bluuebunny/crossref_metadata_2025_split huggingface dataset:
Widespread non-modular overlapping codes in the coding regions*
Authors: Bergman Shaked , Tuller Tamir 
Published: January 2020

Abstract
Messenger RNAs (mRNAs) consist of a coding region (open reading frame (ORF)) and two untranslated regions (UTRs), 5′UTR and 3′UTR. Ribosomes travel along the coding region, translating nucleotide triplets (called codons) to a chain of amino acids. The coding region was long believed to mainly encode the amino acid content of proteins, whereas regulatory signals reside in the UTRs and in other genomic regions. However, in recent years we have learned that the ORF is expansively populated with various regulatory signals, or codes, which are related to all gene expression steps and additional intracellular aspects. In this paper, we review the current knowledge related to overlapping codes inside the coding regions, such as the influence of synonymous codon usage on translation speed (and, in turn, the effect of translation speed on protein folding), ribosomal frameshifting, mRNA stability, methylation, splicing, transcription and more. All these codes come together and overlap in the ORF sequence, ensuring production of the right protein at the right time.
Penetration Depth of Free Falling Intruder into a Particles Bed in Fluid-Immersed Two-Dimension Spherical Particle System
Authors: Viridi S , Sanny T A 
Published: January 2020

Abstract
In a system of spherical particles which is entirely immersed in fluid, an intruder is let free fall into the particles bed consisted of 220 particles with height about 13 particles diameter and width about 15 particles diameter, both are in average. The system is placed in a container with height of 40 cm and width of 15 cm. Bed particles have the same diameter of 1 cm, while the intruder has 4 cm. Water is the fluid with density of 1 g/cm3 and viscosity of 8.90×10−4 Pa·s, which is assumed to constant during the simulation. Intruder initial height is always the same and bed particles are let to be relaxed for about 2 s from its initial random configuration of 20×11 in height and width of bed particle diameter, before the intruder is dropped into the system. Bed particles has always the same density about 2 g/cm3, while intruder density ρ
int is varied from 2 to 4.5 g/cm3 with increment of 0.5 g/cm3. It is observed that higher ρ
int gives higher penetration depth after the density of 2.5 g/cm3. Density of 4.5 g/cm3 and beyond will give similar final result, since the intruder already reached bottom of the container. An empirical model for penetration depth as function of ρ
int is proposed.
Ultraviolet (UV) Activation Effect on Antibacterial Agents of Red Betel (Piper Crocatum) Extract to Streptococcus mutans
Authors: Dyah Astuti Suryani , Dysan Tirtana Rio , Fitriana Mahmud Amalia , Mawaddah Amiliyatul , Abdurachman  , Yasin Moh. 
Published: January 2020

Abstract
Ultraviolet (UV) radiation has caused negative effect on biological environment. As non–moving living things, plants have their own response to reduce the negative effect by increasing flavonoid accumulation, such as red betel (Piper crocatum), which help the plant’s protection from bacteria. In Indonesia, red betel has been used as a herb treatment, especially in oral treatment. This study aims to optimise the antibacterial effect of red betel extract on oral bacteria, Streptococcus mutans, by irradiating UV. Kirby-Bauer method of disk diffusion test was used on this study by showing the bacteria’s diameter of inhibition zone. The samples distribution was devided into two groups, group (L–R+), control group, only used red betel extract without UV irradiation and group (L+R+) treatment combination of UV irradiation and red betel extract. The results showed that group L+R+ had better antibacterial effect on Streptococcus mutans, proven by the bigger inhibition zone, than group L–R+. UV irradiation for 12 hours showed the best result on each treatment with diameter of inhibition zone (15.00 ± 0.05) mm for 10 watt and (15.96 ± 0.05) mm for 15 watt. So, it is proven that UV irradiation can increase the antibacterial effect of red betel extract.
Theoretical Study on Radiationless Decay in Butadiene Isomerization Case using First-principles Calculation
Authors: Fadilla R N , Jannah A N , Febriana F N , Munir S , Zaidan A H 
Published: January 2020

Abstract
This study is to learn the radiation-less decay in butadiene isomerization from skew- to trans- conformation based on energy level diagram. We construct energy level diagram to determine the energy difference of butadiene in transition geometry between ground state and excited state with the basis of first-principles calculations. We use density functional theory for ground state butadiene while configuration interaction and complete active space for the excited state. The result is that the energy difference is 0.005 eV. It implies that there is degeneration occurred at the transition state of butadiene between its ground state and excited state. We conclude that conical intersection may occurs in the butadiene isomerization reaction.
Approximation Rectangular Function as Potential Barrier
Authors: Wardani I , Aisyah N D , Supardi A 
Published: January 2020

Abstract
Quantum tunneling occurs in the isomerization of hydroxymethylene into formaldehyde. Experiments and theory have proven the occurrence of it but both of them have a different result of the half-life of 0.7 hours. The differences the result is the motivation in this study. In theoretical, the probability of quantum tunneling calculates by Wentzel, Kreamer, Berlioun (WKB) approximation. This study calculates probability quantum tunneling use WKB and rectangular function approximation. The calculation of quantum tunneling probability with rectangular function approximation started at 1, 3, 5, 7 until 59 rectangular functions potential barrier use transfer matrix method to simplify the calculation. We use Gaussian function as the potential barrier that the height and width of the potential barrier satisfy the character of the potential barrier in isomerization hydroxymethylene barrier to formaldehyde. And the result, we get the minimum number of rectangular potential barrier to obtain a stable quantum tunneling probability value of 35 potential.
D-band Center Theory for the Case of Hydrogen Atom Adsorption on Fe(100) and Al(100) Surfaces: A Density Functional Study
Authors: Aji Eko Prabowo Wahyu , Khoiroh Nikmatul , Wibisono Satriyaji , Supardi Adri 
Published: January 2020

Abstract
The adsorption process occurs in technology that involves the surface. This study aims at investigating the adsorption of hydrogen atom on iron (Fe) and aluminium (Al) surfaces by using d-band center theory based-on density functional theory (DFT) method. DBC theory has proven very useful to understand the formation bond and the tendency of reactivity of transition metal which can learn by electronic structure system. This study obtained electronic structure system which is described by projected density of states (PDOS) using a system that consist of hydrogen atom adsorbed on Fe and Al surfaces. The result of PDOS used to explain the results of adsorption energy. The antibonding states on Fe surface were unfilled, meanwhile on Al surface were filled. Those results was suitable with the adsorption energy calculation results which showed that the bond between hydrogen and Fe surface was stronger than the bond between hydrogen and Al surface.
Temperature Effect of Chemical Bath Deposition (CBD) to Fabrication and Characterization of Zinc Oxide Nanorods Thin Films Based Gas Sensing: Ethanol
Authors: Ramadhan Adimas , Wulan Septiani Ni Luh , Aji Eko Prabowo Wahyu , Melati Asih 
Published: January 2020

Abstract
Fabrication of zinc oxide (ZnO) nanorods thin films based gas sensing ethanol have been done. Ethanol belongs to volatile organic compound (VOC) that are dangerous if inhaled by humans in high concentrations, so that its detection is necessary. Temperature as kinetic controller of chemical bath deposition (CBD) process take effect to ZnO fabrication and characterization. ZnO nanorods thin films was synthesized onto glass substrate by dip-coating technique. ZnO nanorods was grown using Zn(NO3)2.4H2O and HMTA with ratio 1:1 under CBD condition at temperature 75°C, 83°C, and 87°C. Result of SEM showing ZnO CBD 83°C has nanorods shape with diameter size is 95.56 nm, furthermore at 75°C the formation of the nanorods was not completed yet while at nanorods became deconstructed. XRD result showed all of ZnO sample have hexagonal wurzite which are match well with ICDS-094004 card. Ethanol gas sensing tested at 100°C, 150°C, 200°C showed high sensitivity of the sensor up to 77.31% for ZnO CBD 75°C at 100°C. ZnO CDB 83°C sample at test 200°C have highest response on 2.22 min (tres) and 0.45 min (trec). Time respond and recovery will increase along with increasing of test temperature.
Determination of Infrared Laser Energy Dose for Cancer Cells Inactivation as a Candidate of Photodynamic Therapy
Authors: Kholimatussa’diah Septia , Dyah Astuti Suryani , Apsari Retna 
Published: January 2020

Abstract
The aim of this research is to find out the effect of GaAlAs diode laser 808 nm exposure on MCF-7 breast cancer cells in vitro with and without the addition of a photosensitizer. Methylene blue (C16H18N3SCl) with concentration of 2 µM is used as the photosensitizer based on the preliminary results of cytotoxicity assay. Energy dose is set in the range of 23, 043 to 322, 062 J/cm2. Laser exposure with the addition of the photosensitizer generates the highest percentage of cell death of 20.80% at energy dose of 184, 344 J/cm2 and cell death begin to decrease at energy dose above this value. This behavior is likely caused by photodegradation and photobleaching effect of the photosensitizer due to the longer exposure time. However, the percentage of cell death without the addition of photosensitizer is increased proportionally to the increase of energy dose and achieved 32, 45% cell mortality at 299, 559 J/cm2. This study not only shows that the exposure of infrared laser can be used to inactivate cancer cells but also determines its optimum energy dose, makes it a possible candidate for photodynamic therapy in the future.
Electrospun Collagen-based Scaffold as Therapeutic Agent for Ocular Chemical Injury
Authors: Hasbiyani N A F , Hikmawati D , Siswanto  
Published: January 2020

Abstract
Ocular chemical injury hit on cornea and conjunctiva due to chemical contact. This injury damages to the epithelial surface of the eye, cornea, anterior segment and permanent unilateral or bilateral permanent viscous damage). Nowadays, human amniotic membrane, allograft biomaterials is used as the treatment for the injury. However, this method has many obstacles. Collagen-based Scaffold is a new study of electrospinning membrane made of collagen, hyaluronic acid, and polyethylene oxide. This research is aimed to obtain the optimum concentration of polymer solution that produces the best morphology in the formation of electrospun collagen-based scaffold. The result show that the fiber had mean diameter of 212, 63 nm to 500, 8 nm and mean pore diameter 498, 56 until 2788 nm. FTIR test shows the loss of functional groups Amide A and Amide II indicate successful crosslinking process with glutaraldehyde. The cytotoxicity test showed electrospun collagen-based scaffold was nontoxic.
Expert System for Stroke Classification Using Naive Bayes Classifier and Certainty Factor as Diagnosis Supporting Device
Authors: Ain Khusnul , Hidayati Hanik B. , Aulia Nastiti Olivia 
Published: January 2020

Abstract
Stroke is a disease that has high mortality rate in Indonesia and worldwide. This disease is dangerous if not immediately treated because the brain circulatory disorder can cause a permanent disability or death. Diagnosis process of stroke disease can be assisted by an expert system using Naive Bayes Classifier and Certainty Factor. Decision making by Naive Bayes Classifier uses total probability value of all the diagnostic criteria on the existing database. Certainty Factor uses a weight value combination from measure of believe provided by expert. This expert system research aims to assist in the early diagnosis of a neurologist in diagnosing potential stroke patient from several diagnostic criteria as well as determine the accuracy of the expert system program created. The sample used in this study are the hospital medical records of 130 patients from Dr. Soetomo Hospital of Surabaya consists of 80 stroke patients data and 50 non-stroke patients data. Expert system program uses 12 category for diagnosis as an input and two statement outputs between stroke or non-stroke. Based on the analysis from the 25 testing data of 105 training data we obtained the accuracy of the method Naive Bayes classifier by 96% and of the method of Certainty Factor of 84%. Expert system program using Naive Bayes Classifier and Certainty Factor can be a device for stroke diagnosis.
The nitrogen footprint of organic food in the United States
Authors: Cattell Noll Laura , Leach Allison M , Seufert Verena , Galloway James N , Atwell Brooke , Erisman Jan Willem , Shade Jessica 
Published: January 2020

Abstract
We estimated the reactive nitrogen (Nr) lost per unit food Nr consumed for organic food production in the United States and compared it to conventional production. We used a nitrogen footprint model approach, which accounts for both differences in Nr losses as well as differences in productivity of the two systems. Additionally, we quantified the types of Nr inputs (new versus recycled) that are used in both production systems. We estimated Nr losses from organic crop and animal production to be of comparable magnitude to conventional production losses, with the exception of beef. While Nr losses from organic vegetables are possibly higher (+37%), Nr losses from organic grains, starchy roots, legumes are likely of similar magnitude to conventional production (+7%, +6%, −12%, respectively). Nr losses from organic poultry, pigmeat, and dairy production are also likely comparable to conventional production (+9%, +10%, +12%, respectively), while Nr losses from organic beef production were estimated to be higher (+124%). Due to the high variability and high uncertainty in Nr efficiency in both systems we cannot make conclusions yet on the statistical significance of these potential differences. Conventional production relies heavily on the creation of new Nr (70%–90% of inputs are from new Nr sources like synthetic fertilizer), whereas organic production primarily utilizes already existing Nr (0%–50% of organic inputs are from new Nr sources like leguminous N fixation). Consuming organically produced foods has little impact on an individual’s food N footprint but changes the percentage of new versus recycled Nr in the footprint. With the exception of beef, Nr losses from organic production per unit N in product are comparable to conventional production. However, organic production requires the creation of less new Nr, which could reduce global Nr pollution.
Exploring China’s energy situation through One Belt And One Road
Authors: Gholizadeh Ali , Gong Yilin , Huang Qiang 
Published: January 2020

Abstract
Energy refers to various resources that can be directly obtained or be obtained through processing or conversion, including coal, crude oil, natural gas, coal-bed methane, water energy, nuclear energy, wind energy, solar energy, geothermal energy, biomass energy and other primary energy, electricity, thermal energy, refined oil and other secondary energy, as well as other new and renewable energy. Energy is an important material basis of national economy, and the future national destiny depends on the control of energy. The development and efficient use of energy and per capita consumption are important indicators of production technology and living standards. This paper analyzes the relationship between China’s energy status and One Belt And One Road security from the aspects of China’s energy status, China’s energy consumption in the next 30 years, China’s various energy basic conditions and important energy policies related to countries along the silk road. It is found that “The Belt And Road” strategy provides support and conditions for China’s energy development.
Challenges for product development of wind turbines from the current market situation in Germany
Authors: Wiener Philipp , Nicoleit Thomas 
Published: January 2020

Abstract
The qualitative results of this empirical thesis are the four superior challenges “reduced time for development”, “integration of the value chain”, “reduction of complexity” and “digital transformation”, which apply to the product development of wind turbines. It is assumed that these superior challenges apply to a variety of business areas rather than only for the product development. Recommendations for actions to reduce the time for development are “customized integration of agile approaches”, “break down silo mentality” and “optimization of the innovation culture”. For the integration of the value chain in the product development process, an “establishment of a common basis of trust”, “establishment of multi-company development networks” and an “increase of compatibility of different tools and process automation” are recommended. A reduction of complexity can be achieved with an “expansion of the available capacities in predevelopment” and “development of long-term multi-platform strategies”. The challenges and possible solution approaches for “digital transformation” need further investigation, but it is clear to advise to “ensure access to operational data through digital business models or service contracts”.
Greenhouse gas emissions comparison of solid waste transportation system: a case study in Thailand
Authors: Koiwanit J , Hamontree C 
Published: January 2020

Abstract
During the early periods of civilization, solid waste was conveniently collected transported and disposed because of the low number of population. However, waste generation is expected to increase becasue of rapid population growth and consequently shows an increase in solid waste collection, transportation, and disposal. Waste transportation planning is a difficult task due to the issues of the increasing numbers of garbage vehicles and the fluctuation of fuel prices as well as the cost-effectiveness and health and environmental impacts. An unsustainable waste collection and transportation is heading towards a variety of indirect human health impacts. Accordingly, the vehicle routing problem (VRP) plays a significant role in the field of waste collection and transportation system. This study compares three different Life Cycle Assessment (LCA approaches for the waste transport in Ladkrabang, Bangkok, Thailand. The three scenarios are modelled using GaBi 7 software tool and results are presented based on the CML 2001. The assessment outcomes indicated that the routing optimization with diesel and electric garbage trucks could significantly reduce the GWP impact by 8.51% and 66.44% compared to the baseline scenario, respectively.
Simplified methods of monitoring airborne bacteria for quality and environmental management in the Japanese food industry
Authors: Liu Ze , Tanaka Takehiro , Fujii Shuji 
Published: January 2020

Abstract
Airborne microbes are examined generally by sampling them on culture media and counting the number of their colonies formed. However, because it takes at least two days for bacteria and five days for fungi to be cultivated, reliable data may not be obtained in a time of need. Therefore, the development of simple and quick detection methods is required. In this study, rapid detection methods of indoor airborne bacteria for the improvement of quality and environmental management were reviewed, and a basic study on simplified monitoring techniques of airborne bacteria applicable to food factories was carried out.
Effectiveness of conventional wastewater treatment processes in removing pharmaceutically active compounds
Authors: Maraqa M A , Meetani M , Alhalabi A M 
Published: January 2020

Abstract
Limited work has been done to assess the types and levels of PACs in domestic and treated wastewater in arid and semi-arid countries. In these countries, reuse or artificial recharge of treated sewage effluent is commonly practiced. Thus, the objectives of this study were to quantify the levels of selected PACs in domestic wastewater in the United Arab Emirates (UAE) and to assess the effectiveness of domestic wastewater treatment plants in their removal. An analytical protocol was developed for the analysis of 15 PACs using a UPLC-MS/MS system. Four batches of water and sludge samples were collected from different locations at Al Saad Wastewater Treatment Plant in Al Ain, UAE. Aliquots of each sample were enriched by solid phase extraction. Results show that phenylephrine, dapsone, noscapine, propyl gallate, genistein, and ketoconazole were present in the raw wastewater at low levels (<0.1 μg/L), while acetaminophen and caffeine were present at high levels (>10 μg/L). The overall removal efficiency of the tested PACs from the water stream exceeded 99% for cotinine, acetaminophen, caffeine, naproxen, and ibuprofen, but significantly drops (<50%) for phenylephrine, amoxicillin, dapsone, noscapine, spiramycin, noscapine, genistein and ketoconazole. Analysis of the results indicate that, for highly removed PACs, the main mechanism of removal is possibly aerobic biodegradation. However, for tyramine, dapsone, 9-aminoacridine, noscapine, propyl gallate, and ketoconazole sorption onto the mixed liquor suspended solids first occurs followed by removal by anaerobic digestion. Results of the study should be useful for properly managing treated sewage effluent and sewage sludge.
Characteristics of Cellulose Acetate/Polyethylene Glycol membrane with the addition of Graphene Oxide by using surface coating method
Authors: Nurkhamidah S , Devi B C , Febriansyah B A , Ramadhani A , Nyamiati R D , Rahmawati Y , Chafidz A 
Published: January 2020

Abstract
Fabrication of membrane for desalination process with high performance is the objective of this study. The addition of Graphene Oxide (GO) in cellulose acetate/polyethylene glycol (CA/PEG) with a ratio of 80:20 was prepared by a surface coating method. In this study, the composition of GO was compared, with composition ranging from 0.0025 to 0.0125 wt% to the mass of the solvent. The characteristics of membranes were observed by using Scanning Electron Microscopy (SEM), Fourier-Transformed Infra-Red (FTIR), contact angle analysis and Dynamic Mechanical Analysis (DMA). While its performance was observed by analyzing salt rejection, flux permeate and permeability of the membranes. SEM analysis shows that membrane exhibits asymmetric membrane with sponge-like structure. FTIR results show that the peak area of –OH bonding decreases with the addition of GO. This result is in agreement with the contact angle analysis. The experiment results shows that membrane with the best performance is CA/PEG membrane with the addition of 0.01 wt% GO with salt rejection (%R) of 37%, flux permeate (F) of 1356 L/m2.h, and permeability (P) of 0.0013 L/m2.h.kPa.