bluuebunny/crossref_metadata_2025 huggingface dataset:
Unified phase diagram of reversible–irreversible, jamming, and yielding transitions in cyclically sheared soft-sphere packings
Authors: Das Pallabi , Vinutha H. A. , Sastry Srikanth
Published: April 2020

Significance

The response and self-organization of amorphous matter to externally imposed stresses or deformation is of interest in a variety of contexts. In particular, cyclic-shear deformation has been employed, in computer simulations and experiments, to probe the emergence of irreversibility in colloidal suspensions, yielding and annealing of glasses, jamming, memory formation, etc. We investigate soft-sphere assemblies computationally to obtain a comprehensive understanding of their self-organization and response over a wide range of densities and deformation amplitudes. We find a rich diversity of behaviors and transitions, and obtain a unified phase diagram that exhibits reversible and irreversible regimes and transitions among them that embody yielding, jamming, unjamming, and shear jamming phenomena.
Inhibition of sphingolipid synthesis improves outcomes and survival in GARP mutant
wobbler
mice, a model of motor neuron degeneration
Authors: Petit Constance S. , Lee Jane J. , Boland Sebastian , Swarup Sharan , Christiano Romain , Lai Zon Weng , Mejhert Niklas , Elliott Shane D. , McFall David , Haque Sara , Huang Eric J. , Bronson Roderick T. , Harper J. Wade , Farese Robert V. , Walther Tobias C.
Published: April 2020

Numerous mutations that impair retrograde membrane trafficking between endosomes and the Golgi apparatus lead to neurodegenerative diseases. For example, mutations in the endosomal retromer complex are implicated in Alzheimer’s and Parkinson’s diseases, and mutations of the Golgi-associated retrograde protein (GARP) complex cause progressive cerebello-cerebral atrophy type 2 (PCCA2). However, how these mutations cause neurodegeneration is unknown. GARP mutations in yeast, including one causing PCCA2, result in sphingolipid abnormalities and impaired cell growth that are corrected by treatment with myriocin, a sphingolipid synthesis inhibitor, suggesting that alterations in sphingolipid metabolism contribute to cell dysfunction and death. Here we tested this hypothesis in
wobbler
mice, a murine model with a homozygous partial loss-of-function mutation in
Vps54
(GARP protein) that causes motor neuron disease. Cytotoxic sphingoid long-chain bases accumulated in embryonic fibroblasts and spinal cords from
wobbler
mice. Remarkably, chronic treatment of
wobbler
mice with myriocin markedly improved their wellness scores, grip strength, neuropathology, and survival. Proteomic analyses of
wobbler
fibroblasts revealed extensive missorting of lysosomal proteins, including sphingolipid catabolism enzymes, to the Golgi compartment, which may contribute to the sphingolipid abnormalities. Our findings establish that altered sphingolipid metabolism due to GARP mutations contributes to neurodegeneration and suggest that inhibiting sphingolipid synthesis might provide a useful strategy for treating these disorders.
A widespread toxin−antitoxin system exploiting growth control via alarmone signaling
Authors: Jimmy Steffi , Saha Chayan Kumar , Kurata Tatsuaki , Stavropoulos Constantine , Oliveira Sofia Raquel Alves , Koh Alan , Cepauskas Albinas , Takada Hiraku , Rejman Dominik , Tenson Tanel , Strahl Henrik , Garcia-Pino Abel , Hauryliuk Vasili , Atkinson Gemma C.
Published: April 2020

Under stressful conditions, bacterial RelA-SpoT Homolog (RSH) enzymes synthesize the alarmone (p)ppGpp, a nucleotide second messenger. (p)ppGpp rewires bacterial transcription and metabolism to cope with stress, and, at high concentrations, inhibits the process of protein synthesis and bacterial growth to save and redirect resources until conditions improve. Single-domain small alarmone synthetases (SASs) are RSH family members that contain the (p)ppGpp synthesis (SYNTH) domain, but lack the hydrolysis (HD) domain and regulatory C-terminal domains of the long RSHs such as Rel, RelA, and SpoT. We asked whether analysis of the genomic context of SASs can indicate possible functional roles. Indeed, multiple SAS subfamilies are encoded in widespread conserved bicistronic operon architectures that are reminiscent of those typically seen in toxin−antitoxin (TA) operons. We have validated five of these SASs as being toxic (toxSASs), with neutralization by the protein products of six neighboring antitoxin genes. The toxicity of
Cellulomonas marina
toxSAS FaRel is mediated by the accumulation of alarmones ppGpp and ppApp, and an associated depletion of cellular guanosine triphosphate and adenosine triphosphate pools, and is counteracted by its HD domain-containing antitoxin. Thus, the ToxSAS–antiToxSAS system with its multiple different antitoxins exemplifies how ancient nucleotide-based signaling mechanisms can be repurposed as TA modules during evolution, potentially multiple times independently.
Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis
Authors: Nilsson Avlant , Haanstra Jurgen R. , Engqvist Martin , Gerding Albert , Bakker Barbara M. , Klingmüller Ursula , Teusink Bas , Nielsen Jens
Published: April 2020

Many cancer cells consume glutamine at high rates; counterintuitively, they simultaneously excrete glutamate, the first intermediate in glutamine metabolism. Glutamine consumption has been linked to replenishment of tricarboxylic acid cycle (TCA) intermediates and synthesis of adenosine triphosphate (ATP), but the reason for glutamate excretion is unclear. Here, we dynamically profile the uptake and excretion fluxes of a liver cancer cell line (HepG2) and use genome-scale metabolic modeling for in-depth analysis. We find that up to 30% of the glutamine is metabolized in the cytosol, primarily for nucleotide synthesis, producing cytosolic glutamate. We hypothesize that excreting glutamate helps the cell to increase the nucleotide synthesis rate to sustain growth. Indeed, we show experimentally that partial inhibition of glutamate excretion reduces cell growth. Our integrative approach thus links glutamine addiction to glutamate excretion in cancer and points toward potential drug targets.
Individual differences in trust evaluations are shaped mostly by environments, not genes
Authors: Sutherland Clare A. M. , Burton Nichola S. , Wilmer Jeremy B. , Blokland Gabriëlla A. M. , Germine Laura , Palermo Romina , Collova Jemma R. , Rhodes Gillian
Published: April 2020

People evaluate a stranger’s trustworthiness from their facial features in a fraction of a second, despite common advice “not to judge a book by its cover.” Evaluations of trustworthiness have critical and widespread social impact, predicting financial lending, mate selection, and even criminal justice outcomes. Consequently, understanding how people perceive trustworthiness from faces has been a major focus of scientific inquiry, and detailed models explain how consensus impressions of trustworthiness are driven by facial attributes. However, facial impression models do not consider variation between observers. Here, we develop a sensitive test of trustworthiness evaluation and use it to document substantial, stable individual differences in trustworthiness impressions. Via a twin study, we show that these individual differences are largely shaped by variation in personal experience, rather than genes or shared environments. Finally, using multivariate twin modeling, we show that variation in trustworthiness evaluation is specific, dissociating from other key facial evaluations of dominance and attractiveness. Our finding that variation in facial trustworthiness evaluation is driven mostly by personal experience represents a rare example of a core social perceptual capacity being predominantly shaped by a person’s unique environment. Notably, it stands in sharp contrast to variation in facial recognition ability, which is driven mostly by genes. Our study provides insights into the development of the social brain, offers a different perspective on disagreement in trust in wider society, and motivates new research into the origins and potential malleability of face evaluation, a critical aspect of human social cognition.
Understanding the computation of time using neural network models
Authors: Bi Zedong , Zhou Changsong
Published: April 2020

To maximize future rewards in this ever-changing world, animals must be able to discover the temporal structure of stimuli and then anticipate or act correctly at the right time. How do animals perceive, maintain, and use time intervals ranging from hundreds of milliseconds to multiseconds in working memory? How is temporal information processed concurrently with spatial information and decision making? Why are there strong neuronal temporal signals in tasks in which temporal information is not required? A systematic understanding of the underlying neural mechanisms is still lacking. Here, we addressed these problems using supervised training of recurrent neural network models. We revealed that neural networks perceive elapsed time through state evolution along stereotypical trajectory, maintain time intervals in working memory in the monotonic increase or decrease of the firing rates of interval-tuned neurons, and compare or produce time intervals by scaling state evolution speed. Temporal and nontemporal information is coded in subspaces orthogonal with each other, and the state trajectories with time at different nontemporal information are quasiparallel and isomorphic. Such coding geometry facilitates the decoding generalizability of temporal and nontemporal information across each other. The network structure exhibits multiple feedforward sequences that mutually excite or inhibit depending on whether their preferences of nontemporal information are similar or not. We identified four factors that facilitate strong temporal signals in nontiming tasks, including the anticipation of coming events. Our work discloses fundamental computational principles of temporal processing, and it is supported by and gives predictions to a number of experimental phenomena.
Gd impurity effect on the magnetic and electronic properties of hexagonal Sr ferrites: A case study by DFT
Authors: Taghipour Masomeh , Yousefi Mohammad , Fazaeli Reza , Darvishganji Masoud
Published: April 2020

The electronic and magnetic properties of strontium hexa-ferrite (SrFe12O19) are studied in pure state (SrFe12O19) and with dopant in the positions 2 and 3 of Fe atoms (SrGdFe11O19-I and SrGdFe11O19-II, respectively) by utilizing a variety of the density functional theory (DFT) approaches including the Perdew–Burke–Ernzerhof generalized gradient approximation (PBE-GGA) and GGA plus Hubbard U parameter (GGA+U). The pure SrFe12O19 is a hard magnetic half-metal with an integer magnetic moment of 64.00μ
B, while using the GGA+U functional, the magnetic intensity increases, resulting in a magnetic semiconductor with a high integer magnetic moment of 120μ
B. By doping the Gd atom in the two different positions of Fe, the magnetic moment is increased to 71.68μ
B and 68.00μ
B, respectively. The magnetic moment increases and remains an integer; hence, SrGdFe11O19-II can be very useful for application in magnetic memories. Moreover, applying the Hubbard parameter turns SrGdFe11O19-I and SrGdFe11O19-II to magnetic semiconductors with a magnetic moment of 124μ
B, and the energy gap of both doped structures at spin down is found to be less than the pure case. By studying the electronic density diagram of the atoms of the crystal, it is found that the major effect to create magnetization in the pure case is due to the Fe atom. However, in the doped case, the elements Gd and Fe have the highest moment in the crystal respectively.
Spontaneous growth of the reconnection electric field during magnetic reconnection with a guide field: A theoretical model and particle-in-cell simulations*
Authors: Huang Kai , Lu Quan-Ming , Wang Rong-Sheng , Wang Shui
Published: April 2020

Reconnection electric field is a key element of magnetic reconnection. It quantifies the change of magnetic topology and the dissipation of magnetic energy. In this work, two-dimensional (2D) particle-in-cell (PIC) simulations are performed to study the growth of the reconnection electric field in the electron diffusion region (EDR) during magnetic reconnection with a guide field. At first, a seed electric field is produced due to the excitation of the tearing-mode instability. Then, the reconnection electric field in the EDR, which is dominated by the electron pressure tensor term, suffers a spontaneous growth stage and grows exponentially until it saturates. A theoretical model is also proposed to explain such a kind of growth. The reconnection electric field in the EDR is found to be directly proportional to the electron outflow speed. The time derivative of electron outflow speed is proportional to the reconnection electric field in the EDR because the outflow is formed after the inflow electrons are accelerated by the reconnection electric field in the EDR and then directed away along the outflow direction. This kind of reinforcing process at last leads to the exponential growth of the reconnection electric field in the EDR.
Tuning the alignment of pentacene on copper substrate by annealing-assistant surface functionalization*
Authors: Cao Qiao-Jun , Wen Shuang , Xie Hai-Peng , Shi Bi-Yun , Wang Qun , Lu Cong-Rong , Gao Yongli , Dou Wei-Dong
Published: April 2020

Controlling the alignment and packing structure of organic molecules on solid substrate surfaces at molecule level is essential to develop high-performance organic thin film (OTF) devices. Pentacene, which is a typical p-type semiconductor material usually adopts lying-down geometry on metal substrates owning to π–d coupling between pentacene and metal substrates. However, in this study, we found that pentacene molecules can be adsorbed on an anneal-treated Cu (111) surface with their long axis perpendicular to substrate surface. Highly ordered single-layer pentacene film with stand-up molecular geometry was achieved on this substrate. It was found that the functionalization of Cu surface with C = O groups due to annealing treatment should be accounted for standing-up geometry of pentacene on Cu substrate. This observation shed light on the tuning of the alignment and packing structure of organic molecules.
Influence of bottleneck on single-file pedestrian flow: Findings from two experiments*
Authors: Jin Cheng-Jie , Jiang Rui , Li Da-Wei
Published: April 2020

In order to investigate the influence of bottleneck on single-file pedestrian flow, we conduct two different bottleneck experiments. The first one is on ring road, while the second one is on straight route. For the first one, the global density is always set to be 1.5 ped/m. The corresponding critical flow rate for the bottleneck activation is about 0.57 ped/s. The data of the detectors set at different locations, including the velocities and time-headways, show that the amplitude of the oscillation of the stop-and-go waves gradually increases during the upstream propagation. Besides, when the measured flow rates are the same, the different situations in the single-file experiments with and without bottleneck are compared and discussed. For the second one, lower flow rates are used and the bottleneck is always activated. In all the runs, the system can reach one stable state, and the time needed is nearly the same. Inside the stable area, the statistics of pedestrians’ velocities keeps nearly constant in both time and space. Outside this area, when the waiting time is not long (X = 10 s), the phenomenon observed is similar to that found on ring road, e.g., the statistics of pedestrians’ velocities also gradually increases during the upstream propagation. This phenomenon is similar to that found in vehicular traffic flow, which shows the universality of different traffic flows. But when the waiting time becomes longer (X = 20 s), this situation will be broken since the actions of many pedestrians become much slower. All these results can facilitate understanding more about the influence of bottleneck on single-file pedestrian flow.
Lifshitz transition in triangular lattice Kondo-Heisenberg model*
Authors: Zhang Lan , Zhong Yin , Luo Hong-Gang
Published: April 2020

Motivated by recent experimental progress on triangular lattice heavy-fermion compounds, we investigate possible Lifshitz transitions and the scanning tunnel microscope (STM) spectra of the Kondo–Heisenberg model on the triangular lattice. In the heavy Fermi liquid state, the introduced Heisenberg antiferromagnetic interaction (J
H) results in the twice Lifshitz transition at the case of the nearest-neighbour electron hopping but with next-nearest-neighbour hole hopping and the case of the nearest-neighbour hole hopping but with next-nearest-neighbour electron hopping, respectively. Driven by J
H, the Lifshitz transitions on triangular lattice are all continuous in contrast to the case on square lattice. Furthermore, the STM spectra shows rich line-shape which is influenced by the Kondo coupling J
K, the Heisenberg antiferromagnetic interaction J
H, and the ratio of the tunneling amplitude of f-electron t
f versus conduction electron t
c. Our work provides a possible scenario to understand the Fermi surface topology and the quantum critical point in heavy-fermion compounds.
SiO2 nanoparticle-regulated crystallization of lead halide perovskite and improved efficiency of carbon-electrode-based low-temperature planar perovskite solar cells*
Authors: Liang Zerong , Yang Bingchu , Mei Anyi , Lin Siyuan , Han Hongwei , Yuan Yongbo , Xie Haipeng , Gao Yongli , Zhou Conghua
Published: April 2020

SiO2 nanoparticles were used to regulate the crystallizing process of lead halide perovskite films prepared by the sequential deposition method, which was used in the low-temperature-processed, carbon-electrode-basing, hole-conductor-free planar perovskite solar cells. It was observed that, after adding small amount of SiO2 precursor (1 vol%) into the lead iodide solution, performance parameters of open-circuit voltage, short-circuit current and fill factor were all upgraded, which helped to increase the power conversion efficiency (reverse scan) from 11.44(± 1.83)% (optimized at 12.42%) to 14.01(±2.14)% (optimized at 15.28%, AM 1.5G, 100 mW/cm2). Transient photocurrent decay curve measurements showed that, after the incorporation of SiO2 nanoparticles, charge extraction was accelerated, while transient photovoltage decay and dark current curve tests both showed that recombination was retarded. The improvement is due to the improved crystallinity of the perovskite film. X-ray diffraction and scanning electron microscopy studies observed that, with incorporation of amorphous SiO2 nanoparticles, smaller crystallites were obtained in lead iodide films, while larger crystallites were achieved in the final perovskite film. This study implies that amorphous SiO2 nanoparticles could regulate the coarsening process of the perovskite film, which provides an effective method in obtaining high quality perovskite film.
Ionic liquid gating control of planar Hall effect in Ni80Fe20/HfO2 heterostructures*
Authors: Wang Yang-Ping , Liu Fu-Fu , Zhou Cai , Jiang Chang-Jun
Published: April 2020

We report a tunable transverse magnetoresistance of the planar Hall effect (PHE), up to 48% in the Ni80Fe20/HfO2 heterostructures. This control is achieved by applying a gate voltage with an ionic liquid technique at ultra-low voltage, which exhibits a gate-dependent PHE. Moreover, in the range of 0-V to 1-V gate voltage, transverse magnetoresistance of PHE can be continuously regulated. Ferromagnetic resonance (FMR) also demonstrates the shift of the resonance field at low gate voltage. This provides a new method for the design of the electric field continuous control spintronics device with ultra-low energy consumption.
Comparative study on characteristics of Si-based AlGaN/GaN recessed MIS-HEMTs with HfO2 and Al2O3 gate insulators*
Authors: Zhao Yao-Peng , Wang Chong , Zheng Xue-Feng , Ma Xiao-Hua , Liu Kai , Li Ang , He Yun-Long , Hao Yue
Published: April 2020

Two types of enhancement-mode (E-mode) AlGaN/GaN metal–insulator–semiconductor high-electron-mobility transistors (MIS-HEMTs) with different gate insulators are fabricated on Si substrates. The HfO2 gate insulator and the Al2O3 gate insulator each with a thickness of 30 nm are grown by the plasma-enhanced atomic layer deposition (PEALD). The energy band diagrams of two types of dielectric MIS-HEMTs are compared. The breakdown voltage (V
BR) of HfO2 dielectric layer and Al2O3 dielectric layer are 9.4 V and 15.9 V, respectively. With the same barrier thickness, the transconductance of MIS-HEMT with HfO2 is larger. The threshold voltage (V
th) of the HfO2 and Al2O3 MIS-HEMT are 2.0 V and 2.4 V, respectively, when the barrier layer thickness is 0 nm. The C–V characteristics are in good agreement with the V
th’s transfer characteristics. As the barrier layer becomes thinner, the drain current density decreases sharply. Due to the dielectric/AlGaN interface is very close to the channel, the scattering of interface states will lead the electron mobility to decrease. The current collapse and the R
on of Al2O3 MIS-HEMT are smaller at the maximum gate voltage. As Al2O3 has excellent thermal stability and chemical stability, the interface state density of Al2O3/AlGaN is less than that of HfO2/AlGaN.
Discretizations of the generalized AKNS scheme
Authors: Doikou Anastasia , Sklaveniti Spyridoula
Published: April 2020

We consider space discretizations of the matrix Zakharov–Shabat AKNS scheme, in particular the discrete matrix non-linear Scrhrödinger (DNLS) model, and the matrix generalization of the Ablowitz–Ladik (AL) model, which is the more widely acknowledged discretization. We focus on the derivation of solutions via local Darboux transforms for both discretizations, and we derive novel solutions via generic solutions of the associated discrete linear equations. The continuum analogue is also discussed, and as an example we identify solutions of the matrix NLS equation in terms of the heat kernel. In this frame we also derive a discretization of the Burgers equation via the analogue of the Cole-Hopf transform. Using the basic Darboux transforms for each scheme we identify both matrix DNLS-like and AL hierarchies, i.e. we extract the associated Lax pairs, via the dressing process. We also discuss the global Darboux transform, which is the discrete analogue of the integral transform, through the discrete Gelfand–Levitan–Marchenko (GLM) equation. The derivation of the discrete matrix GLM equation and associated solutions are also presented together with explicit linearizations. Particular emphasis is given in the discretization schemes, i.e. forward/backward in the discrete matrix DNLS scheme versus symmetric in the discrete matrix AL model.
Effects of the alang-alang (Imperata cylindrica) cutting practices to the gall growth
Authors: Syah R F , Hidayat P
Published: April 2020

Alang-alang is an invasive weed species that can grow out of control and harm other plants. The weed control methods commonly applied are burning, cutting, and spraying with herbicides. There is an insect causing alang-alang gall found in Java, namely Orseolia javanica Kieffer & van Leeuwen-Reijnvaan (Diptera: Cecidomyiidae) or known as the alang–alang gall midge. This study was aimed at determining the effects of the alang–alang cutting practice on rice field bunds to the growth of alang–alang galls. The study was done in Cianjur District, West Java. There were several steps done in this study including the preparation of field sites, daily observation of the gall growth, and observation on the duration of the gall midge for emerging. The length of the alang-alang gall on the uncut alang-alang was significantly higher than on the cut alang-alang, while the diameter of the galls was not significantly different. The difference in the length of the galls is believed was due to the different of light exposures. The duration of the emerging time for the alang-alang gall midge was shorter on the cut than the uncut alang-alang which was might be caused by changes in micro climate such as the more sunlight exposures and higher temperature on the habitat. This study suggests that the alangalang cutting practice can shorten the life cycle of the alang–alang gall midge and might have an impact on the biological control effectiveness.
Diversity and species composition of click beetles (Coleoptera: Elateridae) at different land-use types in Harapan Rainforest landscape, Jambi, Indonesia
Authors: Kasmiatun  , Nazarreta R , Hidayat P , Buchori D
Published: April 2020

Click beetles (Family Elateridae) are the largest family of beetles (Order Coleoptera) in superfamily Elateroidea that play an important role in the ecosystem, either as herbivores, predators and rhizophag. Land-use change can have a negative effect on diversity and abundance of click beetles. The aim of this research was to study the diversity and species composition of click beetles at different land-use types in Jambi. This research was carried out in Harapan Rainforest landscape that consists of 4 different land-use, i.e forest, jungle rubber, rubber plantation, and oil palm plantation. Click beetles were collected by fogging method in the morning and fogger directed toward the higher canopy for 20 min. The insect was collected in 16 traps that were installed under plant canopy, then the sample was sorted and identified in the laboratory. In a total of 2.042 individuals click beetles were collected, belonging to 7 subfamilies, 23 genera, and 59 morphospecies. Species richness and abundance of click beetles were higher in forest systems, while the lowest species richness was found in oil palm plantation and the lowest abundance was found in rubber plantation. Common click beetles species found in each land-use have consisted of morphospecies Melanoxanthus sp.01 (Elaterinae: Melanoxanthus). This research showed that different land-use types in Harapan Rainforest influenced the diversity, abundance, and species composition of click beetles. In conclusion, that habitat transformation has an impact on the loss of click beetles communities.
The efficacy of chitosan to control nematode Aphelenchoides besseyi Christie through seed treatment
Authors: Ibrahim A Y , Kurniawati F
Published: April 2020

One of the pathogen that infect rice is white tip nematode (Aphelenchoides besseyi).A. besseyiis a seed-borne pathogen that can cause yield losses 30% to 50%. To overcome this problem, it is necessary to have an effective, efficient, and environmentally friendly control method. The purpose of the research was to study effectiveness of chitosan in controlling white tip nematodes. The experimental design used in this research was completely randomized design. The chitosan concentrations used in this experiment were 0% (control), 0.25%, 0.5%, 0.75%, and 1%. Seeds of each treatment were soaked for 15 min. Each treatment was replicated 5 times, with 25 seeds being used for each replication. Observations including the most effective soaking period, seeds germination, nematodes population, and symptom of morphological damage caused by nematodes. Observations of seed viability were carried out using paper rolls test and directly counting population of nematodes using stereo microscope. The best treatment concentration was determined by % seeds germination and lowest nematodes population. The result showed that chitosan with concentration 0.25% was effective to controlA. besseyiand not significantly different with hot water treatment which is an effective control method to controlA. besseyito date. The treatment was also did not adversely affect to seed germination.
In vitro assays to investigate ethanol extract of Ipomoea batatas leaves as potential biofungicide for controlling Fusarium
Authors: Saputri D D , Utami A W A
Published: April 2020

Fusarium sp. has been known as a pathogenic agent causing fruit rots in chili and potentially decrease annual chili production rates. One plant potentially utilized for controlling Fusarium is purple sweet potato (Ipomoea batatas L.). Purple sweet potato contain active compounds in the form of flavonoids, which has been previously revealed to perform antifungal activity. This study aimed to determine antifungal activity of purple sweet potato (Ipomoea batatas L.) leaves as a bio fungicide for inhibiting the growth of Fusarium sp.-caused chili fruit rots. This work was conducted by testing the ethanol-extracted purple sweet potato leaves extracts against Fusarium sp. with in vitro assays. It was conducted by applying disc-diffusion method to observe the antifungal activity against Fusarium sp. This study showed inhibitory ability of the leaves extract against the growth of Fusarium sp. to range between 46.9 to 89.2%. Besides, in vitro treatment of the leaves extract at 40% concentration was discovered to significantly inhibit the incubation time of Fusarium sp. fruit rot compared to other treatment groups. These findings suggested the leaves extract at 40% concentration to be a potential bio fungicide for controlling Fusarium fruit rots on chili.
The effectiveness of plant growth promoting rhizobacteria isolated from Gunung Ciremai National Park forest to control alternaria blight disease of tomato
Authors: Rizkia N , Wiyono S
Published: April 2020

Tomato is an important horticulture commodity in Indonesia. Alternaria Blight caused by Alternaria solani Ell. & Mart. is an important disease on tomato. Biological control using plant growth promoting rhizobacteria (PGPR) is a promising technique for controlling the disease. One potential source of PGPR is a natural ecosystem area such as forest. This research aimed to determine the effectiveness of 5 PGPR isolated from Gunung Ciremai National Park forest, i.e. AKBR, AKS, C71, KS1, and S2 for controlling Alternaria blight disease on tomato and to assess their effects on plant growth. PGPR was applied by seed coating before planting and bacterial suspension watering on the soils. The research showed that all tested PGPR isolates could delay incubation periods and inhibit the development of blight disease. AKBR and C71 isolates had the highest effectiveness in suppressing A. solani infection with effectiveness rate 68.08% and 62.01% respectively. All tested PGPR isolates increased seed germination and tomato seedling growth. Molecular identification using PCR, followed by sequencing resulted that C71 isolates has 99.8% homology with Lysinibacillus fusiformis (Accession Number: KY910256.1)
Protection of chili pepper from mosaic virus disease and Aphis gossypii by a fermented water extract of compost
Authors: Suwandi S , Irsan C , Muslim A , Herlinda S
Published: April 2020

Mosaic and leaf curl diseases caused by multiple infections of viruses are the most important diseases of chili pepper. Bioactive compounds that are able to improve plant tolerance toward virus infections is promisingly developed for plant protection in organic chili cultivation. The potential of fermentation liquids from enrichment of SWCE (water extract of shrimp waste compost) with shrimp paste (TS, TSN, and TSNJK) that contains amino acids to control mosaic and leaf curl diseases and its aphid vector was demonstrated in a naturally infested curly red chili (Capsicum annuum). Fermentation liquids was sprayed weekly at 2 concentrations on pottedC. annumgrowing in an aphid-infested field. Treatment with all 3 fermentation products significantly reduced disease progression. Disease suppression was demonstrated following spraying at concentration as low as 0.2% and treatment with a higher concentration (2.0%) resulted in a higher suppression. Colonization ofAphis gossypiiwas significantly reduced on plants treated with fermentation liquids. The compost extract containing amino acids showed a remarkable potential to develop into an effective biostimulant for protection from virus disease and its insect vector,Aphis gossypii.
Characteristics of rhizobacteria on healthy and white rot - infected rubber trees
Authors: Febbiyanti T R , Kusdiana A P J
Published: April 2020

White root disease is an important disease in rubber plants caused by the fungus Rigidoporus microporus. The severity of white root disease in smallholder rubber plantations is up to 15%. Various controlling technique has not been effectively eliminate this disease. To develop an integrated white root disease management, a comprehensive study including the ecology and rhizobial characteristic of rubber tree is needed. This study was aimed to describe the characteristics of rhizobacteria on healthy and infected rubber trees. The results showed that the population of antagonistic and non-fluoresence bacteria was higher in the rhizosphere of healthy rubber plants, vice versa. The observation of bacterial morphology showed that the bacterial community was more diverse in the rhizosphere of healthy rubber than the rhizosphere infected by R. microporus.
Green synthesis of silver nanoparticles using leaf and stem bark extract of Pometia pinnata J.R. Forst & G. Forst
Authors: Ningrum A S , Pridyantari A P , Handayani W , Secario K , Djuhana D , Imawan C
Published: April 2020

Pometia pinnata (Matoa) is widely known for its use in traditional medicines and as fruit sources in Indonesia. Stem bark and leaves of Matoa are the most used parts. Each part contains secondary metabolites, including flavonoids, tannins, triterpenoids, glycosides, and saponins. These compounds could act as reducing agents in the biosynthesis of silver nanoparticles. Our research attempts to compare the efficacy of aqueous extracts of Matoa leaf and stem bark in the biosynthesis of silver nanoparticles. We characterized products of silver nanoparticles using UV-Vis spectrophotometer, transmission electron microscope, and particle size analyzer to compare the biosynthesis between the two parts based on ratios of various concentrations of plant extract to silver nitrate (AgNO3). We found that the solution (extract and AgNO3) became darker as the concentration and reaction time increased. Increasing reaction time also caused an increase in absorption peak intensity due to the reduction process of silver ions. The use of leaf and stem bark for biosynthesis resulted in different shapes and sizes of silver nanoparticles; the use of leaves and stem bark resulted in sphere-shaped silver nanoparticles, whereas the use of aqueous leaf extracts triangle-shaped silver nanoparticles formed.
Analysis of the potential application of chitosan to improve vegetative growth and reduce transpiration rate in Amaranthus hybridus
Authors: Berliana A I , Kuswandari C D , Retmana B P , Putrika A , Purbaningsih S
Published: April 2020

Various benefits have been attributed to chitosan in agriculture. This research is aimed at identifying the optimal concentration of chitosan to increase vegetative growth of Amaranthus hybridus L. (green amaranth) and also to determine the effectiveness of chitosan to enable A. hybridus cope with drought stress by acting as an antitranspirant agent. The concentrations of chitosan used to amend the growing medium were 0, 10, 30, 50 and 70 ppm. Results showed that chitosan significantly increased the height of A. hybridus by up to 19.59 % and also significantly increased the number of leaves at 10 ppm. However, chitosan treatment had no effect on chlorophyll content and fresh or dry weight although dosage response was highest at 10 ppm. In addition, chitosan reduced the transpiration rate by 36.66–66.26 %. Therefore, chitosan treatment could be an alternative way to reduce drought stress.
Genetic stability of in vitro propagated transgenic Acacia mangium expressing xyloglucanase
Authors: Utami N , Hartati S , Salamah A
Published: April 2020

In 2011, a gene transformation experiment in A. mangium was carried out to yield transgenic A. mangium that overexpresses the xyloglucanase gene, enabling plants to grow faster. The transgenic A. mangium has been maintained and continuously subcultured since. Here, we tested the stability of the xyloglucanase gene in transgenic A. mangium following in vitro propagation. Molecular and morphological approaches were used. For all specimens tested, the wild-type A. mangium (K) and two lines of transgenic A. mangium named X11 and X21 were positive for the xyloglucanase gene after recurring subculture. Morphological observations did not reveal any alterations, and the cultures had undergone notable physiological deterioration.
Genetic variation in Maturase K (matK) from cacao (Theobroma cacao L.) varieties in Indonesia
Authors: Immanissa S , Faizal I , Salamah A , Sari I A , Susilo A W
Published: April 2020

Cacao is a major agricultural commodity in Indonesia, yet its development is hindered by limited germplasm collections. In this study, the maturase K gene (matK) was used as a marker to determine patterns of genetic variation in Indonesia’s Trinitario and Forastero cacao varieties, with the results showing that the matK sequence does differentiate the varieties. However, the origin of at least one sample is unclear, as it may have been derived from crosses between the Forastero and Trinitario varieties. Similarly, an additional sample appears to be the result of the introduction of Forastero varieties from England, highlighting the importance of careful germplasm collections and molecular studies to identify contaminants.
Identification of maturase K (matK) gene in trinitario cocoa (Theobroma cacao L.) from Lampung Province and Central Java, Indonesia
Authors: Dermawan L P , Faizal I , Salamah A , Sari I A , Susilo A W
Published: April 2020

This research was conducted to determine the genetic variation in Trinitario cocoa (Theobroma cacao L.) accessions obtained from exploration and selection in Lampung Province, named HJ1, HJ2, HJ3, and HJ4, and the earlier Trinitario cocoa accession, named DR2. Identification was performed by comparing the DNA sequence of the matK region in the chloroplast genome. Genomic DNA isolation was performed with samples of old and fresh cocoa leaves. Amplification was conducted using two different primers Mac 02 (872 bp) and Mac 09 (1,153 bp). The sequencing results obtained indicated genetic variation in accession HJ3 amplified using the Mac 09 primer. A dendrogram constructed using the UPGMA method showed that the cocoa accessions from the exploration and selection group (HJ1, HJ2, HJ3, and HJ4) were grouped into one cluster and that DR2 was more ancient than the other four cocoa accessions.
Bioprospection of Diospyros discolor Willd. fruit for the biosynthesis of silver nanoparticles
Authors: Nolia I , Handayani W , Secario K , Djuhana D , Imawan C
Published: April 2020

Leaves from Diospyros discolor Willd. plants can act as a reducing agent in the biosynthesis of silver nanoparticles. This raises the question of whether other parts of the plant can also be used for this purpose. The present study aimed to explore the prospect of D. discolor fruit for the synthesis of silver nanoparticles. The fruit and seeds of the plant were extracted and used for the biosynthesis process, and the resulting silver nanoparticles were characterized using UV–visible light spectrophotometry, Transmission electron microscopy (TEM), and particle size analysis (PSA). During biosynthesis, aqueous extracts from the fruit flesh or seeds were reacted with 1 mM silver nitrate at various ratios. A ratio of 1:2 (v/v) resulted in the highest absorbance values (indicating the greatest production of nanoparticles), and the absorbance at all ratios increased with time. The results were similar for the fruit flesh and seed extracts, with absorbance values observed in the same peak areas for each treatment. However, the use of D. discolor fruit flesh resulted in faster reactions during the initial 24 h.
The effect of pineapple [Ananas comosus (L.) Merr.] juice in extender on Garut ram (Ovis aries L.) spermatozoa quality postcryopreservation
Authors: Isti V A , Setiorini  , Kaiin E M , Gunawan M
Published: April 2020

This study was intended to determine the effect of various concentrations of pineapple [Ananas comosus(L.) Merr.] juice in extender on garut ram (Ovis ariesL.) spermatozoa quality 24 h postcryopreservation. Semen samples were collected from five garut rams once a week using an artificial vagina. The samples were diluted in Tris-egg yolk extender with pineapple juice at concentrations of 0 % (KK), 5 % (KP 1), 10 % (KP 2), 15 % (KP 3), and 20 % (KP 4). The diluted semen samples were loaded into mini straws (0.25 mL) with 50 million cells/ml dosage. Samples were equilibrated at 5 °C for 2 h, and then frozen and stored in liquid nitrogen. Parameters evaluated were motility, viability, membrane integrity, acrosome integrity, and morphological abnormality. One-way ANOVA followed by Duncan’s test showed significant differences (P < 0.05) between KK and KP 3 in the percentage of motile spermatozoa and membrane integrity. Pineapple juice at 15 % could minimize the reduction of spermatozoa quality based on the percentage of motile spermatozoa (52.19 ± 5.32 %) and membrane integrity (38.52 ± 4.85 %).
Direct hydrocarbon indicator (DHI) pitfall assessment in prospecting pliocene globigerina biogenic gas play in “X structure”, Madura Strait, East Java Basin
Authors: Rowi V , Haris A , Riyanto A
Published: April 2020

Direct Hydrocarbon Indicator (DHI) has a major role in the exploration of Pliocene globigerina biogenic gas play in Madura Strait, part of East Java Basin. This study aimed to assess the DHI pitfall within the X Structure which triggered by the drilling result of Well X3 (dry hole) that contradict with Well X1 that successfully discovered gas even though both wells targeted the same reservoir body and DHI features. Low gas saturation that decreases the compressional velocity (Vp) is predicted to be the main reason behind the DHI pitfall. Considering the limitation of qualitative interpretation to investigate the DHI pitfall, this research uses seismic quantitative interpretations, such as fluid substitution modeling, amplitude variations with offset (AVO), seismic inversion, and rock physics analysis to get a full understanding behind the DHI features in X Structure. The 2D marine seismic survey consists of 49 seismic lines and wells data were used in this research. Fluid substitution and Vp-Vs-ρ modelling confirm that the DHI pitfall is related to the non-economic gas saturation (Sg < 10 %) within the reservoir. As for the AVO and inversion analysis indicated that the gas water contact (GWC) level is around 1,389 ms (± 4,023 ft SSTVD). Rock physics analysis shows that the poor reservoir quality is predicted to be the reason behind the low gas accumulation within the reservoir. Several properties cut off for gas zone were derived such as, P-impedance < 5,700 gr/cc*m/s, Vp/Vs < 2.0, porosity > 40 %, dan VCL < 22 %. This research concluded that the seismic quantitative interpretations were successfully used to assess the DHI pitfall and to delineate the economic gas accumulation zone.
Integration of fluid replacement modeling and seismic AVO analysis towards simultaneous seismic inversion to delineate the distribution of Globigerina limestone gas reservoir
Authors: Sumantri I , Haris A , Riyanto A
Published: April 2020

Integration of fluid replacement modelling and seismic AVO analysis towards simultaneous seismic inversion had been done to delineate the distribution of Globigerina limestone gas reservoir in Madura Strait, East Java Basin. This study was using backward modelling or well known as inversion modelling to finish the quantitative analysis. The purpose of the study is to map the distribution of Globigerina limestone gas reservoir so that in the end the final result will be used as a guidance to drill the next exploration well. It started with an optimized low frequency model building by integrating fluid substitution modelling and seismic AVO analysis. By integrating these two methods, the distorted top and bottom reservoir can be compensated, and the low frequency model will be optimized. The availability of the data includes 3D seismic data with acquisition bin size 18.75 m × 12.5 m, with two well logs. The cross plot result showed that the reservoir and non-reservoir lithology can be distinguished by Vp and Vs log. By analysing the acoustic impedance together with Vp/Vs ratio, the character of gas reservoir at surrounding F and H structures can also be delineated. The main cut off for acoustic impedance and Vp/Vs ratio were 5,500 gr/cm3*m/s and 2.0. The final optimizing result of low frequency model showed that the target G structure, which will be the next exploration target, showed an analogue response with its neighbour F and H structures. It is concluded that by integrating both two methods, fluid replacement modelling and AVO seismic analysis, the optimizing of low frequency model can be achieved and the simultaneous seismic inversion can successfully map other gas reservoir.
Identification of gold mineralization zone in “GB” field, Jambi, Indonesia using 3D inversion magnetic data
Authors: Rosid M S , Sari N I , Jaman A P
Published: April 2020

“GB” Field is a gold mineral prospect field located in Jambi, Indonesia. The gold zone is identified using 3D inversion magnetic data. The types of mineralization in this area are high epithermal sulfidation and porphyry copper-gold, which were formed in a hydrothermal environment. Characteristic of this type is a host rock of intermediate-acid igneous rock. This rock comprises mineral ores such as copper-gold and magnetic gangue minerals. Therefore, magnetic methods are very sensitive in identifying the gold prospect areas. Magnetic data were acquired at a 5 m spacing between stations along 51 lines with 100 m spacing between lines. To identify the position, type, and depth of the subsurface structure relating to the gold deposition environment, derivative analysis was performed using first horizontal derivative and Euler deconvolution calculations. Then, a 3D inversion model is constructed to objectively delineate the subsurface structure. Induced polarization as well as geological data are also used to identify the resistivity and chargeability parameters of the prospect zone and its environment. Thus, a gold deposition zone was identified based on the lithocap and intrusion body. The top of the intrusion rock was at a depth of 80 m from the surface.