Miracle-dz/UniFAR-FTUs huggingface dataset:
Fe3+ and Fe2+ partitioning among silicates in metapelites: A synchrotron micro-XANES study

Abstract Synchrotron micro-XANES (X-ray absorption near-edge structure) spectroscopy (SmX) was used to measure Fe3+ and Fe2+ distribution among minerals in standard thin sections with an X-ray beam size of 10 ¥ 15 mm. Measurements were made at beamline X26a, National Synchrotron Light Source, Brookhaven National Lab. Samples studied included metapelites from garnet to upper sillimanite zone rocks that coexist with graphite, graphite/ilmenite, or varying combinations of ilmenite, magnetite, and hematite. SmX results are compared with Mössbauer spectroscopic measurements of Fe3+ on mineral separates from the same rocks. Results show excellent agreement (within ±5-10%) between Mössbauer and SmX for the Fe-rich phases biotite, chlorite, staurolite, and garnet. Mössbauer spectra of muscovite typically show lower values than SmX for Fe3+/SFe (especially at low grades), suggesting contamination of the muscovite separates by fine-grained chlorite. However, heterogeneity of Fe3+ and Fe2+ is probably the chief source of discrepancy between the bulk and micro-scale measurements. The %Fe3+ (relative to total Fe) in these samples ranges from a high of 90% in muscovite to a low of 0-2% in garnet, with Ms > St = Bt = Chl > Tur > Grt in graphite/ilmenitebearing rocks. SmX measurements suggest that the averaged Fe3+/SFe in each mineral species does not change as a function of grade, but varies as a function of buffering assemblage, especially on a very localized scale. This effect shows that the oxygen buffering capacity of mineral assemblages is very large compared to the oxidizing/reducing potential of metamorphic fluids. However, distribution of Fe atoms among phases at each grade also reflects crystal chemistry. Across all grades, the Fe2+/Mg ratio is such that Grt >> St > Bt > Chl > Tur > Ms. Fe3+/Al is highest in biotite in garnet and sillimanite- zone rocks. For Fe3+/Al, Bt > Chl > Tur > St > Ms, and for Fe3+/Fe2+, partitioning behaves as Ms >> Bt ≈ St ≈ Chl > Tur > Grt in graphite/ilmenite-bearing rocks. Overall, partitioning of Fe3+ in any of the minerals of interest reflects both oxide assemblage and crystal-chemical constraints on the amount of Fe3+ that can be substituted into the structure.
Multicolored Electrogenerated Chemiluminescence from Ortho-Metalated Iridium(III) Systems

The electrogenerated chemilumescence (ECL) of F(Ir)pic (bis(3,5-difluoro-2-(2-pyridyl)phenyl-(2-carboxypyridyl))iridium III) and (btp)2Ir(acac) (bis[2,(2‘-benzothienyl)-pyridinato-N,C3‘](acetlyacetonate)Ir(III) has been investigated in acetonitrile (MeCN), mixed MeCN/H2O (50:50, v/v), and aqueous solutions using the oxidative reductive coreactant tri-n-propylamine. ECL was also studied in the presence of the nonionic surfactant Triton X-100 (poly-(ethylene glycol) tert-octylphenyl ether). F(Ir)pic is a blue emitter (λECL ∼ 470 nm), and (btp)2Ir(acac) emits in the red (λECL ∼ 600 nm). The ECL spectrum of each compound is identical to its photoluminescence spectrum, indicating the same metal-to-ligand (MLCT) excited states. The ECL emission spectrum of F(Ir)pic can be distinguished from Ru(bpy)32+ when both are present in the same solution, raising the possibility of using these compounds for detection of multiple analytes in the same solution. ECL intensity increased in the presence of surfactant up to 6-f.
Density functional investigation of the mechanism of the selective catalytic reduction of NO by NH3 over vanadium oxide model clusters

Quantum chemical calculations using the density functional theory were performed to model the mechanism of selective catalytic reduction of NO by NH{sub 3} on a supported vanadium oxide monolayer. In the first step, the adsorption of NH{sub 3} on a bimetallic cluster representative of vanadium oxide, containing a terminal V=O adjacent to a V-OH group, was investigated. The calculations indicate that NH{sub 3} may be strongly adsorbed on V-OH (Broensted acid site) as NH{sub 4(ads)}{sup +}; subsequently, NO reacts with this activated NH{sub 3} to yield the reaction products N{sub 2} and H{sub 2}O. The present results give support to a dual-site Eley-Rideal-type mechanism involving a Broensted site. 38 refs., 5 figs., 2 tabs.
Brownian Dynamics Simulation of the Dynamics of Stretched DNA

DNA is a long flexible polymer and is involved in several fundamental cellular processes such as transcription, replication and chromosome packaging. These processes induce forces and torques in the DNA which deform it. These deformations in turn affect the structure and function of DNA. However, understanding of the dynamic response of DNA to the various forces that act on it is still far from complete. Several experiments have been carried out to study these responses most of which use a micron sized magnetic bead attached to the DNA molecule to both manipulate it and to observe its dynamics. One limitation of this approach is that the dynamics of the DNA molecule has mostly been characterized “indirectly” by observing the dynamics of the magnetic bead. It is also reasonable to expect that, because of the size of the bead relative to that of the DNA, the magnetic bead dynamics will obscure that of the DNA. We adapt existing coarse-grained Brownian dynamics models of DNA to develop a model capable of representing the dynamics of DNA without any of the artifacts inherent to the experiments. This model accounts for bending, torsion, extension, electrostatics, hydrodynamics and the random thermal forces acting on DNA in an electrolyte solution. We then carry out Brownian dynamics simulations with our model to benchmark with well established theoretical results of a stretched polymer in solution. Finally, we employ our model to predict the relaxation time scale for single molecule experiments which sets the framework for future studies in which we plan to further shed light on the dynamics of DNA over long length and time scales. © 2014 ASME
Protein–ligand interaction study of signal transducer smoothened protein with different drugs: molecular docking and QM/MM calculations

In this work, the interaction of signal transducer smoothened (SMO) protein, one of the main members of the Hedgehog (Hh) signaling pathway, with different ligands was studied. Seven hundred molecules, known as SMO ligands in literature, were selected for the docking screens. The site of the antitumor agent LY2940680, present in the X-ray crystal structure of the SMO protein, was selected as the binding site to study the interaction of the selected ligands with the protein. Docking screens only showed ten ligands that can be considered as favorable ligands based on their calculated free binding energies. The amino acid residues responsible for interacting with the ligands were identified. Quantum mechanics/molecular mechanics (QM/MM) calculations were also performed on the structure of the protein interacting with the favorable ligands to obtain more accurate results for their electronic interaction energies. The contribution of the van der Waals (vdW) and electrostatic interaction in the calculated electronic interaction energy of each ligand were calculated by QM/MM calculations. In addition, the effect of the polarization of the wave function of ligand in the active site of the protein on its electronic interaction with the protein was also studied.
Solvent effect in a “solvent free” reaction

Vapour digestion of a mixture of solid [Fe(η5-C5H4–C5H4N)2] and solid pimelic acid HOOC(CH2)5COOH in the presence of solvent vapours generates co-crystals of different stoichiometry depending on the protic or aprotic nature of the solvent. The nature of the products has been ascertained by a combined use of SSNMR and X-ray diffraction.
Conductometric Titration of Latex with Acidic Surface Groups

Abstract In this paper an alternative approach to the calculation of conductometric titration curves is presented. The presented approach does not use the concepts of immobile surface layer, plane of shear, or ζ-potential. Furthermore, it is not necessary to introduce specific chemical binding of counter ions (except protons) to acidic surface groups in order to calculate ionic distributions. The presented approach essentially does not contain any adjustable parameters. Using this approach, it is possible to produce all the features of conductometric titration curves as mentioned in literature. In addition, experimental titration curves are presented which can also be described using the new approach.
Electroencephalographic Study on Sensory Integration in Visually Induced Postural Sway

A periodically reversing optic flow animation, experienced while standing, induces an involuntary sway termed visually induced postural sway (VIPS). Interestingly, VIPS is suppressed during light finger touch to a stationary object. Here, we explored whether VIPS is mediated by parietal field activity in the dorsal visual stream as well as by activity in early visual areas, as has been suggested. We performed a mobile brain/body imaging study using high-density electroencephalographic recording from human participants (11 men and 3 women) standing during exposure to periodically reversing optic flow with and without light finger touch to a stable surface. We also performed recording their visuo-postural tracking movements as a typical visually guided movement to explore differences of cortical process of VIPS from the voluntary visuomotor process involving the dorsal stream. In the visuo-postural tracking condition, the participants moved their center of pressure in time with a slowly oscillating (expanding, shrinking) target rectangle. Source-resolved results showed that alpha band (8–13 Hz) activity in the medial and right occipital cortex during VIPS was modulated by the direction and velocity of optic flow and increased significantly during light finger touch. However, source-resolved potentials from the parietal association cortex showed no such modulation. During voluntary postural sway with feedback (but no visual flow) in which the dorsal stream is involved, sensorimotor areas produced more theta band (4–7 Hz) and less beta band (14–35 Hz) activity than during involuntary VIPS. These results suggest that VIPS involves cortical field dynamic changes in the early visual cortex rather than in the posterior parietal cortex of the visual dorsal stream.
Engineering Nanospaces: Iterative Synthesis of Melamine‐Based Dendrimers on Amine‐Functionalized SBA‐15 Leading to Complex Hybrids with Controllable Chemistry and Porosity

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Doping in solution as an order-inducing tool prior to film formation of regio-irregular polyalkylthiophenes

Favorable alignment of regio-irregular poly(3-alkylthiophene)s in a film can be attained, despite the fact that these polymers lack an intrinsic tendency to form well-ordered supramolecular aggregates. As reported here, alignment can be achieved simply by oxidizing the polymer in solution prior to film formation. A delicate balance between the degree of order and the level of oxidation in solution is observed. These results point to a way to improve charge transport efficiency, which is influenced by intra- and interchain order in the polymer.
Human Serum Albumin Binds Streptolysin O (SLO) Toxin Produced by Group A Streptococcus and Inhibits Its Cytotoxic and Hemolytic Effects

The pathogenicity of group A Streptococcus (GAS) is mediated by direct bacterial invasivity and toxin-associated damage. Among the extracellular products, the exotoxin streptolysin O (SLO) is produced by almost all GAS strains. SLO is a pore forming toxin (PFT) hemolitically active and extremely toxic in vivo. Recent evidence suggests that human serum albumin (HSA), the most abundant protein in plasma, is a player in the innate immunity “orchestra. ” We previously demonstrated that HSA acts as a physiological buffer, partially neutralizing Clostridioides difficile toxins that reach the bloodstream after being produced in the colon. Here, we report the in vitro and ex vivo capability of HSA to neutralize the cytotoxic and hemolytic effects of SLO. HSA binds SLO with high affinity at a non-conventional site located in domain II, which was previously reported to interact also with C. difficile toxins. HSA:SLO recognition protects HEp-2 and A549 cells from cytotoxic effects and cell membrane permeabilization induced by SLO. Moreover, HSA inhibits the SLO-dependent hemolytic effect in red blood cells isolated from healthy human donors. The recognition of SLO by HSA may have a significant protective role in human serum and sustains the emerging hypothesis that HSA is an important constituent of the innate immunity system.
Bringing Real-World Microbiology Experiences to Undergraduate Students in Resource-Limited Environments

Undergraduate microbiology curriculum should be amenable to periodic changes to incorporate new developments and ideas. The curriculum should be used not merely as a way to disseminate facts but also as a way to allow students to experience the process of science. In the context of undergraduate microbiology education in Osmania University (Hyderabad, India), existing curriculum does not explicitly allow students to engage in deeper understanding of concepts and understanding of the process of science, both in lecture and laboratory courses. The assessment methods that are currently used are limited in scope as they only test factual recall and superficial understanding of the subject and very minimally assess critical thinking skills. Another factor hampering innovation in the broader context of undergraduate education is the unavailability and inaccessibility to adequate resources. To address the issue of resource-limitations in implementing activities that expose undergraduate students to real-world microbiology experiences, a collaboration between a research institute and two teaching colleges was formed. This collaboration involved teacher and student workshops on exploring microbial diversity using 16S rRNA analysis with a view of blending novel research questions with technical skills in the undergraduate microbiology lab. This effort is an example of educators providing students with authentic experiences and, helping them gain critical knowledge and research skills in microbiology even under resource constraints, and students demonstrating motivation to participate in similar activities in the future. The collaborative effort described here can be a broadly sustainable model to improve overall undergraduate education in relatively resource-limited environments.
Highly Elastic and Conductive N‐Doped Monolithic Graphene Aerogels for Multifunctional Applications

The simple synthesis of ultralow‐density (≈2.32 mg cm−3) 3D reduced graphene oxide (rGO) aerogels that exhibit high electrical conductivity and excellent compressibility are described herein. Aerogels are synthesized using a combined hydrothermal and thermal annealing method in which hexamethylenetetramine is employed as a reducer, nitrogen source, and graphene dispersion stabilizer. The N‐binding configurations of rGO aerogels increase dramatically, as evidenced by the change in pyridinic‐N/quaternary‐N ratio. The conductivity of this graphene aerogel is ≈11.74 S m−1 at zero strain, whereas the conductivity at a compressive strain of ≈80% is ≈704.23 S m−1, which is the largest electrical conductivity reported so far in any 3D sponge‐like low‐density carbon material. In addition, the aerogel has excellent hydrophobicity (with a water contact angle of 137.4°) as well as selective absorption for organic solvents and oils. The compressive modulus (94.5 kPa; ρ ≈ 2.32 mg cm−3) of the rGO aerogel is higher than that of other carbon‐based aerogels. The physical and chemical properties (such as high conductivity, elasticity, high surface area, open pore structure, and chemical stability) of the aerogel suggest that it is a viable candidate for the use in energy storage, electrodes for fuel cells, photocatalysis, environmental protection, energy absorption, and sensing applications.
Facing Loneliness and Anxiety During the COVID-19 Isolation: The Role of Excessive Social Media Use in a Sample of Italian Adults

The outbreak of coronavirus disease 2019 (COVID-19) prompted people to face a distressing and unexpected situation. Uncertainty and social distancing changed people's behaviors, impacting on their feelings, daily habits, and social relationships, which are core elements in human well-being. In particular, restrictions due to the quarantine increased feelings of loneliness and anxiety. Within this context, the use of digital technologies has been recommended to relieve stress and anxiety and to decrease loneliness, even though the overall effects of social media consumption during pandemics still need to be carefully addressed. In this regard, social media use evidence risk and opportunities. In fact, according to a compensatory model of Internet-related activities, the online environment may be used to alleviate negative feelings caused by distressing life circumstances, despite potentially leading to negative outcomes. The present study examined whether individuals who were experiencing high levels of loneliness during the forced isolation for COVID-19 pandemic were more prone to feel anxious, and whether their sense of loneliness prompted excessive social media use. Moreover, the potentially mediating effect of excessive social media use in the relationship between perceived loneliness and anxiety was tested. A sample of 715 adults (71.5% women) aged between 18 and 72 years old took part in an online survey during the period of lockdown in Italy. The survey included self-report measures to assess perceived sense of loneliness, excessive use of social media, and anxiety. Participants reported that they spent more hours/day on social media during the pandemic than before the pandemic. We found evidence that perceived feelings of loneliness predicted both excessive social media use and anxiety, with excessive social media use also increasing anxiety levels. These findings suggest that isolation probably reinforced the individuals' sense of loneliness, strengthening the need to be part of virtual communities. However, the facilitated and prolonged access to social media during the COVID-19 pandemic risked to further increase anxiety, generating a vicious cycle that in some cases may require clinical attention.
Difference Between Day and Night Temperatures Affects Stem Elongation in Tomato (Solanum lycopersicum) Seedlings via Regulation of Gibberellin and Auxin Synthesis

Temperature is a critical environmental factor governing plant growth and development. The difference between day temperature (DT) and night temperature (NT), abbreviated as DIF, influences plant architecture. Subjecting plants to artificial DIF treatments is an effective strategy in ornamental horticulture. For example, negative DIF (when DT – NT < 0) generally inhibits stem elongation, resulting in dwarf plants. However, the mechanisms underlying stem growth regulation by DIF remains to be completely elucidated. In this study, we aimed to analyze the growth, transcriptome, and phytohormone profiles of tomato (Solanum lycopersicum) seedlings grown under different DIF treatments. Under positive DIF (when DT – NT > 0), in contrast to the control temperature (25°C/20°C, DT/NT), high temperature (30°C/25°C) increased stem length and thickness, as well as the number of xylem vessels. Conversely, compared with the positive high temperature DIF treatment (30°C/25°C), under negative DIF treatment (25°C/30°C) stem elongation was inhibited, but stem thickness and the number of xylem vessels were not affected. The negative DIF treatment decreased the expression of gibberellin (GA)-, auxin-, and cell wall-related genes in the epicotyl, as well as the concentrations of GAs and indole-3-acetic acid (IAA). The expression of these genes and concentrations of these hormones increased under high temperature compared to those under the control temperature positive DIF. Our results suggest that stem length in tomato seedlings is controlled by changes in GA and IAA biosynthesis in response to varying day and night temperatures.
Does Depth Matter? Reproduction Pattern Plasticity in Two Common Sponge Species Found in Both Mesophotic and Shallow Waters

Determining demosponge reproductive strategies is essential to understanding their ecology and life history, as well as for the management of benthic marine environments. This is especially important in mesophotic ecosystems, which have been suggested to serve as a refuge for shallow-water populations and for which knowledge is lacking. Here we compared the reproductive strategies of two common Mediterranean demosponges species: Chondrosia reniformis and Axinella polypoides, which can be found in both shallow and mesophotic habitats along the Israeli coast. Samples were collected over 2 years, via SCUBA diving from the shallow coast (2–32 m) and Remotely Operated Vehicle from the mesophotic sponge grounds (95–120 m). A. polypoides and C. renifornis differed in oocyte morphology and development, but both demonstrated reproductive plasticity with regard to temperature and depth: temperature appears to regulate their reproduction in the shallow water, as both species exhibited seasonality; whereas, in the mesophotic zone, where the temperature amplitude is much smaller, seasonality was not observed for either species. Furthermore, in the mesophotic zone, C. reniformis exhibited low fecundity and probably invests more in asexual reproduction by budding. Mesophotic A. polypoides, in contrast, exhibited enhanced and continuous asynchronous sexual reproduction year-round. Our findings suggest that reproduction plasticity may be a general rule for sponge species that inhabit different habitats; such plasticity could allow sponges to thrive in different environmental conditions. These findings further emphasize the importance of protecting the mesophotic sponge grounds, which can serve as a refuge in the face of the adverse impact of anthropogenic disturbances and rising seawater temperatures.