bluuebunny/crossref_metadata_2025 huggingface dataset:
Polyclonal antibodies production from porcine gelatin and its preliminary study for immunosensor applications
Authors: Astuti A I , Soejoedono R D , Saepudin E , Assaat L D , Ivandini T A
Published: April 2020

Gelatin was extracted from porcine skin and used as an antigen to produce the polyclonal antibodies of porcine gelatin using New Zealand white rabbits for application in the development of an ELISA-based immunosensor for porcine gelatin recognition. The extraction of porcine gelatin from porcine skin was successfully performed with 20.52 % of yield. The characterization performed by using UV and IR spectroscopy indicated that the purified gelatin has a comparable quality against the commercial standard of porcine gelatin. Further analysis of the gelatin with SDS-PAGE method observed five separation lines with molecular weight bands of 57.06; 49.50; 42.94; 33.89; and 29.40 KDa, indicating that the gelatin can be used as an antigen to produce the polyclonal antibodies of porcine gelatin. After five injections of gelatin into the rabbit, ELISA characterization of the purified serum of the blood rabbit showed that the antibody with a concentration of 0.289 mg/mL could be produced.
Preliminary study on carboxylation reaction of phenylacetylene with CO2using nickel catalyst impregnated on mesoporous carbon
Authors: Hadi A , Abdullah I , Krisnandi Y K
Published: April 2020

In this research, carboxylation reaction of phenylacetylene with CO2has been studied using impregnated nickel on mesoporous carbon as catalyst. Mesoporous carbon was successfully synthesized using a soft template method with Pluronic F127 as pore template, and formaldehyde and phloroglucinol as the carbon source. This material was characterized with Fourier Transform Infrared (FTIR), X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM), and Brunauer-Emmett-Teller (BET) analysis. Characterization with XRD shows the presence of two peaks at 24.26° and 42.76° which denotes the typical peak of graphite-like carbon. BET surface area analysis shows that the mesoporous carbon has a pore size distribution of 7.2 nm and surface area of 432.15 m2/g. Modification of mesoporous carbon was carried out by impregnation of Ni metal into mesoporous carbon (Ni@MC) through reduction of Ni(II) with ethylene glycol. The Ni@MC catalyst was used as a catalyst in the carboxylation reaction of phenylacetylene with CO2. The reactions were carried out in a batch reactor under various reaction conditions. High Performance Liquid Chromatography (HPLC) analysis of the product mixtures revealed that the highest yield of trans-cinnamic acid (2.83 %) was achieved at 85 °C for 12 h reaction time.
Effect of surfactants mixing of Tween 80 and Nonidet RK-18 in preparation of microspheres based on polyblend of poly(lactic acid) and polycaprolactone
Authors: Ferrariski A , Budianto E
Published: April 2020

In preparation of microspheres process with solvent evaporation method, microspheres are formed from the oil in water (O/W) emulsion droplets as a template in which the type and concentration of surfactant will affect the stability of the emulsion. This research aims to investigate the effect of composition and concentration of a mixture of Tween 80 and Nonidet RK-18 as a mixed emulsifier in the preparation of microspheres based on polyblend of PLA/PCL. The solvent evaporation method involves emulsification and dispersing the polyblend emulsion in water. The microspheres obtained were characterized using FTIR, stereomicroscopes, and PSA instrumentations. The result of this research shows that the mixed emulsifier produces smaller microspheres compared to the result of using Tween 80 or Nonidet RK-18 individually because of the presence of synergistic effect. When the surfactants mixture is used, the larger Tween 80 ratio in the mixture will increase the ratio of smaller microspheres obtained because of the high hydrophilicity of Tween 80 that can stabilize O/W emulsion. On the other hand, the addition of Nonidet RK-18 in an increasing manner of ratio or concentration may destabilize the emulsion droplets through Ostwald ripening that can occur because Nonidet RK-18 has a low cloud point (17 °C).
Influence of pyrolyzed temperature on the formation of silicon carbide fiber from polycarbosilane in electrospinning method
Authors: Masripah M , Zulys A , Setiawan J
Published: April 2020

The synthesis of silicon carbide (SiC) fibers by electrospinning method was done using polycarbosylane (PCS) as precursor and dimethylformamide (DMF)/toluene as solvent. Knowing the heat treatment of fibers consist of curing and pyrolisis, there were two steps in the major reaction. The curing process is by heating in air to make an oxidative cross-linking of the PCS. The pyrolysis process causes chemical decomposition from organic to inorganic compounds. These composition changes were described through Fourier Transform Infrared FTIR, Thermagravimetric analysis (TGA), X-Ray Diffraction (XRD) and Energy Dispersive X-Ray Spectroscopy (EDS) analysis. The products of electrospinning and curing were characterized by FTIR and TGA. The conversion to ceramic of PCS under various pyrolysis temperatures (1200, 1300, 1400, 1500) °C has been investigated and the products of this process were characterized by FTIR and XRD. Elemental analysis of the fiber as received and after cured showed that the ratio of H and C to Si decreased with holding time at the cure-temperature while the amount of oxygen increased. Meanwhile, the pyrolyzed generally produced silicon oxycarbide SiCxOy. Crystalline SiC β-SiC was found at temperature 1500 °C.
Synthesis and characterization of Au-TiO2 Janus nanostructures
Authors: Mulyantono M F , Gunlazuardi J , Khalil M
Published: April 2020

This work reports a comprehensive study on the synthesis and characterization of Au-TiO2 Janus nanostructures from pre-synthesized Au nanoparticles and anatase TiO2 nanoparticles. Here, well-distributed Au nanoparticles with mean particle diameter of ∼35 nm were successfully prepared using seed-mediated method, which exhibited a unique surface plasmon resonance (SPR) properties at 525.5 nm. Meanwhile, anatase TiO2 nanoparticles with perfectly spherical morphology were synthesized via sol-gel method, which could easily be integrated by the as-prepared Au nanoparticles. Based on the result, it is found that the resultant nanostructured exhibited a Janus heterostructure feature, where Au nanoparticles were efficiently found to be attached on the surface TiO2 nanoparticles. Furthermore, spectroscopic analyses also revealed that the integration of Au nanoparticles could widen the absorption spectrum of TiO2 to visible range due to the presence of SPR phenomenon.
The effect of sorbitan monooleate as surfactant in preparation of polyblend polylactic acid and polycaprolactone microspheres
Authors: Ryofi A N , Budianto E
Published: April 2020

Polyblend of polylactic acid (PLA) and polycaprolactone (PCL) microspheres with polymodal size distribution were synthesized through an emulsification-solvent evaporation method in water-in-oil (W/O) emulsions. Sorbitan monooleate was used as emulsion stabilizer and size controller in preparation of the microspheres. The effect of sorbitan monooleate addition in preparation on the size of the microspheres was studied by varying the volumes of sorbitan monooleate, the stirring speeds of emulsion formation, and dispersion times. The microspheres were characterized using Fourier Transform Infrared (FT-IR) and Particle Size Analyzer (PSA). The results show that there is no chemical interaction between PLA and PCL. This phenomenon can be seen from the FT-IR spectrum, which shows both PLA and PCL component. The particle size of microspheres decreased with the increasing volume of surfactant, emulsion stirring speed, and dispersion time. The size of microspheres obtained ranges from 0.4 μm to 10 µm. Physical forms of microspheres were observed using optical microscope. The result shows that some microspheres are spherical and others are in aggregates form.
Evaluation of dissolution of purified bromelain from pineapple core extract (Ananas comosus [L.] Merr) in the form of chitosan-coated microspheres
Authors: Zahrah T K , Setiasih S , Hudiyono S
Published: April 2020

The aim of this study is to coat the bromelain from pineapple’s core into chitosan microspheres crosslinked by glutaraldehyde to maintain its activity until it reaches the intestines. The crude enzyme was first purified by ammonium sulfate precipitation method, followed by the dialysis. The bromelain fraction of the dialysis has a specific activity of 294.44 U/mg with a purity level of 15.68 fold compared to the crude enzyme. Coating bromelain using glutaraldehyde crosslinked microsphere showed an efficiency of 87.14 %. The dissolution test results showed the release rate of bromelain in artificial gastric fluid is 9.35 % and in artificial intestinal environment is 79.92 %. The result of this study indicates that chitosan-coated microspheres are good enough as bromelain coatings for slow-release matrices.
Synthesis and characterization of Cu2+ imprinted polymer-tannin extract from mango leaf (Mangifera indica L.) for selective separation of Cu2+
Authors: Aribah F A , Nurani D A , Rahayu D U C , Krisnandi Y K
Published: April 2020

Tannins are secondary metabolites in Mango (Mangifera indica L.). This compound has a cluster of polyphenols as functional ligands for chelating Cu(II). Cu(II)-imprinted polymer-tannin (Cu-IP-tannin) was successfully synthesized by polymerization of phenol and formaldehyde with the complex of Cu(II)-tannins in acidic medium. Non-imprinted polymer (NIP) was similarly prepared without the presence of Cu(II) ions. The polymers were characterized by Scanning electron microscopy energy dispersive x-ray spectroscopy (SEM-EDS) and Fourier transform infra-red (FTIR). Cu(II) ions were completely removed by leaching the dried and powder of imprinted polymer with HNO3 0.5 M. The optimum pH of maximum adsorption of Cu(II)-IP-tannin was 7.0 for 120 minutes of contact time. The adsorption of Cu(II)-IP-tannin followed the Freundlich isotherm model with a maximum adsorption capacity of 99.08 mg/g. The relative values of the selectivity factor (αr) of Cu(II)/Ni(II), Cu(II)/Pb(II) and Cu(II)/Fe(II) on a single metal ion selectivity test were 23.89, 55.71 and 26.25, respectively.
Three-component reaction in 1,4-dihydropyridine synthesis catalyzed by Copper(I) Iodide nanoparticles
Authors: Cahyana A H , Ardiansah B , Aisyah N S
Published: April 2020

We have synthesized two 1,4-dihydropyridine derivatives via one-pot three-component reaction. The reactions were catalyzed by copper(I) iodide nanoparticles with crystallite size of 78.4 nm. Formations of cyclocondensation products were confirmed by Fourier Transform Infrared (FTIR), UV-Vis and Gas Chromatography-Mass Spectrometry (GC-MS) spectra.
Hydroprocessing of kemiri sunan oil (reutealis trisperma (blanco) airy shaw) over NiMoCe/γ-Al2O3 catalyst to produce green diesel
Authors: Yulia D , Zulys A
Published: April 2020

Kemiri Sunan is an alternative energy source that has a considerable amount of oil and does not compete for food source. Hydroprocessing of kemiri sunan oil has a big potential for renewable fuels. In this paper, NiMoCe/γ-AL2O3 catalyst is used for hydroprocessing of saturated kemiri sunan oil to produce renewable hydrocarbons. The catalyst was prepared by using wet impregnation method with variations of Ce 1%, 5% and 15%. The characterization of catalyst was used by means of Brunauer-Emmett-Teller (BET), Scanning Electron Microscopy (SEM), X-Ray Diffraction (XRD) and X-Ray Fluorescence (XRF). Hydroprocessing was performed using an autoclave batch reactor under operating conditions of 400° C and 35 bar pressure for 5 hours. GC characterization showed that the product of renewable hydrocarbons is dominated by the C15-C18, alkane chain.
Modification of glassy carbon electrode with NiO nanoparticles prepared using Ocimum sanctum leaf extract as urea sensor
Authors: Arief P R , Yulizar Y , Ivandini T A
Published: April 2020

NiO nanoparticles (NiO NPs) have been prepared with green synthesis method usingOcimum sanctumleaf extract (OSLE), which contains secondary metabolite compounds of alkaloids as a weak base source and capping agent. Characterization using Particle Size Analyser (PSA) showed a particle size of NiO about 52.42 nm. NiO NPs was used as modified on glassy carbon (GC) electrode, and then characterized using cyclic voltammetry (CV) and Scanning Electron Microscopy-Energy Dispersive X-Ray (SEM-EDX). GC-NiO NPs was used for preliminary studies of urea sensor. The results showed that GC-NiO NPs can detect urea with limit of detection (LOD) values of 0.12 mM and linearity R2of 0.97. In addition, the repeatability of urea sensor studies with GC-NiO NPs electrode shows % RSD of 2.854, while its stability shows % RSD of 7.90 for 3 days.
Synthesis Pb(II)-ion imprinted polymer using tannins from mango leaves (Mangifera indica L.)
Authors: Sekarharum C , Rahayu D U C , Nurani D A
Published: April 2020

This work reports the synthesis of Pb(II)–Ion Imprinted Polymer (Pb-IIP) using tannin extract from Mango leaf (Mangifera Indica L.) as functional ligand (chelating agent and monomer). Pb2+ ion found to form a stable compound at 1:1 complex with tannin in aqueous solution. The resulting complex of Pb2+ and tannin extract was polymerized using phenol-formaldehyde as cross-linker in acidic medium. The structure and properties of Pb-IIP were compared to Pb-IIP gallic acid and Non Imprinted Polymer (NIP) that were synthesized with similar conditions. These polymers were charaterized by Fourier Transform Infrared (FTIR) and Scanning Electron Microscopy-Energy Dispersive X-Ray (SEM-EDX). The template of Pb(II) ion was completely removed from the polymeric matrix using 1 mol/L HNO3. The optimum pH of maximum sorption was 5 on IIP-tannin and IIP-gallic acid at 120 mins contact time. Maximum capacity of tannin Pb-IIP, gallic acid Pb-IIP, and NIP were 153.159 mg/g, 147.959 mg/g, and 138.218 mg/g, respectively. It was found that the tannin Pb-IIP sorbent is more selective than gallic acid Pb-IIP and NIP.
In vitro study of DNA-adduct formation (8-OHdG) due to exposure of benzo[a]pyrene and Co(II) through fenton-like reaction
Authors: Wijanarko S A , Budiawan B , Dani I C , Handayani S
Published: April 2020

Severely increasing environmental pollution with an unhealthy pattern of life in the community can increase the source of exposure of carcinogenic substances that can cause cancer. Benzo[a]pyrene and Cobalt (II) are some examples of carcinogenic substances commonly found in the environment. Both materials can simultaneously enter the body through food or polluted air and damage the DNA. In this study, we studied the effect of B[a]P and Co(II) exposure in-vitro on 2’-deoxyguanosine. An increase in the amount of the 8-hydroxy-2’-deoxyguanosin compound is used as an indicator of the occurrence of DNA damage and a cancer risk biomarker. It was found that the synergistic effect on the combination of B[a]P and Co (II) through Fenton-like reaction is influenced by the concentration of H2O2. The amount of 8-OHdG that formed with the combination of B[a]P and Co (II) is 126.23 ppb. It does not vary much with the amount that resulted from B[a]P exposure alone at 136.53 ppb. Exposure of Co(II) through Fenton-like reaction alone gives the highest yield of 8-OHdG formation at 282.67 ppb. Followed by B[a]P and Co(II) at 258.98 ppb, B[a]P and H2O2 at 153.16 ppb.
Electroreduction of carbon dioxide using platinum-iridium modified boron-doped diamond (BDD) with various platinum-iridium ratios
Authors: Saprudin M H , Atriardi S R , Gunlazuardi J , Einaga Y , Ivandini T A
Published: April 2020

Modification of boron-doped diamond (BDD) electrodes with bimetallic platinum-iridium was studied. Combination techniques of wet chemical seeding and electrochemical deposition were performed with various Pt-Ir precursor ratios of (1:1), (1:2) and (2:1). These electrodes were then applied for electrochemical reduction of CO2 dissolved in 0.1 M NaCl solution at the potentials of -1.1 V, -1.2 V, -1.3 V, and -1.5 V (vs Ag/AgCl) for 60 min. Electroreduction of CO2 applied at PtIr(2:1)-BDD at the potential of -1.1 V (vs Ag/AgCl) produced formic acid, methanol and hydrogen as the main products.
Bangka Kaolin and Bayat Zeolite-based ZSM-5 zeolite as heterogeneous catalyst for hexadecane cracking reaction
Authors: Basri E S H , Krisnandi Y K , Ekananda R , Saragi I R
Published: April 2020

Microporous ZSM-5 material was synthesized using natural aluminosilicate minerals, i.e. Bayat zeolite and Bangka kaolin as silica and alumina sources. Prior to use, Bayat zeolite was treated with several treatments, i.e. purification, fragmentation and dealumination. While Bangka Kaolin was used as the source of additional silica, in which the silica was extracted using aqua regia. After that, ZSM-5 zeolite was synthesized using tetrapropylammonium hydroxide (TPAOH) as template. Then, it was characterized using Fourier Transform Infrared (FTIR), X-Ray Diffraction (XRD) and Scanning Electron Microscopy-Energy Dispersive X-Ray (SEM-EDX). Based on XRD pattern, mordenite inverted framework (MFI) structure was obtained. SEM-EDX images showed that the natural aluminosilicate-based ZSM-5, so called ZSM-5 MA, has a coffin-like shape with average crystal size and Si/Al ratio are 1.6 μm and 14.26, respectively. As reference, another as-synthesized ZSM-5 was prepared from pro-analysis reagents, and labelled as ZSM-5MS. It also has mordenite inverted framework (MFI) structure, Si/Al ratio of 21.45 and average crystal size of 0.8 μm. ZSM-5 was tested with micro activity test (MAT) method for hexadecane cracking reaction at 500 °C. Prior to be used, the ZSM-5 was subjected to NH4−
exchanged followed by calcination at 550 °C to obtain H/ZSM-5. The products that obtained from hexadecane cracking reaction are gas (H2, C1–C4) and gasoline (C5–C12) fractions. The catalytic test shows that both H/ZSM-5MA and H/ZSM-5MS gave similar results, despite their differences in Si/Al ratio and particle sizes. Therefore, zeolite synthesis using natural minerals as Si and Al sources is promising to be explored further.
Study of microalgae (Scenedesmus Sp.) utilization as phosphate bioremediator (PO4
3−) in domestic wastewater medium
Authors: Maisarah M , Saefumillah A , Ambarsari H
Published: April 2020

In this research, the use of Scenedesmus sp. as a phosphate bioremediator agent is expected to be applied for lowering the phosphate levels in the water as well as improving the quality of the environment. Scenedesmus sp. used in this research was isolated from Sungai Cideng. Variation of phosphates were tested to see the effect of various types of phosphate found in the waters in the form of a variation of organic phosphates using the Adenosine 5’-monophosphate (AMP), phytic acid and variation of inorganic phosphates using potassium dihydrogen phosphate (KH2PO4) and sodium tripolyphosphate (STPP). It was found that the use of monopotassium phosphate (KH2PO4) was better in decreasing phosphate levels and increasing the number of Scenedesmus sp. cells with a phosphate decrease percentage of 87.5 %. Phosphate test was performed using UV-Vis spectroscopy instrumentation and the abundance of cell count was performed using a microscope and hemocytometer. The environmental quality test parameters are temperature and pH. Direct application in wastewater from Muara Angke was also found the decrease of phosphate levels and increase the number of Scenedesmus sp. cells. Scenedesmus sp. has the ability to reduce nutrients in wastewater to below wastewater quality standard of 86.0 % from the initial phosphate concentration of 0.2255 ppm to 0.0314 ppm.
Chemical vapour deposition (CVD) of molybdenum into medium pore H-zeolites
Authors: Suwardiyanto S , Svelle S , Howe R F
Published: April 2020

Several medium pore H-zeolites (HZSM-5, HIM-5, HTNU-9 and HZSM-11) were evaluated toward molybdenum deposition via chemical vapor deposition using Mo(CO)6 as the molybdenum precursor. The deposition was through a high temperature adsorption of Mo(CO)6 vapor onto dehydrated zeolites. The progress of deposition was monitored gravimetrically. Exsitu infrared (FTIR) spectroscopy was employed to observe the interaction between Mo(CO)6 and the zeolites during the deposition. X-ray photoelectron spectroscopy (XPS) was used to scrutinize the nature of molybdenum deposit within the zeolite. High temperature adsorption of Mo(CO)6 vapor is an irreversible adsorption resulted in a molybdenum deposition onto the zeolites whereas the adsorption conducted at room temperature is a reversible one. Interaction of Mo(CO)6 and the zeolites at high temperature led to the reaction of Mo(CO)6 and hydroxyl group within zeolites i.e. silanol group and Brønsted acid site. The molybdenum dispersion within the zeolites was governed by the particle size of the zeolite. More concentrated molybdenum deposited on zeolite surface occurred on the zeolite with bigger particle size. The highest surface molybdenum deposition was observed on ZSM-11 surface as it has the biggest particle size.
Wood plastic composites from chopped and pelleted waste plastic bags: effect of concentrations and reprocessing on flexural modulus and strength
Authors: Ramadhoni B , Prasetyorini L A , Ujianto O , Wuryanti W
Published: April 2020

The utilization of waste plastic bag, especially as a matrix for wood plastic composites, is expected to reduce the environmental problems throughout the world caused by its use. Wood plastic composites were manufactured via melt mixing of chopped or pelleted waste plastic bags, sawdust and polyethylene grafting maleic anhydrate (MAPE) according to Extreme Lattice Mixture - Design of Experiment (DoE). The effects of concentrations and reprocessing of waste plastic bags on flexural modulus of elasticity and strength of composites were analyzed. In general, flexural modulus of composites from chopped and pelleted waste are increased but still below the value of SNI 8154–2015. Moreover, the flexural strength of the resulted composites from chopped waste also increased than that of the pelleted one. Some of the formulas of composites from chopped waste met the value required by SNI 8154 – 2015. On the contrary, the flexural strengths of composites from pelleted waste are decreased than that of the virgin one. This is probably due to the existence of interaction between pelleted waste and sawdust that prevented the waste plastic to perfectly melted, hence acted as stress concentration sites. Furthermore, the resulted composites were optimized for flexural modulus using response optimizer plot in order to achieve modulus 2000 MPa that required by the standard. However, the optimized flexural modulus of composites from chopped and pelleted waste was in the range of 1500 MPa, which is far below the standard. Therefore, reprocessing of chopped waste into pellets is not necessary due to inferior properties of composites from pelleted waste than that of the chopped one.
Structural and optical properties of La1-xPbxFe0.5Ti0.5O3 (x = 0.1, 0.2, and 0.3) perovskite material prepared by sol-gel method
Authors: Supriyadi Y , Triyono D , Lukmana S K
Published: April 2020

A series of La1-xPbxFe0.5Ti0.5O3 (x = 0.1, 0.2, and 0.3) nanoparticles have been successfully synthesized by sol-gel method. All prepared samples were characterized by X-ray diffraction (XRD), Raman scattering, Fourier Transform Infrared spectroscopy (FTIR), and UV-Vis spectrophotometry (UV-Vis). The X-ray diffraction pattern revealed the orthorhombic crystal structure and the increase of crystallite size with Pb content. The Raman scattering exhibited the similar Raman spectrum indicating the crystal structure remain unchanged due to the Pb substitution; indeed, the difference in lattice vibration phonon modes confirmed the variation in structural parameters with Pb-substitution which is also supported by FT-IR analysis. By using UV-Vis characterization, the optical band gap is found in the range of 2.1 – 2.2 eV.
A study of the poly(dA)-poly(dT) DNA electric field-dependence: density of states (DOS) analysis
Authors: Rahmani F , Yudiarsah E
Published: April 2020

Study of poly(dA)-poly(dT) DNA molecule electronic structure, by analysing its density of states (DOS), had been conducted. This research employed Green’s function method as tool to determine electron DOS of the DNA numerically. Electric field that was applied along z-axis is used as perturbation to modify electron hopping constant between sites in the molecule. In order to include electric field in the calculation, Miller-Abraham formula was used. Medium interaction with backbone molecules was considered as well within the calculation in the form of backbone disorder. By increasing electric field, the band in electron DOS spectrum appeared to become narrower and several states experience the decrement of DOS.
The radiochromic indicator using methyl red dye solution as a high-dose gamma-ray dosimeter application
Authors: Chairunisa W , Imawan C
Published: April 2020

The radiochromic indicator using the methyl red dye solution has been studied as a high-dose gamma-ray dosimeter. The indicator has been tested by irradiating using gamma rays with a 60Co source. The radiation dose was varied from 5 to 100 kGy with a dose rate of 5.5 kGy/h. The color change of the indicator solution caused by the radiation was characterized by using a UV-Visible spectrophotometer and a camera photograph. In addition, the color stability of the indicator is also studied by observing the effect of time and the storage in light and dark conditions. The effect of time after irradiation on the color of the solution has also been investigated. The methyl red solution indicator showed a radiochromic phenomenon color changes from red to dark red for a dose of 5-20 kGy, faded gradually then became colorless at a dose of 25–100 kGy. These color changes correspond to the peak of the UV-Visible absorbance spectrum at a wavelength of 492 nm. The color of the indicator solution is more stable if kept in dark conditions than in the light conditions. The color of the solution also shows its stability for up to 12 days after irradiation. These results conclude that the indicator solution of methyl red can be used as a dosimeter for gamma rays in the dose range of 5–40 kGy.
The sensitivity calculation of localized surface plasmon resonance (LSPR) Au nanorod by applying a boundary element system simulation
Authors: Sofani M , Putra M H , Djuhana D
Published: April 2020

In this study, we have calculated the sensitivity of localized surface plasmon resonance (LSPR) Au nanorod by a public metallic particle simulation based on the boundary element method (Metallic Nano-Particle Boundary Element Method, MNPBEM). The diameter of nanorod D is 20 nm, 60 nm, and 80 nm. The variation of aspect ratio is 1.5 to 3.5. The dielectric of Au nanorod based on the Christine-Johnson experiment. To understand sensitivity sense, we have also varied the refractive index medium by Lorentz-Lorentz approximation from a mixture of water and glycerol concentration. The refractive medium index is n = 1.3334 (100 % water pure), n = 1.3605 (80 % water and 20 % glycerol), n = 1.3881 (60 % water and 40 % glycerol), n = 1.4164 (40 % water and 60 % glycerol), and n = 1.4452 (20 % water and 80 % glycerol). From MNPBEM simulation, we have produced LSPR spectra such as absorption, scattering, and extinction curve as the function of wavelength. Then, the sensitivity of LSPR Au nanorod is determined by the gradient of the peak of wavelength to the refractive index medium variation for all aspect ratio. Interestingly, we have found the LSPR Au nanorod consisted of longitudinal and transversal mode in LSPR Au nanorod curve. The longitudinal mode appeared a higher wavelength than the transversal mode in LSPR spectra. In longitudinal mode, the peak of wavelength increased as the aspect ratio increased (red-shift) while in transversal mode, the peak of wavelength was relatively constant. Furthermore, the sensitivity in longitudinal mode increased as the aspect ratio increased, whereas the sensitivity in transversal decreased as the aspect ratio increased. Increasing the sensitivity in longitudinal mode related to red-shift as the nanorod volume increased and the refractive medium index change. According to the results, the sensitivity determination is useful to understand the refractive index medium changes that it is important to design a sensor device.
Flat optics in high numerical aperture broadband imaging systems
Authors: Werdehausen Daniel , Burger Sven , Staude Isabelle , Pertsch Thomas , Decker Manuel
Published: April 2020

Diffractive optical elements (DOEs) remain highly underutilized in broadband optical systems even though different technologies for DOEs including échelette-type gratings (EGs), multilevel DOEs, and metagratings have been introduced. Specifically, nanocomposite-enabled EGs can achieve efficiencies of close to

100
%

throughout the visible spectrum, but only for relatively small diffraction angles. Therefore, the question remains if they are suitable for high-numerical-aperture (NA) systems. Here we show that this is indeed the case. To this end, we first demonstrate that macroscopic nanocomposite-enabled diffractive lenses (DLs) can achieve perfect broadband focusing up to a NA of 0.03. We then derive analytic relationships and investigate prototypical optical designs to show that this threshold fully covers the requirements of high-end imaging systems with

NA
⩾
1.

This holistic all-system analysis demonstrates that the individual NA of a DL in a broadband imaging system is one to two orders of magnitude lower than the overall system’s NA. This shows that high-NA flat optical elements are not required for high-NA broadband systems. Therefore, nanocomposite-enabled EGs can unlock the full potential of DOEs for broadband optical systems, whereas other technologies cannot fulfill their high efficiency requirements.
Research of selective etching in LiNbO3 using proton-exchanged wet etching technique
Authors: Li Ying , Lan Tian , Yang Dengcai , Xiang Meihua , Dai Jingjing , Li Chong , Wang Zhiyong
Published: April 2020

Lithium niobate material (LN) has shown great application potentials in the fabrication of integrated optical devices due to its excellent physical properties, especially with the occurrence of lithium niobate-on-insulator (LNOI) substrate. However, the greatest challenge of micro/nano optical devices based on LN material lies in the precise etching process and thus limits its applications. In this paper, we comprehensively analyze the etching results treated by the proposed proton-exchanged wet-etching method (PEWE) combining with theoretical simulations and experiments. It is found that the proton-exchanged layer in the LN material can be easily etched after using a mixture acid of HF/HNO3, leading to the improvement of etching rate and surface morphology. The lowest roughness of the optical waveguide is measured to be 0.81 nm, which is beneficial for the performance improvement of LN-based optical devices. Ultimately, a quasi-vertical sidewall of the upper part of optical waveguide with improved surface morphology is successfully realized by utilizing the PEWE. Moreover, this method could also be extended to improve the performance of LNOI-based optical devices and pave the way for ultra-compact photonic integrated circuits based on LNOI.
Terahertz transmission properties of vanadium dioxide films deposited on gold grating structure with different periods
Authors: Gao Min , Wang Xu , Luo Shengxian , Lu Qingjian , Luo Sheng-Nian , Lu Chang , Chen Sihong , Long Fei , Lin Yuan
Published: April 2020

Vanadium dioxide (VO2) is a typical thermal induced phase transition material, exhibiting a transition from metallic phase at high temperature to insulating phase at low temperature, which is also accompanied by a conductivity change of over several orders of magnitude. The transition property makes VO2 prominent to achieve an effective degree of control of terahertz (THz) wave. In this paper, composite films consisting of metal grating with different periods and VO2 film were prepared by polymer assisted deposition method. Although the conductivity change of VO2 films deposited on gold grating structure across phase transition was declined to about two orders of magnitude, the amplitude modulation depth of THz of the composite films can still reach a high value. Furthermore, it was found that the THz modulation depth was related with the grating period. According to theoretical simulation, the fluctuation height of VO2 films, caused by metal grating structure during growth, can be used to regulate THz wave. These results demonstrate an economic and unsophisticated method to fabricate VO2 films with thickness fluctuation structure and then tune the THz waves.
t|ket⟩: a retargetable compiler for NISQ devices
Authors: Sivarajah Seyon , Dilkes Silas , Cowtan Alexander , Simmons Will , Edgington Alec , Duncan Ross
Published: April 2020

We present t|ket⟩, a quantum software development platform produced by Cambridge Quantum Computing Ltd. The heart of t|ket⟩ is a language-agnostic optimising compiler designed to generate code for a variety of NISQ devices, which has several features designed to minimise the influence of device error. The compiler has been extensively benchmarked and outperforms most competitors in terms of circuit optimisation and qubit routing.
Effects of Prehypertensive Losartan Treatment on Resistance Vessel Remodeling and Angiotensin II Type 1 Receptor Expression in Spontaneously Hypertensive Rats
Authors: Wang Ting-jun , Chen Wan-ru , Lin Xu , Lian Gui-li , Xu Chang-sheng , Wang Hua-jun , Xie Liang-di
Published: April 2020

Background

To study the effects of prehypertensive losartan treatment on blood pressure, resistance vessel remodeling, and angiotensin II type 1 receptor (AT1R) expression in adult spontaneously hypertensive rats (SHRs).

Methods

Four-week-old SHR and Wistar-Kyoto rats were randomly divided into losartan-treated and untreated groups. Losartan was administrated by gavage from 4 to 10 weeks old. Blood pressure was monitored by the tail-cuff method till 26 weeks old. The third grade mesenteric arteries were then isolated. Vessel structure, relaxation reactivity, angiotensin II type 1 receptor expression, and angiotensin II levels were analyzed.

Results

Losartan treatment from 4 to 10 weeks of age significantly lowered systolic blood pressure from 10 to 26 weeks in SHR. At 26 weeks old, wall thickness to lumen radius and wall area to lumen area of mesenteric arteries were significantly lower in losartan-treated than untreated SHR (P < 0.01). Maximum relaxation to acetylcholine and its pD2 were increased in losartan-treated compared to untreated SHR (P < 0.01). Angiotensin II type 1 receptor mRNA and protein levels were significantly reduced in losartan-treated SHR (P < 0.01). However, angiotensin II levels in plasma and mesenteric arteries of losartan-treated SHR were higher than those of untreated SHR (P < 0.05). Losartan treatment lowered systolic blood pressure in Wistar-Kyoto at the age of 10 weeks (P < 0.05), but had no significant effect on blood pressure after 14 weeks or mesenteric arteries at 26 weeks.

Conclusions

Blood pressure reduction induced by prehypertensive losartan treatment ameliorates resistance vessel remodeling and downregulates angiotensin II type 1 receptor expression in adult SHR.
Federated sharing and processing of genomic datasets for tertiary data analysis
Authors: Canakoglu Arif , Pinoli Pietro , Gulino Andrea , Nanni Luca , Masseroli Marco , Ceri Stefano
Published: April 2020

Motivation

With the spreading of biological and clinical uses of next-generation sequencing (NGS) data, many laboratories and health organizations are facing the need of sharing NGS data resources and easily accessing and processing comprehensively shared genomic data; in most cases, primary and secondary data management of NGS data is done at sequencing stations, and sharing applies to processed data. Based on the previous single-instance GMQL system architecture, here we review the model, language and architectural extensions that make the GMQL centralized system innovatively open to federated computing.

Results

A well-designed extension of a centralized system architecture to support federated data sharing and query processing. Data is federated thanks to simple data sharing instructions. Queries are assigned to execution nodes; they are translated into an intermediate representation, whose computation drives data and processing distributions. The approach allows writing federated applications according to classical styles: centralized, distributed or externalized.

Availability

The federated genomic data management system is freely available for non-commercial use as an open source project at http://www.bioinformatics.deib.polimi.it/FederatedGMQLsystem/

Contact

{arif.canakoglu, pietro.pinoli}@polimi.it
Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis
Authors: Tao Yifeng , Lei Haoyun , Fu Xuecong , Lee Adrian V , Ma Jian , Schwartz Russell
Published: April 2020

Motivation

Cancer develops and progresses through a clonal evolutionary process. Understanding progression to metastasis is of particular clinical importance, but is not easily analyzed by recent methods because it generally requires studying samples gathered years apart, for which modern single-cell sequencing is rarely an option. Revealing the clonal evolution mechanisms in the metastatic transition thus still depends on unmixing tumor subpopulations from bulk genomic data.

Methods

We develop a novel toolkit called robust and accurate deconvolution (RAD) to deconvolve biologically meaningful tumor populations from multiple transcriptomic samples spanning the two progression states. RAD uses gene module compression to mitigate considerable noise in RNA, and a hybrid optimizer to achieve a robust and accurate solution. Finally, we apply a phylogenetic algorithm to infer how associated cell populations adapt across the metastatic transition via changes in expression programs and cell-type composition.

Results

We validated the superior robustness and accuracy of RAD over alternative algorithms on a real dataset, and validated the effectiveness of gene module compression on both simulated and real bulk RNA data. We further applied the methods to a breast cancer metastasis dataset, and discovered common early events that promote tumor progression and migration to different metastatic sites, such as dysregulation of ECM-receptor, focal adhesion and PI3k-Akt pathways.

Availability and implementation

The source code of the RAD package, models, experiments and technical details such as parameters, is available at https://github.com/CMUSchwartzLab/RAD.

Supplementary information

Supplementary data are available at Bioinformatics online.
Identifiability and experimental design in perturbation studies
Authors: Gross Torsten , Blüthgen Nils
Published: April 2020

Motivation

A common strategy to infer and quantify interactions between components of a biological system is to deduce them from the network’s response to targeted perturbations. Such perturbation experiments are often challenging and costly. Therefore, optimizing the experimental design is essential to achieve a meaningful characterization of biological networks. However, it remains difficult to predict which combination of perturbations allows to infer specific interaction strengths in a given network topology. Yet, such a description of identifiability is necessary to select perturbations that maximize the number of inferable parameters.

Results

We show analytically that the identifiability of network parameters can be determined by an intuitive maximum-flow problem. Furthermore, we used the theory of matroids to describe identifiability relationships between sets of parameters in order to build identifiable effective network models. Collectively, these results allowed to device strategies for an optimal design of the perturbation experiments. We benchmarked these strategies on a database of human pathways. Remarkably, full network identifiability was achieved, on average, with less than a third of the perturbations that are needed in a random experimental design. Moreover, we determined perturbation combinations that additionally decreased experimental effort compared to single-target perturbations. In summary, we provide a framework that allows to infer a maximal number of interaction strengths with a minimal number of perturbation experiments.

Availability and implementation

IdentiFlow is available at github.com/GrossTor/IdentiFlow.

Supplementary information

Supplementary data are available at Bioinformatics online.
Regression-adjusted average treatment effect estimates in stratified randomized experiments
Authors: Liu Hanzhong , Yang Yuehan
Published: April 2020

Linear regression is often used in the analysis of randomized experiments to improve treatment effect estimation by adjusting for imbalances of covariates in the treatment and control groups. This article proposes a randomization-based inference framework for regression adjustment in stratified randomized experiments. We re-establish, under mild conditions, the finite-population central limit theorem for a stratified experiment, and we prove that both the stratified difference-in-means estimator and the regression-adjusted average treatment effect estimator are consistent and asymptotically normal; the asymptotic variance of the latter is no greater and typically less than that of the former. We also provide conservative variance estimators that can be used to construct large-sample confidence intervals for the average treatment effect.
Effects of Growth Phase and Ultraviolet-B Pretreatment in Perilla Leaves on the Two-Spotted Spider Mite
Authors: Tomimori Daichi , Hosokawa Munetaka , Aoki Shinichi , Osakabe Masahiro
Published: April 2020

Perilla, Perilla frutescens (L.) Britton var. crispa (Thunb.) H. Deane, is traditionally cultivated as an edible/medicinal crop in East Asia. Its essential oil contains many bioactive compounds that are expected to have high pharmacological functionality, as well as antimicrobial and insecticidal activity. Spider mites are a major pest group for perilla cultivation. The two-spotted spider mite, Tetranychus urticae Koch, possesses divergent detoxification enzymes and has developed resistance against most acaricides. The essential oil content of perilla halves from the pre-flowering phase to the flowering phase, and ultraviolet (UV)-B radiation generally increases defense compounds. To clarify the effects of this change in essential oil content and the effects of UV-B pretreatment, we investigated the developmental success and egg production of T. urticae on leaves from the preflowering and flowering phases cultivated with and without nighttime UV-B irradiation. Both the parameters significantly increased on leaves from the flowering phase in comparison with that from the preflowering phase, suggesting that constitutively produced essential oil provided protection against mite pests in a growth phase-specific manner. The defense system also extended the developmental period of mites on red perilla leaves, but not on green perilla leaves, in preflowering phase. Although egg production was lower on red perilla leaves pretreated with UV-B, no negative effects were caused on the developmental success and duration on red and green perilla and the egg production on green perilla by UV-B pretreatment. Our findings reveal a significant impact of investment allocation of perilla plants and a small contribution of UV-B irradiation to the plant defense system.
Oesophageal-pericardial fistula: a rare complication of radiation-induced oesophagitis
Authors: Denglos Pauline , Nuytens Frederiek , Piessen Guillaume
Published: April 2020

Oesophageal-pericardial fistula after radiation therapy for lung cancer is a rare complication associated with a high mortality. In this case report, we present the case of 52-year-old women with late radiation-induced oesophagitis after chemoradiotherapy for a pulmonary adenocarcinoma, complicated by an oesophageal-pericardial fistula for which a transthoracic oesophagectomy with pericardial drainage was performed. The postoperative course was complicated by a fatal hypovolaemic shock due to a perforation of the descending aorta near the initial fistula track. In this case report, we illustrate the importance of thorough inspection of diagnostic images in this context and emphasize the role of endovascular repair in case an associated aortic perforation is suspected.
Two-step treatment of dysphagia lusoria: robotic-assisted resection of aberrant right subclavian artery following aortic debranching
Authors: La Regina Davide , Prouse Giorgio , Mongelli Francesco , Pini Ramon
Published: April 2020

A 69-year-old female suffering from severe dysphagia due to an aberrant right subclavian artery was treated with a two-step approach. A right carotid-subclavian bypass was followed 2 weeks later by a robotic-assisted thoracoscopic resection of the aberrant right subclavian artery. The postoperative course was uneventful, and the patient immediately recovered from her dysphagia. In our case, the robotic-assisted technology offered major advantages and, based on our experience, may be useful in the treatment of this rare disease.
Haemorrhagic stroke and major bleeding after intervention with biological aortic valve prosthesis: risk factors and antithrombotic treatment
Authors: Christersson Christina , Ståhle Elisabeth , Lindhagen Lars , James Stefan
Published: April 2020

Introduction

The majority of patients with severe aortic stenosis are recommended intervention with a surgical biological prosthesis (bioSAVR) or a transcatheter aortic valve intervention (TAVI). The antithrombotic strategies after aortic valve intervention vary and include drugs targeting both platelets and the coagulation cascade. Long-term exposure and changes of antithrombotic treatment influence the risk of both bleeding and thromboembolic events.The aim was to describe an unselected sample of patients who have experienced haemorrhagic stroke and other major bleeding events after biological aortic prosthesis, their antithrombotic treatment and changes of treatments in relation to the bleeding event.All patients performing an bioSAVR or a TAVI 2008–2014 were identified in the SWEDEHEART registry and included in the study (n = 10 711). The outcome events were haemorrhagic stroke and other major bleeding event. Information of drug exposure was collected from the dispensed drug registry.The incidence rate of any bleeding event was 2.85/100 patient-years the first year after aortic valve intervention. Heart failure and atrial fibrillation were present more often in patients with a first haemorrhagic stroke or other major bleeding event compared to without. The proportion of exposure to warfarin was 28.7% vs. 21.3% in patients with and without a haemorrhagic stroke. Comparable figures were 31.2% vs. 19.0% in patients with and without other major bleeding event. During 1 month prior a haemorrhagic stroke or other major bleeding event 39.4% and 38.0%, respectively, of the patients not previously exposed to antithrombotic treatment started warfarin or single antiplatelet therapy.Major bleeding events are not uncommon after aortic valve intervention with a biological prosthesis. Evaluation of comorbidities and previous bleeding might improve risk stratification for bleeding in these elderly patients. The pattern of change of antithrombotic treatment was similar in the groups with and without a bleeding event and in most patients the antithrombotic regime was unchanged the month before an event.