bluuebunny/crossref_metadata_2025_split huggingface dataset:
Addressing Disaster Risk Reduction by Analyzing Sea Level Rise in the Aceh Waters
Authors: Setiawan Ichsan , Ilhamsyah Yopi , Miswar Edy , Irham Muhammad 
Published: July 2019

Abstract
Eustatic changes produce changing on global sea levels, such as changes in water volume in the oceans world. This change indirectly affects the balance of water and land and it is very harmful for the archipelago countries which one of them is Indonesia. The two most important effects are the temperature and mass of water stored on land and sea as fresh water in rivers, lakes, glaciers, polar ice caps, and sea ice. Therefore the purpose of this study is to see how far the sea level changes in Aceh waters in relation to disaster risk reduction. To achieve this goal, the method used is to analyze the record of sea level data in the waters of Aceh during the last 25 years. The analysis of sea surface change data in Aceh shows that there has been a linear increase in sea level since 2008 in parallel with the rise in temperature so that it is expected to lose ground in some areas of the Aceh coast.
Numerical Experiments on Tsunami Wave Forces on Open Structures Using Dam-Break Method
Authors: Syamsidik  , Luthfi Mumtaz , Fauzi Amir , Fatimah Eldina 
Published: July 2019

Abstract
Open wall structures, such as those found in mosques, sustained large forces generated by a tsunami as in the case of the 2004 Indian Ocean tsunami. Although the surrounding buildings were flattened, there were a number of mosques in the tsunami affected area could still stand in the middle of the area. These motivated this study to look into more details the hydrodynamic forces generated around the open structures. This research was aimed at investigating the tsunami wave forces on open structures and at knowing relation between the tsunami waves velocity and the pressures on the pillars of the open structures. DualSPHysic was used to simulate the tsunami wave forces on the structures. The DualSPHysic is a smoothed particle hydrodynamic model with mesh-less method. We simulated 12 numerical simulations by constructing a-130 m wave flume equipped with dam-break at one end to generate the tsunami-like flows. A sloping bed was placed in front of an open wall structure. Four pillars were set to imitate a simplified model of open wall structure. Numerical observation points were placed at offshore part of the model, in front of the pillars (lee-side) and at the back of the pillars (wake-side). Simulations were performed for about 6 seconds started from releasing the dam gate and before the flow being reflected by the other end of the flume. This study proved that the impacts of the tsunami-like forces are more significant of the front row of the pillars. Meanwhile, tsunami wave forces at the back row of the pillars group are inconclusive to the wave velocity and wave heights.
Chlorophyll-a, and Sea Surface Temperature (SST) as proxies for Climate Changes: Case Study in Batu Ampar waters, Riau Islands
Authors: Antoni S , Bantan R A , Al-Dubai T A , Lubis M Z , Anurogo W , Silaban R D 
Published: July 2019

Abstract
The condition of Indonesian oceanography is largely determined by the development of the Monsoon Wind and the Indonesian Cross Flow (ARLINDO). The development of marine remote sensing technology that is so fast, able to make it easier to map the condition of waters in Indonesia in an actual way easily and cheaply. This can make it easier to obtain information about climate change approaches to the physical oceanography conditions in Indonesian waters. The purpose of this research is to study the changes of the physical oceanography parameters resulting from climate changes. Based on the results of the research that for the highest Sea Surface Temperature (SST) exist in 2013 (above 30,75 °C). It has increased from the previous year i.e. in 2012 with an increase of SST value of 30 o C. In 2013 SST is spread high on the Batu Ampar Permit - Harbor Bay ferry port. Analyzing the value of chlorophyll-a, sea surface temperature, and sea level to see global climate change in the waters of Batu Ampar. The analysis shows the highest sea level with an elevation of 3.1 meters, with sea surface temperature in the range of 29,5 °C - 29,75 °C, at the time of recording 00:05-02:55 (August 1, 2017 - September 1, 2017). The results of the analysis obtained from the oceanographic conditions in the waters of Batu Ampar did not experience a fluctuating change in global climate change in the waters. The annual SST interval spacing interval of 0.5-0.75 °C and the changing phase relationship could have an impact on subsequent climate change and sea level rise to be concrete evidence. Reduced levels of chlorophyll-a each year will have an impact on the heat of the sea level, thus rising sea levels and indicating a climate with hot temperatures (ice at the poles melt).
Geohazard Identification Using 2-D Resistivity Imaging For Seulawah Agam Volcano, Indonesia
Authors: Syukri Muhammad , Saad Rosli , Marwan  , Tri Anda Sabrian , Safitri R. , Fadhli Zul 
Published: July 2019

Abstract
Common parameter used for delineating geothermal system is resistivity. Hydrothermal alteration of primary minerals depends on temperature distribution and forms various clay minerals with conductivity properties. Clay minerals formed at high temperatures are more resistant than lower temperature. Most geothermal systems within active volcanic regions show low resistivity (1-5 Ohm.m) surrounding an inner core of higher resistivity. 2-D resistivity study conducted at Seulawah Agam active volcano and its vicinity (Aceh) with geothermal sources (Herzt, Ie Jue and Ie Seu’um) flowing from south-east to north-west. Two lines, L1 and L2 were conducted crossing the suspected geothermal flow using ABEM SAS4000 system with 10 m minimum electrode spacing and Pole-Dipole array. Resistivity results indicated two main zones; (i) top layer, <100 m depth with resistivity value of >60 Ohm.m and (ii) cap-rock, 30-100 m depth with resistivity value of 6-50 Ohm.m. Few fractures and low resistivity regions (<5 Ohm.m) were identified in the caprock. Hot water and hot mud have low resistivity value; hence the low resistivity regions were interpreted as geothermal flow and it is convincingly suspected to be a geohazard zone. New extension of Seulawah Agam geothermal flow was identified by 2-D resistivity method.
Tsunami and Earthquake Symbols and Signs on the Children’s Semiotic Understanding
Authors: Moriyanti  , Ismail N M , Yanti F , Rahma E A , Setyana R 
Published: July 2019

Abstract
This qualitative research aims at describing the coastal children’s knowledge and perspective about the Tsunami and earthquake’s symbols and signs. The use and purpose of the signs on the warning board is very important for children on the coastal area as an understanding of disaster preparedness. Consequently, the researchers chose 43 respondents with 8-13 years old who live at the coast of Kampung Jawa, Banda Aceh to respond questionnaire and interview. The questionnaire set contained the verbal and non-verbal symbols and signs about tsunami and earthquake which was formulated in the form open-ended questions. It was found that only 12 children who could answer 80% of the questions correctly from the questionnaire. This implies that their understanding and background knowledge about the tsunami and earthquake’s symbols and signs are very low level even though the symbols and signs are put on their enviroment. Moreover, during interview process, children had wrong interpretation about the signs and symbols and did not know the function because they never get information about the symbols, the way to evacuate and preparation before the disaster happened from their school and enviroment. Consequently, it is suggested that stakeholder should conduct practices for disaster education that can improve their disaster awareness.
Disaster Risk Communication Issues and Challenges: Lessons Learned From the Disaster Management Agency of Banda Aceh City
Authors: Adella Shylvana , Fauzan Nur Muhammad , Nisa Nazriatun , Tirtana Putra Arief , Rizki Ramadhana Fira , Maiyani Fitri , Munadi Khairul , Rahman Alfi 
Published: July 2019

Abstract
The Badan Penanggulan Bencana Daerah (BPBD or Disaster Management Agency) of Banda Aceh City was established through Banda Aceh bylaw (or Qanun) No. 3 of 2011 following the significant 2004 Indian Ocean tsunami. Meanwhile, as Banda Aceh’s population has grown, an increasing number of people have moved to and decided to stay in areas once affected by the tsunami. Given this background, disaster risk communication is indispensable. It is important for the BPBD of Banda Aceh City to disseminate risk messages throughout the community. Disaster risk communication is informed by the communication targets set by the BPBD of Banda Aceh City. The purpose of this study is to explore the issues and challenges in implementing disaster risk communication in the Banda Aceh community and across various sectors. A qualitative research design is applied to gain an insight into the disaster risk communication of the BPBD of Banda Aceh City. Data were collected through interviews and document analysis. The results of this study show that the BPBD of Banda Aceh City has carried out disaster risk communication in accordance with its primary mandated tasks and functions. However, there have been several challenges and issues, namely limited funding and a lack of technology and disaster knowledge. Consequently, the BPBD of Banda Aceh City has been unable to efficiently realize its disaster risk communication goals.
WEBGIS Application for Planning the Tsunami Evacuation Route
Authors: Nizamuddin  , Aldika W A , Ardiansyah  , Hizir  , Muzailin  
Published: July 2019

Abstract
The tsunami that occurred on December 26, 2004 has resulted in massive casualties in Banda Aceh City. As one of the steps to avoid the huge casualty if the tsunami repeats itself, a number of Escape Buildings have been built in the city. In spite of the availability of the Tsunami Escape Buildings, the number of casualties can be reduced only if everyone in the tsunami-prone areas knows the nearest Escape Building from his or her position and the best route to reach the building. The purpose of this research was to build a GIS web application that can help determine the nearest Escape Building from a user-selected location and the best route to reach it. This application utilizes a web service that implements the Dijkstra algorithm to find the closest facility and the best route to the facility. The web GIS application was built using the open source API. The web GIS application developed in this research helps users find the nearest Escape Building and the best route to reach it without the need of any GIS software. The application is easy to use because it provides a user-friendly interface via a web browser.
Post-Disaster Recovery and A New Economic Growth Path: A Comparative Study of Three Provinces in Indonesia
Authors: Nazamuddin B S , Nugroho Agus 
Published: July 2019

Abstract
The purpose of this study is to examine whether there exists a new regional output growth path in post-disaster situation in three provinces of Indonesia affected by relatively large-scale natural disasters, i.e. Aceh, West Sumatera (Sumbar), and Yogyakarta. By using real Gross Regional Domestic Product time series for the period 2001-2017 obtained from the Central Agency of Statistics, a comparative analysis was made from the differences in the effects across those provinces between pre-disaster and post-disaster periods. This study used a simple model with deterministic trend, post-disaster recovery dummy and autoregressive component to estimate changes in the coefficients of trends for each province’s output growth path. The results show that there is no significant difference in the overall effects of trend changes across provinces, while the effects of trend changes between pre-and post-disaster periods vary across provinces and in general post-disaster interventions do not move upward the long-term effects on regional output trends.
Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events
Authors: Huang Xiao-Chen , German Dmitry A , Koch Marcus A 
Published: July 2019

Abstract

Background and Aims
Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution.

Methods
We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness.

Key Results
Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes.

Conclusions
The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant ‘pump’ for continuous and high species diversification.
Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network
Authors: Zeng Wanwen , Wang Yong , Jiang Rui 
Published: July 2019

Abstract

Motivation
Interactions among cis-regulatory elements such as enhancers and promoters are main driving forces shaping context-specific chromatin structure and gene expression. Although there have been computational methods for predicting gene expression from genomic and epigenomic information, most of them neglect long-range enhancer–promoter interactions, due to the difficulty in precisely linking regulatory enhancers to target genes. Recently, HiChIP, a novel high-throughput experimental approach, has generated comprehensive data on high-resolution interactions between promoters and distal enhancers. Moreover, plenty of studies suggest that deep learning achieves state-of-the-art performance in epigenomic signal prediction, and thus promoting the understanding of regulatory elements. In consideration of these two factors, we integrate proximal promoter sequences and HiChIP distal enhancer–promoter interactions to accurately predict gene expression.

Results
We propose DeepExpression, a densely connected convolutional neural network, to predict gene expression using both promoter sequences and enhancer–promoter interactions. We demonstrate that our model consistently outperforms baseline methods, not only in the classification of binary gene expression status but also in regression of continuous gene expression levels, in both cross-validation experiments and cross-cell line predictions. We show that the sequential promoter information is more informative than the experimental enhancer information; meanwhile, the enhancer–promoter interactions within ±100 kbp around the TSS of a gene are most beneficial. We finally visualize motifs in both promoter and enhancer regions and show the match of identified sequence signatures with known motifs. We expect to see a wide spectrum of applications using HiChIP data in deciphering the mechanism of gene regulation.

Availability and implementation
DeepExpression is freely available at https://github.com/wanwenzeng/DeepExpression.

Supplementary information
Supplementary data are available at Bioinformatics online.
QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable
Authors: Berselli Michele , Lavezzo Enrico , Toppo Stefano 
Published: July 2019

Abstract

Motivation
G-quadruplexes (G4s) are non-canonical nucleic acid conformations that are widespread in all kingdoms of life and are emerging as important regulators both in RNA and DNA. Recently, two new higher-order architectures have been reported: adjacent interacting G4s and G4s with stable long loops forming stem-loop structures. As there are no specialized tools to identify these conformations, we developed QPARSE.

Results
QPARSE can exhaustively search for degenerate potential quadruplex-forming sequences (PQSs) containing bulges and/or mismatches at genomic level, as well as either multimeric or long-looped PQS (MPQS and LLPQS, respectively). While its assessment versus known reference datasets is comparable with the state-of-the-art, what is more interesting is its performance in the identification of MPQS and LLPQS that present algorithms are not designed to search for. We report a comprehensive analysis of MPQS in human gene promoters and the analysis of LLPQS on three experimentally validated case studies from HIV-1, BCL2 and hTERT.

Availability and implementation
QPARSE is freely accessible on the web at http://www.medcomp.medicina.unipd.it/qparse/index or downloadable from github as a python 2.7 program https://github.com/B3rse/qparse

Supplementary information
Supplementary data are available at Bioinformatics online.
Extended studies of interspecific relationships in Daucus (Apiaceae) using DNA sequences from ten nuclear orthologues
Authors: Martínez-Flores Fernando , Crespo Manuel B , Geoffriau Emmanuel , Allender Charlotte , Ruess Holly , Arbizu Carlos I , Simon Philipp , Spooner David M 
Published: July 2019

AbstractDaucus has traditionally been estimated to comprise 21–25 species, but a recent study expanded the genus to c. 40 species. The present study uses ten nuclear orthologues to examine 125 accessions, including 40 collections of 11 species (D. annuus, D. arcanus, D. decipiens, D. durieua, D. edulis, D. gracilis, D. minusculus, D. montanus, D. pumilus, D. setifolius and D. tenuissimus) newly examined with nuclear orthologues. As in previous nuclear orthologue studies, Daucus resolves into two well-defined clades, and groups different accessions of species together. Maximum likelihood and maximum parsimony analyses provide concordant results, but SVD quartets reveals many areas of disagreement of species within these two major clades. With maximum likelihood and maximum parsimony analyses Daucus montanus (hexaploid) is resolved as an allopolyploid between D. pusillus (diploid) and D. glochidiatus (tetraploid), whereas with SVD quartets it is resolved as an allopolyploid between D. glochidiatus and an unknown Daucus sp. We propose the new combination Daucus junceus (Durieua juncea) for a neglected species endemic to the south-western Iberian Peninsula often referred to as D. setifolius, and we place D. arcanus in synonymy with D. pusillus. Three lectotypes are also designated.
Study on the performance of titanium film as a diffusion barrier layer for CIGS solar-cell application on stainless-steel substrates
Authors: Jiang Xinxian , Li Boyan , Song Binbin , Zhang Shuwang , Qiu Yang , Zhao Ying , Zhong Dalong 
Published: July 2019

AbstractIn this paper, pure titanium (Ti) thin films deposited by radio frequency sputtering were used as a diffusion barrier layer in a flexible copper indium gallium selenium (CIGS) solar cell on a stainless-steel foil and characterized by X-ray diffraction, scanning electron microscopy and second ion mass spectroscopy measurement methods. The influences of the magnetron sputtering pressure on the surface morphology and preferred crystal orientation of Ti films are discussed. It was found that the Ti film showed a (001) preferred orientation and smooth surface topography at lower deposition pressure, while (002) preferred orientation and relatively rough surface topography at higher deposition pressure. In addition, Ti films made with different process pressures were deposited as the barriers and the second ion mass spectroscopy results indicated that a Ti film with the thickness of 200 nm was able to effectively block Fe and Cr diffusion from the stainless-steel foil into the CIGS absorber across the molybdenum back contact. The Ti barrier significantly improved the conversion efficiency of the CIGS solar cell.
Separation of Unprecedented Degradants of Domperidone by Ultra-Performance Convergence Chromatography and Their Structure Elucidation
Authors: Mutha V V S R N Anji Karun , Chandra Chakravarthy , Vijayabhaskar B , Achanta Prabhakar S , Narkedimilli Jagadeesh , Kaliyaperumal Muralidharan , Korupolu Raghu Babu , Gajbhiye Susheela Bai , Rumalla Chidananda Swamy 
Published: July 2019

Abstract
Domperidone, a gastroprokinetic agent, is a common drug to treat emesis. It was subjected to acid, base-mediated hydrolysis, peroxide-mediated oxidation, photolysis and thermal degradation according to ICH guidelines to observe stability of the selected drug under the stress conditions. Although the drug is resistant to base hydrolysis, photolysis and thermal stressors, two degradants (DP-ISO1 and DP-ISO2) were formed in acid mediated hydrolysis. Oxidation with hydrogen peroxide also resulted in one product (DP-OX). All three degradants were isolated from the crude reaction mixture by preparative high-performance liquid chromatography and supercritical fluid chromatography. Structures of isolated compounds were unambiguously characterized as 5-chloro-1-(1-(3-(6-chloro-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)propyl)piperidin-4-yl)-1,3-dihydro-2H-benzo[d]imidazol-2-one (DP-ISO1), 5-chloro-1-(3-(4-(5-chloro-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)piperidin-1-yl)propyl)-1,3-dihydro-2H-benzo[d]imidazol-2-one (DP-ISO2), 4-(5-chloro-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)-1-(3-(2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)propyl)piperidine 1-oxide (DP-OX) by analysis of mass spectrometry, 1D and 2D nuclear magnetic resonance spectra. To the best of our knowledge, DP-ISO1 and DP-ISO2 are new and DP-OX was previously reported as domperidone impurity.