bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein structure determination as a powerful tool for the sustainable development of agriculture field (and its potential relevance in Indonesia)
Authors: Koesoema A A 
Published: February 2022

Abstract
Traditional agricultural practices, such as classical plant breeding and pest management, have been utilized for many years to increase crop yield and improve its properties. However, more effective and sustainable practices are needed to meet the increasing global demands for agricultural-based products. In the past decades, DNA recombinant technology, and protein structure determination have been employed as a tool for the development of the agricultural field. Protein structure determination enables us to understand the structure-function relationship of a given protein, such as plant hormone, receptor, or growth regulators, thus introducing modifications to improve the properties of the crop. This review introduces the latest development of protein structure determination techniques ranging from X-ray crystallography, protein NMR, and cryo-electron microscopy. Notable examples of how these techniques can be utilized as a powerful tool for the sustainable development of the agricultural field, including their potential relevance in Indonesia, are introduced.
Combination of dry-wet land Preparation to Increase Plant Population and Yield under Direct Seeding Rice
Authors: Susanti Z. , Sakai C. , Sasmita P. , Hikmah Z.M. , Budijaya N. , Shin Y. , Meiyanto S. 
Published: February 2022

Abstract
Rice as a staple food for more than half of the world’s population is commonly grown by transplanting seedlings into puddled soil. Lack of labour and water crisis drive the search for alternative planting system. Direct Seeding Rice (DSR) method may significantly decrease the cost of crop establishment, however, DSR required improvement in land preparation to maintain seed germination. Combination of dry-wet land preparation using Farming Bulldozer (FB) and DSR lead to higher yield due to increasing of plant population. A field experiment was carried out in the 2020 Wet-season at ICRR to examine 2 methods of puddling and different planting system. The study was arranged in a fractional factorial design. The first factor was land preparation which were (L1): land preparation using FB and (L2): hand tractor. The second factor was crop establishment, (D1); DSR using drum seeder with iron-coated seed, (D2) DSR using drum seeder with non-coated seed and (D3): transplanting. Each treatment was set in 5000 m2, with 4 replications. The results showed that (1) combination of dry-wet land preparation and DSR iron-coated yielded at 5478 kg/ha, significantly higher compared to hand tractor (HT) and DSR-non coated seed which yielded at 3698kg/ha. (2) The key yield component that had a large influence on grain yield under direct seeding was the number of productive panicles per m2. Perfect land levelling was crucial to maintain high percentage of seeds germination leaded to sufficient number of standing crop (tiller) per area.
The expression of novel PII-like protein from Lentilactobacillus hilgardii
Authors: Iskhakova Z , Zhuravleva D , Matigorova V , Kayumov A 
Published: February 2022

Abstract
The understanding of molecular mechanisms of bacterial adaptation to environmental changes represents the basis for maintaining the homeostasis of microbiomes of natural and artificial biotopes. Lactic acid bacteria are presented everywhere in the environment and present the indigenous microflora of various fermented substrates, fruits, soil and feces. In natural habitats the starvation by available nitrogen, carbon or energy sources can occur. Nevertheless, the regulation of their nitrogen metabolism remains unexplored and is presented only in a few works. Generally, in the most bacteria the nitrogen metabolism is regulated by PII like proteins in response to the nutrition and energy availability via sensing changes of intracellular level of ATP, ADP, 2-OG and glutamine. Among more than 400 species of Lactobacillaceae known to the date, only seven contain genes encoding for PII homologue. In Lentilactobacilli, the gene of PII-like proteins has unique genetic background being located within the potABCDN operon, which encodes the ABC transporter of spermidine/putrescine, the products of amino acids metabolism. These molecules contain multiple amino groups and thus could also serve as nitrogen source. The maximum expression of the potABCDN operon was observed upon transfer to a medium containing spermidine as solely nitrogen source, while is suppressed upon growth with glutamate and glutamine. This suggests the availability of energy supply as the leading factor determining the level of potABCDN operon transcription in L. hilgardii cells.
Resistance of several Banten local rice varieties (Oryza sativa L) towards brown planthopper (Nilaparvata lugens Stal.) attack as potential genetic resources
Authors: Hastuti D , Yenny R F , Susilawati P N , Welasih A P 
Published: February 2022

Abstract
The purpose of this study was to investigate the genetic resistance of 12 local varieties of rice (Oryza sativa L.) from Lebak, Banten Province, Indonesia to Brown Planthopper (BPH) (Nilaparvata lugens Stal.). The DNA amplification of PCR with SSR marker was analyzed by scaling the emerging tape and the allele size on the associated marker by using the gel analizer software and determined the percentage of polymorphism by calculating the total of polymorphic alleles in each primer. Datas were also analyzed in relation of plant familiarity patterns by using NTSys software to determine the right elders in the assembly of new improved varieties. The results showed that the varieties were suspected to have similar resistance if they had the same allele size with the differential varieties, the Sereh Variety in the Bph1 resistance genes, Tambleg variety in the Bph3 resistance genes, Cireh Gudang variety in the Bph2&3 resistance genes, and Caok Variety in the Bph4 resistance genes. Cireh Gudang varieties are suspected of having horizontal resistance as they are supported by the polygenic resistance genes in the Bph2&3 genes. Tambleg variety have the closest genetic similarities to the differential varieties, so it is presumed to be the best variety to be used as an elderly superior varieties of brown planthopper resistant, followed by Sereh and Cireh Gudang varieties.
The Effect of Bio-Fertilizer Applications Bacillus cereus and Lysinibacillus sp On Paprika Plants (Capsicum annuum L) On Plant Nutrient Content and Cultivation Media
Authors: Sodiq Abdul Hasyim , Setiawati Mieke Rochimi , Santosa Dwi Andreas , Widayat Dedi 
Published: February 2022

Abstract
This study conducted several applications of biofertilizer Bacillus cereus and Lysinibacillus sp on two doses of chemical fertilizer to find out the impact of the use of biofertilizers on paprika cultivation. The design of the research experiment used is a randomized design group of factorial patterns with two factors, the first factor is the use of biofertilizers with seven levels. The second factor is the use of chemical fertilizer doses consisting of two levels. Parameters observed in the laboratory include nutrient content N, P, K plant, and cultivation media. The results showed the nutrient content of P and K plants the highest yields were indicated by bio-fertilizer isolated 2 (P2) and biofertilizer consortium (P4) with a dose of chemical fertilizer 75% (A2). The total nutrient content of the planting media 2 best results are indicated by the treatment of biofertilizer isolated 1 (P1) and biofertilizer isolated 2 (P2) with 100% chemical fertilizer (A1). Bio-fertilizers Isolated Bacillus subtilis 1 and Bacillus subtilis 2 and Lysinibacillus sp. needs to be tested functionally as a nutrient-producing microbe as an absolute technical requirement of biofertilizer products by Ministry of Agriculture standards.
Internal factors and competency on the performance model of self-support agricultural extensional agents in Serang City
Authors: Fauzan A , Mirajiani  , Mulyaningsih A 
Published: February 2022

Abstract
This study was conducted to analyze the internal factors that affect the competence and performance of self-support agricultural extension agents in Serang City. The study was designed as explanatory research, which explains the variables’ position and the causal relationship between variables with a quantitative approach using Partial Least Square (PLS) analysis. Data collection was carried out from April to June 2021 with 34 respondents. The types of data collected were primary and secondary data. The data scale in this study was in the form of ratio data for internal factor variables and ordinal data for competence and performance variables. Based on the data processing results on the performance model of self-support agricultural extension agents in Serang City, it can be concluded that internal factors have a significant direct influence on competence with an influence value of 0.354. Internal factors also significantly influence the performance of self-support agricultural extension agents either directly with a value of 0.297 or indirectly through the competence variable with a value of 0.223. Competence also has a significant effect on performance, with a value of 0.631. Internal factors include training, experience, cosmopolitanism, and social status aspects. Competence must be enhanced to increase the performance of self-supporting agricultural educators. Competence of self-support agricultural teachers refers to the ability and capacity of self-support agricultural instructors to perform their duties. Enhancing the competence and performance of self-supporting agricultural extension workers can be accomplished by boosting their internal factors such as training, experience, and global exposure through training, internships, courses, and coordination meetings. Meanwhile, when recruiting independent agricultural extension workers, socioeconomic status might be considered.
Farmers’ perceptions towards local food in Pandeglang Regency
Authors: Mulyaningsih A , Astuti A , Sari R M 
Published: February 2022

Abstract
Consumption of corn, cassava, and sweet potatoes is closely related to people’s perceptions of local non-rice food. This study was conducted to determine farmers’ perceptions of local food corn, cassava, and sweet potatoes and to explore the obstacles faced in realizing food diversification. The study was conducted from February to April 2021 in Pandeglang Regency, Banten, which is the center of corn, cassava and sweet potato plants. The research method used a survey method to 270 respondents who were selected purposively. Data were analyzed descriptively by making tabulations. The results of the study indicate that the perception of farmers on local food seen from the perception of relative profit is classified as moderate, based on complexity is classified as very low, based on suitability and easy to observe is classified as very high. The obstacles faced by farmers in realizing local food diversification were the availability of raw materials for sweet potato, cassava and corn which is still very volatile because it depends on the cropping pattern and harvest season, cannot be planted continuously in one year because it is vulnerable to pests, the price fluctuating, there is no uniformity of type or variety and quality, and requires storage space for the harvest.
Evaluation on some nitrogen degrading bacteria for culture of glass ell
Authors: Widyastuti Y R , Saputra A , Yosmaniar  , Prihadi T H , Sunarno M T D 
Published: February 2022

Abstract
Nitrogen (N) degrading bacterias are needed for the control of fish culture organic waste. The purpose of the study was to evaluate N- degrading bacterias on survival, growth performance, blood profil, and media water quality for glass eel culture. Twelve aquaria were used at rate of 20 fish/L water. Artemia sp and peleted diet were fed at satiation on test fish for 60 days of experimental period. Completely randomized design with 4 treatments and 3 replications were used. The treatments were different N- degrading bacterias, namely: A) no bacteria (control); B) Nitrobacter sp, C) Pseudomonas sp, and D) Bacillus sp. The parameters tested were survival rate, absolute growth and length, blood profil, and water quality. The results showed that Bacillus sp was the best bacteria for degrading nitrogen to produce the best values of survival rate (90.62±0.40%), total length (9.31±0.59 cm), body weight (1.04±0.17 g/fish), total erythrocytes (1.04×106–1.10×106 cells/mm³) and total leukocytes (7.61×106–8.85×106 cells/mm³). Nitrite, nitrate, ammonia concentrations in culture added bacterias were relatively stable and lower than those at control. It could be stated that adding Bacillus sp can improve survival, growth performance, and blood profil as well as uphold water quality in optimal range conditions.
Thermal and pH Stability of the Red Seaweed (Rhodophyceae) Phycoerythrin Pigments from Kupang, Indonesia
Authors: Munifah Ifah , Musfiroh Siti , Munandar Aris , Surilayani Dini 
Published: February 2022

Abstract
This is a study of a red seaweed sample taken from the seawaters of Kupang, East Nusa Tenggara, Indonesia. Red seaweed utilization as a producer of bioactive compounds is potential to be developed further due to the presence of phycoerythrin (PE) pigment. The phycoerythrin (PE) pigment is extracted using phosphate buffer solvent. The objective of this study is to determine the effect of heat treatment at temperatures ranging from 30° to 80°C on the stability of the antioxidants and proteins in PE pigment. Moreover, the study will also endeavor to learn the effect of adding buffer solutions on the stability of the antioxidants and proteins in PE pigment with pH values ranging from 3 to 8. The study on the stability of K2 red seaweed phycoerythrin (PE) pigment sample from Kupang, East Nusa Tenggara revealed that it remains stable even after being exposed to a 60°C temperature and a fairly wide range of pH buffers. The K2 pigment sample has an R-PE of 0.031 ml/mL. Meanwhile, the R-PE pigment purity index is 0.041 and the yield is 0.042%.
Growth and Feed Digestibility of Sangkuriang Catfish with Corn Gluten Meal-Based Feeding
Authors: Mustahal  , Hermawan D , Syamsunarno M B , Agung L A , Nurhaliza A S , Rachmawati R F , Anggraeni D , Putra A N 
Published: February 2022

Abstract
Diet testing was conducted for 50 days to investigate the growth and feed digestibility of Sangkuriang catfish with corn gluten meal (CGM)-based feeding. This involved 5 treatments with different levels of CGM in the feed 0, 75, 150, 225, and 300 g.kg−1 for three replications. The result showed that the value of SGR ranged from 0.87 to 1.51 %.day−1, the SGR values with CGM at 0, 75 and 150 g.kg−1 were significantly higher than the values in CGM 225 and 300 g.kg−1. The best value of protein and lipid digestibility were recorded with CGM at 0, 75 and 150 g.kg−1 compared to CGM at 225 and 300 g/kg. A greater propensity for higher CGM levels to negatively impact on growth and feed digestibility of Sangkuriang catfish. Therefore, CGM is confirmed to process the potential for application at a level of 150 g.kg−1 in the Sakuriang catfish diet without negatively influencing growth and feed digestibility.
Effectiveness of Different Mesh Size To Release Small Blue Swimming Crab on Trap Fishing
Authors: Nurdin H S , Susanto A , Saputra D Y A 
Published: February 2022

Abstract
Blue swimming crab (Portunus pelagicus) is a fishery commodity with important economic value and also become the main commodity for export needs. However, crab production dominantly comes from fishing activities using traps and gillnet. The fisher use traps without escape gaps so that small crabs have no chance of escaping from the traps. One alternative way to improve the crab trap selectivity is the use of larger mesh sizes on the wall of the trap. This study aimed to determine the effective mesh size for escaping small crabs. This study was conducted in Fisheries Laboratory, University of Sultan Ageng Tirtayasa from July to December 2020. We used different mesh sizes on the trap wall including of 2.0; 2.5; and 3 inches. For all experiments, we used 90 crabs with an average carapace width of 72 mm. The results showed that the pattern of crab when escaping through the net at each mesh size was varied. The crab crept up the netting wall before attempting to escape. The fastest time of crab escapes was found on a 3 inch mesh size with an average time of 10 seconds. Moreover, the highest percentage of crabs that can pass was obtained at the 3-inch mesh size with the value 60%. Based on these results, to increase the catch selectivity we recommend a 3-inch mesh to be used in the collapsible trap wall for blue swimming crab fishing.
Physical properties of bioplastic agar/chitosan blend
Authors: Agusman  , Fransiska D , Murdinah  , Wahyuni T , Irianto H E , Priambudi P , Fateha  , Abdullah A H D , Nissa R D , Firdiana B , Nurhayati  
Published: February 2022

Abstract
Thermoplastic agar/chitosan blend was prepared by a rheomix process, and the effect of concentration agar: chitosan on the material properties forms were investigated. This research aimed to observe the physical properties of bioplastic agar/chitosan produced through rheomix. Bioplastic was produced by mixing 65 % solid material (agar: chitosan) and 35% glycerol, the ration through the melting process at an initial temperature of 100°C. The weight ratio of agar : chitosan was 65% : 0% (F0/control), 52% : 13% (F1), 39 % : 26% (F2), 26 %: 39% (F3). The tensile strength and elongation of bioplastic were decrees with a higher chitosan concentration. The color and the opacity of bioplastic were affected by the ratio of agar: chitosan. The moisture content and the water vapor transmission rate (WVTR) of bioplastic were increased by increasing the chitosan ratio. The SEM micrograph of bioplastic showed that the blend agar and chitosan seem to have a rough and inhomogeneous surface than pure bioplastic agar. The best blend was bioplastic with agar: chitosan 52%: 13% (F1), which have properties of : tensile strength 4.95 ± 0.56 MPa, elongation at break 34.94 ± 0.99 %, moisture content 15.33 ± 0.43%, WVTR 3259.39 ± 28.12 g/m2.24 h.
Retinal age gap as a predictive biomarker of future risk of Parkinson’s disease
Authors: Hu Wenyi , Wang Wei , Wang Yueye , Chen Yifan , Shang Xianwen , Liao Huan , Huang Yu , Bulloch Gabriella , Zhang Shiran , Kiburg Katerina , Zhang Xueli , Tang Shulin , Yu Honghua , Yang Xiaohong , He Mingguang , Zhu Zhuoting 
Published: February 2022

Abstract

Introduction
retinal age derived from fundus images using deep learning has been verified as a novel biomarker of ageing. We aim to investigate the association between retinal age gap (retinal age–chronological age) and incident Parkinson’s disease (PD).

Methods
a deep learning (DL) model trained on 19,200 fundus images of 11,052 chronic disease-free participants was used to predict retinal age. Retinal age gap was generated by the trained DL model for the remaining 35,834 participants free of PD at the baseline assessment. Cox proportional hazards regression models were utilised to investigate the association between retinal age gap and incident PD. Multivariable logistic model was applied for prediction of 5-year PD risk and area under the receiver operator characteristic curves (AUC) was used to estimate the predictive value.

Results
a total of 35,834 participants (56.7 ± 8.04 years, 55.7% female) free of PD at baseline were included in the present analysis. After adjustment of confounding factors, 1-year increase in retinal age gap was associated with a 10% increase in risk of PD (hazard ratio [HR] = 1.10, 95% confidence interval [CI]: 1.01–1.20, P = 0.023). Compared with the lowest quartile of the retinal age gap, the risk of PD was significantly increased in the third and fourth quartiles (HR = 2.66, 95% CI: 1.13–6.22, P = 0.024; HR = 4.86, 95% CI: 1.59–14.8, P = 0.005, respectively). The predictive value of retinal age and established risk factors for 5-year PD risk were comparable (AUC = 0.708 and 0.717, P = 0.821).

Conclusion
retinal age gap demonstrated a potential for identifying individuals at a high risk of developing future PD.
Seizures initiate in zones of relative hyperexcitation in a zebrafish epilepsy model
Authors: Niemeyer James E , Gadamsetty Poornima , Chun Chanwoo , Sylvester Sherika , Lucas Jacob P , Ma Hongtao , Schwartz Theodore H , Aksay Emre R F 
Published: February 2022

Abstract
Seizures are thought to arise from an imbalance of excitatory and inhibitory neuronal activity. While most classical studies suggest excessive excitatory neural activity plays a generative role, some recent findings challenge this view and instead argue that excessive activity in inhibitory neurons initiates seizures.
We investigated this question of imbalance in a zebrafish seizure model with two-photon imaging of excitatory and inhibitory neuronal activity throughout the brain using a nuclear-localized calcium sensor. We found that seizures consistently initiated in circumscribed zones of the midbrain before propagating to other brain regions. Excitatory neurons were both more prevalent and more likely to be recruited than inhibitory neurons in initiation as compared with propagation zones. These findings support a mechanistic picture whereby seizures initiate in a region of hyperexcitation, then propagate more broadly once inhibitory restraint in the surround is overcome.
Cortical thickness differences are associated with cellular component morphogenesis of astrocytes and excitatory neurons in nonsuicidal self-injuring youth
Authors: Cai Suping , Guo Zitong , Wang Xuwen , Huang Kexin , Yuan Kai , Huang Liyu 
Published: February 2022

Abstract
Nonsuicidal self-injury (NSSI) generally occurs in youth and probably progresses to suicide. An examination of cortical thickness differences (ΔCT) between NSSI individuals and controls is crucial to investigate potential neurobiological correlates. Notably, ΔCT are influenced by specific genetic factors, and a large proportion of cortical thinning is associated with the expression of genes that overlap in astrocytes and pyramidal cells. However, in NSSI youth, the mechanisms underlying the relations between the genetic and cell type-specific transcriptional signatures to ΔCT are unclear. Here, we studied the genetic association of ΔCT in NSSI youth by performing a partial least-squares regression (PLSR) analysis of gene expression data and 3D-T1 brain images of 45 NSSI youth and 75 controls. We extracted the top-10 Gene Ontology terms for the enrichment results of upregulated PLS component 1 genes related to ΔCT to conduct the cell-type classification and enrichment analysis. Enrichment of cell type-specific genes shows that cellular component morphogenesis of astrocytes and excitatory neurons accounts for the observed NSSI-specific ΔCT. We validated the main results in independent datasets to verify the robustness and specificity. We concluded that the brain ΔCT is associated with cellular component morphogenesis of astrocytes and excitatory neurons in NSSI youth.