bluuebunny/crossref_metadata_2025 huggingface dataset:
Reinforcement learning-based energy management for hybrid electric vehicle enhanced by velocity prediction
Authors: Luo Shaohua , Bai Qin , Wang Yi , Liu Ning , Ou Yang
Published: June 2024

This paper proposes a novel approach for optimal energy management of engine-battery hybrid electric systems. It addresses two limitations in existing research, namely inaccurate speed prediction and low control accuracy. The proposed method integrates Markov theory and clustering theory to achieve high-precision prediction of future velocity under diverse driving styles. Furthermore, a learning-based energy management strategy is developed using a deep deterministic strategy gradient algorithm. This strategy considers the predicted velocity and aims to minimize engine fuel consumption, battery state fluctuations, and engine start-stop occurrences. Simulation results demonstrate that the proposed algorithm achieves near-optimal performance under specific operating conditions.
Energy sharing mechanisms for multi prosumers considering privacy protection
Authors: Qi Lei , Ai Qian , Ji Wenlu , Li Jiamei , Wang Di , Pan Xiaohui
Published: June 2024

With the rapid development of new renewable energy sources, microgrids, smart buildings and other forms of prosumers have emerged on a large scale. Energy sharing among multi prosumers can improve the overall economic efficiency. Based on taking into account the data privacy of each prosumer, a collaborative operation mechanism for energy sharing among multi prosumers is proposed. First, an internal scheduling model of prosumers with multiple distributed resources is constructed. Then, an iterative mechanism for multi prosumers tariffs is proposed to guide the tariff update by using the supply-demand relationship. Meanwhile, considering the privacy security of the prosumers, a electricity data aggregation method is designed based on Paillier homomorphic encryption algorithm and the secret sharing principle, which is capable of obtaining the system supply and demand information under the premise of protecting the privacy of all parties. Finally, the effectiveness and reasonableness of the proposed mechanism is verified through examples.
Adaptive reactive power control strategy for grid-forming inverter under symmetrical fault
Authors: Mu Longfei
Published: June 2024

Due to the inability of the grid-type control method to compensate for the comprehensive reduction in system inertia, strength, and short-circuit capacity caused by the proportional decrease of synchronous machines, the power grid exhibits insufficient resistance to disturbances, leading to severe stability risks in terms of rotor angle, frequency, and voltage. In response to these challenges, grid-forming inverters have emerged. Under symmetrical faults, the low-voltage ride-through of grid-forming inverters is often accompanied by a frozen reactive power environment, resulting in a direct output of increased voltage and reactive current. However, an elevated reactive power command can cause a sharp increase in the potential amplitude within grid-forming inverters. After the grid fault is cleared, the excessively high internal potential can cause a short-term and rapid increase in terminal voltage, potentially leading to overvoltage, which is detrimental to the operation of grid-connected devices. To address this issue, this paper first employs a grid-forming inverter controlled by a virtual synchronous machine control method. Using the grid positive-sequence voltage as a reference value, it identifies whether a voltage drop fault has occurred. Based on this, an adaptive reactive power control strategy is proposed, which can promptly achieve the same effect as the frozen reactive power environment during faults, while also promptly restoring the reactive power environment after fault clearance, thereby avoiding overvoltage issues. The feasibility of the proposed method is verified through the establishment of a simulation system.
Evaluation of the Nearest and The Longest Shipping Routes in MT. Perla
Authors: Rohman M A , Achmad F
Published: June 2024

Shipping routes are sea transportation from one port to another. There are loading and unloading activities in shipping routes. Loading and unloading activities are the activity of moving cargo from land to ship at the loading port, and moving cargo from ship to land at the unloading port. On ships with irregular routes, loading and unloading activities are random in terms of shipping route, amount of cargo, and length of time required. Evaluation is a process of collecting information to improve and determine quality and performance based on certain considerations and criteria (value and meaning) in implementing a program. This study will discuss the shipping route, amount of cargo, length of shipping time, loading and unloading. The research aimed to evaluate the nearest and the longest shipping routes in MT. Perla. The authors used a quantitative analysis research method where the data was processed and calculated by using Ms. Excel and SPSS was then used to evaluate shipping routes. The research results show that the evaluation of shipping routes for 12 months. Some factors hinder shipping routes, loading, and unloading activities. The researcher’s advice is for all parties to pay attention to the evaluation results and the factors causing those to avoid company losses and to improve the quality of shipping routes.
Biodegradation of bioplastic straws compared to conventional plastic straws
Authors: Limpiteeprakan Pawena , Ratchawong Jirikanya , Kittichaimongkol Natthanida , Tubtimhin Sanga
Published: June 2024

This experimental study aimed to investigate the biodegradation of commercially available bioplastic straws compared to conventional plastic straws using four types of plastic straws: polypropylene (PP), bio-polybutylene succinate (PSB) mixed with polylactic acid (PLA), PLA alone, and bagasse straws. The tubes were cut into small sizes, buried in soil, watered to simulate natural degradation conditions, and placed in the same environment at the College of Medicine and Public Health, Ubon Ratchathani University. The tubes were excavated, weighed, and analyzed using a microscope and scanning electron microscopy. Results showed that the 1 cm small tubes experienced greater weight loss than the 2 cm tubes. Straws made from PSB mixed with PLA showed the highest weight loss of 46%. Bioplastic straws made from PLA alone showed the least weight loss. SEM images showed noticeable surface changes in straws made from natural materials and bioplastics compared to PP straws, especially in the 2 cm tubes. The findings suggest that using biodegradable straws, especially those made from natural materials, can effectively mitigate plastic pollution and preserve the environment.
Research on a circular economy model for biodegradable organic components treatment in municipal solid waste at a household-scale
Authors: Tuyen Duong Kim , Thanh Dang My
Published: June 2024

Since biodegradable components form a major amount of household municipal solid waste (MSW), this study investigated a model of biodegradable organic waste treatment at home scale in order to recycle them into organic fertilizers. The experimental design was carried out in a perforated plastic bin (capacity = 18L) with 2 different models, with and without Trichoderma microbial product (TMP), in order to evaluate the effect of microbial product on the decomposition process and fertilizer quality. The monitored parameters for both models showed a similar trend of changes during the decomposition, however in the model with TMP, it was found that the decomposition process took place faster. The properties included pH (6.2–7.6), temperature (29–44 °C), and moisture content (47–63%). Two models were well matured within 1 month. Fertilizer products are used to grow mung beans (Vigna Radiata). They help in fast-growing plants (height from 20 to 22cm) with good green leaves (leaves width from 3-5 cm). Overall, the model has the potential to be broadly applied, helping to reduce the amount of MSW to be treated, saving costs, and creating a closed cycle towards a circular economy model.
Assessment of indoor air quality of the furniture manufacturers in Binh Duong industrial parks, Vietnam
Authors: Pham A D , Nguyen T T H , Vu T M H
Published: June 2024

Wood furniture and related products are created from raw wood and or wood products that require cutting, sanding, and other handling activities that generate wood dust. Exposure to indoor factory air pollutants can have significant health consequences for workers and nearby communities. Therefore, it was necessary to implement the assessment of indoor air quality in furniture manufacturers. This study mainly aimed to assess the indoor air quality status of physical and chemical aspects at 3 different furniture factories. Each sample was analysed for eight parameters including TSP, PM10, PM2.5, noise, temperature, humidity, wind, and light. Sampling and sample handling techniques were performed based on the usage test methods of Vietnam standards. The concentrations of TSP (194 – 493 μg/m3), PM10 (106.7 – 153.8 μg/m3), PM2.5 (72.8 – 95.6 μg/m3); and, the variables of noise (70.4 – 80.3 dBA), temperature (29.4 – 32.4 °C), humidity (58.0 – 69.4 %), wind (0.29 – 0.49) and light (327 – 573) these considered at 3 furniture manufacturers were within the allowable thresholds of QCVN 02:2019/BYT (Permissible exposure limit value of dust at the workplace), QCVN24:2016/BYT (Permissible exposure levels of noise in the workplace), QCVN26:2016/BYT (Permissible value of microclimate in the workplace); and, QCVN22:2016/BYT (Permissible levels of lighting in the workplace). However, long-term direct exposure of workers to these pollutants would also result in potential health risks. This study also suggested the management and technical control solutions to contribute to improving air quality for furniture manufacturers.
Dynamic Modelling, Simulation, and Sensitive Analysis of Lead Removal in a Fixed-Bed Adsorption Column using Waste-Based Materials
Authors: Gheibi Mohammad , Wacławek Stanisław , Leo Choe Peng , Sadr Seyed , Behzadian Kourosh
Published: June 2024

This study focuses on dynamic modelling and numerical simulation of lead removal from contaminated water using a fixed-bed adsorption column packed with waste-based adsorbents. The pressing need for efficient and sustainable water treatment methods, particularly for heavy metal removal, underscores the significance of this research. Lead contamination in water sources poses severe health risks, necessitating the development of effective removal strategies. The present investigation centres on a comprehensive mathematical model that considers critical parameters, including the column’s physical dimensions, flow rate, initial lead concentration, adsorption rate constant, and adsorbent density. This model is expressed as a partial differential equation (PDE) describing the temporal and spatial evolution of lead concentration along the fixed-bed column. To solve the PDE, the method of lines, a powerful numerical technique that discretises the spatial domain and handles the resulting system of ordinary differential equations (ODEs) using an adaptive solver, is employed. Following that, the effect factors of the simulation process are evaluated by sensitive analysis approach. Simulations are conducted to elucidate the intricate dynamics of lead removal over time and column height. The numerical approach enables the prediction of lead concentration profiles within the column at various time intervals, providing crucial insights into the behavior of the adsorption process.
3D embedded bioprinting of large-scale intestine with complex structural organization and blood capillaries
Authors: Li Yuxuan , Cheng Shengnan , Shi Haihua , Yuan Renshun , Gao Chen , Wang Yuhan , Zhang Zhijun , Deng Zongwu , Huang Jie
Published: June 2024

Accurate reproduction of human intestinal structure and function in vitro is of great significance for understanding the development and disease occurrence of the gut. However, most in vitro studies are often confined to 2D models, 2.5D organ chips or 3D organoids, which cannot fully recapitulate the tissue architecture, microenvironment and cell compartmentalization found in vivo. Herein, a centimeter-scale intestine tissue that contains intestinal features, such as hollow tubular structure, capillaries and tightly connected epithelium with in vivo-like ring folds, crypt-villi, and microvilli is constructed by 3D embedding bioprinting. In our strategy, a novel photocurable bioink composed of methacrylated gelatin, methacrylated sodium alginate and poly (ethylene glycol) diacrylate is developed for the fabrication of intestinal model. The Caco-2 cells implanted in the lumen are induced by the topological structures of the model to derive microvilli, crypt-villi, and tight junctions, simulating the intestinal epithelial barrier. The human umbilical vein endothelial cells encapsulated within the model gradually form microvessels, mimicking the dense capillary network in the intestine. This intestine-like tissue, which closely resembles the structure and cell arrangement of the human gut, can act as a platform to predict the therapeutic and toxic side effects of new drugs on the intestine.
Little prairie under the panel: testing native pollinator habitat seed mix establishment at three utility-scale solar sites in Minnesota
Authors: McCall James , Beatty Brenda , Janski Jake , Doubleday Kate , Martin Jordan , Hartmann Heidi , Walston Leroy J , Macknick Jordan
Published: June 2024

As more land is being utilized for large-scale solar energy projects, there are increasing discussions from stakeholders on how to utilize land under solar panels to promote biodiversity. One path is to plant habitat beneficial to pollinators and other insects, but there have been few long-term studies that examine how different vegetation and seed mixes establish underneath solar panels. This study addresses a scientific gap to determine whether native pollinator seed mixes successfully establish over time under solar arrays using a systematic assessment of eight seed mixes planted at three utility-scale solar sites in Minnesota. We assess establishment with a percent native coverage metric, which is an assessment of native species observations compared to total observations during percent cover analyses in our vegetative test plots. The percent native coverage metric allows for a measurement of how the seed mix established and how the seed mix persists over time. The percent native coverage under and in between the solar photovoltaic (PV) arrays rose from 10% after one year of planting to 58% after three years across all sites, while the native coverage of the full sun control area rose from 9.6% to 70% under the same period, showing that native prairie and pollinator plants successfully established under the array, although to a lesser extent than in full sun conditions. Percent native coverage under the PV arrays rose 5- to 8-fold for each of the three sites from over the course of the study, while the coverage of weeds decreased for all three sites over the same period. Percent native coverage varied by seed mix over the project years, but every seed mix experienced a higher percent native coverage year after year under the PV arrays. Our results did not indicate a difference in establishment across placement within the array; the center, west, and east portions of the areas in between panels had similar establishment rates at two out of three sites, indicating that the same seed mix can be applied throughout the array. Out of 101 plant species seeded, we observed the establishment of 68 species in our vegetative test plots, and we detailed the top 20 observed species to inform future seed mix development. Based on these findings, native pollinator vegetation can establish over time at solar arrays, and it can be suitable for creating habitat at utility-scale solar sites.
Non-invasive stratigraphic analyzes of gelatine-based modern painting materials with linear and nonlinear optical methods
Authors: Quintero Balbas Diego , Maestro-Guijarro Laura , Carmona-Quiroga Paula María , Oujja Mohamed , Castillejo Marta , Bettini Francesca , Porcinai Simone , Striova Jana
Published: June 2024

Stratigraphic analyzes of polychrome surfaces, such as paintings, often need samples to offer consistent results regarding the sequence and composition of the layers. Non-invasive methodologies based on linear and nonlinear optical techniques limit material removal from the objects. Recently, optical coherence tomography (OCT) has become the preferred choice of heritage scientists because it is a safe and fast alternative for studying transparent or semi-transparent layers. Yet, nonlinear optical microscopy (NLOM)) technique in its modality of multiphoton excitation fluorescence (MPEF) has emerged as a promising tool for the same purpose. Here, we explored linear (OCT and confocal Raman microspectroscopy (CRM)) and nonlinear (NLOM-MPEF) optical methods’ capability to investigate gelatine-based layers in mock-up samples and a painting dated 1939 by an artist from the Surrealistic entourage. The optical behavior of mock-up samples that imitate the painting stratigraphy and of six painting fragments detached from the support was also investigated with fiber optics reflectance spectroscopy and laser induced fluorescence (LIF). Thickness values from the mock-ups obtained with OCT, CRM, and MPEF have provided evidence of the complementarity, from a millimetric to a micrometric scale, and the limitations (e.g. strong fluorescence emission in CRM) of the methods. Moreover, the presence of gelatine was ascertained by LIF spectroscopy applied to the painting fragments and NLOM-MPEF confirmed its suitability as a non-invasive technique for investigating gelatine-based stratigraphic systems.
Beyond Moral Fundamentalism
Authors: Fesmire Steven
Published: June 2024

Moral fundamentalism is the habit of acting as though one has access to the exclusively right way to diagnose problems, along with the single approvable practical solution to any particular problem. This approach causes us to oversimplify situations, neglect broader context, take refuge in dogmatic absolutes, ignore possibilities for finding common ground, assume privileged access to the right way to proceed, and shut off honest inquiry. In this way, moral fundamentalism—exacerbated by social media silos—also makes the worst of native impulses toward social bonding and antagonism. This makes it impossible to debate and achieve superordinate social goals, such as public health, justice, security, sustainability, peace, and democracy. Drawing from John Dewey’s pluralistic and pragmatic approach to philosophical questions, this book develops an alternative to both the oversimplification of moral fundamentalism and the arbitrariness of relativism. Pragmatic pluralism is set up as a response to particular conditions and consequences, so it gains practical leverage with complex ethical, political, educational, and policy problems without flattening variability among values or presuming that abstract theories can determine what we ought to do. The book argues that the reductive monistic premise that logically underlies moral fundamentalism is both unwarranted and constrictive, and there is little to be said in favor of the grand philosophical quest for a unifying principle that cannot be accommodated within a wider pluralistic approach. In a concrete and engaging style, the author clarifies and illustrates the promises and challenges of democratic decision-making in societies struggling to grow beyond moral fundamentalism.
Educating for Democracy
Authors: Fesmire Steven
Published: June 2024

Dewey rejected as antidemocratic the notion that we need one educational approach for vocational trainees who will be led, and an essentially different one for elites who will lead. Such an autocratic and class-based approach is fertile ground for moral fundamentalism. Instead, we need to organize schooling so that students gain direct aesthetic fulfillment even as they cultivate competent, forward-looking, open-ended, collaborative, and progressively specialized intelligence. Unfortunately, the increasingly dominant industrial model of education conceives service to the private sector as the overriding goal. It channels energies toward narrow workforce training. This chapter explains, updates, and illustrates Dewey’s alternative, which was to engage occupational callings in a way that contributes to a more humane democratic culture. Nevertheless, even as we continue to debate educational values, the educational pragmatist does not insist upon a shared pre-alignment of ends, diagnoses, and justifications as a prerequisite to participating in public deliberation.
Conclusion
Authors: Fesmire Steven
Published: June 2024

The conclusion recaps the book’s main line of argument. Moral fundamentalist habits, and the reductive monistic philosophical assumption that mostly unintentionally reinforces them, are obstacles to cultivating virtues of inquiry that are suited to dealing with the predicaments that are rapidly transforming our planet. If philosophers and other public intellectuals are to speak more effectively to complex problems in a way that aids public deliberation and social learning, a critical focus on Dewey’s pragmatic pluralism would be salutary. Dewey did not explicitly spell out implications of his approach to ethics and politics for redirecting future theorizing, so the chapter closes with recommendations extrapolated by marrying his writings with a sampling of contemporary pragmatic pluralists who are steeped in his general outlook.
Multidimensional Religiousness and Spirituality Are Associated With Lower Interleukin-6 and C-Reactive Protein at Midlife: Findings From the Midlife in the United States Study
Authors: Vagnini Kaitlyn M , Morozink Boylan Jennifer , Adams Monica , Masters Kevin S
Published: June 2024

Background

Religiousness and spirituality (R/S) are associated with lower morbidity and mortality, yet the physiological mechanisms underlying these associations are under-studied. Chronic inflammation is a plausible biological mechanism linking R/S to downstream health given the sensitivity of the immune system to the social environment and the role of inflammation in many chronic diseases.

Purpose

The purpose of the present study was to examine associations between multiple R/S dimensions and two markers of chronic inflammation, interleukin-6 (IL-6) and C-reactive protein (CRP).

Methods

In this cross-sectional study, data came from biological subsamples of two cohorts from the Midlife in the United States (MIDUS) Study (combined N = 2,118). Predictors include six R/S measures (service attendance, spirituality, private religious practices, daily spiritual experiences, religious coping, and R/S-based mindfulness). Outcomes include log-transformed IL-6 and CRP. Covariates include age, gender, cohort, race, educational attainment, body mass index (BMI), smoking status, and physical activity.

Results

Older adults, women (vs. men), non-White (vs. White) adults, those with higher BMIs, current smokers, and those not meeting physical activity guidelines had significantly higher IL-6 and CRP. In fully adjusted models, greater spirituality, daily spiritual experiences, religious coping, and R/S-based mindfulness were associated with lower IL-6. Higher spirituality was also associated with lower CRP.

Conclusions

Many dimensions of R/S may be health protective for adults given their associations with lower levels of chronic inflammation. Findings underscore the importance of examining multiple dimensions of R/S to understand mechanistic pathways.
Competition and drought affect cleistogamy in a non-additive way in the annual ruderal Lamium amplexicaule
Authors: Stojanova Bojana , Eliášová Anežka , Tureček Tomáš
Published: June 2024

Competition affects mixed-mating strategies by limiting available abiotic or biotic resources such as nutrients, water, space, or pollinators. Cleistogamous species produce closed (cleistogamous, CL), obligately selfed, simultaneously with open (chasmogamous, CH), potentially outcrossed flowers. The effects of intraspecific competition on fitness and cleistogamy variation can range from limiting the production of costly CH flowers because of resource limitation, to favouring CH production because of fitness advantages of outcrossed, CH offspring. Moreover, the effects of competition can be altered when it co-occurs with other environmental variations. We grew plants from seven populations of the ruderal Lamium amplexicaule, originating from different climates and habitats, in a common garden experiment combining drought, interspecific competition, and seasonal variation. All these parameters have been shown to influence the degree of cleistogamy in the species on their own. In spring, competition and drought negatively impacted fitness, but the CL proportion only increased when plants were exposed to both treatments combined. We did not observe the same results in autumn, which can be due to non-adaptive phenotypic variation, or to differences in soil compactness between seasons. The observed responses are largely due to phenotypic plasticity, but we also observed phenotypic differentiation between populations for morphological, phenological, and cleistogamy traits, pointing to the existence of different ecotypes. Our data do not support the hypothesis that CL proportion should decrease when resources are scarce, as plants with reduced growth had relatively low CL proportions. We propose that variation in cleistogamy could be an adaptation to pollinator abundance, or to environment-dependent fitness differences between offspring of selfed and outcrossed seeds, two hypotheses worth further investigation. This opens exciting new possibilities for the study of the maintenance of mixed-mating systems using cleistogamous species as models that combine the effects of inbreeding and reproductive costs.
Characterization of double-stranded RNA and its silencing efficiency for insects using hybrid deep-learning framework
Authors: Cheng Han , Xu Liping , Jia Cangzhi
Published: June 2024

RNA interference (RNAi) technology is widely used in the biological prevention and control of terrestrial insects. One of the main factors with the application of RNAi in insects is the difference in RNAi efficiency, which may vary not only in different insects, but also in different genes of the same insect, and even in different double-stranded RNAs (dsRNAs) of the same gene. This work focuses on the last question and establishes a bioinformatics software that can help researchers screen for the most efficient dsRNA targeting target genes. Among insects, the red flour beetle (Tribolium castaneum) is known to be one of the most sensitive to RNAi. From iBeetle-Base, we extracted 12 027 efficient dsRNA sequences with a lethality rate of ≥20% or with experimentation-induced phenotypic changes and processed these data to correspond to specific silence efficiency. Based on the first complied novel benchmark dataset, we specifically designed a deep neural network to identify and characterize efficient dsRNA for RNAi in insects. The dna2vec word embedding model was trained to extract distributed feature representations, and three powerful modules, namely convolutional neural network, bidirectional long short-term memory network, and self-attention mechanism, were integrated to form our predictor model to characterize the extracted dsRNAs and their silencing efficiencies for T. castaneum. Our model dsRNAPredictor showed reliable performance in multiple independent tests based on different species, including both T. castaneum and Aedes aegypti. This indicates that dsRNAPredictor can facilitate prescreening for designing high-efficiency dsRNA targeting target genes of insects in advance.
racoon_clip—a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data
Authors: Klostermann Melina , Zarnack Kathi
Published: June 2024

Motivation

A vast variety of biological questions connected to RNA-binding proteins can be tackled with UV crosslinking and immunoprecipitation (CLIP) experiments. However, the processing and analysis of CLIP data are rather complex. Moreover, different types of CLIP experiments like iCLIP or eCLIP are often processed in different ways, reducing comparability between multiple experiments. Therefore, we aimed to build an easy-to-use computational tool for the processing of CLIP data that can be used for both iCLIP and eCLIP data, as well as data from other truncation-based CLIP methods.

Results

Here, we introduce racoon_clip, a sustainable and fully automated pipeline for the complete processing of iCLIP and eCLIP data to extract RNA binding signal at single-nucleotide resolution. racoon_clip is easy to install and execute, with multiple pre-settings and fully customizable parameters, and outputs a conclusive summary report with visualizations and statistics for all analysis steps.

Availability and implementation

racoon_clip is implemented as a Snakemake-powered command line tool (Snakemake version ≥7.22, Python version ≥3.9). The latest release can be downloaded from GitHub (https://github.com/ZarnackGroup/racoon_clip/tree/main) and installed via pip. A detailed documentation, including installation, usage, and customization, can be found at https://racoon-clip.readthedocs.io/en/latest/. The example datasets can be downloaded from the Short Read Archive (SRA; iCLIP: SRR5646576, SRR5646577, SRR5646578) or the ENCODE Project (eCLIP: ENCSR202BFN).
HGTDR: Advancing drug repurposing with heterogeneous graph transformers
Authors: Gharizadeh Ali , Abbasi Karim , Ghareyazi Amin , Mofrad Mohammad R K , Rabiee Hamid R
Published: June 2024

Motivation

Drug repurposing is a viable solution for reducing the time and cost associated with drug development. However, thus far, the proposed drug repurposing approaches still need to meet expectations. Therefore, it is crucial to offer a systematic approach for drug repurposing to achieve cost savings and enhance human lives. In recent years, using biological network-based methods for drug repurposing has generated promising results. Nevertheless, these methods have limitations. Primarily, the scope of these methods is generally limited concerning the size and variety of data they can effectively handle. Another issue arises from the treatment of heterogeneous data, which needs to be addressed or converted into homogeneous data, leading to a loss of information. A significant drawback is that most of these approaches lack end-to-end functionality, necessitating manual implementation and expert knowledge in certain stages.

Results

We propose a new solution, Heterogeneous Graph Transformer for Drug Repurposing (HGTDR), to address the challenges associated with drug repurposing. HGTDR is a three-step approach for knowledge graph-based drug repurposing: (1) constructing a heterogeneous knowledge graph, (2) utilizing a heterogeneous graph transformer network, and (3) computing relationship scores using a fully connected network. By leveraging HGTDR, users gain the ability to manipulate input graphs, extract information from diverse entities, and obtain their desired output. In the evaluation step, we demonstrate that HGTDR performs comparably to previous methods. Furthermore, we review medical studies to validate our method’s top 10 drug repurposing suggestions, which have exhibited promising results. We also demonstrated HGTDR’s capability to predict other types of relations through numerical and experimental validation, such as drug–protein and disease–protein inter-relations.

Availability and implementation

The source code and data are available at https://github.com/bcb-sut/HGTDR and http://git.dml.ir/BCB/HGTDR
FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology
Authors: Groza Tudor , Gration Dylan , Baynam Gareth , Robinson Peter N
Published: June 2024

Motivation

Human Phenotype Ontology (HPO)-based phenotype concept recognition (CR) underpins a faster and more effective mechanism to create patient phenotype profiles or to document novel phenotype-centred knowledge statements. While the increasing adoption of large language models (LLMs) for natural language understanding has led to several LLM-based solutions, we argue that their intrinsic resource-intensive nature is not suitable for realistic management of the phenotype CR lifecycle. Consequently, we propose to go back to the basics and adopt a dictionary-based approach that enables both an immediate refresh of the ontological concepts as well as efficient re-analysis of past data.

Results

We developed a dictionary-based approach using a pre-built large collection of clusters of morphologically equivalent tokens—to address lexical variability and a more effective CR step by reducing the entity boundary detection strictly to candidates consisting of tokens belonging to ontology concepts. Our method achieves state-of-the-art results (0.76 F1 on the GSC+ corpus) and a processing efficiency of 10 000 publication abstracts in 5 s.

Availability and implementation

FastHPOCR is available as a Python package installable via pip. The source code is available at https://github.com/tudorgroza/fast_hpo_cr. A Java implementation of FastHPOCR will be made available as part of the Fenominal Java library available at https://github.com/monarch-initiative/fenominal. The up-to-date GCS-2024 corpus is available at https://github.com/tudorgroza/code-for-papers/tree/main/gsc-2024.
hictk: blazing fast toolkit to work with .hic and .cool files
Authors: Rossini Roberto , Paulsen Jonas
Published: June 2024

Motivation

Hi-C is gaining prominence as a method for mapping genome organization. With declining sequencing costs and a growing demand for higher-resolution data, efficient tools for processing Hi-C datasets at different resolutions are crucial. Over the past decade, the .hic and Cooler file formats have become the de-facto standard to store interaction matrices produced by Hi-C experiments in binary format. Interoperability issues make it unnecessarily difficult to convert between the two formats and to develop applications that can process each format natively.

Results

We developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python and R bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.

Availability and implementation

The hictk library, Python bindings and CLI tools are released under the MIT license as a multi-platform application available at github.com/paulsengroup/hictk. Pre-built binaries for Linux and macOS are available on bioconda. Python bindings for hictk are available on GitHub at github.com/paulsengroup/hictkpy, while R bindings are available on GitHub at github.com/paulsengroup/hictkR.
Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana
Authors: Cassan Océane , Lecellier Charles-Henri , Martin Antoine , Bréhélin Laurent , Lèbre Sophie
Published: June 2024

Motivations

Gene regulatory networks (GRNs) are traditionally inferred from gene expression profiles monitoring a specific condition or treatment. In the last decade, integrative strategies have successfully emerged to guide GRN inference from gene expression with complementary prior data. However, datasets used as prior information and validation gold standards are often related and limited to a subset of genes. This lack of complete and independent evaluation calls for new criteria to robustly estimate the optimal intensity of prior data integration in the inference process.

Results

We address this issue for two regression-based GRN inference models, a weighted random forest (weigthedRF) and a generalized linear model estimated under a weighted LASSO penalty with stability selection (weightedLASSO). These approaches are applied to data from the root response to nitrate induction in Arabidopsis thaliana. For each gene, we measure how the integration of transcription factor binding motifs influences model prediction. We propose a new approach, DIOgene, that uses model prediction error and a simulated null hypothesis in order to optimize data integration strength in a hypothesis-driven, gene-specific manner. This integration scheme reveals a strong diversity of optimal integration intensities between genes, and offers good performance in minimizing prediction error as well as retrieving experimental interactions. Experimental results show that DIOgene compares favorably against state-of-the-art approaches and allows to recover master regulators of nitrate induction.

Availability and implementation

The R code and notebooks demonstrating the use of the proposed approaches are available in the repository https://github.com/OceaneCsn/integrative_GRN_N_induction
Problems in Commercial Kits of 25-Hydroxy Vitamin D and the Development of Simple, Robust and Faster HPLC Method
Authors: Saad Syed Muhammad , Khan Abdul Rafiq , Khan Khalid Mohammed , Al-Othaim Ali
Published: June 2024

Vitamin D is a lipid-soluble compound that plays a key role in bone mineral metabolism. The commercial current kits and several published assay methods (High-performance liquid chromatography (HPLC) and Immunoassay) are complicated due to the use of multiple reagents, larger sample volume, high backpressure, longer extraction time, evaporation under nitrogen after extraction, significant interference and antibody cross-reactivity. Here we report a new HPLC method for the determination of 25-hydroxyvitamin D2 (25-OHD2) and 25-hydroxyvitamin D3 (25-OHD3) that is simple (no evaporation), rapid (10-minute run time) and robust. Serum sample (300 μl) is mixed with 300 μl acetonitrile containing lauraphenone as internal standard. After vortexing and centrifugation, the supernatant was loaded into C18 extraction cartridges, washed with 70% methanol and then eluted with 200 μl of a mixture of 70% ethanol and 30% isopropyl alcohol (IPA). The eluent was mixed with 50 μl of water and injected into the HPLC-UV system for analysis. The method proved to be linear in the range of 10–750 nmol/L of 25-OHD2 and 25-OHD3. The intra- and inter-assay precision was less than 10 for both compounds at four different concentrations. The method was compared with (LC–MS/MS) and the correlation coefficients (R2) were 0.9454 and 0.9673 for 25-OHD2 and 25-OHD3 respectively. The proposed HPLC method is simple, rapid, robust and free from the most common problems encountered with commercial kits. It can be used in a high-volume laboratory that uses the HPLC method for the simultaneous determination of 25-OHD2 and 25-OHD3 in serum samples.
Case report of increased left ventricular end-diastolic pressure with pulsatile left ventricular assist device
Authors: de Sá Marchi Mauricio Felippi , Verhemel Sarah , Nuis Rutger-Jan , Van Mieghem Nicolas M
Published: June 2024

Background

Left ventricular assist devices (LVADs) are increasingly utilized in cardiogenic shock and high-risk percutaneous coronary interventions (PCIs). These devices aspirate and expel blood from the left ventricle (LV) into the aorta, consequently reducing left ventricular end-diastolic pressure (LVEDP). We report a case of unexpected LVEDP rise under LV-to-aorta LVAD in the context of transcatheter aortic valve implantation (TAVI) and concomitant multi-vessel PCI.

Case summary

A patient with acute heart failure, severely depressed systolic LV function, severe aortic stenosis, and multi-vessel coronary artery disease underwent TAVI and concomitant PCI under pulsatile LVAD. Notably, the patient experienced unexpected shortness of breath and elevated LVEDP while under LVAD, which normalized immediately upon LVAD removal.

Discussion

Pulsatile LVAD enhances cardiac output by providing pulsatile support through a percutaneous bi-directional flow catheter. Despite expectations of reduced LVEDP and improved myocardial oxygen supply under LVAD support, we observed high LVEDP and clinical complaints of shortness of breath following TAVI and multi-vessel PCI. This case illustrates that an LVAD across the aortic valve may immobilize aortic leaflets and generate acute aortic regurgitation.
Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population
Authors: Leon-Apodaca Ana V , Kumar Manoharan , del Castillo Andres , Conroy Gabriel C , Lamont Robert W , Ogbourne Steven , Cairns Kylie M , Borburgh Liz , Behrendorff Linda , Subramanian Sankar , Szpiech Zachary A
Published: June 2024

Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K’gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K’gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K’gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K’gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROHs)—indicators of inbreeding—are elevated in all sampled dingoes. However, K’gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K’gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.
Pathways to hypermutation in high-grade gliomas: Mechanisms, syndromes, and opportunities for immunotherapy
Authors: Haynes Tuesday , Gilbert Mark R , Breen Kevin , Yang Chunzhang
Published: June 2024

Despite rapid advances in the field of immunotherapy, including the success of immune checkpoint inhibition in treating multiple cancer types, clinical response in high-grade gliomas (HGGs) has been disappointing. This has been in part attributed to the low tumor mutational burden (TMB) of the majority of HGGs. Hypermutation is a recently characterized glioma signature that occurs in a small subset of cases, which may open an avenue to immunotherapy. The substantially elevated TMB of these tumors most commonly results from alterations in the DNA mismatch repair pathway in the setting of extensive exposure to temozolomide or, less frequently, from inherited cancer predisposition syndromes. In this review, we discuss the genetics and etiology of hypermutation in HGGs, with an emphasis on the resulting genomic signatures, and the state and future directions of immuno-oncology research in these patient populations.
Surviving the Game
Authors: Rebillard Fanny
Published: June 2024

Fanny Rebillard discusses the issues surrounding the archiving of video game music. Building over the preexisting research about game preservation and music preservation through recordings in popular music studies and ethnomusicology, Rebillard identifies a number of problems, including those of changes in audio format and the loss of elements related to interactivity and graphics. She discusses how the resolving of these issues during the archiving process, especially through published soundtracks, can provide new perspectives on the wider place of game music. The organization of tracks in such archives is important, and Rebillard closes the chapter with some suggestions for published game music typologies, focusing on the broad categories of completion level and track list organization.
Ludomusical Narrativity
Authors: Grasso Julianne
Published: June 2024

Julianne Grasso’s chapter provides a means to account for music in video games through a narrative perspective. While ludic structures in games (challenges, exploration) are often understood in opposition to narrative structures (story, characters), musical forms help reconcile these experiences for the player. Her aim is to show that, within the perception that musical loops and repetitions (particularly in early video games) promote a feeling of timelessness, the use of music implies narrative form and so enhances the narrativization of the play experience. Indeed, Grasso argues with the aid of case studies, music can be used to shape interactive play and, in some cases, “the enacted narrative is fundamentally musical.”
Hard Limitations and Soft Possibilities
Authors: Burke Kevin R.
Published: June 2024

Kevin R. Burke provides a survey and assessment of the hardware and software that powered early video game sound and analyzes how the hardware limitations and innovative software led to specific compositional styles across platform developers. Throughout, Burke’s focus is on the home consoles of the chiptune era, and he develops a “systematic” approach for the analysis of the audio hardware and software systems, systems that determine the challenges posed, and the possibilities afforded the games’ composers. Burke provides also a glossary of selected digital audio terminology pertinent to the video games industry, a list of video game audio formats, and a table of programmable sound generators used in the video games industry detailing their developer, the number of channels they have, and significant console and PC video games producers using these generators.
Claude Debussy’s Piano Music and the Evocation of Atmosphere and Humor in Video Games
Authors: Bhogal Gurminder Kaur
Published: June 2024

Gurminder Kaur Bhogal’s chapter is an exploration of the influence and direct use of Claude Debussy’s piano music: for instance, how his ethereal “floating sounds” as found in works such as “Clair de Lune” have directed game designers’ attentions toward the creation of various atmospheres and moods in video games, as well as the possibilities that these afford the player. For Bhogal, Debussy’s music and video game compositions that draw from it are effective in creating the virtual spaces players are invited to inhabit, where atmospheres and moods fashioned by the music can touch the player and make them feel.
Music and Sound in Early Film-to-Game Adaptations
Authors: O’Hara William
Published: June 2024

William O’Hara’s chapter examines the use and transformation of sound and music in film-to-game adaptations, focusing on the format’s rise in popularity during the 1980s. O’Hara contends that, rather than assessing the game’s fidelity to the film, game adaptations are best viewed as a new form of media convergence. Using archival evidence, O’Hara sheds light on cross-media relationships during the adaptation process and uncovers cooperation and tension between different industries—changes and compromises had to be made in the games’ audio design due to the exigencies of different technologies and narrative forms and the requirements of intellectual property law and advertising.
Video Games Alive
Authors: Greenfield-Casas Stefan
Published: June 2024

Stefan Greenfield-Casas reviews the growing phenomenon of live concerts of video game music, both offering a typology of these concerts as well as asking if the experience of attending such concerts has an aesthetic effect on the concertgoer’s personal memory of their experience of the game they have played. Greenfield-Casas’s analysis is rooted in the game fans’ experiences, and he constructs a theory of “ludic liveness” to argue that attendance at such concerts provokes experiences of replaying the games—what he calls “replayful listening.” Ultimately, he argues that video game music, remediated through live concerts by way of concert arrangements, becomes ontologically validated in the real world through this process.