bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustainable utilizations of Pohpohan (Pilea melastomoides (Poir.) Wedd) in Tamansari Village, West Java-Indonesia
Authors: Adhiningsih L , Basuni S , Munawir A , Hidayati S , Hartoyo A P P , Sunkar A 
Published: December 2022

Abstract
Forest plays an important role in producing timber and non-timber product to fulfill human beings’ prerequisites and live hood, a source of income for many communities and becomes the solutions to any other challenges. The community in Taman Sari Village cooperates with Gunung Halimun Salak National Park through a conservation partnership program to cultivate and commercialize pohpohan (Pilea melastomoides (Poir.) Wedd) in the traditional zone. This species is known as indigenous fresh aromatic vegetable and contain valuable potential phytochemical such as antibacterial and anti-cancer. Pohpohan is traditionally cultivated by the community since the 1980s in Tamansari village, this culture is still practiced by the community who join as member of the Kelompok Tani Mandiri (KTM). This study aims to document and analyze the sustainable traditional cultivation of pohpohan in Tamansari village by collaborating with all members (56) of the KTM. The study applied mixed qualitative and quantitative methods, to gain more understanding of the community dynamic. Generally, the cultivation and utilization of pohpohan are managed traditionally using manual tools such as hoes and sickles. Yet this approach is considered as environmentally friendly and resourceful for their limited land. A total 34% of pohpohan farmers are in the age class 55-65, indicates the importance of regeneration to verify its sustainability.
Utilization of Kandelia candel (L.) Druce and hypocotyl cutting seedling for mangrove rehabilitation in Indonesia
Authors: Nugraha L A , Kusmana C , Hartoyo A P P 
Published: December 2022

Abstract

Kandelia candel (L.) Druce is one of the rare mangrove species in Indonesia. Additionally, mangrove rehabilitation requires effective and efficient methods. Accelerating the growth of mangrove species using vegetative propagation, specifically hypocotyl cutting, is necessary. The objectives of this study were to investigate the scientific literature on the use of K. candel for mangrove rehabilitation in Indonesia and to analyze the growth of K. candel seedling from hypocotyl cuttings. Scientific literature was collected from 2012 to 2022 in some search engines and library databases. An experimental study was carried out with different treatments (hypocotyl cuttings, planting media, plant growth regulator) and three replications. We found 576 articles on mangrove rehabilitation in Indonesia and only an article uses K. candel (0,002%) as a species in mangrove rehabilitation. There was no study on hypocotyl cutting of K. candel. The best combination of intact hypocotyl treatment was intact hypocotyl, mud+sand growing medium, and growth regulator 15.000 ppm. In contrast, the best combination of cut hypocotyl treatment was bottom hypocotyl, mud+sand planting medium, and growth regulator 15.000 ppm.
The status of bamboo research and development for sustainable use in Indonesia: A systematic literature review
Authors: Ekawati D , Karlinasari L , Soekmadi R , Machfud M 
Published: December 2022

AbstractThe current global situation of bamboo utilization has shifted from traditional to modern bamboo, along with improved technology and innovations. However, the literature on bamboo research and development in Indonesia is still minimal and fragmented. Moreover, it has not yet clearly seen the strategy and direction of future utilization and its sustainability. Therefore, it is urgent to know the current status of bamboo research and development, especially its sustainable use. A systematic literature review was carried out on the research and development of bamboo in Indonesia, examining and comparing publications from both academic and professional works of literature in the period 2001 to 2021. This study was conducted by building insights from past reviews and initial scoping analysis of two decades of bamboo R&D. The findings of this study build upon the research and efforts on the social-cultural, economic, and ecological aspects underpinnings of bamboo utilization and development. Furthermore, the typology and other supporting factors that have already been carried out will be proposed to help connect fragmented and detached aspects into an integrated strategy and direction of research and development. Finally, future orders for progressing and sustainable bamboo utilization and development in Indonesia are identified.
Biomass-based energy potential in Semujur Island, a small remote area in Indonesia
Authors: Siregar U J , Nugroho A , Hartoyo A P P , Siregar C A 
Published: December 2022

Abstract
Electricity has not been spread equally in Indonesia, especially in remote areas. Forest biomass could potentially be utilized as bioenergy and fuel for an electricity generator, particularly in remote areas with no electricity access. The objectives of this research were to identify vegetation species composition and estimate tree biomass’s potential as fuel for power plants in Semujur Island, Bangka Belitung Province, Indonesia. The method used was vegetation analysis throughout the study area. The result showed that Terminalia catappa dominated vegetation species at the seedling, sapling, and pole levels. At tree level was dominated by Ficus caulocarpa with an importance value index (IVI) of 166.81%, while non-tree species was dominated by Cocos nucifera (IVI of 200%) as palm species. Liana and understory that dominated the study site in order were Imperata cylindrica (IVI 52.50%) and Mikania sp. (IVI 143.59%). The total biomass on this island was 2,298.94 tons/ha, which could potentially generate electrical energy amounted to 3,371.78 MWh. This amount of energy can fulfill the electrical needs of the local community for 237 years to the future without any replanting activity. The recommended crops that can be planted on this island are vetiver and sesame to reserve biomass and prevent abrasion.
Study of beam divergence and thrust vector eccentricity characteristics of the Hall thruster based on dual Faraday probe array planes and its applications
Authors: CHEN Xinwei , ZHAO Yong , TIAN Kai , GAO Jun , SUN Mingming , SUN Xinfeng , GUO Ning , ZHANG Hong , WANG Shangmin , FENG Jie , CHEN Tao , GENG Hai , YANG Juntai , SHI Kai 
Published: December 2022

Abstract
The accurate knowledge of the thrust vector eccentricity and beam divergence characteristics of Hall thrusters are of significant engineering value for the beneficial integration and successful application of Hall thrusters on spacecraft. For the characteristics of the plume bipolar diffusion due to the annular discharge channel of the Hall thruster, a Gaussian-fitted method for thrust vector deviation angle and beam divergence of Hall thrusters based on dual Faraday probe array planes was proposed in respect of the Hall thruster beam characteristics. The results show that the ratios of the deviation between the maximum and minimum values of the beam divergence angle and the thrust vector eccentricity angle using a Gaussian fit to the optimized Faraday probe dual plane to the mean value are 1.4% and 11.5%, respectively. The optimized thrust vector eccentricity angle obtained has been substantially improved, by approximately 20%. The beam divergence angle calculated using a Gaussian fitting to the optimized Faraday probe dual plane is approximately identical to the non-optimized one. The beam divergence and thrust vector eccentricity angles for different anode mass flow rates were obtained by averaging the beam divergence and thrust vector eccentricity angles calculated by the dual-plane, Gaussian-fitted ion current density method for different cross-sections. The study not only allows for an immediate and effective tool for determining the design of thrust vector adjustment mechanisms of spacecraft with different power Hall thrusters but also for characterizing the 3D spatial distribution of the Hall thruster plume.
Numerical studies on the influences of gas temperature on atmospheric-pressure helium dielectric barrier discharge characteristics
Authors: HUO Weigang , LIN Jingsong , YU Tanxue , WANG Yuxin , ZHANG Hua 
Published: December 2022

Abstract
A fast-rising gas temperature is due to frequent collisions of the heavy particles in an atmospheric-pressure dielectric barrier discharge. In this paper, a two-dimensional fluid model is applied to investigate the influences of rising gas temperature on an atmospheric-pressure helium dielectric barrier discharge. With the increase in the gas temperature, it is found that: (1) a helium discharge can evolve from the discharge column to a homogeneous discharge; (2) the breakdown time is in advance and the gas breakdown voltage decreases; (3) the spatial distribution evolution of the electron density is similar to that of the helium atom density. The most significant discrepancy between them is that the electron densities are high at some positions where the helium atom densities are nevertheless low. Furthermore, the radial reduced electric fields are obtained under different gas temperatures. The physical reasons for the gas temperature effects are discussed. The simulation results provide a better understanding of the roles of the radial reduced electric field and the heavy particle.
Investigation on the effect of grinding wheel for grinding of AISI D3 tool steel under different conditions
Authors: Ali Syed Mansoor , Johnson Nevan Nicholas , Madhavadas Vaishnav , Giri Anoj , Sahu Jambeswar , Anand Suya Prem , Srivas C S 
Published: December 2022

Abstract
The surface finish of ground samples is highly influenced by the grinding parameters, grinding conditions and the type of grinding wheel. This paper emphasizes on the effect of various grinding factors such as the grinding conditions, the type of grinding wheel and operating process parameters like depth of cut and table speed on the surface roughness of the ground samples. Two types of grinding wheels alumina (Al2O3) and cubic boron nitride (CBN) were used for grinding AISI D3 tool steel under dry and wet conditions. The material removal rate and surface roughness were evaluated for all the ground samples. The results showed that wet grinding outperformed dry grinding and provided a better surface finish while using both grinding wheels. Machine Learning was implemented to optimize the grinding parameters. Multi-objective optimization using genetic algorithm was done and a Pareto frontier chart was made to help determine what values for the input parameters would achieve the required outputs such as material removal rate and surface roughness. Two different approaches Genetic Algorithm and Principle Component Analysis were then compared for multi-objective optimization. The type of grinding wheel used had a dominant effect on the surface roughness of ground samples while the depth of cut had a lesser effect.
Protective responses of older adults for avoiding injury during falls: evidence from video capture of real-life falls in long-term care
Authors: Robinovitch Stephen N , Dojnov Aleksandra , Komisar Vicki , Yang Yijian , Shishov Nataliya , Yu Ying , Bercovitz Ian , Cusimano Michael D , Becker Clemens , Mackey Dawn C , Chong Helen 
Published: December 2022

Abstract

Background
falls are common in older adults, and any fall from standing height onto a rigid surface has the potential to cause a serious brain injury or bone fracture. Safe strategies for falling in humans have traditionally been difficult to study.

Objective
to determine whether specific ‘safe landing’ strategies (body rotation during descent, and upper limb bracing) separate injurious and non-injurious falls in seniors.

Design
observational cohort study.

Setting
two long-term care homes in Vancouver BC.

Methods
videos of 2,388 falls experienced by 658 participants (mean age 84.0 years; SD 8.1) were analysed with a structured questionnaire. General estimating equations were used to examine how safe landing strategies associated with documented injuries.

Results
injuries occurred in 38% of falls, and 4% of falls caused injuries treated in hospitals. 32% of injuries were to the head. Rotation during descent was common and protective against injury. In 43% of falls initially directed forward, participants rotated to land sideways, which reduced their odds for head injury 2-fold. Upper limb bracing was used in 58% of falls, but rather than protective, bracing was associated with an increased odds for injury, possibly because it occurred more often in the demanding scenario of forward landings.

Conclusions
the risk for injury during falls in long-term care was reduced by rotation during descent, but not by upper limb bracing. Our results expand our understanding of human postural responses to falls, and point towards novel strategies to prevent fall-related injuries.
Validation of the Dutch Version of the BODY-Q Measuring Appearance, Health-Related Quality of Life, and Experience of Healthcare in Patients Undergoing Bariatric and Body Contouring Surgery
Authors: de Vries Claire E E , Tsangaris Elena , Makarawung Dennis J S , Mink van der Molen Aebele B , van Veen Ruben N , Hoogbergen Maarten M , Pusic Andrea L , Terwee Caroline B , Cano Stefan , Klassen Anne F 
Published: December 2022

Abstract

Background
The BODY-Q is a patient-reported outcome measure developed for use in bariatric and body contouring surgery.

Objectives
The objective of this study was to examine the validity and reliability of the Dutch version of the BODY-Q.

Methods
The BODY-Q consists of 163 items in 21 independently functioning scales that measure appearance, health-related quality of life, and experience of care. The data used to validate the Dutch BODY-Q were provided by 2 prospective multicenter cohort studies across 3 hospitals in the Netherlands. The BODY-Q was administered before and after surgery at 3 or 4 months and 12 months. Rasch measurement theory (RMT) analysis was used to evaluate the BODY-Q for targeting, category threshold order, Rasch model fit, Person Separation Index, and differential item functioning by language (original English data vs Dutch data).

Results
Data were collected between January 2016 and May 2019. The study included 876 participants, who provided 1614 assessments. Validity was supported by 3 RMT findings: most scales showed good targeting, 160 out of 163 items (98.2%) evidenced ordered thresholds, and 142 out of 163 items (87.1%) fitted the RMT model. Reliability was high with Person Separation Index values &gt;0.70 for 19 out of 21 scales. There was negligible influence of differential item functioning by language on person item locations and the scale scoring.

Conclusions
This study provides evidence for the reliability and validity of the Dutch BODY-Q for use in bariatric and body contouring patients in the Netherlands. The Dutch BODY-Q can be used in (inter)national research and clinical practice.

Level of Evidence: 2
Comparative analysis of thioflavin T and other fluorescent dyes for fluorescent staining ofBacillus subtilisvegetative cell, sporulating cell, and mature spore
Authors: Kuwana Ritsuko , Yamazawa Ryuji , Ito Kiyoshi , Takamatsu Hiromu 
Published: December 2022

ABSTRACTThioflavin T, a cationic benzothiazole dye, is typically used to detect amyloid fibrils. In this study, we analyzed the staining properties of Bacillus subtilis cells using several fluorescent dyes, including thioflavin T analogs, 2-(4ʹ-methylaminophenyl) benzothiazole (BTA-1), and 2-(4-aminophenyl) benzothiazole (APBT). Thioflavin T stained vegetative cells in the early log phase and outer layer structures of forespores and mature spores. The inner parts of forespores and heat-killed mature spores were also stained with thioflavin T. Congo red, auramine O, and rhodamine B stained forespores and mature spores similar to thioflavin T. In contrast, APBT and BTA-1 fluorescence was detected in the outer layers of vegetative cells, mother cells, forespores, and mature spores, indicating that they bind to the cell membrane and/or cell wall. The combination of the fluorescent dyes used in this study will help analyze morphogenetic processes during the sporulation and the damage mechanisms of vegetative cells and spores.
Single-cell RNA sequencing analyses: interference by the genes that encode the B-cell and T-cell receptors
Authors: Sundell Timothy , Grimstad Kristoffer , Camponeschi Alessandro , Tilevik Andreas , Gjertsson Inger , Mårtensson Inga-Lill 
Published: December 2022

Abstract
B and T cells are integral parts of the immune system and are implicated in many diseases, e.g. autoimmunity. Towards understanding the biology of B and T cells and subsets thereof, their transcriptomes can be analyzed using single-cell RNA sequencing. In some studies, the V(D)J transcripts encoding the variable regions of the B- and T-cell antigen receptors have been removed before the analyses. However, a systematic analysis of the effects of including versus excluding these genes is currently lacking. We have investigated the effects of these transcripts on unsupervised clustering and down-stream analyses of single-cell RNA sequencing data from B and T cells. We found that exclusion of the B−/T-cell receptor genes prior to unsupervised clustering resulted in clusters that represented biologically meaningful subsets, such as subsets of memory B and memory T cells. Furthermore, pseudo-time and trajectory inference analyses of early B-lineage cells resulted in a developmental pathway from progenitor to immature B cells. In contrast, when the B−/T-cell receptor genes were not removed, with the PCs used for clustering consisting of up to 70% V-genes, this resulted in some clusters being defined exclusively by V-gene segments. These did not represent biologically meaningful subsets; for instance in the early B-lineage cells, these clusters contained cells representing all developmental stages. Thus, in studies of B and T cells, to derive biologically meaningful results, it is imperative to remove the gene sequences that encode B- and T-cell receptors.
benchdamic: benchmarking of differential abundance methods for microbiome data
Authors: Calgaro Matteo , Romualdi Chiara , Risso Davide , Vitulo Nicola 
Published: December 2022

Abstract

Summary
Recently, an increasing number of methodological approaches have been proposed to tackle the complexity of metagenomics and microbiome data. In this scenario, reproducibility and replicability have become two critical issues, and the development of computational frameworks for the comparative evaluations of such methods is of utmost importance. Here, we present benchdamic, a Bioconductor package to benchmark methods for the identification of differentially abundant taxa.

Availability and implementation
benchdamic is available as an open-source R package through the Bioconductor project at https://bioconductor.org/packages/benchdamic/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Interactive network-based clustering and investigation of multimorbidity association matrices with associationSubgraphs
Authors: Strayer Nick , Zhang Siwei , Yao Lydia , Vessels Tess , Bejan Cosmin A , Hsi Ryan S , Shirey-Rice Jana K , Balko Justin M , Johnson Douglas B , Phillips Elizabeth J , Bick Alex , Edwards Todd L , Velez Edwards Digna R , Pulley Jill M , Wells Quinn S , Savona Michael R , Cox Nancy J , Roden Dan M , Ruderfer Douglas M , Xu Yaomin 
Published: December 2022

Abstract

Motivation
Making sense of networked multivariate association patterns is vitally important to many areas of high-dimensional analysis. Unfortunately, as the data-space dimensions grow, the number of association pairs increases in O(n2); this means that traditional visualizations such as heatmaps quickly become too complicated to parse effectively.

Results
Here, we present associationSubgraphs: a new interactive visualization method to quickly and intuitively explore high-dimensional association datasets using network percolation and clustering. The goal is to provide an efficient investigation of association subgraphs, each containing a subset of variables with stronger and more frequent associations among themselves than the remaining variables outside the subset, by showing the entire clustering dynamics and providing subgraphs under all possible cutoff values at once. Particularly, we apply associationSubgraphs to a phenome-wide multimorbidity association matrix generated from an electronic health record and provide an online, interactive demonstration for exploring multimorbidity subgraphs.

Availability and implementation
An R package implementing both the algorithm and visualization components of associationSubgraphs is available at https://github.com/tbilab/associationsubgraphs. Online documentation is available at https://prod.tbilab.org/associationsubgraphs_info/. A demo using a multimorbidity association matrix is available at https://prod.tbilab.org/associationsubgraphs-example/.
bmVAE: a variational autoencoder method for clustering single-cell mutation data
Authors: Yan Jiaqian , Ma Ming , Yu Zhenhua 
Published: December 2022

Abstract

Motivation
Genetic intra-tumor heterogeneity (ITH) characterizes the differences in genomic variations between tumor clones, and accurately unmasking ITH is important for personalized cancer therapy. Single-cell DNA sequencing now emerges as a powerful means for deciphering underlying ITH based on point mutations of single cells. However, detecting tumor clones from single-cell mutation data remains challenging due to the error-prone and discrete nature of the data.

Results
We introduce bmVAE, a bioinformatics tool for learning low-dimensional latent representation of single cell based on a variational autoencoder and then clustering cells into subpopulations in the latent space. bmVAE takes single-cell binary mutation data as inputs, and outputs inferred cell subpopulations as well as their genotypes. To achieve this, the bmVAE framework is designed to consist of three modules including dimensionality reduction, cell clustering and genotype estimation. We assess the method on various synthetic datasets where different factors including false negative rate, data size and data heterogeneity are considered in simulation, and further demonstrate its effectiveness on two real datasets. The results suggest bmVAE is highly effective in reasoning ITH, and performs competitive to existing methods.

Availability and implementation
bmVAE is freely available at https://github.com/zhyu-lab/bmvae.

Supplementary information
Supplementary data are available at Bioinformatics online.
Invasive Species Policy Must Embrace a Changing Climate
Authors: Bradley Bethany A , Beaury Evelyn M , Fusco Emily J , Lopez Bianca E 
Published: December 2022

AbstractWith increasing impacts of climate change observed across ecosystems, there is an urgent need to consider climate change in all future environmental policy. But existing policy and management might be slow to respond to this challenge, leading to missed opportunities to incorporate climate change into practice. Furthermore, invasive species threats continue to rise and interact with climate change—exacerbating negative impacts. Enabling natural resource managers and individuals to be proactive about climate-driven invasive species threats creates a win–win for conservation. Recommendations include expanding opportunities for information sharing across borders, supporting proactive screening and regulation of high-risk species on the horizon, and incentivizing individual actions that reduce ecological impacts. In addition, invasive species risk should be considered when crafting climate mitigation and adaptation policy to reduce compounding stressors on ecosystems. As we develop much-needed tools to reduce harm, policy and management must consider the combined threats of invasions and climate change.