bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil carbon stocks in various types of land use in West Lombok
Authors: Bakti L A A , Wandiatari F D , Kusumo B H , Sukartono  , Fahrudin  , Virgiawan M A , Suwardji
Published: July 2021

Organic carbon greatly affects soil physical, chemical and biological fertility, so that this soil property is an indicator in determining soil health and quality. The amount of carbon stored in the soil can change due to land use, and its transformation from the ground to the air in the form of CO2, which can lead to global warming. This study aims to determine soil carbon stocks in various types of land use in West Lombok, West Nusa Tenggara Province, Indonesia. A number of soil samples (disturbed and undisturbed samples) were collected from various types of land use (forest, garden, paddy field, dry land and shrubs) using a soil drill (ring diameter 5.8 cm) from 3 depths; 0-10, 10-20, and 20-30 cm. Disturbed samples were dried, ground, sieved with a 2.00 mm sieve diameter, and analysed for their C-organic content using the Walkley and Black methods. Meanwhile, the undisturbed samples were processed in the laboratory to determine the bulk density (BV) of the soil. The results showed that the largest soil carbon stock was found in forests, followed by gardens, rice fields, moorlands, and shrubs. It was also found that the largest carbon stock was at a depth of 0-10 cm in all land use types and decreased with soil depth. These findings can be used as a reference in soil carbon management, considering that the carbon stock in rice fields, moor and shrubs is low to very low, which in turn can reduce soil fertility and productivity.
Combined application of organic and inorganic fertilizer on Alfisol soil fertility and maize growth
Authors: Syamsiyah J , Herdiansyah G , Aisyah N , Mentari F C , Larasati I
Published: July 2021

Fertilizer is an important factor in crop production, but its effectiveness depends on climate and the balance of fertilizers applied. This research aim was to determine the potential use of organic fertilizers to reduce the use of inorganic fertilizers on the growth of maize and Alfisol soil fertility. This research was conducted in the Jumantono, Karanganyar, used the Randomized Block Design with 9 treatments (A = Control, B = NPK standard, C = ¼ NPK + 1 PO, D = ½ NPK + 1 PO, E = ¾ NPK +1 PO, F = 1 NPK + 1 PO, G = ¾ NPK + ¼ PO, H = ¾ NPK + ½ PO, I = ¾ NPK + ¾ PO).The results showed that organic fertilizers at doses ¼, ½ and ¾ accompanied by ¾ NPK standard gives N total, P total, K total, and the plant height, number of leaves and stem diameter which are not different with dose of NPK standard. Organic fertilizers can reduce the use of NPK fertilizers.
Mapping of rain water harvesting potential at Keduang Sub-watershed, Central Java, Indonesia
Authors: Dwiatmojo H R , Komariah  , Ramelan A H , Priyanto E
Published: July 2021

One of the main issues in agriculture in this climate change era is the water crisis. It caused a drought that affected the delay of rice cultivation. A study found that Wonogiri Regency has very critical with a value of 163.1%. Hence, it is necessary to have an alternative solution to overcome it. In this case, utilizing rain by harvesting rainwater (RWH) can be used as an alternative to meet water needs during the dry season and for various other uses. One of the RWH applications is a small-farm reservoir (SFR). To identify the potential locations for RWH is using location suitability modelling based on GIS. The determination of the location depends on biophysical criteria such as rainfall, slope, soil texture, stream order, and land use. The socio-economic attributes consist of the distance to the river, road, settlement, and agriculture. To obtain the suitability location, after all of the maps are generated, next is reclassify the value to 0 and 1. In the end, the maps calculate with a raster calculator to define the suitability location that has value 1. Location and dimension details can find out. This study aims to determine the potential of RWH for agriculture (in specific, SFR) at Keduang Sub-watershed as a consideration for stakeholders’ decision. The results showed 226 areas are potential for SFR implementation and will make it easier for stakeholders to decide by comparing the suitability location map and the long-term strategic map.
Physiology and early growth of introduced robusta coffee clones in wet climate drylands in Bacan, North Maluku
Authors: Sulistiono W , Sugihono C , Hidayat Y , Assagaf M , Abu H L , Brahmantiyo B , Wahab A
Published: July 2021

Climate change, such as a prolonged dry season, will greatly determine the physiological processes and growth of robusta coffee. To overcome this, suitable clonal planting and proper fertilization are required. This study aims to determine the physiological properties and early growth for the suitability of climatic conditions and cultivation treatments. The study was conducted in Latosol soil in the dry land of IP2TP (Instalasi Penelitian dan Pengkajian Teknologi Pertanian) Bacan South Halmahera, North Maluku, from September 2018 to November 2020. The study was arranged in a factorial randomized block design with three replications. The first factor consists of clones of coffee consisting of five clones, namely: BP42, BP409, BP936, BP93 and SA237. The second factor is the fertilizer dosage which consists of 3 levels, namely: (1) 100% chemical NPK (120kg ha−1), (2) 50% chemical NPK + 50% organic and (3) 100% organic. The results showed that the chlorophyll and proline content of leaf was determined by the interaction of clones and fertilization. 50% organic fertilization produced the highest leaf chlorophyll content in clones BP409 and BP936. 50% organic fertilization also produced the lowest leaf proline in clone BP42 which showed more tolerance to drought. Agronomic traits such as plant height are determined by the type of clone. The plant height of BP409 clone highest was significantly different from BP42 and BP936.
Trichoderma biofungicides formulations on shallot growth, yield and fusarium wilt disease resistance
Authors: Sudantha I M , Suwardji S
Published: July 2021

The impact of climate change is an increase in extreme climatic events that make plants susceptible to disease. Fusarium wilt disease is one of the endemic diseases in extreme climatic areas in the high and lowlands. To deal with this climate change adaptation, a study was carried out that aims to determine the effect of the biofungicide Trichoderma spp. in controlling Fusarium wilt disease in several shallot varieties. This study used an experimental method carried out in the Highlands of Sembalun Bumbung Village, East Lombok using a Randomized Block Design with factorial experiments. The main factor is the formulation of biofungicides, namely: without biofungicides (control), liquid biofungicides, tablets and powders. The simple factor is shallot varieties, namely: Bali Karet, Ampenan, Keta Monca, Super Philip, and Super Cross. The results showed that liquid, tablet and powder of biofungicide could suppress Fusarium wilt disease up to 0%, while in control the percentage of disease reached 60%. Bali Karet varieties are very adaptive in the highlands, so they are very resistant to Fusarium wilt, Ampenan and Keta Monca adaptive in the highlands, while Super Philip and Super Cross are less adaptive. Bali Karet varieties showed the highest growth and yield.
Irrigation water management to increase planting index in Boyolali Regency, Indonesia
Authors: Setiapermas M N
Published: July 2021

Climate change will have a negative impact on water resources, agriculture, forestry, health and the vulnerability of public infrastructure and the extinction of various species. Water sources as the main means of agriculture, especially rice fields are the main thing in irrigation. Water sources for irrigation of paddy fields in Boyolali include weirs, trenches, springs that are collected in the form of ponds and a small part is a reservoir. Within 2 years after operation, the use of ponds of water for irrigation was able to accelerate yield increases. With various models of water sources, the cropping patterns include paddy-paddy-paddy, paddy-paddy-palawija (crop planted as 2nd crop in dry season), paddy-palawija-palawija and paddy-palawija-fallow. Water management arrangements in each area that use irrigation channels have an Association of Farmers Using Water who is tasked with making a schedule for the distribution of irrigation between blocks, especially if there is water scarcity such as during the dry season. Types of activities that are usually coordinated by farmer groups are pest control, channel maintenance, and irrigation arrangements. For channel maintenance, usually coordinating with the officers of association of water user farmer and development coordinators in their respective villages.
Characterization of persimmon (Diospyros kaki L.) as biodiversity originated from Indonesia
Authors: Yuniastuti E , Saputro M A A , Nandariyah  , Delfianti M N I
Published: July 2021

Persimmon (Diospyros kaki L.) belongs to the family Ebenaceae is widely grown in the climate zones range in the world. Persimmon grows well in media rich in organic matter with sufficient water content and generally at an altitude above 1000 masl. It is one type of subtropical fruit plant that is classified as rare in Indonesia. It has the potential to be developed for cultivation. The diversity characteristics of persimmon in each region are represented by the qualitative and quantitative. It may be caused by environmental factors or gene changes. Thus, the lack of environmental factors, plant growth will be disorder and will stop. Temperature is one of the factor affecting photosynthesis and plant metabolism at the cellular level. The difference in the temperatur range can be attributed to variations in latitude, topography, proximity to large bodies of water represented. The research aimed to identify morphological characters of persimmon at Selo District and to determine the level of persimmon diversity based on their morphological characters. The research was conducted in February – May 2020 in Selo Village, Boyolali, Central Java Province. This research used 15 samples of persimmon plant. The observation variable include geographical conditions and plant morphological characteristics (trees, stems, leaves, fruits). The data obtained were presented descriptively. The grouping of elements between samples was carried out by cluster analysis with the UPGMA method using the NTSYS. The results of the cluster analysis were presented in the form of dendogram. The results showed that Selo, persommon had various characters but several observation variables showed uniformity. The persimmon similarity coefficient is 0.66.
The role of dolomite and vermicompost in nutrient uptake and production of sweet potato (Ipomoea batatas L) on acid soil
Authors: Nufus N H , Sabrina T. , Hasanah Y
Published: July 2021

Sweet potato production is limited where it is caused by the lack of nutrients needed by the plant, where most of the sweet potato is planted on acid dry land where liming on the soil is an important activity that is sometimes neglected by farmers. so that the need for the nutrients needed is not fulfilled, so that the production of sweet potatoes is lo, by giving Dolomite and Bio-Vermi can help to increase nutrient uptake and plant production. The purpose of this study was to determine the effectiveness of dolomite and Bio-Vemi in optimizing nutrient absorption in the growth and production of sweet potato (Ipomoea batatas L.). The research was conducted in Aras Kabu Village, Beringi District, Deli Serdang Regency, North Sumatra using a randomized block design (RAK) with two factors and three replications. The first factor is the provision of Dolomite with 3 levels, namely D0 (without dolomite), D1 (1.5 ton/ha) and D2 (3 ton/ha). The second factor is the application of Bio-vermi with 4 levels, namely P0 (without Bio-vermi), P1 (100g/plant), P2 (150g/plant), P3 (200g/plant). The results showed that the application of dolomite and bio-vermi could increase soil pH, plant length growth and the number of yams planted. The highest increase in pH was found in D1 (1.5 ton/ha) of 5.57 and P2 (150g/plant) of 5.53, the longest plant length in P3 treatment (200g/plant) along 64.31 and D2 (3 ton/ha) along 64.27, the highest number of planted yams in treatment P1 (100g/plant) was 5.62. There is a significant interaction with dolomite and biovermi in increasing plant growth and nutrient uptake, with the provision of D1 (1.5 ton/ha) can increase soil pH and organic matter by 1% in acid soils, so that the longest plant length in treatment D1P3 is 69, 33 this proves that by giving Dolomite and Bio-vermi can help nutrient uptake and growth and production of sweet potato in acid soils.
Governance of mangrove restoration and conservation to climate change resilience in Bintan Island
Authors: Akbar D , Mariani  , Yudiatmaja W E , Edison
Published: July 2021

Policy of climate change mitigation and adaptation play an important role to socio-economic aspect. Controlling pollution and degradation of environment in coastal area adapted by capacity initiatives to protect marine environment from pollution and climate change. Climate change distributes micro-plastic to the ocean, including the activity of marine debris, fisheries and marine products industry, and shipping line (oil spill). Industry, agriculture in daily life contributes 80% of marine pollution, in addition, hundreds hectares of mangrove deforestation in Kepulauan Riau caused by development. According to Governmental Law No 19 year 1999 of pollution and damage control of the sea and implementation of The Bali Declaration as an adaptation of the 4th Intergovernmental Review Meeting (IGK4) to the Regional Capacity Canter for Clean Seas (RC3S) in Bali by mainstreaming protection of ocean and coastal ecosystem from the threat of chemical, waste, and micro plastic pollution. Mangrove as one of the best alternative of climate change mitigation divided into several zones, namely zone of core, zone utility and zone sustainability. The goals of this research are mapping the destruction factors and rehabilitation efforts, and also to know the interconnected key stakeholders on conserve mangrove and community based ecological mangrove restoration. Restoration and conservation of Mangrove in Kepulauan Riau, especially in Bintan and Batam, to the management of sustainable coastal through the method of Mangrove Restoration Opportunity Evaluation in collaboration between regional government, private sector, civil society, and expert. In recommendation, according to the program of Agency of Peat and Mangrove Restoration (BRGM) of Presidential Decree No 120/2020 by planting, survey, utility and other researches, mangrove sustainability needs consideration of the legality area and common analysis of Ministry and Provincial Government to avoid misunderstanding of taking action between conserve and build, and also taking further action of RZWP3K in Kepulauan Riau.
Snail mucus suppresses anti dsDNA antibodies in lupus mice
Authors: Nurudhin A , Prabowo N A , Ramadhani A
Published: July 2021

Lupus is closely related to weather changes. Changes in extreme weather due to climate changes can trigger lupus flares and cause death. Therefore, many studies are trying to find a drug that can cure lupus. Snail mucus has the properties of suppressing the immune system. The aim of this study is to see how snail mucus affects the levels of anti-dsDNA antibodies in lupus model mice. Experimental study uses a posttest-only group design. The control group was mice with 0.5 cc intraperitoneal (IP) saline. The lupus nephritis group was mice with pristane 0.5 cc IP, and the therapy group was mice with 0.5 cc IP pristane and 0.5 cc snail mucus per day at the 4th month of treatment for 14 days and after that the mice blood serum was taken and examined in the laboratory. The dsDNA antibody examination used the ELISA method. Statistical test with Anova followed by post hoc test. P is significant if it is less than 0.05. There was an increase in the levels of antibody dsDNA (p = 0.016) in the lupus group (75.13 + 22.5mg/dL) compare with the control group (56.96 ± 11.77 mg/dL), but there was a decrease in anti-dsDNA antibodies in the mice with snail mucus (56.01 ± 8.29 mg/dL; p = 0.02), and the methyl prednisolone group (53.47 ± 13.53 mg/dL; p = 0.009) when compared to the lupus group. Snail mucus suppresses anti dsDNA antibody levels in lupus mice.
Morphological characteristics of Temanggung’s robusta coffee (Coffea canephora Pierre ex A. Froehner) at different altitudes
Authors: Pangestika I W , Susilowati A , Purwanto E
Published: July 2021

Temanggung is the center of a coffee plantation in Central Java Province Indonesia since its altitude and cold climate are suitable for the growth and development of the plant. However, due to the climate changes in recent years, the air temperature at a specific altitude is not as cold as before. Vegetation responds to climate change by changing its phenological pattern, i.e., changing morphology. This study aimed to analyze the morphological characters of Temanggung robusta coffee at different altitudes by current climates condition. An exploratory study was conducted on two clusters of altitudes; there are 600 and 900 m asl approximately. Each group repeated in three locations, with each consisting of 5 trees. Fifteen quantitative morphological characters were evaluated using analysis of variance and further test performed using a 5%-LSD-test. Among those, the canopy diameter, plant height, leaf width, fruit length, fruit thickness, bean length, and bean thickness exhibited significant differences. Ten qualitative morphological characters were also evaluated. The characters varied between altitudes, i.e. leaf shape, young leaf color, fruit shape, and ripe fruit color. Meanwhile, there are no significant differences in leaf length and leaf petiole length characters.
The yield of three promising lines cempo ireng black rice M7 generation from gamma-ray irradiation
Authors: Nandariyah  , Sukaya  , Pujiasmanto B , Chasanah U
Published: July 2021

Black rice as a functional food crop contains high anthocyanins to prevent free radicals triggered by global climate change. However, black rice is often uncultivated because of weaknesses such as low yields and long harvest times. Breeding using gamma-ray irradiation is one solution to obtain new high-yielding varieties. This study aims to examine the yield and anthocyanin content of promising lines of cempo ireng black rice M7 generation from gamma-ray irradiation, the yield test is required in plant breeding. The research was conducted from December 2019 to August 2020 at Karanganyar, using different treatment of plant lines: three irradiated lines of black rice and a line without irradiation (control). Observations were made on 30 random sample plants each line. Data were analyzed descriptively and the comparison between mutant and control plant performance using the T-test. Observational variables included plant height, flowering and plant age, number of productive and non-productive tillers, panicle length, number of pithy and empty grains, the weight of 1,000 seeds, productivity, and anthocyanin content. The yield and anthocyanin content of irradiated lines were better than the control line. The highest production value of 8.29 tons/ha and the highest anthocyanin content of 75.04 ppm in line 52.
Laboratory examination to measure antibodies formed after vaccination of COVID-19
Authors: Hasugian A R , Khariri
Published: July 2021

Coronavirus Disease (COVID-19) as the reemerging disease which first discovered on December 2019 in Wuhan, China. World Health Organization (WHO) has designated COVID-19 as a global pandemic on March 11th, 2020. Covid-19 is related with the climate change which influences the environment of life cycle of SARS-CoV2 vector. With there are no drug of choice for Covid-19 until this time, giving vaccination is one of the strategy of prevention to break the transmission and reduce the number of cases. Vaccination can trigger immunity by forming antibodies and protect the individual from antigen which came in to host and can be a marker for future vaccine for disease relates unpredicted climate change. This paper reviews several laboratory methods that can be used to detect antibodies such as Lateral Flow Immunoassay (LFIA), Enzyme-linked Immunosorbent Assay (ELISA) and Electro-Chemiluminescence Immunoassay (ECLIA) and see their ability to protect individuals from COVID-19 after vaccination using neutralization test such as Plaque Reduction Neutralization Test (PNRT) or Surrogate Reduction Neutralization Test (sRNT). The benefit of this reviews is to understand the optimal methods to measure and detect antibody and to improve vaccine development strategy for the disease relate with unpredicted climate change in the future based on antibodies seroconversion and seroprotection.
Farmers’ adaptation in dealing with limited water (A case study on Wonogiri Regency)
Authors: Wardani R I K , Widiyanto  , Rusdiyana E , Rinanto Y , Sudibya
Published: July 2021

The vulnerability of farmers to drought is determined by the interaction of the potential impacts of climate change. The impact of climate change is felt by residents of Paranggupito District, one of which is in Ketos Village in the agricultural sector, especially rainfed land which is very vulnerable to long drought conditions. Farmers ‘losses to drought are determined by the interaction of climate change impacts and farmers’ adaptation. This research aims to find out the adapting strategy the farmers take in dealing with water limitation. The subject of research consisted of farmers in Ketos Village, Paranggupito Sub District, Wonogiri Regency. The research design used was descriptive qualitative one with purposive and snowball sampling techniques. Data collection was carried out using observation, in-depth interview, focus group discussion, and documentation. Data was analyzed using triangulation technique. The result of research shows that to adapt to their condition, the farmers adopt short-and medium-term adapting behaviour, including: determining crop calendar, selecting plant variety, applying intercropping system, determining appropriate planting pattern, controlling pest and disease, determining planting technique, and monitoring continuously.
Effect of supplementary irrigation on rice yield in dry land during rainy season
Authors: Anshori A , Suswatiningsih T E , l Viandari N A , Rajiman  , Mujiyo
Published: July 2021

Climate change causes change in rainfall patterns, which will affect water availability. Water is a limiting factor for rice production on dry land. Increasing rice yields on dry land requires precise water management. This study aimed to investigate the effect of supplementary irrigation when it does not rain on rice yields in dry land during rainy season. The research was conducted on dry land in Playen, Gunung Kidul, Daerah Istimewa Yogyakarta, Indonesia during rainy season of November 2020 to February 2021. The treatments were supplementary irrigation if 1 day without rain (A1), if 2 days without rain (A2) and if 3 days without rain (A3), and they were compared to control without supplementary irrigation (A0). This research used a randomized completely block design, each treatments replicated 4 times. The results showed A1 gave the highest grain yield, namely 7.786 ton ha−1, significant different with other treatments of A2, A3 and A0. Dry straw of A1 was 7.324 ton ha−1, significant different with A2, A3 and A0. Carbon absorption of A1 was 6.860 ton ha−1, consisting of carbon in grain 3.575 ton ha−1 and straw 3.285 ton ha−1, it was significant different with other treatments of A2, A3 and A0 (p<0.05; n=16). B/C A2 1.73 was highest from the others and its farmers have profit Rp. 19,276,360 ha−1.
Identifying the sustainability level of urban slums in the Greater Jakarta, Indonesia using a composite index
Authors: Yuniar A Z , Kristanto G A , Dahlan A V , Kemala D
Published: July 2021

The Republic of Indonesia’s government aims to alleviate slums to mark the start of smart city development. The goals of KotaKu, a national program established to handle slum issues, are 100% access to sanitation and clean water and the reduction of slum areas to zero, which aligns with the nation’s commitment to Sustainable Development Goals to tackle climate change and its impacts. Slum identification and intervention are undertaken through the government’s emphasis on the settlement’s environment, resulting in the wrongful judgment of an area as a slum or vice versa. This study is conducted in four urban slums or kampungs located in the Greater Jakarta area (i.e. Kampung Cikini, Kampung Gedong Pompa, Kampung Cimone-Cincau, and Kampung Markisa). Each area’s sustainability level was calculated using a composite index that used indicators to represent the three pillars of sustainability, i.e., social, economy, and environment. Kampung Cimone-Cincau had the best sustainability (0.75), while Kampung Gedong Pompa had the worst (0.52). Across all the study areas, access to sanitation reached 97% and, access to clean water reached 98%. More thorough indicators to identify slum sustainability can help resolve an area’s wrongful judgment, and a more suitable approach for slum intervention can be made.
Technical efficiency of organic rice farming in Ngawi Regency (The case of the Komunitas Ngawi Organic Center)
Authors: Krisdiyanto R , Harisudin M , Irianto H
Published: July 2021

Soil degradation fertility is a form of environmental damage due to climate change, ironically caused by the agricultural sector as the largest contributor to global warming. One of the efforts to overcome the problem of climate change issues in the agricultural sector is through organic rice farming practices. This study aims to analyze organic rice farming which includes farming profiles, influencing factors, and technical efficiency level of organic rice farming in Ngawi Regency which focuses on the Komunitas Ngawi Organic Center (KNOC). This study used a quantitative descriptive basic method with a census of all active member organic rice farmers of KNOC. The production factors of organic rice were analyzed using the Cobb-Douglass stochastic frontier production function. The results showed that in general the average organic rice farming profile on certified land was superior than non-certified land, with 1.96 R/C ratio on certified land, while 1.41 R/C ratio on non-certified land. The time it takes for land to become certified organic is three consecutive growing seasons applying supervised organic farming. Production factors that positively significantly influence organic rice farming are land area, labor, and organic pesticides. Excessive use of organic fertilizer input can increase the number of wild weeds on organic rice fields which can inhibit the growth of organic rice and reduce grain production. The level of technical efficiency achieved by respondent farmers varies widely between 0.57 - 0.93 with an average of 0.80 which is considered efficient.
Farmers’ conservation behavior in Solo Hulu Watershed
Authors: Anantanyu S , Suwarto  , Winarno J , Wibowo A , Permatasari P
Published: July 2021

Watershed management is an important aspect to support the preservation of surrounding area. The function of upstream area as water catchment area should be protected by keeping the utilization of area from support capability surpassing the environment. Community participation is very necessary to maintain the environment in the ecosystem. This research will provide information about anything related to the profile of farmers, farming, and farming system in Beruk Village. Research is means of providing sustainable livelihood farming programs very useful to the farmer community. The research method used was case study, in which data was collected through in-depth interview, focus group discussion and participatory observation. Participative approach was conducted through in-depth interview, observation and involving farmers in Forum Group Discussion (FGD). The result of research showed that to minimize landslide in the farming area, farmer communities in Beruk Village always consider soil cultivating technique and irrigation system. Irrigation system organization is the farmers’ way of maintaining their land preservation. Farmers do not plant their land with big trees because they are afraid that the trees will shade their vegetables and lead to the death of vegetables. Local leadership in Beruk Village can be seen from presence of community leader.
An approach to gene-based testing accounting for dependence of tests among nearby genes
Authors: Yurko Ronald , Roeder Kathryn , Devlin Bernie , G’Sell Max
Published: July 2021

In genome-wide association studies (GWAS), it has become commonplace to test millions of single-nucleotide polymorphisms (SNPs) for phenotypic association. Gene-based testing can improve power to detect weak signal by reducing multiple testing and pooling signal strength. While such tests account for linkage disequilibrium (LD) structure of SNP alleles within each gene, current approaches do not capture LD of SNPs falling in different nearby genes, which can induce correlation of gene-based test statistics. We introduce an algorithm to account for this correlation. When a gene’s test statistic is independent of others, it is assessed separately; when test statistics for nearby genes are strongly correlated, their SNPs are agglomerated and tested as a locus. To provide insight into SNPs and genes driving association within loci, we develop an interactive visualization tool to explore localized signal. We demonstrate our approach in the context of weakly powered GWAS for autism spectrum disorder, which is contrasted to more highly powered GWAS for schizophrenia and educational attainment. To increase power for these analyses, especially those for autism, we use adaptive $P$-value thresholding, guided by high-dimensional metadata modeled with gradient boosted trees, highlighting when and how it can be most useful. Notably our workflow is based on summary statistics.
DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor
Authors: Xu Zhaochun , Luo Meng , Lin Weizhong , Xue Guangfu , Wang Pingping , Jin Xiyun , Xu Chang , Zhou Wenyang , Cai Yideng , Yang Wenyi , Nie Huan , Jiang Qinghua
Published: July 2021

Accurate prediction of immunogenic peptide recognized by T cell receptor (TCR) can greatly benefit vaccine development and cancer immunotherapy. However, identifying immunogenic peptides accurately is still a huge challenge. Most of the antigen peptides predicted in silico fail to elicit immune responses in vivo without considering TCR as a key factor. This inevitably causes costly and time-consuming experimental validation test for predicted antigens. Therefore, it is necessary to develop novel computational methods for precisely and effectively predicting immunogenic peptide recognized by TCR. Here, we described DLpTCR, a multimodal ensemble deep learning framework for predicting the likelihood of interaction between single/paired chain(s) of TCR and peptide presented by major histocompatibility complex molecules. To investigate the generality and robustness of the proposed model, COVID-19 data and IEDB data were constructed for independent evaluation. The DLpTCR model exhibited high predictive power with area under the curve up to 0.91 on COVID-19 data while predicting the interaction between peptide and single TCR chain. Additionally, the DLpTCR model achieved the overall accuracy of 81.03% on IEDB data while predicting the interaction between peptide and paired TCR chains. The results demonstrate that DLpTCR has the ability to learn general interaction rules and generalize to antigen peptide recognition by TCR. A user-friendly webserver is available at http://jianglab.org.cn/DLpTCR/. Additionally, a stand-alone software package that can be downloaded from https://github.com/jiangBiolab/DLpTCR.
Altered Somatosensory Cortical Activity Is Associated with Cortical Thickness in Adults with Cerebral Palsy: Multimodal Evidence from MEG/sMRI
Authors: Trevarrow Michael P , Lew Brandon J , Hoffman Rashelle M , Taylor Brittany K , Wilson Tony W , Kurz Max J
Published: July 2021

Somatosensory cortical activity is altered in individuals with cerebral palsy (CP). However, previous studies have focused on the lower extremities in children with CP and have given less attention to structural changes that may contribute to these alterations. We used a multimodal neuroimaging approach to investigate the relationship between somatosensory cortical activity and cortical thickness in 17 adults with CP (age = 32.8 ± 9.3 years) and 18 healthy adult controls (age = 30.7 ± 9.8 years). Participants performed a median nerve paired-pulse stimulation paradigm while undergoing magnetoencephalography (MEG) to investigate somatosensory cortical activity and sensory gating. Participants also underwent magnetic resonance imaging to evaluate cortical thickness within the area of the somatosensory cortex that generated the MEG response. We found that the somatosensory responses were attenuated in the adults with CP (P = 0.004). The adults with CP also hypergated the second stimulation (P = 0.030) and had decreased cortical thickness in the somatosensory cortex (P = 0.015). Finally, the strength of the somatosensory response was significantly correlated with the cortical thickness (P = 0.023). These findings demonstrate that the aberrant somatosensory cortical activity in adults with CP extends to the upper extremities and appears to be related to cortical thickness.
Cardiac natriuretic peptide deficiency sensitizes the heart to stress-induced ventricular arrhythmias via impaired CREB signalling
Authors: Hall Eric J , Pal Soumojit , Glennon Michael S , Shridhar Puneeth , Satterfield Sidney L , Weber Beth , Zhang Qinkun , Salama Guy , Lal Hind , Becker Jason R
Published: July 2021

Aims

The cardiac natriuretic peptides [atrial natriuretic peptide (ANP) and B-type natriuretic peptide (BNP)] are important regulators of cardiovascular physiology, with reduced natriuretic peptide (NP) activity linked to multiple human cardiovascular diseases. We hypothesized that deficiency of either ANP or BNP would lead to similar changes in left ventricular structure and function given their shared receptor affinities.

Methods and results

We directly compared murine models deficient of ANP or BNP in the same genetic backgrounds (C57BL6/J) and environments. We evaluated control, ANP-deficient (Nppa−/−) or BNP-deficient (Nppb−/−) mice under unstressed conditions and multiple forms of pathological myocardial stress. Survival, myocardial structure, function and electrophysiology, tissue histology, and biochemical analyses were evaluated in the groups. In vitro validation of our findings was performed using human-derived induced pluripotent stem cell cardiomyocytes (iPS-CMs). In the unstressed state, both ANP- and BNP-deficient mice displayed mild ventricular hypertrophy which did not increase up to 1 year of life. NP-deficient mice exposed to acute myocardial stress secondary to thoracic aortic constriction (TAC) had similar pathological myocardial remodelling but a significant increase in sudden death. We discovered that the NP-deficient mice are more susceptible to stress-induced ventricular arrhythmias using both in vivo and ex vivo models. Mechanistically, deficiency of either ANP or BNP led to reduced myocardial cGMP levels and reduced phosphorylation of the cAMP response element-binding protein (CREBS133) transcriptional regulator. Selective CREB inhibition sensitized wild-type hearts to stress-induced ventricular arrhythmias. ANP and BNP regulate cardiomyocyte CREBS133 phosphorylation through a cGMP-dependent protein kinase 1 (PKG1) and p38 mitogen-activated protein kinase (p38 MAPK) signalling cascade.

Conclusions

Our data show that ANP and BNP act in a non-redundant fashion to maintain myocardial cGMP levels to regulate cardiomyocyte p38 MAPK and CREB activity. Cardiac natriuretic peptide deficiency leads to a reduction in CREB signalling which sensitizes the heart to stress-induced ventricular arrhythmias.
Empirical studies of escape behavior find mixed support for the race for life model
Authors: Wrensford Kwasi , Gutierrez Jahaziel , Cooper William E , Blumstein Daniel T
Published: July 2021

Escape theory has been exceptionally successful in conceptualizing and accurately predicting effects of numerous factors that affect predation risk and explaining variation in flight initiation distance (FID; predator–prey distance when escape begins). Less explored is the relative orientation of an approaching predator, prey, and its eventual refuge. The relationship between an approaching threat and its refuge can be expressed as an angle we call the “interpath angle” or “Φ,” which describes the angle between the paths of predator and prey to the prey’s refuge and thus expresses the degree to which prey must run toward an approaching predator. In general, we might expect that prey would escape at greater distances if they must flee toward a predator to reach its burrow. The “race for life” model makes formal predictions about how Φ should affect FID. We evaluated the model by studying escape decisions in yellow-bellied marmots Marmota flaviventer, a species which flees to burrows. We found support for some of the model’s predictions, yet the relationship between Φ and FID was less clear. Marmots may not assess Φ in a continuous fashion; but we found that binning angle into 4 45° bins explained a similar amount of variation as models that analyzed angle continuously. Future studies of Φ, especially those that focus on how different species perceive relative orientation, will likely enhance our understanding of its importance in flight decisions.
What affects the acceptance of illness in patients with atrial fibrillation?
Authors: Swiatoniowska-Lonc N , Kasperczak D , Jankowska-Polanska B
Published: July 2021

Funding Acknowledgements

Type of funding sources: None.

Background. Patients with atrial fibrillation (AF) have symptoms that require advanced treatment. The most common include palpitations, dyspnea, dizziness, tiredness, chest pain and anxiety. Both the symptoms and treatment and its complications adversely affect the perception of the disease among patients with AF. The research proves that acceptance of illness (AIS) is a factor positively influencing the quality of life, but also the adaptation to the therapeutic recommendations of patients with chronic diseases. There is little research on factors increasing the level of AIS among patients with AF.

The aim of the study is to determine the level of acceptance of illness in patients with AF and factors influencing the level of acceptance of illness.

Material and methods. 84 patients (including 51 men) aged 57.86 ± 17.72 years hospitalized in the cardiology department due to heart rhythm disorders. Standardized tools were used in the study: Acceptance of Illness Scale (AIS) to assess disease acceptance and International Physical Activity Questionnaire (IPAQ) to assess physical activity.  Sociodemographic and clinical data were taken from the hospital register.

Results. In the study group the average result of acceptance of illness (AIS) was 27.67 ± 7.70. 48.8% of patients had a high degree of disease acceptance, 38.09% average, and 13.11% had no acceptance. The examined patients showed a lack of physical activity (IPAQ = 0.92 ± 0.40). In comparative analyses women had lower level of AIS than men (27.36 ± 7.37 vs. 27.86 ± 7.97; p = 0.01), patients more often hospitalized due to AF lower than patients less frequently hospitalized (26.30 ± 6.11 vs. 30.55 ± 8.55; p = 0.02). Lower level of AIS was observed in patients with comorbidities (34 ± 6.25 vs. 22 ± 6.66; p < 0.001). Smokers had higher level of AIS than non-smokers (28.66 ± 6.65 vs. 27.00 ± 7.56; p = 0.02), similarly, physically active persons than inactive ones (26.48 ± 8.27 vs. 23.07 ± 10.58; p = 0.01). In correlation analysis, physical activity turned out to be an important determinant having a positive effect on the level of AIS (r = 0.220; p = 0.03).

Conclusions. Patients with AF have moderate level of acceptance of illness and low level of physical activity. A higher level of AIS is observed in men, without comorbidities, less frequently hospitalized and smokers. The important determinant having positive influence on AIS is physical activity.
The impact of the acceptance of illness on the quality of life of patients with atrial fibrillation
Authors: Jankowska-Polanska B , Kasperczak D , Swiatoniowska-Lonc N , Polanski J
Published: July 2021

Funding Acknowledgements

Type of funding sources: None.

Background. Atrial fibrillation (AF) is the most common supraventricular arrhythmia. AF and the complications associated with it interfere with the physical, mental and social well-being of a person, thus affecting the quality of life. An important factor affecting the quality of life of patients with AF is the acceptance of illness (AI). In spite of the large problem related to this subject, the analysis of the relation between the acceptance of illness and the quality of life of patients with AF is insufficient.

The aim of the study was to assess the impact of the acceptance of illness on the quality of life of patients with AF.

Material and methods. 84 patients (including 51 men) aged 57.86 ± 17.72 years hospitalized in the cardiology department due to heart rhythm disorders. Standardized tools were used in the study: Acceptance of Illness Scale (AIS) to assess the acceptance of illness and Arrhythmia-Specific questionnaire In Tachycardia and Arrhythmia (ASTA) to assess quality of life.

Results. The majority of patients were secondary educated (64.27%), lived in a city (78.58%), were inactive (57.15%), were hospitalized 3-5 times (42.85%), had a cardiostimulator (23.80%) or underwent ablation (22.62%) during the last year. The average result of the acceptance of illness was 27.67 ± 7.70. 48.8% of patients had a high level of the acceptance of illness, 38.09% average, and 13.11% did not accept their illness. The mean result of quality of life for the whole studied group was (ASTA III) 25.64 ± 8.64. As regards the severity of symptoms (ASTA II) the mean result was 17.15 ± 5.89. Correlation analysis showed that the higher the level of the acceptance of illness the higher the quality of life (r = 0.640; p = 0.002) and lower the severity of AF symptoms (r=-0.51, p < 0.001).

Conclusions. Patients with AF present a moderate level of disease acceptance and quality of life. The acceptance of illnessis the independent predictor and significantly increases quality of life of patients with AF.
Quality evaluation of patient educational resources for catheter ablation of atrial fibrillation
Authors: Cano Valls A , Gallagher C , Mont LL , Carro E , Sanders P , Hendriks JM
Published: July 2021

Funding Acknowledgements

Type of funding sources: None.

Background

The prevalence of atrial fibrillation (AF) is increasing rapidly with growing utilisation of catheter ablation (CA) as a treatment strategy. Education of individuals undertaking this procedure is diverse, with varying degrees of information provided and little standardisation. Many individuals utilise the internet as an educational resource. However, there is limited regulation of online patient information.

Aims

The purpose of this study was to evaluate the quality of web based  patient education resources for patients undergoing CA in the management of AF.

Methods

A cross-sectional observational study was performed to obtain all freely accessible online educational resources designed to inform AF patients about CA. from inception until 1st October 2019. Three search engines were used: Google, Yahoo! and Bing, using the search terms "atrial fibrillation" and "catheter ablation" combined with "patient information and patient education" in English and Spanish. The Patient Education Materials Assessment Tool (PEMAT) is a validated tool used to evaluate web-based patient education materials as well as  printable tools. The PEMAT score objectively measures the understandability and actionability of printable tools for audio-visual material.

Results

A total of 17 websites and 15 printable tools were included in the analysis. Non-government organizations developed 19% of materials and 75% were created by private or university hospitals. Nineteen materials (59.3%) were rated as highly understandable and 25 materials (21%) were rated as highly actionable, whilst ten materials had an actionability of 0% (6 websites and 4 printable tools).  Less than a half of the materials evaluated were highly rated by the PEMAT score, with a total of 7 websites (41%) and 7 printable tools (46,6%) scoring >70%.

Conclusion

The overall understandability of educational CA material was high, whilst improvement of actionability is warranted. The addition of summaries, visual aids and tools such as checklists may improve quality. These findings have significant implications for developing new patient educational material for CA in AF.
Pharmacist-led medicines optimisation clinic for implantable cardiac device patients
Authors: Patel M , Fhadil S , Zemrak F , Wright P , Rochford C , Jones S , Earley M , Antoniou S
Published: July 2021

Funding Acknowledgements

Type of funding sources: None.

Background/Introduction: Cardiac implantable electronic devices (CIED) enhance detection of atrial fibrillation (AF), providing a comprehensive measure of AF burden.  Patients with device-detected AF are usually referred for anticoagulation to their local anticoagulation clinic or General Practitioner (GP), which often delays time to initiation, potentially increasing the risk of stroke.  In addition, AF is associated with increased risk of cardiovascular disease and mortality.  Optimising blood pressure, cholesterol and lifestyle choices can significantly reduce the risk of cardiovascular disease and associated mortality in these patients.

Purpose

To develop and evaluate an innovative pathway to allow Specialist Cardiac Pharmacists to promptly assess and initiate anticoagulation in patients with device-detected AF, and additionally address risk factors for prevention of cardiovascular disease.

Methods

As part of a quality improvement initiative, a pathway was developed where patients with AF identified on CIED who require anticoagulation are referred for assessment and management to a pharmacist-led optimisation clinic.  Specialist Cardiac Pharmacists contact patients within 5 days of referral to discuss and initiate or optimise treatment for AF, blood pressure, cholesterol and lifestyle choices.  Patients deemed inappropriate for anticoagulation were referred back to the medical team for further assessment.  All patients received a follow-up telephone consultation at 4-6 weeks to assess tolerability, adherence and response to treatment.

Results

Between September 2020 and February 2021, 22 patients were referred to the optimisation clinic. Mean age was 74.32 +/- 12.34 years and 77% were men.  Mean CHA2DS2VASc was 3.4 +/- 0.8 and mean HASBLED was 1.2 +/- 0.6. The average time from referral to anticoagulation was 3 days compared to 4 weeks prior to implementation of the pathway. All patients were assessed and appropriately anticoagulated, whereas approximately 15% of patients were still not anticoagulated at 3 months prior to implementation of the pathway despite referral to their local clinic. All patients had their blood pressure and cholesterol reviewed, which were optimised in 23% and 41% of patients respectively.  All patients confirmed adherence and suffered no adverse effects on follow-up.

Conclusion(s): We report the safe and successful implementation of a pharmacist-led medicines optimisation clinic.  This has significantly reduced time to anticoagulation without compromising safety, as well as assuring all patients are appropriately anticoagulated.  In addition, over half of patients required blood pressure and/or cholesterol optimisation to reduce the risk of cardiovascular disease, a service not previously provided for this cohort of patients.