bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic stability of in vitro propagated transgenic Acacia mangium expressing xyloglucanase
Authors: Utami N , Hartati S , Salamah A 
Published: April 2020

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractThis 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

Abstract
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

Abstract
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

Abstract
“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.
Shale structure implication in hydraulic fracturing production results: Case study in low resistivity low quality reservoir, offshore North West Java area
Authors: Kusuma D P , Haris A , Astuti T R P , Wibowo R A , Riyanto A , Saputra L I 
Published: April 2020

Abstract
Low-resistivity & low-quality reservoir has been successfully developed in ONWJ area by using hydraulic fracturing stimulation method to optimize production gain due to low-permeability reservoir property. The purpose of this research is to understand implication of shale structure for increasing gain production after hydraulic fracturing stimulation. Implementation of hydraulic fracturing was first completed at BerylE-1 and the well could produce 455 BOPD at 560 psi in reservoir 33 and 35. This reservoir was found in Upper Cibulakan Formation that consists of various lithology’s such as very fine-grained sandstone, shale, siltstone & thin tight carbonate that deposited in shallow marine neritic to littoral environment. Production anomaly occurs after hydraulic fracturing stimulation. Some of well in this reservoir show good incremental production, but in the other well there was no significantly incremental production in this reservoir. There were three types of shale structure classification based on effective porosity distribution: laminated shale, structural shale and dispersed shale. Shale structure for each well has been defined based on Thomas Stieber plot and calibrated using petrographic analysis from 8 sample depth point. Based on this method, reservoir 33 is dominated by structural shale while reservoir 35 is dominated by laminar shale. Production data and shale type from each well has been compared and it shows that hydraulic fracturing simulation will increase effective porosity and will also increase effective permeability value. In BerylD-1 well hydraulic fracturing only completed in reservoir 35 and produced 340 BOPD with initial water cut 0 %. Laminar shale that dominates in reservoir 35 has high factor to increasing production gain after hydraulic fracturing was applied. Release of clay that caused by hydraulic fracturing will increase effective porosity and permeability.
Estimation of rice productivity using Sentinel-2 imagery with NDVI algorithm in Cariu sub-district, Bogor, West Java
Authors: Sahararini A F , Supriatna  , Wibowo A 
Published: April 2020

Abstract
Cariu Sub-District is one of the leading rice producers in Bogor Regency, West Java, Indonesia and in a population of 45,921 in 2017 with a population growth rate of 0.64% based on projection results. The consequence of the increasing population growth rate is increasing rice consumption. Cariu Sub-District has not been able to self-sufficient food. In 2017, Cariu Sub-District had 5,107 hectares of rice harvested area with the productivity of 5.99 ton/hectares. Therefore, it is important to update information about rice planting areas in order to estimate its productivity accurately and to maintain Indonesian especially Cariu Sub-District food needs. This study aims to estimate the rice productivity in Cariu Sub-District, Bogor in 2017 using Sentinel-2 imagery based on remote sensing. In this study, NDVI (Normalized Difference Vegetation Index) method used for determines the rice growth phase. The result shows that the Sentinel-2 image utilization with NDVI algorithm can estimate rice productivity in 2017 in Cariu Sub-District. It was expected that the rice productivity obtained is almost by the data from the Department of Agriculture and Forestry in the Cariu Sub-District.
Estimation of erosion rate in Cileungsi upper watershed Bogor Regency
Authors: Widyasa P A , Kusratmoko E , Marko K 
Published: April 2020

Abstract
Land use of upper watersheds Cileungsi located in Bogor, West Java has always progressed from year to year due to increased human activities that have an impact on land degradation such as erosion. Soil erosion in Java estimated the loss of US $400 million per year. This study aims to estimate of erosion rate by using the Modify Universal Soil Loss Equation (MUSLE) is already integrated into the modeling Soil and Water Assessment Tool (SWAT). SWAT can provide simulation results based on the physical characteristics of the Hydrological Response Unit (HRU) that is considering climate parameters such as rainfall, temperature, solar radiation, humidity, and wind speed. The results showed that the highest rate of erosion on the upstream sub-basin 15 (Ci Janggel) to contribute to the erosion of 184 tons/ha/year classified as heavy erosion. The high rate of erosion occurs on the characteristics of the area with 25–45 % of slope, clay loam soils, land use, and agricultural drylands.
Water quality analysis of Saluran Tarum Barat, West Java, based on National Sanitation Foundation-Water Quality Index (NSF-WQI)
Authors: Cristable R M , Nurdin E , Wardhana W 
Published: April 2020

Abstract
The Saluran Tarum Barat, which is 68.74 kilometers long, starts in Klari, Karawang, West Java, and ends in Cawang, East Jakarta. The Saluran Tarum Barat runs alongside human activities and various environmental conditions. The initial part of the Saluran Tarum Barat is surrounded by agricultural activities, the central part by industrial activities, and the final part by infrastructure development activities. Those various activities and environmental conditions may have different effects on the water quality of the Saluran Tarum Barat. The purpose of this research is to ascertainthe water quality of the Saluran Tarum Barat based on physical, chemical, and biological parameters determined through the National Sanitation Foundation-Water Quality Index (NSF-WQI) method. The results showed that the water quality is classified in the medium category, with a value range of 55.06–67.92.
Exposure pattern of tobacco cultivation places due to climate change in Probolinggo district, East Java
Authors: Sobirin  , Dzikraini F , Indra T L 
Published: April 2020

Abstract
Probolinggo District is one of the centers of tobacco producer in Indonesia, paiton tobacco as local varieties included in dry season type of tobacco (Voor Oogst). Rainfall as well as dry season dynamics in 2015 and 2016 which had already been global, is affected tobacco cultivation and additional values to farmers in Probolinggo district. This research has purpose to identify the exposure patterns of tobacco cultivation places in Probolinggo district related to climate change. Based on daily rainfall data during 1990–2016 from 50 rain gauge stations, parameters of exposure due to climate change are processed by using de Boer method and mapped by using Thiessen polygon method. Determination of level of exposure places are done by scoring method and map overlay technique, then associated with landuse. The analysis results showed that exposure pattern with low level tend to be in the coastal areas and lowlands, stretching from West to East. The higher elevation is, the higher level of exposure places.
Xerostomia and polypharmacy among dependent older New Zealanders: a national survey
Authors: Thomson William Murray , Ferguson Catherine Anna , Janssens Barbara E , Kerse Ngaire M , Ting Graeme S , Smith Moira B 
Published: April 2020

AbstractBackgroundMedication-induced xerostomia is common in older people. We investigated medication use and xerostomia in dependent older New Zealanders.MethodsMedication and xerostomia data analysed from a nationally representative survey of dependent older people. Automatic interaction detection analysis identified medications combinations most strongly associated with xerostomia, and then xerostomia was modelled.ResultsJust over half were taking five to nine different medications; one in five was taking 10+. Xerostomia prevalence (29.4%; 95% confidence interval 26.5, 32.5) was higher among the latter and lowest in psychogeriatric patients. After controlling for age and sex, it was higher among people taking any antidepressant, and higher still with a tricyclic antidepressant and either a steroid or an anticholinergic, or among people taking a bronchodilator without prophylactic aspirin.ConclusionsHealth practitioners should work together to ensure that those with xerostomia are managed in a timely and appropriate manner. Medication review is an important component of that.
Steatohepatitis-Like Changes in Hepatocellular Adenoma
Authors: Liu Yongjun , Zen Yoh , Yeh Matthew M 
Published: April 2020

AbstractObjectivesOur aim was to investigate the frequency of steatohepatitic morphology in hepatocellular adenoma (HCA) and correlate with its clinical parameters and risk factors underlying nonalcoholic fatty liver disease (NAFLD) or nonalcoholic steatohepatitis (NASH).MethodsWe examined a series of 41 liver resection specimens diagnosed with HCA for steatohepatitic changes. Background nonneoplastic liver was also evaluated. Clinical records were reviewed for risk factors of NAFLD/NASH.ResultsSix steatohepatitic HCAs (SH-HCAs) were identified, with an overall prevalence of six (14.6%) of 41, of which three were HNF1α inactivated and three were inflammatory, but none were β-catenin mutated. Five of the six patients with SH-HCA had at least one known risk factor for NAFLD/NASH, including obesity (n = 4; 66.7%), diabetes (n = 5; 83.3%), hypertension (n = 3; 50%), and dyslipidemia (n = 1; 16.7%). Compared with the patients without SH-HCA, the patients with SH-HCA had a higher frequency of type 2 diabetes, obesity, and hypertension. Of the six SH-HCAs, background nonneoplastic liver showed significant steatosis in three (50%) cases and steatohepatitic changes in one (16.7%) case.ConclusionsApproximately 15% of HCAs in our series demonstrated steatohepatitic changes. Lack of such morphology in β-catenin–mutated subtype suggests reassurance in this morphologic variant of HCA.
‘They know they’re not coming back’: resilience through displacement in the riskscape of Southwest Washington, DC
Authors: DiValli Jesse , Perkins Tracy 
Published: April 2020

Abstract
The lack of a strong national US strategy to respond to the threat of climate change places significant responsibility on urban areas to mitigate their risks through resilience planning. However, urban riskscapes include a complex and unequal layering of risks, with historically disadvantaged populations often bearing the brunt of many forms of cumulative risk while realising the fewest benefits from urban amenities. This article contributes to scholarship on resilience planning through an analysis of current development plans and resident perceptions in a neighbourhood in Southwest Washington, DC, by integrating insights on social inequality from the study of urban development, social capital and riskscapes.
Quantifying technical confounders in microbiome studies
Authors: Bartolomaeus Theda U P , Birkner Till , Bartolomaeus Hendrik , Löber Ulrike , Avery Ellen G , Mähler Anja , Weber Daniela , Kochlik Bastian , Balogh András , Wilck Nicola , Boschmann Michael , Müller Dominik N , Markó Lajos , Forslund Sofia K 
Published: April 2020

Abstract

Aims
Recent technical developments have allowed the study of the human microbiome to accelerate at an unprecedented pace. Methodological differences may have considerable impact on the results obtained. Thus, we investigated how different storage, isolation, and DNA extraction methods can influence the characterization of the intestinal microbiome, compared to the impact of true biological signals such as intraindividual variability, nutrition, health, and demographics.

Methods and results
An observative cohort study in 27 healthy subjects was performed. Participants were instructed to collect stool samples twice spaced by a week, using six different methods (naive and Zymo DNA/RNA Shield on dry ice, OMNIgene GUT, RNALater, 95% ethanol, Zymo DNA/RNA Shield at room temperature). DNA extraction from all samples was performed comparatively using QIAamp Power Fecal and ZymoBIOMICS DNA Kits. 16S rRNA sequencing of the gut microbiota as well as qPCRs were performed on the isolated DNA. Metrics included alpha diversity as well as multivariate and univariate comparisons of samples, controlling for covariate patterns computationally. Interindividual differences explained 7.4% of overall microbiome variability, whereas the choice of DNA extraction method explained a further 5.7%. At phylum level, the tested kits differed in their recovery of Gram-positive bacteria, which is reflected in a significantly skewed enterotype distribution.

Conclusion
DNA extraction methods had the highest impact on observed microbiome variability, and were comparable to interindividual differences, thus may spuriously mimic the microbiome signatures of various health and nutrition factors. Conversely, collection methods had a relatively small influence on microbiome composition. The present study provides necessary insight into the technical variables which can lead to divergent results from seemingly similar study designs. We anticipate that these results will contribute to future efforts towards standardization of microbiome quantification procedures in clinical research.