bluuebunny/crossref_metadata_2025 huggingface dataset:
Bioaccumulation of lead (Pb) and mercury (Hg) in green mussel Perna viridis (Linnaeus, 1758) in Cengkok Coastal Waters, Banten Bay, Indonesia
Authors: Melinda T , Samosir A M , Sulistiono  , Simanjuntak C P H
Published: July 2021

Banten Bay potentially receives pollutants such as heavy metals from various anthropogenic activities operating around the bay. Cengkok Coastal Waters, as part of Banten Bay, has a variety of fishery commodities, including green mussels (Perna viridis). This paper identifies the risks of heavy metal contamination by quantifying the bioaccumulation of Pb and Hg in the green mussel tissue. The study was conducted from March to August 2019. Analytical results indicate concentrations of Pb and Hg in the range of 0.005-0.044 mg/kg and 0.012-0.036 mg/kg, respectively. These results were still below the established national standards by SNI (2009) for fresh food and BPOM (2018) for processed food. These concentrations suggest that green mussel found in Cengkok Coastal Waters and surrounding areas are still suitable for consumption by the local community as long as they do not exceed the permissible limits, namely, 0.7 kg meat/week (for children) and 2.4 kg meat/week (for adults).
The effectiveness of the electricity and LPG for the sustainability of Sandfishes Holothuria scabra drying process on small islands
Authors: Pramana R , Akhirman  , Irawan H
Published: July 2021

The small islands are suitable as Aquaculture location for Sandfishes Holothuria scabra, because of the pristine water conditions. The harvested Sandfishes sometimes marketed dried, but most of it marketed fresh because the drying process took a long time using the sun heat, and needs fully standby if use heat from firewood. Both methods have conditions that depend on nature; if in rainy weather, the sun heat is unavailable and firewood becomes wet, that makes fire unavailable so that the drying process should stop. The alternative energy sources on the small island potentially used for drying the Sandfishes are the communal electricity, which commonly operates for 12 hours, and the Liquid Petroleum Gas (LPG) 3 Kg that is regularly using for daily cooking purposes. Using electric energy and LPG for drying can apply to an oven. Drying experiment results at a temperature of 50 °C for 12 hours in an electric oven gained average weight shrinkage of 83.9%, and LPG gained an average weight loss of 87.8% were significantly different based on the Independent Samples t-Test. Cost for 12 hours of electricity consumption is IDR 3,960 lower than the LPG consumption, which is IDR 5,833. Oven production capacity is 32 fresh Sandfishes weight of 500 g, which produces Sandfishes dry weight around 2 kg within the selling price class of IDR 2.2 million/kg.
Evaluation of crude ethanolic extract of aquatic plants as inhibition zone against Flavobacterium columnare
Authors: Novita H , Nugraha M F I , Firmania kn R , Fadjar M. , Radjamuddin M A L
Published: July 2021

Three different aquatic plants Selaginellaplana (Desv. Ex. Poir) Hieron, Ludwigiaadscendens (L.) H. Hara, dan Ephitemabenthamii C. B. Clarke were collected from South Sulawesi and crude extracts all of plants parts were prepared in ethanol. This extracts were checked for the presence of inhibitory zone by agar well diffusion method against gram negative Flavobacteriumcolumnare bacterial. Furthermore Minimum Inhibitory Concentration (MIC), Minimum bactericidal concentrations (MBC) testing has been done for crude extract of plants. Extracts of three plants prepared in ethanol showed relatively inhibitory zone to Flavobacterium columnareand two extracts of above plants were positive in MIC and MBC.
Potential of antibacterial compound from extract of the green algae Bornetella sp
Authors: Bahrun  , Soekamto N H , Firdaus  , Akbar A
Published: July 2021

Antibiotics resistance has become an obstacle in the treatment of various types of diseases caused by bacterial infections. The investigation of secondary metabolites from macroalgae as antibiotic reference compounds can be done as an effort to overcome this problem. Potential test for antibacterial compounds from green algae Bornetellasp has been carried out against Escherecia coli and Staphylococcus aureus bacteria. The secondary metabolite extraction process was carried out using a multilevel maceration method using n-hexane, chloroform, ethyl acetate and methanol as solvents. The extract obtained was then tested for phytochemicals and their activity against the tested bacteria by the paper disc diffusion method. The test results obtained showed that the chloroform extract had the highest activity with an inhibition zone diameter of 16.33 ±1.18 mm against E. coli and 14.26 ±0.69 mm against S. aureus. The presence of secondary metabolites of the alkaloid, steroid, phenolic and flavonoid groups based on the results of phytochemical screening is the cause of this activity.
Control of bacterial leaf blight disease in several varieties of rice plants (Oryza sativa L.) by using bacteria of Paenibacilus polymyxa Mace
Authors: Sopialena  , Suyadi  , Jannah R , Tantiani D
Published: July 2021

Bacterial Leaf Blight Disease caused by bacteriaXanthomonas oryzaepv.Oryzaeis an endemic disease found in all rice plantation in Indonesia. The bacteria infects plants from the vegetative to generative phase and is able to reduce production by up to 30%. Most of farmers control the disease by using chemical pesticides that cause pollution to the environment. While this study offers control by using biological pesticides with the bacteriaPaenibacilus polymyxaMace. The research aims to control Bacterial Leaf Blight Disease usingP. polymyxaMace in several varieties of rice plants (Oryza sativaL.) as well as to obtain effective concentrations ofP. polymyxaMace Bio agent to control Bacterial Leaf Blight Disease. Experiments were conducted using Split-plot design with 3 (three) replication. The main plot was the Concentration ofP. PolymyxaMace consist of 4 levels, they were P0=Control/Untreated, P1=2.5 mL.L-1 water, P2=5 mL.L-1 water, P3=7.5 mL.L-1 water, and as a Sub Plot was a Variety (V) consist of 3 levels, they were V1=Cibogo Variety, V2=Mekongga Variety, V3=Ciherang Variety. The results showed that that the Mekongga variety is the most resistant variety to the pathogenXanthomonas oryzaepv. Oryzae. The use ofP. PolymyxaMace as biological agents effective to control Bacterial Leaf Blight caused by the pathogenX oryzaepv. Oryzae on several rice plant varieties (Oryza sativaL.), and the best concentration ofP. PolymyxaMace to control Bacterial Leaf Blight disease was 5 mL.L-1 water.
Water-system changes in swampy rice agro-ecosystems area and their economic impacts on farmers in South Sumatra, Indonesia
Authors: Purbiyanti E , Sjarkowi F , Adriani D , Antoni M , Alamsyah I , Yulius  , Yudhistira N , Utami G
Published: July 2021

Conversion of land encompasses not only changes inthe use of land for cultivation of food to non-food product but also includes the conversion of land in use to unused land. Changes in the management of water in the area of agro-ecosystem in Ogan Komering Ilir (OKI) District has resulted in a change of use of paddy swampy land. Research was aimed :1) to analyze the differences in the income of farmers of rice due to the changes management water in the area of agro-ecosystems; and 2) to analyze the level of welfare of the rice farmers after adapting to the current environmental conditions. Research was carried out in the Belanti Village, Sirah Pulau Padang District, Ogan Komering Ilir District, South Sumatra Province, Indonesia. Location was selected purposively as the village was exposed to routine annual flood since 2008. The farmers has experinced crop and harvest failure, despite the fact that it has served as rice granary since 1992. As survey method with structured questionaires was applied in this research. Sampling was conducted purposively against 42 rice farmers who experienced crop failure. The primary and secondary data were collected and then subjected to land rent value analysis and t-test analysis. Results showed that: 1) changes in water management have reduced household income of farmers by 50.06%; and 2) the level of welfare of rice farmers is still low even though they have made adaptation efforts. To improve the quality of living for farmers affected by flooding, there is a need for integrated cooperation between the government of the country, palm plantation companies, and farmers.
Innovation study of the leading commodity agroecological zone in the Central Aceh Region
Authors: Nasution A , Alemina E
Published: July 2021

The Central Region of Aceh including of Bener Meriah, Central Aceh, Gayo Lues and Southeast Aceh districts, are the highland area of Aceh which has the potential to produce various agricultural commodities. However, the development of agricultural patterns in changing land uses has an impact on a sustainable agricultural system. This Agroecological Zone Innovation study aims to identify development priorities for leading agricultural commodities and the suitability of commodities cultivated by farmers with existing land. The results of the study show that the plants are included in the main development priority group, exist in the community, are proposed for development by farmers and are suitable for development based on the analysis of the expert system in Bener Meriah are coffee, tomatoes, avocados and oranges; in Central Aceh does not exist, in Gayo Lues are shallots and red chilies; and in Southeast Aceh is corn. Expert system analysis with agroecological zone input shows that in general the four districts in the Central Region of Aceh are suitable for the development of plantation, paddy and secondary, vegetables and fruits crops where their locations are spread across almost all sub-districts of Aceh Central Region.
Corporate social responsibility reporting of agriculture companies: evidence from Indonesia
Authors: Ika S R , Akbar FA , Puspitasari D , Sumbodo B T , Widagdo A K
Published: July 2021

This research investigates the extent of corporate social responsibility (CSR) reporting of agriculture companies listed on the Indonesia Stock Exchange (IDX). Specifically, this research attempts to compare the level of CSR reporting before and after the issuance of The Capital Market and Financial Institution Supervisory Agency (Bapepam LK) Regulation No X.K.6 in 2012 related to the content of CSR disclosure in the corporate annual report. This research also examines company characteristics, which may influence the extent of corporate CSR reporting, namely, profitability and firms size. The annual report of 12 agriculture companies for three years (2011 to 2013) was used as a sample. The CSR reporting level was analyzed using content analysis based on an index under the Global Reporting Initiative (GRI) G3 sustainability framework. The index consists of voluntary and mandatory disclosure under the X.K.6 regulation. The paired-sample t-test indicates that the CSR disclosure level increased in 2012, immediately after the regulation issuance (significant at 5 per cent level). When this study categorizes the disclosure into mandatory and voluntary, the results suggest that both disclosures after the new rule are greater than those before the rule comes. These results indicate that the new rule’s issuance imposes companies to do more CSR activities, thereby improving the company’s annual report’s disclosure level. In terms of factors influencing CSR reporting, size positively influence CSR reporting in the agriculture industry. The result indicates that the larger the firm, the more resources available for the firm to do CSR activities reported in the company annual report.
Genetic variation of seven years old Araucaria cunninghamii progeny test in Bondowoso East Java
Authors: Setiadi D , Mashudi  , Hadiyan Y , Susanto M , Baskorowati L , Pujiono S , Adinugraha H A , Sulaeman M
Published: July 2021

Araucaria cunninghamii is conifer trees with great commercial value for tropical and sub-tropical region. The genetic variation in growth i.e: height, diameter, volume was examined on 7 years old of A. cunninghamii progeny test at the area of Forest for Special Purpose (KHDTK) in Bondowoso, East Java. The progeny trial included 80 families from six provenances, with four replications and four trees in each row plots. The analysis showed that there were great variations of genetic growth within provenances and between provenances. It was discovered that A. cunninghamii from Fak-fak Papua had the best height growth (mean height= 10.65 m with volume mean annual increments =8.39 m 3 ha-1 year-1), while A. cunninghamii from Serui Papua had the best diameter growth (mean diameter =15.84 cm). The individual heritability for height and diameter were classified as moderate (h 2i = 0.16; 0.30). The genetic correlation between the height and diameter was quite strong (r g = 0.79). As a result of the findings, the future genetic program strategy in the research will focus on increasing genetic biodiversity for the species in order to increase Mean Annual Increment (MAI) for supplying Indonesia’s wood demand.. The genetic diversity will be achieved through some steps in the strategy i.e: best genetic growth selection within provenances; combining of genetic of the best growth between provenances; and establishment of the progeny trial for next generations.
The role of urban household wood product consumption on forest management and its impact: a system modelling simulation approach in Bogor City
Authors: Abdulah L , Suhendang E , Purnomo H , Matangaran J R
Published: July 2021

The term consumption of wood products has not yet become a significant consideration in regulating timber forest products in Indonesia. The result is that tree harvesting is not based on the size of its utilization. This situation will impact the piling up of harvested wood and reduce the price of wood and forested land’s economic value. Otherwise, timber needs are not fulfilled to carry out illegal logging to meet their needs. Errors in using basic data will improve environmental damage like carbon storage. This problem must be seen as a system. For this reason, this study aims to recommend strategies for meeting the needs of trees and timber to maintain forest productivity. The method used is system dynamics analysis. The results showed that emissions from wood products’ utility in households are 14 t in natural forests and only 2 t from plantation forests. The scenario of promoting the use of wood is carried out, the community will use solid wood and composite wood products more widely, and the use of wood in roof construction tends to be constant.
Resilience of forest village communities in the implementation of the community forest policy
Authors: Tjoa M , Iskar  , Latukau S H
Published: July 2021

The implementation of the Community Forestry (HKm) program in a community group causes changes in community land management and becomes a challenge for sustainable forest management. This study aims to determine the level of ability (resilience) of the community to survive in the face of changes in community forestry policies. The approach used in this research is qualitative and quantitative. The survey method was used by conducting interviews to collect data from groups and other community members as well as key informants. The results showed that the level of community resilience in implementing Social Forestry policies adhered to indicators of natural resources, socio-culture, and economics concluded that there were several aspects that became the reasons for group members to stay in HKm including system functioning parameters (average 65%), income (average 37%), participation (average 88%) and capacity (average 82%).
The role of stakeholders in ecotourism development in Marsegu Island Nature Tourism Park (MINTP) in Western Seram Regency, Eastern Indonesia
Authors: Lelloltery H , Puttileihalat M M S , Sitanala M , Seipalla B B , Kunda R M
Published: July 2021

This study aimed to 1) Identifying stakeholders involved in ecotourism activities and 2) Analyze the role of stakeholders in support ecotourism activities in MINTP Western Seram Regency. A survey method with interview technique and Focus Group Discussions The data were analyzed descriptively qualitatively using stakeholder analysis. The stakeholder identification results showed that the primary stakeholder is the community in coastal villages around Kotania Bay. The key stakeholder is Nature Conservation Agency, Maluku and North Maluku. Supporting stakeholders are the private sector and academics, supporting capital dan facilities, and providing education and natural resources research. The results showed that each stakeholder is performed functions partially; therefore, it is necessary to have a collaboration management.
Coral reef condition in the coastal waters of Kei Besar Island, Southeast Maluku-Indonesia
Authors: Sahetapy D , Limon G V , Tetelepta J M S , Pattikawa J A , Rijoly F , Masrikat J A N , Loupatty S R
Published: July 2021

A study on coral reefs condition in the coastal waters of Kei Besar Island was conducted in 2019 with the aimed to provide data on taxa composition, density and colony diameter of stony corals, coral reefs condition, and ecological indices of the coral community. It was found during the study that there are 17 families of stony coral, which consist of 62 genera and 206 species. Among those species of stony coral, 79 species are classified as protected species and 50 species as ornamental coral. Coral families of Acroporidae, Faviidae, Fungiidae, and Poritidae have high species richness. The density of stony coral colonies between reef stations ranged from 3.0 colonies m−2 (low) with a relatively large colony diameter until 16.3 colonies m−2 (high) with a small coral colony diameter. The only one reef station was in Excellent condition, while seven reef stations in Good, four reef stations in Fair, and two coral reef sites were in Poor condition. The coral community in the coastal waters of Kei Besar Island had moderate species diversity of stony coral and low species dominance with stable condition.
Diversity of parrotfish in Ambon Island waters, Eastern Indonesia
Authors: Loupatty S R , Limmon G V , Rijoly F , Tetelepta J M S , Pattikawa J A
Published: July 2021

Ambon is small island belongs to Maluku Province, Eastern Indonesia. The waters of this island has great potential of marine resources such as Echinoderms, Molluscs, Crustaceans, and Fishes. Coral reef ecosystem in this area make its marine waters has variety of reef fishes. One of the reef fish is parrotfish, which is important economically and ecologically. This research was conducted to study diversity of parrotfishes in Ambon Island waters. Samples were collected through UVC method and purposive sampling method at fish markets and fish landing sites in 2015-2017. It was found that parrotfish in Ambon Island waters consist of 29 species and 6 genera i.e. 15 species and four genera from UVC sampling and 25 species and six genera from sampling at fish markets and fish landing sites. 15 of those parrotfish has been successfully validated by DNA barcoding. Total density of parrotfish in the southern waters of Ambon Island was 318 ind./ha.
Density and abundance of sea cucumber at seagrass ecosystem in Paperu Waters, Saparua Bay, Maluku
Authors: Manuputty G D , Luhulima Y , Pattinasarany M M
Published: July 2021

Sea cucumbers, Holothurians, are high economic value resources according to their utilization for food and medicine. Due to the roles affect the increasing of sea cucumber exploitation in natural, the sea cucumbers are consequently categorized as endangered species. People in Saparua Island have been utilized the resources for years, including people in Paperu. Hence, the research was carried out to analyze the density and abundance of sea cucumber species at the seagrass ecosystem on Paperu Waters Saparua Bay. The research was conducted in October 2017 by using the linear transect method which consisted of three stations and 9 transects. The results showed that no less than eight species were found on the site, which were classified into one order, two families, and three genera. The eight species are approximately found in various densities and abundance, i.e. Bohadschia bivittata, B. marmorata, B. vitiensis, Holothuria atra, H. edulis, H. leucospilota, H. scabra, and Stichopus horrens. The highest density and abundance was found at species Bohadschia vitiensis and B. bivittata, respectively 0,16 ind.m−2 and 5.336 ind, while the lowest density and abundance were found at species H. leucospilota (0,04 ind.m−2 and 1.334 ind).
Marine fisheries zoning based on adat sasi indigenous local wisdom: A technical overview
Authors: Djunarsjah E , Putra A P
Published: July 2021

On Haruku Island, Maluku Province, there is Adat Sasi where fishing activities and their use are regulated based on the culture of the local community from hereditary inherited from their ancestors. Adat Sasi is a prohibition against taking natural products in the form of agriculture and marine fisheries before the specified time so that the environment is preserved. On the other hand, Law Number 23 of 2014 concerning Regional Government regulates the boundaries of provincial authority in the sea area. The question is whether the fishing zone which is bound by Adat Sasi follows the National regulation? In this paper, Marine Fisheries Zoning Based on Adat Sasi Indigenous Local Wisdom is technically reviewed based on the principle of hydrography, which is one of the scientific fields related to positioning activities at sea. The methodology used is to search for information on the boundaries of the fishing zone that is tied to Adat Sasi, and then quantify it numerically to be compared with the Sea Boundary Map of Maluku Province. The results of the study indicate that the fishing zone boundary which is related to Adat Sasi is approximately 5.04 km from the coastline. While the provincial authority in the sea area is as far as 22.2 km. Thus, the Provincial Government has the opportunity to expand the fishing zone based on Adat Sasi or have other alternatives to determine zoning for coastal areas by considering Adat Sasi in the framework of sustainable nature conservation.
The vulnerability of reef fishes to environmental exposure in Komodo National Park and its surrounding waters
Authors: Oktaviani D , Sulaiman P S , Puspasari R
Published: July 2021

Komodo National Park (KNP) is administratively located in the Komodo district, West Manggarai Regency, East Nusa Tenggara Province. The geographical position is connected to the coast of the Flores Sea and the Indian Ocean. Fishing is the main livelihood for approximately 13% of the district population. There are 60 reef fish species found in the area, and small scale fishers were mostly operated to support their livelihood. This study aims to determine the vulnerability of five high-value reef fish species to environmental exposure, i.e., Plectropomus leopardus (Lacepède, 1802); Variola louti (Forsskål, 1775); Epinephelus fuscogutattus (Forsskål, 1775); Lutjanus malabaricus (Bloch & Schneider, 1801); and Lutjanus gibbus (Forsskål, 1775). The observation was carried out during 2019. The analysis was performed by the method for assessing the vulnerability of marine fish and shellfish species to a changing climate. The approach consisted of sensitivity attribute and exposure factor based on reasonable time series data availability. The results indicated that the vulnerability indices of P. leopardus, V. louti, and E. fuscoguttatus to aquatic environment variabilities were high. This means that the three populations are strongly influenced by environmental conditions on the coral reef ecosystem. The vulnerability indices of L. malabaricus and L. gibbus to the aquatic environment variables were moderate or sufficiently affected by environmental conditions to the coral reef ecosystem. One should be considered that these findings with the data-quality scoring at a category 2 and 3 or limited data to adequate data. These indices showed that necessary to manage and protect the marine and coastal ecosystems of Komodo National Park and its surroundings from anthropogenic pressures and adapt to environmental exposure factors. This should be supported by the identification of grouper and snapper spawning aggregation areas in the National Park.
Analysis of water pollution in microbiology aspect of some watersheds at Ambon City, Maluku Province
Authors: Kaihena M , Talakua C M , Pagaya J , Talakua S M
Published: July 2021

This research aims to study the factors that affect water pollution and the difference in water pollution microbiology at several watersheds in Ambon City. This research used the sample of well water and river water at Wai Ila, Wai Batu Merah, and Wai Ruhu watersheds. The sample obtained was analyzed using the method of determining MPN and water pollution method. The data obtained were analyzed with the use of regression - correlation test and analysis of variance (ANOVA). The correlation and regression test indicates the factors which affect the pollution of well water from microbiological aspects in terms of the number of coliform bacteria and E. coli is the factor of the utilization of the well, the distance to the well, septic tank and its structure, the frequency of cleaning wells and income level, with P-value in the ANOVA of 0.049. While the factors that affect water pollution of the river from the aspect of microbiology are the population, average income head of the family, absence of livestock farming, and sanitation around the river, with a P-value in ANOVA of 0.050. One Way ANOVA test results against the average number of coliform and E.coli in river Wai Ila, Wai Batu Merah, and Wai Ruhu watersheds shows there is a significant difference between the pollution from the aspect of environmental microbiology especially the number of bacteria coliform and E.coli in river water of the three watersheds with P-value value each of 0.048 and 0.028 (a < 0.05).
Lactic acid bacteria profile isolated from “laor” worms (Polychaeta) fresh from Lawena Beach, Ambon Maluku
Authors: Mailoa M N , Sormin R B D , Leiwakabessy J , Wattimena M L
Published: July 2021

This study aimed to determine the characteristics of lactic acid bacterial isolates (LAB) from fresh laor worms. LAB isolation was carried out by using a multilevel dilution technique with 0.9% NaCl diluent then grown on MRS Agar media with 1% CaCO3 added and incubated at 37°C for 48 hours. This research was using descriptive methods of morphological characterization and biochemical tests on LAB isolates. The total LAB on fresh laor worms was 6.8 x 104-7.4 x104 CFU/g. The morphological and biochemical characterization showed that LAB isolates were three categories: round colony shape, small size, milky white color with convex elevation, round cell shape, short chain (isolate Bl 6); short stem cell shape (isolate Bl 2, Bl 3, Bl 4); the form of short chain stem cells (isolate Bl 3). The catalase test interpretation of the isolates showed a negative results and the Gram staining showed LAB isolates were Gram positive. Two genera of lactic acid bacteria were suspected as Lactobacillus and Streptococcus.
‘I’ll Get You, Tom and Jerry. And That Little Dog, Too!’: Adaptation, Transmedia, and Franchise Management in theTom and JerryandWizard of OzCrossovers
Authors: McGowan David
Published: July 2021

This article will offer a close reading of two Warner Bros. direct-to-video animated features—Tom and Jerry & the Wizard of Oz (2011) and Tom and Jerry: Back to Oz (2016)—as an example of the transmedia tendencies of studios in the conglomerate era. Although The Wizard of Oz (1939) and Tom and Jerry were originally MGM productions, the modern distribution of these works provides an insight into the complicated post-‘Golden Age’ trajectories of studio archives. Ted Turner’s brief takeover of MGM in the mid-1980s stripped the studio of many of its assets, while the merger of Turner’s company with Warner Bros. in 1996 brought these MGM properties under Warner control. The Tom and Jerry/Wizard of Oz crossover films heavily reference the 1939 MGM movie (the songs, the ruby slippers, and so on)—something that other adaptations of Baum’s novels have not been permitted to do. This paper will suggest that these new extensions of old brands subtly rewrite MGM’s industrial history in favour of establishing them as Warner Bros. franchises, while also re-establishing the brand identity of the 1939 film at a time where Oz adaptations are facing greater competition, particularly from the successful stage musical Wicked (2003).
Hear it through the grapevine
Authors:   The ECN committee comprises:, Bowman Dominic M , Maunder Megan , Richards Fred , Boubert Douglas , O'Brien Áine
Published: July 2021

Dominic M Bowman and the ECN Committee share their perspective of the RAS Early Career Network's first career event: postdoctoral career advice from the community
Electromagnetic counterparts of gravitational-wave signals
Authors: Nuttall Laura K , Berry Christopher P L
Published: July 2021

Laura Nuttall and Christopher Berry review the potential of multimessenger astronomy with gravitational-wave observations
Things are looking up
Authors: Bowler Sue
Published: July 2021

Sue Bowler discovers how RAS 200 outreach with The Prince's Trust has inspired two young people
quincunx: an R package to query, download and wrangle PGS Catalog data
Authors: Magno Ramiro , Duarte Isabel , Maia Ana-Teresa
Published: July 2021

Motivation

The Polygenic Score (PGS) Catalog is a recently established open database of published polygenic scores that, to date, has collected, curated and made available 721 polygenic scores from over 133 publications. The PGS Catalog REST API is the only method allowing programmatic access to this resource.

Results

Here, we describe quincunx, an R package that provides the first client interface to the PGS Catalog REST API. quincunx enables users to query and quickly retrieve, filter and integrate metadata associated with polygenic scores, as well as polygenic scoring files in tidy table format.

Availability and implementation

quincunx is freely available under an MIT License, and can be accessed from https://github.com/maialab/quincunx.

Supplementary information

Supplementary data are available at Bioinformatics online.
Dynamic Microwave-Assisted Micelle Extraction Coupled with Cloud Point Preconcentration for the Determination of Triazine Herbicides in Soil
Authors: Wu Lijie , Li Zhanchao , Hu Mingzhu
Published: July 2021

A green and simple method, dynamic microwave-assisted micelle extraction coupled with cloud point preconcentration, was developed for the determination of triazine herbicides in soil samples. The method has the advantages of those two extraction procedures, which could eliminate the interferences from complex soil samples greatly. Non-ionic surfactant Triton X-114 aqueous solution used as extraction solvent was continuously pumped into soil samples. The resulting extract was heated and centrifuged in the presence of NaCl. After centrifugation, the analytes were enriched into the surfactant-rich phase. No filtration or cleaning steps were required. Several key parameters were investigated. The Box–Behnken design was applied to optimize the experimental factors involved in the dynamic microwave-assisted micelle extraction. Good linearity was observed in the range of 1.00–250.00 μg kg−1. The limits of detection were ranged between 0.26 and 1.71 μg kg−1. The recoveries of analytes ranged from 80.3 to 98.3% with the relative standard deviations ranging from 1.1 to 6.6%.
Thin-Layer Chromatography Gradient Optimization Strategy for Wet Load Adsorption Flash Chromatography
Authors: Kręcisz Paweł , Czarnecka Kamila , Szymański Paweł
Published: July 2021

Chromatography is one of the most popular methods for the separation of compounds in modern pharmaceutical industry and science. Despite the extensive use of the reversed phase chromatography in analytical and preparative applications, the normal phase adsorption chromatography has a special place in purifying post-reaction mixtures or the separation of natural extracts, especially in wet load mode, because of simplicity and high velocity of preparation. Complex mixtures, more difficult to separate, require gradient methods to obtain better results of separations. These methods can be developed by external software, but the automatic methods are often not very accurate and the negative impact of wet load application on separation quality is considerable in them. Therefore, we present the thin-layer chromatography (TLC) gradient optimization strategy for wet load separations to obtain repeatable results of separations for different compounds without worrying about negative impact of wet loading on separation quality. The strategy provides information about an elution model of desired compound, which is used to develop the gradient method. The strategy also allows to standardize the separation length, because gradient methods performed by the TLC gradient optimization strategy have a very similar duration time in column volumes. The method can also be simply scaled because of using the column volume as a base unit in calculations.
What Might (Finally) Kill the Jus ad Bellum?
Authors: Hakimi Monica
Published: July 2021

There is a long tradition of international relations and legal scholars warning of the demise of the jus ad bellum—the body of international law that governs when states may use force across national borders. I argue in this Lecture, presented at The University College London Faculty of Laws in October 2020, that these warnings have mostly been wrong. The reason they have been wrong is that they have misdiagnosed the main threat to the jus ad bellum, or at least, they have myopically focused on and grossly overstated the seriousness of a particular kind of threat. And in doing so, they have diverted attention away from other challenges that might actually push the contemporary jus ad bellum to the breaking point—and that we might now confront.
Time outweighs the effect of host developmental stage on microbial community composition
Authors: Dibner Reilly R , Weaver A Monique , Brock Marcus T , Custer Gordon F , Morrison Hilary G , Maignien Lois , Weinig Cynthia
Published: July 2021

Thousands of microbial taxa in the soil form symbioses with host plants, and due to their contribution to plant performance, these microbes are often considered an extension of the host genome. Given microbial effects on host performance, it is important to understand factors that govern microbial community assembly. Host developmental stage could affect rhizosphere microbial diversity while, alternatively, microbial assemblages could change simply as a consequence of time and the opportunity for microbial succession. Previous studies suggest that rhizosphere microbial assemblages shift across plant developmental stages, but time since germination is confounded with developmental stage. We asked how elapsed time and potential microbial succession relative to host development affected microbial diversity in the rhizosphere using monogenic flowering-time mutants of Arabidopsis thaliana. Under our experimental design, different developmental stages were present among host genotypes after the same amount of time following germination, e.g. at 76 days following germination some host genotypes were flowering while others were fruiting or senescing. We found that elapsed time was a strong predictor of microbial diversity whereas there were few differences among developmental stages. Our results support the idea that time and, likely, microbial succession more strongly affect microbial community assembly than host developmental stage.
Staphylococcal trafficking and infection—from ‘nose to gut’ and back
Authors: Raineri Elisa J M , Altulea Dania , van Dijl Jan Maarten
Published: July 2021

Staphylococcus aureus is an opportunistic human pathogen, which is a leading cause of infections worldwide. The challenge in treating S. aureus infection is linked to the development of multidrug-resistant strains and the mechanisms employed by this pathogen to evade the human immune defenses. In addition, S. aureus can hide asymptomatically in particular ‘protective’ niches of the human body for prolonged periods of time. In the present review, we highlight recently gained insights in the role of the human gut as an endogenous S. aureus reservoir next to the nasopharynx and oral cavity. In addition, we address the contribution of these ecological niches to staphylococcal transmission, including the roles of particular triggers as modulators of the bacterial dissemination. In this context, we present recent advances concerning the interactions between S. aureus and immune cells to understand their possible roles as vehicles of dissemination from the gut to other body sites. Lastly, we discuss the factors that contribute to the switch from colonization to infection. Altogether, we conclude that an important key to uncovering the pathogenesis of S. aureus infection lies hidden in the endogenous staphylococcal reservoirs, the trafficking of this bacterium through the human body and the subsequent immune responses.
MiR-592 activates the mTOR kinase, ERK1/ERK2 kinase signaling and imparts neuronal differentiation signature characteristic of Group 4 medulloblastoma
Authors: Paul Raikamal , Bapat Purna , Deogharkar Akash , Kazi Sadaf , Singh Satish Kumar Vishram , Gupta Tejpal , Jalali Rakesh , Sridhar Epari , Moiyadi Aliasgar , Shetty Prakash , Shirsat Neelam Vishwanath
Published: July 2021

Medulloblastoma, a common malignant brain tumor in children, consists of four molecular subgroups WNT, SHH, Group 3 and Group 4. Group 3, Group 4 tumors have an overlap in their expression profiles and genetic alterations but differ significantly in their clinical characteristics, with Group 3 having the worst 5-year overall survival of <60%. MiR-592 is overexpressed predominantly in Group 4 tumors. MiR-592 expression reduced the anchorage-independent growth, invasion potential and tumorigenicity of Group 3 medulloblastoma cells. DEPTOR, an endogenous inhibitor of the mTOR kinase, and EML1 were identified as novel targets of miR-592. The miR-592 mediated decrease in the DEPTOR expression levels activated both mTORC1 and mTORC2 complex in medulloblastoma cells. However, the miR-592 expression also decreased the AKT kinase activity, likely to be due to the activation of the inhibitory feedback of the mTOR signaling. MiR-592 expression upregulated several neuronal differentiation-related genes, a characteristic of Group 4 medulloblastoma in Group 3 cell lines. The expression of miR-592 also upregulated the activity of ERK1/ERK2 kinases indicating activation of the MAPK signaling pathway. The inhibition of MAPK signaling by the ERK1/ERK2 inhibitor and mTOR signaling by rapamycin abrogated the miR-592-mediated upregulation of neuronal differentiation-related genes. Group 4 medulloblastomas showed higher activity of the mTOR and MAPK signaling compared to Group 3 tumors. Thus, miR-592 overexpression appears to be a driver event and a determining factor of Group 4 biology, which activates the mTOR and MAPK signaling pathways and thereby imparts its characteristic expression profile of neuronal differentiation-related genes.
Understanding Drivers of Variation and Predicting Variability Across Levels of Biological Organization
Authors: McEntire Kira D , Gage Matthew , Gawne Richard , Hadfield Michael G , Hulshof Catherine , Johnson Michele A , Levesque Danielle L , Segura Joan , Pinter-Wollman Noa
Published: July 2021

Differences within a biological system are ubiquitous, creating variation in nature. Variation underlies all evolutionary processes and allows persistence and resilience in changing environments; thus, uncovering the drivers of variation is critical. The growing recognition that variation is central to biology presents a timely opportunity for determining unifying principles that drive variation across biological levels of organization. Currently, most studies that consider variation are focused at a single biological level and not integrated into a broader perspective. Here we explain what variation is and how it can be measured. We then discuss the importance of variation in natural systems, and briefly describe the biological research that has focused on variation. We outline some of the barriers and solutions to studying variation and its drivers in biological systems. Finally, we detail the challenges and opportunities that may arise when studying the drivers of variation due to the multi-level nature of biological systems. Examining the drivers of variation will lead to a reintegration of biology. It will further forge interdisciplinary collaborations and open opportunities for training diverse quantitative biologists. We anticipate that these insights will inspire new questions and new analytic tools to study the fundamental questions of what drives variation in biological systems and how variation has shaped life.
Convex X-ray spectra of PKS 2155-304 and constraints on the minimum electron energy
Authors: Jagan Sitha K , Sahayanathan S , Rieger Frank M , Ravikumar C D
Published: July 2021

The convex (concave upward) high-energy X-ray spectra of the blazar PKS 2155-304, observed by XMM-Newton, is interpreted as the signature of subdominant inverse-Compton emission. The spectra can be well fitted by a superposition of two power-law contributions which imitate the emission due to synchrotron and inverse-Compton processes. The methodology adopted enables us to constrain the photon energy down to a level where inverse-Compton emission begins to contribute. We show that this information supplemented with knowledge of the jet Doppler factor and magnetic field strength can be used to constrain the low-energy cut-off γminmec2 of the radiating electron distribution and the kinetic power Pj of the jet. We deduce these quantities through a statistical fitting of the broad-band spectral energy distribution of PKS 2155-304 assuming synchrotron and synchrotron self-Compton emission mechanisms. Our results favour a minimum Lorentz factor for the non-thermal electron distribution of γmin ≳ 60, with a preference for a value around γmin ≃ 330. The required kinetic jet power is of the order of Pj ∼ 3 × 1045 erg s−1 in case of a heavy, electron–proton dominated jet, and could be up to an order of magnitude less in case of a light, electron–positron dominated jet. When put in context, our best-fitting parameters support the X-ray emitting part of blazar jets to be dominated by an electron–proton rather than an electron–positron composition.
A mechanical model for magnetized relativistic blastwaves
Authors: Ai Shunke , Zhang Bing
Published: July 2021

The evolution of a relativistic blastwave is usually delineated under the assumption of pressure balance between forward- and reverse-shocked regions. However, such a treatment usually violates the energy conservation law, and is inconsistent with existing magnetohydrodynamic numerical simulation results. A mechanical model of non-magnetized blastwaves was proposed in previous work to solve the problem. In this paper, we generalize the mechanical model to the case of a blastwave driven by an ejecta with an arbitrary magnetization parameter $\sigma_{\rm ej}$. We test our modified mechanical model by considering a long-lasting magnetized ejecta and found that it is much better than the pressure-balance treatment in terms of energy conservation. For a constant central engine wind luminosity $L_{\rm ej} = 10^{47} {\rm erg ~ s^{-1}}$ and $\sigma_{\rm ej}<10$, the deviation from energy conservation is negligibly small at small radii but only reaches less than $25{{\ \rm per\ cent}}$ even at 1019 cm from the central engine. For a finite lifetime of the central engine, the reverse shock crosses the magnetized ejecta earlier for the ejecta with a higher $\sigma_{\rm ej}$, which is consistent with previous analytical and numerical results. In general, the mechanical model is more precise than the traditional analytical models with results closer to those of numerical simulations.
Age at onset in axial spondyloarthritis around the world: data from the Assessment in SpondyloArthritis international Society Peripheral Involvement in Spondyloarthritis study
Authors: Boel Anne , López-Medina Clementina , van der Heijde Désirée M F M , van Gaalen Floris Alexander
Published: July 2021

Objective

Age at onset is useful in identifying chronic back patients at an increased risk of axial SpA (axSpA). However, the majority of data on which the criterion of age at onset <45 years is based originates from Europe. Therefore it is unknown if this criterion applies in other parts of the world. We aimed to assess the age at onset of axSpA and its relationship with HLA-B27 and gender across the world.

Methods

Analyses were applied to patients from 24 countries across the world with an axSpA diagnosis and known age at onset of axial complaints. Cumulative probability plots were used to display the cumulative distribution of age at onset of axial symptoms. Linear regression models were built to assess the effect of HLA-B27 and gender on age at onset of axial symptoms.

Results

Of 2579 axSpA patients, 92% had an age at onset of axial symptoms <45 years, with only small variations across the geographical regions [Asia, n = 574 (94%); Europe and North America, n = 988 (92%); Latin America, n = 246 (89%); Middle East and North Africa, n = 771 (91%)]. Age at onset of axial symptoms was consistently lower in HLA-B27-positive patients {median 25 years [interquartile range (IQR) 19–32] vs 31 [IQR 22–39]} and male patients [median 25 years (IQR 19–33) vs 28 (IQR 21–37)], but in multivariable models an additional statistically significant effect of male gender independent of HLA-B27 was only found in Asia.

Conclusion

Around the world, the great majority of axSpA patients had an age at onset of axial disease of <45 years, with HLA-B27 and male gender associated with earlier disease onset.
Aspergillus flavus Infections in Children With Leukemia Despite Liposomal Amphotericin-B Prophylaxis
Authors: Vissing Nadja Hawwa , Lausen Birgitte , Hutchings Hoffmann Marianne , Als-Nielsen Bodil , Schmiegelow Kjeld , Helweg-Larsen Jannik , Arendrup Maiken Cavling , Nygaard Ulrikka
Published: July 2021

Liposomal amphotericin-B (L-AmB) prophylaxis is used in children with leukemia when azoles are contraindicated, but its effect is debated. We reviewed cases of invasive aspergillosis despite L-AmB 2.5 mg/kg twice weekly in children with high-risk leukemia during 2012-2019. Ten (16%) of 62 children had proven or probable aspergillosis. Thus, L-AmB prophylaxis offered insufficient protection for Aspergillus, in particular for Aspergillus flavus.