bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of siam orange (Citrus nobilis Lour.) and pineapple (Ananas comosus (L.) Merr.) juices combination in extender on Garut Ram (Ovis aries L.) spermatozoa quality post-cryopreservation
Authors: Saoemi H A , Kaiin E M , Setiorini S , Gunawan M 
Published: January 2020

Abstract
The research aimed to find out the effect of various concentrations of siam orange (Citrus nobilis Lour.) and pineapple (Ananas comosus (L.) Merr.) juices combination (1:1) in extender on garut ram (Ovis aries L.) spermatozoa quality 24 hours post-cryopreservation. 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 siam orange and pineapple juices combination 0 %, 5 %, 10 %, 15 %, and 20 %. Diluted semen samples were loaded into mini straws (0.25 mL) with 50 million cells/ml dosage. Samples were equilibrated at 5°C for two hours, then frozen and stored in liquid nitrogen. The one factor ANOVA and continued with Duncan test showed a significant differences (P<0.05) between control and sample with 10 % juices combination in the percentage of spermatozoa motility and membrane integrity, a significant difference (P<0.05) between control and sample with 5 % along with 10 % juices combination in the percentage of spermatozoa viability. Siam orange and pineapple juices combination 10% in extender was able to minimize the reduction of spermatozoa quality post-cryopreservation based on the percentage of spermatozoa motility (68.06 ± 2.34 %), viability (41.47 ± 6.64 %) and membrane integrity (46.00 ± 5.65 %).
The effect of siam orange juice (Citrus nobilis Lour.) in extender on Garut Ram (Ovis aries L.) spermatozoa quality post-cryopreservation
Authors: Gunawan M , Setiorini S , Fitri H N , Kaiin E M 
Published: January 2020

Abstract
The research aimed to find out the effect of Siam Orange juice in extender on Garut Ram spermatozoa quality 24 hours post-cryopreservation. Semen was collected from five rams once a week using an artificial vagina. Semen sample was diluted in Tris-egg yolk-based extender containing 0 % (KK), 5 % (KP 1), 10 % (KP 2), 15 % (KP 3) and 20 % (KP 4) Siam orange juice. Semen was packed in 0.25 ml straw with a final concentration of 50x106 spermatozoa/mL. Sperm was equilibrated at 5° C for two hours then frozen and stored in liquid nitrogen (LN2) tube. Sperm parameters, including motility, viability, membrane integrity, acrosome integrity, and abnormality, were assessed. One-way ANOVA test results showed significant differences between treatment groups on the percentage of motility, viability, and membrane integrity (p <0.05). Duncan test results indicated that KP 2 had significant differences in all treatment groups. Therefore, orange juice at 10 % concentration (KP 2) was the best concentration that was able to minimize the reduction of ram spermatozoa quality post-cryopreservation based on motility [(58.68 ± 0.68) %], viability [(59.73 ± 6.47) %], and membrane integrity [(54.87 ± 5.58) %].
Purification of NS2B-NS3 dengue virus serotype 3 protein as raw material for dengue virus vaccine
Authors: Arisanti M , Faizal I , Abinawanto A , Bowolaksono A 
Published: January 2020

Abstract
Dengue virus serotype 3 has been recognized as the predominant serotype in many occurrences of Dengue Hemorrhagic Fever (DHF) in Indonesia. Performing DHF prevention could be done with vaccination. BPPT institution was developing a vaccine, which is made from NS2B-NS3 recombinant protein. This protein is one of the non-structural proteins that arrange the genome of DENV and it has a molecular weight of 83 kDa. This research aims to isolate and purify NS2B-NS3 protein DENV-3 from transformant cell of Saccharomyces cerevisiae. Purification of NS2B-NS3 protein is done with HisPur Ni-NTA Magnetic Beads method. Optimization of purification is done by increasing the concentration of imidazole as protein binder in the elution buffer starting from 250 mM until 500 mM. The validity of purified protein was tested qualitatively with Sodium Dodecyl Sulfate-Polyacrilamide Gel Electrophoresis (SDS-PAGE) method and quantified by Bichinconinic Acid (BCA) method. The results revealed us that NS2B-NS3 protein was purified optimally at 300 mM imidazole by HisPur Ni-NTA Magnetic Beads method. SDS-PAGE analysis showed that there was a specific band with size 83 kDa in lane result of elution with 300 mM imidazole and based on the result of protein quantification obtained that it has the highest percentage of purification effectiveness is 16.38 %.
Water mass along eastern pathway of Indonesia Throughflow from a CTD Argo Float
Authors: Rahma A , Atmadipoera A S , Naulita Y 
Published: January 2020

Abstract
Eastern pathway of the Indonesia Throughflow (ITF) conveys a secondary ITF inflow that brings North/South Pacific water entering interior Indonesian Seas. The transformation occurred along the Pacific water mass journey towards the Indonesian sea. For the first time since 2016, CTD Argo float measurement is available following the ITF path – along Maluku-Seram- Banda Seas, providing prime datasets to be able seen change of ITF water. This paper aims to investigate transformation of ITF water masses and the percentage of water mass contribution (with Optimum MultiParameter method) along its eastern path of ITF between Maluku – Seram and Banda Seas. The result shows that along the path, North Pacific water origin is predominant in Southern Banda Sea, but lower thermocline water of South Pacific water origin in South Maluku and Seram Sea. Large transformation of ITF water is indicated with salty upper-thermocline water in Maluku-Seram Seas, but fresh thermocline water in Banda Sea. Spatial variation of mixing layer depth and thermocline depth is also found. The percentage of the water mass contribution of the North Pacific water NPSW and NPIW gets bigger along the journey to the Banda Sea, while the dominant of SPSLTW was found in Maluku Sea and Seram Sea.
Anti-mycobacterium compound derived from Erythrobacter sp. isolated from Callyspongia aurizusa
Authors: Murniasih T , Cindhy C I , Yunovilsa P M , Sukara E 
Published: January 2020

Abstract
Pathogenic bacteria, especially Mycobacterium, to be one of the causes of disease in society. Sponge bacterial symbionts are one of the potential sources for producing new antibacterial compounds. This study was carried out for investigating the antimycobacterial compounds derived from the Callyspongia aerizusa’s bacterial symbiont. Antimycobacterial compound isolation was done by growing selected bacteria SP.PP.3 in marine broth then continued for active compound separation. The separation of an active compound was carried out using High Performance Liquid Chromatography (HPLC), whereas the antibacterial activity was tested using agar diffusion method against Mycobacterium smegmatis. The compounds were identified by spectroscopy method (LC-MS). An antimycobacterial compound was detected in the HPLC fraction with code FH8. LC-MS and 1HNMR analysis predicted that there was a bromophycolide compound that contained active fractions. 16S rRNA molecular identification indicated that the strain SP.PP.3 was closely related to Erythrobacter sp. with 99% homology similarity.
Assessing coral reefs condition for rehabilitation site selection using diver-towed survey in an island of Anambas Islands
Authors: Arafat D , Affandy A , Subhan B , Rikardi N , Madduppa H , Putra E R , Santoso P , Setiawan A , Aprizan M , Zulfikar R , Prabowo B , Muhammad F , Hashri M S 
Published: January 2020

Abstract
To select a rehabilitation area of coral reefs in Pahat Island within Anambas Islands, this study was conducted to asses coral reefs condition using diver-towed or manta tow surveys and underwater photo transects (UPT). The results of the manta tow surveys showed coral cover dominated by hard corals percentage ranged between 11% and 50% (categories 2 and 3) in the western, northern and southern parts of Pahat Island. Distribution of hard coral percentage with more than 50% (Category 4: 51% - 75% and 5: 76% -100%) was observed in the eastern part of Pahat Island. While results from UPT showed the hard coral percentage of 62.5%, 33.67% and 17% in the eastern, western and northern of Pahat Island, respectively. There are similarities in the results of coral reef cover Obtained by the manta tow and UPT methods. Conclusions, this study recommends western Pahat Island as a good alternative for a rehabilitation site as the coral coverage was in poor condition.
Fish larva distribution and profusion in Mangunharjo and Timbulsloko mangrove ecosystem
Authors: Kurniawan N A , Ambariyanto  , Suprijanto J 
Published: January 2020

Abstract
Mangrove area as nursery grounds for the fish larvae in Semarang and Demak. Fish larvae were collected during August - February representing dry and rainy seasons from three mangrove station swamps by a beach seine net. The net was dragged on the bottom for 100 m three times. A total of 291 fish larvae were collected, representing 5 families. The most abundant species formed about 76 % of all collected fishes. Two fish larvae family were collected for the first time from mangrove areas in the Timbulsloko. Most of the collected fishes are economically important fishes. Moreover five families were belonging to demersal fishes. The highest species richness value was recorded in Timbulsloko mangroves at night in the river. This Finding showed that mangroves could support the life history of many demersal and pelagic fish.
Acoustic impedance model-based inversion to identify target reservoir: a case study Nias Waters
Authors: Erryansyah M , Nainggolan T B , Manik H M 
Published: January 2020

Abstract
Seismic method is a good geophysical method in imaging the subsurface conditions using the principle of seismic wave propagation. This method is often used in hydrocarbon exploration. One important step in hydrocarbon exploration is seismic interpretation. In the stages of seismic interpretation, a good basic knowledge of geophysical and geological knowledge is needed regarding the existence and characterization of hydrocarbon reservoirs. One method used in interpreting seismic data is the acoustic impedance inversion method. In this study, 2D seismic inversion was carried out to determine the reservoir characteristics of the MCL-1 well in the Nias basin. This study uses model-based on inversion which aims to obtain the value of acoustic impedance which is useful for the identification of distribution, porosity values and reservoir conditions of the target zone. The results obtained are the target reservoir zone at a depth of 6649-7434 feet or 1705-1810ms for MCL-1 wells with a range of acoustic impedance values of 25556 ((ft/s) * (g/cc)) - 46885 ((ft/s) * (g/cc)) with the type of rock that fills the reservoir is the type of limestone rock. The correlation value for model-based inversion has a relatively small error. This can characterize the hydrocarbon reservoir well.
Coral reefs ecosystem degradation at Nusa Penida, Bali
Authors: Tito C K , Ampou E E 
Published: January 2020

Abstract
Coral reefs interference by multiple threats from local and global source. The aggregate effects of local stressors such as tourism activity, pollution, overfishing, and coral harvesting can decrease resilience of the reefs. Furthermore, increased ocean temperatures, changing ocean chemistry, and sea level rise are the greatest global threats to coral reef ecosystems. The objective of this work is to assess coral reefs ecosystem degradation at Nusa Penida (NP), Bali. In this works, monitoring of coral reef ecosystem was conduct by transect photographs on May and October 2018. We observed the evidence of coral reefs degradation in the site, particularly on the northern and southern reefs area. We also found that algal cover much higher than our previous monitoring activities, linked to higher coral mortality at these locations.
Plant defense-related gene expression analysis of canker-infected lime seedling
Authors: Sudyoung N , Tokuyama S , Krajangsang S , Pringsulaka O , Yeesin P , Koto R , Sarawaneeyaruk S 
Published: January 2020

Abstract
A serious problem for Paan-lime production in Thailand is a citrus canker disease caused by the bacterium Xanthomonas citri subsp. citri (Xcc). The use of antagonist against pathogenic Xcc is increasingly becoming popular. In this study, we investigated the effect of pathogenic Xcc and a bacterial antagonist on defense-related gene expression of Paan-lime. The ability of Xcc and the antagonist Pseudomonas aeruginosa SWUC02 to induce defense-related gene expression, including PR-1, Pt14, LRR8, and LOX gene, was assessed. We assured that all four defense-related genes are present in Paan-lime by analyzing the similarity of nucleotide sequences in parts of the genes against other citrus species. Using reverse-transcription PCR (RT-PCR), we showed that the antagonist is able to induce the expression of LRR8 gene at 24 hours post-inoculation, while Xcc induces PR-1 and LOX gene expression at the same time. Our results suggest that these defense-related genes alter their expressions in response to canker disease infection. Thus, we could use this group of genes as a biomarker for screening canker-resistance Paan-lime tree.
Additive manufacturing in radiation oncology: a review of clinical practice, emerging trends and research opportunities
Authors: Tino Rance , Leary Martin , Yeo Adam , Kyriakou Elizabeth , Kron Tomas , Brandt Milan 
Published: January 2020

Abstract
The additive manufacturing (AM) process plays an important role in enabling cross-disciplinary research in engineering and personalised medicine. Commercially available clinical tools currently utilised in radiotherapy are typically based on traditional manufacturing processes, often leading to non-conformal geometries, time-consuming manufacturing process and high costs. An emerging application explores the design and development of patient-specific clinical tools using AM to optimise treatment outcomes among cancer patients receiving radiation therapy. In this review, we:
• highlight the key advantages of AM in radiotherapy where rapid prototyping allows for patient-specific manufacture
• explore common clinical workflows involving radiotherapy tools such as bolus, compensators, anthropomorphic phantoms, immobilisers, and brachytherapy moulds; and
• investigate how current AM processes are exploited by researchers to achieve patient tissue-like imaging and dose attenuations.
Finally, significant AM research opportunities in this space are highlighted for their future advancements in radiotherapy for diagnostic and clinical research applications.
New horizons in appetite and the anorexia of ageing
Authors: Cox Natalie J , Morrison Leanne , Ibrahim Kinda , Robinson Sian M , Sayer Avan A , Roberts Helen C 
Published: January 2020

AbstractAppetite drives essential oral nutritional intake. Its regulation is complex, influenced by physiology, hedonism (the reward of eating) and learning from external cues within a person’s society and culture. Appetite loss is common in the older population and not always attributable to medical conditions or treatment. Although the physiological basis of the anorexia of ageing (loss of appetite due to the ageing process) has been established, the effect of ageing on hedonism and external cues, which may be equally important, is less well understood. The anorexia of ageing is associated with reductions in dietary diversity and oral intake, and increased risk of malnutrition, sarcopenia and frailty. Early identification of poor appetite could allow timely intervention before weight loss occurs. There is no standardised tool for assessing appetite in clinical settings at present but the 4-item Simplified Nutritional Appetite Questionnaire (SNAQ) has the potential to be used in this way. This review, designed for clinicians, will discuss the regulation of appetite and the pathogenesis of the anorexia of ageing. It will describe the current evidence for interventions to manage the anorexia of ageing, which is limited, with little benefit reported from individual studies of education, physical activity and medication. There is some positive evidence for flavour enhancement, fortified food and oral nutritional supplements but mainly within single studies. Looking ahead, the aim is to develop multicomponent approaches to the treatment of the anorexia of ageing based on growing understanding of the role of physiological signalling, hedonism and external cues.
Use of medication among nursing home residents: a Danish drug utilisation study
Authors: Lundby Carina , Jensen John , Larsen Søren Post , Hoffmann Helene , Pottegård Anton , Reilev Mette 
Published: January 2020

Abstract

Background
Data on drug utilisation patterns in nursing home populations is scarce. We aimed to describe drug use patterns in Danish nursing home residents.

Methods
We established a cohort of 5,179 individuals (63% women; median age of 84 years) admitted into 94 nursing homes across Denmark during 2015–2017. Data on prescription drug use and other census data were obtained from the nationwide Danish health registries.

Results
The total number of drug classes filled increased from a median of 6 drugs (interquartile range [IQR] 3–9) at 18–24 months before nursing home admission to a median of 8 drugs (IQR 6–11) just after admission, with the most common drug classes comprising paracetamol (61%), platelet inhibitors (41%), proton pump inhibitors (34%), statins (33%) and potassium supplements (31%). The incidence rate of new drug treatments increased from 21 new treatments/100 residents/month at 12–24 months before admission to a peak of 71 new treatments/100 residents/month in the month prior to admission, while it levelled off to about 34 new treatments/100 residents/month after 6–9 months. The drug classes primarily responsible for this peak were laxatives, antibiotics and analgesics. The largest absolute increases were seen for laxatives (53%), paracetamol (43%) and antidepressants (36%), all showing a marked increase up to and following admission. A high proportion of residents remained on therapy in the 3-year period following admission, with users of antidepressants and antidementia drugs being most persistent.

Conclusion
Nursing home admission is associated with an increase in use of both predominantly preventive and non-preventive drug classes.
DEEPrior: a deep learning tool for the prioritization of gene fusions
Authors: Lovino Marta , Ciaburri Maria Serena , Urgese Gianvito , Di Cataldo Santa , Ficarra Elisa 
Published: January 2020

Abstract

Summary
In the last decade, increasing attention has been paid to the study of gene fusions. However, the problem of determining whether a gene fusion is a cancer driver or just a passenger mutation is still an open issue. Here we present DEEPrior, an inherently flexible deep learning tool with two modes (Inference and Retraining). Inference mode predicts the probability of a gene fusion being involved in an oncogenic process, by directly exploiting the amino acid sequence of the fused protein. Retraining mode allows to obtain a custom prediction model including new data provided by the user.

Availability and implementation
Both DEEPrior and the protein fusions dataset are freely available from GitHub at (https://github.com/bioinformatics-polito/DEEPrior). The tool was designed to operate in Python 3.7, with minimal additional libraries.

Supplementary information
Supplementary data are available at Bioinformatics online.
Collaboration across Time and Space in the LTER Network
Authors: Huang Tian-Yuan , Downs Martha R , Ma Jun , Zhao Bin 
Published: January 2020

AbstractThe scale of ecological research is getting larger and larger. At such scales, collaboration is indispensable, but there is little consensus on what factors enable collaboration. In the present article, we investigated the temporal and spatial pattern of institutional collaboration within the US Long Term Ecological Research (LTER) Network on the basis of the bibliographic database. Social network analysis and the Monte Carlo method were applied to identify the characteristics of papers published by LTER researchers within a baseline of papers from 158 leading ecological journals. Long-term and long-distance collaboration were more frequent in the LTER Network, and we investigate and discuss the underlying mechanisms. We suggest that the maturing infrastructure and environment for collaboration within the LTER Network could encourage scientists to make large-scale hypotheses and to ask big questions in ecology.
Reduction of colitis-associated colon carcinogenesis by a black lentil water extract through inhibition of inflammatory and immunomodulatory cytokines
Authors: Mazewski Candice , Luna-Vital Diego , Berhow Mark , Gonzalez de Mejia Elvira 
Published: January 2020

Abstract
The objective was to compare the impact of black lentil (BL) water and delphinidin 3-O-(2-O-β-d-glucopyranosyl-α-l-arabinopyranoside) (D3G)-rich lentil extracts on tumor development, inflammation and immune response in an azoxymethane (AOM)/dextran sodium sulfate (DSS) model. C57BL/6 mice were randomly separated into four groups: healthy control (n = 6), AOM/DSS control (n = 14), AOM/DSS + BL (600 mg/kg body wt, n = 12) and AOM/DSS + D3G (41 mg/kg body wt, equivalent to D3G concentration in BL, n = 12). Mice were given treatments for 11 weeks using a voluntary jelly administration. AOM/DSS + BL presented a lower (P &lt; 0.05) disease activity index, throughout and at the end (2.4) compared with AOM/DSS (6.3). AOM/DSS + BL mice had an average of 7.8 neoplasms versus 12.8 for the AOM/DSS (P &lt; 0.05). Proinflammatory cytokines were downregulated in the colon mucosa: interleukin (IL)-1β (−77.5%, −70.7%) and IL-6 (−44.4%, −44.9%) by AOM/DSS + BL and AOM/DSS + D3G, respectively, compared with AOM/DSS. IL-6 protein expression was decreased by BL in plasma (−72.6%) and gene expression in colon polyps (fold change: −4.0) compared with AOM/DSS. AOM/DSS + D3G non-polyp tissue gene expression clustered with the healthy control tissue with only four genes modified (secreted phosphoprotein 1 and CXC motif chemokine ligands 2, 5 and 10). AOM/DSS + BL downregulated programmed death-ligand 1 protein expression in colon tissue (−54.7%) and gene expression by 2.8-fold compared with the AOM/DSS control. In fecal samples, gallic and protocatechuic acids and epicatechin were found, and concentration of most amino acids was lower and unsaturated fatty acids were higher for AOM/DSS + BL and AOM/DSS + D3G. BL and D3G-rich extracts showed anti-inflammatory and proimmune response effects while BL additionally prevented growth of neoplasia.