bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the Fisheries Business Orientation of the Duano Tribe Based on Socio-Culturalism in Tanah Merah Subdistrict, Indragiri Hilir, Indonesia
Authors: Metalisa R , Yanti C W , Bathara L , Arief H , Novikarumsari N D 
Published: December 2022

Abstract
Business in the fisheries sector is the only business run by the duano tribes from their predecessors. Initially, the duano tribes was a cultural community whose lives moved according to the direction of the sea breeze and schools of fish. As the duano tribes community developed, they began to occupy an area to live permanently, build a family, and carry out business to meet the necessities of life. The business is offered by the duano tribe in the fisheries sector. The purpose of this study was to analyze the orientation of the fishery business carried out by the duano tribe based on social and culture. The research uses a survey with an explanatory research approach. The analysis technique uses quantitative and qualitative descriptive with as many as 54 respondents. The fishery business carried out by the duano tribe is still oriented to the subsystem, namely fishery products produced only to meet the family’s daily needs, so the category of duano fishermen is still classified as traditional fishermen. The categorization of duano fishermen is based on the use of fishing gear, utilization of labor, and productivity.
Preliminary Study Of Marine Debris Composition From Fisherman Activities : A Case Study On Cikidang Fishing Port, Pangandaran
Authors: Prasetiawan N R , Sudirman N , Salim H L , Ati R N A , Kepel T L , Daulat A , Kusumaningtyas M A , Permana S M , Setiawan A , Pranowo W S , Rustam A , Suryono D D , Jayawiguna M H , Sukoraharjo S S 
Published: December 2022

Abstract
Marine debris pollution has become an important issue in recent years. It has an impact on marine environment and marine life, as well as effecting human health. The objective of this study was to identify the composition of waste that was produced from the fishermen’s activities. The research was conducted in Cikidang Fishing Port, Pangandaran. The data of waste types from fishing vessel were grouped based on the vessel’s dimension. The result show that plastics dominated the waste composition, and based on the vessel dimension when compared the amount of waste generated, the amount of waste from one day fishing (small vessel) was greater than the ten days fishing (big vessel). The amount of waste generated from small vessel was 0.009 tons-1.vessel-1.year-1, meanwhile from big vessel was 0.09 tons-1.vessel-1.years-1. This indicates that the fishers habit to dispose waste not in the right place can become a potential source of marine debris pollution. Maintaining the quality of fishery products is very important starting from improving the fisherman behaviour to the fishing port facilities to achieve the sustainability fishery product.
Degradation of chlorobenzene by non-thermal plasma coupled with catalyst: influence of catalyst, interaction between plasma and catalyst
Authors: SHI Xiujuan , LIANG Wenjun , YIN Guobin , LIU Jia 
Published: December 2022

Abstract
Non-thermal plasma (NTP) is considered to be a promising technology for the removal of volatile organic compounds; however, its application is limited by low CO2 selectivity and undesirable by-products. To overcome these issues, this paper discusses the degradation of chlorobenzene (CB) in systems of NTP coupled with catalysts, and the influence of catalyst locations in the NTP was investigated. In addition, the interaction between plasma and catalyst was also explored. The results indicated that the degradability of CB was remarkably improved through the combination of NTP with catalysts, and the formation of ozone was effectively inhibited. The degradation efficiency increased from 33.9% to 79.6% at 14 kV in the NTP-catalytic system, while the ozone concentration decreased from 437 to 237 mg m−3, and the degradation efficiency of in plasma catalysis (IPC) systems was superior to that of the post plasma catalysis system, while the inhibition ability of ozone exhibited an opposing trend. In the IPC system, the degradation efficiency was 87.7% at 14 kV, while the ozone concentration was 151 mg m−3. Besides, the plasma did not destroy the pore structure and crystal structure of the catalyst, but affected the surface morphology and redox performance of the catalyst. Thus, NTP coupled catalytic system could improve the degradation performance of CB. Furthermore, the plasma discharge characteristics played a major role in the NTP synergistic catalytic degradation of CB. Finally, based on the experiment analysis results, the general reaction mechanism of CB degradation in an IPC reaction system was proposed.
Daylight entanglement-based quantum key distribution with a quantum dot source
Authors: Basso Basset F , Valeri M , Neuwirth J , Polino E , Rota M B , Poderini D , Pardo C , Rodari G , Roccia E , Covre da Silva S F , Ronco G , Spagnolo N , Rastelli A , Carvacho G , Sciarrino F , Trotta R 
Published: December 2022

Abstract
Entanglement-based quantum key distribution can enable secure communication in trusted node-free networks and over long distances. Although implementations exist both in fiber and in free space, the latter approach is often considered challenging due to environmental factors. Here, we implement a quantum communication protocol during daytime for the first time using a quantum dot source. This technology presents advantages in terms of narrower spectral bandwidth—beneficial for filtering out sunlight—and negligible multiphoton emission at peak brightness. We demonstrate continuous operation over the course of three days, across an urban 270 m-long free-space optical link, under different light and weather conditions.
Learning single-cell chromatin accessibility profiles using meta-analytic marker genes
Authors: Kawaguchi Risa Karakida , Tang Ziqi , Fischer Stephan , Rajesh Chandana , Tripathy Rohit , Koo Peter K , Gillis Jesse 
Published: December 2022

AbstractMotivationSingle-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) is a valuable resource to learn cis-regulatory elements such as cell-type specific enhancers and transcription factor binding sites. However, cell-type identification of scATAC-seq data is known to be challenging due to the heterogeneity derived from different protocols and the high dropout rate.ResultsIn this study, we perform a systematic comparison of seven scATAC-seq datasets of mouse brain to benchmark the efficacy of neuronal cell-type annotation from gene sets. We find that redundant marker genes give a dramatic improvement for a sparse scATAC-seq annotation across the data collected from different studies. Interestingly, simple aggregation of such marker genes achieves performance comparable or higher than that of machine-learning classifiers, suggesting its potential for downstream applications. Based on our results, we reannotated all scATAC-seq data for detailed cell types using robust marker genes. Their meta scATAC-seq profiles are publicly available at https://gillisweb.cshl.edu/Meta_scATAC. Furthermore, we trained a deep neural network to predict chromatin accessibility from only DNA sequence and identified key motifs enriched for each neuronal subtype. Those predicted profiles are visualized together in our database as a valuable resource to explore cell-type specific epigenetic regulation in a sequence-dependent and -independent manner.
GSCA: an integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels
Authors: Liu Chun-Jie , Hu Fei-Fei , Xie Gui-Yan , Miao Ya-Ru , Li Xin-Wen , Zeng Yan , Guo An-Yuan 
Published: December 2022

Abstract
Cancer initiation and progression are likely caused by the dysregulation of biological pathways. Gene set analysis (GSA) could improve the signal-to-noise ratio and identify potential biological insights on the gene set level. However, platforms exploring cancer multi-omics data using GSA methods are lacking. In this study, we upgraded our GSCALite to GSCA (gene set cancer analysis, http://bioinfo.life.hust.edu.cn/GSCA) for cancer GSA at genomic, pharmacogenomic and immunogenomic levels. In this improved GSCA, we integrated expression, mutation, drug sensitivity and clinical data from four public data sources for 33 cancer types. We introduced useful features to GSCA, including associations between immune infiltration with gene expression and genomic variations, and associations between gene set expression/mutation and clinical outcomes. GSCA has four main functional modules for cancer GSA to explore, analyze and visualize expression, genomic variations, tumor immune infiltration, drug sensitivity and their associations with clinical outcomes. We used case studies of three gene sets: (i) seven cell cycle genes, (ii) tumor suppressor genes of PI3K pathway and (iii) oncogenes of PI3K pathway to prove the advantage of GSCA over single gene analysis. We found novel associations of gene set expression and mutation with clinical outcomes in different cancer types on gene set level, while on single gene analysis level, they are not significant associations. In conclusion, GSCA is a user-friendly web server and a useful resource for conducting hypothesis tests by using GSA methods at genomic, pharmacogenomic and immunogenomic levels.
Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments
Authors: Hu Ruyun , Fu Lihao , Chen Yongcan , Chen Junyu , Qiao Yu , Si Tong 
Published: December 2022

Abstract
Directed protein evolution applies repeated rounds of genetic mutagenesis and phenotypic screening and is often limited by experimental throughput. Through in silico prioritization of mutant sequences, machine learning has been applied to reduce wet lab burden to a level practical for human researchers. On the other hand, robotics permits large batches and rapid iterations for protein engineering cycles, but such capacities have not been well exploited in existing machine learning-assisted directed evolution approaches. Here, we report a scalable and batched method, Bayesian Optimization-guided EVOlutionary (BO-EVO) algorithm, to guide multiple rounds of robotic experiments to explore protein fitness landscapes of combinatorial mutagenesis libraries. We first examined various design specifications based on an empirical landscape of protein G domain B1. Then, BO-EVO was successfully generalized to another empirical landscape of an Escherichia coli kinase PhoQ, as well as simulated NK landscapes with up to moderate epistasis. This approach was then applied to guide robotic library creation and screening to engineer enzyme specificity of RhlA, a key biosynthetic enzyme for rhamnolipid biosurfactants. A 4.8-fold improvement in producing a target rhamnolipid congener was achieved after examining less than 1% of all possible mutants after four iterations. Overall, BO-EVO proves to be an efficient and general approach to guide combinatorial protein engineering without prior knowledge.
Computational analyses reveal fundamental properties of the AT structure related to thrombosis
Authors: Lopes Tiago J S , Rios Ricardo A , Rios Tatiane N , Alencar Brenno M , Ferreira Marcos V , Morishita Eriko 
Published: December 2022

Abstract

Summary
Blood coagulation is a vital process for humans and other species. Following an injury to a blood vessel, a cascade of molecular signals is transmitted, inhibiting and activating more than a dozen coagulation factors and resulting in the formation of a fibrin clot that ceases the bleeding. In this process, antithrombin (AT), encoded by the SERPINC1 gene is a key player regulating the clotting activity and ensuring that it stops at the right time. In this sense, mutations to this factor often result in thrombosis—the excessive coagulation that leads to the potentially fatal formation of blood clots that obstruct veins. Although this process is well known, it is still unclear why even single residue substitutions to AT lead to drastically different phenotypes. In this study, to understand the effect of mutations throughout the AT structure, we created a detailed network map of this protein, where each node is an amino acid, and two amino acids are connected if they are in close proximity in the three-dimensional structure. With this simple and intuitive representation and a machine-learning framework trained using genetic information from more than 130 patients, we found that different types of thrombosis have emerging patterns that are readily identifiable. Together, these results demonstrate how clinical features, genetic data and in silico analysis are converging to enhance the diagnosis and treatment of coagulation disorders.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Tracing weak neuron fibers
Authors: Liu Yufeng , Zhong Ye , Zhao Xuan , Liu Lijuan , Ding Liya , Peng Hanchuan 
Published: December 2022

Abstract

Motivation
Precise reconstruction of neuronal arbors is important for circuitry mapping. Many auto-tracing algorithms have been developed toward full reconstruction. However, it is still challenging to trace the weak signals of neurite fibers that often correspond to axons.

Results
We proposed a method, named the NeuMiner, for tracing weak fibers by combining two strategies: an online sample mining strategy and a modified gamma transformation. NeuMiner improved the recall of weak signals (voxel values &lt;20) by a large margin, from 5.1 to 27.8%. This is prominent for axons, which increased by 6.4 times, compared to 2.0 times for dendrites. Both strategies were shown to be beneficial for weak fiber recognition, and they reduced the average axonal spatial distances to gold standards by 46 and 13%, respectively. The improvement was observed on two prevalent automatic tracing algorithms and can be applied to any other tracers and image types.

Availability and implementation
Source codes of NeuMiner are freely available on GitHub (https://github.com/crazylyf/neuronet/tree/semantic_fnm). Image visualization, preprocessing and tracing are conducted on the Vaa3D platform, which is accessible at the Vaa3D GitHub repository (https://github.com/Vaa3D). All training and testing images are cropped from high-resolution fMOST mouse brains downloaded from the Brain Image Library (https://www.brainimagelibrary.org/), and the corresponding gold standards are available at https://doi.brainimagelibrary.org/doi/10.35077/g.25.

Supplementary information
Supplementary data are available at Bioinformatics online.
igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)
Authors: Robinson James T , Thorvaldsdottir Helga , Turner Douglass , Mesirov Jill P 
Published: December 2022

Abstract

Summary
igv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a single line of code and has no external dependencies. The viewer runs completely in the web browser, with no backend server and no data pre-processing required.

Availability and implementation
The igv.js JavaScript component can be installed from NPM at https://www.npmjs.com/package/igv. The source code is available at https://github.com/igvteam/igv.js under the MIT open-source license. IGV-Web, the end-user application built around igv.js, is available at https://igv.org/app. The source code is available at https://github.com/igvteam/igv-webapp under the MIT open-source license.

Supplementary information
Supplementary information is available at Bioinformatics online.
Nanocrystalline fluorapatite mineralization in the calciphile rock-boring bivalve Lithophaga: functional and phylogenetic significance
Authors: Taylor John D , Glover Emily A , Ball Alexander D , Najorka Jens 
Published: December 2022

Abstract
Phosphate mineralization as a skeletal material is uncommon in invertebrate animals and rare in Mollusca. Remarkably, apatite minerals were first reported more than 30 years ago in the periostracum of two species of the mytilid bivalve Lithophaga where shells are mostly constructed of calcium carbonate. This discovery extended the range of biominerals secreted by molluscs but has attracted no subsequent research. In this study we review the occurrence of phosphate mineralization in Lithophaga and putatively allied taxa. Lithophagine bivalves, particularly Lithophaga and the more diverse Leiosolenus species, are well known for their endolithic chemical dissolution of calcareous rocks and corals with calcium-binding lipoproteins secreted by mantle glands. Fluorapatite was identified by X-ray diffraction in an outer layer of the periostracum in six species of Lithophaga. Morphological study by scanning electron microscopy of four species showed the fluorapatite crystals embedded in periostracal material in a layer 10–20 µm thick. Dilute bleach treatment revealed the crystals as densely packed euhedral prisms 250–400 nm in size. The succeeding inner layers of the periostracum were unmineralized. Observations of the developing periostracum of Lithophaga teres suggest that the initial mineralization is in the form of amorphous granules that coalesce and transform into euhedral crystals. Periostracal phosphate was not recorded in other members of the Lithophaginae – Leiosolenus, Botula or Zelithophaga species. Leiosolenus species characteristically have extraperiostracal aragonitic encrustations that can be thick and structurally complex. Published molecular phylogenies of Mytilidae bivalves show a division into two major clades with Lithophaga species in one clade and Leiosolenus species in the other, indicating that the subfamily Lithophaginae as presently understood is polyphyletic. This result implies that the two genera have independent evolutionary pathways to endolithic occupation of calcareous substrates although using similar mantle gland secretions to excavate their crypts. Because fluorapatite is considerably less soluble and harder than calcium carbonate, it is suggested that the phosphate layer of Lithophaga is a functional adaptation to protect their shells from self-dissolution from their rock-dissolving glandular secretions and may also act as defence against other shell-eroding organisms.
Automatic Multi-Plug Filtration Cleanup Tip-Filtration with Ultra-Performance Liquid Chromatography/Tandem Mass Spectrometry Detection For 22 Pesticide Residues in Typical Vegetables
Authors: Ma Lili , Cao Lihua , Feng Yuechao , Jia Li , Liu Cong , Ding Qi , Liu Jia , Shao Peng , Pan Canping 
Published: December 2022

Abstract
An automatic multi-plug filtration cleanup (m-PFC) tip-filtration method was developed to reduce the manual operation workload in sample preparation. In this work, m-PFC was based on multi-walled carbon nanotubes mixed with primary secondary amines and anhydrous magnesium sulfate (MgSO4) in a packed column for analysis of pesticide residues followed by ultra-performance liquid chromatography coupled with tandem mass spectrometry. Method validation was performed on 22 pesticide residues in carrot, spinach and leek, at spiked levels of 5, 10 and 50 μg/kg, respectively. The average recoveries were between 70.1 and 119.5% with associated relative standard deviations &lt;20% (n = 6) indicating satisfactory accuracy and repeatability. Matrix-matched calibration curves were performed with the correlation coefficients (R2) higher than 0.9903 within a linearity range of 5–100 ng/mL. The limits of quantification were 5 μg/kg for all the pesticides in carrot, spinach and leek matrices. The developed method was successfully used to determine pesticide residues in market samples.
The use of blended learning in postgraduate education in orthodontics: student versus teacher perception
Authors: Maes Désirée Martine , Zong Chen , Begnoni Giacomo , Verdonck Anna , Willems Guy , Cadenas de Llano-Pérula Maria 
Published: December 2022

SummaryObjectiveTo investigate the use of blended learning (BL) in Postgraduate Education in Orthodontics.MethodsA self-developed online questionnaire was sent to 244 teaching staff members of the European Orthodontic Departments. They were asked to answer it and share it with their postgraduate students. 18 questions for teaching staff and 27 for postgraduate students evaluated the use, perceptions, feedback options, learning outcomes, and teacher’s role in BL. The answers of teaching staff and students were statistically compared by Fisher’s Exact Test, Chi-Square Test, Unpaired t-test, and Mann–Whitney Test.Results124 completed questionnaires were received, 44 from teaching staff and 80 from postgraduate students. Teaching staff is more acquainted with BL than students (P = 0.001). Both groups found BL courses a good alternative to traditional courses (P = 0.654). The use of interactive multimedia was more appreciated by students (P = 0.015). Both groups found students’ results not to change with BL, but teaching staff had a more negative perception (P = 0.012). In general, teaching staff perceived feedback and interaction as less essential than postgraduates in BL. Teaching staff felt more like coaches when using BL, while postgraduates did not perceive any changes in teachers’ roles (P = 0.006). Limitations: Due to the General Data Protection Regulation it was not possible to directly contact the postgraduate students in Postgraduate Orthodontic Programs throughout Europe. Therefore, this study completely relied on the goodwill of the teaching staff being contacted.ConclusionThe main differences in perception between teaching staff and postgraduate students were student results, teachers’ role, use, and importance of feedback and interactive multimedia. Although both groups found BL courses to stimulate students’ learning and to be a relevant cost-effective addition to traditional courses, they were hesitant to fully replace them with BL.
Change of pulmonary function tests in hospitalized COVID-19 patients at third and sixth month follow-up
Authors: Kafkas Meltem Karakulak , Tüzün Sabah , Hacıağaoğlu Nazlı , Çetin Hüseyin , Cömert Sevda Şener , Şimşek Engin Ersin 
Published: December 2022

Abstract

Background
The effect of COVID-19 infection on pulmonary function is unknown.

Objective
This study aimed to evaluate pulmonary function tests (PFTs) of patients hospitalized with the diagnosis of COVID-19 pneumonia at 3 and 6 months post-discharge.

Methods
Patients aged 18 years and over who had positive COVID-19 PCR test results and were hospitalized in the pandemic service between 1 May 2020 and 31 October 2020, were included in the study. All patients were evaluated with PFTs FVC, FEV1, FEV1/FVC, and FEF25–75 at 3 and 6 months after discharge.

Results
The mean age of 34 patients included in the study was 47.7 ± 12.7 years. The FVC, FEV1, FEV1/FVC, and FEF25–75 measurements at 3 and 6 months post-discharge showed no significant difference (P = 0.765, P = 0.907, P = 0.707, and P = 0.674, respectively). There was no significant difference in any PFT measurements at the third month follow-up, regardless of the pharmacological treatment protocols applied during hospitalization (P &gt; 0.05). However, FEV1/FVC and FEF25–75 levels were 83.1 [3.4]% and 91.0 [10.0]%, respectively, in those who received systemic steroid treatment, and 78.3 ± 8.5% and 72.5 ± 25.7% in those who did not (P = 0.019 and P = 0.048, respectively). In addition, FVC and FEV1 levels increased significantly from the third to the sixth month follow-up in patients who received systemic steroid therapy (P = 0.035 and P = 0.018, respectively).

Conclusion
Although there is no significant difference in PFT measurements from 3 to 6 months in COVID-19 patients, systemic steroid therapy may have a beneficial effect on respiratory function in COVID-19 patients.