bluuebunny/crossref_metadata_2025 huggingface dataset:
Prey-size plastics are invading larval fish nurseries
Authors: Gove Jamison M. , Whitney Jonathan L. , McManus Margaret A. , Lecky Joey , Carvalho Felipe C. , Lynch Jennifer M. , Li Jiwei , Neubauer Philipp , Smith Katharine A. , Phipps Jana E. , Kobayashi Donald R. , Balagso Karla B. , Contreras Emily A. , Manuel Mark E. , Merrifield Mark A. , Polovina Jeffrey J. , Asner Gregory P. , Maynard Jeffrey A. , Williams Gareth J.
Published: November 2019

Life for many of the world’s marine fish begins at the ocean surface. Ocean conditions dictate food availability and govern survivorship, yet little is known about the habitat preferences of larval fish during this highly vulnerable life-history stage. Here we show that surface slicks, a ubiquitous coastal ocean convergence feature, are important nurseries for larval fish from many ocean habitats at ecosystem scales. Slicks had higher densities of marine phytoplankton (1.7-fold), zooplankton (larval fish prey; 3.7-fold), and larval fish (8.1-fold) than nearby ambient waters across our study region in Hawai‘i. Slicks contained larger, more well-developed individuals with competent swimming abilities compared to ambient waters, suggesting a physiological benefit to increased prey resources. Slicks also disproportionately accumulated prey-size plastics, resulting in a 60-fold higher ratio of plastics to larval fish prey than nearby waters. Dissections of hundreds of larval fish found that 8.6% of individuals in slicks had ingested plastics, a 2.3-fold higher occurrence than larval fish from ambient waters. Plastics were found in 7 of 8 families dissected, including swordfish (Xiphiidae), a commercially targeted species, and flying fish (Exocoetidae), a principal prey item for tuna and seabirds. Scaling up across an ∼1,000 km
2
coastal ecosystem in Hawai‘i revealed slicks occupied only 8.3% of ocean surface habitat but contained 42.3% of all neustonic larval fish and 91.8% of all floating plastics. The ingestion of plastics by larval fish could reduce survivorship, compounding threats to fisheries productivity posed by overfishing, climate change, and habitat loss.
mRNA structure regulates protein expression through changes in functional half-life
Authors: Mauger David M. , Cabral B. Joseph , Presnyak Vladimir , Su Stephen V. , Reid David W. , Goodman Brooke , Link Kristian , Khatwani Nikhil , Reynders John , Moore Melissa J. , McFadyen Iain J.
Published: November 2019

Messenger RNAs (mRNAs) encode information in both their primary sequence and their higher order structure. The independent contributions of factors like codon usage and secondary structure to regulating protein expression are difficult to establish as they are often highly correlated in endogenous sequences. Here, we used 2 approaches, global inclusion of modified nucleotides and rational sequence design of exogenously delivered constructs, to understand the role of mRNA secondary structure independent from codon usage. Unexpectedly, highly expressed mRNAs contained a highly structured coding sequence (CDS). Modified nucleotides that stabilize mRNA secondary structure enabled high expression across a wide variety of primary sequences. Using a set of eGFP mRNAs with independently altered codon usage and CDS structure, we find that the structure of the CDS regulates protein expression through changes in functional mRNA half-life (i.e., mRNA being actively translated). This work highlights an underappreciated role of mRNA secondary structure in the regulation of mRNA stability.
Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis
Authors: Chekan Jonathan R. , Ongpipattanakul Chayanid , Nair Satish K.
Published: November 2019

Enzymes that generate ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products have garnered significant interest, given their ability to produce large libraries of chemically diverse scaffolds. Such RiPP biosynthetic enzymes are predicted to bind their corresponding peptide substrates through sequence-specific recognition of the leader sequence, which is removed after the installation of posttranslational modifications on the core sequence. The conservation of the leader sequence within a given RiPP class, in otherwise disparate precursor peptides, further supports the notion that strict sequence specificity is necessary for leader peptide engagement. Here, we demonstrate that leader binding by a biosynthetic enzyme in the lasso peptide class of RiPPs is directed by a minimal number of hydrophobic interactions. Biochemical and structural data illustrate how a single leader-binding domain can engage sequence-divergent leader peptides using a conserved motif that facilitates hydrophobic packing. The presence of this simple motif in noncognate peptides results in low micromolar affinity binding by binding domains from several different lasso biosynthetic systems. We also demonstrate that these observations likely extend to other RiPP biosynthetic classes. The portability of the binding motif opens avenues for the engineering of semisynthetic hybrid RiPP products.
A DNA virus-encoded immune antagonist fully masks the potent antiviral activity of RNAi in
Drosophila
Authors: Bronkhorst Alfred W. , Vogels Rob , Overheul Gijs J. , Pennings Bas , Gausson-Dorey Valérie , Miesen Pascal , van Rij Ronald P.
Published: November 2019

Coevolution of viruses and their hosts may lead to viral strategies to avoid, evade, or suppress antiviral immunity. An example is antiviral RNA interference (RNAi) in insects: the host RNAi machinery processes viral double-stranded RNA into small interfering RNAs (siRNAs) to suppress viral replication, whereas insect viruses encode suppressors of RNAi, many of which inhibit viral small interfering RNA (vsiRNA) production. Yet, many studies have analyzed viral RNAi suppressors in heterologous systems, due to the lack of experimental systems to manipulate the viral genome of interest, raising questions about in vivo functions of RNAi suppressors. To address this caveat, we generated an RNAi suppressor-defective mutant of invertebrate iridescent virus 6 (IIV6), a large DNA virus in which we previously identified the 340R protein as a suppressor of RNAi. Loss of 340R did not affect vsiRNA production, indicating that 340R binds siRNA duplexes to prevent RNA-induced silencing complex assembly. Indeed, vsiRNAs were not efficiently loaded into Argonaute 2 during wild-type IIV6 infection. Moreover, IIV6 induced a limited set of mature microRNAs in a 340R-dependent manner, most notably miR-305–3p, which we attribute to stabilization of the miR-305–5p:3p duplex by 340R. The IIV6 340R deletion mutant did not have a replication defect in cells, but was strongly attenuated in adult
Drosophila
. This in vivo replication defect was completely rescued in RNAi mutant flies, indicating that 340R is a bona fide RNAi suppressor, the absence of which uncovers a potent antiviral immune response that suppresses virus accumulation ∼100-fold. Together, our work indicates that viral RNAi suppressors may completely mask antiviral immunity.
Hepatocyte nuclear factor-1β regulates Wnt signaling through genome-wide competition with β-catenin/lymphoid enhancer binding factor
Authors: Chan Siu Chiu , Zhang Ying , Pontoglio Marco , Igarashi Peter
Published: November 2019

Hepatocyte nuclear factor-1β (HNF-1β) is a tissue-specific transcription factor that is essential for normal kidney development and renal tubular function. Mutations of HNF-1β produce cystic kidney disease, a phenotype associated with deregulation of canonical (β-catenin–dependent) Wnt signaling. Here, we show that ablation of HNF-1β in mIMCD3 renal epithelial cells produces hyperresponsiveness to Wnt ligands and increases expression of Wnt target genes, including
Axin2
,
Ccdc80
, and
Rnf43
. Levels of β-catenin and expression of Wnt target genes are also increased in HNF-1β mutant mouse kidneys. Genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) in wild-type and mutant cells showed that ablation of HNF-1β increases by 6-fold the number of sites on chromatin that are occupied by β-catenin. Remarkably, 50% of the sites that are occupied by β-catenin in HNF-1β mutant cells colocalize with HNF-1β–occupied sites in wild-type cells, indicating widespread reciprocal binding. We found that the Wnt target genes
Ccdc80
and
Rnf43
contain a composite DNA element comprising a β-catenin/lymphoid enhancer binding factor (LEF) site overlapping with an HNF-1β half-site. HNF-1β and β-catenin/LEF compete for binding to this element, and thereby HNF-1β inhibits β-catenin–dependent transcription. Collectively, these studies reveal a mechanism whereby a transcription factor constrains canonical Wnt signaling through direct inhibition of β-catenin/LEF chromatin binding.
Fast fit-free analysis of fluorescence lifetime imaging via deep learning
Authors: Smith Jason T. , Yao Ruoyang , Sinsuebphon Nattawut , Rudkouskaya Alena , Un Nathan , Mazurkiewicz Joseph , Barroso Margarida , Yan Pingkun , Intes Xavier
Published: November 2019

Fluorescence lifetime imaging (FLI) provides unique quantitative information in biomedical and molecular biology studies but relies on complex data-fitting techniques to derive the quantities of interest. Herein, we propose a fit-free approach in FLI image formation that is based on deep learning (DL) to quantify fluorescence decays simultaneously over a whole image and at fast speeds. We report on a deep neural network (DNN) architecture, named fluorescence lifetime imaging network (FLI-Net) that is designed and trained for different classes of experiments, including visible FLI and near-infrared (NIR) FLI microscopy (FLIM) and NIR gated macroscopy FLI (MFLI). FLI-Net outputs quantitatively the spatially resolved lifetime-based parameters that are typically employed in the field. We validate the utility of the FLI-Net framework by performing quantitative microscopic and preclinical lifetime-based studies across the visible and NIR spectra, as well as across the 2 main data acquisition technologies. These results demonstrate that FLI-Net is well suited to accurately quantify complex fluorescence lifetimes in cells and, in real time, in intact animals without any parameter settings. Hence, FLI-Net paves the way to reproducible and quantitative lifetime studies at unprecedented speeds, for improved dissemination and impact of FLI in many important biomedical applications ranging from fundamental discoveries in molecular and cellular biology to clinical translation.
Mutant p53 antagonizes p63/p73-mediated tumor suppression via Notch1
Authors: Zhang Jin , Sun Wenqiang , Kong Xiangmudong , Zhang Yanhong , Yang Hee Jung , Ren Cong , Jiang Yuqian , Chen Mingyi , Chen Xinbin
Published: November 2019

Significance

Despite studies have shown that mutant p53 acquires its GOF by suppressing p63 and p73, the hypothesis has not been tested in vivo and the underlying mechanism is not fully understood. Here, by using mutant p53-R270H knockin and
TAp63/p73
-deficient mouse models, we showed that KI mutant p53-R270H antagonizes p63/p73 to shorten mouse life span and to promote T lymphoblastic lymphomagenesis. Mechanistically, we showed that mutant p53 collaborates with the Notch1 intracellular domain (NICD) to abrogate p63/p73-mediated repression of HES1 and ECM1. As a result, HES1 and ECM1 are overexpressed, leading to lymphomagenesis. Thus, we identify a context where mutant p53 contributes to pathogenesis of T lymphoblastic lymphoma by collaborating with the Notch1 pathway to hijack the p63/p73-regulated transcriptional program.
Neural progenitor cells mediated by H2A.Z.2 regulate microglial development via Cxcl14 in the embryonic brain
Authors: Li Zhongqiu , Li Yanxin , Jiao Jianwei
Published: November 2019

Microglia, the resident immune cells of the central nervous system, play an important role in the brain. Microglia have a special spatiotemporal distribution during the development of the cerebral cortex. Neural progenitor cells (NPCs) are the main source of neural-specific cells in the early brain. It is unclear whether NPCs affect microglial development and what molecular mechanisms control early microglial localization. H2A.Z.2, a histone variant of H2A, has a key role in gene expression regulation, genomic stability, and chromatin remodeling, but its function in brain development is not fully understood. Here, we found that the specific deletion of H2A.Z.2 in neural progenitor cells led to an abnormal increase in microglia in the ventricular zone/subventricular zone (VZ/SVZ) of the embryonic cortex. Mechanistically, H2A.Z.2 regulated microglial development by incorporating G9a into the promoter region ofCxcl14and promoted H3k9me2 modification to inhibit the transcription ofCxcl14in neural progenitor cells. Meanwhile, we found that the deletion of H2A.Z.2 in microglia itself had no significant effect on microglial development in the early cerebral cortex. Our findings demonstrate a key role of H2A.Z.2 in neural progenitor cells in controlling microglial development and broaden our knowledge of 2 different types of cells that may affect each other through crosstalk in the central nervous system.
Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration
Authors: Voigt Andrew P. , Mulfaul Kelly , Mullin Nathaniel K. , Flamme-Wiese Miles J. , Giacalone Joseph C. , Stone Edwin M. , Tucker Budd A. , Scheetz Todd E. , Mullins Robert F.
Published: November 2019

The human retinal pigment epithelium (RPE) and choroid are complex tissues that provide crucial support to the retina. Disease affecting either of these supportive tissues can lead to irreversible blindness in the setting of age-related macular degeneration. In this study, single-cell RNA sequencing was performed on macular and peripheral regions of RPE-choroid from 7 human donor eyes in 2 independent experiments. In the first experiment, total RPE/choroid preparations were evaluated and expression profiles specific to RPE and major choroidal cell populations were identified. As choroidal endothelial cells represent a minority of the total RPE/choroidal cell population but are strongly implicated in age-related macular degeneration (AMD) pathogenesis, a second single-cell RNA-sequencing experiment was performed using endothelial cells enriched by magnetic separation. In this second study, we identified gene expression signatures along the choroidal vascular tree, classifying the transcriptome of human choriocapillaris, arterial, and venous endothelial cells. We found that the choriocapillaris highly and specifically expresses the regulator of cell cycle gene (
RGCC
), a gene that responds to complement activation and induces apoptosis in endothelial cells. In addition,
RGCC
was the most up-regulated choriocapillaris gene in a donor diagnosed with AMD. These results provide a characterization of the human RPE and choriocapillaris transcriptome, offering potential insight into the mechanisms of choriocapillaris response to complement injury and choroidal vascular disease in age-related macular degeneration.
Probing the rice Rubisco–Rubisco activase interaction via subunit heterooligomerization
Authors: Shivhare Devendra , Ng Jediael , Tsai Yi-Chin Candace , Mueller-Cajar Oliver
Published: November 2019

During photosynthesis the AAA+ protein and essential molecular chaperone Rubisco activase (Rca) constantly remodels inhibited active sites of the CO
2
-fixing enzyme Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) to release tightly bound sugar phosphates. Higher plant Rca is a crop improvement target, but its mechanism remains poorly understood. Here we used structure-guided mutagenesis to probe the Rubisco-interacting surface of rice Rca. Mutations in Ser-23, Lys-148, and Arg-321 uncoupled adenosine triphosphatase and Rca activity, implicating them in the Rubisco interaction. Mutant doping experiments were used to evaluate a suite of known Rubisco-interacting residues for relative importance in the context of the functional hexamer. Hexamers containing some subunits that lack the Rubisco-interacting N-terminal domain displayed a ∼2-fold increase in Rca function. Overall Rubisco-interacting residues located toward the rim of the hexamer were found to be less critical to Rca function than those positioned toward the axial pore. Rca is a key regulator of the rate-limiting CO
2
-fixing reactions of photosynthesis. A detailed functional understanding will assist the ongoing endeavors to enhance crop CO
2
assimilation rate, growth, and yield.
Challenging battles of plants with phloem-feeding insects and prokaryotic pathogens
Authors: Jiang Yanjuan , Zhang Chuan-Xi , Chen Rongzhi , He Sheng Yang
Published: November 2019

Significance

Piercing-sucking insects and phloem-inhabiting prokaryotic pathogens contribute to some of the world’s most disastrous crop losses, including those caused by the brown plant hopper in rice or citrus greening in citrus. For historic and technical reasons, our knowledge of phloem–insect/pathogen interactions remains fragmentary. We highlight recent progress and areas of deficiency in the study of phloem-associated prokaryotic pathogens and insects. Increased efforts are needed to make major advances in this historically understudied area of research.
Covariant BSSN formulation in bimetric relativity
Authors: Torsello Francesco , Kocic Mikica , Högås Marcus , Mörtsell Edvard
Published: November 2019

Numerical integration of the field equations in bimetric relativity is necessary to obtain solutions describing realistic systems. Thus, it is crucial to recast the equations as a well-posed problem. In general relativity, under certain assumptions, the covariant BSSN formulation is a strongly hyperbolic formulation of the Einstein equations, hence its Cauchy problem is well-posed. In this paper, we establish the covariant BSSN formulation of the bimetric field equations. It shares many features with the corresponding formulation in general relativity, but there are a few fundamental differences between them. Some of these differences depend on the gauge choice and alter the hyperbolic structure of the system of partial differential equations compared to general relativity. Accordingly, the strong hyperbolicity of the system cannot be claimed yet, under the same assumptions as in general relativity. In the paper, we stress the differences compared with general relativity and state the main issues that should be tackled next, to draw a roadmap towards numerical bimetric relativity.
Quantum confined Rydberg excitons in reduced dimensions
Authors: Konzelmann Annika , Frank Bettina , Giessen Harald
Published: November 2019

In this paper we propose first steps towards calculating the energy shifts of confined Rydberg excitons in

Cu

2

O

quantum wells, wires, and dots. The macroscopic size of Rydberg excitons with high quantum numbers

n

implies that already μm sized lamellar, wire-like, or box-like structures lead to quantum size effects, which depend on the principal Rydberg quantum number

n
.

Such structures can be fabricated using focused ion beam milling of cuprite crystals. Quantum confinement causes an energy shift of the confined object, which is interesting for quantum technology. We find in our calculations that the Rydberg excitons gain a potential energy in the μeV to meV range due to the quantum confinement. This effect is dependent on the Rydberg exciton size and, thus, the principal quantum number

n
.

The calculated energy shifts in the μeV to meV energy range should be experimentally accessible and detectable.
Progress of physics understanding for long pulse high-performance plasmas on EAST towards the steady-state operation of ITER and CFETR
Authors: Huang J , Gong X , Garofalo A M , Qian J , Chen J , Wu M , Li M , Yuan Q , Wang L , Pan C , Lin X , Yang Q , Ekedahl A , Maingi R , Holcomb C T , Li E , Zeng L , Zhang B , Chang J F , Zhang X J , Goniche M , Peysson Y , Zhu X , Sun Y , Xu G , Zang Q , Zhang L , Liu H , Lyu B , Ding R , Ren Q , Ding B , Guo W , Ding S , Xiang N , Liang Y , Liu F , Zhao Y , Xiao B , Hu J , Hu C , Hu L , Gao X , Fu P , Song Y , Zhang X D , Chan V , Li J , Wan B
Published: November 2019

Recently, the first ever 100 s long, steady-state H-mode discharge with good control of impurities, core and edge MHD stabilities, and heat exhaust was demonstrated in the Experimental Advanced Superconducting Tokamak (EAST) using the ITER-like (International Tokamak Experimental Reactor) tungsten upper divertor. Using both radio frequency (RF) power and neutral beam injection (NBI) heating, EAST has demonstrated fully non-inductive scenarios with an extension of fusion performance at high density and low rotation: β
P ∼ 2.5, β
N ∼ 2.0, H98,y2 ∼ 1.2, bootstrap current fraction fBS ∼50% at q95 ∼ 6.8. With pure RF power heating, plasmas have been maintained for up to 21 s (over 40 times the current relaxation time) with zero loop voltage and small edge localized modes (ELMs) at high density (ne/nGW ∼ 0.6–0.8), β
P ∼ 2.0, β
N ∼ 1.6, and ƒBS ∼47%. Experimental investigations show how plasma current profiles, turbulent transport and radiation properties self-consistently evolve toward fusion relevant steady state conditions. Modeling and physics experiments have confirmed the synergistic effects between electron cyclotron heating (ECH) and low hybrid wave (LHW), where ECH enhances the heating and current drive from LHW injection, enabling fully non-inductive operation at higher density. Small/no ELMs facilitate the RF power coupling in the H-mode phase and reduce divertor erosion. A low tungsten concentration was observed at high β
P with a hollow profile in the core. Reduction of the peak divertor heat flux with f
rad of up to 40% was compatible with the high β
P scenario by using active radiation feedback control. With features such as dominant electron heating, zero/low NBI torque and an ITER-like tungsten divertor, fully non-inductive high-performance experiments on EAST offer unique contributions towards the succesful operation of ITER and CFETR (the Chinese Fusion Engineering Testing Reactor).
Computational Analysis of Fluid Behaviour Around Airfoil With Navier-Stokes Equation
Authors: Tulus  , Khairani C , Marpaung T.J. , Suriati
Published: November 2019

A study of the development models and shapes of aircrafts component that undergo refinement process over time, must go through the analysis phase. The analysis can be solved by computation method which is supported by the development of numerical method. One important component of aircraft is airfoil. Airfoil is a part that influences the lifting force on the wing of the aircraft. Therefore, in this study should be conducted a study of three different forms of airfoil, about the behaviour of the fluid flow around it, numerically. The approach to fluid flow behaviour can be done using the Navier-Stokes equation. The airflow velocity around the airfoil is the fluid flow behaviour to be analysed, so the numerical solution can be obtained through Finite Element Method (FEM), then it is simulated with COMSOL Multiphysics 5.2a software. Thus, the simulation results will show the interrelations between the angle of attack (α) which varies with the maximum velocity distribution on each airfoil surface, and can be seen the most stable maximum velocity distribution among the three airfoil forms.
Comparison of Waves Reduction by Mangrove Avicennia Marina in East Lampung and Indah Kapuk Beach, Indonesia
Authors: Herison A , Bengen D G , Romdania Y , Kurniawati R
Published: November 2019

Mangrove Avicennia Marina has important role in wave reduction. The purpose of this research were: (1) To know wave energy ratio in Indah Kapuk Beach and East Lampung Regency, Indonesia. (2) To know the influence of Avicennia Marina mangrove’s respiratory roots on wave energy reduction. Measurement of wave in Indah Kapuk Beach used SBE26, in East Lampung used SBE26 and RBRDUO TD. Parameters were the structure of mangrove vegetation and wave energy reduction. The wave observed in Indah Kapuk Beach tends to be smaller than in East Lampung, so the influence of respiratory root in reducing wave in Indah Kapuk Beach was less visible while the influence of respiratory root in East Lampung was more clearly seen. The muffled wave in the Indah Kapuk Beach research was less visible due to the presence of inhibitors obstructing the incoming waves, while the reduced wave was more clearly measured in the study in East Lampung because without an inhibitors of wave coming.
Estimation of Settlement Induced Land Subsidence of Marine Clay on Kamal Muara Area, Northern Jakarta, Based on the Change of Pore Water Pressure
Authors: Taqwa F M L , Hutabarat L E , Ilyas T , Prakoso W A
Published: November 2019

Land subsidence phenomena which occurred in last 30 years in Jakarta affected by groundwater extraction, settlement of high compressibility soil such as marine clay, natural consolidation of alluvial soil or tectonic subsidence. Over the period of 1982–1997, the subsidence occurred from 20 to 200 cm, with the rates of about 1 to 15 cm/year, in several places. This paper discusses settlement induced land subsidence of shallow marine clay deposits on Kamal Muara area, based on the pore water pressure changes based on the piezometer’s measurement located at 19 meters and 32 meters depth. Consolidation parameters (Cv and Cc) tested by cyclic load consolidation test. The estimation of on-site land subsidence is performed using the Terzaghi’s 1-D consolidation theory and the secondary compression theory. Ranges of estimated values, as well as their relevant statistical properties, were identified. The results shown as follow: Without water extraction, settlement on soil layer #1 and #2 estimated as 0.647 meters and 0.305 meters respectively, with average subsidence rate is 9.832 cm/year and 1.07 cm/year. Total settlement estimated as 1.01 meters, with average subsidence rate is 5.07 – 5.42 cm/year. With water extraction, settlement on soil layer #1 and #2 estimated as 0.658 meters and 0.395 meters respectively, with average subsidence rate is 10.005 cm/year and 31.88 cm/year. The subsidence on Kamal Muara estimated as 0.68 – 1.05 meters, with subsidence rate 5 – 20.9 cm/year. The results placed on the lower range of field geodetical measurements, due to specific values of surface load and pore water measurement on Kamal Muara is used specifically.
The Analysis of Modified of Cakar Ayam (CAM) Designed with Concrete Plate Thickness Variation in Soft Soil
Authors: Jannah A , Setiawan B , Djarwanti N
Published: November 2019

Modified of Cakar Ayam System (CAM) is a system that uses galvanized steel pipes as stiffener plate. This system had been implemented on the trial road of Pamanukan-Indramayu, Indonesia. Many advantages are obtained from the use of this system, for example reduction on deflection, durability, and application on road pavement. Full scale trials had been conducted in Indonesia, for the examples, the Waru-Surabaya Highway and Section IV Highway, Makassar. Despite this system is widely used but there are still many problems occur such as deflection and crack due to less plate thickness. This research will discuss about the deflection, moment and shear force of plate model on soft base ground using Finite Element Method (FEM). The system configurations for concrete plate applied in this research were 7.25 m in width and 14.0 m in length with thickness was varied by 0.15 m, 0.18 m and 0.22 m using 21 cakars. The loads represented semi-trailer truck loading with the weight of each axle propagated into 2 equal uniform loads. The position of test loading points were made in several variations to determine the largest deflection value. If the plate got thicker then, its stiffness value would increase and the deflection accorded smaller result. By using CAM System, cakar could function as a load restraint and plate grip. The stiffness of the plate would increase when the plate was applied with the CAM System and could reduce deflection by 2.74% to 39.77%. On the effect on the moment and shear force, it was found that the thicker the plate, the greater the moment and shear force value obtained. The difference in the value of the moment obtained from the comparison between the plate using the CAM System and the plate without the CAM System was 0.23% to 1.60%, while for shear force values, the difference was 7.56% to 11.19%.
Sensitivity Analysis of Soil Parameters on Slope Stability using Simplified Bishop Method (Case Study in Grobogan, Central Java, Indonesia)
Authors: Surjandari N S , Riyadinata F D , Purwana Y M
Published: November 2019

Slope instability can occur due to the influence of soil parameter values. The value of soil parameters is a random phenomenon that is uncertain and tends to a certain range. This study attempts to analyze the sensitivity of soil parameters on a slope with a height of 6 m. Sensitivity analysis includes several ranges of soil parameter data based on the Soil Investigation Report in Grobogan, Central Java, Indonesia. Slope failure is based on Mohr-Coulomb theory and slope stability analysis using simplified Bishop method. The analysis will produce how much influence from the variation of soil parameter values to the safety factor on the slope. The results of the influence of the variation of parameter values are recapitulated and processed, so that the sensitivity percent of each soil parameter is obtained against the safety factor of slopes. The results showed that the most sensitive soil parameters were soil cohesion.
Retinal Blood Vessel Segmentation using Gaussian Filter
Authors: Maison  , Lestari T , Luthfi A
Published: November 2019

Retinal diseases are a visual disorder that can cause human vision problems, such as blindness and low vision. Early detection of this disease is important to prevent visual impairment. In ophthalmology, segmentation of blood vessels is a major component of color retinal fundus images analysis for monitoring and diagnosing retinal diseases, like diabetic retinopathy, hypertensive retinopathy, age-related macular degeneration and arteriosclerotic. This process is effective to identify retinal diseases more accurately. This paper using Gaussian Filter to segmenting blood vessel on retinal images because this method is effective to remove noise and make blood vessels on images more clearly. These methods are applied to color fundus images from DRIVE database. These databases contain color fundus image are used to evaluate this method. The performance is evaluated by accuracy, sensitivity and specificity. The proposed method has the average of accuracy, sensitivity and specificity at 95.72%, 96.90% and 82.10%.
Herd vaccination threshold for rabies disease with fuzzy transmission coefficient
Authors: Wiraningsih E D , Amarti Z , Supriatna A K
Published: November 2019

This paper considers a deterministic model for the transmission dynamics of rabies virus in the wild dogs-human zoonotic cycle. The endemic equilibrium is found and its existence depends on the value of the basic reproduction number. The effect of vaccination in dogs is considered on the model. We then also present the effective reproduction number in the presence of the vaccination. Further we developed the formula to obtain the minimum level of the vaccination to eliminate the endemic equilibrium, which is called the herd vaccination threshold. We found the relation between this herd vaccination threshold and the basic reproduction number. The effect of some fuzzy parameters to the herd vaccination threshold is also investigated.
Model Design of Tomato Sorting Machine Based on Artificial Neural Network Method Using Node MCU Version 1.0
Authors: Istiadi A , Sulistiyanti S R , Herlinawati  , Fitriawan H
Published: November 2019

Tomatoes have different quality and maturity, this is a problem in sorting because it is often wrong on put the grade of tomato marketing and takes a long time in sorting. One solution offered to overcome this problem is a tomato sorting system based on artificial neural network method that can minimizes the sorting time and also places the tomato according to grade. In this research, the model of artificial neural network system backpropagation method on microcontroller NodeMCU Lua version 1.0. The artificial neural network method is used to process the image of tomato objects moving through conveyor in the form of RGB value and captured by color sensor TCS 3200, the image obtained can classify the grade of tomatoes into unripe, half ripe and ripe. This research compared the results of training and testing of artificial neural networks between Matlab R2015a and NodeMCU Lua version 1.0. The outputs or decisions of artificial neural networks will be forwarded to the control system in the form of hardware and software used in this research. The results showed that the tomato sorting model successfully classified the tomato grade, and was able to control motor servo & DC motor automatically based on RGB value with processing time about 5 seconds and error 8.3%.
Effect of Bed Thickness on the Drying Rate of Paddy Rice in an Up-flow Fixed Bed Dryer
Authors: Kumoro A C , Lukiwati D R , Praseptiangga D , Djaeni M , Ratnawati R , Hidayat J P , Utari F D
Published: November 2019

Rice has played its important role as the world’s major source of food for human and animals. In order to sustain the food supply, many efforts have been conducted to increase the production of paddy rice per acre. The management of highly moist paddy rice during the harvesting period for preserving the paddy rice quality, increase in yield and reduce postharvest losses is greatly challenging. Drying process is one of the postharvest technologies for preserving the quality and extending the storage time of paddy rice. Moisture is removed to retard the development of a favorable environment for growth of molds and insects that lead to cause spoilage. In this paper, an experimental work and development of a simple mathematical model in a fixed bed drying of highly moist paddy rice have been conducted. Effect of bed thickness (6 cm to 12 cm) on the paddy rice drying rate was investigated by flowing drying air at 5.5 m/s with 37.45 % relative humidity at 40°C for 10 to 130 minutes. Drying of paddy rice using 8 cm bed thickness for 60 minutes was found to be the best drying condition to obtain acceptable moisture content of paddy rice for safe storage. The proposed non-equilibrium has shown its suitability for predicting the moisture content of paddy rice with variation of height of a fixed bed under unsteady state conditions. The drying rate constant was found to be a logarithmic function of bed thickness.
Prompt active restoration of peatlands substantially reduces climate impact
Authors: Nugent Kelly A , Strachan Ian B , Roulet Nigel T , Strack Maria , Frolking Steve , Helbig Manuel
Published: November 2019

Restoration of peatlands after peat extraction could be a benefit to the climate system. However a multi-year ecosystem-scale assessment of net carbon (C) sequestration is needed. We investigate the climate impact of active peatland restoration (rewetting and revegetating) using a chronosequence of C gas exchange measurements across post-extraction Canadian peatlands. An atmospheric perturbation model computed the instantaneous change in radiative forcing of CO2 and CH4 emissions/uptake over 500 years. We found that using emission factors specific to an active restoration technique resulted in a radiative forcing reduction of 89% within 20 years compared to IPCC Tier 1 emission factors based on a wide range of rewetting activities. Immediate active restoration achieved a neutral climate impact (excluding C losses in the removed peat) about 155 years earlier than did a 20 year delay in restoration. A management plan that includes prompt active restoration is key to utilizing peatland restoration as a climate change mitigation strategy.
Magnetic and Electromagnetic Wave Absorption Characteristics of BaFe11Ti0.5Zn0.5O19 in X Band
Authors: Dedi  , Idayanti Novrita , Kristiantoro Tony , Sudrajat Nanang , Gustinova Arighi , Primadona Indah
Published: November 2019

Research has been made on BaFe11Ti0.5Zn0.5O19 compound by high energy milling (HEM) with variation of milling t = 2, 8, and 12 hours. This research was conducted to find out the influence of milling time on magnetic and electromagnetic wave absorption properties of BaFe11Ti0.5Zn0.5O19 compound. Materials were characterized by X-Ray Diffraction (XRD), Permagraph C, Scanning Electron Microscope (SEM), and Vector Network Analyzer (VNA). XRD patterns of bulk sample had shown the material forms a single phase BaFe12O19 (Barium hexaferrite). A SEM image of bulk sample shows hexagonal structure. A VNA spectrum obtained from 12 hours milling exhibit the highest electromagnetic wave absorption compared with 2 and 8 hours milling, with 99,19% absorption at frequency 11,7 GHz in X-band. Agglomeration occurs on the sample powder may due to electrostatic force among particles and a SEM image confirmed it. Based on that results, the addition of milling time can improve the electromagnetic wave absorption of BaFe11Ti0,5Zn0,5O19 powder.
Selected Application of Linear Composites Containing Side Emitting Optical Fibres
Authors: Křemenáková Dana , Militký Jiří , Mishra Rajesh , Venkataraman Mohanapriya , Petru Michal
Published: November 2019

The main aim of this contribution is description of side emitting plastic optical fibres basic properties and their efficient embedding into fibrous structures for creation of textile structures with active visibility in shadows. For preparation of textile structures containing side emitting plastic optical fibres the special weaving technology is used. Illumination system with light emitting diode (LED) is used as light source. Light intensity of textile structures is compared with light intensity of fibres. Incorporation of side emitting plastic optical fibres into fibrous tube provides sufficient side emission especially for plastic optical fibres with larger diameters. The corresponding technology has been developed and the possible applications were proved in real conditions. The use of side emitting POF in textile tube are still in the first stage of industrial realization and it will be necessary to optimize their composition and functionality for various targeted applications including surface effects, doping and use of special dyestuffs.
The Thickness Effect on LSPR Spectra of Au-Nanorod Coated TiO2and SiO2Studied by MNPBEM
Authors: Kuddah Muhammad Sujak Mansur , Putra Miftahussurur Hamidi , Djuhana Dede
Published: November 2019

We have studied the effect on localized surface plasmon resonance (LSPR) of Au-nanorod (AuNR) coated TiO2(Au@TiO2) and SiO2(Au@SiO2). The length and diameter of AuNR are 70 nm and 20 nm, respectively. For this purpose, then AuNR was coated by TiO2and SiO2with thickness varying from 2nm to 20nm with increment 2nm. The LSPR exhibited two modes, transverse mode (TM) and longitudinal mode (LM) as commonly was found in a rod-shaped particle. Interestingly, the peak of extinction red-shift as the thickness increased both TM and LM. Increasing volume and refractive index around AuNR contributed to red-shift, therefore the rate of decreasing energy TiO2faster than SiO2. Furthermore, we have also observed the peak of LSPR extinction curve of Au@TiO2have a similar trend to Au@SiO2as the thickness increased, but its beginning to decrease at ∼8nm. In the LM, for a given thickness, we found the peak of extinction curve Au@TiO2show more than one peak present around ∼2-3nm and ∼8nm. However, only one peak happened in Au@SiO2. In a sense, Au coated TiO2can be fully utilized to enhance photocatalytic activity under visible light of AuNR and useful in photocatalytic activity, on the other hand, SiO2plays an insignificant role for a certain limit thickness under visible light – near-infrared.
Study of Domain Wall Propagation in FePt and FePd Nanowires Driven by Sub-nanosecond Pulse of Magnetic Field by Micromagnetic Simulation
Authors: Hawibowo Sulaiman , Kurniawan Candra , Djuhana Dede
Published: November 2019

In this study, we investigated the domain wall propagation behavior in FePt and FePd nanowires by micromagnetic simulation based on LLG equation. A rectangular shape nanowire model was generated with a fixed length of 2000 nm and varied thicknesses of 2.5 nm and 5 nm. The wire widths were varied of 50 nm, 100 nm, and 150 nm. The 500 ps length of magnetic-pulse was applied in-plane to a transverse type domain wall. We observed the Walker Breakdown field (H
WB), which means the maximum domain wall velocity before it was abruptly decreased. The transverse DW structure was maintained below H
WB while vortex/antivortex wall structure was formed in the higher magnetic field. Interestingly, the H
WB value of both FePt and FePd were decreased as the width and thickness of the nanowires increased. We have also analyzed the changing of the demagnetization and exchange energy for the domain wall structure transition from transverse wall to vortex/anti-vortex wall.
Study of Temperature and Holding Time of Second Stage in Two-stages Thermal Upgrading of Lateritic Nickel Ore
Authors: Suharno B , Sa’adah A , Shofi A , Nurjaman F
Published: November 2019

A two-stage thermal upgrading process with the addition of 10 wt.% sodium sulfate and sodium chloride followed by magnetic separation was conducted for treatment low-grade nickeliferous laterite ore to produce a ferronickel product. The aim of this experiment was to investigate the effect of reduction temperature and holding time in two-stage thermal upgrading process, which was carried out from 950°C to 1150°C for 30 to 90 minutes, into the grade and recovery of nickel also the morphology of ferronickel particle. A wet magnetic separation with 500 gauss magnet was conducted to produce ferronickel in concentrate. Increasing the reduction temperature of nickel laterite increased the nickel grade and recovery. The nickel grade and recovery also increased along with the longer holding time in the reduction process. Nevertheless, it decreased the iron recovery.
Microstructure, Phases Transformation and Hardness of Sintered Fe-Mo-Si Alloys Prepared by Powder Metallurgy Technique
Authors: Ciswandi  , Riastuti Rini , Wismogroho Agus Sukarto , Hermanto Bambang , Sudiro Toto
Published: November 2019

The transition-metal silicides are attractive materials for high-temperature applications due to its mechanical properties and resistance to oxidation-corrosion at high temperature. In this paper, the development of silicides alloy based on ferromolybdenum (Fe-Mo) and ferrosilicon (Fe-Si) lumps as starting materials were discussed. The Fe-Mo and Fe-Si lumps were manually crushed into small granules. Afterwards, the small granule of Fe-Mo and Fe-Si were separately milled into fine powder and were then mixed by using Wet-High Energy Milling technique for 4h and 2h, respectively. The powders were compacted and then sintered at 1200°C for 2h in a vacuum. The microstructure of sintered alloys was observed by using SEM-EDX. Meanwhile, the formation of silicides phases was identified by using XRD. The Vickers hardness testing was performed to measure the hardness of sintered alloys. According to the results, the MoSi2 phase was detected in the (Fe-Si)-30(Fe-Mo) alloy. When the Fe-Si concentration was decreased to 40 % at, the FeMoSi phase was formed. The detail results of this study are presented and discussed in this paper.
Role of Zn Substitution on Improvement of Electromagnetic and Microwave Absorption Characteristics of BaTi(1-x) ZnxO3 (x = 0; 1/3; ½; 2/3; 1)
Authors: Zainal Yuda Bakti , Kristiantoro Tony , Dedi  , Manaf Azwar
Published: November 2019

In the current study, we have explored the electromagnetic and microwave absorption characteristics, especially the permeability, permittivity and reflection loss of magnetoelectric BaTi(1-x)ZnxO3 with x = 0; 1/3; ½; 2/3; 1. The composition was selected to include the effect of structural change when Ti is substituted with Zn in BaTi(1-x)ZnxO3 material system. When x = 0, the Zn free BaTiO3 posesses a tetragonal phase with lattice parameters a = b = 3.996361 Å and c = 4.030751 Å. The lattice parameters changed when x > 0 and phase transformation as well as material structure change occurred when x = 1. In addition, the effect of the geometric effect of replacing Ti ions with Zn which has a bigger ion radius will increase the absorption of electromagnetic waves.
Production of Nanobiocontrol Agent in Molasses and Tofu Liquid Waste Media by Streptomyces sp. TT10
Authors: Desak Gede Sri Andayani , I Dewa Hermida Putu , Hidayat Novik Nur , Kristiantoro Toni , Tirta Andini Desak Gede
Published: November 2019

The objective of this study has processed the waste of agriculture into high economic value materials using fermentation technology byStreptomyces sp.TT 10 in the form of new materials in Nano size. In this study, anti-phytopathogenic agents would be produced using fermentation technology in the form of antifungal that fought fungi that often infected strawberries. The research series consisted of the fermentation process for seven days, 30°C, pH 7 on molasses and tofu liquid waste medium. The broth of fermentation was extracted using ethyl acetate. Concentrated ethyl acetate extracts were ground using a shaker mill PPF-UG to obtain the size up to 100 nm. Furthermore, Nano sizes were characterized using (particle size analyzer) PSA and (scanning electron microscope) SEM. The anti-phytopathogenic agent was analyzed by agar diffusion and microdilution. The results showed that activity of ethyl acetate extract ofStreptomyces sp.TT10 was increased up to 80% after milling process, against pathogenic strawberry that isPenicillium sp., Aspergillus sp., Rhodotorula sp., Kluyveromyces sp., Candida krusei, Candida pseudotropicalisandFusarium oxysporumwith inhibitory diameter (mm), minimum inhibition concentrations (MIC) (ppm) and the minimum fungicidal concentration (MFC) (ppm) value (%) are respectively (82.85:50;50), (81.29;50;50), (82.85;50;50), (83.87;50;50), (74.07;50;50), (79.95;50;50), and (83.33; 50; 50).
Preparation of Polyvinyl Alcohol/Cellulose Nano fiber Nanocomposite Isolated from Empty Oil Palm Fruit Bunches
Authors: Gea Saharman , Indra  , Muis Yugia , Panindia Nami , Hutapea Yasir Arafat
Published: November 2019

This research was aimed to manufacture polyvinyl alcohol (PVA)/cellulose nanofiber (CNF) nanocomposite which was isolated from oil palm empty fruit bunches (OPEFB) through steam explosion method combined with a hydrolysis process involving HCl 10%. The isolation process was performed in 2 steps; α-cellulose isolation from empty fruit bunches fibers and then cellulose nanofiber isolation from α-cellulose which was hydrolyzed with acid using ultrasonicator and homogenized in rotational speed of 8000 rpm. The functional group and morphology of nanofibres cellulose were characterized. FT-IR spectrum resulted an absorptions for C-O-C group at wavelength of 1059.99 cm-1 which indicated a glycoside bond. Then, C-H group at 2900.94 cm-1 and O-H group at 3348.62 cm-1 were revealed to indicate the cellulose nanofiber. Moreover, TEM was used for morphological analysis and showing a decrease in fibres diameters after experiencing a chemical-mechanical treatment which lead to nanofibres with final diameter size of 20-30 nm. PVA/CNF nanocomposite with the percentage ratio of 80:20 gave a tensile strength of 17.41 Mpa and Modulus Young of 0.9 Gpa. Finally, the product was also morphologically analyzed with SEM and indicating an even distribution on the PVA surface.