bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissemination of angling vessels in the eastern Indian Ocean: a remote sensing perspective
Authors: Syah A F , Inayah Z , Partadisastra M A , Yehezkiel R 
Published: October 2020

Abstract
Dissemination of angling vessels extracted from Vessels Monitoring System (VMS) platform and the Visible Infrared Imaging Radiometer Suite (VIIRS) boat detection (VBD) data in the eastern Indian Ocean. The data of angling vessels derived VMS platform and VBD data was provided by Ministry of Maritime Affairs and Fisheries Indonesia and Earth Observation Group, respectively. The results showed the number of angling vessels that operated during southeast monsoon was higher than others monsoon. The dissemination of angling vessels originating from the VMS platform with VIIRS-VBD has a similar pattern, especially from Bali – Nusa Tenggara. In the general, the dissemination variety of angling vessels from VMS showed that angling vessels mostly appeared in the waters of Bali – Nusa Tenggara while the angling vessels from VBD appeared from West Java - Nusa Tenggara. The VMS and VBD data opening up a variety of possible future applications for more calculable data analysis of fisheries.
Maritime archeology resources potential in Belitung waters
Authors: Novita A , Adhityatama S , Ramadhan A S , Manurung Y H M , Prasetya W H 
Published: October 2020

Abstract
In the national development agenda, the government is committed to building Indonesia to become the world’s maritime axis. The commitment aims to restore the identity of Indonesia as a maritime nation which includes the development of infrastructure, political, socio-cultural, legal, security, and economic aspects. Archaeological research conducted by Balai Arkeologi Sumatera Selatan shows the Belitung waters have potential cultural material resources related to past maritime trade. The issue in this paper is to discuss maritime archeological resources found in Belitung waters through library research from the results of archeological research. This paper aims to provide an overview of Belitung waters which caused shipwrecks that crossing these shipping lanes in the past.
The effect of tomato juice (Lycopersicon esculentum) as natural antioxidant to fertilization rate spermatozoa of kancra fish (Tor soro) 24 hours postcryopreservation
Authors: Muhiardi I , Abinawanto  , Subagja J , Arifin O Z , Anabella N A , Arief M Z 
Published: October 2020

Abstract
Kancra fish (Tor soro) is one of endemic freshwater fish which is originated from Sumatera island. Nowdays, the population of kancra fish is declining because of over fishing in the habitat. Therefore, it is necessary to preserve kancra fish by doing spermatozoa cryopreservation. The objective of present study is to evaluated the effect of tomato juice on fertilization rate 24 hour after spermatozoa cryopreservation. The study used a completely randomized design with four treatments and six replications. Four treatments consisted of 0% tomato juice + 10% DMSO (0% SBt); 10% tomato juice + 10% DMSO (10% SBt); 20% tomato juice + 10% DMSO (20% SBt); and 30% tomato juice + 10% DMSO (SBt 30%). Data was analysed by One Way Analyses of Variance test followed by Tukey test. The results showed that there was the tomato juice effect (P<0.05) on the fertilization rate after spermatozoa was deep frozen in liquid nitrogen (LN) for 24 hours has significant difference (P <0.05) in the average value of the percentage of fertilization rate. The results showed that the 10% of tomato juice was optimum concentration that showed the highest fertilization rate (81.25 ± 6.07%).
Utilization of marine resources in prehistoric era at Pawon Cave West Java
Authors: Yondri L , Oscandar F , Malinda Y 
Published: October 2020

Abstract
Pawon Cave is one of the locations for prehistoric life discovery in West Java. Archaeological research at Pawon Cave was done since 2003 until now. Seven human skeletons from prehistoric era had been found there. Five sample for carbon dating analysis for cultural chronology show the time between 5600-11700 BP. Besides human skeletons, from archaeological excavation at Pawon Cave also found various artefactual made various of stone like chert, obsidian, and andesite, bone tools as deer antlers, and pig teeth. Bone tools are processed into single piercings, double piercings, and spatulas, jewelry from shark teeth, animal fangs, and mollusks. Food indication can know from bone fragments from various animals bone fragment, and mollusks from both freshwater and marine. Based on the results of the forensic odontology analysis, an understanding about types of materials consumed by Pawon Man is more diverse. hunting and collecting food of Pawon Man in the past, not only show by the excavation findings like animal bones remains, more specifically known from the analysis of calculus (plaque) attached to Pawon Man teeth. Based on archeological found in excavation and the result of calculus analysis can be show the Pawon Man in the prehistoric time also used as artifact and consume some source from marine.
Application of asexual reproduction techniques and grow ability of the sandfish Holothuria scabra
Authors: Pattinasarany M M , Pattiasina B J 
Published: October 2020

Abstract
Sea cucumber population in nature is reported to have experienced exploitation pressure in various places. Natural sea cucumber reproduction (sexual) takes a long time to produce a new adult individual. This is feared to be the cause of the extinction of sea cucumbers. Sandfish, Holothuria scabra, do not include sea cucumber species which are categorized as capable of asexual reproduction. However, several laboratory-scale studies state that sandfish can be induced for asexual reproduction. This study aims to determine the level of life graduation and the growth of sandfish produced by asexual reproduction. Individual sandfish is tied with rubber bands about 60% from the anterior to the posterior. The result showed that the sandfish were successfully induced to undergo asexual reproduction which is known as “fission”. The time needed for a sandfish to break itself into 2 new individuals takes less than 2 days. The first days after dividing the body seem to be a critical period. Only 13.64% of new individuals survive the critical phase. It concluded that the growth of asexual reproduction sandfish is slow because it takes time to regenerate the scattered internal organs during the process of division.
Modeling the impact of the COVID-19 pandemic on air emissions indicators of climate change originating from solid waste management in coastal settlements
Authors: Tassakka M I S , Musrianton M , Alsita I , Runtu K G A , Normayasari  , Ndahawali D H 
Published: October 2020

Abstract
COVID-19 was first reported in Indonesia on March 2, 2020. Several actions have been taken, such as limiting population mobility and prohibiting almost all activities that can be avoided. This policy has environmental consequences, especially the amount of solid waste generation. This study provides a view of the effect of COVID-19 on the amount of solid waste generation and composition in coastal settlements, the impact on air quality which has implications for climate change, and provides the most efficient solid waste management solution. Measurement of solid waste data using SNI 19-3964-1994 and air emissions analysis using the IWM2 software. On the basis of this quantitative analysis, we reached the following conclusions: (1)the reduction of solid waste generation is 15,47% with the composition during the pandemic namely organic 41,4%; wood 3,4%; fabric/textile 1,1%; rubber/leather 13,4%; plastic 21,3%, iron 5,5%; Glass 3,9%, paper 0,2% and residue 6,8%, (2) the resulting air emissions decreased by parameters CO2 of 32.33 tons/year (37.97%), CH4 of 14.37 tons/year (38.14%), and Global Warming Potential (GWP) of 334.01 tons/year (38.12%), (3) the most efficient management of solid waste for coastal settlements during the COVID-19 pandemic period is the process of recycling, biological processing, and bringing residues to landfill.
Potency of jellyfish alkaloid (Aeginura sp) on kidney histopathology and relative percent survival (RPS) of tiger grouper (Epinephelus fuscoguttatus) against Vibrio harveyi
Authors: Andayani S , Fadjar M , Rahayu A P , Rahman M F , Kurniati E 
Published: October 2020

Abstract
The purpose of this research were to determine the effect of alkaloid jellyfish compounds on kidney histopathology and to know the best doses to the Relative Percent Survival (RPS) of tiger grouper. The method of this research was descriptive and treatment with Completely randomized design. The treatment of active alkaloid compound on feed was given for 28 days. And then challenge-tested to 107 cells.ml−1 of Vibrio harveyi into the media for one day. Using alkaloids compound of Aeginura sp. on the feed with the doses of Control= 0 g alkaloid / kg feed; A = 0.5 g alkaloid / kg feed; B = 0.75 g alkaloid / kg feed; C = 1.0 g alkaloid / kg feed; Alkaloid D = 1.25 g / kg feed. The result of the scoring shows that the 4 treatment with given alkaloid dosage are able to decrease the damage level on the tissues of the fish’ kidneys. The average total damage of treatment C =1gr Alkaloid dosage is found to have the lowest value compared to another treatment with the percentage damages of 13,47% which is categorized low. Those results show better value than the infected fish without any medication with total damage of 42.27% within the medium category. The best RPS was found at a treatment of C with the value of 100%. For further study, it was suggested using a dose of 1 g alkaloid / kg feed for the best result. It was proved by an absent of the damage on kidney and the value of RPS reached 100%.
Updating of baseline radionuclides concentration in Jakarta Bay
Authors: Priasetyono Y , Makmur M , Yahya M N , Putra D I P , Prihatiningsih W R , Suseno H 
Published: October 2020

Abstract
Jakarta Bay receives a variety of pollutants including radioactive substances originating from industry and operating the Serpong nuclear area in South Tangerang. Radionuclide types that have the potential to enter Jakarta Bay are anthropogenic or primordial radionuclides originating from the Serpong nuclear area and factory. Whereas the input of natural radionuclides originating from the use of industrial raw materials and terrestrial run-off. Monitoring is carried out twice a year on the coast of the bay of Jakarta. Monitoring results showed primordial radionuclide concentrations were in normal condition and originated from global fallout. This is shown from the ratio of 226Ra concentration which is the character of the Pacific Ocean before the nuclear accident at Fukushima. On the other hand, artificial radionuclides are in normal conditions and do not exceed the threshold.
Functional Connectivity Network Disruption Underlies Domain-Specific Impairments in Attention for Children Born Very Preterm
Authors: Wheelock M D , Lean R E , Bora S , Melzer T R , Eggebrecht A T , Smyser C D , Woodward L J 
Published: October 2020

Abstract
Attention problems are common in school-age children born very preterm (VPT; &lt; 32 weeks gestational age), but the contribution of aberrant functional brain connectivity to these problems is not known. As part of a prospective longitudinal study, brain functional connectivity (fc) was assessed alongside behavioral measures of selective, sustained, and executive attention in 58 VPT and 65 full-term (FT) born children at corrected-age 12 years. VPT children had poorer sustained, shifting, and divided attention than FT children. Within the VPT group, poorer attention scores were associated with between-network connectivity in ventral attention, visual, and subcortical networks, whereas between-network connectivity in the frontoparietal, cingulo-opercular, dorsal attention, salience and motor networks was associated with attention functioning in FT children. Network-level differences were also evident between VPT and FT children in specific attention domains. Findings contribute to our understanding of fc networks that potentially underlie typical attention development and suggest an alternative network architecture may help support attention in VPT children.
A Comparative Analysis of Statistical Methods to Estimate the Reproduction Number in Emerging Epidemics, With Implications for the Current Coronavirus Disease 2019 (COVID-19) Pandemic
Authors: O’Driscoll Megan , Harry Carole , Donnelly Christl A , Cori Anne , Dorigatti Ilaria 
Published: October 2020

AbstractBackgroundAs the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues its rapid global spread, quantification of local transmission patterns has been, and will continue to be, critical for guiding the pandemic response. Understanding the accuracy and limitations of statistical methods to estimate the basic reproduction number, R0, in the context of emerging epidemics is therefore vital to ensure appropriate interpretation of results and the subsequent implications for control efforts.MethodsUsing simulated epidemic data, we assess the performance of 7 commonly used statistical methods to estimate R0 as they would be applied in a real-time outbreak analysis scenario: fitting to an increasing number of data points over time and with varying levels of random noise in the data. Method comparison was also conducted on empirical outbreak data, using Zika surveillance data from the 2015–2016 epidemic in Latin America and the Caribbean.ResultsWe find that most methods considered here frequently overestimate R0 in the early stages of epidemic growth on simulated data, the magnitude of which decreases when fitted to an increasing number of time points. This trend of decreasing bias over time can easily lead to incorrect conclusions about the course of the epidemic or the need for control efforts.ConclusionsWe show that true changes in pathogen transmissibility can be difficult to disentangle from changes in methodological accuracy and precision in the early stages of epidemic growth, particularly for data with significant over-dispersion. As localized epidemics of SARS-CoV-2 take hold around the globe, awareness of this trend will be important for appropriately cautious interpretation of results and subsequent guidance for control efforts.
Effectiveness of Contact Precautions to Prevent Transmission of Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococci in Intensive Care Units
Authors: Khader Karim , Thomas Alun , Huskins W Charles , Stevens Vanessa , Keegan Lindsay T , Visnovsky Lindsay , Samore Matthew H 
Published: October 2020

Abstract

Background
Contact precautions for endemic methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) are under increasing scrutiny, in part due to limited clinical trial evidence.

Methods
We retrospectively analyzed data from the Strategies to Reduce Transmission of Antimicrobial Resistant Bacteria in Intensive Care Units (STAR*ICU) trial to model the use of contact precautions in individual intensive care units (ICUs). Data included admission and discharge times and surveillance test results. We used a transmission model to estimate key epidemiological parameters, including the effect of contact precautions on transmission. Finally, we performed multivariate meta-regression to identify ICU-level factors associated with contact precaution effects.

Results
We found that 21% of admissions (n = 2194) were placed on contact precautions, with most for MRSA and VRE. We found little evidence that contact precautions reduced MRSA transmission. The estimated change in transmission attributed to contact precautions was –16% (95% credible interval, –38% to 15%). VRE transmission was higher than MRSA transmission due to contact precautions, but not significantly. In our meta-regression, we did not identify associations between ICU-level factors and estimated contact precaution effects. Importation and transmission were higher for VRE than for MRSA, but clearance rates were lower for VRE than for MRSA.

Conclusions
We found little evidence that contact precautions implemented during the STAR*ICU trial reduced transmission of MRSA or VRE. We did find important differences in the transmission dynamics between MRSA and VRE. Differences in organism and healthcare setting may impact the efficacy of contact precautions.
Commercial Serology Assays Predict Neutralization Activity against SARS-CoV-2
Authors: Suhandynata Raymond T , Hoffman Melissa A , Huang Deli , Tran Jenny T , Kelner Michael J , Reed Sharon L , McLawhon Ronald W , Voss James E , Nemazee David , Fitzgerald Robert L 
Published: October 2020

AbstractBackgroundIt is unknown whether a positive serology result correlates with protective immunity against SARS-CoV-2. There are also concerns regarding the low positive predictive value of SARS-CoV-2 serology tests, especially when testing populations with low disease prevalence.MethodsA neutralization assay was validated in a set of PCR-confirmed positive specimens and in a negative cohort. In addition, 9530 specimens were screened using the Diazyme SARS-CoV-2 IgG serology assay and all positive results (N = 164 individuals) were reanalyzed using the neutralization assay, the Roche total immunoglobin assay, and the Abbott IgG assay. The relationship between the magnitude of a positive SARS-CoV-2 serology result and neutralizing activity was determined. Neutralizing antibody titers (50% inhibitory dilution, ID50) were also longitudinally monitored in patients confirmed to have SARS-CoV-2 by PCR.ResultsThe SARS-CoV-2 neutralization assay had a positive percentage agreement (PPA) of 96.6% with a SARS-CoV-2 PCR test and a negative percentage agreement (NPA) of 98.0% across 100 negative control individuals. ID50 neutralization titers positively correlated with all 3 clinical serology platforms. Longitudinal monitoring of hospitalized PCR-confirmed patients with COVID-19 demonstrated they made high neutralization titers against SARS-CoV-2. PPA between the Diazyme IgG assay alone and the neutralization assay was 50.6%, while combining the Diazyme IgG assay with either the Roche or Abbott platforms increased the PPA to 79.2 and 78.4%, respectively.ConclusionsThese 3 clinical serology assays positively correlate with SARS-CoV-2 neutralization activity observed in patients with COVID-19. All patients confirmed SARS-CoV-2 positive by PCR develop neutralizing antibodies.
A Reappraisal of Outcome of Elective Surgery After Successful Non-Operative Management of an Intra-Abdominal Abscess Complicating Ileocolonic Crohn’s Disease: A Subgroup Analysis of a Nationwide Prospective Cohort
Authors: Collard M K , Benoist S , Maggiori L , Zerbib P , Lefevre J H , Denost Q , Germain A , Cotte E , Beyer-Berjot L , Corté H , Desfourneaux V , Rahili A , Duffas J P , Pautrat K , Denet C , Bridoux V , Meurette G , Faucheron J L , Loriau J , Souche R , Vicaut E , Panis Y , Brouquet A 
Published: October 2020

AbstractBackground and AimsFew prospective data exist on outcomes of surgery in Crohn’s disease [CD] complicated by an intra-abdominal abscess after resolution of this abscess by antibiotics optionally combined with drainage.MethodsFrom 2013 to 2015, all patients undergoing elective surgery for CD after successful non-operative management of an intra-abdominal abscess [Abscess-CD group] were selected from a nationwide multicentre prospective cohort. Resolution of the abscess had to be computed tomography/magnetic resonance-proven prior to surgery. Abscess-CD group patients were 1:1 matched to uncomplicated CD [Non-Penetrating-CD group] using a propensity score. Postoperative results and long-term outcomes were compared between the two groups.ResultsAmong 592 patients included in the registry, 63 [11%] fulfilled the inclusion criteria. The abscess measured 37 ± 20 mm and was primarily managed with antibiotics combined with drainage in 14 patients and nutritional support in 45 patients. At surgery, a residual fluid collection was found in 16 patients [25%]. Systemic steroids within 3 months before surgery [p = 0.013] and the absence of preoperative enteral support [p = 0.001] were identified as the two significant risk factors for the persistence of a fluid collection. After propensity score matching, there was no significant difference between the Abscess-CD and Non-Penetrating-CD groups in the rates of primary anastomosis [84% vs 90% respectively, p = 0.283], overall [28% vs 15% respectively, p = 0.077] and severe postoperative morbidity [7% vs 7% respectively, p = 1.000]. One-year recurrence rates for endoscopic recurrence were 41% in the Abscess-CD and 51% in the Non-Penetrating-CD group [p = 0.159].ConclusionsSurgery after successful non-operative management of intra-abdominal abscess complicating CD provides good early and long-term outcomes.
Genetic interaction analysis in microbial pathogens: unravelling networks of pathogenesis, antimicrobial susceptibility and host interactions
Authors: Halder Viola , McDonnell Brianna , Uthayakumar Deeva , Usher Jane , Shapiro Rebecca S 
Published: October 2020

ABSTRACT
Genetic interaction (GI) analysis is a powerful genetic strategy that analyzes the fitness and phenotypes of single- and double-gene mutant cells in order to dissect the epistatic interactions between genes, categorize genes into biological pathways, and characterize genes of unknown function. GI analysis has been extensively employed in model organisms for foundational, systems-level assessment of the epistatic interactions between genes. More recently, GI analysis has been applied to microbial pathogens and has been instrumental for the study of clinically important infectious organisms. Here, we review recent advances in systems-level GI analysis of diverse microbial pathogens, including bacterial and fungal species. We focus on important applications of GI analysis across pathogens, including GI analysis as a means to decipher complex genetic networks regulating microbial virulence, antimicrobial drug resistance and host–pathogen dynamics, and GI analysis as an approach to uncover novel targets for combination antimicrobial therapeutics. Together, this review bridges our understanding of GI analysis and complex genetic networks, with applications to diverse microbial pathogens, to further our understanding of virulence, the use of antimicrobial therapeutics and host−pathogen interactions.
Unique genomic traits for cold adaptation inNaganishia vishniacii, a polyextremophile yeast isolated from Antarctica
Authors: Nizovoy Paula , Bellora Nicolás , Haridas Sajeet , Sun Hui , Daum Chris , Barry Kerrie , Grigoriev Igor V , Libkind Diego , Connell Laurie B , Moliné Martín 
Published: October 2020

ABSTRACTCold environments impose challenges to organisms. Polyextremophile microorganisms can survive in these conditions thanks to an array of counteracting mechanisms. Naganishia vishniacii, a yeast species hitherto only isolated from McMurdo Dry Valleys, Antarctica, is an example of a polyextremophile. Here we present the first draft genomic sequence of N. vishniacii. Using comparative genomics, we unraveled unique characteristics of cold associated adaptations. 336 putative genes (total: 6183) encoding solute transfers and chaperones, among others, were absent in sister species. Among genes shared by N. vishniacii and its closest related species we found orthologs encompassing possible evidence of positive selection (dN/dS &gt; 1). Genes associated with photoprotection were found in agreement with high solar irradiation exposure. Also genes coding for desaturases and genomic features associated with cold tolerance (i.e. trehalose synthesis and lipid metabolism) were explored. Finally, biases in amino acid usage (namely an enrichment of glutamine and a trend in proline reduction) were observed, possibly conferring increased protein flexibility. To the best of our knowledge, such a combination of mechanisms for cold tolerance has not been previously reported in fungi, making N. vishniacii a unique model for the study of the genetic basis and evolution of cold adaptation strategies.