bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping of Road Network, Land Use, and Pedestrian Ways in CBD of Semarang
Authors: Rakhmatulloh A R , Dewi D I K 
Published: August 2019

Abstract
The more human activities in the city increase mobility, demand of circulation route and adequate transportation system. Semarang City Government has already provided the transportation facilities: BRT (Bus Rapid Transit) and pedestrian ways. However, the connectivity of pedestrian ways (door to door service) is still not properly used according to the safety, convenience, and the needs of urban society. As a result, the travel cost becomes expensive and mobility activities from one place to another is not efficient. The purpose of this research is about the study of integrated road networks, land use, and pedestrian ways in the center of Semarang City. The method of this research, using GIS application for mapping and planning the connectivity of land use and pedestrian ways towards public transportation or BRT (Bus Rapid Transit) route in Semarang City. The aim of the research is mapping the connectivity of pedestrian ways in order to create easy access to public transportation.
Mapping of Space compatibility for Street Vendors in Urban Public Space, Taman Tirto Agung, Banyumanik, Semarang
Authors: Widjajanti R , Dewi S P , Khadiyanta P 
Published: August 2019

Abstract
The high competition to be able to work in the formal sector makes some people more absorbed in the informal sector, one of them in the field of commerce/service, namely as street vendors. The activity of street vendors occupying the public space is often considered as troublemakers because the government does not have a clear reference to arrange the location that can be used by them and in accordance with the characteristics of its activity. As well as street vendors in Taman Tirto Agung, Indonesia. who grow and develop to fill the park have degraded the visual quality of space and changed the function of the public space. The arrangement of street vendors should consider their space behaviors so that the space they use is compatible with their activities. The aim of this research is to identify the space that compatible with street vendors in Taman Tirto Agung. By using the GIS mapping and quantitative method with survey and questionnaire techniques, showed that street vendors choose compatible trade location in Taman Tirto Agung are determined by various activities around the park; activity time lasts for 24 hours; numbers of passing visitors; the flow of visitors; and settled space use.
Mapping community environmental sanitation issue using household spatial cognition: A case of Bulu Lor Subdistrict, Semarang, Indonesia
Authors: Artiningsih A , Nugroho P , Perdana S A J , Khairunisa M U 
Published: August 2019

Abstract
Recently, a community in cities has played a key role in practicing an inclusive sustainable development with other stakeholders. However, the city government has a limitation in data spatial collection and documentation of urban environmental sanitation services, for instance. At the local scale, this data particularly relates to the local community knowledge and experiences. Unfortunately, the role of community as spatial data resource has not been encouraged yet. Instead, this condition has got worsened due to the lack of community spatial literacy. Nevertheless, this strive is important for data input on the planning process which illustrated how community recognizes their environmental changes. This paper attempts to build a simple mapping method based on household spatial cognition on urban environmental sanitary problems using GIS. Inductive mapping method applied to capture the community knowledge and experiences with a case study approach. In-depth interview was conducted with several key informants on Bulu Lor Subdistrict, part of North Semarang District, Indonesia. The reconstruction of household spatial cognition demonstrates transformation phase on the sanitation improvement due to community knowledge elevation on their health awareness and creation on their communal sanitation governance.
Determining the Spatial Connectivity of Surabaya’s Peri-urban Area towards Urban Rural Linkage Framework Based on Population Movement Relation
Authors: Aulia B U , Santoso E B , Hapsari A D , Safitri E W 
Published: August 2019

Abstract
The rapid development and becoming the most dominant growing center at East Java Province, Surabaya City is affected by its periphery areas. This fact is shown by the core area act as an economic center and the periphery act as a settlement support, resulting in urban area widening, known as peri-urban area. This also indicate a domination of periphery area movement toward the core area in the form of people’s flow or population movement. However, the result of the observation shows a tendency of peri-urban problem occurrences such as traffic jam, flood, and slum area. Thus, it is necessary to determine its connectivity between the core area and its support area in urban-rural linkage framework for the aim of having a formulated anticipation effort to face those problems in the future. The analysis was done by quantitative and qualitative approach resulting Normalized Difference Built-Up Index (NDBI) of the year 2002 until 2018 which the conversion reach out 43,95% of non-built-up area to build up area due of the urban area widening. Also, the spatial interaction from the Gravity Model shows the strongest interaction force occurred at Sidoarjo Regency’s districts which directly adjacent with Surabaya City. It can be concluded that the peri-urban area at southern Surabaya have a significant urban rural linkage interaction strength from the population movement. This imply that prioritizing the infrastructure development is a step forward to solve the occurred problems. With a hope by understanding these facts will encourage the government to formulate the sectoral policies.
Mapping of Child Friendly Parks Availability for Supporting Child Friendly City in Semarang
Authors: Prihantini P. , Kurniawati W 
Published: August 2019

Abstract
Semarang is one of a city that gets an award as a child-friendly city. A child-friendly city is a city that has recognized the existence of children’s rights, which implements it in policy, including in the development of its city. The availability of service facilities that consider children’s needs such as children’s playgrounds can contribute to the realization of a child-friendly city. Semarang has 33 active parks in 2014 and continues to grow by approximately 20 parks now, but not all parks provide children’s ground. The purpose of this study is to know that the availability of child-friendly parks can support Semarang as a Child-Friendly City. This study uses a qualitative descriptive approach, using a scoring analysis tool. The results of the analysis show that the availability of child-friendly parks is sufficient to influence the predicate of a child-friendly city because child-friendly parks are a representation of the attention and recognition of children’s rights.
Land Subsidence Monitoring in Semarang and Demak Coastal Areas 2016-2017 Using Persistent Scatterer Interferometric Synthetic Aperture Radar
Authors: Azeriansyah R , Prasetyo Y , Yuwono B D 
Published: August 2019

Abstract
Land subsidence is a problem faced in coastal areas of Java Island especially coastal areas of Semarang and Demak that caused by various natural and human factors. One method that can be used for this is by utilizing the method of Persistent Scatterer Interferometric Synthetic Aperture Radar (PS-InSAR). PS-InSAR is a remote sensing technique that is the development of the DInSAR method that can monitor the movement of the ground surface that allows users to perform regular measurements and monitoring of fixed objects on the surface of the earth. One of PS-InSAR method is Standford Method of Persistent Scatterers (StaMPS). StaMPS identify and extract the deformation signal even in the absence of bright scatterers. StaMPS is also applicable in areas undergoing non-steady deformation, with no prior knowledge of the variations in deformation rate. In addition, this method can also cover a large area. From the PS-InSAR method can be known the impact on the existing area in Semarang and Demak region per year from 2016 to 2017 by utilizing the image of Sentinel-1A. The result of PS-InSAR is done comparison of result from GNSS survey data.
Land Subsidence Of Semarang City Using Permanent Scatterer Interferometric Synthetic Aperture Radar (Ps-Insar) Method In Sentinel 1a Between 2014-2017
Authors: Prasetyo Y , Firdaus H Sugiastu , Diyanah  
Published: August 2019

Abstract
Environmental changes resulting from the impact of land use and underwater changes that may occur is the land subsidence. The main idea of this study is to measure and analyse land subsidence in Bandung City by processing SENTINEL 1A satellite images using the PS-InSAR technique. PS-InSAR technique is an effective technique for measuring crustal deformation. We processed 7 pair imageries of SENTINEL 1A images (at level 1.0) acquired from September 2014 to 2017. For time series of interferogram analyse, we analysed 7 pairs possibility of PS-InSAR interferogram using SNAP open source program. To get better result, we computed the best baseline estimation to reduce fringes from baseline between master and slave data. The 1-arcsec (30 m) Shuttle Radar Topography Mission (SRTM) used to remove the topographic contribution as Digital Elevation Model (DEM) reference. Whereas for observing land subsidence using the PS-InSAR method. Overlapping method was used to correlate the effect of changes in land subsidence into land use region in Semarang City. Observations in the deep aquifer used correlation seen from the increase and decrease of the graph of the inner MAT aquifer and the average increase and decrease in ground surface of PS-InSAR. The result of PS- InSAR processing showed the average value of the decrease in the face of the soil with a range of -4.4 ± 3.4 cm up. +2,2 ± 3,4 cm and from result of processing got information of the biggest decrease in land surface is in Sub District Semarang Utara, Semarang Barat, Pedurungan and Genuk. To verify the result of PS-InSAR results, we used secondary data GPS observation[6] in 2013 and 2016 with a 3 observation benchmark points.
Estimation of Ecological Footprint for Sidoarjo Regency and its Implication towards Spatial Development
Authors: Santoso E B , Aulia B U , Aninditya D N 
Published: August 2019

Abstract
Sidoarjo Regency is one of buffer zones of Surabaya City in which directly adjacent with Surabaya at the south part of it. The highly economic growth of Surabaya has many direct y for Sidoarjo regency, mainly due to population growth and urban sprawl that bring negative impacts on sustainability. Decreasing of the productivity because of conversion of agricultural land into settlements and air pollution are major issues that occur in Sidoarjo regency. Regional development should be in line by efforts to conserve the environment so that take environmental carrying capacity into account is a must. Ecological footprint is one of approaches in the calculation of sustainability by identifying the components of consumption and emissions resulting from human activities for subsequent comparison with the availability of natural resources (biocapacity). Biocapacity consists of components of land productivity, ie agricultural land, forestry land, terrestrial fisheries, and constructed land that is processed using satellite imagery as resource. The difference between the ecological footprint calculation and the biocapacity indicates the sustainability of the Sidoarjo Regency. In conclusion, Sidoarjo regency has experienced ecological deficit level 1 with biocapacity value of 25,665 and ecological footprint value of 111,962. It is resulted that natural resources in Sidoarjo Regency are only able to accommodate approximately one-fourth of total consumption in Sidoarjo regency. This prediction could be used as consideration on spatial planning as well as spatial policies in terms of sustainability.
Investigation of Crude Palm Oil as an Alternative Processing Oils in Natural Rubber : Effect of the Unsaturated Fatty Acid
Authors: Abbas Khaliesah , Ong S.K. 
Published: August 2019

AbstractPetroleum based processing oils is the hydrocarbon oils derived from petroleum refining process and commonly used as extender or processing oils to improve the rubber processability. Hydrocarbon oils can be classified as paraffins, aromatics, naphthene and olefins oil based on their molecular structure. The studies on replacement of hydrocarbon oils with natural processing oils had been studied by vast number of researchers due to finite resources and the toxicity of the hydrocarbon oils which enhanced awareness in using natural based oils. These natural processing oils are from vegetable or animal. The vegetable oils contain mainly unsaturated fatty acids. Studies showed that the unsaturated fatty acids affect the cure characteristics and the mechanical properties of the filled vulcanizates as these fatty acids took part during the vulcanization and promote the filler-rubber interaction. In this study, natural rubber (NR) of grade Standard Malaysian Rubber 20 (SMR 20) with the loadings of paraffin oil (PO) and crude palm oil (CPO) between 1 to 5 phr was investigated. Within the loadings of PO and CPO studied, the unsaturated fatty acid in CPOs were reported to results in plasticizing effect which results in lower minimum and maximum torques. Though that the unsaturated fatty acid which took part during the vulcanization prolonged the cure time, it resulted in higher CB-SMR 20 interaction. The tensile properties, tear strength, hardness and abrasion resistance of the CPO recipes were affected by combination of plasticizing effect and better CB-SMR 20 interaction.
Generation Method of Air Defense Missile Weapon Interception Scheme
Authors: Guibao Song , Jiaming Song , Runa Jia , Zijie Jiang , Zhan Liu 
Published: August 2019

Abstract
The research on the generation method of the anti-aircraft missile interception scheme before the war can lay the foundation for the rational allocation of the next air defense missile. In this paper, the clustering algorithm based on fuzzy C-means is used to cluster anti-ship missiles. Based on this, the number of anti-aircraft missiles launched during the first interception is determined. Then, by analyzing the depth of the launching area and the interception process, the number of interception of each layer of air defense missiles in the air defense interception operation is calculated. Finally, the anti-aircraft interception scheme that can achieve the expected damage probability of anti-ship missiles can be solved. The case is verified by the case that the calculation efficiency is relatively high and has certain application value.
A comparison and assessment of computational method for identifying recombination hotspots inSaccharomyces cerevisiae
Authors: Yang Hui , Yang Wuritu , Dao Fu-Ying , Lv Hao , Ding Hui , Chen Wei , Lin Hao 
Published: August 2019

AbstractMeiotic recombination is one of the most important driving forces of biological evolution, which is initiated by double-strand DNA breaks. Recombination has important roles in genome diversity and evolution. This review firstly provides a comprehensive survey of the 15 computational methods developed for identifying recombination hotspots in Saccharomyces cerevisiae. These computational methods were discussed and compared in terms of underlying algorithms, extracted features, predictive capability and practical utility. Subsequently, a more objective benchmark data set was constructed to develop a new predictor iRSpot-Pse6NC2.0 (http://lin-group.cn/server/iRSpot-Pse6NC2.0). To further demonstrate the generalization ability of these methods, we compared iRSpot-Pse6NC2.0 with existing methods on the chromosome XVI of S. cerevisiae. The results of the independent data set test demonstrated that the new predictor is superior to existing tools in the identification of recombination hotspots. The iRSpot-Pse6NC2.0 will become an important tool for identifying recombination hotspot.
ChaperISM: improved chaperone binding prediction using position-independent scoring matrices
Authors: Gutierres M B B , Bonorino C B C , Rigo M M 
Published: August 2019

Abstract

Motivation
Understanding the mechanisms of client protein interaction with Hsp70 chaperones is essential to analyze the complex dynamics in the context of normal or dysregulated metabolism. Because Hsp70 can bind millions of proteins, including key molecules involved in processes of stemness, tumorigenesis and survival, in silico prediction of Hsp70 interactions has great value in validating possible new clients. Currently, two algorithms are available to predict binding to DnaK—the bacterial Hsp70—but both are based on amino acid sequence and energy calculations of qualitative information—binders and non-binders.

Results
We introduce a new algorithm to identify Hsp70 binding sequences in proteins—ChaperISM—a position-independent scoring matrix trained on either qualitative or quantitative chemiluminescence data previously published, which were obtained from the interaction between DnaK and different ligands. Both versions of ChaperISM, qualitative or quantitative, resulted in an improved performance in comparison to other state-of-the-art chaperone binding predictors.

Availability and implementation
ChaperISM is implemented in Python version 3. The source code of ChaperISM is freely available for download at https://github.com/BioinfLab/ChaperISM.

Supplementary information
Supplementary data are available at Bioinformatics online.
Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach
Authors: Wu Yufeng 
Published: August 2019

Abstract

Motivation
Cells in an organism share a common evolutionary history, called cell lineage tree. Cell lineage tree can be inferred from single cell genotypes at genomic variation sites. Cell lineage tree inference from noisy single cell data is a challenging computational problem. Most existing methods for cell lineage tree inference assume uniform uncertainty in genotypes. A key missing aspect is that real single cell data usually has non-uniform uncertainty in individual genotypes. Moreover, existing methods are often sampling based and can be very slow for large data.

Results
In this article, we propose a new method called ScisTree, which infers cell lineage tree and calls genotypes from noisy single cell genotype data. Different from most existing approaches, ScisTree works with genotype probabilities of individual genotypes (which can be computed by existing single cell genotype callers). ScisTree assumes the infinite sites model. Given uncertain genotypes with individualized probabilities, ScisTree implements a fast heuristic for inferring cell lineage tree and calling the genotypes that allow the so-called perfect phylogeny and maximize the likelihood of the genotypes. Through simulation, we show that ScisTree performs well on the accuracy of inferred trees, and is much more efficient than existing methods. The efficiency of ScisTree enables new applications including imputation of the so-called doublets.

Availability and implementation
The program ScisTree is available for download at: https://github.com/yufengwudcs/ScisTree.

Supplementary information
Supplementary data are available at Bioinformatics online.
MALDI-TOF MS protein fingerprinting of mixed samples
Authors: Reeve Michael A , Bachmann Denise 
Published: August 2019

Abstract
Analytical techniques currently available for the characterization of mixtures of microorganisms are generally based on next-generation sequencing. Motivated to develop practical and less-expensive methods for characterizing such mixtures, we propose, as an alternative or complement, the use of matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS), which is capable of high-resolution discrimination between species and even between biotypes within species. Potential approaches employing this technique for such characterization are discussed along with impediments to their successful employment. As a consequence, our rationale has been to capitalize on the powerful algorithms currently available for spectral comparison. Following this rationale, the first priority is to ensure the generation of MALDI-TOF MS spectra from mixtures of microorganisms that contain manageable peak complexities and that can be handled by the existing spectral comparison algorithms, preferably with the option to archive and re-run sample preparations and to pipette replicates of these onto MALDI-TOF MS sample plates. The second priority is to ensure that database entry is comparably facile to sample preparation so that large databases of known microorganism mixture MALDI-TOF MS spectra could be readily prepared for comparison with the spectra of unknown mixtures. In this article, we address the above priorities and generate illustrative MALDI-TOF MS spectra to demonstrate the utility of this approach. In addition, we investigate methods aimed at chemically modulating the peak complexity of the obtained MALDI-TOF MS spectra.
Citywide Transmission of Multidrug-resistant Tuberculosis Under China’s Rapid Urbanization: A Retrospective Population-based Genomic Spatial Epidemiological Study
Authors: Jiang Qi , Liu Qingyun , Ji Lecai , Li Jinli , Zeng Yaling , Meng Liangguang , Luo Geyang , Yang Chongguang , Takiff Howard E , Yang Zheng , Tan Weiguo , Yu Weiye , Gao Qian 
Published: August 2019

Abstract

Background
Population movement could extend multidrug-resistant tuberculosis (MDR-TB) transmission and complicate its global prevalence. We sought to identify the high-risk populations and geographic sites of MDR-TB transmission in Shenzhen, the most common destination for internal migrants in China.

Methods
We performed a population-based, retrospective study in patients diagnosed with MDR-TB in Shenzhen during 2013–2017. By defining genomic clusters with a threshold of 12–single-nucleotide polymorphism distance based on whole-genome sequencing of their clinical strains, the clustering rate was calculated to evaluate the level of recent transmission. Risk factors were identified by multivariable logistic regression. To further delineate the epidemiological links, we invited the genomic-clustered patients to an in-depth social network investigation.

Results
In total, 105 (25.2%) of the 417 enrolled patients with MDR-TB were grouped into 40 genome clusters, suggesting recent transmission of MDR strains. The adjusted risk for student to have a clustered strain was 4.05 (95% confidence interval, 1.06–17.0) times greater than other patients. The majority (70%, 28/40) of the genomic clusters involved patients who lived in different districts, with residences separated by an average of 8.76 kilometers. Other than household members, confirmed epidemiological links were also identified among classmates and workplace colleagues.

Conclusions
These findings demonstrate that local transmission of MDR-TB is a serious problem in Shenzhen. While most transmission occurred between people who lived distant from each other, there was clear evidence that transmission occurred in schools and workplaces, which should be included as targeted sites for active case finding.
The average residential distance between genomic-clustered cases was more than 8 kilometers, while schools and workplaces, identified as sites of transmission in this study, deserve increased vigilance for targeted case finding of multidrug-resistant tuberculosis.