Miracle-dz/UniFAR-FTUs huggingface dataset:
1,2,4,5-Tetrachloro-3,6-diiodobenzene benzene monosolvate

The title compound, C6Cl4I2·C6H6, crystallizes from benzene solution as cube-shaped crystals in the triclinic space group P\overline{1} with Z = 1. The asymmetric unit of the crystal structure contains one half of each molecule. In the crystal, the benzene ring is almost orthogonal to the perhalobenzene ring and the molecules are linked by C—I. π interactions, with a close contact between the iodine atom and the benzene ring of 3.412 (1) Å.
Does conjugation strategy matter? Cetuximab-conjugated gold nanocages for targeting triple-negative breast cancer cells

The efficient targeting of cancer cells depends on the success of obtaining the active targeting of overexpressed receptors. A very accurate design of nanoconjugates should be done via the selection of the conjugation strategy to achieve effective targeted nanoconjugates. Here, we present a detailed study of cetuximab-conjugated nonspherical gold nanocages for the active targeting of triple-negative breast cancer cells, including MDA-MB-231 and MDA-MB-468. A few different general strategies were selected for monoclonal antibody conjugation to the nanoparticle surface. By varying the bioconjugation conditions, including antibody orientation or the presence of a polymeric spacer or recombinant protein biolinker, we demonstrate the importance of a rational design of nanoconjugates. A quantitative study of gold content via ICP-AES allowed us to compare the effectiveness of cellular uptake as a function of the conjugation strategy and confirmed the active nature of nanoparticle internalization in cancer cells via epidermal growth factor receptor recognition, corroborating the importance of the rational design of nanomaterials for nanomedicine.
PHENOLIC COMPOUNDS IN LAUREL WOOD: A NEW SOURCE OF PROANTHOCYANIDINS

Laurel tree (Laurus nobilis L.) wood is a byproduct of the pruning of this tree widely cultivated for its aromatic leaves. The phenolic composition of laurel wood has not been reported yet. The aim of this work was to study the phenolic profile of an ethyl acetate extract of laurel wood in order to know its potential as a source of antioxidants and valuable compounds. Three flavan-3-ols, 4 dimeric B-type proanthocyanidins, and 2 trimeric A-type procyanidins were isolated by preparative column chromatography and semi-preparative HPLC, using a fast online post-column radical scavenging detection technique as guidance. All isolated compounds were fully characterized by spectroscopic (NMR, IR, UV) and spectrometric (MS) techniques. In addition, 17 minor proanthocyanidins were tentatively identified by liquid chromatography coupled to mass spectrometry (HPLC–ESI–MS). The extract was dominated by the presence of cinnamtannin B-1, a bioactive trimeric A-type procyanidin reported as a strong antioxidant of commercial value. According to the chemical composition found, it can be concluded that laurel wood is a renewable source of potential bioactive phenolic compounds.
Regulation of Neuronal Network Dynamics through Ionic and Synaptic Homeostasis

Author(s): Gonzalez, Oscar Christian | Advisor(s): Bazhenov, Maxim | Abstract: The regulation of transmembrane ionic and synaptic currents is crucial for maintaining physiological neural activity and allow brain networks to be resilient to external perturbations. To this effect, the brain implements many homeostatic mechanisms by which it can control neuronal excitability and communication by maintaining ionic concentration gradients and synaptic strengths within a physiological range. Indeed, there exist many membrane-bound transporter proteins which function to move ions across the plasma membrane to re-establish resting ionic gradients following changes in neuronal spiking. Similarly, the nervous system has developed homeostatic mechanisms by which it can regulate the strength of synaptic connections by augmenting the number of excitatory post-synaptic receptors present in an activity-dependent manner. It is traditionally thought that a breakdown of these mechanisms may underlie various neurological and psychiatric disorders. Though much has been learned about ionic and synaptic regulation of single neuron activity, how these homeostatic mechanisms give rise to or influence physiological and pathological brain states remains to be fully understood. Here we explore the roles of ionic and synaptic homeostasis in the regulation of network dynamics. We begin by first demonstrating that in the pathological brain (i.e. one riddled with K-channelopathies or suffering traumatic brain injury) these network stabilizing mechanisms can overcompensate for the chronic network perturbations resulting in hyperexcitability and lowered thresholds for seizure generation. We then demonstrate that the regulation of ionic concentration gradients in the healthy brain can give rise to infra-slow network fluctuations, which may underlie various brain-state transitions and cognitive states. Together these studies highlight the importance of proper ionic and synaptic regulation for the maintenance of physiological activity and transitions to pathological states and provides new insight into the development of interventions that can be used to treat epileptic seizures.
Process-yield-structure-bioconversion of Organosolv Lignin from Wheat straw

Lignocellulosic-based bio-refineries are essential for secure energy in future. Lignin degradation is vital for carbon recycling and the production of renewable chemicals. In the first part of this study, biodegradation of organosolv lignin by a white-rot fungus, Bjerkandera adusta, was established. The FTIR spectra of lignin, before and after treatment with fungus, displayed modification by changing the structure of lignin. Some of the functional groups have disappeared, and some novel bands appeared in the spectra. The SDS-PAGE chromatographs also displayed that the fungus protein has a molecular weight of 44 kDa. This molecular weight increased to 46 kDa after the treatment of lignin by the fungus. The heavier molecular weight occurred due to the bonding of fungus protein with lignin. The results from surface morphology also showed the attachments of lignin molecules to fungus mycelia. As a result, the extracted lignin after treatment with B. adusta showed significant changes in its physical and chemical structure, which makes it a novel candidate for yielding value-added products and refinery of lignin waste in pulp and paper industries. In the second part of this study, the ability of B. adusta to produce the extracellular and intracellular enzymes and transform the isolated lignin into small molecules was investigated. The results from the spot tests confirmed that the fungus had the ability to produce laccase in the presence or absence of lignin, but for manganese peroxidase secretion, the presence of lignin is essential. Based on the results from size exclusion chromatography, MALDI-TOF and SDSPAGE, for lignin biotransformation, the attachments between fungal protein (particularly laccase) and lignin was essential. Ultimately, B. adusta, by producing lignin peroxidases,
Effect of Synthesis Condition on the Structural Features of Ni-Ce Bimetallic Catalysts Supported on Functionalized Multi-Walled Carbon Nanotubes

In this paper, screening study in regards to preparation of functionalized multi-walled carbon nanotubes (FMWNT)-supported bi-metallic catalyst is discussed. Functional groups such as hydroxyl and carboxylic acid are introduced on multi-walled carbon nanotubes (MWCNT) surface using acid treatment method with the aid of probe-type ultrasonication. It is done by varying the concentration of nitric acid (HNO3) and sulphuric acid (H2SO4), acid volume ratio and treatment duration. Catalysts with different ratios of cerium and nickel nanoparticles which are either loaded inside or outside of MWCNT were prepared via ultrasonic-assisted co-precipitation method (NiCe/CNT). This is done to study the effect of cerium loadings. The characterization of the FMWNT and catalysts are carried out using transmission electron micrographs (TEM), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), Brunauer-Emmett-Teller (BET), X-ray diffraction (XRD), and Raman spectroscopy. The results showed that the treatment in concentrated HNO3/H2SO4 with volume ratio of 3:1 for 8 h was the most suitable condition to generate large amount of surface oxygen group with minimal defects. The observations for each used condition were discussed thoroughly. Decoration of MWCNT with different metal loadings resulted in different distribution and dispersion of metal on nanotubes surface.
Fundamental study of heterogeneous KCl sulfation under oxy‐fuel combustion conditions

Under oxy‐fuel combustion condition, SO2 in the flue gas would be accumulated by recirculation, which is conducive to the heterogeneous sulfation reaction of alkali metals. In the present study, experiments were conducted in a fixed bed to investigate the effects of operating parameters and mineral additives (SiO2, CaO, and Fe2O3) on the heterogeneous sulfation of potassium chloride under oxy‐fuel combustion atmosphere. According to the results here, the heterogeneous sulfation reaction was a kinetically controlled process, with the activation energy of 93.6 kJ/mol. The reaction orders with respect to SO2, O2, and H2O were determined as 1, 0.6 and 0 (H2O involved in the reaction). While the reaction would be promoted obviously in the absence of H2O. The rate law of heterogeneous sulfation of potassium chloride was derived based on the experimental data. Compared with air combustion, the heterogeneous sulfation rate was lower under oxy‐fuel combustion. All the mineral additives employed would affect the sulfation reaction. The sulfation reaction can be catalyzed by Fe2O3. While CaO would suppress the reaction by competing for SO2 with KCl. The reaction between CaO and SO2 could also be catalyzed by Fe2O3. Besides, SO2 was more reactive towards CaO than KCl.
Coordination in Compounds

Compounds are generally divided in those that involve a dependency (subordinate and attributive) relation of one constituent upon the other and those where there is coordination, for which there is much controversy on delimiting the exact borders. This article offers an overview of compounds belonging to the second type, for which the term ‘coordinative’ is adopted, as more general and neutral, drawn from a wide range of terms that have been proposed in the literature. It attempts to provide a definition on the basis of structural and semantic criteria, describes the major features of coordinative compounds and discusses crucial issues that play a significant role to their formation and meaning, such as those of headedness, the order of constituents, and compositionality. Showing that languages vary with respect to the frequency and types of coordinative compounds, being unclear in which way these constructions are distributed and used cross-linguistically, it tries to give a classification with extensive exemplification from genetically and typologically diverse languages.
Chloroquine sensitizes MDA-MB-231 cells to osimertinib through autophagy–apoptosis crosstalk pathway

Background: Triple-negative breast cancer (TNBC) is a breast cancer that tests negative for estrogen receptor (ER), progesterone receptors, and human epidermal growth factor receptors 2 (HER2). It is aggressive and invasive in nature and lacks targeted therapy. Purpose: The EGFR is frequently overexpressed in TNBC, and the EGFR-overexpressing TNBC presumably escapes EGFR inhibitor therapy by upregulating autophagy and inhibiting apoptosis. Methods: To parse the autophagy–apoptosis crosstalk pathway as a potential targeted therapy in TNBC, the activity of an EGFR inhibitor, osimertinib, alone and in combination with an autophagy inhibitor, chloroquine, was examined in EGFR-overexpressing TNBC cell line, MDA-MB-231. The nature of interaction between both drugs at various concentrations was determined by calculating combination indexes (CI) using CompuSyn software. Temporal changes in the expression of the autophagy marker, LC3B-II, and several apoptosis signaling molecules were measured using Western blot and luminex assay with MAGPIX® after exposure to drugs. A synergistic interaction (CI <1) was identified with combinations of 4–6.5 μM osimertinib with 30–75 μM chloroquine. Results: A combination of osimertinib (6 μM) with chloroquine (30 μM) resulted in a 6-fold increase of LC3B-II relative to control compared to 2.5-fold increase for either drug alone. The caspase-3 expression increased 2-fold compared to a 0.5-fold decrease with chloroquine and 1.5-fold increase with osimertinib. Conclusion: Our results indicate that inhibition of the autophagic flux via chloroquine improves the effectiveness of osimertinib in TNBC cancer cells, warranting further investigations of this combination in vivo.
Determination of heavy metals in olive fruits as an indicator of environmental pollution

ABSTRACT Characterization of olive fruits according to their heavy metal composition was carried out with a chemometric approach. The concentrations of Pb, Cd, Cr, Mn, Fe, Ni and Co in the olive samples were determined by high-resolution continuum source atomic absorption spectrometer (HR-CS AAS). Heavy metal contamination in twenty-three olive samples collected from different regions (industrialized and non-industrialized) of Hatay province in Turkey was evaluated. Analytical performance and reliability of the method were checked by validation parameters. The results demonstrated that the mean content of heavy metals in the olive samples were ranged between 0.046 and 17.229 mg kg−1. The analytical data was examined by principal component analysis (PCA) and cluster analysis (CA) for the classification studies. The olive samples were classified into three groups reflecting the groups of unpolluted, industrial polluted and non-industrial polluted stations. This model can be a useful tool for the olive industry to emphasize product quality and naturalness.
Effect of Biological and Liquid Hot Water Pretreatments on Ethanol Yield from Mengkuang (Pandanus artocarpus Griff)

1) This study aimed to increase the sugar and ethanol yield from the mengkuang plant biomass through biological and liquid hot water (LHW) pretreatment and their combination. The results showed that biological pretreatments with 5% inoculum of the fungus Trametes versicolor resulted in the highest alpha cellulose content incubated for 30 days, and 10% inoculum resulted in the lowest lignin content. LHW pretreatment decreased the hemicellulose content of pulps from 10.17% to 9.99%. T. versicolor altered the structure of the mengkuang pulp by degrading the lignin and lignocellulose matrix. The resulting delignification and cellulose degradation facilitate the hydrolysis of cellulose into sugars. The alpha cellulose content after biological-LHW pretreatment was higher (78.99%) compared to LHW-biological pretreatment (76.85%). Scanning electron microscopy analysis showed that biological–LHW combinated treatment degrades the cell wall structures. The ethanol yield for biological–LHW pretreated sample was observed 43.86% (13.11 g/L ethanol by weight of the substrate, which is much higher than that of LHW–biological pretreatment (34.02%; 9.097 g/L). The highest reducing sugar content about 45.10% was observed with a resulting ethanol content of 15.5 g/L at LHW pretreatment temperature of 180°C for 30 min.
Content of Photosynthetic Pigments and Leaf Gas Exchanges of Young Coffee Plants under Light Restriction and Treated with Paclobutrazol

The use of shading and paclobutrazol in coffee plants can be an important cultivation strategy to mitigate the negative effects of high solar radiation and atmospheric temperature. Therefore, the levels of photosynthetic pigments and foliar gas exchanges of young coffee plants submitted to doses of paclobutrazol were evaluated, in environments with artificial light restriction. Five experiments were performed: one in full sunlight and four in artificially shaded environments with black polyethylene meshes at 20%, 40%, 60% and 80% levels of light restriction. In each of these environments, an experiment was carried out, consisting of five treatments, defined by the application of paclobutrazol via substrate, at doses of 0, 10, 20, 30 and 40 mg of active ingredient per plant. Joint analysis of experiments and analysis of variance of the regression were made, for the study of levels of shading and doses of paclobutrazol. The light restriction optimized the photosynthetic apparatus of the plants, mainly at levels close to 60%, and considerably favored leaf gas exchanges of arabica coffee. The application of paclobutrazol in the studied dosages resulted in little or no effect on photosynthetic pigment contents and did not influence leaf gas exchanges of coffee plants.
POSSIBLE PROTECTIVE EFFECT OF ALPHA LIPOIC ACID AGAINST RICIN INDUCED HEPATOTOXICITY IN ADULT MALE ALBINO RATS

Introduction: Ricin is one of the most potent and deadly plant toxins known. It induces oxidative stress and was exploited as a poison for bioterrorism due to its characters. Developing an effective antidote for ricin toxicity becomes a reliable way against its potential biothreat. Alpha lipoic acid (ALA) being an ideal antioxidant, was chosen as protection against ricin toxicity. Aim of the work: The current study was carried out to confirm the hepatotoxic effect of ricin using the electron microscope (EM) and to assess the potential protective effect of ALA against ricin hepatotoxicity and lethality. Material and methods: The current study was conducted on 60 adult male albino rats. Rats were divided into four groups. The first group (10 rats) was used as control group. Group II (10 rats) was injected with ALA (100mg/kg intraperitoneal). Group III (20 rats) was injected once with ricin (25ug/kg subcutaneous). Group IV was injected with ALA (100 mg/kg) 15 minute prior to and immediately after ricin injection. Survival time was recorded and liver samples were taken for examination under EM. Results: Injection of ALA together with ricin significantly prolonged the survival time of the rats in group IV more than those in group III. Electron microscopic examination of liver specimens obtained from group III revealed hepatocytes with either euchromatic nuclei, shrunken hyperchromatic nuclei or nuclei with marginated chromatin. Hugely dilated degranulated rough endoplasmic reticulum (RER), many lipid droplets and electron dense mitochondria were detected. Treatment of animals with ALA resulted in less ultra structure damage. The hepatocytes showed either euchromatic nuclei or nuclei with marginated chromatin. Their cytoplasm exhibited slightly dilated RER, electron dense mitochondria and some vacuoles. Conclusion: It was concluded that ricin is a hepatotoxic substance causing ultra structure damage. Furthermore, ALA proved to be beneficial in prolonging the survival time and decreasing the toxic effect of ricin on the liver. Recommendations: Further studies are recommended to detect the underlying mechanism of ricin hepatotoxicity and to find more protective substances against ricin toxicity
Physicochemical properties and bioactive compounds of fermented pomegranate juice as affected by high-pressure processing and thermal treatment

ABSTRACT High-pressure processing (HPP) is a novel non-thermal processing technology, ensuring the safety of food products, as well as preserving their nutritional and functional characteristics, and avoiding the harmful effects of traditional thermal technologies. This study examined the inactivation of microorganisms and the HPP kinetic model in fermented pomegranate juice (FPJ) at different pressures (400 MPa, 500 MPa, and 600 MPa), and different treatment times (3 min, 5 min, 7 min, and 10 min). Moreover, HPP and thermal processing (TP) (65 °C/20 min) treatment responsible for a similar microbial inactivation activity, were compared by examining their impact on bioactive compounds, volatile compounds, and various quality attributes to provide a theoretical basis for FPJ processing. The inactivation curves of the microorganisms as a result of HPP were fitted using the Weibull model. Furthermore, HPP at or over 600 MPa/3 min inactivated the microorganisms and sufficiently retained the microbial populations investigated in this study below the detection limit. Following HPP and TP treatment, the total color difference (ΔE) values, total soluble solids (TSS), pH and titratable acidity (TA) had not significantly (p>0.05) changed. For total flavonoids, total phenols, anthocyanins, and antioxidant activity, the maximal retention of 91.18%, 97.52%, 95.69%, and 95.89% was achieved at 600 MPa/3 min, which was 4.62%, 24.61%, 26.83%, and 7.08% higher than in the TP-treated sample. The main volatile compounds in FPJ were esters and alcohols, and the FPJ treated at 600 MPa/3 min exhibited the highest alcohol content, while the esters were 2.27% higher than in the control. Considering the pasteurization effect and quality maintenance abilities of HPP and TP treatment, 600 MPa/3 min could be considered as an optimal condition in facilitating FPJ processing.
Catabolism of Extracellular Protein by Pancreatic Cancer Cells

All cells require amino acids to support protein synthesis and cell growth. Until recently, mammalian cells were thought to depend on monomeric amino acids in the environment. I showed that pancreatic tumor cells can use extracellular protein as a source of amino acids. These cells take up intact protein via macropinocytosis and catabolize it in lysosomes. This process – “protein eating” – enables cultured pancreatic cancer cells to grow in amino acid-deficient environments. In this thesis, I present my work on protein eating. To show that protein eating is capable of fueling growth, I cultured murine pancreatic cancer cells in medium lacking leucine (an essential amino acid) and supplemented with a physiological concentration of serum albumin. Many cells cells died in this medium, but some survived and grew to confluence. I passaged these survivors for months, and they gradually adapted to growth fueled by protein eating. This proved that protein eating is a viable form of amino acid uptake. I developed isotope tracer-based methods to quantitatively measure protein eating. Cells are grown in medium with stable isotope-labeled amino acids and unlabeled serum protein. Mass spectrometry enables distinction of amino acids taken up as monomers (labeled) from amino acids taken up as intact protein and catabolized (unlabeled). I conducted genome-wide screens to systematically identify genes essential for growth fueled by protein eating. The most essential gene was GCN2, which suppresses translation initiation in cells starved for amino acids. I discovered that loss of GCN2 impairs catabolism in amino acid-deprived cells. I propose that GCN2 supports catabolism by directing amino acids emerging from lysosomes into newly synthesized proteins that increase the catabolic capacity of the cell – for example, the lysosomal hydrolase cathepsin L.