bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitro propagation of six selected sugarcane mutant clones through leaf explants
Authors: Purnamaningsih R , Sukmadjaja D , Suhesti S , Rahayu S 
Published: October 2021

Abstract
Six mutant clones of sugarcane with high productivity have been produced through tissue culture techniques combined with mutations using gamma-ray irradiation and Ethyl Methane Sulfonate. The six mutant clones have been tested for stability in the field. They are proven to have high productivity and yields, so that they are very potential to be developed as superior varieties. To support the planting material sufficiency of these clones, an efficient propagation method was needed. Media formulations with different physical properties and composition of growth regulators were tested to obtain high seedling propagation rates. The media formulation for callus induction was Murashige dan Skoog (MS) + 3 mg/l 2,4-D + 3 g/l casein hydrolysate + 3% sucrose and for shoot regeneration was MS + 0,5 mg/l BA + 0,1 mg/l IBA + 100 mg/l PVP and 2% sucrose. Shoot proliferation was carried out on MS liquid (1, ½) + (0.3; 0.5 mg/l) BA + 0.1 mg/l IBA + 1 mg/l Kinetin + (0; 0.5 mg/l) GA3+ sucrose 2%. The results showed that callus induction, callus regeneration, and shoot proliferation of sugarcane mutant clones were influenced by the genotype and medium composition. The fastest callus induction was obtained from the MSP-4 clone (5.82 days), and the longest was MSB-7 (8.82 days). The largest callus diameter was obtained from MSB-6 clone on MS medium containing 1 mg/l BA, 100 mg/l PVP, and 2% sucrose. The highest number of shoots was obtained from the MSB-6 clone, while the least number of shoots conducted from the MSB-8 clone. The MSB-8 clones were more difficult to regenerate compared to the others. The best media formulation for shoot proliferation was ½ MS containing 0.5 mg/l BA, 1 mg/l Kinetin, and 0.1 mg/l IBA, while the best formulation for rooting was ½ MS.
Performance of native chicken fed on ration containing fermented sago waste
Authors: Ralahalu T N , Latupeirissa CH C E , Hehanussa S CH H , Fredriksz S. 
Published: October 2021

Abstract
The use of fermented sago waste (9 days incubation time) in the ration of native chicken is studied. 100 chicks of 7 days old native chicken were used. The experiment is being conducted in a completely randomized design in which the animals were divided into four treatments of ration. Each treatment was replicated five times. The experimental rations are: R0 (0% fermented sago waste), R1 (5% fermented sago waste), R2 (10% fermented sago waste) and R3 (15% fermented sago waste). Parameters measured were feed intake, feed conversion, body weight gain and carcass percentage. It appeared from this experiment that feeds intake were similar between birds. In grower birds, the use of fermented sago waste in the rations had no significant effect on feed intake. In both, starter and grower birds body weight gain was higher for birds consuming control ration than for those consuming ration with fermented sago waste. The use of 5 up to 15 percent fermented sago waste in the rations significantly affects feed conversion and carcass percentage in both, starter and grower birds.
Identification of endophytic and rhizosphere bacteria in rice (Oryza sativa L.) in the experimental field at Payakumbuh State Agriculture Polytechnic, West Sumatra, Indonesia
Authors: Sondang Y , Siregar R , Anty K 
Published: October 2021

Abstract
The decrease of soil fertility and fewer soil microorganisms will lower crop production, particularly rice, thus threatening the national food security program. This study is (a) to isolate and identify the bacteria in the endophytic and rhizosphere of rice plants (b) to study the bacteria from the endophytic and rhizosphere of rice plants which potentially stimulate plant growth. The experiment was carried out at the Laboratory of Food Crop Cultivation at Payakumbuh State Agriculture Polytechnic, Limapuluh Kota Regency, West Sumatra for four months. The sampling method was carried out by random sampling at rice planting in the Payakumbuh State Agriculture Polytechnic Experimental Field. Endophytic bacteria were taken from the root tissue of rice plants, and rhizosphere bacteria were taken from a layer of soil around rice roots. Isolation of bacteria was carried out by using the pour plate and scratchplate methods. Four bacteria were identified using the 16S rRNA sequencing method. The identification results showed that in the rice root tissue found the bacteria Chromobacterium rhizoryzae and Brevibacillus brevis. In the rice rhizosphere, Bacillus pseudomycoides and Bacillus thuringiensis are found. Bacteria are dominated by the Bacillus genera which can stimulate plant growth.
The physicochemical characteristics of gandaria (Bouea macrophylla) leather with sugar concentration treatment
Authors: Lawalata V N 
Published: October 2021

Abstract
Gandaria leather is a kind of fruit leather processed by gandaria fruit in the form of thin sheets with a thickness of 2-3 mm and has a specific consistency and taste according to gandaria fruit. The purpose of this study was to determine the effect of added sugar on the physicochemical characteristics of gandaria leather. This study used a single-factor completely randomized design, with 0%, 5%, 10%, and 15% sugar concentrations. The results showed that the sugar concentration had a very significant effect on the parameters of water content, total sugar, total acid, vitamin C, and water activity (aw), and had a significant effect on the tensile strength of gandaria leather. The physicochemical characteristics of gandaria leather from various sugar concentration treatments are as follows: water content (14.05% -20.13%), total sugar (80.56% - 84.90%), total acid (3.10 - 12.37 mg/100g), vitamin C (59.44 - 78.48 mg/100g), water activity (0.48 - 0.62), and tensile strength (0.20-0.37 N). The resulting gandaria leather qualifies as good fruit leather, and the treatment with a 10% sugar concentration is recommended for gandaria leather which has the potential to be developed and commercialized.
The utilization of agro-industrial waste for soil amendment and liquid biofertilizer mixed bacterial antagonist in eggplant production
Authors: Boonraeng S , Punyoyai N 
Published: October 2021

Abstract
This research aimed to improve soil fertility with soil amendment, prepared from agro-industrial waste, and application of antagonistic bacteria for controlling bacterial wilt disease. The experiments were tested on sandy-to-sandy loam soil with low organic matter and nutrients for planting eggplants. Besides the soil improvement with spent mushroom waste and mango peel mixed kernel, the results showed that soil pH, soil organic matter, nitrogen, phosphorus, and potassium increased as available levels. Also, two species of bacterial antagonist named Bacillus subtilis and B. amyloliquifaciens were cultured and mixed in liquid biofertilizer. It was spiked for soil preparation before planting and during crop growth every week, which was affected by eggplant survival from bacterial wilt by 100% and 97% in plot and field-tested, respectively. The results from testing on sandy loam with the use of liquid biofertilizer three times/week showed that Ralstonia solanacearum in soil suppressed to the reduction of 1,000-10,000 times. The yield increased by 25.9%. The optimum harvesting time was 12-15 days of fruit growth with the antioxidant activity. Finally, this study has excellent potential to be extended for farmers who organically grown.
Moringa oleifera milk powder as a supplementary food for malnutrition children (SUSUKE)
Authors: Djoko S W , Kembauw E , Kapelle I B D 
Published: October 2021

Abstract
Moringa oleifera are known throughout the world as a nutrition plants, WHO has introduced moringa as an alternative food to overcome malnutrition. In Africa and Asia Moringa leaves are recommended as a nutrient-rich supplements for nursing mothers and children during infancy phase. Moluccas is one of the top 5 regions with quite high rates of malnutrition, while rich in natural products, the lack of knowledge and poor processing method results in nutrients unable to be properly absorbed. Moringa milk-powder can be the answers to malnutrition problems. Methods: This Study used a Nested case-control design, subject were all children aged 1 month-12 years who were diagnosed with malnutrition using WHO and CDC chart during reseach. Result: Sample size was 60 children’s 30 subjects are using malnutrition treatment and moringa milk powder and 30 subjects are using only malnutrition treatment. Conclusion: Moringa milk powder have a benefit for malnutrition children.
Clove processing as a source of increasing business income in Ambon City
Authors: Kembauw E , Mahulette A S , Kakisina A P , Tuhumury M T F , Umanailo M C B , Kembauw M G I 
Published: October 2021

Abstract
Clove is one of the important plantation commodities in Maluku, especially in Ambon City. Clove processing diversification will provide opportunities to increase business income. This study aims to determine the factors that support the diversification of clove processing on the income of entrepreneurs in the city of Ambon. The method used was purposive sampling. The results showed that the diversification of clove processing gave a large enough contribution to income, but the percentage contribution of processing diversification was not visible because the income outside of processing was relatively large. The results showed that the greater the number of species produced, the greater the capital. Based on the analysis, it is known that the level of raw materials available to entrepreneurs to support diversification activities.
A simple discrete-element model for numerical studying the dynamic thermal response of granular materials
Authors: Wu Ze-Xiang , Yang Lei , Wang Zhe , Zhuang Ying-Chun , Tu Dong-Mei 
Published: October 2021

Abstract
This paper aims to investigate the influence of periodicity temperature change on the properties of dry granular materials in macroscopic and microscopic. A series of cyclic thermal consolidation tests have been carried out based on the discrete element method (DEM) that incorporate particles’ volumetric thermal expansion coefficient. The simulation of the direct shear test was carried out on the samples after thermal cycling. Results showed that thermally-induced volumetric strain accumulation of the specimen can be calculated by the DEM model, based on the two-dimensional particle flow code (PFC2D) software. The lateral pressure degraded concomitantly thanks to decreases in particles’ horizontal contact during periodic thermal cycling. In addition, the shear dilatancy level decreases during the shearing process with the number of thermal cycles. Both the size and anisotropy of the normal contact force and contact number and the force chain are affected by the temperature cycle. Finally, the results of this paper have a certain reference for the engineering practice, such as thermal piles or others, when granular materials are subjected to thermal cycling.
Integrated approach in treatment of solid olive residue and olive wastewater
Authors: Altalhi Tariq , El-moemen A Abd , Ibrahim Mohamed M , Mezni Amine , Alsohaimi Ibrahim Hotan , Mahmoud M H H , Kumeria Tushar , Mersal Gaber A M , Mostafa Nasser Y 
Published: October 2021

Abstract
Generally olive oil generated two forms of waste by-products: solid olive residue (SOR) and olive wastewater (OWW). In the present study a promising solution is given to treat both SOR and OWW waste by-products. The first process consists of converting the solid olive residue to activated carbon using pyrolysis process at 600 °C, followed by steam activation procedure at three different temperatures. The attained activated carbon was examined by different experimental techniques such as FTIR, SEM, BET and iodine number. The surface area was increased by increasing stream activation temperature (reach 1020 m2 g−1 BET). However, the steam activation at 700 °C was found to be ideal for environmental and economic performance. On the other hand, the activated carbon at 700 °C displayed high removal capacity of both polyphenolic compounds and COD from olive wastewater. In fact, after 2 h of treatment, 95.5% of COD and 84.2% of polyphenolic compounds were completely removed.
A systematic review of life cycle assessment of hydrogen for road transport use
Authors: Rinawati Dyah Ika , Keeley Alexander Ryota , Takeda Shutaro , Managi Shunsuke 
Published: October 2021

Abstract
This study conducted a systematic literature review of the technical aspects and methodological choices in life cycle assessment (LCA) studies of the use of hydrogen for road transport. More than 70 scientific papers published during 2000–2021 were reviewed, in which more than 350 case studies of the use of hydrogen in the automotive sector were found. Only some studies used hybrid LCA and energetic input–output LCA, whereas most studies addressed attributional process-based LCA. A categorization based on the life cycle scope distinguished case studies that addressed the well-to-tank (WTT), well-to-wheel (WTW), and complete life cycle approaches. Furthermore, based on the hydrogen production process, these case studies were classified into four categories: thermochemical, electrochemical, thermal–electrochemical, and biochemical. Moreover, based on the hydrogen production site, the case studies were classified as centralized, on-site, and on-board. The fuel cell vehicle passenger car was the most commonly used vehicle. The functional unit for the WTT studies was mostly mass or energy, and vehicle distance for the WTW and complete life cycle studies. Global warming potential (GWP) and energy consumption were the most influential categories. Apart from the Greenhouse Gases, Regulated Emissions, and Energy Use in Transportation model and the Intergovernmental Panel on Climate Change for assessment of the GWP, the Centrum voor Milieukunde Leiden method was most widely used in other impact categories. Most of the articles under review were comparative LCA studies on different hydrogen pathways and powertrains. The findings provide baseline data not only for large-scale applications, but also for improving the efficiency of hydrogen use in road transport.
Levels of Parental Drinking in the Presence of Children: An Exploration of Attitudinal Correlates
Authors: Bowden Jacqueline A , Delfabbro Paul , Room Robin , Miller Caroline L , Wilson Carlene 
Published: October 2021

Abstract

Aims
This study aimed to examine perceived social norms, the effect of parental drinking on these norms, alcohol use in front of children, and how norms and consumption vary based on child age and gender of the parent.

Methods
A cross-sectional online panel survey was undertaken with n = 1000 Australian adults (including 670 parents) aged 18–59 years. The survey assessed: alcohol consumption in front of children; normative attitudes towards drinking in the presence of children; and perceived social norms.

Results
Overall, 33.9% of parents reported drinking a glass of alcohol each day or a couple of times a week, 18.2% reported getting slightly drunk and 7.8% indicated getting visibly drunk each day or a couple of times a week with their children present. In total, 37.5% reported drinking in front of their children at least weekly. Fathers were more likely to drink in front of children than mothers. Most parents deemed drinking small amounts of alcohol in front of children as acceptable but did not accept drunkenness. Respondents were less concerned about a father drinking one or two drinks in front of their children than a mother. Social expectations were not related to child age, but norms related to others’ perceived behaviour were.

Conclusions
Many parents, particularly fathers consume alcohol in front of their children. There is a need to target health promotion strategies to adults and parents consuming in excess of health guidelines, and to the many parents who are consuming alcohol at higher levels in front of their children.
Neuropsychological Screening in Pediatric Multidisciplinary Clinics: Group Characteristics and Predictive Utility
Authors: Wolfe Kelly R , Hutaff-Lee Christa , Wilkening Greta 
Published: October 2021

Abstract

Objective
To evaluate the feasibility of administering caregiver-report neuropsychological screening measures in pediatric multidisciplinary clinics (MDCs) and investigate predictive utility for cognitive and academic difficulties on follow-up testing.

Method
The Pediatric Perceived Cognitive Functioning (Peds PCF) and Colorado Learning Difficulties Questionnaire (CLDQ) were administered to caregivers of youth with history of brain tumor (BT), non-central nervous system (CNS) cancer, or Fontan circulation as part of routine neuropsychological consultation in MDCs from 2017 to 2019. We examined cross-sectional differences on screening measures, and relationships between screening and intellectual and academic test performance in a subset who presented for follow-up neuropsychological evaluation. Receiver operating characteristic (ROC) curve analysis was used to identify suggested cut scores on screening measures for predicting who would most benefit from further evaluation.

Results
Screening was completed with 192 families. Children with history of non-CNS cancer (n = 29) had fewer parent-reported cognitive and academic concerns compared with either BT (n = 88) or Fontan (n = 75) groups. Peds PCF and CLDQ scores were related to intellectual and academic test performance in the group presenting for neuropsychological evaluation (n = 68). ROC curve analysis identified cut scores across screening measures with maximal sensitivity and specificity for detecting neuropsychological difficulties.

Conclusions
It is feasible to utilize parent rating measures during neuropsychological consultation in pediatric MDCs. The Peds PCF and CLDQ demonstrated sensitivity to intellectual and academic difficulties in children with significant medical histories. Screening may be a helpful tool for pediatric neuropsychologists and other professionals during MDC consultation to inform clinical management.
Peakhood: individual site context extraction for CLIP-seq peak regions
Authors: Uhl Michael , Rabsch Dominik , Eggenhofer Florian , Backofen Rolf 
Published: October 2021

Abstract

Motivation
CLIP-seq is by far the most widely used method to determine transcriptome-wide binding sites of RNA-binding proteins (RBPs). The binding site locations are identified from CLIP-seq read data by tools termed peak callers. Many RBPs bind to a spliced RNA (i.e. transcript) context, but all currently available peak callers only consider and report the genomic context. To accurately model protein binding behavior, a tool is needed for the individual context assignment to CLIP-seq peak regions.

Results
Here we present Peakhood, the first tool that utilizes CLIP-seq peak regions identified by peak callers, in tandem with CLIP-seq read information and genomic annotations, to determine which context applies, individually for each peak region. For sites assigned to transcript context, it further determines the most likely splice variant, and merges results for any number of datasets to obtain a comprehensive collection of transcript context binding sites.

Availability and implementation
Peakhood is freely available under MIT license at: https://github.com/BackofenLab/Peakhood.

Supplementary information
Supplementary data are available at Bioinformatics online.
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data
Authors: Creed Jordan H , Wilson Christopher M , Soupir Alex C , Colin-Leitzinger Christelle M , Kimmel Gregory J , Ospina Oscar E , Chakiryan Nicholas H , Markowitz Joseph , Peres Lauren C , Coghill Anna , Fridley Brooke L 
Published: October 2021

Abstract

Summary
Multiplex immunofluorescence (mIF) staining combined with quantitative digital image analysis is a novel and increasingly used technique that allows for the characterization of the tumor immune microenvironment (TIME). Generally, mIF data is used to examine the abundance of immune cells in the TIME; however, this does not capture spatial patterns of immune cells throughout the TIME, a metric increasingly recognized as important for prognosis. To address this gap, we developed an R package spatialTIME that enables spatial analysis of mIF data, as well as the iTIME web application that provides a robust but simplified user interface for describing both abundance and spatial architecture of the TIME. The spatialTIME package calculates univariate and bivariate spatial statistics (e.g. Ripley’s K, Besag’s L, Macron’s M and G or nearest neighbor distance) and creates publication quality plots for spatial organization of the cells in each tissue sample. The iTIME web application allows users to statistically compare the abundance measures with patient clinical features along with visualization of the TIME for one tissue sample at a time.

Availability and implementation
spatialTIME is implemented in R and can be downloaded from GitHub (https://github.com/FridleyLab/spatialTIME) or CRAN. An extensive vignette for using spatialTIME can also be found at https://cran.r-project.org/web/packages/spatialTIME/index.html. iTIME is implemented within a R Shiny application and can be accessed online (http://itime.moffitt.org/), with code available on GitHub (https://github.com/FridleyLab/iTIME).

Supplementary information
Supplementary data are available at Bioinformatics online.
Topical antibiotic prophylaxis for surgical wound infections in clean and clean-contaminated surgery: a systematic review and meta-analysis
Authors: Chen Po-Jung , Hua Yi-Ming , Toh Han Siong , Lee Mei-Chuan 
Published: October 2021

Abstract

Background
Topical antibiotics are widely prescribed as prophylaxis for surgical site infection (SSI). Despite giving high drug concentrations at local wound sites, their efficacy remains controversial. This study is a systematic review and meta-analysis designed to compare the efficacy and safety of topical antibiotics with non-antibiotic agents in preventing SSI.

Methods
Randomized controlled trials (RCTs) comparing topical antibiotics in patients with clean and clean-contaminated postsurgical wounds were included. Relevant trials published before 30 September 2020, were searched in the PubMed, Embase, and Cochrane databases, without language restrictions. The primary outcome was the incidence of SSIs, presented as the event rate. The secondary outcome was the incidence of contact dermatitis (safety outcome). Data were synthesized using the random-effects model, with the results expressed as risk ratio (RR) with 95 per cent confidence intervals (c.i.).

Results
Thirteen RCTs were included. The incidence of SSIs and contact dermatitis showed no significant difference between topical antibiotics and non-antibiotic agents (RR 0.89, 95 per cent c.i. 0.59 to 1.32 (P = 0.56, I2 = 48 per cent); and RR 2.79, 95 per cent c.i. 0.51 to 15.19 (P = 0.24, I2 = 0 per cent), respectively). In the subgroup analyses, a reduction in SSIs was also not observed in dermatological (RR 0.77, 95 per cent c.i. 0.39 to 1.55; P = 0.46, I2 = 65 per cent), ocular (RR 0.08, 95 per cent c.i. 0.00 to 1.52; P = 0.09), spinal (RR 1.34, 95 per cent c.i. 0.65 to 2.77; P = 0.43, I2 = 0 per cent), orthopaedic (RR 0.69, 95 per cent c.i. 0.37 to 1.29; P = 0.25, I2 = 0 per cent), or cardiothoracic surgeries (RR 1.60, 95 per cent c.i. 0.79 to 3.25; P = 0.19).

Conclusion
Given the current evidence, the routine application of topical antibiotics to surgical wounds did not reduce the incidence of SSI. Further trials are needed to assess their effectiveness in high-risk surgeries or in selected patient groups.