bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxygen is a better predictor of macroinvertebrate richness than temperature—a systematic review
Authors: Croijmans L , De Jong J F , Prins H H T
Published: June 2020

Despite ongoing loss of diversity in freshwater ecosystems, and despite mitigation measures to halt this loss, it is still not clear what ecological drivers underlies lotic biodiversity. A complicating factor is that two of the main drivers, oxygen and temperature, are correlated, and hence studies towards drivers of lotic diversity are confounded. Here, we undertook a systematic review, consisting of both qualitative and quantitative analyses, to disentangle these two drivers. We accessed two literature repositories and assessed papers for eligibility using a set of predetermined criteria. For the qualitative part of this systematic review, we used results on patterns of taxonomic richness and multivariate ordination analyses to expose effects of temperature and dissolved oxygen concentration on biodiversity. For the meta-analysis, we could only use raw data of a few papers in generalized linear models. The qualitative analysis did not show strong consistent effects of either dissolved oxygen concentration or temperature on diversity. However, the meta-analysis showed that taxonomic richness is positively related with dissolved oxygen concentration. Inversely a negative correlation with temperature was found, but adding temperature to a model which already included dissolved oxygen content did not significantly improve the model. These results show the strength of a systematic review and meta-analysis over a conventional review without a meta-analysis; we found no pattern with the qualitative analysis, but a strong pattern with the quantitative analysis.
Bamboo architecture as a learning project for community development of rural area in Indonesia
Authors: Nurdiah E A , Juniwati A
Published: June 2020

Concrete and steel have become common building materials in Indonesia and used as main building materials by both local people as well as architects in their design project. In Indonesia, common people in urban and rural areas, engineers and architects are also more familiar with the utilization of industrial building materials rather than local materials. However, industrial building materials area often questionable as sustainable materials. While bamboo, as local material, has been known as a sustainable material. Therefore, the usage of bamboo in nowadays architecture need to be elaborated and taught to the young generation and the society for the community development project. This paper aims to discuss the method of using bamboo as local material for community development in Indonesia while involving students from architectural education for the design process. The case study was taken during the community service project for Jarak Village’s residents which was done by students and lecturer from Petra Christian University. By discussing the issue and methods, in the future bamboo architecture will present not only as a building that provides space for activities but also as an instrument of the learning process and community development.
Traditional architecture translation of Dhurung Barn to Bawean’s Airport, East Java, Indonesia
Authors: Samodra F X T B , Putro C M A
Published: June 2020

The tropical architecture of island city, Bawean, has been known as a cross-cultural result. The archipelago environment is exposed to high solar radiation and wind, thermal potency and problems are accumulated with the noise problem of the building. Therefore, this study aims to provide the design proposal and analysis for the contemporary architecture with pioneer airport design as an object through re-interpreting traditional channel approach of Bawean architecture as a case. In the transformation process and its thermal interference in the design is evaluated by the Flow Design simulation program to evaluate the proposed design wind flow and a noise control evaluation. The concept of Bawean architecture, mainly the Dhurung Barn, is applied by implying its original form into the modern form without losing the conveyed meaning. The results of this airport design show the locality of shape, space, and zoning, and the formation of thermal and acoustic design integration.
Concerning digital design in architectural pedagogy
Authors: Tedjosaputro M A
Published: June 2020

The emerging field of digital design in architecture has changed the way designers think and the way it should be taught. This paper looks at six design educational exercises which have adopted digital tools using various systems. Discussions are rooted in digital design cognition, digital design eco-system and pedagogy. This paper attempts to observe the change of ways of making within these themes using design cognition lens. It is proposed that digital design tool affordances is a pertinent concept to support this emerging field, both pedagogically and with regard to software development. It is also suggested that the digital eco-system framework need to include the dialogue between analogue and digital design tools.
The evaluation of city landmarks through the study of place attachment in Surabaya, Indonesia
Authors: Damayanti R , Tampubolon A C , Kusumo C
Published: June 2020

The presence of landmarks is one form of city identity. The city landmark is a symbol of pride that describes the city history, power, and future dream; it also reflects characteristics of the city and society. Theoretically, the identity or symbol creates a bonding with the society called as place attachment; since it represents the true meaning of the people and place characteristics. This research aims to evaluate current city landmarks of Surabaya through the place attachment study of specific young adults aged 19 yr to 22 yr. The implementation of mixed qualitative-quantitative research method is used to understand the respondents’ spatial perception by observing their social life and place preferences in the city to define social and physical symbols. The social symbols and physical symbols were compared to reveals the current value of the city landmarks. This research found that the attachment of the young adults to the Surabaya’s landmarks is weak. Young adults recognized the city landmarks in term of strong intrinsic value. It gives them a pleasant feeling by seeing the place. However, they were not engaged in the place. To improve its place attachment, the city landmarks should provide the affordance of desired and desirable activities.
Spatial pattern of the social space in self-built and core house post-disaster housing in Yogyakarta, Indonesia
Authors: Marcillia S M , Wulansari M A D
Published: June 2020

The main purpose of this article is to understand the spatial pattern for social space in post-disaster housing reconstruction in Yogyakarta as an actualization of their important socio-spatial space in Javanese dwellings through an in-depth examination and comparative analyses between two-real cases of post-disaster housing in Yogyakarta. The methodology of this research is based on several periods of on-field observation, which including physical data documentary, interview and literature reviews. Items related to development of space pattern and its relation to the activities and social interaction behaviors in the spaces were assessed. Based on the cases, a discussion on how residents adjusted their post-disaster housing were performed, and in conclusion, results suggest that modification were being made in their development of spatial pattern to accommodate their needs of social space in order to maintain users’ personal and social lifestyles.
Compare the growth and productivity of I. aquatic species on hydroponic subsystems within an aquaponic system
Authors: Quí T P , Ardi A , Chaniago I
Published: June 2020

The growth and productivity of two the Water Spinach varieties [Kangkung Unggul BikaR and Kangkung Bangkok LP-1R] had already been an experiment on two different Hydroponic culture subsystems [Floating Raft and Pumice Bed] of an Aquaponic circulatory system, where mineral nutrients of the Water Spinach vegetables were absorbed from biochemical processes occurring in solid wastes of fish and excess feeds. Consequently, this study showed individual functions of these two different Hydroponic culture subsystems from new established dates no significant differences at the 7th test date, until increasingly significant difference for the Hydroponic culture subsystem of Floating Raft is less effective than Hydroponic system of Pumice Bed based on the height of shoot, length of petiole and width of leaf on the 14th test date and the height of shoot, length of petiole, length of leaf, the number of leaf and length of root on the 21st test date. Nonetheless, Hydroponic subsystems did not support the growth and productivity of the Water Spinach varieties in all stages of testing about statistical significance. In addition, in term of productivity criteria and growth criteria on the 7th, 14th and 21st dates of testing, no significant difference were observed between two Water Spinach varieties. Finally, the advice of the study does not choose the treatment [Floating Raft Hydroponic culture subsystem and Kangkung Unggul BikaR variety] due to the poor result for the height of the shoot, length of petiole and reality of yield of Kangkung Unggul BikaR variety are probably at the 21st test date.
Evaluation and selection of salacca hybrid population based on fruit characters
Authors: Budiyanti T , Hadiati S , Fatria D
Published: June 2020

The variety assembly of new superior salacca leads to the character preferred by consumers which is sweet, thick flesh, not smelling and productive. These idiotypes can be obtained by hybridizing between the local elders and being selected variety based on the superior character. This research was aimed to evaluate and select salacca progenies with the characteristics of sweetness, not astringent, aromatic, high edible portion, thick flesh, and productive of 50 salacca hybrid populations. The research was conducted from January to December 2018 at the Agriculture Seed Center in Sei Lekop sub-district, East Bintan District, Bintan Regency, Riau Islands Province. The characterization and selection results got four progenies with scores above 20 points. The selected progenies were accessions with numbers 24, 524, 189, 500. The four selected progenies were further propagated by air layering the sucker as material to form a population for the observation test of prospective new superior varieties.
Optimization of the flowering stage by using stimulants of calcium carbide and paclobutrazol on pineapple at post tin mining area
Authors: Lestari T , Mustikarini E D , Apriyadi R , Hutahean B P
Published: June 2020

Bangka Island is the potential to increase pineapple production because of the availability of marginal land caused by tropical tin mining. The success of pineapple cultivation is determined by the formation of flowers that will become fruit. The flowering process can be accelerated using carbide and paclobutrazol. This research aimed to study the effect of Calcium carbide and paclobutrazol application as a flowering stimulant for flowering initiation and yield of pineapple in the post tin mining area. This research was conducted from January 2018 – July 2019 located in post tin mining area owned by PT Timah Tbk, Dwi Makmur Village, Merawang Subdistrict, Bangka Island using an experimental method with randomized block design with a single factor which was a type of flowering stimulant consist of calcium carbide [Calcium carbide] [P0] and paclobutrazol [P1]. The result showed that both of flowering stimulant gave significant effect to flowering time, fruit diameter, fruit length, fruit weight with crown, and fruit weight without the crown of pineapple. The fastest flowering duration showed in the pineapple with Carbide application in the post tin mining area.
Identification of gambier plant [Uncaria gambir [Hunter] Roxb] pollination system
Authors: Zainal A , Anwar A , Lopita S
Published: June 2020

The gambier plant pollination system needs to be understood for a breeding program to be conducted. The purpose of this study was to determine the percentage of self-pollination [autogamy and geitonogamy] and cross-pollination, both natural and artificial allogamy, in these plants. This research was conducted in the Experimental Garden of the Faculty of Agriculture, Andalas University, Padang and used a survey method [identifying samples, conducting pollination, observing samples and collecting data obtained in the field] together with non-probabilistic purposive sampling. Observations made include pollen adhesion to the stigma and fruit formation. Data were analyzed using simple statistics. Fruit production was highest following artificial allogamous cross-pollination [86%], followed by natural allogamous cross-pollination [51%] and geitonogic self-pollination [22%]. Autogamic self-pollination failed to produce fruit. Gambier plants are cross-pollinating plants able to undergo geitonogamous but not autogamous self-pollination.
A comparison of microwave and ultrasonic treatment on swelling power and water solubility of tapioca
Authors: Pratama F , Sari I P , Ridhowati S , Arsyad F S
Published: June 2020

Analysis of swelling power [SP] and water solubility index [WSI] of tapioca starch as affected by microwave and ultrasonic treatments was determined. The moisture content of the native tapioca starch was adjusted to 30%, 40% and 50% [wb]. The microwave treatment was performed at the power level of 450 W for 2 minutes, and the ultrasonic treatment was carried out at 40 kHz of 40°C for 30 minutes. Analysis of variance showed that the method of modification had a significant effect on SP and WSI. It was found that the microwave treatment decreased the SP and WSI, whereas the ultrasonic treatment increased the SP and WSI at a higher moisture content of native tapioca starch.
The potency of active components containing on andaliman fruit [Zanthoxylum acanthopodium] for increasing the quality of salted eggs
Authors: Silaban R , Harahap A U , Harahap A S
Published: June 2020

A type of spice that is still limited to use with primary commodities is andaliman [Zanthoxylum acanthopodium DC]. Geographically, the spice is only found in the district of Toba Samosir which is closed to Lake Toba. The herb plant is a group of family Rutaceae and has identified with the name of Andaliman [Batak pepper]. The chemical compound that is thought to have the most role in various biological activities of andaliman fruit as an antioxidant and antimicrobial for food processing. Research conducted to determine the phytochemical compounds, the group of secondary metabolites within the extraction, and the influence of antimicrobial compounds from essential oils on salted eggs. Parameters were chemical compounds from different extracted and quality of the eggs. The chemical composition of each extract was examined by both the Harborne method and GC-MS. Results showed that phytochemical contents contained steroid and triterpenoid for three types of extraction with no detect for saponin. Antimicrobial compounds sourcing from andaliman extracts can inhibit the Staphylococcus aureus. Besides, the quality profile of salted eggs by ripening with andaliman extracts was significantly influenced comparing with control. It can be concluded that the active components of andaliman extract have potentially affected the quality of salted eggs.
Isolation of Chitinase B [ChiB] gene from Serratia plymutica strain UBCF_13
Authors: Oktavioni M , Winata S R , Syafriani E , Syukriani L , Jamsari J
Published: June 2020

The utilization of synthetic fungicides harms the environment. Several studies have been carried out to control disease in plants using biocontrol agents and bio fungicides that more environmentally friendly. Laboratory tests showed that bacterial isolates UBCF_13 can act as biocontrol of pathogenic fungi that have been identified as Serratia plymutica bacteria. This bacteria is capable of producing chitinase enzymes that can degrade pathogenic fungal cell walls. The study was aimed to isolate the chitinase B gene from Serratia plymuticha strain UBCF_13. Cloning of the chitinase B [ChiB] gene from the bacterial genome UBCF_13 was carried out using a PCR-based cloning strategy using specific primers. The UBCF_13 ChiB gene was successfully isolated and identified with a sequence of 1583 bp covering ORF of 1500 bp which encodes 499 amino acids. Domain analysis exhibited 2 functional domains, namely catalytic and the chitin-binding domain. The 3D analysis of the ChiB protein structure indicates a similar function with the c1ur88 template which is identified as ChiB. Further research is necessary to determine the optimal method to express and determine its detailed function.
The pET-Rep recombinant plasmid construction and geminivirus Rep [C1] gene expression in Escherichia coli strain BL21
Authors: Gozalia E N , Syukriani L , Renfiyeni R , Jamsari J
Published: June 2020

Geminivirus Rep [C1] gene produces a replication protein [Rep] that interacts with Retinoblastoma-related protein [RBR] when Geminivirus infect the plants. That interactions interfere with RBR and transcription factor function. So the mechanism of chili plant defense against symptoms of Pepper Yellow Leaf Curl Disease is blocked. The NPR1 gene is a transcriptional co-activator involved in the regulation defense mechanism of Systemic Acquired Resistance [SAR] in chili plants. In silico, Rep protein blocks the SAR mechanism that is regulated by the NPR1 gene. This study aimed to obtain a construction of pET-28a+ plasmid expression recombinant Rep [C1] gene and Rep protein that can be expressed in E.coli BL21. This research is useful to study the interaction of Geminivirus with transcription co-activator in chili plants. The construction was done by ligating plasmid and Rep genes which have been cut using restriction enzymes BamHI and SacI. The construction of a recombinant pET-Rep plasmid is confirmed by amplification and verification of the nucleotide sequence through sequencing techniques. Nucleotide sequence verification results proved that the Rep [C1] gene is successfully constructed into a pET-28a+ plasmid with proper position and orientation. The pET-Rep recombinant proceeds to the expression test using the E.coli BL21 host. Expression was performed using the induction method with IPTG. Proteins Rep is purified using the MagnehisTM Protein Purification System. Rep protein is visualized with SDS-PAGE. Visualization showed that Rep protein was successfully expressed in E.coli BL21 where protein size is estimated of 41,03 kDa in size.
Prediction of secondary, tertiary protein structure and interaction eIF4E from Capsicum annum with Rep Geminivirus
Authors: Hidayati R , Nova B , Jamsari J
Published: June 2020

The eIF4E gene is a gene that plays a role in the initiation of protein translation. This gene is relatively conserved and is present in all organisms. In humans, this gene functions as a proto-oncogene, its expression and activation are associated with transformation and tumorigenesis. The eIF4E protein takes a role in the translation initiation by recruiting ribosomes to the 5’-cap structure. In some conditions, it functions as an initiator in the process of translation and co-factor of the plant’s defense system from virus attacks. The eIF4E protein also can bind with the genome linked viral protein to turnip mosaic virus [TuMV] in Capsicum annum. Their interaction is effective for virus infectivity and upregulated genome amplification. Understanding the tertiary structure of the eIF4E protein and its ligands will help in elucidating its interactions with viruses. So that it can be used to avoid spreading the virus in chili plants.
Effects of the entomopathogen concentration of Beauveria Bassiana [Bals] Vuil for biological control of Helicoverpa armigera Hubner [Lepidoptera : Noctuidae]
Authors: Nelly N , Reflin R , Hidayat Y A
Published: June 2020

Beauveria bassiana is an entomopathogenic fungus found in the rhizosphere, known to affect the mortality of H. Armigera. The research was conducted at the Laboratory of Biological Control, Department of Plant Protection, Faculty of Agriculture, Andalas University, from January 2019 to March 2019. The aim of this study, therefore, is to obtain an effective concentration with the optimal characteristics of controlling H. armigera, utilizing a completely randomized design, with 4 treatments and 5 replications. In addition, the treatment required the application of B. bassiana suspension, at a concentration of [A] 5×107 conidia/ml, [B] 1×108 conidia/ml, [C] 5×108 conidia/ml and [D] control [distilled water]. The results showed the treatment with the highest concentration [5×108 conidia/ml] possessed the ability to increase the mortality rate by 68% in the larvae of H. armigera, at an LT50 of 5.82 days. Hence, a higher concentration affects the lifespan, and nature of pupae, and adult pests formed.
West Sumatera brown rice resistance to brown planthopper
Authors: Busniah M , Kasim M , Winarto W
Published: June 2020

Rice is the main staple food for half of the world’s global population. One of the superior rice variety indicators is resistance to brown planthopper. The study was aimed to analyze several West Sumatera rice varieties against brown planthopper. The research was conducted in the screen house, Faculty of Agriculture, Andalas University, Padang, Indonesia from April to October 2018. A completely randomized design was used in this study. Nine rice genotypes and one control variety were used in this assay. The treatment was replicated three times. The result showed that Batang Sungkai was the best genotype in resistance based on the attack intensity.
Effectiveness of the combination of attractants and colors in trapping fruit flies [Bactrocera spp] on chili plant [Capsicum annuum L.]
Authors: Suwinda S , Wilyus W , Novalina N
Published: June 2020

The research was carried out to examine the effect of attractants and the color of traps in trapping fruit flies [Bactrocera spp.]. The research was done by using Randomized Block Design [RBD] with 2 factors and 3 replications. The first factor was the type of attractants consisted of 3 levels; A0 [methyl eugenol + water], A1 [methyl eugenol + guava juice], and A2 [methyl eugenol + starfruit juice]. The second factor was the colors of trap consisted of 4 levels; B0 [without color [transparent]], B1 [red], B2 [yellow], and B3 [green]. The result shows that: trap A1B3 [methyl eugenol and guava juice as an attractant, green trap] was a type of trap that has the broadest spectrum to attract and trap various species of fruit flies. There was no significant effect of adding color to traps in attracting and trapping male fruit flies. Male fruit flies generally were more attracted and more trapped in traps with methyl eugenol as attractants than the traps added with fruit juice. Female fruit flies were attracted and trapped only in a trap with attractants containing fruit juice as an attractant.
Diversity of Hymenopteran parasitoid in agricultural and primary forest in Lubuk Kilangan, Padang, West Sumatera, Indonesia
Authors: Busniah M , Hakiki A , Martinius M
Published: June 2020

A hymenopteran parasitoid is an important natural enemy for many orders of insect pests. This group can control pests specifically in the agricultural ecosystem. The research aimed to study the diversity of hymenopteran parasitoids in the agricultural and primary forest ecosystems. A purposive random sampling method was used to determine the research location. Malaise and yellow trap were used to collect the samplings. The research location was agricultural and primary forest ecosystems. The result showed that families of the hymenopteran parasitoid in the dominant number of individuals and morphospecies were Braconidae, Ichneumonidae, and Scelionidae. According to the result, the diversity index in both ecosystems was high [4.879 for primary forest and 4.675 for agricultural]. The evenness index in both ecosystems was also high [0.905 for primary forest dan 0.887 for agricultural forest]. The similarity index in both ecosystems was classified as high [0.607 respectively].
Application of solid and liquid organic matter to increase P availability in Inceptisol
Authors: Banamtuan E , Suwardi S , Iskandar I , Sumawinata B
Published: June 2020

Phosphorus is an essential nutrient for plant growth, but its supply in the soil is limited by two constraints, namely small in amount and small in its availability. In acidic soil, P is tied up by Al and Fe, while in high soil pH, P is bound by Ca. Thus, to increase the availability of P in the soils, prepared organic matter may be added. The quality of prepared organic matter depends on the type of source material, composting process, and the method of application. To find out the effects of applying solid and liquid organic matter on the availability of P in the soil, this glasshouse experiment involving the application of five treatments of organic matter on corn, which was planted in Inceptisol, was conducted. Two organic matters used were solids: cow manure compost [CMC] and goat manure compost [GMC]; and the other three were in liquid form: composted cow manure extract [CCME], composted goat manure extract [CGME], and humic substance [HS]. Based on the results on the observed parameters, at 7 weeks after planting, the application of CMC produced the highest increase in available-P in the soil, followed by GMC, HS, CGME, and CCME, in that order. In either solid or liquid form, the applied organic matter significantly raised available-P, total-N, organic-C, cation exchange capacity [CEC], soil electrical conductivity [EC], and exchangeable bases in the soil, with the solid organic matters performing better, overall, than their liquid counterparts. Future research on closely related technical and economic aspects is recommended.
Organic carbon sequestration at different age of tea [Camelia sinensis] plantation under the wet tropical area
Authors: Yulnafatmawita Y , Yasin S , Haris Z A
Published: June 2020

Soil organic carbon [OC] sequestration is affected by some factors, one of which is the vegetation living on it. Tea is a crop on which the part being harvested is the leaves, which are supposed to contribute to soil OC. The objective of the research was to determine the amount of OC sequestered at different crop age under tea plantation in wet tropical areas. The soil samples were taken from 3 different crop ages [36, 21, and 9 years old] under the same slope [>45%] and soil [volcanic] at ≥ 1,400 m asl. As a comparison, the soil was also sampled from the secondary forest around the research site. At each crop age and the forest, the soil was sampled for 100 cm depth with a 20 cm increment. Undisturbed soil samples were taken for soil BD and disturbed soil samples for OC. The result showed that SOC content decreased by soil depth, and the soil BD was not significantly different among the depths. Therefore, the amount of OC sequestered declined by decreasing soil depth. The SOC sequestration rate decreased by increasing the age of tea crop from 1.67 to 0.49 Mg/Ha/y/1-m depth respectively between 9-21 and 21-36 years old. Compared to the secondary forest, however, the OC sequestration under tea plantation improved by 1.50, 1.71, and 1.79 times as the age of tea crop increased from 9, to 21, and to 36 years old, respectively. It seems that tea cultivation is the potential to sequester OC even though the leaves are regularly harvested.
Effect of biochar from young coconut waste to improve chemical properties of ultisols and growth coffee [Coffea arabica L.] plant seeds
Authors: Herviyanti H , Maulana A , Prima S , Aprisal A , Crisna S D , Lita A L
Published: June 2020

This study aims to determine the effect of biochar from young coconut [Cocus nucifera L.] waste to improve the chemical properties of Ultisols and the growth of coffee [Coffea arabica] plant seeds. The research has been carried out at the Laboratory of Chemistry and Soil Fertility and Experimental wirehouse of the Faculty of Agriculture, Andalas University, Padang. This research used a Completely Randomized Design [CRD] with 3 replications. The formulation is biochar of young coconut waste/8 kg of soil ie: A = 0.0%; B = 0.5% [173 g]; C = 1.0% [348 g]; D = 1.5% [520 g]; and E = 2.0% [693 g]. The results of the utilization of young coconut waste as a source of biochar could improve the chemical properties of Ultisols. Addition 2% [693 g.8kg/lof soil] of biochar young coconut waste can increase pH and decrease Al and H-exch, so that increase available P, organic C and CEC by 1.70 ppm; 0.99% and 9.12 cmol[+].kg−1; compared to 0% of biochar. Application 1.5% [520g.8kg/lof soil] almost the same 2% of biochar young coconut waste to increase total N and exchangeable of the cation [K, Ca, and Mg]. Whereas addition up to 2% of biochar young coconut waste has not shown a significant increase in growth coffee [Coffee arabica L.] plant seed at the age of 3 months [12 after week planting].
Soybean seed [Glycine max L.] coated by fertile soil-applied sodium bicarbonate at alluvial soil
Authors: Jamilah J , Irawan N , Thesiwati A S , Ernita M
Published: June 2020

Soybean yields in Indonesia tend to be low, on average <1.5 Mg ha−1 and many of the needs are met through soybean imports. The purpose of this study was to determine the effect of seed coating and sodium bicarbonate on the growth and yield of soybeans in alluvial soils. The experiment was carried out at Alluvial soil in Padang, with an altitude of 10 m above sea level. The experiments were arranged in a completely randomized design in the factorial form. The first-factor was the application of coating material to soybean seeds consisting of 2 levels; uncoated and coated. The second factor was the application of sodium bicarbonate in the leaves of the plant consisting of 4 concentrations; 0%; 0.125%; 0.250% and 0.375%, with 3 replications. Data were analyzed statistically using F-tests 5% significance level. If the treatment had a significant effect, it will continue using the LSD test 5% significance level. The parameters of observations were made; plant height when the generative phase, the number of primary branches, the number of nodules, the number of pith pods, the weight of 100 seeds, dry weight of seeds per plot. The result showed that the application of coating materials on soybean seeds and 0.125% sodium bicarbonate sprayed on the leaves increase the growth and yield of soybean Anjasmoro variety with the highest seed yield was 1.90 Mg ha−1.
Soil chemical characteristics at three slope positions in the smallholder’s Piper nigrum L. in Lhokseumawe City, Aceh Province
Authors: Yusra Y , Khusrizal K , Diannastiti F A
Published: June 2020

The spatial variation of soil properties is significantly influenced by several factors. Slope position belongs to a component of topography as one soil-forming factor which would be influenced by soil development. The purpose of this study is to understand the pedogenesis of soil chemical characteristics on the diversity of slope positions in the smallholder’s Piper nigrum L. in Lhokseumawe City Aceh Province, start from October to December 2017. The research was conducted using the descriptive survey method and fifteen soil samples from three slope positions, i.e. upper slope position [33%], middle slope position [22%], and lower slope position [6.6%] were collected. The soil samples were analyzed using appropriate methods such as soil pH using pH meter, soil organic carbon using Walkley and Black, total nitrogen using Kjehdahl, available phosphorus using Bray II, and potassium exchangeable using Morgan. This research has studied the correlation between soil chemical properties and the differentiation of soil chemical characteristics at each slope position by the DMRT test method. The result showed that the slope position affected soil chemical properties. The slope position had affected water movement from the upper to the lower slope position and this process caused variation of soil chemical characteristic formation. The value of soil pH, soil organic carbon, total nitrogen, available phosphorus, and potassium exchangeable was higher in the lower slope position than those in the middle and upper slope positions.
Palm Oil Fuel Ash [POFA]: innovative potential applications as heavy metal removal materials in gold mining wastewater
Authors: Riduan A , Rainiyati R , Heraningsih S F
Published: June 2020

Gold mining wastewater contains heavy metals hazardous to the environment. The alternative solution to overcome the contamination problems was using adsorbent to reduce the amount of heavy metal content in the wastewater. Palm oil fuel ash [POFA] as a potential adsorbent to absorb the heavy metal content. This current study focused on the application of palm oil fuel ash [POFA] for the removal of heavy metal in the environment. The technology used in this study was the combination of adsorption and precipitation methods. Gold mining wastewater and supernatant were analyzed using Inductively Coupled Plasma [ICP] mass spectrometers. The result of this study showed that the level of heavy metals in the gold mining wastewater was successfully reduced at large amounts and that the POFA had a good adsorption capability.
Marketing performance of Kopi Solok Radjo in industrial revolution 4.0 [a case study of Solok Radjo cooperative in Solok District
Authors: Yusmarni Y , Putri A , Paloma C
Published: June 2020

The concept of marketing is currently experiencing development along with the advancement of society and technology. A company needs to be transformed into an intelligent organization to achieve the best business results. Nowadays we enter the digital transformation of the industry which is called Industry 4.0. In terms of marketing, recently digital technology plays a significant role in expanding the market and increasing the company sale. A company can advertise and sell their product using various internet platforms such as social media, websites, blogs, and online market application that can reach consumers all over the world. This research aimed to describe the performance of the marketing mix of Kopi Solok Radjo from the consumers’ point of view and to analyze the effect of the marketing mix on the consumers’ decision to purchase. The study finds that the performance of Kopi Solok Radjo’s marketing mix is good, where a score of all variables is in the category of high. Moreover, this study used multiple regression analysis to assess the effect of the marketing mix on consumers’ decision to purchase Kopi Solok Radjo. The research finds that all variables simultaneously affect the consumers’ decision to purchase. However, a partially only variable of promotion affects the purchasing decision. Solok Radjo Cooperative has employed digital promotion to reach the wider market. The digital marketing and promotion employed by the cooperative are the website, social media application [Instagram, Twitter and Facebook], and online marketing applications [Tokopedia and Shopee]. Ever since the cooperative used online promotion, the market has reached international markets such as Singapore, Australia, and the USA.
The existence of traditional medicinal plants in megapolitan city communities
Authors: Siregar R S , Pulungan D R , Khairani L , Lubis S
Published: June 2020

The purpose of this study is to explain and analyze people’s perceptions of medicinal plants in Medan seen from personal factors, group influence factor, cultural factor, cultivation and marketing of medicinal plants in Medan. The population was all people of Medan who used traditional medicinal plants that were randomly selected to be used as research samples. Primary data were obtained using a questionnaire and using a Likert Scale analysis tool and confirmatory factor analysis using AMOS software. The results showed that people’s perception of traditional medicinal plants in the city of Medan was positive. All factors that support people’s perception of medicinal plants are proven to be accepted and approved. People of Medan believe in medicinal plants in curing various diseases and increasing body immunity. This has an impact on the use of home yards and agricultural land as a location for the cultivation of traditional medicinal plants, as well as selling to various districts in the Province of North Sumatra.
The influences of driving forces on behaviors of Na+ and H2O in cyclic octa-peptide nanotube: investigated by steered molecular dynamics
Authors: Shan Tianjiao , Zhao Xiaoguang , Liang Haihai
Published: June 2020

The behaviors of Na+ and H2O in cyclic peptide nanotube (CPN) under different conditions are important for their applications. In this study, a series of driving forces has been applied to Na+ and H2O constrained in the self-assembled nanotube of {cyclo[(-D-Ala-L-Ala)4-]}10, to understand the influence on the transport properties and behaviors of Na+ and H2O using steered molecular dynamics (SMD). The results show that H2O need less driving force (0.4 kcal mol−1 Å−1) to migrate in the nanotube than that of Na+ (2.3 kcal mol−1 Å−1). Under the same driving force, the transport speed of H2O is about 135 times faster than that of Na+. The instantaneous velocity curves reveal that water adopts a kind of irregular hopping transport mode which does not change with the driving force, while Na+ transports in an obvious hopping mode changing with driving force in three different types. Particularly, the instantaneous velocity curves of Na+ under the driving force of 3.2–5.2 kcal mol−1 Å are roughly similar to the pulse signal, which is of great significance to the treatment of human diseases and the detection of electrolytes. The transport resistance mainly comes from electrostatic interaction. Results in this work show that cyclic octa-peptide nanotubes have excellent performance sensitive to external driving forces and are good potential materials for drug design, biosensors, ion transmembrane transport and ion probe for the detection of Na+ in organisms.
Synthesis of Mn-doped CsPbClxBr3−x perovskite nanocrystals using ultrasonic irradiation-promoted with decrease of reaction order
Authors: Xu Shuhong , Zhang Ruohu , Wu Hao , Cui Yiping , Wang Chunlei , Shao Haibao
Published: June 2020

The incorporation of impurity cation as a way of introducing various novel functionalities provides an additional level of control over the electronic and optical properties of perovskite nanocrystals (NCs). However, the conventional post-synthetic cation exchange approaches suffer from large time and energy consumption. In this work, we developed a novel one-pot method to synthesize Mn-doped CsPbClxBr3−x NCs by merit of sonochemical technique, achieving dramatically rapid reduce of time and energy consumption. The localized hot spots with high transient temperature, pressure, and cooling rate, as well as an excellent stirring action of ultrasonic preparation facilitate the diffusion of Mn2+ in perovskite lattice. Besides, further reaction kinetics investigation reveals an apparent decrease of reaction order from original method (2.4) to our ultrasound-assisted method (1.0).
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook
Authors: Foerster Hartmut , Battey James N D , Sierro Nicolas , Ivanov Nikolai V , Mueller Lukas A
Published: June 2020

Manually curated metabolic databases residing at the Sol Genomics Network comprise two taxon-specific databases for the Solanaceae family, i.e. SolanaCyc and the genus Nicotiana, i.e. NicotianaCyc as well as six species-specific databases for Nicotiana tabacum TN90, N. tabacum K326, Nicotiana benthamiana, N. sylvestris, N. tomentosiformis and N. attenuata. New pathways were created through the extraction, examination and verification of related data from the literature and the aid of external database guided by an expert-led curation process. Here we describe the curation progress that has been achieved in these databases since the first release version 1.0 in 2016, the curation flow and the curation process using the example metabolic pathway for cholesterol in plants. The current content of our databases comprises 266 pathways and 36 superpathways in SolanaCyc and 143 pathways plus 21 superpathways in NicotianaCyc, manually curated and validated specifically for the Solanaceae family and Nicotiana genus, respectively. The curated data have been propagated to the respective Nicotiana-specific databases, which resulted in the enrichment and more accurate presentation of their metabolic networks. The quality and coverage in those databases have been compared with related external databases and discussed in terms of literature support and metabolic content.
DeepEventMine: end-to-end neural nested event extraction from biomedical texts
Authors: Trieu Hai-Long , Tran Thy Thy , Duong Khoa N A , Nguyen Anh , Miwa Makoto , Ananiadou Sophia
Published: June 2020

Motivation

Recent neural approaches on event extraction from text mainly focus on flat events in general domain, while there are less attempts to detect nested and overlapping events. These existing systems are built on given entities and they depend on external syntactic tools.

Results

We propose an end-to-end neural nested event extraction model named DeepEventMine that extracts multiple overlapping directed acyclic graph structures from a raw sentence. On the top of the bidirectional encoder representations from transformers model, our model detects nested entities and triggers, roles, nested events and their modifications in an end-to-end manner without any syntactic tools. Our DeepEventMine model achieves the new state-of-the-art performance on seven biomedical nested event extraction tasks. Even when gold entities are unavailable, our model can detect events from raw text with promising performance.

Availability and implementation

Our codes and models to reproduce the results are available at: https://github.com/aistairc/DeepEventMine.

Supplementary information

Supplementary data are available at Bioinformatics online.
Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes versus disordered proteins
Authors: Zhang Jian , Ghadermarzi Sina , Kurgan Lukasz
Published: June 2020

Motivation

There are over 30 sequence-based predictors of the protein-binding residues (PBRs). They use either structure-annotated or disorder-annotated training datasets, potentially creating a dichotomy where the structure-/disorder-specific models may not be able to cross-over to accurately predict the other type. Moreover, the structure-trained predictors were shown to substantially cross-predict PBRs among residues that interact with non-protein partners (nucleic acids and small ligands). We address these issues by performing first-of-its-kind comparative study of a representative collection of disorder- and structure-trained predictors using a comprehensive benchmark set with the structure- and disorder-derived annotations of PBRs (to analyze the cross-over) and the protein-, nucleic acid- and small ligand-binding proteins (to study the cross-predictions).

Results

Three predictors provide accurate results: SCRIBER, ANCHOR and disoRDPbind. Some of the structure-trained methods make accurate predictions on the structure-annotated proteins. Similarly, the disorder-trained predictors predict well on the disorder-annotated proteins. However, the considered predictors generally fail to cross-over, with the exception of SCRIBER. Our study also reveals that virtually all methods substantially cross-predict PBRs, except for SCRIBER for the structure-annotated proteins and disoRDPbind for the disorder-annotated proteins. We formulate a novel hybrid predictor, hybridPBRpred, that combines results produced by disoRDPbind and SCRIBER to accurately predict disorder- and structure-annotated PBRs. HybridPBRpred generates accurate results that cross-over structure- and disorder-annotated proteins and produces relatively low amount of cross-predictions, offering an accurate alternative to predict PBRs.

Availability and implementation

HybridPBRpred webserver, benchmark dataset and supplementary information are available at http://biomine.cs.vcu.edu/servers/hybridPBRpred/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Closure coefficients in scale-free complex networks
Authors: Stegehuis Clara
Published: June 2020

The formation of triangles in complex networks is an important network property that has received tremendous attention. The formation of triangles is often studied through the clustering coefficient. The closure coefficient or transitivity is another method to measure triadic closure. This statistic measures clustering from the head node of a triangle (instead of from the centre node, as in the often studied clustering coefficient). We perform a first exploratory analysis of the behaviour of the local closure coefficient in two random graph models that create simple networks with power-law degrees: the hidden-variable model and the hyperbolic random graph. We show that the closure coefficient behaves significantly different in these simple random graph models than in the previously studied multigraph models. We also relate the closure coefficient of high-degree vertices to the clustering coefficient and the average nearest neighbour degree.
Are Quality Metrics in Inflammatory Bowel Disease Rooted in Substantial Quality Evidence? A Systematic Review
Authors: Weissman Simcha , Goldowsky Alexander , Mehta Tej I , Sciarra Michael A , Feuerstein Joseph D
Published: June 2020

Background and Aims

Quality metrics were established to develop standards to help assess quality of care, yet variation in inflammatory bowel disease [IBD] clinical practice exists. We performed a systematic review to assess the overall quality of evidence cited in formulating IBD quality metrics.

Methods

A systematic search was performed on PubMed, MEDLINE, and EMBASE. All major national and international IBD societies were included. Quality metrics were assessed for evidence quality and categorised as category A [guideline based], category B [primarily retrospective and observational studies], or category C [expert opinion]. Quality metrics were examined for the type of metric, and the quality, measurability, review, existing conflicts of interest [COI], and patient participation of the metric. Statistical analysis was conducted in R.

Results

A total of 143 distinct, and an aggregate total of 217 quality metrics were included and analysed; 68%, 3.2%, and 28.6% of IBD quality metrics were based on low, moderate, and high quality of evidence, respectively. The proportion of high-quality evidence across societies was significantly different [p <0.01]. Five organisations included patients in quality metric development, three reported external review, not all reported measurable outcomes or stated the presence of a COI. Finally, 43% of quality metrics were published more than 5 years ago.

Conclusions

Quality metrics are important to standardise practice. As more than two-thirds of the quality metrics in IBD are based on low-quality evidence, further studies are needed to improve the overall quality of evidence supporting the development of quality measures.