202 research outputs found
Multivariate Quantitative Representativeness and Constituency Analysis of Ecological Observation Networks
No full textCite this code as: Kumar, J. (2023). Multivariate Quantitative Representativeness and Constituency Analysis of Ecological Observation Networks (Version 1.0) [Computer software]. https://doi.org/10.5281/zenodo.8048530
Multivariate Quantitative Representativeness and Constituency Analysis of Ecological Observation Networks
Author: Jitendra (Jitu) Kumar ([email protected]), Oak Ridge National Laboratory
Regional and global ecological research networks, representing coordinated and standardized as well as adhoc networks of observation sites, provide valuable observations necessary for ecological modeling and synthesis studies. Studies conducted across observational networks strive to scale up their results to larger areas, trying to reach conclusions that are valid throughout regional, continental, and even global scales. Network representativeness and constituency can show how well conditions at those locations represent conditions elsewhere within a larger area containing the network and can be used to help scale-up results over larger regions.
Representativeness: Euclidean distance between two sites plotted in multivariate environmental space can be used as an inverse measure of multivariate similarity to quantify representativeness. Close sites in environmental space have a similar combination of environmental factors, and therefore are highly representative of each other.
Constituency: For any site in the network, its Constituency represent all locations that are best represented by the multivariate environmental drivers at that site.
Code Compilation:
make
Edit the ```makefile``` as needed for your platform.
CC=gcc
CFLAGS= -O3
hpea: network_representativeness.o\
utility.o
(CFLAGS) *.o -lm -o network_representativeness
.o:
(CFLAGS) -c $<
clean:
\rm *.o network_representativeness
Running the representativeness analysis:
Usage: network_representativeness -infile input data file [ASCII]
-coordsfile coordinate file name
-clustfile coordinate file name [OPTIONAL -- must be used with -siteclustfile]
-sitefile site data file name
-siteclustfile site data file name [OPTIONAL -- must be used with -clustfile]
-nsites No. of sites
-minmaxfile minmax file name
-outfile output file name
-nrows No. of rows in input data
-ncols No. of variables
-details [OPTIONAL -- turn on output representativeness for each site, default is to write network representativeness and constituency only.]
-help program usage help.
Publications using ```network_reprentativeness``` code:
Kumar, J., Coffin, A. W., Baffaut, C., Ponce-Campos, G., Witthaus, L., and Hargrove, W. W. (2023) "Quantitative Representativeness and Constituency of the Long-Term Agroecosystem Research Network, and Analysis of Complementarity with Other Existing Ecological Networks", Environmental Management (in press)
M. M. T. A. Pallandt, J. Kumar, M. Mauritz, E. A. G. Schuur, A.-M. Virkkala, G. Celis, F. M. Hoffman, and M. Göckede. Representativeness assessment of the pan-arctic eddy covariance site network and optimized future enhancements. Biogeosciences, 19(3):559--583, 2022. https://doi.org/10.5194/bg-19-559-2022
J. Kumar, F. M. Hoffman, W. W. Hargrove, and N. Collier. Understanding the representativeness of FLUXNET for upscaling carbon flux from eddy covariance measurements. Earth System Science Data Discussion, 2016:1--25, August 2016. https://doi.org/10.5194/essd-2016-36.If you use this software, please cite it as below.
Kumar, J. (2023). Multivariate Quantitative Representativeness and Constituency Analysis of Ecological Observation Networks (Version 1.0) [Computer software]. https://doi.org/10.5281/zenodo.804853
Particle and cluster analyses of silica powders via small angle neutron scattering
No full textData source: Supplementary data, https://doi.org/10.1016/j.powtec.2017.12.061Small angle neutron scattering (SANS) responses of particulate silica as disordered and ordered porous and non-porous powders were obtained. Each classification provided distinct scattering patterns which were fitted and analysed using Guinier-Porod and mass-surface fractal (msf) models. The resulting particle dimensions showed good agreement with the same from nitrogen gas adsorption analyses. Additionally, the excellent fit of the msf model to the non-porous silica scattering response resulted in an agreement between the mass and surface fractal dimension values for it and similar analyses and results published previously for fumed silica. The msf fitting gave additional insight into particle and cluster scattering dimensions with particle dimensions being consistent with those from the G-P analyses.S. Hadi Madani, Ian Harvey Arellano, Jitendra P. Mata, Phillip Pendleto
Nanoplastics and Protein Corona - Investigating the Corona Structure and their Biological Impacts
No full textThis thesis explores the chemical and biological bases behind the reported effects of nano-scale
plastics (nanoplastics) on organisms. Surface characteristics play a key role in controlling
interactions between nanoplastics and biological systems, and key amongst these for
nanoparticles is the protein complex formed on the surface of nanoplastics when nanoplastics
are exposed to biological fluids, the protein corona. However, there are few studies focussing
on the nanoparticle-biological interface in the current literature and thus a lack of understanding
of the key principles that govern the formation and properties of protein coronae, or how the
properties of protein coronae affect the response of biological systems.
This work has approached this challenge by first investigating the physical structures that are
formed on nanoplastics in the presence of proteins, and then introducing nanoplastic and
nanoplastic/protein complexes to in vitro cells and model lipid membranes to investigate their
impact. Collectively, the contributory factors were critically assessed – nanoplastic size and
charge, and the nature of the protein corona.
The initial study involved comparing bare polystyrene (PS) nanoplastics (both large and small,
and with both positive and negative surface charge), with the nanoplastics coated with protein
coronae formed by exposure to the human serum abundant proteins human serum albumin
(HSA), and lysozyme (LYS). The protein coronae were studied using neutron scattering
techniques and both hard and soft coronae were found to be produced depending on the
conditions (when PS and protein carry same or opposite surface charges, respectively). Soft
corona complexes are characterised by a structure where the nanoplastics were surrounded by
a loose protein layer (~ 2-3 protein thick, observed for LYS soft corona formed around small
PS(+) nanoplastics). In most cases hard-corona coated nanoplastics also formed fractal-like
aggregates in solution (except for the HSA hard corona complex with PS(+)large). Nanoplastic
size affected the structures of both the protein corona and the intrinsic protein: the selfassociation
forces holding the nanoplastic/protein complex together were stronger, and the hard
corona proteins underwent significant conformational change, for smaller nanoplastics (20 nm)
compared to larger nanoplastics (200 nm).
Bare nanoplastics and nanoplastic/protein corona complexes were introduced to cellular
environments of human alveolar epithelial (A549) cells and tethered POPC lipid bilayers. For bare nanoplastics the introduction of bare PS nanoplastics to the A549 cells in serum-free
media caused mild cytotoxicity, although there was no clear correlation between cell death and
the physical properties of the nanoplastics (size or surface charge). When the nanoplastics were
exposed to in vitro cells they had strong association with cells, and were clearly shown to be
adhering to the cellular membrane. On the POPC tethered bilayer damage was observed which
was nanoplastic size-dependent and charge-independent — small nanoplastics (20 nm) showed
membrane thinning, disruption in headgroup packing, and resistivity decrease, while the large
particles (200 nm) did not cause any membrane disruption.
Both HSA and LYS protein coronae (soft and hard) altered the way the nanoplastics interacted
with in vitro cells and lipid bilayers. In most cases, the presence of the protein corona reduced
the bilayer disruption and the extent of cytotoxicity; this reduction was greater for soft corona,
independent of the protein type or the nanoplastic size. An exception was found for the LYS
hard corona complexes with small PS nanoplastics, where the cytotoxicity effect was not
mitigated. The difference may be related to the fractal-like morphology of hard corona
nanoplastic/protein complexes, which are known to be harmful to cells.
The nanoplastic interaction with cells was not limited to membrane adhesion, however, particle
uptake into the cells was indicated in flow cytometry experiments and confirmed with
fluorescence microscopy. Three-dimensional reconstructed images of cells showed that some
of the uptaken nanoplastics were localised around the cell nuclei, apparently adhering to the
nuclear membrane surface, they did not penetrate the nuclei. There was also an indication that
chromosomes were found close to the small polystyrene nanoparticles, but not the larger
particles. Since these nanoplastics have been associated with reports of delayed reproduction
and transgenerational effects, this cellular level observation demonstrates the possibility that
small PS nanoplastics (20 nm) could be interacting with DNA.
This work therefore determined protein corona formation around PS nanoplastics is mainly
dictated by electrostatic interactions and soft and hard protein coronae adopt distinctively
different geometries. The presence of protein corona, of different types, can have the impact
on cytotoxicity and membrane disruption differently. These findings contribute to the literature
surrounding nanoplastic toxicity by establishing the link between molecular level interactions
and biological consequences
Structural evolution of photocrosslinked silk fibroin and silk fibroin-based hybrid hydrogels: A small angle and ultra-small angle scattering investigation
No full textAbstract not availableJasmin L. Whittake r, Rajkamal Balu, Robert Knott, Liliana de Campo, Jitendra P .Matac, Christine Rehm, Anita J. Hill, Naba K .Dutta, Namita Roy Choudhur
Native disulphide-linked dimers facilitate amyloid fibril formation by bovine milk alpha(S2)-casein
No full textData source: Supplementary information, https://doi.org/10.1016/j.bpc.2020.106530Bovine milk α(S2)-casein, an intrinsically disordered protein, readily forms amyloid fibrils in vitro and is implicated in the formation of amyloid fibril deposits in mammary tissue. Its two cysteine residues participate in the formation of either intra- or intermolecular disulphide bonds, generating monomer and dimer species. X-ray solution scattering measurements indicated that both forms of the protein adopt large, spherical oligomers at 20 °C. Upon incubation at 37 °C, the disulphide-linked dimer showed a significantly greater propensity to form amyloid fibrils than its monomeric counterpart. Thioflavin T fluorescence, circular dichroism and infrared spectra were consistent with one or both of the dimer isomers (in a parallel or antiparallel arrangement) being predisposed toward an ordered, amyloid-like structure. Limited proteolysis experiments indicated that the region from Ala⁸¹ to Lys¹¹³ is incorporated into the fibril core, implying that this region, which is predicted by several algorithms to be amyloidogenic, initiates fibril formation of α(S2)-casein. The partial conservation of the cysteine motif and the frequent occurrence of disulphide-linked dimers in mammalian milks despite the associated risk of mammary amyloidosis, suggest that the dimeric conformation of α(S2)-casein is a functional, yet amyloidogenic, structure.David C. Thorn, Elmira Bahraminejad, Aidan B. Grosas, Tomas Koudelka, Peter Hoffmann, Jitendra P. Mata, Glyn L. Devlin, Margaret Sunde, Heath Ecroyd, Carl Holt, John A. Carve
Polymeric ionic liquid nanoparticle emulsions as a corrosion inhibitor in anticorrosion coatings
No full textIn this contribution, we report the facile preparation of cross-linked polymerizable ionic liquid (PIL)-based nanoparticles via thiol–ene photopolymerization in a miniemulsion. The synthesized PIL nanoparticles with a diameter of about 200 nm were fully characterized with regard to their chemical structures, morphologies, and properties using different techniques, such as Fourier transform infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy, and transmission electron microscopy. To gain an in-depth understanding of the physical and morphological structures of the PIL nanoparticles in an emulsion, small-angle neutron scattering and ultra-small-angle neutron scattering were used. Neutron scattering studies revealed valuable information regarding the formation of cylindrical ionic micelles in the spherical nanoparticles, which is a unique property of this system. Furthermore, the PIL nanoparticle emulsion was utilized as an inhibitor in a self-assembled nanophase particle (SNAP) coating. The corrosion protection ability of the resultant coating was examined using potentiodynamic polarization and electrochemical impedance spectroscopy. The results show that the PIL nanoparticle emulsion in the SNAP coating acts as an inhibitor of corrosion and is promising for fabricating advanced coatings with improved barrier function and corrosion protection.Mona Taghavikish, Surya Subianto, Naba Kumar Dutta, Liliana de Campo, Jitendra P. Mata, Christine Rehm, and Namita Roy Choudhur
Experimental studies on the generation and evolution of mineral porosity during fluid-mediated mineral replacement reactions
No full textThe porosity in minerals contributes to enhanced permeability for fluid flow in natural systems and engineering processes. Porosity can be created by fluid-mediated mineral replacement reactions. Such reaction-induced porosity can evolve with time, yet the mechanisms and kinetics of porosity creation and evolution remain poorly understood. This thesis presents experimental investigations on the creation and evolution of mineral porosity in two model replacement reactions, i.e., the replacement of calcite by gypsum and anhydrite with a positive volume change and the replacement of pentlandite by violarite and millerite with a negative volume change. These replacement reactions were conducted under mildly acidic hydrothermal conditions for up to 18 months, and the mineralogy, microstructure and porosity of the reaction products were quantitatively analysed by powder X-ray diffraction, (ultra) small-angle neutron scattering, high resolution scanning electron microscopy, focused-ion beam scanning electron microscopy, and X-ray micro-tomography. The results showed that porosity creation and evolution are highly dependent on mineral systems and reaction conditions.
In the calcite-gypsum-anhydrite mineral system, the experiments at 25-60 °C produced intragranular nanopores in gypsum replacing calcite. Because of the positive volume change, gypsum overgrowth also occurred on the grain surface, and the gypsum in the overgrowth region contained intergranular micropores. Porosity coarsening was rapid (a few weeks) in the replacement region, leading to the formation of micro-voids in the core of gypsum grains. The replacement reaction was sensitive to temperature. When the experiments were conducted at a higher temperature of 220 °C, anhydrite was formed instead of gypsum. Porosity evolution in anhydrite was different when compared to gypsum at lower temperatures.
In the pentlandite-violarite-millerite mineral system, only replacement occurred, likely because the negative volume change does not require overgrowth for additional space. The replacement was sensitive to temperature and solution pH. The experiments conducted at 125 °C and pH 4 produced permeable nanopores leading to the complete replacement of pentlandite; these nanopores coarsened slowly during the 17 months of experiment and occurred preferentially near the grain surface. However, in experiments conducted at 125 °C and pH 5, violarite became impermeable in partially replaced grains due to hematite precipitation in the pore space, blocking the fluid flow. At a higher temperature of 220 °C and pH 4, the formation of millerite in addition to violarite resulted in faster porosity coarsening and formed micropores within 4 weeks.
Fundamentally, these complex porosity creation and evolution phenomena observed in the two model mineral replacement reactions are controlled by the interplay between dissolution, precipitation, epitaxial nucleation, and Ostwald ripening processes which are all sensitive to reaction conditions. This understanding should generally be applicable to other mineral replacement reactions.
Finally, a case study of the application of porosity control was presented. The leaching of chalcopyrite is often kinetically inhibited by surface passivation layers, which are formed by the replacement of chalcopyrite during leaching. Common passivation layers are elemental sulphur and jarosite. Our leaching experimental results showed that surface sulphur could be removed by adding sulphur-dissolving solvent tetrachloroethylene (TCE) into the sulfuric acid leaching solution. The removal of surface sulphur significantly improved the leaching rate by almost 6 times compared with TCE-free leaching. At the later stage of leaching, chalcopyrite was replaced by potassium jarosite. The jarosite shell did not passivate TCE-free leaching due to its porous structure. However, the jarosite shell became nearly impermeable in TCE-assisted leaching because elemental sulphur filled the pores in the jarosite. This case study suggests that chalcopyrite leaching can be significantly enhanced by either removing the surface passivating layer or by controlling the porosity and permeability of the surface layers formed on the chalcopyrite surface
Effects of crowding and environment on the evolution of conformational ensembles of the multi-stimuli-responsive intrinsically disordered protein, Rec1-Resilin: a small-angle scattering investigation
No full textData source: Supporting information, http://pubs.acs.org.access.library.unisa.edu.au/doi/suppl/10.1021/acs.jpcb.6b02475In this study, we explore the overall structural ensembles and transitions of a biomimetic, multi-stimuli-responsive, intrinsically disordered protein (IDP), Rec1-resilin. The structural transition of Rec1-resilin with change in molecular crowding and environment is evaluated using small-angle neutron scattering and small-angle X-ray scattering. The quantitative analyses of the experimental scattering data using a combination of computational models allowed comprehensive description of the structural evolution, organization, and conformational ensembles of Rec1-resilin in response to the changes in concentration, pH, and temperature. Rec1-resilin in uncrowded solutions demonstrates the equilibrium intrinsic structure quality of an IDP with radius of gyration Rg ∼ 5 nm, and a scattering function for the triaxial ellipsoidal model best fit the experimental dataset. On crowding (increase in concentration >10 wt %), Rec1-resilin molecules exert intermolecular repulsive force of interaction, the Rg value reduces with a progressive increase in concentration, and molecular chains transform from a Gaussian coil to a fully swollen coil. It is also revealed that the structural organization of Rec1-resilin dynamically transforms from a rod (pH 2) to coil (pH 4.8) and to globular (pH 12) as a function of pH. The findings further support the temperature-triggered dual-phase-transition behavior of Rec1-resilin, exhibiting rod-shaped structural organization below the upper critical solution temperature (∼4 °C) and a large but compact structure above the lower critical solution temperature (∼75 °C). This work attempted to correlate unusual responsiveness of Rec1-resilin to the evolution of conformational ensembles.Rajkamal Balu, Jitendra P. Mata, Robert Knott, Christopher M. Elvin, Anita J. Hill, Namita R. Choudhury and Naba K. Dutt
3D printed graphene aerogels using conductive nanofibrillar network formulation
No full textDespite recent progress in 3D printing of graphene, formulation of aqueous 3D printable graphene inks with desired rheological properties for direct ink writing (DIW) of multifunctional graphene macrostructures remains a major challenge. In this work, we develop a novel 3D printable pristine graphene ink in aqueous phase using conductive nanofibrillar network formulation by controlling the interfacial interactions between graphene and PEDOT:PSS nanofibrils. The formulated inks, tailored for energy applications, provide excellent 3D printability for fabricating multilayer 3D structures (up to 30 layers) with spanning features and high aspect ratio. The 3D printed aerogels, comprising interconnected networks of graphene flakes and PEDOT:PSS nanofibrils, exhibit excellent electrical conductivity as high as ∼630 S m − 1 and can be converted into conductive hydrogels via swelling in water/electrolyte. The formulated graphene inks were used for fabricating 3D printed supercapacitor electrodes (power density of 11.3 kW kg−1 and energy density of 7.3 Wh kg−1) with excellent performance and durability.Full Tex
rekabentuk bahan pembelajaran penyelesaian masalah matematik berdasarkan schema-based instruction dalam kalangan pelajar disleksia
No full textDisleksia merupakan masalah pembelajaran spesifik yang disebabkan oleh masalah neurologi. Kekeliruan dalam menyahkod sesuatu perkataan menyebabkan gangguan semasa sesi pembelajaran dan emosi pelajar. Masalah matematik tidak hanya bergantung dengan penggunaan nombor dan simbol semata-mata. Terdapat juga domain matematik yang menggunakan perkataan dan pada kebiasaannya dalam bentuk soalan penyelesaian masalah. Tujuan kajian ini adalah bagi mereka bentuk bahan bantu mengajar yang menggunakan schema–based instruction (Jitendra, 2010) sebagai strategi pembelajaran masalah matematik. Pembelajaran bagi pelajar disleksia direka bentuk bagi pembangunan aplikasi bahan bantu mengajar. Rekabentuk ini dilakukan khususnya untuk membantu pelajar disleksia menyelesaikan masalah matematik yang berbentuk perkataan
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