bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolates of nitrifying and denitrifying bacteria activities that derived from catfish, Pangasius sp. culture pond
Authors: Yosmaniar  , Setiadi E , Novita H 
Published: June 2021

AbstractNitrifying and denitrifying bacteria are very fruitful for controlling water quality in fish culture because they have a role in converting toxic chemical compounds into non-toxic compounds. The purpose of this experiment is to determine the isolates of nitrifying and denitrifying bacteria in terms of oxidizing ammonia, accumulating total nitrite, and accumulating total nitrate activities. Eight isolates of bacteria consist of four nitrifying bacteria (NP1, NP2, NP3, and NP4), and four denitrifying bacteria (DP1, DP2, DP3, and DP4) were inoculated with the density of 102CFU/ml. The result showed that NP1, NP2, NP3, and NP4 isolates have almost similar ability to oxidize ammonium of 99.57, 99.37, 99.89, and 99.83%, respectively. The NP1-NP4 isolates on the total nitrite accumulated were 0.06, 0.05, 0.06, and 0.06%, while the total nitrate accumulated were 1.56, 1.65, 2.08, and 1.65%, respectively. The isolates of DP1, DP2, DP3, and DP4 can reduce total nitrate by 99.9, 100.0, 99.9, and 99.9%, respectively, while accumulated total nitrite was 0.01, 0.04, 0.00, and 0.00%. Isolates of NP2 and DP2 are recommended for controlling chemical compounds in the pond water.
The influence of moon period day to paperek fish (Leiognathus spp) cathed and it’s connection with physical waters of boat live nets at Dodinga Bay, West Halmahera Districs
Authors: Karuwal J , Budiman B 
Published: June 2021

Abstract
The aims of this research are to know the influence of the moon day period on paperek (Leiognathus spp ) catches and it’s relation to waters physical factors of the boat liftnets in the Dodinga bay. The oceanographic parameter data are sea surface temperature, waters salinity, brightness, current velocity, wind speed and peperek catches that was in situ collected. Data analysis was done descriptively and statistics to explain the relationship among variables by using multiple linear regression. The result of F test gets the Fcount is 0.974 is greater than Ftable value is 0.442. This showing that all physical parameter waters were together to exert an influence upon the presence of paperek fish in waters. The formed of regression equation model are ŷ = 6.675 – 0.22x
1 + 0.70x
2 – 0.126x
3 – 0.58x
4 – 0.806x
1 + e; where: ŷ = total anchovies fish catch; X1 = temperature (°C ); X2 = salinity (o/oo ); X3 = wind speed (ms -1); X4 = brightness (m ); X5 = current velocity ( ms -1 ) and e = standard error. Furthermore the obtained of the paperek (Leiognathus spp ) catches were many caught on Dodinga bay waters with boat liftnets at water temperature are 25.00-25.09 °C. salinities are 30.0-31.0 ppt. current velocity are 0.05 0.18 m s-1. brightness value are 8.97-10 meters and wind speed are 1.83 3.05 ms -1.
The fishery of sea-cucumber Holothuridae in Kilbat Village, Central Maluku Regency, Indonesia
Authors: Lewerissa Y A , Ongkers O T S , Pattikawa J A , Tetelepta J M S , Divinubun A 
Published: June 2021

Abstract
Sea cumber is one of the valuable high economic resources. Worldwide, most sea cucumber fisheries are ineffectively managed, leading to declining stocks and potentially eroding the resilience of fisheries. The local fishermen of Kilbat Village have been exploiting sea cucumber for a long time with un-proper management pan. This study was aimed to investigate the utilization of sea cumber and assess its sustainability, and propose a sustainable management strategy. Field observation was used to analyze sea cucumber utilization, the Rapid appraisal to Fisheries (Rapfish) approach was used to assess its sustainability, whilst DPSIR was applied to perform a sustainable management strategy. The result shows that the local sea cucumber fishermen utilize sea cucumber as a source of income and self-consumption. The average sustainability was 61.17% of 100% sustainable scale and considered as fair sustain with institutional dimension being unsustain. There are 8 strategies proposed for sea cumber sustainable management with responses at D, P, S, and I level, A traditional indigenous knowledge (sasi) has been proposed for sea cucumber community-based fishery management.
Antibacterial activity of Rhizophora apiculata extract originated from Inner Ambon Bay against selected pathogen bacteria
Authors: Sormin R B D , Nendissa D M , Mailoa M N , Rieuwpassa F , Wenno M R 
Published: June 2021

Abstract
Inner Ambon bay, Ambon Island, Maluku Province, is a good place for mangrove to growth. Some mangroves have been known as a source of germplasm that has antimicrobial properties. This research goals to study the antibacterial activity of various extract of Rhizophora apiculata from the coast of the Inner Ambon Bay, against several pathogenic bacteria. The experimental design was complete random design with two factors, firstly, the type of extract solvent was extract namely methanol, ethyl acetate and n-hexane, and the second four strains of bacteria consist of Gram positive strains: Bacillus cereus and Gram negative strains: Escherichia coli, Salmonella typhi Staphylococcus aureus.The highest antibacterial activity was resulted by ethyl acetate extracts with an average value of inhibition zone was 18.64±3.88b mm, then followed by methanol extract 15.02±5.17b mm and n-hexane extract 8.48±1.25a mm. The strongest extract against the bacterial pathogen was ethyl acetate extract. The most susceptible bacteria to the three extracts tested with an inhibition zone was (18.02±7.49b) mm, followed by B. cereus, E. coli and S. aureus with the inhibition zones were (13.48±4.50a) mm, (12.94±4.69a) mm and (11.74±3.90a) mm, respectively.
Utilization of garlic as traditional fish handling in Molluccas Islands: case study on layang fish (Decapterus macrosoma, BLECKER)
Authors: Wenno M R , Kaya A O W , Lewerissa S , Wattimena M L , Sormin R B D , Nanlohy E E E M 
Published: June 2021

Abstract
Fish form part of a highly nutritional diet and provide a source of essential proteins. However, they can rapidly degrade, particularly when in a fresh state and not handled properly. Degradation can occur either biochemically or microbiologically. Various methods can be implemented to maintain the quality of fresh fish; for example, the utilization of natural preservatives such as garlic. Garlic is a herb which has been proven to inhibit the growth of microorganisms. Tubers of garlic contain antimicrobial compounds such as allicin (diallyl thiosulfinate) and ajoene. This study aimed to determine the effect of immersion duration in a garlic solution on the freshness level of shortfin scad fish. The Total Volatile Base Nitrogen (TVBN) values ranged from 25.33 mg%N to 78.66 mg%N, the bacterial TPC (Total Plate Count) was 7.5×101 to 1.6×105 CFU/g, and the pH 5.9 to 8.0. Visibility ranged from 4.64 to 8.33, odor 3.47 to 8.75, and texture 3.62 to 8.20. This study found that immersion treatment using garlic can maintain fish quality for eight hours, with a 20-minute immersion treatment obtaining optimal parameter values.
Nutrition content and amino acid profile of paper squid (Loligo edulis)
Authors: Loppies C R M , Apituley D A N , Tentua E 
Published: June 2021

Abstract
One of the ways to diversify squid products into ready to eat food that has the potential to be developed is paper squid. The main stages in paper squid processing are drying under the sun, pressing, and drying in oven. This research aims to determine the proximate and the amino acid profile contained in paper squid (Loligo edulis, Hoyle). The proximate analysis results showed that paper squid contains 8.25% of moisture content, 3.65% of ash content, 72.28% of protein content, and 11.96% of carbohydrates content. Amino acids detected in paper squid are 15 types of amino acids consisting of 9 essential amino acids and 6 non-essential amino acids. The highest essential amino acid in paper squid is arginine containing 6.24% and the lowest is histidine which is 1.43%. The highest non-essential amino acid in paper squid is glutamic acid which is 12.13% and the lowest is tyrosine which is 2.49%.
Chemical properties of dried anchovy (Stolephorus sp) from Buru Island
Authors: Savitri I K E , Tohata V D , Sormin R B D , Lalopua V M N , Mailoa M N , Rieuwpassa F 
Published: June 2021

Abstract
The objective of this study was determined proximate, amino acid and some minerals of dried anchovy from Kayeli bay Buru Island. Dried anchovy from Buru island has a good quality indexes and a good feasibility business while the nutritional composition unexplored, so determine the proximate, amino acid and ash content are appropriate to complete its nutritional data. Protein in dried anchovy is relatively high, almost 60% and the amino acids profile were Phenylalanine, Valine, Threonine, Isoleucine, Methionine, Histidin, Lysine, Leucine, Arginine, Aspartic, Tyrosine, Serine, Glutamate and Glysine. There are 8 essential amino acids, 1 semy essential amino acid and 6 non essential amino acids and the highest non essential amino acid is Glutamate and followed by Aspartic. Dried anchovy has a good amino acid profile especially essential group with a good taste and also highly Phosphorous, Calcium, Iron and Iodine.
Boundedness for finite subgroups of linear algebraic groups
Authors: Shramov Constantin , Vologodsky Vadim 
Published: June 2021

We show the boundedness of finite subgroups in any anisotropic reductive group over a perfect field that contains all roots of

1
1

. Also, we provide explicit bounds for orders of finite subgroups of automorphism groups of Severi–Brauer varieties and quadrics over such fields.
Urban renewal in Ibadan, Nigeria: World class but essentially Yoruba
Authors: Roelofs Portia 
Published: June 2021

Abstract
Urban renewal is central to ‘world-class’ city aspirations on the African continent: demolitions and evictions exemplify the power of the state to restructure urban space, prioritizing elite forms of accumulation and enforcing aesthetic norms of cleanliness, order and modernity. The ubiquity of world-class city-making has been taken by urban studies scholars as evidence of African leaders’ converging on a unitary aspirational urban imaginary. This article contends that the concept of world class should instead be understood as a key terrain on which African governments’ distinctive and diverse ideational ambitions are expressed. In Oyo State, southwest Nigeria, vernacular political traditions—in this case Yoruba cultural nationalism centred on the ideas of Obafemi Awolowo—were deployed by the state governor to legitimize urban renewal. Drawing on the Yoruba notion that elitism can be ‘generalized’, the cultivation of globalized urban forms was not only a project of becoming ever more homogenously ‘international’ but a historically grounded aspiration to become ever more essentially Yoruba. Thus, beyond commonalities across the discourses used to legitimize neoliberal urban development—world class, international and global—these universal sounding imaginaries may at the same time express much more particularistic political projects.
Translingual Discrimination: Skilled Transnational Migrants in the Labour Market of Australia
Authors: Dovchin Sender , Dryden Stephanie 
Published: June 2021

Abstract
Drawing on linguistic ethnographic data, this study examines the language-based discriminatory experiences of skilled transnational migrants in the labour market of Australia. Moving beyond two main concepts of ‘interlingual’ and ‘intra-lingual’ discrimination in applied linguistics, this article points out the concept of ‘translingual discrimination’, which refers to inequality based on transnational identities’ specific linguistic repertoires and backgrounds that are substantiated by the national order of things. Translingual discrimination adds intensity to transnational processes, with the skilled migrants showing particular potential for exclusion regarding two factors: translingual ‘name discrimination’ and ‘English discrimination’. ‘Translingual name discrimination’ is a homogenous form of ‘name’ policing, evident in multiple examples where the skilled transnational migrants’ job applications are often largely rejected on the grounds of their ‘birth name’ written on their curriculum vitae. ‘Translingual English discrimination’ is another common form of discrimination, where the skilled transnational migrants become subject to discrimination based on their English proficiency and their overall language skills, leading to ‘the paradoxes of migration’—discrepancies between the imagination and the reality—where they fall from ‘hero to zero’ in the host society.
A 3-Level Impaction Technique for Dorsal Reshaping and Reduction Without Dorsal Soft Tissue Envelope Dissection
Authors: Finocchi Valerio , Vellone Valentino , Mattioli Rubens Giorgio , Daniel Rollin K 
Published: June 2021

Abstract

Background
Preservation rhinoplasty (PR) techniques are continuously evolving and many variations of established techniques have been proposed since Daniel coined this term in 2018.

Objectives
The aim of this study was to describe indications for a new “3-level impaction” technique, allowing, in selected cases, a complete profile correction and dorsal reduction without dissection of the dorsal soft tissue envelope (STE).

Methods
Three hundred and fifty primary closed rhinoplasty cases were retrospectively studied from January 2018 and October 2019. Age, sex, race, technical details, surgical time, and complications were registered. Ninety-five dorsa were reduced and shaped without dissecting the dorsal STE by combining: (1) a swinging-door septoplasty with low septal strip resection, (2) endonasal bony cap mosaic osteotomies, and (3) let-down or push-down operation.

Results
All patients showed a dramatic change in profile height and shape without either dorsal STE dissection or bony cartilage dorsal tissue resection. Mosaic osteotomies converted the dorsal keystone area from S- to V-shaped dorsum, let-down-operation and low septal strip resection enabled impaction, and profile setting was achieved by quadrangular cartilage flap rotation. The average follow-up time was 14 months (range, 12-16 months).

Conclusions
In selected patients, dorsum can be preserved without STE dissection. By combining multiple endonasal maneuvers it is possible to obtain a dramatic change without dissecting the STE, while simultaneously avoiding any dorsal tissue resection. This method offers a versatile technique in selected patients, which leads to fast recovery and natural results.

Level of Evidence: 4
Eight genes are necessary and sufficient for biogenesis of quinohemoprotein amine dehydrogenase
Authors: Nakai Tadashi , Tanizawa Katsuyuki , Okajima Toshihide 
Published: June 2021

ABSTRACT
Quinohemoprotein amine dehydrogenase (QHNDH) containing a peptidyl quinone cofactor, cysteine tryptophylquinone, is produced in the periplasm of Gram-negative bacteria through an intricate process of post-translational modification that requires at least 8 genes including those encoding 3 nonidentical subunits and 3 modifying enzymes. Our heterologous expression study has revealed that the 8 genes are necessary and sufficient for the QHNDH biogenesis.
Involvement of an FNR-like oxygen sensor in Komagataeibacter medellinensis for survival under oxygen depletion
Authors: Watanabe Seiji , Shirai Mutsunori , Kishi Mikiya , Ohnishi Yasuo 
Published: June 2021

ABSTRACT
During acetic acid fermentation, acetic acid bacteria face oxygen depletion stress caused by the vigorous oxidation of ethanol to acetic acid. However, the molecular mechanisms underlying the response to oxygen depletion stress remain largely unknown. Here, we focused on an oxygen-sensing FNR homolog, FnrG, in Komagataeibacter medellinensis. Comparative transcriptomic analysis between the wild-type and fnrG-disrupted strains revealed that FnrG upregulated 8 genes (fold change &gt;3). Recombinant FnrG bound to a specific DNA sequence only when FnrG was reconstituted anaerobically. An operon consisting of acetate kinase and xylulose-5-phosphate/fructose-6-phosphate phosphoketolase genes was found to be an FnrG regulon involved in cell survival under oxygen-limiting conditions. Moreover, a strain that overexpressed these 2 genes accumulated more acetic acid than the wild-type strain harboring an empty vector. Thus, these 2 genes could be new targets for the molecular breeding of acetic acid bacteria with high acetic acid productivity.
MultiDTI: drug–target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network
Authors: Zhou Deshan , Xu Zhijian , Li WenTao , Xie Xiaolan , Peng Shaoliang 
Published: June 2021

Abstract

Motivation
Predicting new drug–target interactions is an important step in new drug development, understanding of its side effects and drug repositioning. Heterogeneous data sources can provide comprehensive information and different perspectives for drug–target interaction prediction. Thus, there have been many calculation methods relying on heterogeneous networks. Most of them use graph-related algorithms to characterize nodes in heterogeneous networks for predicting new drug–target interactions (DTI). However, these methods can only make predictions in known heterogeneous network datasets, and cannot support the prediction of new chemical entities outside the heterogeneous network, which hinder further drug discovery and development.

Results
To solve this problem, we proposed a multi-modal DTI prediction model named ‘MultiDTI’ which uses our proposed joint learning framework based on heterogeneous networks. It combines the interaction or association information of the heterogeneous network and the drug/target sequence information, and maps the drugs, targets, side effects and disease nodes in the heterogeneous network into a common space. In this way, ‘MultiDTI’ can map the new chemical entity to this learned common space based on the chemical structure of the new entity. That is, bridging the gap between new chemical entities and known heterogeneous network. Our model has strong predictive performance, and the area under the receiver operating characteristic curve of the model is 0.961 and the area under the precision recall curve is 0.947 with 10-fold cross validation. In addition, some predicted new DTIs have been confirmed by ChEMBL database. Our results indicate that ‘MultiDTI’ is a powerful and practical tool for predicting new DTI, which can promote the development of drug discovery or drug repositioning.

Availability and implementation
Python codes and dataset are available at https://github.com/Deshan-Zhou/MultiDTI/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Linear functional organization of the omic embedding space
Authors: Xenos A , Malod-Dognin N , Milinković S , Pržulj N 
Published: June 2021

Abstract

Motivation
We are increasingly accumulating complex omics data that capture different aspects of cellular functioning. A key challenge is to untangle their complexity and effectively mine them for new biomedical information. To decipher this new information, we introduce algorithms based on network embeddings. Such algorithms represent biological macromolecules as vectors in d-dimensional space, in which topologically similar molecules are embedded close in space and knowledge is extracted directly by vector operations. Recently, it has been shown that neural networks used to obtain vectorial representations (embeddings) are implicitly factorizing a mutual information matrix, called Positive Pointwise Mutual Information (PPMI) matrix. Thus, we propose the use of the PPMI matrix to represent the human protein–protein interaction (PPI) network and also introduce the graphlet degree vector PPMI matrix of the PPI network to capture different topological (structural) similarities of the nodes in the molecular network.

Results
We generate the embeddings by decomposing these matrices with Nonnegative Matrix Tri-Factorization. We demonstrate that genes that are embedded close in these spaces have similar biological functions, so we can extract new biomedical knowledge directly by doing linear operations on their embedding vector representations. We exploit this property to predict new genes participating in protein complexes and to identify new cancer-related genes based on the cosine similarities between the vector representations of the genes. We validate 80% of our novel cancer-related gene predictions in the literature and also by patient survival curves that demonstrating that 93.3% of them have a potential clinical relevance as biomarkers of cancer.

Availability and implementation
Code and data are available online at https://gitlab.bsc.es/axenos/embedded-omics-data-geometry/.

Supplementary information
Supplementary data are available at Bioinformatics online.
CStreet: a computed

C

ell

S

tate

tr

ajectory inf

e

r

e

nce method for

t

ime-series single-cell RNA sequencing data
Authors: Zhao Chengchen , Xiu Wenchao , Hua Yuwei , Zhang Naiqian , Zhang Yong 
Published: June 2021

Abstract

Motivation
The increasing amount of time-series single-cell RNA sequencing (scRNA-seq) data raises the key issue of connecting cell states (i.e. cell clusters or cell types) to obtain the continuous temporal dynamics of transcription, which can highlight the unified biological mechanisms involved in cell state transitions. However, most existing trajectory methods are specifically designed for individual cells, so they can hardly meet the needs of accurately inferring the trajectory topology of the cell state, which usually contains cells assigned to different branches.

Results
Here, we present CStreet, a computed Cell State trajectory inference method for time-series scRNA-seq data. It uses time-series information to construct the k-nearest neighbor connections between cells within each time point and between adjacent time points. Then, CStreet estimates the connection probabilities of the cell states and visualizes the trajectory, which may include multiple starting points and paths, using a force-directed graph. By comparing the performance of CStreet with that of six commonly used cell state trajectory reconstruction methods on simulated data and real data, we demonstrate the high accuracy and high tolerance of CStreet.

Availability and implementation
CStreet is written in Python and freely available on the web at https://github.com/TongjiZhanglab/CStreet and https://doi.org/10.5281/zenodo.4483205

Supplementary information
Supplementary data are available at Bioinformatics online.