Miracle-dz/UniFAR-FTUs huggingface dataset:
Effective Viscosity of Lightly UVO-Treated Polystyrene Films on Silicon with Different Molecular Weights

Recently, we found that a brief, 1 s exposure to ultraviolet ozone (UVO) can cause the effective viscosity, ηeff, of polystyrene films supported by oxide-coated silicon (PS-SiOx) to increase by more than 100 times. In this experiment, we study the phenomenon with different PS molecular weights, Mw, from 2.4 to 451 kg/mol. We found that ηeff was increased for all Mw’s when the film thickness, h0, was decreased below an onset thickness comparable to the radius of gyration, Rg, of the polymer. For h0 greater than the onset thickness, the ηeff versus h0 dependence varies with Mw. Specifically, for Mw ≥ 60K g/mol ηeff was constant, equal to the bulk viscosity. For Mw < 60K g/mol, ηeff decreased with decreasing h0 in the same way as that of the pristine counterparts. X-ray photoelectron spectroscopy (XPS) shows that oxygenated groups are formed in the films after the UVO treatment. We propose that the oxygenated groups can interact with the OH groups on the SiOx surface to produce increases in ηeff. Correspondi.
Templating Porphyrin Anisotropy via Magnetically Aligned Carbon Nanotubes.

The preparation and characterisation of a novel three-dimensional organic material consisting of porphyrin arrays on carbon nanotubes embedded in an organogel is reported. Firstly, the porphyrin array was prepared through metal-ligand coordination of a ditopic ligand (1,2-bis(4-pyridyl)ethane) and two bis-Zn(II) porphyrins, linked through a pyrene core, and was studied through UV-Vis, NMR and diffusion spectroscopies. Secondly, the porphyrin supramolecular architecture was adsorbed on pristine carbon nanotubes, greatly improving the dispersibility of the latter in organic solvents. The hybrid material was characterised by means of UV-Vis spectroscopy, microscopic techniques and thermogravimetric analysis. Finally, by exploiting the anisotropic magnetic susceptibility of carbon nanotubes, the hybrid material was aligned under a magnetic field, the organisation of which could be maintained by in situ gelation. The resultant hybrid organogel exhibited notable optical anisotropy, suggesting an anisotropic arrangement of the porphyrin-CNTs architectures in the macroscopic material.
Impact of aggregation triggering ultrashort self-assembling peptide motifs on the solubility of proteins

Intracellular solubility and folding of proteins are influenced by numerous extrinsic and intrinsic factors. One of the intrinsic parameters is the presence of aggregating motif within the amino acid sequence of the protein which makes the protein intrinsically disorder. Here we have studied the effect of ultrashort self-assembling peptide (SSP) motif consisting of four amino acids Isoleucine-Valine-Phenylalanine-Lysine, having aggregation propensity on intracellular expression and folding of small ubiquitin-like modifier (SUMO) protein by c-terminally conjugating SSP motif. Conjugation of SSP motif directed SUMO accumulation into the inclusion bodies of E. coli. SSP conjugated inclusion bodies of SUMO have revealed highly ordered, fibrous rich structure, when observed under scanning electron microscopy. FTIR analysis of SSP conjugated SUMO has also confirmed that the composition of self-assembling fibrous material is mainly beta sheet rich. This observation has confirmed our hypothesis that SSP motifs, when exposed to favourable conditions can lead to the aggregation of soluble proteins. *Correspondence to: Hauser CAE, Ph.D, Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, Tel: +966 12 808 2524; E-mail: charlotte.hauser@kaust.edu. sa
Optimal coding of blended seismic sources for 2D full waveform inversion in time

Full Waveform Inversion (FWI) schemes are gradually becoming more common in the oil and gas industry, as a new tool for studying complex geological zones, based on their reliability for estimating velocity models. FWI is a non-linear inversion method that iteratively estimates subsurface characteristics such as seismic velocity, starting from an initial velocity model and the preconditioned data acquired. Blended sources have been used in marine seismic acquisitions to reduce acquisition costs, reducing the number of times that the vessel needs to cross the exploration delineation trajectory. When blended or simultaneous without previous de-blending or separation, stage data are used in the reconstruction of the velocity model with the FWI method, and the computational time is reduced. However, blended data implies overlapping single shot-gathers, producing interference that affects the result of seismic approaches, such as FWI or seismic image migration. In this document, an encoding strategy is developed, which reduces the overlap areas within the blended data to improve the final velocity model with the FWI method.
Synthesis of Benzoxazoles, Benzimidazoles, and Benzothiazoles Using a Brønsted Acidic Ionic Liquid Gel as an Efficient Heterogeneous Catalyst under a Solvent-Free Condition

Herein, we introduce a reusable Brønsted acidic ionic liquid gel (BAIL gel) obtained by treating 1-methyl-3-(4-sulfobutyl)-1H-imidazolium hydrogen sulfate with tetraethyl orthosilicate (TEOS). The grafting of the Brønsted acidic ionic liquid to the surface of TEOS has increased the catalytic activity of the material and also simplified catalyst recovery from the reaction mixture. This reaction has a wide substrate scope, and the BAIL gel represents a new catalyst for the synthesis of benzoxazoles, benzimidazoles, and benzothiazoles. The method shows attractive characteristics such as high yields, recyclable catalyst, and work-up simplicity. More importantly, no additional additives or volatile organic solvent and inert atmosphere are required for the reaction, and the BAIL gel has shown a great promise for industrial applications. To the best of our knowledge, the synthesis of benzoxazoles, benzimidazoles, and benzothiazoles using a recyclable heterogeneous ionic liquid gel was not previously reported in the literature.
A Brief History of Single-Particle Tracking of the Epidermal Growth Factor Receptor

Single-particle tracking (SPT) has been used and developed over the last 25 years as a method to investigate molecular dynamics, structure, interactions, and function in the cellular context. SPT is able to show how fast and how far individual molecules move, identify different dynamic populations, measure the duration and strength of intermolecular interactions, and map out structures on the nanoscale in cells. In combination with other techniques such as macromolecular crystallography and molecular dynamics simulation, it allows us to build models of complex structures, and develop and test hypotheses of how these complexes perform their biological roles in health as well as in disease states. Here, we use the example of the epidermal growth factor receptor (EGFR), which has been studied extensively by SPT, demonstrating how the method has been used to increase our understanding of the receptor’s organization and function, including its interaction with the plasma membrane, its activation, clustering, and oligomerization, and the role of other receptors and endocytosis. The examples shown demonstrate how SPT might be employed in the investigation of other biomolecules and systems.
Photodynamic Inactivation of Escherichia coli with Cationic Porphyrin Sensitizers

The activity of singlet-oxygen sensitizers for photodynamic inactivation (PDI) of microorganisms and photodynamic therapy of tumor cells has been evaluated using Escherichia coli , Saccharomyces cerevisiae , and human cancer cell lines. In this chapter, drug resistance of E. coli was examined based on the PDI activity of a variety of RPy-P-porphyrin sensitizers with different number of ionic valence and different hydrophobic characters. The PDI activities toward E. coli were evaluated using the minimum effective concentrations ([ P ]) of the porphyrin sensitizers. It was found that the [ P ] value for E. coli was larger than that for S. cerevisiae . E. coli has drug-resistance toward hydrophobic and mono-cationic porphyrins. However, E. coli has weak drug-resistance toward the porphyrins with both polycationic character and hydrophobicity. Since the outer membrane mainly consists of lipopolysaccharides and phospholipids that are negatively charged, cationic porphyrins are able to adsorb to the outer leaflet. Then the cationic porphyrins with hydrophobic character can interact with not only the outer leaflet but also inner leaflet of the outer membrane and the plasma membrane. Thus, porphyrins may be incorporated inside E. coli cells via the self-promoted uptake pathway. Moreover, polycationic porphyrins can interact with DNA and proteins by strong binding affinities.
Méthodes d’estimation de la reproductibilité

Dans de nombreuses situations en medecine, il est necessaire de disposer d’une mesure fiable des parametres etudies, que ce soit un parametre biologique, un signe clinique, ou un score a une echelle de qualite de vie. La reproductibilite est l’aptitude d’un instrument de mesure a fournir des resultats identiques dans des conditions de recueil identiques ; elle s’apprecie en mesurant la concordance de deux mesures repetees. Plusieurs methodes d’evaluation de la concordance peuvent etre utilisees, le choix de la methode dependant de la nature de la mesure effectuee, quantitative ou qualitative. Les methodes d’evaluation les plus courantes sont : dans le cas d’une variable qualitative, le coefficient kappa ; dans le cas d’une variable quantitative, le coefficient de correlation intra-classe et la methode graphique de Bland et Altman. Les resultats de ces indices de concordance sont a interpreter en tenant compte des caracteristiques de la population dans laquelle ils ont ete obtenus et du contexte et des objectifs d’utilisation de l’outil de mesure concernee.
Bioethanol Production from Dilute-acid Pre-treated Wheat Straw Liquor Hydrolysate by Genetically Engineered Saccharomyces cerevisiae

Sustainable recycling of lignocellulosic biomass includes utilization of all carbohydrates present in its hydrolysates. Since wheat straw is a xylose-rich raw material, utilization of xylose from obtained liquid part (liquor) of hydrolysates improves overall bioprocess efficiency. In this work, dilute acid pre-treatment of wheat straw was performed in high-pressure reactor at different temperatures (160 °C – 200 °C), residence times (1 min – 10 min), and acids (H2SO4 and H3PO4) concentrations. During dilute acid pre- treatment, hemicellulose is degraded to pentose sugars that cannot be used by industrial ethanol- producing yeasts. Therefore, genetically engineered Saccharomyces cerevisiae strain that can utilize xylose was used. Fermentations were performed on different xylose-rich liquor wheat straw hydrolysates in shake-flasks and in horizontal rotating tubular bioreactor. The efficiency of fermentations carried out in shake flasks using xylose- rich liquor wheat straw hydrolysates were in the range of 19.61 – 74.51 %. However, the maximum bioprocess efficiency (88.24 %) was observed during fermentation in the HRTB on the liquor wheat straw hydrolysate obtained by pre- treatment with 2 % w/w phosphoric acid.
Characterization of Chromatin Interaction in Mammalian Cells

Higher-order chromatin organization in cell nucleus is mysterious. Microscopy and highthroughput sequencing technologies have been applied to reveal the connections between genome structure and gene transcription, which is the main topic of my thesis. Higher-order chromatin organization differs across cell types and species, giving an insight into disease genesis and tumorigenesis. Despite an enormous progress has been made recently in epigenomic study, lots of things remain unknown. My dissertation reviews the current understanding of epigenomics, characterizes chromatin interaction in mammalian cells using different technologies, investigates chromatin reorganization in breast cancer cells, analyzes integrated genomic and epigenomic data in breast cancer metastasis and discusses results and future directions. Dissertation Jacqueline Jufen Zhu i Characterization of Chromatin Interaction in Mammalian Cells Jacqueline Jufen Zhu B.E. , Nanjing Agricultural University, 2010 M.S., Chinese Academy of Sciences, 2013 A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy at the University of Connecticut
Chiral Liquid‐Crystalline Ionic Liquid Systems Useful for Electrochemical Polymerization that Affords Helical Conjugated Polymers

Ionic liquids bearing both liquid crystallinity and chirality are potentially applicable for chiral electrochemical syntheses and polymerizations. In this study, two types of chiral nematic liquid‐crystalline ionic liquids (N*‐LCILs) are developed to achieve asymmetric electrochemical polymerization without a supporting electrolyte and even a chiral dopant. N*‐LCILs are prepared i) by adding an axially chiral binaphthyl derivative as an external chiral dopant to imidazolium cation–based LCILs or ii) by incorporating a chiral binaphthyl phosphate as a counter anion in LCILs. Helical poly(3,4‐ethylenedioxythiophene) (H‐PEDOT) films are successfully synthesized through electrochemical polymerization of a dimer‐ or trimer‐type 3,4‐ethylenedioxythiophene (EDOT) monomer in an N*‐LCIL, where N*‐LCIL plays the role of both an asymmetric solvent and a supporting electrolyte. H‐PEDOT films have helically π‐stacked structures of conjugated chains and spiral morphologies consisting of one‐handed screwed fibril bundles. The plausible mechanism of the asymmetric electrochemical polymerization of EDOT in N*‐LCIL is proposed to elucidate the correlation of helical sense between the helically π‐stacked chains, screwed fibril bundles, and N*‐LCIL. The two present types of N*‐LCILs are the first to enable supporting electrolyte–free asymmetric electrochemical polymerization, and they have potential applications in various types of chiral electrochemical syntheses, expanding the potential utility of ionic liquids.
Recent developments in purification techniques and industrial applications for whey valorization: A review

Abstract Whey is considered as a by-product of dairy industries and commonly regarded as waste. Despite being a good source of nutrients (lactose, minerals, and bioactive peptides), it is commonly discarded as effluent. Innovative techniques such as membrane filtration, chromatography (affinity and ion exchange), chemical treatments, and/or combination of these are used for the extraction of these constituents. The presence of these components in whey makes it functional in food and pharmaceutical industries. This article is aimed at supplementing recent information to available literature about different novel techniques used for the separation of whey constituents and their industrial application. In future, information reviewed will be helpful for the processors to select the best technique for the separation of individual constituents for the attainment of maximum yield and purity.
Heat pump drying of grape pomace: Performance and product quality analysis

Abstract Grape is one of the most popular fruits and various types of grape have been cultivated by more than 100 countries around the World. The wine and juice industry produces large quantities of by-product, called grape pomace (GP) as an industrial waste and it consists of skins, seeds, and stems. Various processes such as separation, pressing, drying, and milling are applied to benefit from its health effects. In this study, the seeded black GP Kalecik karası (Vitis vinifera) was dried in an assisted closed cycle heat pump dryer (HPD) designed for high-moisture products to investigate the drying behaviors of GP. The effects of drying air temperature on bioactive properties and the drying characteristics of GP, and performance of system have discussed. Experiments were carried out at two different temperatures (45 and 50°C) and air velocity of 1.0 m/s. It was seen that increasing temperature decreased the drying time, coefficient of performance of whole system (COPws), and specific energy consumption (SEC). The average values of COPws for temperatures 45°C and 50°C were calculated as 3.28 and 3.10, respectively. The drying efficiencies (DE) at drying air temperature of 45°C and 50°C ranged from 2 to 12% and from 2 to 15%, respectively. Additionally, result of analysis has indicated that using a HPD at lower temperatures increases performance of system despite of higher energy input. Bioactive properties of dried samples at drying air temperature of 45°C are better than 50°C. The results show that drying the GP at low temperature is more suitable for product quality. For this reason, heat pump may be preferred. It shows that this drying system with higher capacities in the future can be recommended as an alternative technique in terms of energy usage, drying time, and performance of system.
The role of post translational modification in regulating Human Papillomavirus (HPV) E6 functions

The Human Papillomavirus (HPV) E6 oncoprotein from cancer-causing HPV types is highly multi-functional, capable of targeting many different cellular partners and pathways. Integral to this multi-functionality is its regulation by phosphorylation. Here I describe studies to firstly investigate when E6 is phosphorylated within the PDZ binding motif (PBM), and demonstrate a complex pattern of phosphorylation events which take place upon the exposure of the cells to different forms of stress. Most important of which is phosphorylation by kinases belonging to the core of the DNA Damage Response (DDR) machinery. Functionally this redirects E6 from interaction with PDZ substrates to association with 14-3-3 proteins. This in turn appears to contribute towards the ability of E6 to inhibit p53 transcriptional activity on a subset of p53 responsive promoters, thereby linking DDR signaling to the function of the E6 PBM. Functionally I have also been able to precisely dissect the sequence constraints within the E6 PBM governing phosphorylation by different kinases, PDZ recognition and interaction with different 14-3-3 isoforms. I also show that phospho-regulation of the E6AP ubiquitin ligase can also play a role in these pathways, and can be utilized and redirected by different HPV E6 oncoproteins with varying degrees of efficiency. Depending upon the specific HPV E6 protein, I also show the first evidence for phosphorylation at a site outside of the PBM and provide insights into the potential functional consequences thereof. Taken together, these studies shed new light on the role of E6 phosphorylation in a range of different biological activities, and begin to explain the multi-functional nature of the high risk HPV E6 proteins.
The simultaneous effects of image force and diffusion on ultrafine particle deposition onto vegetation: A wind tunnel study

Abstract Atmospheric ultrafine particles (UFP) and their associated sources and sinks continue to attract significant research attention in climate and air pollution science. Vegetation is an important sink for UFP given its large area coverage. What remains a subject of inquiry are the aerodynamic and electromagnetic processes governing the aforementioned vegetation sink. Single fiber theory can explain deposition of zero charged UFP onto vegetation by treating vegetation as filter media. However, the ability of single fiber theory to predict deposition of charged UFP onto vegetation remains to be explored and frames the scope here. Wind tunnel experiments were used to investigate UFP dry deposition onto Juniper branches (Juniperus chinesis) under three different wind speeds (0.3, 0.6, and 0.9 m/s). Results indicate that the single fiber theory can describe the deposition of singly charged particles onto vegetation if both the image force and Brownian diffusion are simultaneously considered. The image force can be expressed by when the image force dimensionless number (KIM) is smaller than 10−8. It is shown that the single fiber filtration model and the wind tunnel measurements mostly agree to within 20%. The main finding here is that the image force at smaller KIM (10−10 ∼ 10−8) increases deposition of charged UFP onto vegetation. Because filtration theory can be readily accommodated in fluid transport formulations as a boundary condition, the findings regarding charge enhance UFP deposition schemes that can be used in air quality and climate models. Copyright © 2019 American Association for Aerosol Research
Reconstitution of basic mitotic spindles in cell-like confinement

Bipolar organization of the mitotic spindle is the result of forces generated by dynamic microtubules and associated proteins in interaction with chromosomes and the cell boundary1–4. Biophysical experiments on isolated spindle components have provided important insights into the force-generating properties of different components5–8, but a quantitative understanding of the force balance that results from their concerted action is lacking. Here we present an experimental platform based on water-in-oil emulsion droplets that allows for the bottom-up reconstitution of basic spindles. We find a typical metaphase organization, where two microtubule asters position symmetrically at moderate distance from the mid-zone, is readily obtained even in the absence of chromosomes. Consistent with simulations, we observe an intrinsic repulsive force between two asters that can be counterbalanced alternatively by cortical pulling forces, anti-parallel microtubule crosslinking, or adjustment of microtubule dynamics, emphasizing the robustness of the system. Adding motor proteins that slide anti-parallel microtubules apart drives the asters to maximum separation, as observed in cells during anaphase9,10. Our platform offers a valuable complementary approach to in vivo experiments where essential mitotic components are typically removed, instead of added, one by one.
Effect of surfactants on swelling capacity and kinetics of alginate-chitosan/CNTs hydrogel

Nanocomposite hydrogels of alginate-chitosan matrix with nanofillers, functionalized multi-walled carbon nanotubes (COOH-MWCNTs) were first time synthesized in cationic, anionic, mixture of cationic and anionic surfactants and in the absence of surfactants by employing solution casting method. Whole process of synthesis was carried out under greener source of heating i.e., ultrasonic waves. Synthesized films were evaluated by Fourier transform infrared spectroscopy and scanning electron microscopy which reveal uniform dispersion of nanofillers in matrix. Synthesized hydrogels were also newly explored for swelling capacity. Swelling ratio of hydrogels was measured in distilled water, saline solutions and in solutions of different pH. Swelling pattern of prepared films indicates that these materials are very stable and can show best performance in different pH and kinds of solutions. Effect of concentration ratio of nanofillers to matrix and nature of surfactants on swelling ability was also appraised and indicated that trace amount of nanofillers gives fascinating results. Process of swelling and deswelling of synthesized films was taken place by super case-II transport mechanism, which is effected by amount of nanofillers and nature of surfactant.