bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of teak plantation areas on water yield and peak discharge from five catchments in Blora Regency
Authors: Basuki T M , Pramono I B 
Published: August 2020

Abstract
Teak plantation occupies 67% of plantation areas in Java-Indonesia; however, its impact on hydrological responses has not been studied in detail. Therefore, a study to assess the impact of teak areas on water yield and peak discharge was conducted in Blora, Central Java. Five catchments with different percentages of the mature teak plantation from 53% to 82% were chosen. Five stream water level recorders were installed at the outlet of the catchments to measure stream water level (SWL). The SWL data were converted into a discharge. Based on 2008-2018 data, the results showed that the lowest monthly (8-41 mm mo−1) and annual (140-445 mm yr−1) water yield were found in Modang catchment with teak areas (82%), and the highest monthly (41-107 mm mo−1) and annual (526-1,500 mm yr−1) water yield occurred in Kejalen catchment with teak areas (74%). Generally, all the catchments had the highest water yield in 2010 and the lowest in 2012. It was found that the broader the teak areas, the lower the peak discharge. Although the catchments with the highest (82%) teak areas produced less monthly and annual water yield compared to the catchments with less teak coverage, however, the catchments with high teak coverage can control peak discharge.
Effects of biopore infiltration holes and cross drain on soil properties on skidding roads and natural production forest
Authors: Prameswari D , Supriyanto  , Saharjo B H , Wasis B , Pamoengkas P 
Published: August 2020

Abstract
Logging activities in natural production forests tend to have negative impacts on soil quality. This study aims to examine the effect of biopore infiltration holes and cross drains on the chemical and physical properties of the soil both on skid trails and in natural forests. The study was conducted at a natural production forest in West Kalimantan. The results showed that there was no significant change in the chemical properties of the soil in both the skid trails and natural forest, except for the higher organic C parameter in the natural forest. There was an increase in organic C from 1.16% to 2.04% (<3%) on the skid trails before and after one year. In general, there was a change in the physical properties of the soil on the skid trails. In the natural forest, the bulk density is lower than that on the skid trails and tends to increase with soil depth. Porosity in the center of the skid trails decreases by 24% compared to that in the natural forests at a depth of 0-10 cm. The phenomenon of degradation is also apparent in the parameters of available water, soil permeability, and drainage pores in the middle of the skid trails.
The effects of arbuscular mycorrhizal inoculation to growth and survivability of micropropagated Eucalyptus pellita and Acacia crassicarpa in nursery
Authors: Agustini L , Irianto R S B , Indrayadi H , Tanna R D , Fahrizawati  , Faulina S A , Hidayat A , Tjahjono B , Priatna D , Turjaman M 
Published: August 2020

Abstract
Inoculation of arbuscular mycorrhizal (AM) fungi into micropropagated Eucalyptus pellita and Acacia crassicarpa, that may have poor root structures, was conducted. The study aimed to investigate the effects of Acaulospora sp., Acaulospora tuberculata, Entrophospora sp., Gigaspora sp., and two different isolates of Glomus maculosum inoculations on the growth parameters of 21-days old plantlets of Eucalyptus pellita and Acacia crassicarpa. After 120 days of acclimatization in the nursery, E. pellita seems to be more responsive to mycorrhizal inoculation than A. crassicarpa. The survival rate of E. pellita was almost three times of the control. Although there was no significant difference between treatments, inoculation of Glomus maculosum RD.1.5.1 and Acaulospora sp. GB.10.A2 showed the highest impact on plant height (54-56 cm), stem diameter (4.3-4.4 mm), and root dry-weight (2.03-2.05 gr) of E. pellita; and Entrophospora sp. RB.10.3.1 on plant height, stem diameter, and root dry-weight of A. crassicarpa (41.46 cm, 2.96 mm, and 1.34 gr, respectively). This study also revealed that the benefits of AM fungi association were not always related to the level of root colonization.
The effects of several planting media on the red jabon (Anthocephalus macrophyllus (Roxb.) Havil) growth
Authors: Irawan A , Kinho J , Hidayah H N 
Published: August 2020

AbstractForest plantation establishment covers not only in the areas with optimum conditions but also in the marginal land areas. The selection of appropriate tree species is required when the plantation will be established in the marginal areas. This study aimed to determine the effects of several planting media, which is similar to the condition of the marginal/extreme conditions, on the growth of red jabon seedlings. The trials were conducted in a factorial complete randomized design with two tested factors, i.e.,planting media (M) and watering conditions (P), in which each factor has three levels. The first factor consists of topsoil medium (M1) as control, subsoil ultisol + topsoil medium (M2), and sandy soil + topsoil medium (M3); while the second factor consists of: watered with tap water (P1), watered with salted-water (P2), and waterlogged condition (P3). The best growth response was shown by the red jabon seedlings, which were planted in the subsoil ultisol + topsoil with a waterlogged condition (M2P3). The growth response of red jabon seedlings in the M2 treatment was similar (2.35 cm height, 0.26 mm diameter) and was not significantly different from the control (2.36 cm height, 0.26 mm diameter). The waterlogged condition (2.6 cm height, 0.28 mm diameter) also resulted in similar growth response to the control treatment (2.39 cm height, 0.29 mm diameter). The sandy soils and salted-watering conditions showed inferior growth responses compare to the other treatments. Thus, the seedlings showed its preference both to the fertile topsoil and subsoil ultisol media with adequate to high moisture levels rather than sandy medium with salted-watering conditions.
Choices of crops on establishing of agroforestry plot in peatland in Rasau Jaya Dua Village, West Kalimantan, Indonesia
Authors: Sanudin  , Widyaningsih T S , Fauziyah E 
Published: August 2020

Abstract
Information about the choices of crops is essential to understand what is the community’s preferences and consideration to understand the existence of crops on their community land. The research aimed to find out farmers’ preferences and choices of crops on establishing an agroforestry plot in the peatland area. The research was conducted in Rasau Jaya Dua Village, Kubu Raya District, from August to November 2017. The primary data on this research were the community’s socioeconomic condition and their preference for crops. Data on socioeconomic conditions were collected through in-depth interviews with 46 respondents. Data in choices of crops were collected through the Participatory Rural Appraisal (PRA) method using the ranking matrix of 20 farmers group members who involved in the development of the agroforestry plot on peatlands. The result showed that farmer has a preference of crops for their agroforestry plots on peatland. Corn is the most favorite crop to be planted on agroforestry plots. Corn is easy to grow, has a stable selling price, and has a short harvesting period (4 months). Meanwhile, for perennial tree crops, pulai (Alstonia pneumatophora), jelutung rawa (Dyera polyphylla), and gerunggang (Cratoxylum glaucum Korth) were the most favorite choices. Those trees have initially been grown on peatland, but the planting stocks were challenging to be found, and they need a more extended period to be harvested.
Spines growth responses of dragon blood (Daemonorops draco) rattan seedlings in several compositions of organic media
Authors: Nugroho A W 
Published: August 2020

AbstractCultivation ofDaemonorops dracois one of the conservation strategies to conserve its population in nature. Complete data and information about morphology are needed to support cultivation techniques. There has been much research on the morphology ofD. draco, but the research of rattan spines is lack. Rattan spines have an important function in protecting themselves against herbivores or seed predators. Growing media is one of the factors that influence the growth of rattan spines. We studied the growth of rattan spines from several compositions of organic media in nurseries. The experiment was arranged in a completely randomized design, with five treatments and three replications. The treatments were compositions of organic media content, i.e.: 0%, 25%, 50%, 75%, and 100%. The variables observed were the number of rattan spines, spines color, and spines angle. Our results showed that the media composition of 75% organic matter tends to show higher spines growth response even though statistically not significantly different with 100% mineral soils. Spine’s color was light green to yellow. Spines angle was pointed downward towards the grounds.
Effect of plant extracts and chemical fungicide on viability and percentage of seed-borne fungal infection on calliandra (Calliandra callothyrsus) seed
Authors: Suharti T , Nugraheni Y M M A , Suita E , Sumarni B 
Published: August 2020

Abstract
Calliandra (Calliandra callothyrsus) is one of the potential tree species that can be used as bio-energy resources. Unfortunately, fungi are one of the factors that can infect and decrease the viability of calliandra seeds. Some efforts are needed to improve the viability and inhibit fungal infection through biological or chemical treatments. The study was conducted to determine the effects of various plant extracts and chemical fungicide on the germination capability, as well as the inhibition of fungal infection in calliandra seeds. Parameters observed in this study were seed germination and fungi infection percentage. Seeds were treated by immersing them in hot water (five minutes) followed by chemical fungicides (i.e., benomyl, mancozeb) or plant extracts (i.e., ginger, onion, garlic, turmeric) for one hour. The study design used was a completely randomized design. The results showed that all the treatments could increase seed viability significantly. The treatment with immersion in onion, ginger and mancozeb was more effective on seed germination ability (88.67%, 8.33%, 86%) and reduced in fungal infections (11.33%, 5.33%, 0%). These treatments resulted in a significant difference between seed germination compared with the hot water and turmeric treatments. The best germination and reduction of fungal infection on calliandra seeds were showed on treatment by onion and mancozeb, respectively. The results revealed that garlic, onion, turmeric have a significant effect in inhibiting all fungal species compared to the hot water treatment. Ginger and onion extracts were effective treatments for increasing seed germination and controlling the fungal infection.
The influence of vegetation compositions on Asian giant honey bee (Apis dorsata Fabr.) in Kampar Regency
Authors: Pribadi A 
Published: August 2020

Abstract
Five essential types of vegetation in Kampar regency are considered to influence the number of Apis dorsata population, namely natural forests, forest plantations (Acacia and Eucalyptus), oil palm plantations, rubber plantations, and river existence. The objective of the study was to determine the effect of vegetation types on the number of A. dorsata population. This study was conducted from April to November 2016 and covered all districts categorized as the center of wild honey production in Kampar regency. Each sialang tree was observed for the number of A. dorsata. Sialang trees are big giant trees that are usually inhabited by A. dorsata colonies. The number of populations of A. dorsata for each tree was approached by using linear regression equations. By using all types of equations, the influence of different types of vegetation compositions (natural forests, Acacia and Eucalyptus plantations, oil palm plantations, rubber plantations and river existence) on the number of A. dorsata colony could be determined. The results, in respective of the vegetation types, were 28.17%, 21.51%, 14.81%, 21.32% and 14.82%. Moreover, the number of A. dorsata population in each sialang tree reached its maximum population above 60,000 ha in natural forest. Surprisingly, the number of A. dorsata colonies inhabited each sialang tree showed a positive correlation with the increase of the oil palm plantations area.
Cu based Metal Organic Framework (Cu-MOF) for electrocatalytic hydrogen evolution reaction
Authors: Nivetha Ravi , Sajeev Aparna , Mary Paul Aleena , Gothandapani Kannan , Gnanasekar Subashini , Bhardwaj Preetam , Jacob George , Sellappan Raja , Raghavan Vimala , N Krishna Chandar , Pitchaimuthu Sudhagar , Jeong Soon Kwan , Nirmala Grace Andrews 
Published: August 2020

Abstract
Hydrogen production using novel catalysts is regarded as one of the most needed technology for the future economic needs and water splitting to give H2 gas, which is a challenging task for large-scale production. This work reports the synthesis of Meso-Cu-BTC metal organic framework and further used for understanding its role in electrochemical hydrogen evolution reaction (HER) in 1 M NaOH solution. Meso-Cu-BTC electrocatalyst showed a less overpotential of 89.32 mV and an onset potential of 25 mV with an appreciable current density. Results show a low Tafel slope of 33.41 mVdec−1 and long-term durability. Thus, the overall results show that Meso-Cu-BTC acted as a good candidate for electrocatalysis towards hydrogen evolution.
Effect of heat treatments on the microstructure and mechanical properties of Zn-15 wt% Al alloy
Authors: Song Zhenya , Yan Ming , Jin Shenchao , Liu Yong , Ren Yanbiao , Shi Tiesheng , Zhang Lincai 
Published: August 2020

Abstract
The effect of heat treatment on the micro-structural and mechanical properties of Zn-15wt%Al alloys was investigated systematically in this work. After being annealed below 275 °C, granular α particles were distributed homogeneously in the η phase matrix, while a lamellar microstructure along with isolated η grains was observed when the alloys were annealed above 275 °C, followed by an air cooling (AC) treatment. A subsequent tensile test showed that the strength of alloys always increased with the annealing temperature. However, when the alloys were annealed above 275 °C, followed by a water-quenched (WQ) treatment, their strength firstly decreased with the aging time and then became unchanged. It was revealed by an in situ investigation that the γ′ phase retained from quenching decomposed gradually into an equiaxed microstructure during aging, leading to a reduction in the strength. Transmission electron microscopic (TEM) studies showed that dislocations were rarely inspected after a severely plastic deformation in the WQ-treated alloys, indicating that grain boundary sliding and rotation would be a dominant deformation mechanism. However, for the AC-treated alloys, dislocation tangles were easily found in lamellas due to the severe plastic deformations, demonstrating that in addition to grain boundary sliding and rotation, dislocation slip was another important deformation mechanism. A strength model, incorporating phase transformation dynamics with the law of mixtures, was established for the WQ-treated alloys annealed above 275 °C. Meanwhile, the number of α particles in the γ′ phase was assumed to be a key parameter for understanding the evolution of mechanical properties of Zn-15wt%Al alloys during the heat treatments. The more α particles in a unit volume of the γ′ phase, the easier plastic deformation the alloys is prone to, a lower strength and a larger elongation of the alloys will be.
Local modulation of Neurofilament transport at Nodes of Ranvier
Authors: Jia Zelin , Li Yinyun 
Published: August 2020

Abstract
Neurofilaments (NFs) are the most abundant cytoskeletal filaments undergoing ‘slow axonal transport’ in axons, and the population of NFs determines the axonal morphology. Both in vitro and ex-vivo experimental evidences show that the caliber of node is much thinner and the number of NFs in the node is much lower than the internode. Based on the Continuity equation, lower population of NFs indicates faster transport velocity. We propose that the local acceleration of NFs transport at node may result from the higher on-track rate

γ

o
n

or higher transition rate

γ

01

from pausing to running. We construct a segment of axon including both node and internode, and inject NFs by a fixed flux into it continuously. By upregulating transition rate of either

γ

o
n

or

γ

01

locally at the Node of Ranvier in the ‘6-state’model, we successfully accelerate NFs velocity and reproduce constriction of nodes. Our work demonstrates that local modulation of NF kinetics can change NFs distribution and shape the morphology of Node of Ranvier.
Enhanced repulsively bound atom pairs in topological optical lattice ladders
Authors: Flannigan Stuart , Daley Andrew J 
Published: August 2020

Abstract
There is a growing interest in using cold-atom systems to explore the effects of strong interactions in topological band structures. Here we investigate interacting bosons in a Cruetz ladder, which is characterised by topological flat energy bands where it has been proposed that interactions can lead to the formation of bound atomic pairs giving rise to pair superfluidity. By investigating realistic experimental implementations, we understand how the lattice topology enhances the properties of bound pairs giving rise to relatively large effective pair-tunnelling in these systems which can lead to robust pair superfluidity, and we find lattice supersolid phases involving only pairs. We identify schemes for preparation of these phases via time-dependent parameter variation and look at ways to detect and characterise these systems in a lattice. This work provides a starting point for investigating the interplay between the effects of topology, interactions and pairing in more general systems, with potential future connections to quantum simulation of topological materials.
reconCNV: interactive visualization of copy number data from high-throughput sequencing
Authors: Chandramohan Raghu , Kakkar Nipun , Roy Angshumoy , Parsons D Williams 
Published: August 2020

Abstract

Summary
Copy number variation (CNV) is an important category of unbalanced structural rearrangement. While methods for detecting CNV in high-throughput targeted sequencing have become increasingly sophisticated, dedicated tools for interactive and dynamic visualization of CNV from these data are still lacking. We describe reconCNV, a tool that produces an interactive and annotated web-based dashboard for viewing and summarizing CNVs detected in next-generation sequencing (NGS) data. reconCNV is designed to work with delimited result files from most NGS CNV callers with minor adjustments to the configuration file. The reconCNV output is an HTML file that is viewable on any modern web browser, requires no backend server, and can be readily appended to existing analysis pipelines. In addition to a standard CNV track for visualizing relative fold change and absolute copy number, the tool includes an auxiliary variant allele fraction track for visualizing underlying allelic imbalance and loss of heterozygosity. A feature to mask assay-specific technical artifacts and a direct HTML link out to the UCSC Genome Browser are also included to augment the reviewer experience. By providing a light-weight plugin for interactive visualization to existing NGS CNV pipelines, reconCNV can facilitate efficient NGS CNV visualization and interpretation in both research and clinical settings.

Availability and implementation
The source code and documentation including a tutorial can be accessed at https://github.com/rghu/reconCNV as well as a Docker image at https://hub.docker.com/repository/docker/raghuc1990/reconcnv.

Supplementary information
Supplementary data are available at Bioinformatics online.
SPEARS: Standard Performance Evaluation of Ancestral haplotype Reconstruction through Simulation
Authors: Manching Heather , Wisser Randall J 
Published: August 2020

AbstractMotivationAncestral haplotype maps provide useful information about genomic variation and insights into biological processes. Reconstructing the descendent haplotype structure of homologous chromosomes, particularly for large numbers of individuals, can help with characterizing the recombination landscape, elucidating genotype-to-phenotype relationships, improving genomic predictions and more. Inferring haplotype maps from sparse genotype data is an efficient approach to whole-genome haplotyping, but this is a non-trivial problem. A standardized approach is needed to validate whether haplotype reconstruction software, conceived population designs and existing data for a given population provides accurate haplotype information for further inference.ResultsWe introduce SPEARS, a pipeline for the simulation-based appraisal of genome-wide haplotype maps constructed from sparse genotype data. Using a specified pedigree, the pipeline generates virtual genotypes (known data) with genotyping errors and missing data structure. It then proceeds to mimic analysis in practice, capturing sources of error due to genotyping, imputation and haplotype inference. Standard metrics allow researchers to assess different population designs and which features of haplotype structure or regions of the genome are sufficiently accurate for analysis. Haplotype maps for 1000 outcross progeny from a multi-parent population of maize are used to demonstrate SPEARS.Availabilityand implementationSPEARS, the protocol and suite of scripts, are publicly available under an MIT license at GitHub (https://github.com/maizeatlas/spears).Supplementary informationSupplementary data are available at Bioinformatics online.
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control
Authors: Osorio Daniel , Cai James J 
Published: August 2020

Abstract

Motivation
Quality control (QC) is a critical step in single-cell RNA-seq (scRNA-seq) data analysis. Low-quality cells are removed from the analysis during the QC process to avoid misinterpretation of the data. An important QC metric is the mitochondrial proportion (mtDNA%), which is used as a threshold to filter out low-quality cells. Early publications in the field established a threshold of 5% and since then, it has been used as a default in several software packages for scRNA-seq data analysis, and adopted as a standard in many scRNA-seq studies. However, the validity of using a uniform threshold across different species, single-cell technologies, tissues and cell types has not been adequately assessed.

Results
We systematically analyzed 5 530 106 cells reported in 1349 annotated datasets available in the PanglaoDB database and found that the average mtDNA% in scRNA-seq data across human tissues is significantly higher than in mouse tissues. This difference is not confounded by the platform used to generate the data. Based on this finding, we propose new reference values of the mtDNA% for 121 tissues of mouse and 44 tissues of humans. In general, for mouse tissues, the 5% threshold performs well to distinguish between healthy and low-quality cells. However, for human tissues, the 5% threshold should be reconsidered as it fails to accurately discriminate between healthy and low-quality cells in 29.5% (13 of 44) tissues analyzed. We conclude that omitting the mtDNA% QC filter or adopting a suboptimal mtDNA% threshold may lead to erroneous biological interpretations of scRNA-seq data.

Availabilityand implementation
The code used to download datasets, perform the analyzes and produce the figures is available at https://github.com/dosorio/mtProportion.

Supplementary information
Supplementary data are available at Bioinformatics online.