bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil as A Fundamental Element of Silviculture for Sustainable Tropical Rain Forest Management
Authors: Munawar A , Wiryono  
Published: December 2019

Abstract
Soil is a fundamental element of a forest ecosystem. It provides physical support for plants, absorbs and retains water, retains and supplies essential nutrients and other chemical compounds for plant growth, and provides nutrients cycling services and habitats for organisms. Soils underlying tropical rainforest ecosystems have distintive characteristics. The soils are old and highly-weathered and leached, highly-acidic, lacking of weatherable minerals and nutrient reserves, and dominated by low-activity clays with poor retention capacity to nutrients. Under such conditions, rainforest productivity relies heavily on the top layer of the soils, consisting of decaying plant materials and animal remains in which most biological activities such as nutrient cycling occur. These characteristics indicate that rainforest ecosystem is very fragile. When the forest trees overlying such soils are cut down, the logged over areas lose this thick layer and then the forest will seriously degrade. Therefore maintaining vegetation on soil surface is imperative. This paper aims to discuss properties of soils in the tropical rainforests, to identify soil-related damages due to silvicultural practices, and to find preventive and currative actions in order to promote sustainable tropical rainforest management.
The use of Analytical Network Process (ANP) Approach to Assess the Health of Natural Production Forest
Authors: I Putra Erianto , Supriyanto  , Purnomo Herry , Haneda Noor F , Matangaran Juang R 
Published: December 2019

Abstract
The need of the sustainable forest management has become the world most demand in a recent to face the climate change issue. Monitoring the health of forest thus should be done properly as one of indicators for achieving sustainable forest management. Forest Health Monitoring (FHM) is one of the methods applied to monitor the status, change and trends of forest health condition by using the ecological indicators. Here, we re-introduce the used of Analytical Networking Process (ANP) approach to scoring the health condition of natural production forest. We weighted the-four ecological indicators of Forest Health Monitoring (FHM), e.g. forest productivity in term of quality and quantity, forest health and vitality (tree-damage and crown condition), site quality, and biodiversity. Final score of forest health is obtained by combining indicator weights and relative score of each indicator. This work has been published in 2008, but reintroducing the method is taking a high importance as it needed for better developing the health assessment for different forest type and function.
Identifying forest fires causes in Kawah Kamojang Nature Reserve (Mount Guntur), Garut, West Java
Authors: Lestari K G , Putra E I , Matangaran J R. 
Published: December 2019

Abstract
Forest and land fires have caused losses on social, economic, and ecological aspects in Indonesia. Forest and land fires management will not be optimal without knowing factors causing them. Mount Guntur which belong to Kawah Kamojang Nature Reserve (Mount Guntur) (KKNR) is suffering from forest and land fires almost every year. This study aims to identify the factors causing forest and land fires in KKNR. The research used field observation, in-depth interviews, and field data collection. The results indicate that the factors causing forest and land fires are human factors from sand mining, land preparation, and bird poaching. Drought due to long dry season trigger the fire occurrences. Here, we strongly suggest increasing the knowledge and awareness of forest fire to the people in KKNR to prevent the area from the further destructive forest fire.
Quality of kapok honey in some areas of Apis mellifera honey cultivation in Central Java and East Java Province
Authors: Adalina Y , Heryati Y , Yuniati D 
Published: December 2019

AbstractJava Island is a center for developingApis melliferabee cultivation due to the availability of honey bee feed plants. The most reliable plant species producing honey is kapok plant (Ceiba petandra), because the flowering period is around 2.5 months. This study aims to determine the quality ofA.melliferakapok honey from Central and East Java. Sampling was carried out by purposive sampling method in Pati District and Jepara District (Central Java Province) and Pasuruan District (East Java Province), which were the centers of honey production. To find out the quality of kapok honey, laboratory analysis of 9 honey samples from honey producers was done. The results showed that the acidity, hydroxymethylfurfural (HMF), reducing sugar and sucrose levels of all honey samples met SNI 8664-2018 standards, except honey water content which exceeded the SNI limit (maximum 22%). Kapok honey is acidic with a pH value of 4.0 to 4.5, white to light amber with an intensity value of 20 to 73 mm Pfund. The results of the phytochemical analysis that showed that the kapok honey in Pati District contained saponin active compounds, whereas honey from Jepara and Pasuruan District contained saponins and flavonoids which had the potential to be anti-bacterial and antioxidant.
The Best Practices of Stingless Bee Farming in Kapuas Hulu Regency, West Kalimantan Province, Indonesia
Authors: Ashari R , Karyaatmadja B , Sutedja I G N N , Rakhmadi D , Abidin S 
Published: December 2019

Abstract
Utilization of non-timber forest products can provide income for the community. Through the Forest and Climate Change Programme – Financial Cooperation Module (FORCLIME - FC), communities in 15 villages in the Kapuas Hulu Regency, West Kalimantan Province began developing stingless beekeeping in 2017. The purpose of this study were to measure the success rate of beekeeping and obtain the best practices for stingless beekeeping. Currently the community is developing 544 boxes of stingless bee colonies (Apidae: Apinae: Trigona) which colonies were obtained from forests in each village. From a number of these colonies, the success rate was 65%. This success depends on the location of cultivation, the technique of extracting and distributing colonies from the forest, and the maintenance process when the colonies have been moved.
Species Grouping of Shorea spp. Based On Responsive Scale of Periodic Individual Diameter Increment
Authors: Susanty F H 
Published: December 2019

Abstract
The purpose of this research was to determine species grouping of Shorea sp. based on the characteristics of periodic individual diameter increment on natural forest. The study was conducted on Labanan forest research station located in Berau, East Kalimantan. This study was using data series on logged over forest permanent plots with total of 8 ha along 1990-2018. Shorea spp. species group was determined based on the number of classes (5 classes) as responsive scale of periodic diameter increment rates. The consistency assessment analysis was conducted using compares of two approaches which as by interval class and euclidean distance method. The identified results of measuring 26 species of Shorea, 16 species can be further analyzed into species grouping based on their increment. The interval class rates approach has different scale with euclidean distance rates for cluster similarity method. Shorea parvifolia, S. johorensis, S. pinanga and S. scrobiculata were recommended as very responsive or fast-growing species. Whereas S. patoiensis, S. beccariana and S. smithiana were in the slow growing species group. This result is providing the recommendation of selection of priority species based on the increment rates characteristic for increasing the productivity especially on production forest stand.
Traditional Cultivation Of Laccifer lacca Kerr. in Alor, East Nusa Tenggara
Authors: Kadha F , Supriyanto  , Haneda N F 
Published: December 2019

Abstract
Lac is a resin produced by secretion of small insect of Laccifer lacca in Kesambi trees. Lac resin is important for paint, ink, pharmacy, cosmetic, electricity, coating (candy, fruits, and vegetables), textile and candle industries. Lac price in the market is IDR 10,000.00/kg in 2019, while the lac price in 2005 – 2006 was IDR 60,000.00/kg. The decrease of lac price in Alor Island due to lack of technology in increasing the lac quantity, quality and no special institution to facilitate lac marketing. The objective of this survey was to study the traditional practices of lac cultivation in Alor Island. The method was done by field survey in the farmer gardens and interviewed the farmers. The result showed that lac cultivation in Alor Island is done traditionally and low technological inputs. Insect inoculation is done on young branches at 1 m above ground of 16 years old of Kesambi trees as a host. The maintenance of Kesambi trees is done by cutting old branches. Lac harvesting is done in June, July and in December by cutting the colonized branches into small size, and dried under sunlight. Lac resin is crushed into granular sizes, and packed into plastic bags for post-harvesting technology.
Soil Disturbance by Logging Operation of Industrial Plantation Forest in Indonesia
Authors: Matangaran J R , Putra E I , Mashitha M W , Diatin I , Mujahid M , Adlan Q 
Published: December 2019

Abstract
Logging concessions in natural forest and industrial plantation forest are the main producers of logs in Indonesia. Several companies of industrial plantation forest have been successfully planted with fast-growing species such as Acacia mangium for pulpwood. These plantation forests have entered their annual harvesting period. Some options of timber harvesting machines such as forwarder, harvester, feller buncher, and excavator are chosen to remove timber from stump to the log landing site. The negative impact of such machines includes the loss of topsoil and soil compaction. The objectives of the research were to analysis soil compaction by excavator with log carrier in forwarding log from stump to landing site. Bulk density, cone index and deep of rut were measured after logging operation at the harvesting site at one of industrial plantation forest of South Kalimantan. The result showed that soil bulk density increase with the increase in the number of excavator with log carrier passes. The rut was formed on several places on the soil surface, particularly near landings and under the log carrier. The ground pressure of the excavator and log carrier caused the formation of the rut on the soil surface. Weight of excavator plus loads had caused pressure on the track of the contact with the ground. Rut formed and high soil bulk density indicated the soil compaction occurred by the harvesting operation.
Land Management in Optimizing Productivity of Limited Land to Deal with Rural Food, Feed and Fuel (3F) Security
Authors: Widyati E , Darwiati W , Yulianti M 
Published: December 2019

Abstract
Study aims to observe the best practice in optimizing land productivity for successing rural food and energy sovereignity. This study was carried out in Majalengka District on 2 ha land, arranged as monoculture calliandra plantation (2 × 3 m spacing), agroforestry (2 × 5 m spacing), and agro-sylvo-pasture (2 × 5 m spacing). Calliandra planted in agroforestry was combined with maize, beans, and peas; while agro-silvo-pasture planted with the same commodities mixed with utilizing waste of corn and calliandra for forage of cattle or goats. Calliandra were harvested in 2 years age by applying coppice system. Yield of 2 years fire-woods, annual (food crops), and 6 months coppice sprouting capacity of calliandra, were calculated as land productivity. The result showed that productivity of grown in monoculture was 28 tons/ha, higher than agroforestry (15) or agro-silvo-pasture (13.8). However, agro-silvo-pasture could significantly improve number of 6 months age coppice (diameter 4-6 cm) by 8-10 coppices/trees higher than agroforestry (6-8) or monoculture (3-5). Agroforestry was also successfuly improve land productivity; such as produced corn grain (8.4 tons), mung bean (1.6 tons), groundnut grain (2.5 tons), pigeon pea (0.8 tons), respectively, per year. Income for farmer can be calculated per years per hectar, as 3,050,000 IDR (monoculture); 26,575,000 IDR (agroforestry), and 28,375,000 IDR (agro-silvo-pasture). Whereas agro-silvo-pasture was not significantly different in increasing land productivity compare to agroforestry, nevertheless, cattle or goat breeder not only gained 3 tons maize waste and 2.2 tons leaf during a season but also saved fertilizers due to manure production. It can be concluded that developing energy plantation forest through agroforestry or agrosylvopasture can be the promissing program to realize the rural food, feed, fuel security.
Human embryo gene editing: God's scalpel or Pandora's box?
Authors: Zhou Qi , Zhang Yan , Zou Yujie , Yin Tailang , Yang Jing 
Published: December 2019

AbstractGene editing refers to the site-specific modification of the genome, which mainly focuses on basic research, model organism construction and treatment and prevention of disease. Since the first application of CRISPR/Cas9 on the human embryo genome in 2015, the controversy over embryo gene editing (abbreviated as EGE in the following text) has never stopped. At present, the main contradictions focus on (1) ideal application prospects and immature technologies; (2) scientific progress and ethical supervision; and (3) definition of reasonable application scope. In fact, whether the EGE is ‘God's scalpel’ or ‘Pandora's box’ depends on the maturity of the technology and ethical supervision. This non-systematic review included English articles in NCBI, technical documents from the Human Fertilization and Embryology Authority as well as reports in the media, which performed from 1980 to 2018 with the following search terms: ‘gene editing, human embryo, sequence-specific nuclease (SSN) (CRISPR/Cas, TALENT, ZFN), ethical consideration, gene therapy.’ Based on the research status of EGE, this paper summarizes the technical defects and ethical controversies, enumerates the optimization measures and looks forward to the application prospect, aimed at providing some suggestions for the development trend. We should regard the research and development of EGE optimistically, improve and innovate the technology boldly and apply its clinical practice carefully.
Logomaker: beautiful sequence logos in Python
Authors: Tareen Ammar , Kinney Justin B 
Published: December 2019

Abstract

Summary
Sequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA and protein sequences, yet it is currently difficult to generate and customize such logos within the Python programming environment. Here we introduce Logomaker, a Python API for creating publication-quality sequence logos. Logomaker can produce both standard and highly customized logos from either a matrix-like array of numbers or a multiple-sequence alignment. Logos are rendered as native matplotlib objects that are easy to stylize and incorporate into multi-panel figures.

Availability and implementation
Logomaker can be installed using the pip package manager and is compatible with both Python 2.7 and Python 3.6. Documentation is provided at http://logomaker.readthedocs.io; source code is available at http://github.com/jbkinney/logomaker.
Anatomy and Physiology of Macaque Visual Cortical Areas V1, V2, and V5/MT: Bases for Biologically Realistic Models
Authors: Vanni Simo , Hokkanen Henri , Werner Francesca , Angelucci Alessandra 
Published: December 2019

AbstractThe cerebral cortex of primates encompasses multiple anatomically and physiologically distinct areas processing visual information. Areas V1, V2, and V5/MT are conserved across mammals and are central for visual behavior. To facilitate the generation of biologically accurate computational models of primate early visual processing, here we provide an overview of over 350 published studies of these three areas in the genus Macaca, whose visual system provides the closest model for human vision. The literature reports 14 anatomical connection types from the lateral geniculate nucleus of the thalamus to V1 having distinct layers of origin or termination, and 194 connection types between V1, V2, and V5, forming multiple parallel and interacting visual processing streams. Moreover, within V1, there are reports of 286 and 120 types of intrinsic excitatory and inhibitory connections, respectively. Physiologically, tuning of neuronal responses to 11 types of visual stimulus parameters has been consistently reported. Overall, the optimal spatial frequency (SF) of constituent neurons decreases with cortical hierarchy. Moreover, V5 neurons are distinct from neurons in other areas for their higher direction selectivity, higher contrast sensitivity, higher temporal frequency tuning, and wider SF bandwidth. We also discuss currently unavailable data that could be useful for biologically accurate models.
Do Audits Deter or Provoke Future Tax Noncompliance? Evidence on Self-Employed Taxpayers
Authors: Beer Sebastian , Kasper Matthias , Kirchler Erich , Erard Brian 
Published: December 2019

AbstractThis article employs unique tax administrative data and operational audit information, including risk scores used for audit selection, from a sample of approximately 7500 self-employed US taxpayers to investigate the effects of operational tax audits on future reporting behavior. Our estimates indicate that audits can have substantial deterrent or counter-deterrent effects, depending on the audit outcome. In the aggregate, taxable income is estimated to increase by roughly 15% 1 year after an operational audit. However, this figure masks substantial heterogeneity within the population. Among those taxpayers who receive an additional tax assessment, reported taxable income is estimated to be 64% higher in the first year after the audit (44% after 3 years) than it would have been in the absence of the audit. In contrast, among those taxpayers who do not receive an additional tax assessment, reported taxable income is estimated to be approximately 15% lower the year after the audit (21% 3 years later) than it would have been had the audit not taken place. Our results suggest that improved targeting of audits toward noncompliant taxpayers would not only yield more direct audit revenue but also pay dividends in terms of future tax collections.
Global Burden of Hepatitis B Infection in People Living With Human Immunodeficiency Virus: A Systematic Review and Meta-analysis
Authors: Leumi Steve , Bigna Jean Joel , Amougou Marie A , Ngouo Anderson , Nyaga Ulrich Flore , Noubiap Jean Jacques 
Published: December 2019

Abstract

Background
This meta-analysis was conducted to estimate the global burden of hepatitis B virus (HBV) infection in people living with human immunodeficiency virus (PLWH).

Methods
We searched multiple databases for studies published between January 1990 and December 2017. HBV infection (hepatitis B surface antigen) was diagnosed with serological assays. A random-effects meta-analysis served to pool data.

Results
We included 358 studies (834 544 PLWH from 87 countries). The pooled prevalence of HBV infection was 8.4% (95% confidence interval [CI], 7.9%–8.8%), among which 26.8% (95% CI, 22.0%–31.9%) was positive to hepatitis B e antigen. HBV prevalence (with 95% CIs) differed according to region: West and Central Africa, 12.4% (11.0%–13.8%); Middle East and North Africa, 9.9% (6.0%–14.6%); Asia and the Pacific, 9.8% (8.7%–11.0%); Eastern and Southern Africa, 7.4% (6.4%–8.4%); Western and Central Europe and North America, 6.0% (5.5%–6.7%); and Latin America and the Caribbean, 5.1% (4.2%–6.2%) (P &lt; .0001). The prevalence decreased from 10.4% in low-developed to 6.6% in highly developed countries (P &lt; .0001) and increased from 7.3% in countries with HIV prevalence ≤1% to 9.7% in countries with HIV prevalence &gt;1% (P &lt; .0001). Globally, we estimated that there were 3 136 500 (95% CI, 2 952 000–3 284 100) cases of HBV in PLWH, with 73.8% of estimated regional cases from sub-Saharan Africa and 17.1% from Asia and the Pacific.

Conclusions
This study suggests a high burden of HBV infection in PLWH, with disparities according to region, level of development, and country HIV prevalence.
Estimates of the Time From Seroconversion to Antiretroviral Therapy Initiation Among People Newly Diagnosed With Human Immunodeficiency Virus From 2006 to 2015, New York City
Authors: Robertson McKaylee M , Braunstein Sarah L , Hoover Donald R , Li Sheng , Nash Denis 
Published: December 2019

Abstract

Background
We estimated the time from human immunodeficiency virus (HIV) seroconversion to antiretroviral therapy (ART) initiation during an era of expanding HIV testing and treatment efforts.

Methods
Applying CD4 depletion parameters from seroconverter cohort data to our population-based sample, we related the square root of the first pretreatment CD4 count to time of seroconversion through a linear mixed model and estimated the time from seroconversion.

Results
Among 28 162 people diagnosed with HIV during 2006–2015, 89% initiated ART by June 2017. The median CD4 count at diagnosis increased from 326 (interquartile range [IQR], 132–504) cells/µL to 390 (IQR, 216–571) cells/µL from 2006 to 2015. The median time from estimated seroconversion to ART initiation decreased by 42% from 6.4 (IQR, 3.3–11.4) years in 2006 to 3.7 (IQR, 0.5–8.3) years in 2015. The time from estimated seroconversion to diagnosis decreased by 28%, from a median of 4.6 (IQR, 0.5–10.5) years to 3.3 (IQR, 0–8.1) years from 2006 to 2015, and the time from diagnosis to ART initiation reduced by 60%, from a median of 0.5 (IQR, 0.2–2.1) years to 0.2 (IQR, 0.1–0.3) years from 2006 to 2015.

Conclusions
The estimated time from seroconversion to ART initiation was reduced in tandem with expanded HIV testing and treatment efforts. While the time from diagnosis to ART initiation decreased to 0.2 years, the time from seroconversion to diagnosis was 3.3 years among people diagnosed in 2015, highlighting the need for more effective strategies for earlier HIV diagnosis.
Clinical Impact of Rapid Drug Susceptibility Testing to Accompany Fluoroquinolone-Containing Universal Tuberculosis Regimens: A Markov Model
Authors: Kendall Emily A , Malhotra Shelly , Cook-Scalise Sarah , Dowdy David W , Denkinger Claudia M 
Published: December 2019

Abstract

Background
To appropriately treat tuberculosis (TB) with regimens that combine novel and older drugs, evidence-based, context-specific strategies for drug-susceptibility testing (DST) will be required.

Methods
We created a Markov state-transition model of 100 000 adults with TB receiving a novel, fluoroquinolone (FQ)–containing regimen. We estimated clinical outcomes and resource utilization with no FQ-DST, universal FQ-DST, or FQ-DST only for patients with rifampin-resistant TB (“targeted FQ-DST”). We considered scenarios of stronger (South Africa) and weaker (Southeast Asia) correlation of fluoroquinolone resistance with rifampin resistance, with sensitivity analysis for other setting and regimen characteristics.

Results
Relative to no FQ-DST, targeted FQ-DST increased cure of FQ-resistant TB by 7.5% (interquartile range [IQR], 6.7%–9.2%) in South Africa and 1.7% (IQR, 0.7%–2.5%) in Southeast Asia. However, rare FQ resistance among the more prevalent rifampin-susceptible TB accounted for 50% of FQ-resistant TB in South Africa and 83% in Southeast Asia. As a result, universal FQ-DST further increased cure of FQ-resistant TB by 3.4% (IQR, 2.3%–5.4%) in South Africa and 5.8% (IQR, 5.1%–6.3%) in Southeast Asia. With targeted FQ-DST, 1 additional patient was cured per 50 (IQR, 42–70) tests in South Africa and 44 (IQR, 37–51) in Southeast Asia. When expanding from targeted to universal FQ-DST, 1 additional cure required 3500 (IQR, 2300–5500) tests in South Africa and 410 (IQR, 370–450) in Southeast Asia.

Conclusions
FQ-DST improved patient outcomes and was particularly important for high-risk patient groups and less robust regimens. A universal strategy was favored in generalized epidemics of fluoroquinolone resistance.