased in ISO treated rats. COMB Pre-treatment significantly reversed the ISO actions. Histopathological studies of simple and TEM were also co-related with the above biochemical parameters. Docking studies with NF-kB were also performed. Evidence has shown for the first time in this approach that COMB pre-treatment ameliorated ISO induced cardio-toxicity in rats and revealed cardio-protection.
Agricultural productivity in relation to climate and cropland management in West Africa
Authors: Mechiche-Alami Altaaf , Abdi Abdulhakim M.
Published: February 2020

The climate of West Africa is expected to become more arid due to increased temperature and uncertain rainfall regimes, while its population is expected to grow faster than the rest of the world. As such, increased demand for food will likely coincide with declines in agricultural production in a region where severe undernutrition already occurs. Here, we attempt to discriminate between the impacts of climate and other factors (e.g. land management/degradation) on crop production across West Africa using satellite remote sensing. We identify trends in the land surface phenology and climate of West African croplands between 2000 and 2018. Using the combination of a an attribution framework and residual trend anlaysis, we discriminate between climate and other impacts on crop productivity. The combined effect of rainfall, land surface temperature and solar radiation explains approximately 40% of the variation in cropland productivity over West Africa at the 95% significance level. The largest proportions of croplands with greening trends were observed in Mali, Niger and Burkina Faso, and the largest proportions with browning trends were in Nigeria, The Gambia and Benin. Climate was responsible for 52% of the greening trends and 25% of the browning trends. Within the other driving factors, changes in phenology explained 18% of the greening and 37% of the browning trends across the region, the use of inputs and irrigation explained 30% of the greening trends and land degradation 38% of the browning trends. These findings have implications for adaptation policies as we map out areas in need of improved land management practices and those where it has proven to be successful.
Analysis of membrane fouling by Brunauer-Emmett-Teller nitrogen adsorption/desorption technique
Authors: Virtanen Tiina , Rudolph Gregor , Lopatina Anastasiia , Al-Rudainy Basel , Schagerlöf Herje , Puro Liisa , Kallioinen Mari , Lipnizki Frank
Published: February 2020

Membrane fouling is the major factor limiting the wider applicability of the membrane-based technologies in water treatment and in separation and purification processes of biorefineries, pulp and paper industry, food industry and other sectors. Endeavors to prevent and minimize fouling requires a deep understanding on the fouling mechanisms and their relative effects. In this study, Brunauer-Emmett-Teller (BET) nitrogen adsorption/desorption technique was applied to get an insight into pore-level membrane fouling phenomena occurring in ultrafiltration of wood-based streams. The fouling of commercial polysulfone and polyethersulfone membranes by black liquor, thermomechanical pulping process water and pressurized hot-water extract was investigated with BET analysis, infrared spectroscopy, contact angle analysis and pure water permeability measurements. Particular emphasis was paid to the applicability of BET for membrane fouling characterization. The formation of a fouling layer was detected as an increase in cumulative pore volumes and pore areas in the meso-pores region. Pore blocking was seen as disappearance of meso-pores and micro-pores. The results indicate that the presented approach of using BET analysis combined with IR spectroscopy can provide complementary information revealing both the structure of fouling layer and the chemical nature of foulants.
Quantum dynamics studies of isotope effects in the Mg+(3p) + HD → MgH+/MgD+ + D/H insertion reaction
Authors: Mao Ye , Yuan Jiuchuang , Yang Zijiang , Chen Maodu
Published: February 2020

The time-dependent wave packet quantum dynamics studies for the Mg+(3p) + HD → MgH+/MgD+ + D/H diabatic reaction are carried out for the first time on recently developed diabatic YHWCH potential energy surfaces [Phys. Chem. Chem. Phys., 2018, 20, 6638–6647]. The results of reaction probabilities and total integral cross sections show a dramatic preference to the formation of MgD+ over MgH+ owing to the insertion reaction mechanism in the title reaction. The MgD+/MgH+ branching ratio witnesses a monotonic decrease from 10.58 to 3.88 at collision energy range of 0.01 to 0.20  eV, and at the collision energy of 0.114  eV, it is close to the experimental value of 5. The rovibrational state-resolved ICSs of the two channels show the products MgD+ have higher vibrational excitation and hotter rotational state distributions. The opacity function P(J) suggests that the MgH+ + D channel and MgD+ + H channel are dominated by high-b and low-b collisions, respectively. Both forward and backward scattering peaks are found in the differential cross section curves, whereas the angle distributions of products are not strictly forward-backward symmetric because of the short lifetime of the complex in the reaction.
New perspectives on analysing data from biological collections based on social network analytics
Authors: de Siracusa Pedro C. , Gadelha Luiz M. R. , Ziviani Artur
Published: February 2020

Biological collections have been historically regarded as fundamental sources of scientific information on biodiversity. They are commonly associated with a variety of biases, which must be characterized and mitigated before data can be consumed. In this work, we are motivated by taxonomic and collector biases, which can be understood as the effect of particular recording preferences of key collectors on shaping the overall taxonomic composition of biological collections they contribute to. In this context, we propose two network models as the first steps towards a network-based conceptual framework for understanding the formation of biological collections as a result of the composition of collectors’ interests and activities. Building upon the defined network models, we present a case study in which we use our models to explore the community of collectors and the taxonomic composition of the University of Brasília herbarium. We describe topological features of the networks and point out some of the most relevant collectors in the biological collection as well as their taxonomic groups of interest. We also investigate their collaborative behaviour while recording specimens. Finally, we discuss future perspectives for incorporating temporal and geographical dimensions to the models. Moreover, we indicate some possible investigation directions that could benefit from our approach based on social network analytics to model and analyse biological collections.
Plasmonic Manipulation of DNA using a Combination of Optical and Thermophoretic Forces: Separation of Different-Sized DNA from Mixture Solution
Authors: Shoji Tatsuya , Itoh Kenta , Saitoh Junki , Kitamura Noboru , Yoshii Takahiro , Murakoshi Kei , Yamada Yuto , Yokoyama Tomohiro , Ishihara Hajime , Tsuboi Yasuyuki
Published: February 2020

We demonstrate the size-dependent separation and permanent immobilization of DNA on plasmonic substrates by means of plasmonic optical tweezers. We found that a gold nanopyramidal dimer array enhanced the optical force exerted on the DNA, leading to permanent immobilization of the DNA on the plasmonic substrate. The immobilization was realized by a combination of the plasmon-enhanced optical force and the thermophoretic force induced by a photothermal effect of the plasmons. In this study, we applied this phenomenon to the separation and fixation of size-different DNA. During plasmon excitation, DNA strands of different sizes became permanently immobilized on the plasmonic substrate forming micro-rings of DNA. The diameter of the ring was larger for longer DNA (in base pairs). When we used plasmonic optical tweezers to trap DNA of two different lengths dissolved in solution (φx DNA (5.4 kbp) and λ-DNA (48.5 kbp), or φx DNA and T4 DNA (166 kbp)), the DNA were immobilized, creating a double micro-ring pattern. The DNA were optically separated and immobilized in the double ring, with the shorter sized DNA and the larger one forming the smaller and larger rings, respectively. This phenomenon can be quantitatively explained as being due to a combination of the plasmon-enhanced optical force and the thermophoretic force. Our plasmonic optical tweezers open up a new avenue for the separation and immobilization of DNA, foreshadowing the emergence of optical separation and fixation of biomolecules such as proteins and other ncuelic acids.
The association of Chlamydia trachomatis and Mycoplasma genitalium infection with the vaginal metabolome
Authors: Borgogna Joanna-Lynn C. , Shardell Michelle D. , Yeoman Carl J. , Ghanem Khalil G. , Kadriu Herlin , Ulanov Alexander V. , Gaydos Charlotte A. , Hardick Justin , Robinson Courtney K. , Bavoil Patrik M. , Ravel Jacques , Brotman Rebecca M. , Tuddenham Susan
Published: February 2020

Chlamydia trachomatis (CT) and Mycoplasma genitalium (MG) are two highly prevalent bacterial sexually transmitted infections (STIs) with a significant rate of co-infection in some populations. Vaginal metabolites are influenced by resident vaginal microbiota, affect susceptibility to sexually transmitted infections (STIs), and may impact local inflammation and patient symptoms. Examining the vaginal metabolome in the context of CT mono (CT+) and CT/MG co-infection (CT+/MG+) may identify biomarkers for infection or provide new insights into disease etiology and pathogenesis. Yet, the vaginal metabolome in the setting of CT infection is understudied and the composition of the vaginal metabolome in CT/MG co-infected women is unknown. Therefore, in this analysis, we used an untargeted metabolomic approach combined with 16S rRNA gene amplicon sequencing to characterize the vaginal microbiota and metabolomes of CT+, CT+/MG+, and uninfected women. We found that CT+ and CT+/MG+ women had distinct vaginal metabolomic profiles as compared to uninfected women both before and after adjustment for the vaginal microbiota. This study provides important foundational data documenting differences in the vaginal metabolome between CT+, CT+/MG+ and uninfected women. These data may guide future mechanistic studies that seek to provide insight into the pathogenesis of CT and CT/MG infections.
Aluminosilicate Nanocomposites from Incinerated Chinese Holy Joss Fly Ash: A Potential Nanocarrier for Drug Cargos
Authors: Ramanathan Santheraleka , Gopinath Subash C. B. , Md Arshad M. K. , Poopalan Prabakaran , Anbu Periasamy , Lakshmipriya Thangavel
Published: February 2020

An incredible amount of joss fly ash is produced from the burning of Chinese holy joss paper; thus, an excellent method of recycling joss fly ash waste to extract aluminosilicate nanocomposites is explored. The present research aims to introduce a novel method to recycle joss fly ash through a simple and straightforward experimental procedure involving acidic and alkaline treatments. The synthesized aluminosilicate nanocomposite was characterized to justify its structural and physiochemical characteristics. A morphological analysis was performed with field-emission transmission electron microscopy, and scanning electron microscopy revealed the size of the aluminosilicate nanocomposite to be ~25 nm, while also confirming a uniformly spherical-shaped nanostructure. The elemental composition was measured by energy dispersive spectroscopy and revealed the Si to Al ratio to be 13.24 to 7.96, showing the high purity of the extracted nanocomposite. The roughness and particle distribution were analyzed using atomic force microscopy and a zeta analysis. X-ray diffraction patterns showed a synthesis of faceted and cubic aluminosilicate crystals in the nanocomposites. The presence of silica and aluminum was further proven by X-ray photoelectron spectroscopy, and the functional groups were recognized through Fourier transform infrared spectroscopy. The thermal capacity of the nanocomposite was examined by a thermogravimetric analysis. In addition, the research suggested the promising application of aluminosilicate nanocomposites as drug carriers. The above was justified by an enzyme-linked apta-sorbent assay, which claimed that the limit of the aptasensing aluminosilicate-conjugated ampicillin was two-fold higher than that in the absence of the nanocomposite. The drug delivery property was further justified through an antibacterial analysis against Escherichia coli (gram-negative) and Bacillus subtilis (gram-positive).
Cretaceous gnetalean yields first preserved plant gum
Authors: Roberts Emily A. , Seyfullah Leyla J. , Loveridge Robert F. , Garside Paul , Martill David M.
Published: February 2020

Some liquid plant exudates (e.g. resin) can be found preserved in the fossil record. However, due to their high solubility, gums have been assumed to dissolve before fossilisation. The visual appearance of gums (water-soluble polysaccharides) is so similar to other plant exudates, particularly resin, that chemical testing is essential to differentiate them. Remarkably, Welwitschiophyllum leaves from Early Cretaceous, Brazil provide the first chemical confirmation of a preserved gum. This is despite the leaves being exposed to water twice during formation and subsequent weathering of the Crato Formation. The Welwitschiophyllum plant shares the presence of gum ducts inside leaves with its presumed extant relative the gnetalean Welwitschia. This fossil gum presents a chemical signature remarkably similar to the gum in extant Welwitschia and is distinct from those of fossil resins. We show for the first time that a water-soluble plant exudate has been preserved in the fossil record, potentially allowing us to recognise further biomolecules thought to be lost during the fossilisation process.
Glycation changes molecular organization and charge distribution in type I collagen fibrils
Authors: Bansode Sneha , Bashtanova Uliana , Li Rui , Clark Jonathan , Müller Karin H. , Puszkarska Anna , Goldberga Ieva , Chetwood Holly H. , Reid David G. , Colwell Lucy J. , Skepper Jeremy N. , Shanahan Catherine M. , Schitter Georg , Mesquida Patrick , Duer Melinda J.
Published: February 2020

Collagen fibrils are central to the molecular organization of the extracellular matrix (ECM) and to defining the cellular microenvironment. Glycation of collagen fibrils is known to impact on cell adhesion and migration in the context of cancer and in model studies, glycation of collagen molecules has been shown to affect the binding of other ECM components to collagen. Here we use TEM to show that ribose-5-phosphate (R5P) glycation of collagen fibrils – potentially important in the microenvironment of actively dividing cells, such as cancer cells – disrupts the longitudinal ordering of the molecules in collagen fibrils and, using KFM and FLiM, that R5P-glycated collagen fibrils have a more negative surface charge than unglycated fibrils. Altered molecular arrangement can be expected to impact on the accessibility of cell adhesion sites and altered fibril surface charge on the integrity of the extracellular matrix structure surrounding glycated collagen fibrils. Both effects are highly relevant for cell adhesion and migration within the tumour microenvironment.
Supervised deep learning for real-time quality monitoring of laser welding with X-ray radiographic guidance
Authors: Shevchik Sergey , Le-Quang Tri , Meylan Bastian , Farahani Farzad Vakili , Olbinado Margie P. , Rack Alexander , Masinelli Giulio , Leinenbach Christian , Wasmer Kilian
Published: February 2020

Laser welding is a key technology for many industrial applications. However, its online quality monitoring is an open issue due to the highly complex nature of the process. This work aims at enriching existing approaches in this field. We propose a method for real-time detection of process instabilities that can lead to defects. Hard X-ray radiography is used for the ground truth observations of the sub-surface events that are critical for the quality. A deep artificial neural network is applied to reveal the unique signatures of those events in wavelet spectrograms from the laser back-reflection and acoustic emission signals. The autonomous classification of the revealed signatures is tested on real-life data, while the real-time performance is reached by means of parallel computing. The confidence of the quality classification ranges between 71% and 99%, with a temporal resolution down to 2 ms and a computation time per classification task as low as 2 ms. This approach is a new paradigm in the digitization of industrial processes and can be exploited to provide feedbacks in a closed-loop quality control system.
FKBP5-associated miRNA signature as a putative biomarker for PTSD in recently traumatized individuals
Authors: Kang Hyo Jung , Yoon Sujung , Lee Suji , Choi Koeul , Seol Sihwan , Park Shinwon , Namgung Eun , Kim Tammy D. , Chung Yong-An , Kim Jungyoon , Han Jung-Soo , Lyoo In Kyoon
Published: February 2020

The epigenetic regulation of microRNA (miRNA) expression related to the FK506-binding protein 5 (FKBP5) gene may contribute to the risk of stress-related disorders such as posttraumatic stress disorder (PTSD). Here, we identified candidate miRNAs derived from FKBP5 knockout mice as a potential diagnostic biomarker of PTSD. Using a translational approach, candidate miRNAs found to alter in expression within the medial prefrontal cortex of FKBP5 knockout mice were selected. Each candidate miRNA was examined in the serum of 48 recently traumatized individuals with PTSD and 47 healthy individuals. Multimodal imaging was also conducted to identify the neural correlates for the expression of candidate exosomal miRNAs in response to trauma exposure. Differential miRNA expression was found according to PTSD diagnosis in two composite marker groups. The differential miRNA expression between the composite marker groups contributed to PTSD symptom severity, which may be explained by differential recruitment of prefrontolimbic activity in brain imaging. The present study reveals that a set of circulating exosomal miRNAs showing altered expression in FKBP5 knockout mice play a potential role as epigenetic markers of PTSD. The corroborative evidence from multiple levels including molecular, brain, and behavioral indicates that these epigenetic biomarkers may serve as complementary measures for the diagnosis and prognosis prediction of PTSD in recently traumatized individuals.
Cold atmospheric plasma generated reactive species aided inhibitory effects on human melanoma cells: an in vitro and in silico study
Authors: Yadav Dharmendra Kumar , Adhikari Manish , Kumar Surendra , Ghimire Bhagirath , Han Ihn , Kim Mi-Hyun , Choi Eun-Ha
Published: February 2020

Malignant melanoma is considered to be a heterogeneous disease that arises from altered genes and transformed melanocytes. In this study, special softjet cold atmospheric plasma was used to treat three different human melanoma cells using air and N2 gases to check the anti-melanoma activity. The physical effects by plasma revealed an increase in the temperature with the gradual reduction in pH at 60 sec, 180 sec and 300 sec air and N2 plasma treatment. Cellular toxicity revealed a decreased in cell survival (~50% cell survival using air gas and <~60% cell survival using N2 gas at 60 sec plasma treatment in G-361 cells). Gene analysis by q-PCR revealed that 3 min and 5 min air and N2 plasma treatment activated apoptotic pathways by triggering apoptotic genes in all three melanoma cell lines. The apoptosis was confirmed by DAPI staining and its related pathways were further explored according to protein-protein docking, and their probable activation mechanism was revealed. The pathways highlighted that activation of apoptosis which leads to cellular cascades and hence stimulation ASK1 (docking method) revealed that softjet plasma can be an effective modality for human melanoma treatment.
Determination of Kaurenoic Acid in Acanthopanax trifoliatus by Ultra-High Performance Liquid Chromatography Coupled with Tandem Mass Spectrometry (UHPLC-MS/MS)
Authors: Peng Qun , Chen Jianyuan , Duan Hanying , Wang Chao
Published: February 2020

Acanthopanax trifoliatus (L.) Merr. (A. trifoliatus) belongs to the family Araliaceae, which is called “Le Cai”, and is an indigenous plant to Guangdong Province that has been prevalently planted for years. A. trifoliatus is used in folk medicine and has ginseng-like activity. Kaurenoic acid ((−)-kaur-16-en-19-oic acid, KA) is a kaurane-type diterpenoid that is regarded as a major compound in A. trifoliatus. Early studies have reported the determination of KA by HPLC capillary electrophoresis. However, KA could not be completely separated from other components in the plant extract by HPLC because of their similar molecular structures and physical and chemical properties. UHPLC-MS/MS could be a useful tool to identify and quantify KA. In the present work, a UHPLC-ESI-MS/MS method for determining KA in A. trifoliatus was developed and validated. KA was extracted from lyophilized A. trifoliatus leaves by ultrasound-assisted extraction and further purified by solid phase extraction (SPE). KA was quantified and separated on an Accucore C18 LC column. Mass spectrometry with multi-reaction monitoring (MRM) and quantitative fragment ion/product ion (m/z: 301.3/301.3) in ESI negative mode was used for quantification. The intra-assay and inter-assay relative standard deviation (R.S.D.) were 2.8% and 3.2%, respectively. The inter-person R.S.D. on the same day was 3.6%. The inter-instrument R.S.D. with the same model on the same day was 2.9%. The recoveries evaluated upon spiking three different concentrations of KA were above 97%. A minor matrix effect of 94% was observed. This method has been applied successfully for the determination of KA in A. trifoliatus leaves.
Topical recombinant human Nerve growth factor (rh-NGF) is neuroprotective to retinal ganglion cells by targeting secondary degeneration
Authors: Guo Li , Davis Benjamin M. , Ravindran Nivedita , Galvao Joana , Kapoor Neel , Haamedi Nasrin , Shamsher Ehtesham , Luong Vy , Fico Elena , Cordeiro M. Francesca
Published: February 2020

Optic neuropathy is a major cause of irreversible blindness worldwide, and no effective treatment is currently available. Secondary degeneration is believed to be the major contributor to retinal ganglion cell (RGC) death, the endpoint of optic neuropathy. Partial optic nerve transection (pONT) is an established model of optic neuropathy. Although the mechanisms of primary and secondary degeneration have been delineated in this model, until now how this is influenced by therapy is not well-understood. In this article, we describe a clinically translatable topical, neuroprotective treatment (recombinant human nerve growth factor, rh-NGF) predominantly targeting secondary degeneration in a pONT rat model. Topical application of rh-NGF twice daily for 3 weeks significantly improves RGC survival as shown by reduced RGC apoptosisin vivoand increased RGC population in the inferior retina, which is predominantly affected in this model by secondary degeneration. Topical rh-NGF also promotes greater axonal survival and inhibits astrocyte activity in the optic nerve. Collectively, these results suggest that topical rh-NGF exhibits neuroprotective effects on retinal neurons via influencing secondary degeneration process. As topical rh-NGF is already involved in early clinical trials, this highlights its potential in multiple indications in patients, including those affected by glaucomatous optic neuropathy.
Clinical significance of circulating soluble immune checkpoint proteins in sorafenib-treated patients with advanced hepatocellular carcinoma
Authors: Dong Minh Phuong , Enomoto Masaru , Thuy Le Thi Thanh , Hai Hoang , Hieu Vu Ngoc , Hoang Dinh Viet , Iida-Ueno Ayako , Odagiri Naoshi , Amano-Teranishi Yuga , Hagihara Atsushi , Fujii Hideki , Uchida-Kobayashi Sawako , Tamori Akihiro , Kawada Norifumi
Published: February 2020

In hepatocellular carcinoma (HCC), the clinical significance of soluble immune checkpoint protein levels as predictors of patient outcomes or therapeutic responses has yet to be defined. This study profiled the baseline levels of sixteen soluble checkpoint proteins and their changes following sorafenib treatment for HCC. Plasma samples were obtained from 53 patients with advanced HCC at baseline, week 1, 2 and 4 of sorafenib treatment and tested the concentrations of 16 soluble checkpoint proteins using multiplexed fluorescent bead-based immunoassays. Multivariate analysis showed high sBTLA levels at baseline were an independent predictor of poor overall survival (p = 0.038). BTLA was highly expressed in T cells and macrophages in peritumoral areas. At week 2, sCD27 levels were decreased compared to baseline. By contrast, the concentrations of most inhibitory proteins, including sBTLA, sLAG-3, sCTLA-4, sPD-1, sCD80, sCD86 and sPD-L1, had significantly increased. The fold-changes of soluble checkpoint receptors and their ligands, including sCTLA-4 with sCD80/sCD86, sPD-1 with sPD-L1; and the fold-changes of sCTLA-4 with sBTLA or sPD-1 were positively correlated. sBTLA may be a good biomarker for predicting overall survival in HCC patients. Sorafenib treatment in patients with advanced HCC revealed dynamic changes of soluble checkpoint protein levels.
Ni-based catalysts supported on Mg–Al hydrotalcites with different morphologies for CO2 methanation: exploring the effect of metal–support interaction
Authors: Ren Jie , Mebrahtu Chalachew , Palkovits Regina
Published: February 2020

Ni-based Mg–Al hydrotalcite catalysts with perfect morphologies were proven to be highly active and stable during CO2 methanation.
Effects of collagen peptides from skate (Raja kenojei) skin on improvements of the insulin signaling pathway via attenuation of oxidative stress and inflammation
Authors: Woo Minji , Seol Bo Gyeong , Kang Keon-Hee , Choi Yung Hyun , Cho Eun Ju , Noh Jeong Sook
Published: February 2020

It has been well established that hepatic insulin signaling is significantly affected by the antioxidative status of the liver.
Synthesis of acrolein by oxidative coupling of alcohols over spinel catalysts: microcalorimetric and spectroscopic approaches
Authors: Folliard Vincent , Postole Georgeta , Marra Livia , Dubois Jean-Luc , Auroux Aline
Published: February 2020

Oxidative coupling of methanol and ethanol is becoming a promising alternative to produce sustainable acrolein.