Miracle-dz/UniFAR-FTUs huggingface dataset:
A Combined DNA/RNA-based Next-Generation Sequencing Platform to Improve the Classification of Pancreatic Cysts and Early Detection of Pancreatic Cancer Arising From Pancreatic Cysts

Objective: We report the development and validation of a combined DNA/RNA next-generation sequencing (NGS) platform to improve the evaluation of pancreatic cysts. Background and Aims: Despite a multidisciplinary approach, pancreatic cyst classification, such as a cystic precursor neoplasm, and the detection of high-grade dysplasia and early adenocarcinoma (advanced neoplasia) can be challenging. NGS of preoperative pancreatic cyst fluid improves the clinical evaluation of pancreatic cysts, but the recent identification of novel genomic alterations necessitates the creation of a comprehensive panel and the development of a genomic classifier to integrate the complex molecular results. Methods: An updated and unique 74-gene DNA/RNA-targeted NGS panel (PancreaSeq Genomic Classifier) was created to evaluate 5 classes of genomic alterations to include gene mutations (e.g., KRAS, GNAS, etc.), gene fusions and gene expression. Further, CEA mRNA (CEACAM5) was integrated into the assay using RT-qPCR. Separate multi-institutional cohorts for training (n=108) and validation (n=77) were tested, and diagnostic performance was compared to clinical, imaging, cytopathologic, and guideline data. Results: Upon creation of a genomic classifier system, PancreaSeq GC yielded a 95% sensitivity and 100% specificity for a cystic precursor neoplasm, and the sensitivity and specificity for advanced neoplasia were 82% and 100%, respectively. Associated symptoms, cyst size, duct dilatation, a mural nodule, increasing cyst size, and malignant cytopathology had lower sensitivities (41–59%) and lower specificities (56–96%) for advanced neoplasia. This test also increased the sensitivity of current pancreatic cyst guidelines (IAP/Fukuoka and AGA) by >10% and maintained their inherent specificity. Conclusions: PancreaSeq GC was not only accurate in predicting pancreatic cyst type and advanced neoplasia but also improved the sensitivity of current pancreatic cyst guidelines.
Growth response of cabbage plants to transition elements under water culture conditions : I Titanium, Vanadium, Chromium, Manganese, and Iron

Abstract Cabbage plants were water-cultured under 4 levels of titanium (0,0,4,4,20 ppm), vanadium (0, 0.4,4, 20 ppm), chromium (0, 0.2, 2, 10 ppm), manganese (0, 0.4, 4, 20 ppm), and iron (0, 1, 10, 50 ppm), and the effects of the elements supplied on the growth of the plants and on the distribution of the elements in the plants were studied. The dry weight of a whole plant and of inner leaves (yield) without the addition of Ti, V, and Cr did not decrease, while that without the addition of Mn and Fe decreased slightly. The addition of Ti, V, Cr, Mn, and Fe (more than 0.4, 0.4, 2, 4, and 10 ppm, respectively) decreased the yield. Slight transition element-induced chlorosis was observed in the plots at high levels of Ti, Cr, and Mn. The contents of the elements in the plants increased with an increase in the concentration of each element in the culture solution. The critical contents of Mn and Fe in plant-tops which resulted in a slight decrease in the yield due to the deficient injury were estimated to be.
Temperature effects on the toxicity of four trace metals to adult spotted Babylonia snails (Babylonia areolata)

A study was conducted to determine the median lethal toxicity of four heavy metals on the marine gastropod Babylonia areolata. Median lethal toxicity tests were conducted to observe the sensitivity of this gastropod to metals and how variations in temperature might affect toxicity of test elements. Four heavy metals were used in the study. It was observed that the 96-hr LC50 (in mg/L) for the different metals was found to be nickel (Ni) 33.53 (35.22–28.43), copper (Cu) 44.59 (46.43–41.53), cadmium (Cd) 21.53 (23.43–18.37), and zinc (Zn) 27.34 (28.81–24.24) at room temperature 24 °C. With temperature as a variable, median lethal concentration (LC50) values were observed to increase from 22.41 mg/L at 10 °C to 27.34 mg/L at 28 °C and reduce to 18.43 mg/L at 30 °C and a further rise in toxicity was observed at 35 °C where LC50 value was 12.7 mg/L as seen in the case of Zn. It was also observed that at 40 °C thermal and chemical toxicity overlapped as 100% mortality was observed in controls. This trend was noted in all metals for Babylonia areolata indicating that temperature played an important role in determining LC50 values of toxicants.
Effect of the metal ion on the anti T. cruzi activity and mechanism of action of 5-nitrofuryl-containing thiosemicarbazone metal complexes

Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, is a major health problem worldwide. In this work, we report the development of palladium and platinum metal complexes with 5-nitrofuryl-containing thiosemicarbazones (L) as bioactive ligands against T. cruzi and PTA (1,3,5-triaza-7-phosphaadamantane) as co-ligand. Eight new complexes of the formula [MCl(L)(PTA)] with M = Pd or Pt were synthesized and fully characterized. Most complexes showed similar activities against T. cruzi to those of the corresponding free thiosemicarbazone ligands. No significant differences between palladium and platinum complexes were observed. Metal compounds with the phenylthiosemicarbazone derivative were the most active ones (IC50 = 9.84 ± 0.32 and 4.94 ± 0.24 μM for Pd2+ and Pt2+, respectively). The prepared complexes were not toxic on mammalian cells, showing selective indexes of more than 10–20. The ability of the complexes to be reduced in the parasite, which leads to toxic free radical species, was confirmed by the detection of OH· and nitroanion free radical species by ESR spectroscopy experiments. Gel electrophoresis and fluorescence experiments were consistent with an intercalating-like mode of DNA interaction for the complexes, but DNA interaction does not seem to be the main mechanism of anti T. cruzi action for these compounds. The results obtained show that complexation of the bioactive ligands with the selected metals is a valid strategy to obtain improved metal-based antiparasitic compounds.
Partitioning of free energy contributions in the estimation of binding constants : Residual motions and consequences for amide-amide hydrogen bond strengths

Any bimolecular association is entropically unfavorable because of degrees of freedom of translation and rotation lost when two molecules come together to form a complex. For a ligand of molecular weight 200, the formation of a «rigid» dimer (one in which there is no residual relative motion of the associating components A and B in the complex A.B) opposes binding by ca. 10 -9 to 10 -10 M -1 in binding constant
Measurement of the Free Concentration Using Solid-Phase Microextraction: Binding to Protein

A method is described to measure freely dissolved compounds, using solid-phase microextraction (SPME) as sampling technique. Currently applied techniques, like solvent extraction, have the disadvantage of extracting the total amount of a compound that is present in a sample. For many applications, though, the freely dissolved fraction of a compound is of more interest than the overall amount. The procedure described in this work is based on the principle that only the freely dissolved compound is available for partitioning to the SPME fiber. By extracting only a small amount of the freely dissolved fraction, the equilibrium between the fraction of a compound bound to a matrix and the fraction dissolved in the aqueous phase is not perturbed. The procedure was applied to study the binding of four polar compounds, i.e., aniline, nitrobenzene, 4-chloro-3-methylphenol, and 4-n-pentylphenol, to bovine serum albumin to illustrate the possibilities of the method.
Similarity in air and nitrogen I. Breakdown voltages

Measurements of the static breakdown voltage Vs of air and nitrogen have been made under uniform field conditions for values of N in the range 165×1019-99×1019 cm−3 and 033×1020 less-than-or-eq, slant Nds less-than-or-eq, slant 264×1020 cm−2 (N is the gas number density and ds the sparking distance.) The measurements show that Paschen's Law, Vs=f(Nds), is obeyed in nitrogen, but an interesting deviation is revealed in air. The observed deviations from Paschen's Law are in good agreement with the deviations which were calculated by Daniel et al. in 1969 from measurements of the spatial growth of pre-breakdown ionization currents.
Advances on biomass pretreatment using ionic liquids: An overview

Petroleum is currently being used as a major source for chemicals, materials, and fuels, but poses major concerns in terms of its future utilisation due to resource limitation, increasing costs and associated environmental issues. An alternative raw material for chemicals and biofuels production is lignocellulosic biomass. The conversion of biomass to biofuels begins with biomass pretreatment in which chemical and/or physical treatments are utilised to remove or weaken the tight linkages among cell-wall components, making biomass easier to degrade. The use of ionic liquids–salts (mixtures of cations and anions that melt below 100 °C) has been described as a new potentially viable development in this area due to the increasing interest in the use of such compounds to pretreat lignocellulosic materials and to catalyse the dissolution of cellulose. This manuscript aims to provide an overview on the major representative progress and development of the use of ionic liquids systems for biomass pretreatment and cellulose dissolution. A comparison of the environmental impact of different ionic liquids for the conversion of carbohydrates into useful biofuel intermediates will be described, with their inherent advantages for biomass valorisation processes in terms of unique and tuneable physico-chemical properties.
Application of near infrared reflectance spectroscopy to the compositional analysis of biscuits and biscuit doughs

The possible use of near infrared (n.i.r.) diffuse reflectance spectroscopy in the monitoring of automatic metering equipment used for fat, sucrose, dry flour and water in short dough biscuit production has been investigated. The experimental design involved randomisation of a standard pilot scale Lincoln biscuit recipe to produce calibration and prediction samples and comparison of n.i. r. results with the levels of ingredients determined from the recipe. The use of several strategies based on regression analysis for selection of the ‘best’ wavelengths for reflectance measurements for each analyte was investigated. A novel strategy based on computing the regressions on analyte concentration of all possible pairs of reflectance readings across the spectrum at given intervals is presented. The results of the experiments demonstrate that the precision of the n.i. r. method is excellent for all four constituents, but only the calibrations for fat are sufficiently accurate to be capable of detection of metering errors of ±5% relative to the total amount of fat in the recipe.
Disappearance of aerially applied fenitrothion in rice crop waters

The disappearance of fenitrothion under real environmental conditions was studied. Fenitrothion was applied in the rice crop field of the Ebre Delta (Tarragona, Spain) during July 1995 by helicopter spray ing at a rate of 148 mL/ha Tionfos 50 LE (50% of pure fenitrothion). For monitoring fenitrothion residues in water, two different analytical techniques were used: enzyme-linked immunosorbent assay (ELISA) and automated on-line solid-phase extraction (Prospekt) followed by liquid chromatography/diode array detection (LC/DAD). The unequivocal identification of fenitrothion, fenitrooxon, 3-methyl-4-nitrophenol, and s-methyl isomer of fenitrothion was achieved by liquid chromatography/mass spectrometry (LC/MS) using an atmospheric pressure chemical ionization (APCI) interface in the negative ionization (NI) mode. The residue levels of fenitrothion in rice crop field waters varied from 119−178 μg/L down to 3.8−1.5 μg/L after 48 h of helicopter application. The half-lifetimes t1/2 were calculated by both anal.
Mass Absorption Cross-Section of Ambient Black Carbon Aerosol in Relation to Chemical Age

Three differing techniques were used to measure ambient black carbon (BC) aerosols in downtown Toronto through 20 December 2006 to 23 January 2007. These techniques were thermal analysis, as performed by a Sunset Labs OCEC Analyzer (OCEC); light attenuation, as performed by an Aethalometer (AE); and photoacoustic analysis, as performed by a Photoacoustic Instrument (PA). These measurements of ambient PM 2.5 were used to investigate the effects of coating thickness on BC Mass Absorption Cross-section (MAC). MAC values were determined by comparing 880 nm and 370 nm AE measurements and PA measurements of b abs (absorption coefficient, Mm–1) to the OCEC measurements. Based on mass size distributions and supporting criteria, the PM 2.5 was classified as fresh, semi-aged, or aged. The average MAC values in these categories, based on the PA measurements, were 9.3 ± 1.8, 9.9 ± 2.0, and 9.3 ± 2.2 m 2 /g (mean ± standard deviation), respectively, suggesting that any difference in coating thickness as a result of aging, on the time scale observed, did not produce a difference in MAC. In a second type of experiment, a thermodenuder was installed upstream of the AE, PA, and OCEC and samples were heated to 340°C in order to evaporate volatile and semi-volatile components within the coating. Based on the PA measurements, the average MAC values of these heated samples, for the fresh, semi-aged, and aged categories were 7.7 ± 2.2, 6.9 ± 2.2, and 9.1 ± 2.0 m 2 /g, respectively. Similar differences in MAC were also observed by the AE. The decrease in MAC in the fresh and semi-aged samples was interpreted in terms of the degree of coating of the PM 2.5 . Results agreed well with predictions made by absorption amplification theory and had ramifications for calibration of filter-base attenuation and photoacoustic instruments.
OPTIMIZATION OF PROCESS VARIABLES FOR ACCELERATED AGING OF BASMATI RICE

Experiments were conducted to develop a process for accelerated aging of aromatic rice. Freshly harvested clean paddy of “Pusa Basmati” variety was conditioned as per the experimental design. Response surface methodology for three variables at five levels was used. Central composite rotatable design was used to optimize the temperature (30–50C), relative humidity (50–90%) and aging period (3–14 days) to accelerate the aging process for paddy. The optimum levels of process variables were based on the desired milling and cooking quality indices. The quality attributes included milling yield, kernel elongation ratio, volume expansion ratio, solid loss, amylose content, gel consistency and aroma. A complete second-order polynomial model was fitted to the data and the adequacy of the model was tested. The models were then used to interpret the effect of various input parameters on the response. The total effect of individual input variables and combined effect of all these variables at linear and quadratic level on head yield was significant at 1% level. Similar interpretation of the effect of various input parameters on the responses have been done in details. The common optimum condition for accelerated aging of paddy was found to be 43.4C, 71.0% relative humidity (RH) and 11.4 days. PRACTICAL APPLICATION Freshly harvested rice is less preferred by consumers because of poor cooking properties like less kernel elongation and volume expansion ratio with more solids loss and softer gel consistency. Aging brings about progressive desirable changes in the grain. The natural aging process is time-consuming and also requires proper storage. Therefore, the aging process may be accelerated by subjecting the grains to appropriate environmental conditions to bring about the acceptable properties so that the full potential of domestic as well as export market may be explored at the right time with a relatively high price. The information obtained from this study may be used in designing thermal processing to obtain aged rice within a short period.
Applicability of Different Indices to Evaluate Nutrient Status of Winter Wheat in the Organic System

ABSTRACT Nitrogen (N), phosphorus (P), and potassium (K) nutrient status of two winter wheat cultivars (Kobra and Juma) in the organic crop production system was compared with integrated and conventional systems. This research was conducted between 1998 and 2000 at the Experimental Station in Osiny (Lublin province, Poland) on a grey-brown podzolic soil. To determine N, P, and K contents shoot samples of wheat were taken at the shooting and earing growth stages. Measurements of chlorophyll content were performed with a chlorophyll meter (SPAD) to estimate N nutrient status. Four different methods [Nitrogen Nutrient Index (NNI), Soil Plant Analysis Development (SPAD), Diagnostic Recommendation Integrated System (DRIS), and Sufficiency Range (SR)] of nutrient status evaluation were compared. Nitrogen (N) and potassium (K) nutrient status of wheat cultivated in the organic system was lower compared with the other farming systems. Assuring sufficient supply of nitrogen to cereals under the conditions of organic farming is particularly difficult in early growth stages. In the integrated and conventional systems wheat was sufficiently supplied with NPK. Kobra cv. proved to be more adapted to the organic system. Results indicate that classical nutrient status indices are of lesser use for organic farming.
Membranes of Palmitoyloleoylphosphatidylcholine and C 12 E 4 A Lattice Model Simulation

The structure of the lamellar phase of the ternary system of palmitoyloleoylphosphatidylcholine (POPC)/tetra(ethylene oxide) monododecyl ether (C12E4) has been characterized in detail by a X-ray and neutron scattering and by 2H NMR spectroscopy. The addition of small amounts of surfactant to the POPC bilayers causes the bilayer to become more rigid, while the addition of large amounts of surfactants induces a fluidization of the structure. Here, we report a Monte Carlo study of the underlying mechanisms yielding these changes in the orientational order of POPC/C12E4 bilayers. The study employs a lattice Monte Carlo dynamics algorithm that rests on the assumption that the conformational dynamics of chain molecules can be described as the superposition of local structural rearrangements involving short-chain segments. This approach is particularly useful for following structural and conformational changes on time scales longer than those associated with the gauche/trans isomerization of hydrocarbon chains.
Adsorptive properties of acid-heat activated rectorite for Rhodamine B removal: equilibrium, kinetic studies

Abstract The acid-heat activated sodium rectorite (AH-R) was prepared and used to remove Rhodamine B (RhB) from aqueous solution. The AH-R showed higher adsorbility than the raw sodium rectorite and the rectorite modified by acid or by heat treatment. The effects of pH, adsorbent dosage, initial dye concentration, reaction temperature and ionic strength were studied. The Rhodamine B adsorption on the AH-R was a fast process and the equilibrium was reached in 60 min. The Langmuir and Freundlich isotherm models were applied to the equilibrium data and the Langmuir model was applied to the equilibrium data better. The maximun adsorption capacity was found to be 59.1 mg/g, and the kinetic data followed the pseudo-second-order kinetics. Thermodynamic parameters were obtained and it was found that the adsorption of Rhodamine B dye onto the AH-R was an endothermic and spontaneous process at the temperatures under investigation.
Effects of Fulvic Acid on Fe(II) Oxidation by Hydrogen Peroxide

Iron redox cycling can catalyze the oxidation of humic substances and increase the rate of oxygen consumption in surface waters rich in iron and organic carbon. This study examines the role of Fenton's reaction [oxidation of Fe(II) by hydrogen peroxide] in this catalytic cycle. A number of competing processes were observed in model systems containing dissolved Fe, hydrogen peroxide, and Suwannee River fulvic acid. First, the effective rate constant of Fenton's reaction increased with increasing fulvic acid concentration, indicating the formation of Fe(II)−fulvate complexes that react more rapidly with hydrogen peroxide than Fe(II)−aquo complexes. This effect was significant at pH 5 but negligible at pH 3. A second effect was scavenging of the HO• radical produced in Fenton's reaction by fulvic acid, forming an organic radical. The organic radical reduced oxygen to HO2•/O2•-, which then regenerated hydrogen peroxide by reaction with Fe(II). Finally, Fe(III) was reduced by a dark reaction with fulvic acid, .
Investigating the Gas Sorption Mechanism in an rht-Metal–Organic Framework through Computational Studies

Grand canonical Monte Carlo (GCMC) simulations were performed to investigate CO2 and H2 sorption in an rht-metal–organic framework (MOF) that was synthesized with a ligand having a nitrogen-rich trigonal core through trisubstituted triazine groups and amine functional groups. This MOF was synthesized by two different groups, each reporting their own distinct gas sorption measurements and crystal structure. Electronic structure calculations demonstrated that the small differences in the atomic positions between each group’s crystal structure resulted in different electrostatic parameters about the Cu2+ ions for the respective unit cells. Simulations of CO2 sorption were performed with and without many-body polarization effects and using our recently developed CO2 potentials, in addition to a well-known bulk CO2 model, in both crystallographic unit cells. Simulated CO2 sorption isotherms and calculated isosteric heats of adsorption, Qst, values were in excellent agreement with the results reported previousl.
Understanding the Catalytic Behavior of Zeolites: A First-Principles Study of the Adsorption of Methanol

Zeolites are microporous aluminosilicate materials used as industrial catalysts, and there is much interest in understanding their catalytic behavior. The adsorption of methanol in the catalytically active zeolite chabazite and in sodalite was examined by performing ab initio calculations within periodic boundary conditions. A direct correlation between zeolite structure and chemical activation of the adsorbate was found. Methanol was protonated without an activation energy by a Brønsted acid site, provided the molecule was situated in the eight-ring window of chabazite, whereas the same molecule was only physisorbed in more open cage regions, such as those found in sodalite.