bluuebunny/crossref_metadata_2025 huggingface dataset:
Site selection for the development of organic farming for conservation purposes in the upstream of Air Bengkulu watershed, Bengkulu
Authors: Lovita V , Sulistyo B , Listyowati E A
Published: April 2022

Awareness of the dangers posed by the use of synthetic chemicals in farming attracts attention. The development of organic agriculture requires a suitable location. However, sometimes, suitable land is very limited. This study aims to select the site for the development of organic agriculture, as well as to function in overcoming the existence of critical land, especially in the Upstream of Air Bengkulu Watershed, Bengkulu. The research method carried out is by compiling a Map of Conservation Activity Plan (CAP) based on a model developed by the then Ministry of Environment and Forestry. Maps used for input to CAP are EHL (Erosion Hazard Level), Soil Depth, Slope, Population Pressure, and the Recommended Landuse. From the CAP Map, the sites that are estimated to be used for organic farming development locations will be obtained. Results show that the sites for CAP to support organic farming is divided, broadly, into 2 categories: (1) mixed cultivation, minimum tillage, planting of ground cover, management of organic matter and application of agroforestry covers 9.32% in Semidang Lagan and Karang Tinggi District, and (2) mixed cropping, minimum tillage, ground cover planting, organic matter management, permanent vegetation and application of agroforestry covers 38.79% in Taba Penanjung District, Bajak Dua, Jambu and Rindu Hati Village. While 51.89% of the study area in Taba Penanjung District should be used for protected area.
Modeling of Sandy Soil Compaction and Water Holding Capacity Due to Biogas Slurry Ameliorant
Authors: Yudhistira D.T. , Ngadisih  , Karyadi J.N.W. , Tirtalistyani R. , Ismail M.H. , Mawandha H.G.
Published: April 2022

Model could be used to study the behavior of real systems such as hydrosphere (soil system) for improving their performance as basis of decision-making that promote the sustainability. Here, the study focused on SDGs point 15, how the agriculture particularly soil management should keep the life on land. Biogas slurry (BS) is a liquid-solid mix waste from livestock that useful for soil improving soil quality. Sandy soil has some limitations when used as media of plant cultivation, mainly poor in water holding capacity and less of organic content. This study aimed to measure and explore the sandy soil quality (soil compaction, SC and water holding capacity, WHC) due to BS application. A completely randomized design (CRD) in laboratory was adopted in this study where soil and BS put in a pot of diameter and height of 8.2 cm and 12 cm, respectively. The experiment was carried out with treatment of sandy soil as control (K), sandy soil and BS dose15 ton/ha (D1), 30 ton/ha (D2), and 45 ton/ha (D3). The soil was incubated 84 days that every 14 days (incubation time, IT) the SC and WHC were measured. Mathematical model and Two Ways ANOVA Test were applied to analyze the data. Logistic equation was acceptable (R2 > 80%) to describe soil compaction behavior in sandy soil with BS ameliorant. The SC rate of K, D1, D2, and D3 treatments were - 0.0251, -0.0524, -0.0280, and -0.0360, respectively. This study revealed BS and IT significantly affect SC and WHC of sandy soil with BS ameliorant.
The capacity of agroforestry and food crop system for C stock and sequestration (case study on Saobi Island Madura)
Authors: Mandasari P A , Adim M , Aisjah St , Supriyadi S , Murniyanto E
Published: April 2022

Reducing CO2 emission is basically simultaneous processes between suppressing the carbon (C) release and increasing C sequestration. These can be carried out by plants as they have capability to fix CO2. The objective of this study was to investigate the C stock and sequestration in dryland with two systems, namely teak tree-based agroforestry and food crop system on Saobi Island, Madura. Data were collected from three measuring plots of each system, which were determined purposively. For the agroforestry system, the employed plot was the one having relatively regular tree spacing; while for the food crop system, the plot compromised the border where the jaran trees planted. Teak tree biomass and C stock were calculated by employing allometric equations, while for food crops, undergrowth, and litter were determined by using destructive methods. Carbon stock was calculated by an allometric equation and conversion from biomass weight. The results showed that agroforestry and food crop systems produced biomass up to 11.59 and 14.97 t/ha respectively. Although the biomass of both systems was quite similar, the C stock in the agroforestry system was higher than that of the food crop system; as the agroforestry one could sequestrate CO2 as much as 2308.23 t/ha, and 20.96 t/ha in existing conditions.
Improving coffee quality through yeast addition in the fermentation process to support sustainable coffee production
Authors: Mariyam S , Kistanti A , Karyadi J N W , Widiyastuti R J
Published: April 2022

Indonesia is the fourth largest country in the world as a coffee producer. Coffee has complex chemical structure with volatile and non-volatile compounds, this composition has an important role in the distinctive coffee’s taste. Fermentation is an important stage in coffee processing, it has a direct effect on the coffee’s quality. So far, many people have done traditional fermentation relying on natural microbes in fresh coffee. The purpose of this study was to improve coffee’s quality by controlled fermentation using added yeast, thereby encouraging the sustainability of coffee production. The coffee cherries were taken from a coffee plantation in Merapi mountain area, Yogyakarta. Yeast isolates used were Saccharomyces cerevisiae and Pichia kudriavzevii. The experimental processes of fermentation were carried out on three different environmental variables, namely: fermentation in bioreactor with inoculum, fermentation in bioreactor without inoculum, and traditional fermentation in an open container. Coffee cherries were peeled by pulper machine then kept underwater for 72 hours, except for fermentation in an open container. Data logger was used to monitor the temperature changes, the moisture content, brix, PH, and color change were measured for each 24 hours during fermentation. From the data analyzed, the moisture content and brix were increased during fermentation. The result indicated that fermentation by yeast addition raised acidity in the final coffee result, this can be shown from the PH result that eventually decreased from 5.83 to 5.49 and 6.15 to 4.29, respectively. The maximum temperature for both yeast species addition was reached at a 24 to 48 hours period. The result showed that the color parameter (LAB) was elevated, except the lightness value from Pichia kudriavzevii fermentation. Result in this study revealed that the type of microorganism will determine the characteristics of the coffee produced, such as the acidity. The specific taste and aroma compound were generated during fermentation by different yeast species.
Stable and unstable carbon fraction under different vegetable farming system on Mt. Merbabu’s andisols, Central Java
Authors: Palayukan G D , Hanudin E , Purwanto B H
Published: April 2022

This study aims to find out the effect of vegetable cultivation systems that are managed organically, semi-organic, and conventionally on the unstable and stable carbon fraction of Andisol soil on the north slope of Merbabu. Field research was carried out using a sampling method in 3 different farming systems, namely organic (O), semi-organic (SO), and conventional (K) and 3 soil depths, namely 0-20 cm, 20-40 cm, and 40-60 cm. The parameters measured include the physical, chemical, and biological properties of the soil. The physicochemical properties of the soil analyzed included texture, volume weight of soil, pH-H2O, pH-NaF, organic matter, cation exchange capacity, total-N, Al/Fe extracted oxalate and pyrophosphate. The carbon fractions analyzed included particulate organic matter carbon, water-soluble carbon, soil organic carbon mineralization, microbial biomass carbon, humic acid, and fulvic acid. Analysis of Variance (ANOVA) was conducted to determine the effect of farming system and soil depth on soil physicochemical properties, while the difference between the two-treatment means was analyzed by DMRT. Regression-correlation analysis was carried out to determine the close relationship between the independent and dependent variables. The results showed that the farming system and soil depth had a significant effect on soil physical and chemical properties. Parameters of soil chemical properties that significantly affect the farming system and soil depth are pH-H2O, pH NaF, organic matter, cation exchange capacity, total-N, and Al/Fe pyrophosphate extracted. Organic farming systems have an unstable and stable organic carbon fraction that is more dominant than semi-organic and conventional farming systems. Parameters of soil chemical properties such as organic matter, total organic carbon, and total-N are closely related to particulate organic matter carbon, water-soluble carbon, microbial biomass carbon, soil organic carbon mineralization, soil humic and fulvic acid. The organic farming system has been proven to improve the physical and chemical properties of the soil and increasing the availability of organic carbon fraction in Andisol soil.
Relationship between plant residue removal and soil carbon in soils of smallholder nutmeg plantations in Ternate Island, Indonesia
Authors: Ishak L , Sarni  , Erwin
Published: April 2022

A poor plant residue management in the nutmeg plantation system in the Ternate Island is claimed as the major factor causing the decline of soil organic carbon (SOC), and hence the low production of nutmeg. The present study was conducted with the aim of examining the relationship between SOC and plant residue removal activity in nutmeg croplands. An interview method was used to collect data from 140 farmers about their knowledge on SOC and the models of plant residue management adopted in their cropland. A snap-shot field survey was also undertaken at 14 plantation sites to collect soil samples from the depth of 0-20 cm and 20-30cm soil layer to be analyzed. The result of interview was analyzed descriptively, whilst the soil variable data were analyzed using regression models. The findings revealed that all the respondents remove plant residue from the soil surface and burned it. About 80% of the respondents applied it four times a year, whilst the rest 20% did it twice a year. The SOC content in the soils treated with the four times residue removal practice was lower than ones with less frequency of plant residue removal, and thereby has triggered the formation of subsoil compaction.
Contribution of semi-organic shallot to sustainable value chain: case study of marginal land in Selopamioro village, Bantul, Yogyakarta, Indonesia
Authors: Dewayanti R , Irham  , Perwitasari H
Published: April 2022

Shallot is one of three main vegetable commodities in Indonesia, highly potential to be developed, both in terms of consumption and trade. However, shallot from sustainable cultivation is still scarcely available in the market. Therefore, this study aims to analyse the semi-organic shallot value chain in order to identify constraints on production and marketing, also to assess its value chain sustainability performance, with case of marginal land in Selopamioro village, Bantul district, Yogyakarta. The research involves multi-stakeholders along the chain, including three farmer groups i.e. Lestari Mulyo, Sekar Mulyo, and Bumi Mukti. These groups have consistently developed semi-organic shallot production for the past few years, using different bulb varieties, due to their soil characteristics. Snowball sampling is applied in mapping the value chain actors, followed with survey, key informant interview within guided questionnaire, and market observations. Data analysis covers descriptive analysis, PESTEC analysis for constraint identification and improvement recommendation, while value chain sustainability performance is assessed through selected indicators of economic, social, and environment related to the study area. Results describe actors, supporters, and influencers of the existing value chain. In terms of production constraints, results identify: poor marginal land fertility, same time harvesting, discontinuous supply, impatient farming activities, women role equality in farming activities, lack of processing sources, virus contamination risk, longer seedling, and limited source for shifting fuel into electrical machineries. As marketing constraints, results identify: on farm government focus, lack of selling skill and sustainable commodity campaign, unreliable off-takers linkage, limited alternative market information, consumer price sensitivity, verbal agreement transaction, minor young farmer membership, poor e-commerce skill, weak branding effort and processing focus, and business unit unavailability at farmer group. Recommendation highlights the triple helix approach in strengthening the collaboration within the chain. Further the value chain is considered sustainable, with sustainability performance of the value chain related to Lestari Mulyo and Sekar Mulyo is good, and Bumi Mukti is moderate.
The sustainability level of semi organic shallot farming based on farmers perception : a case study in Bantul district, Daerah Istimewa Yogyakarta, Indonesia
Authors: Utami T W , Irham  , Abdurofi I
Published: April 2022

Shallot is one of the greatest agricultural commodities in Bantul District. Along with the increasing of citizens awareness about the sustainable agricultural products, the farmer group in Bantul District produce the semi organic shallots named GLOWING (Gede Lebih Original Berwawasan Lingkungan) and provide the advantages such as the minimal use of chemical fertilizers and pesticides. The sustainability of shallot farming is a multidimensional concept that requires a balance on the economic, ecological and social aspects. This study aims to measure the sustainability level of shallot farming in the core aspects such as economics, ecological and social based on shallot farmers perception in Bantul District, Daerah Istimewa Yogyakarta. The research location was determined purposively in Bantul District, Daerah Istimewa Yogyakarta. The research sample was taken using census method and designed as a descriptive study from 153 members of Lestari Mulyo and Bumi Mukti Farmer Group in Bantul District. Data were collected using interview, observation, and literature review then analyzed using qualitative descriptive analysis and farming sustainability index. The results showed that the sustainability level of semi organic shallot farming based on farmers perception in Bantul District at the economic is quite sustainable and at the social, ecology aspects is very sustainable
Feasibility study of a tropical sweet corn farming at the Center of Innovation and Agrotechnology Universitas Gadjah Mada
Authors: Waluyati L R , Fadhliani Z , Anjani H D , Siregar A P , Susilo K R. , Setyowati L
Published: April 2022

Sweet corn is a tropical plant that is widely grown by farmers in Indonesia. The sweet corn market is wide open to the retail level since it is popular for its sweet taste. It can be consumed directly for vegetables, roasted corn or steamed corn. In terms of price, sweet corn offers a higher value than field corn, thus encouraging the enthusiasm of farmers to plant sweet corn. The Center for Agrotechnology Innovation Universitas Gadjah Mada (PIAT UGM) has developed sweet corn farming using a superior seed called Bonanza Now F1, which is expected to be introduced and adopted by farmers. However, it is paramount to conduct a feasibility analysis of sweet corn farming utilizing this seed to ascertain whether the farming can benefit farmers so that it is feasible to cultivate. This study aims to (1) determine the cost and the revenue of sweet corn farming, 2) analyze the income of the sweet corn farming, and 3)determine the feasibility of the sweet corn farming. We utilize sweet corn farming data in 2020 from PIAT UGM to conduct cost-income and feasibility analyses using the R/C ratio. The results show that: 1) The cost and the revenue of sweet corn farming carried out by PIAT UGM is 8,425,649 IDR and 36,050,195 IDR per hectare, respectively, 2) The sweet corn farming generated income around 27,624,546 IDR per hectare, and 3) The value of the R/C ratio in sweet corn farming is 4.28, indicating that for every expenditure of 1.00 IDR, the farmers will get a revenue of 4.28 IDR. Thus, sweet corn farming at PIAT UGM is feasible to cultivate.
Web-based spatial information system to support land use planning in achieving sustainable and precision agriculture at regional scale
Authors: Amelia V , Sinaga S , Bhermana A
Published: April 2022

Today’s, the need of land resource information is prerequisite for agricultural development especially for land use planning. The existence web-based information system is an integral part of IoT technology can then be implemented to assist spatial planning process for agriculture development. This study was conducted to develop spatial information for land use planning process. Technology of geographical information system (GIS) was applied in this study to develop and manage database system. Land evaluation consisted of land capability evaluation (LCE) and land suitability evaluation (LSE) was used in methodology to determine arable lands based on their capability and suitability including land allocation for commodity group as agriculture system for food crops and estate crops. The result showed that food crops development areas are mainly located along the rivers (113,841 hectares). Meanwhile, for estate crops, they occupy 79.17% of total arable lands (432,632 hectares). The resulting database format and land evaluation integrated into web-based environment can then be used for delivering information purposes in accordance with location geographically. Therefore, it can be directly accessed anytime and anywhere by stakeholders located at concerning areas for planning process while at the same time, they can also provide the feedback for updating data.
The Biokinetic Parameters for the Removal of the Biochemical Demand of Oxygen and Coliforms in the Domestic Wastewater Treatment Plant of Pisco
Authors: Córdova-Mendoza Pedro , Barrios-Mendoza Teresa , Zuzunaga-Morales Ramiro , Córdova-Barrios Isis , Lévano-Moran José , Zuzunaga-Concha Emily
Published: April 2022

The objective of the research was to determine the biokinetic parameters that significantly influence the removal of the biochemical oxygen demand and coliforms in the domestic wastewater treatment plant. Material and methods, primary documentation was used, using the analytical-explanatory method, applied research. Results: The technical standard OS.090, for wastewater treatment plants establishes the maximum permissible limits and the average values of the oxidation lagoon were obtained, with a pH between 8-9, temperature 30.9 ° C, it was evidenced that the oxygen utilization rate values (VUO), for 5h (VUO = -0.1301), 15h (VUO = -0.1257), 35 h (VUO = -0.1187), 60h (VUO = -0.0958) and 80h (VUO = - 0.0885). Discussion: With the consumption of dissolved oxygen, the microbial ecological balance was reached on the third day in the reactor, which allowed obtaining the biokinetic parameters with a K = 0.0097 L/mg * d, Ks = 149.132 mg/l, qmax = 0.0698 h-1, a = 0.041 kgO2 / DBOr and b = 0.0365. Conclusion: The complete mixture of the removal of BOD5 is in a range of 85-95, the tests in the sample at 80 hours reached for the BOD5 of 27 mg/l.
Impact of Vehicle Light on Physical Properties of Particulate Matters Emitted from Vehicles
Authors: Ghadikolaei Meisam Ahmadi , Wong Pak Kin , Chen Shou Hao , Ng Kar Wei , Xu Jin Cheng
Published: April 2022

Gasoline and diesel vehicles are one of the main sources of PMs generation which are harmful to human health and the environment. The light emitted from the headlights of these vehicles may cause to make the PMs more/less/not dangerous than the raw PMs to human health and the environment by changing their properties. However, there is no information available in this field. Therefore, this research is presented to investigate the effect of light emitted from one of the most common vehicle headlights (Halogen type) on the physical properties of PMs. Three PM samples taken directly from one diesel vehicle operating at an idle condition, and inside of a diesel particulate filter and gasoline vehicle exhaust pipe (engine was off) were exposed to the vehicle headlight for 6 hrs at 10 cm distance. It is observed that the vehicle light has the potential to change the structure, shape, and size of the PMs, while the fresh PMs from diesel vehicle receives more changes (43.5% increase in particle diameter) compared with the other two samples containing mature/aged PMs (increases of 3.6 and 9.9%, respectively). Also, the effect of the beam from the scanning electron microscope on the PM physical properties is presented.
Policy and Legal Issues of the Environmental and Social Inspection in Fishery-Solar Energy
Authors: Hsiung Ku-Hsiu
Published: April 2022

Taiwan serves as the mainly research object in this paper. Due to the positive promotion of photovoltaic installation in Taiwan, the installed capacity of photovoltaic power station with Fishery-Solar Hybrid System is scheduled to 4GW. Photovoltaic power station installed upon the fish pond can achieve the effect of renewable energy generation and fish farming. However, the large area of photovoltaic power station into the fishing village, also have an impact on the original fishing village life. For example, the change of fish farming methods, landscape and ecological impact. Therefore, Taiwan established the “Solar Fishery and Electricity Symbiosis Auditing” in 2020, and this paper will discuss the procedure and law issues of this measure.
High Andean Woody Plants, between Nursing and Competition Effects in a High Andean Polylepis Forests
Authors: Alvarez-Montalván C , Parra C , Alvarez J , Córdova-Mendoza P , Julian-Laime E , Laredo I
Published: April 2022

The diversity of Plants in the Andes is a complex stochastic network, this diversity is characterized by being distributed in three main families: Asteraceae, Poaceae and Rosaceae. The first two are the most diverse and have the Gynoxis and Chusquea genera respectively as the most dominant woody individuals in the last altitudinal floors above 3200 m. a. s. l. However, the Rosaceae family has less richness, it includes the genus Polylepis, present in the last tree line limit above 4300 m.a.s.l. This is the case of mono-specific forests of Polylepis rodolfo-vasquezii, a species highly threatened by anthropogenic impacts such as logging, burning, and llama-sheep farming. These forests are relict and generate a nurse effect, which allows the existence of important diversity such as Gynoxis nitida, Miconia latifolia, Bomarea dulcis and Displostephium rupestri and Brachyotum rostratum. However, the impacts generate complex plants diversity responses, where the nurse effect can become into a competition effect, especially with Gynoxis nítida, which can take advantage of the ecological niche to promote the increase in abundance of its young individuals against those of P. rodolfo-vasquezii, which is reduced by anthropic activities.
Smart Fashion Economy through a Data-Driven Circular Ecosystem: A Case Study
Authors: Ghoreishi Malahat , Bhandari Kajal , Franconi Alessio
Published: April 2022

While Circular Economy (CE) strategies have been discussed as solutions for negative environmental impacts, companies are facing various challenges in applying CE strategies and redefining their business models. Recent research articulates that to achieve the CE goals, businesses should collaborate with each other within an ecosystem in which values are equally captured among all the stakeholders by governing and managing data flows. In this ecosystem, all the actors and stakeholders can share data, information and solutions regarding to CE to help each other through the path and co-create CE values. Regardless of the transition towards CE, fashion and textile industry is still following the linear economy model (take, make, use, dispose), where only less than 1% of the recycled clothes get back to use cycle. For textile and fashion industry, data plays a key role in providing transparent flow of information on product’s lifecycle, from circular material resources and design all the way to the recycling and waste management. In this regard, a data-driven ecosystem in which various stakeholders can access the source of right data, can ensure the success of circularity of the entire supply chain. A data-driven strategy can help to engage and train all organizations to build a data-literacy ecosystem towards a common goal. The purpose of this paper is to identify the important role of a data-driven CE ecosystem in fashion industry within the case study of the circularity. ID® a solution developed by-circular fashion.
Oxidation of copper electrodes on flexible polyimide substrates for non-enzymatic glucose sensing
Authors: Liu Shijia , Ay Ayse , Luo Qiaochu , Hu Xiangqi , Białas Katarzyna , Dutta Gorachand , Moschou Despina , Regoutz Anna
Published: April 2022

The integration of non-enzymatic glucose sensing entities into device designs compatible with industrial production is crucial for the broad take-up of non-invasive glucose sensors. Copper and its oxides have proven to be promising candidates for electrochemical glucose sensing. They can be fabricated in situ enabling integration with standard copper metallisation schemes for example in printed circuit boards (PCBs). Here, copper oxide electrodes are prepared on flexible polyimide substrates through direct annealing of patterned electrode structures. Both annealing temperature and duration are tuned to optimise the sensor surface for optimum glucose detection. A combination of microscopy and spectroscopy techniques is used to follow changes to the surface morphology and chemistry under the varying annealing conditions. The observed physico-chemical electrode characteristics are directly compared with electrochemical testing of the sensing performance, including chronoamperommetry and interference experiments. A clear influence of both aspects on the sensing behaviour is observed and an anneal at 250 °C for 8 h is identified as the best compromise between sensor performance and low interference from competing analytes.
Intensive Blood Pressure Treatment Goals: Evidence for Cardiovascular Protection From Observational Studies and Clinical Trials
Authors: Whelton Paul K , Bundy Joshua D , Carey Robert M
Published: April 2022

Epidemiologic studies have consistently identified a strong, progressive relationship between blood pressure (BP) and cardiovascular disease (CVD) events, in a range of systolic BP (SBP) from as low as 90 mm Hg to as high as 180 mm Hg. Clinical trials have demonstrated greater prevention of CVD with more compared with less intensive antihypertensive drug treatment. Meta-analyses of randomized controlled trials provide strong evidence for more intensive antihypertensive drug therapy down to an SBP of 130 mm Hg, and to an SBP 120–124 mm Hg in the meta-analysis with the greatest statistical power. In the Systolic Blood Pressure Intervention Trial (SPRINT) randomization to an SBP treatment goal of <120 mm Hg compared with <140 mm Hg in persons with high CVD risk not only reduced the rate of CVD but also all-cause mortality. These benefits were noted in all of the prestated subgroups of interest, including those ≥65 years of age at baseline. In addition, cognitive impairment was less common in those randomized to the intensive compared with standard treatment. Most clinical practice guidelines recommend an SBP treatment target <130 mm Hg in adults with a high risk of CVD, which is the norm for many patients seen in clinical practice, especially those who are older, have diabetes mellitus, or chronic kidney disease.
Interspecific morphological variation in Juglandoideae resting bud organization: a winter’s tale?
Authors: Schoonderwoerd Kristel M , Friedman William E
Published: April 2022

Background and Aims

Dormant resting buds are frequently regarded as static units, with protective cataphylls on the outside and embryonic foliage leaves on the inside. How the presence of cataphylls influences the dynamic, cyclical, annually repeating sequence of leaf forms that a resting bud gives rise to has rarely been interrogated. To examine the connection between dormant structure and growing-season development, we compare the complete seasonal heteroblastic sequence of leaf forms of six species of temperate Juglandaceae with distinctly different vegetative resting bud structures. These include buds with cataphylls; buds without cataphylls; and buds with caducous cataphylls that are lost before the onset of winter.

Methods

In a common garden setting over a 7-month growing season, the dimensions of 2249 individual vegetative metamers were tracked from first exposure to abscission along the shoots of saplings and mature trees. The timing of metamer initiation within terminal buds was investigated using micro-CT scanning. Character state transitions of resting bud types were estimated using a phylogenetic tree of Juglandaceae.

Key Results

The presence of cataphylls within a heteroblastic sequence is associated with a single cohort of foliage leaves that flush and abscise synchronously. This growing pattern is highly determinate, with next year’s terminal-bud cataphylls already initiated before spring leaf out. In contrast, in sequences without cataphylls, shorter-lived foliage leaves appear and abscise in a staggered fashion. Despite these differences in leaf demography, all examined heteroblastic sequences produce a series of small, caducous leaf forms that precede terminal bud set.

Conclusions

The ubiquity of caducous leaf forms in Juglandoideae may point to the importance of shoot tip protection far beyond the dormant season. In addition, the presence or absence of cataphylls in resting buds is indicative of distinct shoot ontogenetic patterns, and functional strategies, in summer.
Mining hidden knowledge: embedding models of cause–effect relationships curated from the biomedical literature
Authors: Krämer Andreas , Green Jeff , Billaud Jean-Noël , Pasare Nicoleta Andreea , Jones Martin , Tugendreich Stuart
Published: April 2022

Motivation

We explore the use of literature-curated signed causal gene expression and gene–function relationships to construct unsupervised embeddings of genes, biological functions and diseases. Our goal is to prioritize and predict activating and inhibiting functional associations of genes and to discover hidden relationships between functions. As an application, we are particularly interested in the automatic construction of networks that capture relevant biology in a given disease context.

Results

We evaluated several unsupervised gene embedding models leveraging literature-curated signed causal gene expression findings. Using linear regression, we show that, based on these gene embeddings, gene–function relationships can be predicted with about 95% precision for the highest scoring genes. Function embedding vectors, derived from parameters of the linear regression model, allow inference of relationships between different functions or diseases. We show for several diseases that gene and function embeddings can be used to recover key drivers of pathogenesis, as well as underlying cellular and physiological processes. These results are presented as disease-centric networks of genes and functions. To illustrate the applicability of our approach to other machine learning tasks, we also computed embeddings for drug molecules, which were then tested using a simple neural network to predict drug–disease associations.

Availability and implementation

Python implementations of the gene and function embedding algorithms operating on a subset of our literature-curated content as well as other code used for this paper are made available as part of the Supplementary data.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Prediction of RNA–protein interactions using a nucleotide language model
Authors: Yamada Keisuke , Hamada Michiaki
Published: April 2022

Motivation

The accumulation of sequencing data has enabled researchers to predict the interactions between RNA sequences and RNA-binding proteins (RBPs) using novel machine learning techniques. However, existing models are often difficult to interpret and require additional information to sequences. Bidirectional encoder representations from transformer (BERT) is a language-based deep learning model that is highly interpretable. Therefore, a model based on BERT architecture can potentially overcome such limitations.

Results

Here, we propose BERT-RBP as a model to predict RNA–RBP interactions by adapting the BERT architecture pretrained on a human reference genome. Our model outperformed state-of-the-art prediction models using the eCLIP-seq data of 154 RBPs. The detailed analysis further revealed that BERT-RBP could recognize both the transcript region type and RNA secondary structure only based on sequence information. Overall, the results provide insights into the fine-tuning mechanism of BERT in biological contexts and provide evidence of the applicability of the model to other RNA-related problems.

Availability and implementation

Python source codes are freely available at https://github.com/kkyamada/bert-rbp. The datasets underlying this article were derived from sources in the public domain: [RBPsuite (http://www.csbio.sjtu.edu.cn/bioinf/RBPsuite/), Ensembl Biomart (http://asia.ensembl.org/biomart/martview/)].

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Semaglutide for treatment of obesity in hemodialysis patients waiting for a kidney transplant: new hope?
Authors: Touzot Maxime , Ureña-Torres Pablo , Dupuy Olivier
Published: April 2022

Obesity limits the access to kidney transplantation and increases the risk of complications and mortality posttransplantation. Usual noninvasive measures, including lifestyle changes and dietary education, do not provide long-term and consistent body weight reduction. In many cases, only bariatric surgery allows patients to significantly reduce body weight. We here report two cases of obese hemodialysis (HD) patients who were successfully treated with off-labeled semaglutide, a glucagon-like peptide receptor agonist (GLP-1RA). The first patient had a body mass index (BMI) of 45.7 kg/m2 despite a history of partial gastrectomy. The second patient had a history of type 2 diabetes mellitus and a BMI of 36.5 kg/m2. Both patients started semaglutide at the maximal subcutaneous dose of 1 mg/week, which was clinically well tolerated. During the 9-month follow-up, body weight loss ranged from 6.5 to 9.0 kg, ∼1 kg/month. GLP-1RAs, such as semaglutide or liraglutide, could be a novel pharmacological alternative to bariatric surgeries for these HD patients.
A mitochondrial long-chain fatty acid oxidation defect leads to transfer RNA uncharging and activation of the integrated stress response in the mouse heart
Authors: Ranea-Robles Pablo , Pavlova Natalya N , Bender Aaron , Pereyra Andrea S , Ellis Jessica M , Stauffer Brandon , Yu Chunli , Thompson Craig B , Argmann Carmen , Puchowicz Michelle , Houten Sander M
Published: April 2022

Aims

Cardiomyopathy and arrhythmias can be severe presentations in patients with inherited defects of mitochondrial long-chain fatty acid β-oxidation (FAO). The pathophysiological mechanisms that underlie these cardiac abnormalities remain largely unknown. We investigated the molecular adaptations to a FAO deficiency in the heart using the long-chain acyl-CoA dehydrogenase (LCAD) knockout (KO) mouse model.

Methods and results

We observed enrichment of amino acid metabolic pathways and of ATF4 target genes among the upregulated genes in the LCAD KO heart transcriptome. We also found a prominent activation of the eIF2α/ATF4 axis at the protein level that was independent of the feeding status, in addition to a reduction of cardiac protein synthesis during a short period of food withdrawal. These findings are consistent with an activation of the integrated stress response (ISR) in the LCAD KO mouse heart. Notably, charging of several transfer RNAs (tRNAs), such as tRNAGln was decreased in LCAD KO hearts, reflecting a reduced availability of cardiac amino acids, in particular, glutamine. We replicated the activation of the ISR in the hearts of mice with muscle-specific deletion of carnitine palmitoyltransferase 2.

Conclusions

Our results show that perturbations in amino acid metabolism caused by long-chain FAO deficiency impact cardiac metabolic signalling, in particular the ISR. These results may serve as a foundation for investigating the role of the ISR in the cardiac pathology associated with long-chain FAO defects.

Translational Perspective: The heart relies mainly on mitochondrial fatty acid β-oxidation (FAO) for its high energy requirements. The heart disease observed in patients with a genetic defect in this pathway highlights the importance of FAO for cardiac health. We show that the consequences of a FAO defect extend beyond cardiac energy homeostasis and include amino acid metabolism and associated signalling pathways such as the integrated stress response.
Frequent premature atrial contractions as a signalling marker of atrial cardiomyopathy, incident atrial fibrillation, and stroke
Authors: Farinha José Maria , Gupta Dhiraj , Lip Gregory Y H
Published: April 2022

Premature atrial contractions are a common cardiac phenomenon. Although previously considered a benign electrocardiographic finding, they have now been associated with a higher risk of incident atrial fibrillation (AF) and other adverse outcomes such as stroke and all-cause mortality. Since premature atrial contractions can be associated with these adverse clinical outcomes independently of AF occurrence, different explanations have being proposed. The concept of atrial cardiomyopathy, where AF would be an epiphenomenon outside the causal pathway between premature atrial contractions and stroke has received traction recently. This concept suggests that structural, functional, and biochemical changes in the atria lead to arrhythmia occurrence and thromboembolic events. Some consensus about diagnosis and treatment of this condition have been published, but this is based on scarce evidence, highlighting the need for a clear definition of excessive premature atrial contractions and for prospective studies regarding antiarrhythmic therapies, anticoagulation or molecular targets in this group of patients.
Markups and Financial Shocks
Authors: Meinen Philipp , Soares Ana Cristina
Published: April 2022

This paper analyses the impact of financial frictions on markup adjustments at the firm level. We use a rich panel data set that matches information on banking relationships with firm-level data. By relying on insights from recent contributions in the literature, we obtain exogenous credit supply shifters and markups that are both firm specific and time varying. We uncover new findings at this level. In particular, firms more exposed to liquidity risks tend to raise markups in response to negative bank-loan supply shocks, while less exposed firms generally reduce them. Further empirical analyses suggest that our findings are mostly consistent with models featuring a sticky customer base, where financially constrained firms have an incentive to raise markups in order to sustain liquidity without losing too many customers. Our results have important economic implications regarding the cyclicality of the aggregate markup.
Hidden Costs of Fire Exclusion in Longleaf Pine Forests Linked to Duff And Carbon Management
Authors: Susaeta Andres , Fill Jennifer , Crandall Raelene , Varner J Morgan
Published: April 2022

The reintroduction of fire to long-unburned pine ecosystems is a silvicultural tool to restore their ecological and economic value. However, if prescribed fire is used after long periods of fire exclusion, high amounts of duff consumed during fire can result in tree stress and mortality. Prescribed burning with a focus on managing duff has therefore been recommended for mitigating negative impacts on overstory trees when fire is reintroduced. We modeled the economic outcomes of different forest management scenarios related to burning for duff management in even-aged longleaf pine stands. We considered five management scenarios in which we varied prescribed fire use, thinnings, mortality rates, and salvage logging. Our findings indicate that burning for duff management without and with thinnings can be considered the most economically viable strategy ($1593/ha–$966/ha).
Reduction in leaf size at higher altitudes across 39 broad-leaved herbaceous species on the northeastern Qinghai-Tibetan Plateau
Authors: Ke Xinran , Kang Huixing , Tang Yanhong
Published: April 2022

Leaf size varies conspicuously within and among species under different environments. However, it is unclear how leaf size would change with elevation, whether there is a general elevational pattern, and what determines the altitudinal variation of leaf size. We thus aimed to address these questions by focusing on the broad-leaved herbaceous species at high altitudes on the northeastern Qinghai-Tibetan Plateau. We measured the leaf size, leaf length, leaf width and leaf mass per area for 39 broad-leaved herbaceous species inhabited in the open areas along two mountain slopes from 3200 to 4400 m at the Lenglongling and the Daban Mountain, the northeastern Qinghai-Tibetan Plateau. We analyzed the altitudinal patterns in leaf size in relation to leaf inclination and leaf surface features, and applied a leaf energy balance model to discuss the underlying mechanisms. Leaf size decreased significantly at higher altitudes. The altitudinal reduction of leaf size was mainly attributed to the reduction of leaf length, and differed in different species, and in leaves with different inclination and leaf surface features. A leaf energy balance model with local environmental measurements demonstrates that leaf temperature tracks air temperature more closely in small than in large leaves, and that the leaf-size impact is stronger at higher latitudes. Based on the observational findings, we propose that the distribution upper-limit for broad-leaved herbaceous species would be at an elevation of about 5400 m on the northeastern Qinghai-Tibetan Plateau.
The importance of ecotype diversity on duckweed growth with and without salt stress
Authors: van Moorsel Sofia J
Published: April 2022

The pollution of freshwater ecosystems is threatening freshwater plant species diversity worldwide. Freshwater plants, such as the common duckweed (Lemna minor), are potentially sensitive to novel stressful environments. To test if ecotype diversity could increase resistance to stressful environments, I used seven L. minor populations and measured their growth rates with and without moderate salt stress across an ecotype diversity gradient. The L. minor populations were grown over 5 months in 92 experimental mesocosms, either in ecotype monocultures or in polyculture with either one or three conspecific ecotypes (23 unique compositions). After growing the duckweed in unperturbed conditions (phase 1), the cultures were subjected to moderate salt stress (50 mmol/L NaCl) for several weeks (phase 2). The experiment was conducted in the presence of the natural epimicrobial community associated with the different ecotypes. In phase 2, a subset of these algae added an unintentional second stressor to the experiment. The ecotypes differed in their growth rates, the fastest growing at twice the rate of others. The diversity context further shaped the ecotype growth rates. Ecotype polycultures showed higher abundances towards the end of the experiment, thus over time, as the environment deteriorated, ecotype diversity gained in importance. These findings show that within-species variation in growth rates can translate to a positive effect of ecotype diversity on population abundance. Exposure of L. minor to moderate salt levels did not significantly impact growth rates, although the effect may have been masked by reduced algal stress in the saline environments.
Machine-learning of complex evolutionary signals improves classification of SNVs
Authors: Labes Sapir , Stupp Doron , Wagner Naama , Bloch Idit , Lotem Michal , L. Lahad Ephrat , Polak Paz , Pupko Tal , Tabach Yuval
Published: April 2022

Conservation is a strong predictor for the pathogenicity of single-nucleotide variants (SNVs). However, some positions that present complex conservation patterns across vertebrates stray from this paradigm. Here, we analyzed the association between complex conservation patterns and the pathogenicity of SNVs in the 115 disease-genes that had sufficient variant data. We show that conservation is not a one-rule-fits-all solution since its accuracy highly depends on the analyzed set of species and genes. For example, pairwise comparisons between the human and 99 vertebrate species showed that species differ in their ability to predict the clinical outcomes of variants among different genes using conservation. Furthermore, certain genes were less amenable for conservation-based variant prediction, while others demonstrated species that optimize prediction. These insights led to developing EvoDiagnostics, which uses the conservation against each species as a feature within a random-forest machine-learning classification algorithm. EvoDiagnostics outperformed traditional conservation algorithms, deep-learning based methods and most ensemble tools in every prediction-task, highlighting the strength of optimizing conservation analysis per-species and per-gene. Overall, we suggest a new and a more biologically relevant approach for analyzing conservation, which improves prediction of variant pathogenicity.