bluuebunny/crossref_metadata_2025 huggingface dataset:
Low-cost of shoot propagation of pineapple (Ananas comosus l. Merr) cv Queen using gandasil-D and AB-mix
Authors: Rosmaina  , Mufadillah A , Zam S I , Zulfahmi
Published: June 2024

Media composition is the main factor in the success of plant tissue culture. This study aims to find alternative media formulas using AB-Mix and Gandasil-D for shoot propagation of pineapple. The study used a factorial completely randomized design (CRD). The first factor was the AB-Mix concentration consisting of: 2.5 ml/L, 5.0 ml/L, and 7.5 ml/L. The second factor was the concentration of Gandasil-D consisting of 1.0 g/l, 1.5 g/l, and 2.0 g/l. Each treatment medium added 2 ppm BAP and 0.5 ppm NAA as plant regulators. Parameters observed included the time of shoot emergence, the number of shoots, the number of roots, and leaves number. The results showed that the concentration of AB-Mix affected all observed parameters, while Gandasil-D and the interaction between Gandasil-D and AB-Mix had no significance. AB-Mix 7.5 ml/l was the best treatment because it resulted in shoot emergence time (30.55 days after induction), number of shoots (3.55 shoots/explant), number of roots (2.05 roots/explant), and number of leaves (14.66 leaves/explant) were not significantly from MS media. Based on the regression analysis carried out, it is still possible to increase the concentration of AB-Mix to increase the number of shoots produced.
Understanding the impact and driver of digital divide to support rural development policy: a review
Authors: Ihsaniyati Hanifah , Sarwoprasodjo Sarwititi , Muljono Pudji , Gandasari Dyah
Published: June 2024

Rural development requires the internet and digital technologies for sustainable development. There is ample evidence that rural communities have less contact with the internet and digital technologies than urban communities. This digital divide will hinder development. Therefore, efforts to bridge the digital divide are essential for better development policies. On the other hand, studies on impacts and the factors that drive this gap have not been explored. This study aims to explain the digital gap’s impacts and its causal factors in rural development. This research is a narrative review of 16 articles from reliable sources such as scopus.com. The results of the literature review are summarized to answer research questions. The study found that the digital divide impacts rural socio-economy, rural socio-culture, rural socio-politics, and rural environments. This study’s drivers of the digital divide include demographics, human resource capabilities, geographical conditions, limited infrastructure, internet networks, uneven economic development, and policy failure. The impacts and drivers of the digital gap described in this study contribute to some of our efforts to bridge the digital divide while providing insights for future research.
Cost and revenew analysis of arrowroot farming in Yogyakarta, Indonesia
Authors: Sundari M T , Rahayu E S , Irianto H , Handayani S M , Setyowati  , Widadie F
Published: June 2024

Arrowroot is a commodity that has been cultivated for generations in Yogyakarta. Arrowroot can grow on land that is exposed to little sunlight that can be planted on yard or even developed on a large scale on land under crop stands so that it can increase land productivity and increase farmers’ income. Arrowroot can be used as raw material for flour. As a result, Garut is a viable local food source with economic potential that should be considered in future. This study aimed to determine the costs, revenues, incomes, profits, and efficiency of arrowroot farming in Yogyakarta, Indonesia. The basic research method used in this research is descriptive and analytical. This study used survey techniques to conduct door-to-door interviews with arrowroot farmers. The purposive sampling method was used to select the sample, with respondents being farmers who actively cultivated arrowroot every year and were registered in Department of Agriculture and Food Security of Yogyakarta. The total research sample was 92 farmers spread across 3 sub-districts in Yogyakarta. Cost analysis, revenue, income, farm profit, and the R/C ratio were all used in the analysis. The results showed that the average farming costs in one growing season consisted of explicit costs of IDR 1,634,728.07/ha and implicit costs of IDR 21,034,373.62/ha. The average farm revenue was IDR 13,491,298.19/ha. The average farm income was IDR 11,856,570.12/ha. The average farm profit was -IDR 9,177,803.50/ha. The average R/C ratio on explicit costs was 8.25, meaning the farm is efficient, and the average R/C ratio on total costs was 0.60, meaning the farm is inefficient.
Productivity of elephant grass pakchong (Pennisetum purpureum cv Pakchong) and elephant grass taiwan (Pennisetum purpureum cv Taiwan) cultivated based on different stem cutting sizes
Authors: Fanindi A , Sutedi E , Sajimin  , Herdiawan I , Harmini  , Pamungkas F A , Kusumaningrum D A , Baehaki  , Karya  , Setiawan A , Solihat I , Mulyadi A
Published: June 2024

In Indonesia, elephant grass seeds used by farmers are in the form of cuttings or vegetative material. Currently, there is no standard for the cuttings used to produce high-productivity elephant grass. Therefore, research was conducted to determine the optimal size of cuttings for achieving good elephant grass productivity. The study was conducted in the field station area of Rancamaya, Bogor. A factorial group randomized design with 5 replications was employed for the research. The first factor was the type of elephant grass, consisting of 1) Pakchong and 2) Taiwan, while the second factor was the size of the cuttings, consisting of 1) 5 cm long cuttings, one node, 2) 10 cm long cuttings, one node, 3) 15 cm long cuttings, one node, and 4) control (two nodes as per usual farmer practice). The research results indicated that there was an interaction between the type of elephant grass and the size of cuttings for leaf length, fresh and dry leaf weight, dry stem weight, and total dry weight. The 5 cm cuttings of Pakchong had the highest fresh and dry leaf weights (P<0.05). The highest dry stem and total weight were obtained with the control size cuttings of Pakchong. The number of tillers was influenced by the size of cuttings, with the control size cuttings having the highest number of tillers, although not significantly different from the number of tillers for the 5 cm and 15 cm cuttings. The highest total fresh weight was obtained with the 5 cm cuttings and Pakchong. This study indicates that 5 cm cuttings can be used as cutting material to produce Pakchong and Taiwan with optimal forage production. Further research is needed to assess the forage quality.
Relationship between chlorophyll and yield of two rice varieties in different farming systems
Authors: Syamsiyah J , Ariyanto D P , Herawati A , Dewayani R A , Permata D I
Published: June 2024

Rice is the staple food of Indonesian society which continues to increase in demand due to population growth. Currently, there are 3 agricultural systems in rice cultivation, namely organic, semi-organic, and conventional. The three systems provide changes in soil physical, chemical, and biological properties, but there is not much information related to chlorophyll levels in plants. This study aims to assess chlorophyll levels and their relationship with the yield of two rice varieties in various farming systems, especially the IR64 and Mentik Wangi varieties. This research is a field survey study followed by laboratory analysis. Determination of sampling locations by purposive sampling on organic, semi-organic, and conventional rice fields with two varieties of rice. Observation parameters include chlorophyll content, harvest dry grain weight, and milled dry grain weight. The results showed that the levels of chlorophyll A in IR64 and Chlorophyll B in IR 64 and Mentik Wangi varieties with organic farming systems were higher than in semi-organic and conventional farming systems. There was a positive correlation between chlorophyll levels and the yield of two rice varieties in different farming systems.
Disease Incidence of Leaf Rust of Soybean Caused by Phakopsora pachyrizi Planted in Mahogany Agroforestry System
Authors: Widono S , Dewi F C
Published: June 2024

Soybean (Glycine max L.) is one of the agricultural commodities needed in high quantities in Indonesia. Using agroforestry systems for soybean cultivation can solve the domestic fulfillment of soybean needs. The moist environmental conditions of agroforestry plantings due to shading make soybeans susceptible to leaf rust disease. The pathogen Phakopsora pachyrhizi causes leaves to fall off early, inhibiting soybean seed pod growth. Research on the incidence of leaf rust disease in several soybean varieties is essential to optimize soybean production in agroforestry systems. The study was conducted from June to October 2023 in the Special Purpose Forest Area (KHDTK) of Alas Bromo, Karanganyar, Central Java, Indonesia. The experiment used a randomized experimental design (RAK) with seven soybean varieties: Anjasmoro, Agromulyo, Dena-1, Dena-2, Denasa-1, Denasa-2, and Devon-1. Disease incidence observation was based on visual symptoms. The disease incidence was in the range of 3.33-26.67%. The highest incidence occurred in the Denasa-1 and Dena-2 varieties, while the lowest was in the Anjasmoro and Dena-1 variety.
Resource-based typology to facilitate sustainable growth of agricultural start-up companies in ASEAN
Authors: Akbar Maulana , Kusnandar
Published: June 2024

Startup companies have had a significant influence on the growth of the economy. Nevertheless, they are prone to failure. Resources, both tangible and intangible, are essential for the sustainable growth of start-up companies. The main objective of this study is to gain a thorough comprehension of the classification of agricultural startup companies in ASEAN countries, taking into account their available resources. This study employs data sourced from Crunchbase, a comprehensive database including information on 201 agricultural startup companies operating in ASEAN countries. The study primarily focuses on analyzing two main variables: tangible and intangible sources. The study employed the K-means clustering algorithm to analyze the attributes of agricultural startup companies. The study’s results indicate that startup companies in ASEAN countries can be categorized into three distinct clusters. The first cluster is made up of players who have a great deal of experience and who have the highest levels of income, funding, and personnel count. The second cluster is made up of players with a moderate amount of experience who have a low CB Rank, Funding, and Estimated Revenue, but they have a moderate number of employees. Inexperienced players make up the third cluster, which has a higher total quantity of investment and income but a very small number of employees. This group is characterized by greater total investment and income.
Carbon stocks estimation in the KGPAA Mangkunagoro I Forest Park at collection zone area
Authors: Nugroho U J , Nufus M , Rahmadwiati R , Ekayanti N P , anggraini Y D , Zaidan M N , Risdiana I , Mufidah A K Z
Published: June 2024

Mangkunagoro I Forest Park is a nature conservation area for plant collection purposes and preserving biodiversity. Moreover, Forest park as a forest also can absorb and store carbon as biomass. It makes forest park play a role in the mitigation of climate change. This research aimed to determine the amount of carbon stock in the Mangkunagoro I Forest Park collection zone. There are 35 plots in total with 20 x 20 m in size taken using systematic sampling. A non-destructive method with allometric equations was used to estimate total biomass and carbon stocks. In the Mangkunagoro I forest park collection zone, 11 species of trees and 3 species of bamboo were found with a total density of 79 trees/ha. Estimated biomass, carbon stocks, and carbon sequestration in the site were 304.24 ton/ha, 142 ton/ha, and 299.68 ton/ha, respectively.
Growth of matoa (Pometia pinnata JR Forst & G Forst) seedlings at various application times of chitosan
Authors: Yuniastuti E , Nugrahaningrum A , Manurung IR , Pujiasmanto B
Published: June 2024

Matoa (Pometia pinnata JR Forst & G Forst) has potential as a biodiesel raw material. Chitosan can increase plant growth by stimulating the biosynthesis of auxin and tryptophan. This research aimed to get the chitosan application time and the matoa type that can increase matoa growth. The method used was a completely randomized design (CRD) with two factors. The first was the application time of chitosan (without chitosan application, morning, afternoon, a combination of morning and evening) and the second was matoa type (red, green, and yellow). Chitosan was given at a concentration of 4%. Data analysis used analysis of variance and continued with Duncan’s Multiple Range Test (DMRT) at the 5% significance level. The results showed that chitosan application in the morning time gave the best results on the photosynthetic rate, the afternoon gave the best results on the height and photosynthetic rate, and the morning and afternoon gave the best results on the stem diameter. The interaction of chitosan application time in the afternoon with green matoa species gave the best results on the plant height and in the afternoon with red matoa and in the morning with green matoa gave the best results on the photosynthetic rate.
The diversity and significance of wild edible vegetable plants in Aceh Tamiang, Indonesia
Authors: Adnan  , Navia Z I , Jamil M , Suwardi A B
Published: June 2024

Wild vegetable species are native or naturalized plants that thrive in their natural habitat. This study aims to look into indigenous knowledge about using plants as vegetables and how it affects food security and diversity in the Aceh Tamiang region. Plant material was randomly collected from three subdistricts in Aceh Tamiang, Indonesia. Ethnobotanical data was collected through investigations and semi-structured interviews. A total of 90 respondents, 30 from each sub-district, were selected randomly. Data was cross-checked and verified using the informant context approach and group discussions. The data were examined employing descriptive statistics and quantitative ethnobotanical approaches. We discovered 42 different species of wild vegetables. The majority of these plants are harvested from the wild by consumers in the area. These findings suggest that various plants are able to be consumed raw, which could be a valuable resource for the local community during times of food insecurity.
Leaf Rust Infection Phakopsora pachyrhizi on Seven Soybean Varieties in Pine Agroforestry System
Authors: Septariani D N , Supyani  , Jannah M
Published: June 2024

The agroforestry farming system is an alternative to increasing soybean production in Indonesia. However, in its cultivation, there are obstacles in the form of attacks by leaf rust pathogens. Leaf rust caused by the P. pachyrhizi fungus can reduce soybean production, depending on the variety and environmental conditions. This research was conducted from June to September 2023 on the KHDTK (Kawasan Hutan dengan Tujuan Khusus) Forestry Alas Bromo, Karanganyar, Central Java, Indonesia, to explore the leaf rust incidence in soybean varieties. This research used a completely randomized block design (CRBD) consisting of seven soybean variety treatments: Anjasmoro, Argomulyo, Dena-1, Dena-2, Denasa-1, Denasa-2, and Devon-1, and repeated three times. The variable observed was disease incidence. The results showed that all soybean varieties tested could be infected with the leaf rust pathogen. The lowest leaf rust infection was found in the Devon-1 variety (6.0%), and the highest infection occurred in the Dena-1 variety (20.0%). This is thought to be related to genetic traits and environmental conditions strongly influencing the growth and development of the P. pachyrhizi pathogen.
Atomicity of Boolean algebras and vector lattices in terms of order convergence
Authors: Avilés Antonio , Bilokopytov Eugene , Troitsky Vladimir
Published: June 2024

We prove that order convergence on a Boolean algebra turns it into a compact convergence space if and only if this Boolean algebra is complete and atomic. We also show that on an Archimedean vector lattice, order intervals are compact with respect to order convergence if and only the vector lattice is complete and atomic. Additionally we provide a direct proof of the fact that uo convergence on an Archimedean vector lattice is induced by a topology if and only if the vector lattice is atomic.
Rods, tubes, wires, and sheets
Authors: Dierking Ingo , Martins Figueiredo Neto Antônio
Published: June 2024

More lyotropic phase forming rod-like and plate-like materials are introduced, not so much natural mineral materials but rather laboratory made modern materials and biomaterials. Rod-like systems that are discussed are the classic example of the tobacco mosaic viruses, cellulose nanocrystals which have more recently attracted much attention, gold nanorods with their plasmonic properties, titanium dioxide, and cadmium selenide. These are followed by carbon nanotubes, ZnO, silver, and boron nitride nanowires, before several different nanosheet materials are discussed, such as graphene and graphene oxide, as well as other plate-like nanostructures such as MoS2 and MXenes. Their applications as fibres and in fabrics is pointed out.
Prior infections and effectiveness of SARS-CoV-2 vaccine in test-negative studies: a systematic review and meta-analysis
Authors: Tsang Tim K , Sullivan Sheena G , Huang Xiaotong , Wang Can , Wang Yifan , Nealon Joshua , Yang Bingyi , Ainslie Kylie E C , Cowling Benjamin J
Published: June 2024

Prior infection with SARS-CoV-2 can provide protection against infection and severe COVID-19. We aimed to determine the impact of preexisting immunity on vaccine effectiveness (VE) estimates. We systematically reviewed and meta-analyzed 66 test-negative design studies that examined VE against infection or severe disease (hospitalization, intensive care unit admission, or death) for primary vaccination series. Pooled VE among studies that included people with prior COVID-19 infection was lower against infection (77%; 95% CI, 72-81) and severe disease (86%; 95% CI, 83-89) compared with studies that excluded people with prior COVID-19 infection (pooled VE against infection: 87% [95% CI, 85-89]; pooled VE against severe disease: 93% [95% CI, 91-95]). There was a negative correlation between VE estimates against infection and severe disease, and the cumulative incidence of cases before the start of the study or incidence rates during the study period. We found clear empirical evidence that higher levels of preexisting immunity were associated with lower VE estimates. Prior infections should be treated as both a confounder and effect modificatory when the policies target the whole population or are stratified by infection history, respectively.
Characterizing an amidase and its operon from actinomycete bacteria responsible for paraben catabolism
Authors: Takenoya Mihoko , Hiratsuka Yoshiaki , Shimamura Kaho , Ito Shinsaku , Sasaki Yasuyuki , Yajima Shunsuke
Published: June 2024

Hydrazidase from Microbacterium hydrocarbonoxydans was revealed to catalyze synthetic hydrazide compounds, enabling the bacteria to grow with them as a sole carbon source, but natural substrates have remained unknown. In this study, kinetic analyses of hydrazidase with parabens showed that the compounds can be substrates. Then, methylparaben induced gene expressions of the operon containing hydrazidase and ABC transporter, and the compound as a sole carbon source was able to grow the bacteria. Furthermore, homology search was carried out revealing that several actinomycetes possess hydrazidase homologs in the operon. Among those bacteria, an amidase from Pseudonocardia acaciae was subjected to a kinetic analysis and a structure determination revealing similar but not identical to those of hydrazidase. Since parabens are reported to exist in plants and soil, and several actinomycetes code the homologous operon, the enzymes with those operons may play a physiologically important role for bacterial survival with use of parabens.
Assay for okadaic acid O-acyl transferase using HPLC-FLD
Authors: Terauchi Masato , Komazaki Yuki , Yoshino Atsushi , Cho Yuko , Kudo Yuta , Yotsu-Yamashita Mari , Konoki Keiichi
Published: June 2024

Dinophysistoxin 1 (DTX1, 1) and okadaic acid (OA, 2), produced by the dinoflagellates Dinophysis spp. and Prorocentrum spp., are primary diarrhetic shellfish toxins (DSTs), which may cause gastric illness in people consuming such as bivalves. Both compounds convert to dinophysistoxin 3 (DTX3, 3; generic name for 1 and 2 with fatty acids conjugated at 7-OH) in bivalves. The enzyme okadaic acid O-acyl transferase (OOAT) is a membrane protein found in the microsomes of the digestive glands of bivalves. In this study, we established an in vitro enzymatic conversion reaction using 4-nitro-2,1,3-benzoxadiazole (NBD)-OA (4), an OA derivative conjugated with (R)-(-)-4-nitro-7-(3-aminopyrrolidin-1-yl)-2,1,3-benzoxadiazole (NBD-APy) on 1-CO2H, as a substrate. We detected the enzymatically produced 3, NBD-7-O-palmitoyl-OA (NBD-Pal-OA), using high-performance liquid chromatography-fluorescence detection. We believe that an OOAT assay using 4 will facilitate the fractionation and isolation of OOAT in the future.
OLB-AC: toward optimizing ligand bioactivities through deep graph learning and activity cliffs
Authors: Yin Yueming , Hu Haifeng , Yang Jitao , Ye Chun , Goh Wilson Wen Bin , Kong Adams Wai-Kin , Wu Jiansheng
Published: June 2024

Motivation

Deep graph learning (DGL) has been widely employed in the realm of ligand-based virtual screening. Within this field, a key hurdle is the existence of activity cliffs (ACs), where minor chemical alterations can lead to significant changes in bioactivity. In response, several DGL models have been developed to enhance ligand bioactivity prediction in the presence of ACs. Yet, there remains a largely unexplored opportunity within ACs for optimizing ligand bioactivity, making it an area ripe for further investigation.

Results

We present a novel approach to simultaneously predict and optimize ligand bioactivities through DGL and ACs (OLB-AC). OLB-AC possesses the capability to optimize ligand molecules located near ACs, providing a direct reference for optimizing ligand bioactivities with the matching of original ligands. To accomplish this, a novel attentive graph reconstruction neural network and ligand optimization scheme are proposed. Attentive graph reconstruction neural network reconstructs original ligands and optimizes them through adversarial representations derived from their bioactivity prediction process. Experimental results on nine drug targets reveal that out of the 667 molecules generated through OLB-AC optimization on datasets comprising 974 low-activity, noninhibitor, or highly toxic ligands, 49 are recognized as known highly active, inhibitor, or nontoxic ligands beyond the datasets’ scope. The 27 out of 49 matched molecular pairs generated by OLB-AC reveal novel transformations not present in their training sets. The adversarial representations employed for ligand optimization originate from the gradients of bioactivity predictions. Therefore, we also assess OLB-AC’s prediction accuracy across 33 different bioactivity datasets. Results show that OLB-AC achieves the best Pearson correlation coefficient (r2) on 27/33 datasets, with an average improvement of 7.2%–22.9% against the state-of-the-art bioactivity prediction methods.

Availability and implementation

The code and dataset developed in this work are available at github.com/Yueming-Yin/OLB-AC.
Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases
Authors: Gualdi Francesco , Oliva Baldomero , Piñero Janet
Published: June 2024

Motivation

Understanding the genetic basis of complex diseases is one of the main challenges in modern genomics. However, current tools often lack the versatility to efficiently analyze the intricate relationships between genetic variations and disease outcomes. To address this, we introduce Genopyc, a novel Python library designed for comprehensive investigation of how the variants associated to complex diseases affects downstream pathways. Genopyc offers an extensive suite of functions for heterogeneous data mining and visualization, enabling researchers to delve into and integrate biological information from large-scale genomic datasets.

Results

In this work, we present the Genopyc library through application to real-world genome wide association studies variants. Using Genopyc to investigate the functional consequences of variants associated to intervertebral disc degeneration enabled a deeper understanding of the potential dysregulated pathways involved in the disease, which can be explored and visualized by exploiting the functionalities featured in the package. Genopyc emerges as a powerful asset for researchers, facilitating the investigation of complex diseases paving the way for more targeted therapeutic interventions.

Availability and implementation

Genopyc is available on pip https://pypi.org/project/genopyc/.The source code of Genopyc is available at https://github.com/freh-g/genopyc. A tutorial notebook is available at https://github.com/freh-g/genopyc/blob/main/tutorials/Genopyc_tutorial_notebook.ipynb. Finally, a detailed documentation is available at: https://genopyc.readthedocs.io/en/latest/.
Multimodal pretraining for unsupervised protein representation learning
Authors: Nguyen Viet Thanh Duy , Hy Truong Son
Published: June 2024

Proteins are complex biomolecules essential for numerous biological processes, making them crucial targets for advancements in molecular biology, medical research, and drug design. Understanding their intricate, hierarchical structures, and functions is vital for progress in these fields. To capture this complexity, we introduce Multimodal Protein Representation Learning (MPRL), a novel framework for symmetry-preserving multimodal pretraining that learns unified, unsupervised protein representations by integrating primary and tertiary structures. MPRL employs Evolutionary Scale Modeling (ESM-2) for sequence analysis, Variational Graph Auto-Encoders (VGAE) for residue-level graphs, and PointNet Autoencoder (PAE) for 3D point clouds of atoms, each designed to capture the spatial and evolutionary intricacies of proteins while preserving critical symmetries. By leveraging Auto-Fusion to synthesize joint representations from these pretrained models, MPRL ensures robust and comprehensive protein representations. Our extensive evaluation demonstrates that MPRL significantly enhances performance in various tasks such as protein–ligand binding affinity prediction, protein fold classification, enzyme activity identification, and mutation stability prediction. This framework advances the understanding of protein dynamics and facilitates future research in the field. Our source code is publicly available at https://github.com/HySonLab/Protein_Pretrain.
Rates of Resistance to Ceftazidime-Avibactam and Ceftolozane-Tazobactam Among Patients Treated for Multidrug-Resistant Pseudomonas aeruginosa Bacteremia or Pneumonia
Authors: Shah Sunish , Kline Ellen G , Haidar Ghady , Squires Kevin M , Pogue Jason M , McCreary Erin K , Ludwig Justin , Clarke Lloyd G , Stellfox Madison , Van Tyne Daria , Shields Ryan K
Published: June 2024

Among consecutive patients with multidrug-resistant Pseudomonas aeruginosa bacteremia or pneumonia we found those treated with ceftazidime-avibactam were more likely to develop resistance (defined as ≥4-fold increased MIC) than those treated with ceftolozane-tazobactam (40% vs 10%; P = .002). Ceftazidime-avibactam resistance was associated with new mutations in ampC and efflux regulatory pathways.
Limited efficacy of a commercial microbial inoculant for improving growth and physiological performance of native plant species
Authors: Wong Wei San , Ruscalleda-Alvarez Jaume , Yong Jean W H , Stevens Jason C , Valliere Justin M , Veneklaas Erik J
Published: June 2024

Soil microbial inoculants are increasingly being explored as means to improve soil conditions to facilitate ecological restoration. In southwestern Western Australia, highly biodiverse Banksia woodland plant communities are increasingly threatened by various factors including climate change, land development and mining. Banksia woodland restoration is necessary to conserve this plant community. The use of microbial inoculation in Banksia woodland restoration has not yet been investigated. Here, we evaluated the efficacy of a commercial microbial inoculant (GOGO Juice, Neutrog Australia Pty Ltd) for improving the performance of 10 ecologically diverse Banksia woodland plant species in a pot experiment. Plants were subjected to one of two watering regimes (well-watered and drought) in combination with microbial inoculation treatments (non-inoculated and inoculated). Plants were maintained under these two watering treatments for 10 weeks, at which point plants in all treatments were subjected to a final drought period lasting 8 weeks. Plant performance was evaluated by plant biomass and allocation, gas exchange parameters, foliar carbon and nitrogen and stable isotope (δ15N and δ13C) compositions. Plant xylem sap phytohormones were analysed to investigate the effect of microbial inoculation on plant phytohormone profiles and potential relationships with other observed physiological parameters. Across all investigated plant species, inoculation treatments had small effects on plant growth. Further analysis within each species revealed that inoculation treatments did not result in significant biomass gain under well-watered or drought-stressed conditions, and effects on nitrogen nutrition and photosynthesis were variable and minimal. This suggests that the selected commercial microbial inoculant had limited benefits for the tested plant species. Further investigations on the compatibility between the microorganisms (present in the inoculant) and plants, timing of inoculation, viability of the microorganisms and concentration(s) required to achieve effectiveness, under controlled conditions, and field trials are required to test the feasibility and efficacy in actual restoration environments.
Who will take the bait? Using an embedded, experimental study to chart organization-specific phishing risk profiles and the effect of a voluntary microlearning among employees of a Dutch municipality
Authors: Spithoven Remco , Drenth Anthonie
Published: June 2024

Phishing can lead to data leaks or infiltration of computer networks. Protection against the risks of phishing is particularly important for public organizations such as municipalities, that process a large amount of sensitive personal information and whose operational processes can have major societal impact. This makes phishing a direct threat to operational continuity and the reputation of the organization and raises the question of how public organizations can combat this effectively and which resources they can deploy to mitigate the risks of phishing. In this experiment, two test phishing emails were sent to the total population of one of the 15 largest Dutch municipalities. We performed an embedded experiment, with employees experiencing the risks of phishing first hand with extensive attention for the ethics of this approach. Senior and middle-aged employees clearly run the biggest risk of becoming victims of phishing at this specific organization, but they are not automatically prepared to do an online, educational microlearning on phishing. This is also the case for young staff. Less voluntary education should be aimed at these groups of employees in this organization to make them and the organization, more resilient to the risks of phishing. Also, the microlearning did not have an effect on the results of our participants. We advocate a tailor-made approach of offline training to raise awareness and resilience against phishing among employees of public organizations, municipalities, and organizations in general. Our experimental design can be reused in this direction. We conclude to also look at how never-clickers think and act, with further theoretical substantiation and research into the application of the human-as-solution approach..
Genome report: First reference genome of Vaccinium floribundum Kunth, an emblematic Andean species
Authors: Albuja-Quintana Martina , Pozo Gabriela , Gordillo-Romero Milton , Armijos Carolina E , Torres Maria de Lourdes
Published: June 2024

Vaccinium floribundum Kunth, known as “mortiño,” is an endemic shrub species of the Andean region adapted to harsh conditions in high-altitude ecosystems. It plays an important ecological role as a pioneer species in the aftermath of deforestation and human-induced fires within paramo ecosystems, emphasizing its conservation value. While previous studies have offered insights into the genetic diversity of mortiño, comprehensive genomic studies are still missing to fully understand the unique adaptations of this species and its population status, highlighting the importance of generating a reference genome for this plant. ONT and Illumina sequencing were used to establish a reference genome for this species. Three different de novo genome assemblies were generated and compared for quality, continuity and completeness. The Flye assembly was selected as the best and refined by filtering out short ONT reads, screening for contaminants and genome scaffolding. The final assembly has a genome size of 529 Mb, containing 1,317 contigs and 97% complete BUSCOs, indicating a high level of integrity of the genome. Additionally, the LTR Assembly Index of 12.93 further categorizes this assembly as a reference genome. The genome of V. floribundum reported in this study is the first reference genome generated for this species, providing a valuable tool for further studies. This high-quality genome, based on the quality and completeness parameters obtained, will not only help uncover the genetic mechanisms responsible for its unique traits and adaptations to high-altitude ecosystems but will also contribute to conservation strategies for a species endemic to the Andes.
Acute kidney injury after radical gastrectomy: incidence, risk factors, and impact on prognosis
Authors: Zhang Benlong , Li Li , Gao Yunhe , Wang Zijian , Lu Yixun , Chen Lin , Zhang Kecheng
Published: June 2024

Background

Acute kidney injury (AKI) is a serious adverse event often overlooked following major abdominal surgery. While radical gastrectomy stands as the primary curative method for treating gastric cancer patients, little information exists regarding AKI post-surgery. Hence, this study aimed to ascertain the incidence rate, risk factors, and consequences of AKI among patients undergoing radical gastrectomy.

Methods

This was a population-based, retrospective cohort study. The incidence of AKI was calculated. Multivariate logistic regression was used to identify independent predictors of AKI. Survival curves were plotted by using the Kaplan–Meier method and differences in survival rates between groups were analyzed by using the log-rank test.

Results

Of the 2,875 patients enrolled in this study, 61 (2.1%) developed postoperative AKI, with AKI Network 1, 2, and 3 in 50 (82.0%), 6 (9.8%), and 5 (8.2%), respectively. Of these, 49 patients had fully recovered by discharge. Risk factors for AKI after radical gastrectomy were preoperative hypertension (odds ratio [OR], 1.877; 95% CI, 1.064–3.311; P = 0.030), intraoperative blood loss (OR, 1.001; 95% CI, 1.000–1.002; P = 0.023), operation time (OR, 1.303; 95% CI, 1.030–1.649; P = 0.027), and postoperative intensive care unit (ICU) admission (OR, 4.303; 95% CI, 2.301–8.045; P < 0.001). The probability of postoperative complications, mortality during hospitalization, and length of stay in patients with AKI after surgery were significantly higher than those in patients without AKI. There was no statistical difference in overall survival (OS) rates between patients with AKI and without AKI (1-year, 3-year, 5-year overall survival rates of patients with AKI and without AKI were 93.3% vs 92.0%, 70.9% vs 73.6%, and 57.1% vs 67.1%, respectively, P = 0.137).

Conclusions

AKI following radical gastrectomy is relatively rare and typically self-limited. AKI is linked with preoperative hypertension, intraoperative blood loss, operation time, and postoperative ICU admission. While AKI raises the likelihood of postoperative complications, it does not affect OS.
Robotic-assisted thoracic surgery training in France: a nation-wide survey from young surgeons
Authors: Clermidy Hugo , Fadel Guillaume , Bottet Benjamin , Belaroussi Yaniss , Eid Maroua , Armand Elsa , Baste Jean-Marc , Pages Pierre-Benoit , Fourdrain Alex , Al Zreibi Charles , Madelaine Leslie , Saiydoun Gabriel ,   AJCTCV, Bernard Chloé , Jungling Marie , Aiouaz Hayat , Vasse Solenne , Buschiazzo Antoine , Borchiellini Paul , Cattan Johann , Saade Saadé
Published: June 2024

OBJECTIVES

Evaluate theoretical and practical training of thoracic surgeons-in-training in robotic-assisted thoracic surgery (RATS) in France.

METHODS

A survey was distributed to thoracic surgeons-in-training in France from November 2022 to February 2023.

RESULTS

We recruited 101 thoracic surgeons-in-training (77% response rate). Over half had access to a surgical robotics system at their current institution. Most (74%) considered robotic surgery training essential, 90% had attended a robotic procedure. Only 18% had performed a complete thoracic robotic procedure as the main operator. A complete RATS procedure was performed by 42% of fellows and 6% of residents. Of the remaining surgeons, 23% had performed part of a robotic procedure. Theoretical courses and simulation are well developed; 72% of residents and 91% of fellows had undergone simulation training in the operating room, at training facilities, or during congress amounting to <10 h (for 73% of the fellows and residents), 10–20 h (17%), 20–30 h (8%) or >30 h (3%). Access to RATS was ≥1 day/week in 71% of thoracic departments with robotic access. Fellows spent a median of 2 (IQR 1–3) semesters in departments performing robotic surgery. Compared with low-volume centres, trainees at high-volume centres performed significantly more complete robotic procedures (47% vs 13%; P = 0.001), as did fellows compared with residents.

CONCLUSIONS

Few young surgeons perform complete thoracic robotic procedures during practical training, and access remains centre dependent. Opportunities increase with seniority and exposure; however, increasing availability of robotic devices, theoretical formation, and simulation courses will increase opportunities.
A transform-based technique for solving boundary value problems on convex planar domains
Authors: Hulse Jesse J , Lanzani Loredana , Llewellyn Smith Stefan G , Luca Elena
Published: June 2024

A new technique is presented that can be used to solve mixed boundary value problems for Laplace’s equation and the complex Helmholtz equation in bounded convex planar domains. This work is an extension of Crowdy (2015, CMFT, 15, 655–687) where new transform-based techniques were developed for boundary value problems for Laplace’s equation in circular domains. The key ingredient of the method is the analysis of the so-called global relation, which provides a coupling of integral transforms of the given boundary data and of the unknown boundary values. Three problems which involve mixed boundary conditions are solved in detail, as well as numerically implemented, to illustrate how to apply the new approach.
Use of All of Us data to increase health literacy and research skills in high school students
Authors: Yamazaki Katrina Go , Taylor Amy , Asikin-Garmager Asih , Han Sharon , Bartlett Laura
Published: June 2024

Objective

This case study describes how an All of Us engagement project returned value to community by strengthening high school students’ capacity to serve as health advocates.

Materials and Methods

Project activities included health literacy education and research projects on the influence of environmental, societal, and lifestyle factors on community health disparities. The research project involved use of the Photovoice method and All of Us data. At project’s end, students presented their research to the community.

Results

The project’s success was measured by students’ participation in the research poster session and comparison of pre- and post-project scores from the Health Literacy Assessment Scale for Adolescent. Data analysis suggests the project succeeded in meeting its goal of increasing students’ health literacy.

Discussion and Conclusion

Through education and research activities, students learned about community health issues and the importance of participation in medical research programs, like All of Us, to address issues.
A novel approach to patient portal activation data to power equity improvements
Authors: Muniyappa Anoop , Weia Benjamin , Ling Nicole , O’Brien Julie , Tamerat Mariamawit , Soulsby William Daniel , Yim Joanne , Oates Aris
Published: June 2024

Background

There are significant disparities in access and utilization of patient portals by age, language, race, and ethnicity.

Materials and Methods

We developed ambulatory and inpatient portal activation equity dashboards to understand disparities in initial portal activation, identify targets for improvement, and enable monitoring of interventions over time. We selected key metrics focused on episodes of care and filters to enable high-level overviews and granular data selection to meet the needs of health system leaders and individual clinical units.

Results

In addition to highlighting disparities by age, preferred language, race and ethnicity, and insurance payor, the dashboards enabled development and monitoring of interventions to improve portal activation and equity.

Discussion and Conclusions

Data visualization tools that provide easily accessible, timely, and customizable data can enable a variety of stakeholders to understand and address healthcare disparities, such as patient portal activation. Further institutional efforts are needed to address the persistent inequities highlighted by these dashboards.
Matrix first, minerals later: fine-tuned dietary phosphate increases bone formation in zebrafish
Authors: Cotti Silvia , Di Biagio Claudia , Huysseune Ann , Koppe Wolfgang , Forlino Antonella , Witten P Eckhard
Published: June 2024

Bone matrix formation and mineralization are two closely related, yet separated processes. Matrix formation occurs first, mineralization is a second step strictly dependent on the dietary intake of calcium and phosphorus (P). However, mineralization is commonly used as diagnostic parameter for bone-related diseases. In this context, bone loss, often characterized as a condition with reduced bone mineral density, represents a major burden for human health, for which increased dietary mineral intake is generally recommended. Using a counterintuitive approach, we use a low-P diet followed by a sufficient-P intake to increase bone volume. We show in zebrafish by histology, qPCR, micro-CT, and enzyme histochemistry that a two-months period of reduced dietary P intake stimulates extensive formation of new bone matrix, associated with the upregulation of key genes required for both bone matrix formation and mineralization. The return to a P-sufficient diet initiates the mineralization of the abundant matrix previously deposited, thus resulting in a striking increase of the mineralized bone volume as proven at the level of the vertebral column, including vertebral bodies and arches. In summary, bone matrix formation is first stimulated with a low-P diet, and its mineralization is later triggered by a sufficient-P dietary intake. In zebrafish, the uncoupling of bone formation and mineralization by alternating low and sufficient dietary P intake significantly increases the bone volume without causing skeletal malformations or ectopic mineralization. A modification of this approach to stimulate bone formation, optimized for mammalian models, can possibly open opportunities to support treatments in patients that suffer from low bone mass.
Effects of high dose aspartame-based sweetener on the gut microbiota and bone strength in young and aged mice
Authors: Cyphert Erika L , Liu Chongshan , Morales Angie L , Nixon Jacob C , Blackford Emily , Garcia Matthew , Cevallos Nicolas , Turnbaugh Peter J , Brito Ilana L , Booth Sarah L , Hernandez Christopher J
Published: June 2024

In a recent study examining the effects of manipulating the gut microbiome on bone, a control group of mice in which the microbiome was altered using a non-caloric, aspartame-based sweetener resulted in whole bone strength being 40% greater than expected from geometry alone, implicating enhanced bone tissue strength. However, the study was not designed to detect changes in bone in this control group and was limited to young male mice. Here we report a replication study examining how changes in the gut microbiome caused by aspartame-based sweetener influence bone. Male and female C57Bl/6 J mice were untreated or treated with a high dose of sweetener (10 g/L) in their drinking water from either 1 to 4 mo of age (young cohort; n = 80) or 1 to 22 mo of age (aged cohort; n = 52). Sweetener did not replicate the modifications to the gut microbiome observed in the initial study and did not result in an increase in bone tissue strength in either sex at either age. Aged male mice dosed with sweetener had larger bones (+17% femur section modulus, p<.001) and greater whole bone strength (+22%, p=.006) but the increased whole bone strength was explained by the associated increase in body mass (+9%, p<.001). No differences in body mass, whole bone strength, or femoral geometry were associated with sweetener dosing in males from the young cohort or females at either age. As we were unable to replicate the gut microbiota observed in the initial experiment, it remains unclear if changes in the gut microbiome can enhance bone tissue strength. Although prior work studying gut microbiome–induced changes in bone with oral antibiotics has been highly repeatable, the current study highlights the variability of nutritional manipulations of the gut microbiota in mice.
Environmental Damage in Ukraine as Environmental War Crime under the Rome Statute
Authors: Maruf Shah
Published: June 2024

The Russian invasion of Ukraine has caused irreparable damage to the natural environment. Despite being a topic of wide discussion, an analysis of whether the attacks causing such damage can be tried at the International Criminal Court (ICC) as an environmental war crime (EWC) under Article 8(2)(b)(iv) of the Rome Statute remained grossly inadequate. Even after the Kakhovka Dam destruction in June 2023, the most significant incident of environmental damage since the war started, no comprehensive analysis of the incident from an EWC perspective was made. The present article fills this void and thoroughly analyses whether the dam breach can qualify as an EWC under Article 8(2)(b)(iv), the most ecocentric provision in the entire international criminal law (ICL) framework. After providing an overview of the environmental damage caused and a synopsis of the EWC, this article applies the EWC provision to the incident and discusses the prospects and the challenges of characterizing it as an EWC. This article suggests that Russia’s intentional attack on the dam can be a potential case of EWC under Article 8(2)(b)(iv) as it caused ‘widespread, long-term and severe’ environmental damage in contrast to little military advantage — which was arguably known to Russia. At the same time, however, the article identifies some challenges that the ICC Prosecutor may face in proving the case, like determining the ‘attack’ question, satisfying the ‘long-term’ damage criterion, and establishing the mental elements, particularly the ‘knowledge’ element. It also briefly discusses the broader implications of the assessment and the identified challenges. The article concludes that the challenges can be surmounted and, in any case, bringing such a charge will offer the ICC an avenue to clarify the existing uncertainties surrounding Article 8(2)(b)(iv), which will ensure legal certainty and help ensuring environmental justice through the ICL regime in future.