bluuebunny/crossref_metadata_2025 huggingface dataset:
Staying Afloat: Operating Tourism in Disaster-Prone Areas of Mesilou, Sabah
Authors: Kamarudin K H , Wahid S N A , Chong N O
Published: January 2020

Multi-hazards and disasters affect our lives greatly and therefore it become everyone’s business. Every time disaster hit a community, it left substantial damages to physical and nonphysical components (particularly economic and social aspects) that shaped our livelihood. From the community-based rural tourism (CBRT) point of view, disaster occurrences often led to significant decrease to destination image and reputation, increase fear of safety, damaging infrastructure and agriculture land. These led to the declining of tourist arrivals which affect income generation and revenue from tourism to the community. Failure to acknowledge these direct and indirect effects might weaken the tourism community’s capacity in coping with future disasters. Based on previous studies on CBRT in disaster-prone areas, researchers have uncovered unique cases whereby some rural communities that operates tourism as a vital income are able to raise above adversity and become resilient. In this light, a tourism community in Mesilou Village in Sabah, Malaysia is selected as a case study. This community was badly affected by 6.0-magnitude earthquake that hit Kota Belud in June 2015. At the time, a study of the post-earthquake has been conducted by a group of researchers from UTM in October 2015 and discovered that Mesilou had about 20 homestay operators. For nearly six months after the earthquake, the majority of CBRT operators were affected with high booking cancellation, damages of infrastructure (main road, bridges), disruption of water and electricity supplies and local transportation which hindered tourists from coming to their village. In October 2018, an impact study had been conducted by the same researchers from UTM and found that CBRT in Mesilou not only recovered from the disaster, but remarkably has been booming since then. This is evident from the survey which indicated a growing number of homestays from 20 full time operators (until 2015) to 40 homestays by October 2018. Two general conclusions can be made from the result of data analysis; (1) disaster did not deter the tourists from visiting Mesilou after the earthquake; (2) the CBRT operators pose strong social, economic and environmental capitals to “bounce back” from adversity and rebuilt the community prior to the disasters. This paper will discuss the lessons learned from CBRT operators in Mesilou regarding business recovery and resiliency prior to disaster.
The Importance of Cultural Heritage Conservation in Society: A Review and Prospect for Future Cities, with Bandar Lampung as Cased Study
Authors: Nugroho A C , Hardilla D
Published: January 2020

This paper introduces the special feature of cultural heritage documentation; conservation and society entitled “The Importance of Cultural Heritage Conservation in Society”. The Netherlands Indies Government developed a cultural heritage in 1778 after establishment of Bataviaasch Genootschapvan Kunsten en Wetenschappen and De Outdheidkundige Diest at 1913 – 1928 in Lampung Region. Cultural heritage draw from a theory based in living system, developing strategies both for adopting impact and mitigation those threats by sustaining building and natural environment. Cities like Bandar Lampung are high complex living organism and are subjects to continue transformation produced by the requirement that vary from multi-ethnic of community, the political, economical, cultural and above all changing climate factored. All of factors are able to maintain normative developmental task that occur at various stage of live in the future. However, the preliminary problem of developing future cities in Bandar Lampung is related to existing social condition of modern society, which threatens the existence of local social community. We must prevent the loss of cultural heritage, through conservation and coordination of counterterrorism. To overcome this shortage, we need understanding factors affecting issue, including neighbourhood characteristic such as socio economic factor, residential pattern, social value, and stressful life events and insufficient resources. This paper investigate paradigm the role of cultural heritage conservation in society and become an important approach in develop innovation in both architecture and urban design. With present paper we aim to increase the awareness of learning cultural diversity form cultural heritage conservation and re interpreting them in establishment of urban system strategies for future cities.
The Economic Sustainability Model of Community Based Tourism in Batik Kampong Semarang
Authors: Dewi S P , Ristianti N S , Kurniati R
Published: January 2020

The dualism of the existence of kampong heritage and urban activities led to increasingly eroded villages in developments in the downtown. This was marked by the increasingly disappearing of historic buildings in the old town's kampong and changed into functions of modern buildings and activities. In line with the existence of Batik Kampong Semarang. At present the government has tried to develop these kampongs into tourist destinations. But the economic sustainability side has not been significantly achieved. Therefore, the research question is "What is the economic sustainability model of community based tourism in Batik Kampong Semarang?". This research has goal to develop a economic sustainability model of community based tourism in Batik Kampong Semarang. The method is qualitative. The analysis stage is to identify the potential of Batik Kampong as a tourist destination, the process of developing activities and space, identify CBT and SWOT in Batik Kampong. From this concept, a sustainable model for the preservation of historic tourism villages will be formulated economically in a sustainable manner. The output of this research is the economic sustainability model of community-based tourism in Batik Kampong Semarang in the dualism context of modern versus cultural heritage transformation.
Revealing Malay Royal Town Identity: Seri Menanti, Negeri Sembilan
Authors: Shukri S M , Wahab M H , Amat R C
Published: January 2020

Malay royal town in Malaysia have been establish dating from the 16th century with a unique and significant identity that creates the image of these towns. Malay Royal town identity constitutes the physical environment, human activities, cultural and meaning that creates social phenomenon and place genius loci. Nevertheless, identity in Malaysia's royal towns were facing alteration which resulted to places are becoming less meaningful, placelessness and lose their identity. A case study was carried out in Sri Menanti, Negeri Sembilan, which is one of the royal towns in Malaysia. Thus, this paper discusses the components that characterised the Malay royal town identity of Seri Menanti, Negeri Sembilan. The study methodology involves a historical map overlay, site observations and also the use of semi-structured interviews. The paper concludes that the vitality of these components contributed to identity of the Malay Royal towns in Seri Menanti, Negeri Sembilan.
Designating Urban Rivers as National Heritage: A case study of Sungai Kelang and Sungai Gombak, Kuala Lumpur, Malaysia
Authors: Nayan N M , Jones D S , Bahaluddin A , Ghani I , Rahman N A
Published: January 2020

Rivers were places where civilizations arose and aided the foundations of their economic fortunes. However, most urban rivers have today been abused and undervalued, and thus little conserved or re-opened up to celebrate these waterways. Malaysia is one of a number of countries whom have witnessed the former. In 2011, the River of Life (RoL) Entry Points Projects (EPP) was introduced to address this issue aimed towards revitalizing the Klang River into a heritage riverscape and a reinvigorated linear commercial centre for Greater Kuala Lumpur and the Klang Valley (GKL/KV). This paper discusses the heritage fabric at the confluence of the Klang and Gombak Rivers in portraying and narrating the importance of these rivers to the cultural identity of this precinct. Recognising these qualities will result in highlighting the cultural heritage values that need to be considered in recognizing this riverscape as a National Heritage asset. This paper also explored the historical and potential elements of the urban river in Malaysia through the mix method approach (Convergent Parallel). Research data was obtained from Malaysian authorities, using a top-down approach, through interview and visitor participant questionnaires to obtain convergence and divergence perceptions and patterns between these two sources of data. Data obtained sought to elucidate the cultural identity of this urban riverscape and its fabric from the perspective of both official participants perceived responsibilities and the interpretation of the riverscape from local respondent perspectives. The results of data from both participant types is crucial in offering new viewpoints towards a new to better adapt the government’s visions and visitor expectation about the future of this riverscape. This information could better enhance the tourism aspects of this area that has been highlighted as ‘National Key Economic Area (NKEA) 06: Tourism’, and to foster the integration of cultural heritage in an urban setting.
The Centrum-Bandung : Adaptive Reuse at Heritage Building as Sustainable Architecture
Authors: Permata D D , Kuswandy A S , Riza A I , Sakti P F , Diana T I
Published: January 2020

Historic buildings which are the remains of the Dutch Colonial period from the glorious past era still exist in some cities in Indonesia. These buildings can be easily recognized from their typical architectural style in which a mixture of European architecture adjusted to the country’s tropical climate known as Indische Architecture. The style is obvious in parts of the cities in which the Dutch carried out their activities such as districts for offices, trading centres, housing complexes as well as recreational areas. One colonial building in Bandung infamously implementing the style is The Centrum. The building which originally functioned as a recreational vicinity was built in 1920s. Designed by C.P. Wolff Schoemaker, it served as swimming pool or bathhouse where the people of Dutch residing in or visiting the city spent their leisure time. The Centrum, of which facilities the Indonesian in the colonial period were prohibited to even used, has become a cultural heritage landmark located in historic military base. A cultural heritage should be conserved to preserve the valuable generation-to-generation history, and one of the favoured ways to do it is adaptive re-use, or reusing of existing building as part of the concept of sustainable architecture. This paper discusses adaptive re-use implemented in The Centrum building, which has undergone the process of function shifting from swimming pool to restaurant and wedding venue, and lastly to selfie spot. Using qualitative approach along with comparative descriptive method, the study applies the theory of adaptive re-use to investigate the changes in function of The Centrum from period to period. It is found that the function shifts of The Centrum from time to time is the result of situational adjustment to the change of its owner/user, architectural needs as well as current trends such as selfie tourism.
Is Tehran’s Public Spaces Disability Friendly?
Authors: Esfandfard E , Wahab M H , Amat R B C
Published: January 2020

Public space act like a living spaces of the cities where people gather to socialize, communicate with each other and where urban activities being carried out. It defined the character of the city and play important role to connect people to the city. Comfortable and accessible public spaces lead to vitality and livability to the city. Lack of the maintenance and attention to public spaces could reduce the comfort level and livability to the city. United Nations Convention emphasized that the people with disability have the same rights to access the public spaces, where World Health Organization declare that about 10% of world population are disabled. The eight years war between Iran and Iraq had increased disability rate among the citizens. Tehran as capital of Iran and the most populous city in Iran need to improve facilities and accessibility in order to support the need of the people with disability to live actively in the society. The purpose of this paper is to analyze the need of urban public space for people with disability in Tehran. Among the identified obstacles for people with disability in Tehran are related to lack of application of Universal Design (UD) elements on the urban spaces and public facilities. This study is based on applied theory and quantitative method for evaluating satisfaction of people with disability. This research focused on two type of disability group, visual impairment and wheelchair users. One of the city district in Tehran is chosen as a case study. The findings of this study obtain will be analyses to provide UD solutions in urban public spaces for them.
Identification of Urban Vitality at Bus Rapid Transit (BRT) Halte in Semarang City Centre
Authors: Medina I D , Dewi D I K , Rakhmatullah A R
Published: January 2020

The urban vitality theory is one of urban design theories from Jane Jacobs (1960) stated that a city where can live for 24 hours should be equipped with good built environment refers to pedestrians.. This research has been conducted in Semarang City Centre Area which is the center of Semarang City. Semarang City Centre is Pandama area consists of Jalan Pandanaran, Jalan Pemuda, and Jalan Gajah Mada. This area consists of the central government, trade and services, residential areas, and already has public transportation, one of them is Trans Semarang BRT. However, the interest of Trans Semarang BRT users has not yet dominated can be influenced by several factors such as environmental conditions that have not supported pedestrians, affecting individual behavior on foot. This study used a quantitative method approach by first calculating values of the indicators at all Bus Rapid Transit (BRT) Halte on Semarang City Centre and then used ranking method to perform comprehensive comparative analysis to identification urban vitality. The results from this study shows that the Hotel Santika Halte has the highest urban vitality level, followed by Balaikota halte has the second rank and Theresia Halte has the third rank of urban vitality.
Characteristic of pro delta environment on coal seam PAF and NAF, warukin formation, South Kalimantan
Authors: Agustin F , Barkah A , Sulastri A , Abdullah C I , Santoso A B , Adiputra R N
Published: January 2020

Coal seam of the Kusan Bawah block, Warukin Formation, Asam-Asam Basin, South Kalimantan has age middle Miosen to Late Miosen. The purpose of this study is to investigate the characteristic of the coal, PAF, and NAF, the depositional environment. The method used in this research is taking rock samples from core drilling and then testing the quality of rock geochemistry by using Net Acid Generating test. Rock geochemical analysis results are entered into modeling software to determine its distribution based on stratigraphic principle. Results of rock geochemical quality analysis based on SNI 6597- 2011 to Non-Acid Forming and Potential Acid Forming. The advantages of identification PAF or NAF value are about preventive activity to decrease acidic pollutant material in the environment. Potential Acid Forming material is above seam G and is between EL and seam D. The percentage of Potential Acid Forming material is 33.17% and NAF 66.83%. The depositional environment of the Kusan Bawah block is interpreted in pro delta and transgressive conditional.
Decreasing the ash coal and sulfur contents of sawahlunto subbituminous coal by using “minyak jelantah”
Authors: Prabowo H , Prengki I
Published: January 2020

Ash and sulfur caused low calorific value of coal and difficult to ignite the coal. The ash of the combustion product will pollute the environment. Through the conducted experiments the results of sulfur analysis on the coal tested were obtained. Five (5) experiments were conducted with different sample weights in the laboratory. In sample 1, the weight of the original coal sample of 0.2500 grams generated a level of sulfur content of 1.23%. In sample 2, the sample weight of 0.2500 grams of coal + 5ml of oil generated a level of sulfur content of 0.976%. In Sample 3, Coal + 10 ml of oil, where the sample weight was 0.2500 grams generated a level of sulfur content of 0.802%. In Sample 4, Coal + 15ml of oil, where sample weight was 0.2500 grams generated sulfur content of 0.609%. In Sample 5, Coal + 20 ml of “minyak jelantah” (used cooking oil), where the sample weight was 0.2500 grams generated a sulfur content of 0.428% and also a decrease in the value of the ash content. The coal was originally 62.80 and after the addition of refined” minyak jelatah” (used cooking oil) the lowest value generated was 35.78.
Riverine biota as environmental indicators of artisanal small-scale and large-scale gold mining impacts on riverine ecosystems in Brong Ahafo Region, Ghana
Authors: Macdonald KF , Lund M , vanEtten E
Published: January 2020

A study on two adjacent small ephemeral river systems in the upper Tano River Basin in Brong Ahafo, Ghana; one impacted by ASGM and the other by a modern large gold mining (LSM), showed that impacts of mining on river sediment and water quality and quantity were reflected in the macroinvertebrate and microbial communities. This study investigated the impacts of ASGM on the ecology of the Surow River and that of a large-scale mining (LSM, the Ahafo mine) on the Subri River between February 2013 and April 2014 Macroinvertebrate communities responded to the shift in river water and sediment qualities, whilst microbial communities tended to respond to water quality only. Bioaccumulation and biomagnification of mercury were evident in fishes in the river system impacted by ASGM, although mercury was barely detected in river water and sediment. The study confirmed that impact assessment of ASGM or the modern LSM on rivers should not be limited to the physical and chemical properties of water and sediment, but also include its riverine biota.
Carbon footprint comparison of three different mine tailings management using a life cycle assessment approach
Authors: Adiansyah J S
Published: January 2020

One of the potential risks in the mining operation is tailings management. Some environmental incidents occurred were associated with tailings. This paper investigated the carbon footprint of three different mine tailings management using life cycle assessment (LCA) and The Australian indicator set method was applied to assess the carbon footprint. Those three different mine tailings management were tailings paste (OPT 1), thickened tailings (OPT 2) and OPT 1 improvement. The extended strategies for OPT 1 were also proposed by improving flotation technology and introducing renewable energy sources (OPT 1A-G). These strategies changed fine coal segregation technology from column flotation to stack cell (OPT 1A) and substituted fossil fuels to renewable energy with the various reduction percentage of 10%, 30%, 50% (OPT 1B-G). The results of the analyses show that OPT 1 generated the highest carbon footprint compared to the base case scenario (OPT 2). Replacing column flotation with stack cell contributed to the reduction of carbon footprint by 18%. The renewable energy (the wind and solar) utilization of 10%, 30%, and 50% affected vary on the carbon footprint reduction from 24% to 44%.
Kampoeng Reklamasi: a case study of the designation reclamation type of an ex-tin minein Bangka Island, Indonesia
Authors: Syauqi A , Sudrajat J , Anbiyak N , Hutahaean B , Adnis R
Published: January 2020

Air Jangkang mine is one of tin mines operated by PT TimahTbk in Bangka Island. Decades of mining operation produced piles of tailing which mainly composed of silica sand. The soil samples taken from the area indicate acidic soil, poor organic content, and low values of cation changing capacity in addition to low levels of phosphor and potassium. The low pH value also plays pivotal roles regarding the leaching and mobilization of heavy metals that accumulated in the water and soil. This study explains how the planning and implementation of other designation reclamation type as specified in the regulation. The critical stage in this reclamation area is the recovery and enrichment of nutrient-deficient soil so that the nutrients are available for plant uptake. In terms of food safety from the reclamation area, PT TimahTbk gives serious attention through implementing series of toxicity tests on crops and fish. The result illustrates that the toxic metal concentration in the vegetables, fruit, and fish are vary with the highest concentration of Pb and As are found in the vegetables. Samples taken from radish and spinach show Pb concentration at 6.1 ppm and 2.01 ppm respectively, exceeding Indonesian national standard at 0,5. This result suggests that heavy metals are mainly accumulated in the roots of a plant.
Danau Seran, a pit lake in an ex-mining area as an opportunity for sustainable tourism
Authors: Caesarina H M , Hirsan F P
Published: January 2020

The mining activities left so many environmental impacts on its ex-mining areas. Some of the abandoned open-cut mines often filled by groundwater or rainwater and turn into pit lakes. Despite its toxic water and other environmental problem, this pit lakesbecome a tourist attraction in some areas. This research aimed to analyse whether a pit lake in the ex-mining area is potential for sustainable tourism and how it impacts the environment and local community. This research took DanauSeran (Seran Lake), ex-diamond mining as a case study. Some field research and interviews with local communities were done during this research. The environmental condition of the area shows that the water of Danau Seran is acidic and harmful for long term daily use. No green plantation is seen in the area. Based on 3A tourism principle (Attractiveness, Amenity, Accessibilities), Danau Seran has fulfilled almost all principles of 3A. The result shows that Danau Seran as a pit lake needs to improve its environmental quality and community development through reclamation. Hence, this will create an opportunity for sustainable tourism.
Good mining practices toward a good mine management: a case of mining business permit issuance
Authors: Haris O K , Djamiati T S , Adiansyah J S
Published: January 2020

Maladministration fundamentally starts from the misconduct of public officials. It then extends to providing bad service ranging from acceptance, process, and administration execution, which includes the issuance of permit in mining sector. Mining management plays an important role in meeting people’s needs. The management also serves an important function to provide added value to national economic growth and sustainable regional development. This study aims to examine the correct method to find the philosophy of Mining Business Permit (IUP) issuance, norm formulation of government authority to grant IUP, and government authority to issue IUP that carries implication for criminal offense. The methods combine two approaches, namely legal and problem approach. The application of such method can contribute to the formulation of an integrated holistic policy to issue IUP and optimize collective strategic resources for the greater good of human life. This study found that maladministration of mining business permit has engendered complexities and overlapping decisions in both vertical and horizontal levels. In vertical level, conflict of authority and overlapping decisions occuredin central and regional government.
Community understanding and attitude levels on the implementation of illegal sand mining on the Induk Beach, West Lombok
Authors: Rochayati N , Mahsup  , Ibrahim  , Herianto A , Johari H I
Published: January 2020

Taman Ayu Village in Gerung, West Lombok District, has a prospect as an up-coming tourist area. It is unfortunate if the coastal sand mining activities damage the coastal regions. The research conducted aims to describe the level of understanding and attitude of the community towards the impact of mining illegally. This research method is descriptive, with a qualitative approach by using observation, in-depth interviews. The results of the study show that mining is carried out by the community, because of the need for beach sand for building materials, especially as the final content for making ornaments or home decorations. Coastal sand mining caused a decrease in the beach surface, potential disasters, and coastal abrasion. The positive impact of these activities is increasing the income of the mining community. The community has understood that sand mining activities cause damage to coastal areas, but due to economic demands, the community continues to carry out these activities. In tackling illegal mining on the central coast, the role and responsibility of the Government is integral. Banning and giving warnings in the form of installing warning boards around the mining site as well as providing specialized training for mining officials to provide an understanding to stop the mining activities.
A basic study on artificial aging in Mg-10Al12Si+1Pb alloy
Authors: Cicek Bunyamin , Aydogmus Tuna , Sun Yavuz
Published: January 2020

In this study, research has been made on the aging of metal matrix composite materials produced by the in situ casting system. Mg matrix composite material was produced by the in situ casting system. In this study, 90%Mg + 10% Al12Si (wt) ingot casting was performed for alloy formation and 1% Pb was added as an alloying element to the melted structure. This study aims to examine the effect of the artificial aging (AA) process on hardness and microstructure after alloying and composite of Mg metal. The in situ casting system was used in the casting of Mg alloy under the Ar gas atmosphere. The material after required casting homogenization process; for the AA process, they were embedded in a powder graphite filled vessel and kept at 350 °C for 1 h and then quenched (with 25 °C water). Later; after quenching, the materials were kept at 150 °C for 2, 4, 12, 16 and 24 h and aged samples were obtained. Microstructure images were obtained from the samples by scanning electron microscope (SEM) and light optical microscope (LOM) and then the hardness values of the micro hardness device were measured. Grain structure because of AA heat treatment; showed changes according to un-aging material. The hardness value is directly proportional to the increasing aging time of the materials applied to the AA process; it was found that the levels increased approximately to 45% (86HV to 125HV) compared to the un-aging material and passed to the fixing phase.
On flexural and pull out properties of 3D printed PLA based hybrid composite matrix
Authors: Kumar Sudhir , Singh Rupinder , Singh T P , Batish Ajay
Published: January 2020

Fused deposition modelling (FDM) has been widely explored for number of commercially available virgin thermoplastics (such as: poly lactic acid (PLA), nylon, acrylonitrile butadiene styrene (ABS) etc), thermoplastic based composites and printing conditions. But hitherto little has been reported on flexural and pull-out properties of 3D printed PLA based hybrid composite matrix (having magnetostrictive properties) especially in structural engineering applications. In the present work an effort has been made for 3D printing of PLA hybrid composite matrix (having magnetic characteristics) to investigate the flexural and pull out properties. The photo micro-graphic analysis and Shore D hardness has been performed on the printed samples and multifactor optimization tool has been used for optimizing the printing conditions. From multifactor optimization viewpoint it has been ascertained that infill density 100%; infill angle 45°; and infill speed 90 mm s−1 are the best printing conditions. Further from morphological testing it has been observed that mechanical properties (flexural and pull out) are dependent upon the hardness, surface porosity and surface roughness (Ra). The creo structural analysis supported with photomicrographs have been performed on the samples prepared at best setting of input parameters and it has been found that strain increases downward along the thickness and is maximum at lowest layer due to which the failure starts from the base line in flexural testing.
PEGlatyon-SPION surface functionalization with folic acid for magnetic hyperthermia applications
Authors: Piazza Rodolfo Debone , Viali Wesley Renato , dos Santos Caio Carvalho , Nunes Eloiza S , Marques Rodrigo Fernando C , Morais Paulo C , da Silva Sebastião William , Coaquira José Antonio H , Jafelicci Miguel
Published: January 2020

Superparamagnetic iron oxide nanoparticles (SPION) are of great interest for application in magnetic fluid hyperthermia (MFH) due to their heat generation capability in an external alternating magnetic field, besides biocompatibility, and surface properties. MFH has emerged as a promisor therapeutic approach for cancer treatment and is based in controlled heating tumor tissue through the accumulation of SPIONs within cancer cells. This work describes a new route for the preparation of folate-conjugated PEGylated SPIONs, which involves the attachment of such molecules at the surface through polycondensation reactions, without the need for coupling agents or prior modification on the species involved. The size of iron oxide cores obtained by transmission electron microscopy was about 12 nm. The conjugation of folate onto SPIONs was confirmed by FTIR spectroscopy. The folate conjugated nanoparticles were colloidal stable in PBS, presenting a hydrodynamic diameter of 109 ± 1 nm and PDI 0.148. The obtained folate-targeted PEGylated SPIONs showed superparamagnetic behavior with a saturation magnetization of 73.1 emu·g−1 at 300 K. Their specific absorption rate (SAR) ranged from 32.8 to 15.0 W g−1 in an alternating magnetic field of 10–16 kA m−1 and frequency of 420–203 kHz. The heat generated was sufficient to raise the sample temperature to the therapeutic range used in MFH establishing this system as promising candidates for use in MFH treatment.
Variation in seed traits among Mediterranean oaks in Tunisia and their ecological significance
Authors: Amimi Nabil , Dussert Stéphane , Vaissayre Virginie , Ghouil Hana , Doulbeau Sylvie , Costantini Carlo , Ammari Youssef , Joët Thierry
Published: January 2020

Background and Aims

Oaks are the foundation and dominant tree species of most Mediterranean forests. As climate models predict dramatic changes in the Mediterranean basin, a better understanding of the ecophysiology of seed persistence and germination in oaks could help define their regeneration niches. Tunisian oaks occupy distinct geographical areas, which differ in their rainfall and temperature regimes, and are thus a valuable model to investigate relationships between seed traits and species ecological requirements.

Methods

Seed morphological traits, desiccation sensitivity level, lethal freezing temperature, embryonic axis and cotyledon sugar and lipid composition, and seed and acorn germination rates at various constant temperatures were measured in Quercus canariensis, Q. coccifera, Q. ilex and Q. suber, using seeds sampled in 22 Tunisian woodlands.

Key Results

Only faint differences were observed for desiccation sensitivity in the oak species studied. By contrast, the species differed significantly in sensitivity to freezing, germination rates at low temperature and base temperature. Quercus ilex and Q. canariensis, which occur at high elevations where frost events are frequent, showed the lowest freezing sensitivity. A significant correlation was found between hexose contents in the embryonic axis and freezing tolerance. Significant interspecific differences in the time for seeds to germinate and the time for the radicle to pierce the pericarp were observed. The ratio of pericarp mass to acorn mass differed significantly among the species and was negatively correlated with the acorn germination rate. Quercus coccifera, which is frequent in warm and arid environments, showed the highest acorn germination rate and synchrony.

Conclusions

Seed lethal temperature, seed germination time at low temperatures, the ratio of pericarp mass to acorn mass and the embryonic axis hexose content appeared to be key functional traits that may influence the geographical ranges and ecological requirements of Mediterranean oaks in Tunisia.
Socio-ecological factors shape the opportunity for polygyny in a migratory songbird
Authors: Canal David , Schlicht Lotte , Manzano Javier , Camacho Carlos , Potti Jaime
Published: January 2020

Why females pair with already mated males and the mechanisms behind variation in such polygynous events within and across populations and years remain open questions. Here, we used a 19-year data set from a pied flycatcher (Ficedula hypoleuca) population to investigate, through local networks of breeding pairs, the socio-ecological factors related to the probability of being involved in a polygynous event in both sexes. Then, we examined how the breeding contexts experienced by individuals shaped the spatial and temporal separation between broods of polygamous males. The probability of polygyny decreased with the distance between nests. Indeed, secondary females were often close neighbors of primary females, although the distance between both nests increased slightly with increasing synchrony between them. The probability of polygyny was also related to the breeding time of individuals because early breeding males were more likely to become polygynous with late-breeding females. Throughout the season, there was substantial variation in the temporal separation between primary and secondary broods, and this separation was, in turn, related to the breeding asynchrony of the polygamous males (in the primary nest) relative to the neighbors. Polygynous males that bred late relative to their neighbors had a short time window to attract a second female and, thus, the breeding interval between their primary and secondary broods was reduced. Overall, the spatial proximity between polygynous males’ broods and, if the opportunity existed, their temporal staggering are compatible with a male strategy to maximize paternity and reduce the costs of caring for two broods, though the effect of female’s interest, either primary or secondary, cannot be fully ruled out. We highlight that a comprehensive assessment of the breeding contexts faced by individuals is essential to understand mating decisions and reconcile the discrepancies raised by previous work on social polygyny.
BiORSEO: a bi-objective method to predict RNA secondary structures with pseudoknots using RNA 3D modules
Authors: Becquey Louis , Angel Eric , Tahi Fariza
Published: January 2020

Motivation

RNA loops have been modelled and clustered from solved 3D structures into ordered collections of recurrent non-canonical interactions called ‘RNA modules’, available in databases. This work explores what information from such modules can be used to improve secondary structure prediction. We propose a bi-objective method for predicting RNA secondary structures by minimizing both an energy-based and a knowledge-based potential. The tool, called BiORSEO, outputs secondary structures corresponding to the optimal solutions from the Pareto set.

Results

We compare several approaches to predict secondary structures using inserted RNA modules information: two module data sources, Rna3Dmotif and the RNA 3D Motif Atlas, and different ways to score the module insertions: module size, module complexity or module probability according to models like JAR3D and BayesPairing. We benchmark them against a large set of known secondary structures, including some state-of-the-art tools, and comment on the usefulness of the half physics-based, half data-based approach.

Availability and implementation

The software is available for download on the EvryRNA website, as well as the datasets.

Supplementary information

Supplementary data are available at Bioinformatics online.
Gapsplit: efficient random sampling for non-convex constraint-based models
Authors: Keaty Thomas C , Jensen Paul A
Published: January 2020

Gapsplit generates random samples from convex and non-convex constraint-based models by targeting under-sampled regions of the solution space. Gapsplit provides uniform coverage of linear, mixed-integer and general non-linear models.

Availability and implementation

Python and Matlab source code are freely available at http://jensenlab.net/tools.

Supplementary information

Supplementary data are available at Bioinformatics online.
Cytomegalovirus (CMV) Cell-Mediated Immunity and CMV Infection After Allogeneic Hematopoietic Cell Transplantation: The REACT Study
Authors: Chemaly Roy F , El Haddad Lynn , Winston Drew J , Rowley Scott D , Mulane Kathleen M , Chandrasekar Pranatharthi , Avery Robin K , Hari Parameswaran , Peggs Karl S , Kumar Deepali , Nath Rajneesh , Ljungman Per , Mossad Sherif B , Dadwal Sanjeet S , Blanchard Ted , Shah Dimpy P , Jiang Ying , Ariza-Heredia Ella
Published: January 2020

Background

Cytomegalovirus (CMV) infection remains an important cause of morbidity and mortality in allogeneic hematopoietic cell transplant (allo-HCT) recipients. CMV cell-mediated immunity (CMV-CMI) as determined by a peptide-based enzyme-linked immunospot (ELISPOT) CMV assay may identify patients at risk for clinically significant CMV infection (CS-CMVi).

Methods

The CS-CMVi was defined as CMV viremia and/or disease necessitating antiviral therapy. CMV-CMI was characterized as high when the intermediate-early 1 (IE-1) antigen spot counts (SPCs) were >100 (cutoff 1) or when the IE-1 and phosphoprotein 65 antigen SPCs were both >100 SPCs per 250 000 cells (cutoff 2), and a low CMV-CMI when SPCs were below these thresholds. In this prospective multicenter study, we evaluated CMV-CMI every 2 weeks from the pretransplant period until 6 months posttransplantation in 241 allo-HCT recipients with positive CMV serostatus. The primary endpoint was CS-CMVi occurring within 2 weeks of the last measurement of CMV-CMI.

Results

CS-CMVi occurred in 70 allo-HCT recipients (29%). CMV-CMI was low in patients who experienced CS-CMVi (94%), whereas those who had a high CMV-CMI were less likely to have CS-CMVi (P < .0001). Patients with CS-CMVi had higher all-cause mortality (P = .007), especially those with low CMV-CMI (P = .035). On multivariable analysis, CMV-CMI, sex, race, antithymocyte globulin, and steroid use were independent predictors of CS-CMVi, and the time from transplant to engraftment was the only predictor of mortality.

Conclusions

Measurement of CMV-CMI using a novel ELISPOT assay would be useful clinically to monitor allo-HCT recipients and distinguish between those at risk of developing CS-CMVi and requiring antiviral prophylaxis or therapy and those who are protected.
Cost-effectiveness of a Pharmacogenomic Test for Stratified Isoniazid Dosing in Treatment of Active Tuberculosis
Authors: Rens Neil E , Uyl-de Groot Carin A , Goldhaber-Fiebert Jeremy D , Croda Julio , Andrews Jason R
Published: January 2020

Background

There is marked interindividual variability in metabolism and resulting toxicity and effectiveness of drugs used for tuberculosis treatment. For isoniazid, mutations in the N-acetyltransferase 2 (NAT2) gene explain >88% of pharmacokinetic variability. However, weight-based dosing remains the norm globally. The potential clinical impact and cost-effectiveness of pharmacogenomic-guided therapy (PGT) are unknown.

Methods

We constructed a decision tree model to project lifetime costs and benefits of isoniazid PGT for drug-susceptible tuberculosis in Brazil, South Africa, and India. PGT was modeled to reduce isoniazid toxicity among slow NAT2 acetylators and reduce treatment failure among rapid acetylators. The genotyping test was assumed to cost the same as the GeneXpert test. The main outcomes were costs (2018 US dollars), quality-adjusted life-years (QALYs), and incremental cost-effectiveness ratios.

Results

In Brazil, PGT gained 19 discounted life-years (23 QALYs) and cost $11 064 per 1000 patients, a value of $476 per QALY gained. In South Africa, PGT gained 15 life-years (19 QALYs) and cost $33 182 per 1000 patients, a value of $1780 per QALY gained. In India, PGT gained 20 life-years (24 QALYs) and cost $13 195 per 1000 patients, a value of $546 per QALY gained. One-way sensitivity analyses showed the cost-effectiveness to be robust to all input parameters. Probabilistic sensitivity analyses were below per capita gross domestic product in all 3 countries in 99% of simulations.

Conclusions

Isoniazid PGT improves health outcomes and would be cost-effective in the treatment of drug-susceptible tuberculosis in Brazil, South Africa, and India.
Prospective Evaluation of the Frequency and Severity of Symptoms in Lyme Disease Patients With Erythema Migrans Compared With Matched Controls at Baseline, 6 Months, and 12 Months
Authors: Wormser Gary P , McKenna Donna , Karmen Carol L , Shaffer Keith D , Silverman Jesse H , Nowakowski John , Scavarda Carol , Shapiro Eugene D , Visintainer Paul
Published: January 2020

Background

Erythema migrans is the most common clinical manifestation of Lyme disease. Despite antibiotic therapy, typically at least 10% of adult patients with erythema migrans experience persistence of at least 1 subjective symptom for ≥6 months (posttreatment Lyme disease symptoms [PTLDS]).

Methods

This study was designed to determine whether the frequency and severity (based on a visual analogue scale) of 12 particular symptoms in patients with erythema migrans (n = 52) differed from matched control subjects (n = 104) followed prospectively for 12 months.

Results

At baseline, patients with Lyme disease were more likely than controls to have at least 1 symptom (P = .006). Among symptomatic subjects, Lyme disease patients had a higher mean number of symptoms (P < .001) and a higher mean total symptom severity score (P < .001). At both 6 and 12 months, however, there were no significant differences for these variables and no significant differences in the frequency or severity of any of the 12 individual symptoms assessed. However, 10 patients were clinically assessed as having possible PTLDS.

Conclusions

Patients with erythema migrans were more likely than matched control subjects to be symptomatic at baseline with a greater symptom severity score, but this was not found at ≥6 months. Use of symptom survey data alone, however, was less likely to identify patients with possible PTLDS compared with individual clinical assessments. Because it is very challenging to be certain that the presence of long-term symptoms in a particular patient is correctly attributable to having had Lyme disease, an objective biomarker would be highly desirable.
Two Clinical Prediction Tools to Improve Tuberculosis Contact Investigation
Authors: Li Ruoran , Nordio Francesco , Huang Chuan-Chin , Contreras Carmen , Calderon Roger , Yataco Rosa , Galea Jerome T , Zhang Zibiao , Becerra Mercedes C , Lecca Leonid , Murray Megan B
Published: January 2020

Background

Efficient contact investigation strategies are needed for the early diagnosis of tuberculosis (TB) disease and treatment of latent TB infections.

Methods

Between September 2009 and August 2012, we conducted a prospective cohort study in Lima, Peru, in which we enrolled and followed 14 044 household contacts of adults with pulmonary TB. We used information from a subset of this cohort to derive 2 clinical prediction tools that identify contacts of TB patients at elevated risk of progressing to active disease by training multivariable models that predict (1) coprevalent TB among all household contacts and (2) 1-year incident TB among adult contacts. We validated the models in a geographically distinct subcohort and compared the relative utilities of clinical decisions based on these tools to existing strategies.

Results

In our cohort, 296 (2.1%) household contacts had coprevalent TB and 145 (1.9%) adult contacts developed incident TB within 1 year of index patient diagnosis. We predicted coprevalent disease using information that could be readily obtained at the time an index patient was diagnosed and predicted 1-year incident TB by including additional contact-specific characteristics. The area under the receiver operating characteristic curves for coprevalent TB and incident TB were 0.86 (95% confidence interval [CI], .83–.89]) and 0.72 (95% CI, .67–.77), respectively. These clinical tools give 5%–10% higher relative utilities than existing methods.

Conclusions

We present 2 tools that identify household contacts at high risk for TB disease based on reportable information from patient and contacts alone. The performance of these tools is comparable to biomarkers that are both more costly and less feasible than this approach.
Efficacy and Safety of Switching to Dolutegravir/Lamivudine Fixed-Dose 2-Drug Regimen vs Continuing a Tenofovir Alafenamide–Based 3- or 4-Drug Regimen for Maintenance of Virologic Suppression in Adults Living With Human Immunodeficiency Virus Type 1: Phase 3, Randomized, Noninferiority TANGO Study
Authors: van Wyk Jean , Ajana Faïza , Bisshop Fiona , De Wit Stéphane , Osiyemi Olayemi , Portilla Sogorb Joaquín , Routy Jean-Pierre , Wyen Christoph , Ait-Khaled Mounir , Nascimento Maria Claudia , Pappa Keith A , Wang Ruolan , Wright Jonathan , Tenorio Allan R , Wynne Brian , Aboud Michael , Gartland Martin J , Smith Kimberly Y
Published: January 2020

Background

The 2-drug regimen dolutegravir (DTG) + lamivudine (3TC) is indicated for treatment-naive adults with human immunodeficiency virus type 1 (HIV-1). We present efficacy and safety of switching to DTG/3TC in virologically suppressed individuals.

Methods

TANGO is an open-label, multicenter, phase 3 study that randomized adults (1:1, stratified by baseline third agent class) with HIV-1 RNA <50 copies/mL to switch to once-daily fixed-dose DTG/3TC or remain on a tenofovir alafenamide (TAF)–based regimen. The primary end point was proportion of participants with HIV-1 RNA ≥50 copies/mL at week 48 (US Food and Drug Administration Snapshot algorithm) in the intention-to-treat–exposed population (4% noninferiority margin).

Results

743 adults were enrolled; 741 received ≥1 dose of study drug (DTG/3TC, N = 369; TAF-based regimen, N = 372). At week 48, proportion of participants with HIV-1 RNA ≥50 copies/mL receiving DTG/3TC was 0.3% (1/369) vs 0.5% (2/372) with a TAF-based regimen (adjusted treatment difference [95% confidence interval], −0.3 [−1.2 to .7]), meeting noninferiority criteria. No participants receiving DTG/3TC and 1 receiving a TAF-based regimen met confirmed virologic withdrawal criteria, with no emergent resistance at failure. Drug-related grade ≥2 adverse events and withdrawals due to adverse events occurred in 17 (4.6%) and 13 (3.5%) participants with DTG/3TC and 3 (0.8%) and 2 (0.5%) with a TAF-based regimen, respectively.

Conclusions

DTG/3TC was noninferior in maintaining virologic suppression vs a TAF-based regimen at week 48, with no virologic failure or emergent resistance reported with DTG/3TC, supporting it as a simplification strategy for virologically suppressed people with HIV-1.

Clinical Trials Registration

NCT03446573.