bluuebunny/crossref_metadata_2025 huggingface dataset:
The sustainable agricultural mechanization of rice farming and its impact on land productivity and profit in Lampung Tengah Regency
Authors: Haryono D , Hudoyo A , Mayasari I
Published: April 2021

The mechanization of rice farming has been fast developing since implementing the special effort (Upsus) program in 2015. Through this program, many combine harvesters and four-wheel tractors had been distributed to the farmer groups. This study’s objectives were to know the practice of sustainable agricultural mechanization, know its impact on land productivity and profit for rice farming, and know whether sustainable agricultural development in Lampung Tengah Regency. This study was conducted at three sub-districts, Central Lampung Regency, in August and September 2020. Respondents were 108 farmers with 359 observations since each respondent was interviewed for 3-4 previous planting seasons, and an observation was a rice farm in a planting season. To know the practice of the mechanization, the data were analyzed descriptively. To know its impact, the data were analyzed using two multiple regression analysis models, each of which the dependent variable is productivity and profit. The independent variables for these two models were the mechanization types, the treatment variables, and the planting seasons and location, which were the control variables. The results revealed that the 4-wheel tractors were more efficient than that of the 2-wheel tractors. Combining harvester (CH) was the most efficient in harvesting than that of manual cutting and thresher and full manual harvesting. The results revealed that statistically, with the level of significance (α) by 1%, the combined harvester’s use increased the average productivity by 0.16 tonnes/ha or almost 3%, i.e., from 5.51 tonnes/ha to 5.67 tonnes/ha. They increased the average profit by IDR2.44 million/ha or 40%, i.e., from IDR6.10 million/ha to IDR8.54 million/ha. These findings revealed that the use of a tractor together with a combine harvester was sustainable agricultural development.
Static and dynamic panel models: Which is better? (Case study: Poverty data in Indonesia 2012-2019)
Authors: Sihombing P R , Arsani A M
Published: April 2021

Indonesia’s poverty rate continues to decline from year to year; however, the decline in the percentage of poor people is slowing down continuously, following the law of diminishing returns. Many factors influence poverty, including HDI, Gini ratio, and the open unemployment rate. This study model static and dynamic panel data on Indonesia’s poverty cases in 2012-2019 to explain the relationship between HDI, Gini ratio, and the unemployment rate to poverty. It also compares poverty modeling with static and dynamic panel data regression. The results show that the Gini ratio has a significant and positive relationship to poverty. HDI has a significant and negative relationship to poverty. However, there is insufficient evidence to suggest that unemployment affects poverty. Using static panel data regression, the selected model is a fixed effect model but still experiences violations of the classic autocorrelation assumption. The dynamic panel data model gives better results than the static panel data regression model when viewed from the r-square value and the number of variables that significantly affect. From the results of this study, it can be implemented that an increase in economic growth without an increase in equity has no impact on poverty. So, it needs extra efforts by the government in economic equality for all regions of Indonesia. Also, there is a need for additional actions by the government and the community to improve education, health, purchasing power, and community competitiveness.
Perceptions, attitudes and lifestyles of students of Madrasah Ibtidaiyah Teacher Education Study Program about education for sustainable development
Authors: Emilzoli M , Ali M , Rusman
Published: April 2021

This study discusses students’ perceptions, attitudes, and lifestyles of the Madrasah Ibtidaiyah Teacher Education Program at Siliwangi Islamic College regarding Education for Sustainable Development (ESD). The research was conducted in October 2019 involving 86 students of PGMI study program through a survey that focused on knowledge of ESD, attitudes, and lifestyles of st sustainable development concepts. This research uses descriptive analysis. In terms of understanding found inconsistency of respondent’s knowledge of ESD, it can be seen from 74.4% of students have heard the term ESD, 70% stated understanding of ESD, but only 24.4% of respondent were right when asked about the definition of ESD. In terms of attitude, respondents are in a very good category (85.63%) it means that respondents understand how to behave according to the ESD values in daily activity. But this is not in line with the curriculum in Madrasah Ibtidaiyah Teacher Education Program at Siliwangi Islamic College. The curriculum, especially mandatory subjects at the Madrasah Ibtidaiyah (MI) or elementary school, does not contain the values or activities related to ESD. While on the other hand, the concept and program of ESD have been introduced since 2002 by UNESCO and participated in by many countries through educational programs ranging from primary education to higher education. This research is very important to produce a picture of ESD competence integrated into the curriculum in the madrasah ibtidaiyah teacher education program.
The effect of the type of planting medium and the dosage of vermicompost fertilizer on the growth and yield of bean (Phaseolus vulgaris L.) Kenya varieties
Authors: Sudrajat A , Rachmawati Y S , Qurani C N N , Akmaliya  , Sarbini
Published: April 2021

The superiority of the Kenya variety of beans has the opportunity to increase export value; with good market prospects, it is necessary to increase the production of Kenyan varieties of beans. This study aims to determine the effect of the type of planting medium and the dosage of vermicompost fertilizer on the growth and yield of green beans. This research was conducted from February until April 2020 in Ngamprah, Kab. West Bandung, West Java. This research was conducted using an experimental design in the form of a factorial randomized block design (RBD) with three replications consisting of two factors. The first factor is the type of planting media which consists of 3 levels (m0 = soil, ml = soil + rice husk charcoal (1 : 1), m2 = soil + cocopeat (1:1)). The second factor was vermicompost consisting of 4 levels (k0 = 0 t ha-1, k1 = 7.5 t ha-1, k2 = 15 t ha-1, and k3 = 22.5 t ha-1). Based on the study results, there was an interaction between the soil planting media with a dosage of 15 t ha-1 of vermicompost on the growth and yield of upright beans. Soils with a silty loam texture and high P nutrient content in vermicompost can support growing places and sufficient nutrient availability for the growth and yield of upright beans.
Genetic diversity of local durian from Tidore Island based on morphological and moleculer data for tropical fruit conservation in North Maluku
Authors: Sundari  , Mas’ud A , Wahyudi D , Arumingtyas E L , Hakim L , Azrianingsih R
Published: April 2021

Durian is a tropical fruit that has substantial economic value. One of the durian production centers in North Maluku is Tidore Island. This study’s objective was to identify genetic diversity, taxonomic status, and local durian conservation models in North Maluku. Data collection method with purposive sampling technique. Morphological data, including 142 characters (stems, leaves, flowers, and fruit), were analyzed descriptively and arranged by UPGMA dendrogram with the outgroup (D. kutezensis). Molecular data were obtained by using the PCR RAPD technic. Genetic diversity of local durian Tidore based on morphological characters produced 7 clusters with the closest genetic distance to local durian (R4-R10) with a similarity value of 0.887. Genetic diversity of local durian Tidore based on PCR RAPD technic produced 5 clusters with the closest genetic distance to local durian (R10-R12) with a similarity value of 0.977. The value of Tidore’s local durian dissimilarity is close to 10%; it can be assumed that the genetic diversity of Tidore’s local durian is at the level of intraspecies diversity. Gap analysis recommends that Tidore’s local durian conservation model is appropriate with the durian breeding program through an in-situ selection of superior traits and conservation..
Utilization of rice husk silica as solid catalyst in the transesterification process for biodiesel production
Authors: Banurea I R , Setyawan N , Yuliani S , Herawati H , Hoerudin
Published: April 2021

Biodiesel from palm oil is a promising renewable fuel for substitute petro-diesel either be used directly or as a diesel mixture. To improve reaction rate and biodiesel yield, adding a catalyst with excess alcohol is needed in transesterification process. The high content of silica in rice husks is very prospective for the development of a heterogeneous catalyst. The study was carried out to investigate catalytic activity of the silica from rice husk produced by the impregnation process and various calcination temperatures at various amounts of it in the transesterification process for biodiesel production. A preliminary study was carried out to determine the amount of catalyst in the transesterification process. The amount of catalyst producing the highest yield of biodiesel was used in the next study. In the main study, the catalyst from rice husk silica was synthesized through an impregnation process used 1 N KOH and calcination processes at 200, 300, 400, and 500 °C. The experimental result showed the crystallinity degree of the catalyst first increased and then decreased with increases in calcination temperatures. The calcination at 300 °C resulted in the highest surface area of the catalyst (7.21 m2/g). The biodiesel produced through transesterification process using catalyst from rice husk silica with impregnation of KOH 1N and calcination at 300 °C resulted in the highest methyl ester (94.39 %), total acid number of 0.09 mg KOH/g, total glycerol of 0.57 %, saponification number of 186.76 %, free glycerol of 0.01 %, and moisture content of 650.55 ppm.
Reflector and passive cooler for optimization of solar panel output
Authors: Siregar W P H , Fawaid M , Abizar H , Nurtanto M , Suhendar  , Suyitno
Published: April 2021

The objectives of this study were (1) To determine the effect of using passive reflectors and coolers on the output power produced by solar panels. The research method used was an experimental method with a true experimental design model, namely in this design there were 2 systems, the first system was treated, the second system was not given treatment. The variations in treatment in this study are as follows; (1) Solar panels without using passive cooling reflectors and (2) Solar panels using reflectors and passive cooling. Data were collected for 4 days from (08.00-14.00) with a sample of 50 Wp solar modules. The data collection technique used was literature study, performance and testing documentation. The results showed that the results of the solar panel testing power with 2 variations of treatment, namely, (1) The solar panel without using a reflector and passive cooling produces an average power of 47.68 Watts and (2) Solar panels using a reflector and passive cooler are 59.63 Watts. The results of this study indicate that solar panels using reflectors and coolers increase the power by 25.07% of solar panels without using reflectors and passive cooling.
Speckle noise reduction of Sentinel-1 SAR data using fast fourier transform temporal filtering to monitor paddy field area
Authors: Kustiyo  , Rokhmatuloh  , Saputro A H , Kushardono D
Published: April 2021

Synthetic Aperture Radar (SAR) images have the ability to work in any weather situation. It is mostly impossible to get cloud free optical image monthly in Indonesia, especially in Subang. So, the use of SAR imagery for the monthly monitoring of paddy is recommended. The disadvantage of the SAR images is noise, known as speckle noise. This noise reduces the quality of the image; reducing the speckle noise is necessary. This research proposes the FFT algorithm to remove the speckle noise. Because the frequency pattern of FFT is periodic, and the research focuses on the paddy field area, so the one year of paddy growth was used. There are many planting times in the research area, from one to three planting times a year; most of the area is twice planting time a year. Six scenarios of the FFT filter were proposed and investigated to select the optimum scenario. The scenarios use the number of FFT results to implement in filtering. The first scenario used FFT1 to FFT2, and the sixth scenario used FFT-1 to FFT-8. The performance results were measure by the correlation value of the original image and the results of FFT filtering. The results show that by increasing the number of FFT in the filtering process, the correlation increase. The minimal FFT filtering is FFT1-FFF3 filtering, with the average correlation is 87%, but some acquisition still has the correlation less than 85%. The optimum is FFT1- FFT5 filtering, with the average correlation, is 92%, and all correlations are above 85% for all data during a year. Using the optimum scenario, the backscattered trend of paddy growth could be identified better and easier, so this technique is recommended for paddy growth monitoring.
Google earth engine and landsat data for detecting inundation changes in Limboto lake
Authors: Lahay R J , Koem S
Published: April 2021

Limboto Lake has environmental degradation due to the high sedimentation rate. Based on that fact, monitoring of inundation change is needed for upcoming lake management. The dynamics of Limboto lake inundation can be detected by utilizing remote sensing data. The emergence of cloud computing-based geospatial technology allows its users to automatize remote sensing data preparation and processing procedures. The study attempted to investigate the dynamics of Limboto lake inundation within the time frame of 2001-2019. The detection was conducted by incorporating the Landsat data and water index method through Google Earth Engine (hence, GEE) interface. The observation year was chosen to start from 2001 due to the Landsat 7 ETM + images were completely available for a year (11 months). The results displayed that the lake’s inundation area’s dynamics during the observed time frame tended to show a trend of shrinkage in size. The shrinkage mostly took place at the west and northwest part of Limboto lake. The shrinkage that occurred at the lake inundation area is to be treated as a warning sign for decision-makers to formulate a decision to handle the potential negative impacts of the lake inundation shrinkage.
Application of GIS to define a juridical bay as part of Indonesia’s internal waters
Authors: Rachma T R N , Turmudi  , Kardono P
Published: April 2021

Indonesia is an archipelagic state bordered by archipelagic baselines. Based on the Law of the Sea Convention (LOSC), Indonesia has two maritime zones within the baseline, namely internal waters and archipelagic waters. It is necessary to make clear boundaries because there are different jurisdictions between the two areas. This study aims to identify Indonesian internal waters and a drawing closing line in the juridical bay. GIS software is used to identify the juridical bay, referring to the terms of the juridical bay in LOSC. The results of the research show that (1) several bays in Indonesia do not meet the criteria of juridical bays, (2) a juridical bay can consist of several smaller bays, (3) a large bay cannot be fully claimed as a juridical bay because there are limitations of the maximum length of the closing line, and (4) there are several juridical bays that do not have the name.
The Role of Urban Land Management on the Informal Settlements
Authors: Fouad Zina , Sati Abbas Sana
Published: April 2021

The research deals with the concept of the Informal settlements, as they are unauthorized subdivisions of lands in the urban environment that start with a sudden invasion on the lands of others without legal capacity, for a specific group of individuals, where they reside their houses, without official permission from the owner They are located in city centers or urban vacancies. So the paper aims to build a comprehensive theoretical framework for solving and addressing the problem of Informal settlements through the Programs and strategies of the urban land management system. The problems of the Informal settlements (security of tenure, ownership issues, increased demand for shelter, violation of the scheme of land use, basic services) are the main issues and tasks of urban land management. The research defines urban land management as the responsible authority in the urban sector that has the responsibility to solve and address obstacles that prevent achieving urban development aims, including these obstacles (informal settlements, housing, and infrastructure services). The research problem was represented by The lack of a clear perception of the role of urban land management programs and strategies in solving and addressing the problem of the Informal Settlements, while the research hypothesis was that Solving and addressing the problem of Informal Settlements is through the programs and strategies of the urban land management system, which is represented by the formal urban land management programs for informal settlements, a sustainable urban land management system and urban land management development in varying proportions. The paper built a theoretical framework for solving and addressing the problem of Informal settlements through the Programs and strategies of the urban land management system. The research concluded that The importance of programs and strategies for each of (formal urban land management approach, sustainable urban land management system, decentralized urban land management system and urban land management development), including (securing tenure for informal settlement dwellers, developing informal settlement areas and converting them into formal areas, providing basic infrastructure services, developing Participatory approaches between the public and private sectors, community participation, recognition of the right to decent housing), in solving and addressing the problem of informal settlements, albeit partially, which contributes to reducing or limiting the resort to informal settlements and thus their gradual disappearance.
Theoretical structure of Eco-cities: subject review
Authors: Khalid Zainab , Radi Abaas Zaynab
Published: April 2021

Given the importance of ecology and its entry into various fields in general and the urban environment particularly; ecological cities take wide ranges of application at multiple regional and global levels. However, it repeatedly noted that there was a state of cognitive confusion and overlapping in the term ecology comes from the diversity of implementation within several disciplines. Architects, designers, and planners have instilled biological development directly into the formal principles as well as the social structures of the ecological cities. Therefore, the research presents a rapid review of the most relevant areas that dealt with the ecological cities by research and analysis at various levels, from the concept and definition of the term, architecture, direction, design, planning, and housing to know the most significant similarities and differences of ecological cities within the various urban specialties. The findings reveal the application of the term Eco-city is branched and fallen under several names within one main goal to preserve the ecosystems and the natural environment while developing an appropriate microclimatic zone and achieving sustainable and healthy comfort levels for their residents through different urban indicators and techniques.
Evaluation of Road Networks Based on Traffic Accidents in Erbil City
Authors: Arshad Abdulwahab Azad
Published: April 2021

The traffic accidents threats humans live and its increases during the time. For this reason, this paper tries to analysis the traffic accidents by assessment of accident situations. Also, study the effect of road design elements and regulations coincide with case study in two methods applied first the five parameters individually tested. Then effective parameters tested together, correlation between accidents and the parameter, the roads and streets must design carefully and according to specifications and criteria. In this paper trying to indicate the weak points of road network and fixing this points to avoid them in the future. The ring road have a negative aspect because it extends the path and collecting local roads more than the straight paths. Also, restriction of sight distance occurs, the topographic of Erbil city is helpful in avoiding vertical curves, but the horizontal curves presented with concentric ring roads.
Role of Architecture in overcoming visual distortions. In the context of needs and social changes
Authors: Wannnous Hussien M. , Jishi Mohammad H.
Published: April 2021

This paper sheds light on the visual distortions that urban communities suffer due to neglect and weak law enforcement and their impact on the economic, environmental and social aspects. Architecture has a major role in addressing sagging and deformations that affect buildings, reviving them and making them more sustainable instead of consuming new lands, Contrary to the principles of sustainable and irreplaceable resources. The study relies on selecting four examples from 32 projects that deal with different issues related to the visual distortions that Lebanon’s suburbs and rural areas suffer from, and to provide serious and affordable solutions in order to change the existing stereotype in the urban environment. This study focuses on the importance of the role of architecture, especially the involvement of architecture students in local universities in reformulating the scenery in the streets of the community to which they belong. This experience will have a positive impact on society and improving its livelihood and environment.
Measuring pedestrian quality standards: a case study of Al-Khourng walkway and Al-Rawan Street
Authors: Hassan Alwan Kareem , Waheed Hadi Dhuha
Published: April 2021

Streets are an important component of the urban form and the most popular urban space in the city. Therefore, our streets deserve to be more than just traffic lanes because the negative impact of car-centered lifestyles has led to the reduction of urban spaces and their inadequacy with human needs, as it creates a social burden. We are also increasingly aware of the devastating cost of car air pollution, to our health. Cities are starting to realize that by encouraging more people to walk by reducing the number of car trips, as in old cities. A healthier and equal society can be created, business and investment attracted, and streets become a vital space for pedestrians and need to be governed effectively and efficiently to promote a conducive, sustainable and friendly environment for all. The aim of this study is to find out the difference between a pedestrian street scene and a car based on the characteristics of a pedestrian-friendly environment. The study area that will be covered in the research in the practical side is the Al-Khoranq walkway in the old city of Najaf with an organic planning and Al-Rawan Street in the modern districts of Najaf with network planning. As for the practical side of the research, geographic information systems technology was used with field surveys and image capture of the study area. The study reached a conclusion that the planning of our city around cars left many streets unattractive places for walking or hiking due to the failure to achieve safety and comfort for pedestrians, unlike pedestrian streets that were planned for the person and achieve his well-being when using the street.
Will the Covid-19 Pandemic Transform Our Urban Habitat? A Microalgae Photobioreactors Labyrinth-Garden as an answer for The Post-Covid Sustainable City
Authors: Cervera Rosa , Villalba Ma. Rosa
Published: April 2021

The epidemics of the first half of the 19th century made sanitation an essential point in the urban life. It laid the way for a city based on sunlight, ventilation and an urban planning of straight-lined, wide street and green areas. Until the beginning of 2020 we have lived in the belief that this urban model protected us. However, there were already many indications that the city was not capable of giving a satisfactory answer to the parameters of the 21st century, such as pollution, the heat island effect and the excessive consumption of energy and resources. Now, the coronavirus COVID-19, has put a stop to the city movement and with it, to the pollution it involves, revealing the level of contamination to which we were exposed. Therefore, it has become a priority to minimize energy consumption, energy dependence and pollution to improve the health and quality of life of its citizens. As answers to these demands, buildings with living organisms, such as microalgae, make the city a sustainable and Self-Sufficient environment. Giving an answer to the problem above, the design of the Park-Labyrinth proposes the installation of an intensive cultivation of microalgae that not only helps reduce CO2 emissions, transforming it into a product that generates interest, but also generates benefits to society in terms of recreation, energy production, reduction of polluting gases and use of space.
Groundwater Quality Study Based on the Existence of Escherichia coli as Bioindicator
Authors: Rinanti A , Fachrul M F , Hendrawan D I , Anisah U , Alreekabi N K
Published: April 2021

The research aim was to observe the distribution pattern of Escherichia coli as groundwater pollution indicator in the most populous area, Matraman Sub-District Area in Jakarta, Indonesia (106°49’35” EL and 06°10’37” SL) consists of six (6) Urban Villages. The existence of Escherichia coli was measured with Most Probable Number (MPN) method as mentioned in Indonesian Standard Number 01-2332.1-2006. This research was also measure pollution parameter of Dissolved Oxygen (DO) and pH, and topography analyses used as well to determine groundwater flow direction. Groundwater sampling was conducted in several housings that have low, middle, and high income as indicator of sanitation quality which causes groundwater pollution by Escherichia coli bacteria. The research result showed that the level of average Escherichia coli was 345,9778, 310,0556, and 727,1389 MPN/100 mL. Escherichia coli distribution pattern was headed from southeastern to northwestern area, in correspondence with Matraman Sub-District topography. The average pH level, temperature and DO0 in whole area respectively were 6.3, 24.7°C and 2.238 mg/L, that exceeded minimum water quality standards in Indonesian Minister of Health Regulation Number 492/MENKES/PER/IV/2010 regarding drinking water quality requirements. This study could be a reference for daily groundwater utilization in Matraman Sub-District and to provide information for further research.
Planning sustainable environmental neighborhoods is a step towards the direction of sustainable cities
Authors: Khalifa Mohammed Ali Nada , Abbas Ahmed Zainab
Published: April 2021

The sustainable environmental neighborhoods is sustainable development of neighborhoods that include considerations related to transport, density, urban forms, and environmental buildings and especially those related to social and functional integration, and civil society participation, This standard, which did not attract the attention of specialists in the 1990s, has today become a center of attention for all those interested in urbanism and sustainability. The problem of the research is the existence of urban problems in residential neighborhoods that lead to lack of sustainability in the city, and the research aims to explain the role and importance of environmental sustainability of residential neighborhoods in achieving city sustainability assuming that environmental sustainability of residential neighborhoods leads to the sustainability of the city, and as a general methodology for the research, the descriptive analytical method was adopted. The research included sustainable environmental neighborhoods, neighborhood definition, and definition of sustainable neighborhoods, characteristics of sustainable neighborhoods, types of sustainable neighborhoods, goals and standards for sustainable neighborhoods, Sweden’s experience, and the research reached the following main conclusions:

1 - Sustainable environmental neighborhoods are modern neighborhoods that appeared most often in industrial sites that suffer from pollution to give a positive image of these sites to be new neighborhoods that enjoy social, participatory, economic and environmental quality and they are urban poles characterized by density and interconnection and respond to the principle of sustainability in terms of general quality.

2 - The achievement of sustainable neighborhoods is one of the stages towards achieving sustainable cities because it is a test of the principles and directions before achieving the sustainable city.

3 - There are common characteristics of sustainable neighborhoods, including density, functional integration, sustainable transportation, the high quality of the perimeter, intergenerational and social inclusion, prosperity, ease of communication, and control of values and community participation.
Loss of Methylthioadenosine Phosphorylase by Immunohistochemistry Is Common in Pulmonary Sarcomatoid Carcinoma and Sarcomatoid Mesothelioma
Authors: Terra Simone , Roden Anja C , Yi Eunhee S , Aubry Marie Christine , Boland Jennifer M
Published: April 2021

Objectives

Differentiating malignant pleural mesothelioma from benign reactive mesothelial processes can be quite challenging. Ancillary tests such as BRCA1-associated protein 1 (BAP1) immunohistochemistry and p16 fluorescence in situ hybridization (FISH) are helpful tools to aid in this distinction. Immunohistochemistry for methylthioadenosine phosphorylase (MTAP) has recently been proposed as an effective surrogate marker for p16 FISH and is an attractive alternative test due to shorter turnaround time. There are little data regarding the specificity of MTAP loss for mesothelioma or whether it may be useful to distinguish mesothelioma from the most common entity in the differential diagnosis, sarcomatoid carcinoma.

Methods

We studied well-characterized cases of sarcomatoid carcinoma (n = 34) and sarcomatoid mesothelioma (n = 62), which were stained for MTAP (clone 2G4) and BAP1 (clone C-4).

Results

Loss of MTAP expression was observed in 17 (50%) of 34 pulmonary sarcomatoid carcinomas; BAP1 expression was retained in all of the cases in which it was performed (n = 31). MTAP expression was lost in 38 (61%) of 62 sarcomatoid mesotheliomas; BAP1 was lost in 6 (10%) of 62. In the six cases with BAP1 loss, five also had loss of MTAP, while MTAP expression was retained in one.

Conclusions

Loss of MTAP expression by immunohistochemistry is common in pulmonary sarcomatoid carcinoma, as it is present in half of cases. This rate is similar to what is observed in sarcomatoid mesothelioma (61%). Therefore, this stain is not useful to distinguish between these two malignancies. MTAP loss is more common than BAP1 loss in the setting of sarcomatoid mesothelioma (61% vs 10%, respectively).
MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition
Authors: Zuo Zeyuan , Cao Liu , Nothia Louis-Félix , Mohimani Hosein
Published: April 2021

Motivation

Untargeted mass spectrometry experiments enable the profiling of metabolites in complex biological samples. The collected fragmentation spectra are the metabolite’s fingerprints that are used for molecule identification and discovery. Two main mass spectrometry strategies exist for the collection of fragmentation spectra: data-dependent acquisition (DDA) and data-independent acquisition (DIA). In the DIA strategy, all the metabolites ions in predefined mass-to-charge ratio ranges are co-isolated and co-fragmented, resulting in multiplexed fragmentation spectra that are challenging to annotate. In contrast, in the DDA strategy, fragmentation spectra are dynamically and specifically collected for the most abundant ions observed, causing redundancy and sub-optimal fragmentation spectra collection. Yet, DDA results in less multiplexed fragmentation spectra that can be readily annotated.

Results

We introduce the MS2Planner workflow, an Iterative Optimized Data Acquisition strategy that optimizes the number of high-quality fragmentation spectra over multiple experimental acquisitions using topological sorting. Our results showed that MS2Planner increases the annotation rate by 38.6% and is 62.5% more sensitive and 9.4% more specific compared to DDA.

Availability and implementation

MS2Planner code is available at https://github.com/mohimanilab/MS2Planner. The generation of the inclusion list from MS2Planner was performed with python scripts available at https://github.com/lfnothias/IODA_MS.

Supplementary information

Supplementary data are available at Bioinformatics online.
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model
Authors: Hosoda Shion , Fukunaga Tsukasa , Hamada Michiaki
Published: April 2021

Motivation

Accumulating evidence has highlighted the importance of microbial interaction networks. Methods have been developed for estimating microbial interaction networks, of which the generalized Lotka–Volterra equation (gLVE)-based method can estimate a directed interaction network. The previous gLVE-based method for estimating microbial interaction networks did not consider time-varying interactions.

Results

In this study, we developed unsupervised learning-based microbial interaction inference method using Bayesian estimation (Umibato), a method for estimating time-varying microbial interactions. The Umibato algorithm comprises Gaussian process regression (GPR) and a new Bayesian probabilistic model, the continuous-time regression hidden Markov model (CTRHMM). Growth rates are estimated by GPR, and interaction networks are estimated by CTRHMM. CTRHMM can estimate time-varying interaction networks using interaction states, which are defined as hidden variables. Umibato outperformed the existing methods on synthetic datasets. In addition, it yielded reasonable estimations in experiments on a mouse gut microbiota dataset, thus providing novel insights into the relationship between consumed diets and the gut microbiota.

Availability and implementation

The C++ and python source codes of the Umibato software are available at https://github.com/shion-h/Umibato.

Supplementary information

Supplementary data are available at Bioinformatics online.
Model learning to identify systemic regulators of the peripheral circadian clock
Authors: Martinelli Julien , Dulong Sandrine , Li Xiao-Mei , Teboul Michèle , Soliman Sylvain , Lévi Francis , Fages François , Ballesta Annabelle
Published: April 2021

Motivation

Personalized medicine aims at providing patient-tailored therapeutics based on multi-type data toward improved treatment outcomes. Chronotherapy that consists in adapting drug administration to the patient’s circadian rhythms may be improved by such approach. Recent clinical studies demonstrated large variability in patients’ circadian coordination and optimal drug timing. Consequently, new eHealth platforms allow the monitoring of circadian biomarkers in individual patients through wearable technologies (rest-activity, body temperature), blood or salivary samples (melatonin, cortisol) and daily questionnaires (food intake, symptoms). A current clinical challenge involves designing a methodology predicting from circadian biomarkers the patient peripheral circadian clocks and associated optimal drug timing. The mammalian circadian timing system being largely conserved between mouse and humans yet with phase opposition, the study was developed using available mouse datasets.

Results

We investigated at the molecular scale the influence of systemic regulators (e.g. temperature, hormones) on peripheral clocks, through a model learning approach involving systems biology models based on ordinary differential equations. Using as prior knowledge our existing circadian clock model, we derived an approximation for the action of systemic regulators on the expression of three core-clock genes: Bmal1, Per2 and Rev-Erbα. These time profiles were then fitted with a population of models, based on linear regression. Best models involved a modulation of either Bmal1 or Per2 transcription most likely by temperature or nutrient exposure cycles. This agreed with biological knowledge on temperature-dependent control of Per2 transcription. The strengths of systemic regulations were found to be significantly different according to mouse sex and genetic background.

Availability and implementation

https://gitlab.inria.fr/julmarti/model-learning-mb21eccb.

Supplementary information

Supplementary data are available at Bioinformatics online.
SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning
Authors: Singh Jaspreet , Litfin Thomas , Paliwal Kuldip , Singh Jaswinder , Hanumanthappa Anil Kumar , Zhou Yaoqi
Published: April 2021

Motivation

Knowing protein secondary and other one-dimensional structural properties are essential for accurate protein structure and function prediction. As a result, many methods have been developed for predicting these one-dimensional structural properties. However, most methods relied on evolutionary information that may not exist for many proteins due to a lack of sequence homologs. Moreover, it is computationally intensive for obtaining evolutionary information as the library of protein sequences continues to expand exponentially. Here, we developed a new single-sequence method called SPOT-1D-Single based on a large training dataset of 39 120 proteins deposited prior to 2016 and an ensemble of hybrid long-short-term-memory bidirectional neural network and convolutional neural network.

Results

We showed that SPOT-1D-Single consistently improves over SPIDER3-Single and ProteinUnet for secondary structure, solvent accessibility, contact number and backbone angles prediction for all seven independent test sets (TEST2018, SPOT-2016, SPOT-2016-HQ, SPOT-2018, SPOT-2018-HQ, CASP12 and CASP13 free-modeling targets). For example, the predicted three-state secondary structure’s accuracy ranges from 72.12% to 74.28% by SPOT-1D-Single, compared to 69.1–72.6% by SPIDER3-Single and 70.6–73% by ProteinUnet. SPOT-1D-Single also predicts SS3 and SS8 with 6.24% and 6.98% better accuracy than SPOT-1D on SPOT-2018 proteins with no homologs (Neff = 1), respectively. The new method’s improvement over existing techniques is due to a larger training set combined with ensembled learning.

Availability and implementation

Standalone-version of SPOT-1D-Single is available at https://github.com/jas-preet/SPOT-1D-Single. Direct prediction can also be made at https://sparks-lab.org/server/spot-1d-single. The datasets used in this research can also be downloaded from GitHub.

Supplementary information

Supplementary data are available at Bioinformatics online.
Impact of Immunosuppressive Agents on Clinical Manifestations and Outcome of Staphylococcus aureus Bloodstream Infection: A Propensity Score–Matched Analysis in 2 Large, Prospectively Evaluated Cohorts
Authors: Camp Johannes , Glaubitz Lina , Filla Tim , Kaasch Achim J , Fuchs Frieder , Scarborough Matt , Kim Hong Bin , Tilley Robert , Liao Chun-Hsing , Edgeworth Jonathan , Nsutebu Emmanuel , López-Cortés Luis Eduardo , Morata Laura , Llewelyn Martin , Fowler Vance G , Thwaites Guy , Seifert Harald , Kern Winfried V , Kuss Oliver , Rieg Siegbert
Published: April 2021

Background

Staphylococcus aureus bloodstream infection (SAB) is a common, life-threatening infection. The impact of immunosuppressive agents on the outcome of patients with SAB is incompletely understood.

Methods

Data from 2 large prospective, international, multicenter cohort studies (Invasive Staphylococcus aureus Infections Cohort [INSTINCT] and International Staphylococcus aureus Collaboration [ISAC]) between 2006 and 2015 were analyzed. Patients receiving immunosuppressive agents were identified and a 1:1 propensity score–matched analysis was performed to adjust for baseline characteristics of patients. Overall survival and time to SAB-related late complications (SAB relapse, infective endocarditis, osteomyelitis, or other deep-seated manifestations) were analyzed by Cox regression and competing risk analyses, respectively. This approach was then repeated for specific immunosuppressive agents (corticosteroid monotherapy and immunosuppressive agents other than steroids [IMOTS]).

Results

Of 3188 analyzed patients, 309 were receiving immunosuppressive treatment according to our definitions and were matched to 309 nonimmunosuppressed patients. After propensity score matching, baseline characteristics were well balanced. In the Cox regression analysis, we observed no significant difference in survival between the 2 groups (death during follow-up: 105/309 [33.9%] immunosuppressed vs 94/309 [30.4%] nonimmunosuppressed; hazard ratio [HR], 1.20 [95% confidence interval {CI}, .84–1.71]). Competing risk analysis showed a cause-specific HR of 1.81 (95% CI, .85–3.87) for SAB-related late complications in patients receiving immunosuppressive agents. The cause-specific HR was higher in patients taking IMOTS (3.69 [95% CI, 1.41–9.68]).

Conclusions

Immunosuppressive agents were not associated with an overall higher mortality. The risk for SAB-related late complications in patients receiving specific immunosuppressive agents such as IMOTS warrants further investigations.
Vasoplegia induces high energy demand and depletes cardiac energetics: a new insight into physiological concepts of cardiac work and a model for acute heart failure?
Authors: Watson W , Neubauer S , Rider OJ
Published: April 2021

Funding Acknowledgements

Type of funding sources: Other. Main funding source(s): British Heart Foundation

Background / Introduction

Hearts subjected to constant high workload will, over time, fail.  We hypothesized vasoplegia would create a high cardiac energy demand and deplete cardiac energy reserves, a mechanism causing failure. With 31Phosphorus Magnetic Resonance Spectroscopy, we can measure energy: ATP usage (via creatine kinase flux) and reserves of phosphocreatine (PCr/ATP ratio).

Methods: Ten healthy volunteers were recruited

mean age 37, mean BMI 22.4, 5 male, 5 female.  A nitrate vasodilator (Glyceryl trinitrate, GTN) was used to induce vasoplegia, with MRI and MRS measurements taken before and during.

Results

There was reduced preload (falls in end diastolic volume and right atrial area) and afterload (mean blood pressure fall 14mmHg, p <0.0001).  Subjects mounted reflex tachycardia (mean heart rate rise 9bpm, p < 0.0001) and inotropy (mean baseline ejection fraction increase 5%, p = 0.0002) hence cardiac output and rate pressure product were maintained (baseline CO 6.24 ± 1.45 L/min vs GTN 6.49 ± 1.43 L/min, p = 0.37; baseline RPP = 6929 ± 976 mmHg.bpm vs GTN 7214 ± 1051 mmHg.bpm, p = 0.06).

There was a 58% increase in Creatine Kinase activity (kf) (baseline 0.158 s-1 vs GTN 0.249 s-1, p = 0.006) and CK flux (baseline 1.79 ± 0.78 umol/g/s vs GTN 2.59 ± 1.07 umol/g/s, p = 0.03), demonstrating increased ATP transfer.  PCr/ATP fell (from 2.17 ± 0.2 to 1.99 ± 0.22, p = 0.027).  Baseline PCr/ATP positively correlated with the change in stroke volume (R2 = 0.66, p = 0.005) during administration of GTN. In addition, whilst at rest, CK kf correlated with rate pressure product (R2 = 0.56, p = 0.03), there was no correlation seen during GTN.  

Conclusions 

We have shown vasoplegia increases energy demand upon the heart, despite unchanged cardiac output and rate pressure product.  Further, we have shown a fall in Phosphocreatine/ATP ratio, suggesting this ATP transfer outstripped oxidative phosphorylation and the phosphocreatine pool was depleted in order to maintain ATP delivery.  We speculate that progressive depletion of energetics in the context of high energy demand drives hearts under constant stress into failure.

In addition, we demonstrate that the magnitude of the resting phosphocreatine pool relates to ability to augment stroke volume during stress and suggest that this may be protective against a decline into failure.  Further work is needed, but PCr/ATP may be an important biomarker for treatments that target myocardial energetics to protect against failure. Abstract Figure 1
Prevalence of undiagnosed pre-diabetes or diabetes in patients with HFpEF presenting in the emergency department
Authors: Stratinaki M , Milaki K , Stavrakis S , Pitarokoilis M , Rogdakis E , Charitakis E , Kafarakis P , Garidas G , Stavratis S , Korela D , Katsiavos A , Thanasia A , Lamprogiannakis E , Foukarakis E
Published: April 2021

Funding Acknowledgements

Type of funding sources: None.

Introduction

Heart failure with preserved ejection fraction (HFpEF) has become a common cause of visiting the emergency department (ED). Type 2 diabetes mellitus (T2DM) is one of the important predisposing factors.

Purpose

To study the prevalence of undiagnosed pre-diabetes or T2DM in the patients visiting the ED due to HFpEF.

Methods

93 consecutive patients without known history of T2DM visited the ED with signs and symptoms of heart failure. Left ventricular ejection fraction (LVEF) was calculated using bedside ECHO. LVEF > 50% was used to classify HFpEF patients. HbA1c was measured to all patients and the cutoff for T2DM was HbA1c > 6.5% and for pre-diabetes 5.7-6.4%. Body mass index (BMI), brain natriuretic peptide (BNP) , creatinine  and  hemoglobin (Hb) were also recorded. Results are interpreted as mean ± SD.

Results

Mean age was 56 ± 11.8 years. 64/93 (68.8%) were female and 29/93(26.97%) male. Mean BMI was 36.52 ± 7.34 kg/m2 and mean Hb 13.51 ± 3.45 g/dl. Mean BNP was 584.82 ± 212.97 pg/ml. Mean creatinine was 1.11 ± 0.36mg/dl. 19/93 (17.67%) patients had HbA1c > 5.7-6.4% and were classified as pre-diabetics and 23/93(21.93%) had HbA1c > 6.5% and were classified as diabetics. We did not identify any correlation between the rest of the parameters.

Coclusion

44.64% of the patients that visited ED due to signs or symptoms of HFpEF were identified as having either pre-diabetes or T2DM. Taking into consideration the importance of the presence of T2DM in the prognosis of the patients with HFpEF, it would be reasonable to screen all patients with HFpEF for T2DM and suggest specialized treatment.