bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate prediction of protein–ligand interactions by combining physical energy functions and graph-neural networks
Authors: Hong Yiyu , Ha Junsu , Sim Jaemin , Lim Chae Jo , Oh Kwang-Seok , Chandrasekaran Ramakrishnan , Kim Bomin , Choi Jieun , Ko Junsu , Shin Woong-Hee , Lee Juyong 
Published: November 2024

AbstractWe introduce an advanced model for predicting protein–ligand interactions. Our approach combines the strengths of graph neural networks with physics-based scoring methods. Existing structure-based machine-learning models for protein–ligand binding prediction often fall short in practical virtual screening scenarios, hindered by the intricacies of binding poses, the chemical diversity of drug-like molecules, and the scarcity of crystallographic data for protein–ligand complexes. To overcome the limitations of existing machine learning-based prediction models, we propose a novel approach that fuses three independent neural network models. One classification model is designed to perform binary prediction of a given protein–ligand complex pose. The other two regression models are trained to predict the binding affinity and root-mean-square deviation of a ligand conformation from an input complex structure. We trained the model to account for both deviations in experimental and predicted binding affinities and pose prediction uncertainties. By effectively integrating the outputs of the triplet neural networks with a physics-based scoring function, our model showed a significantly improved performance in hit identification. The benchmark results with three independent decoy sets demonstrate that our model outperformed existing models in forward screening. Our model achieved top 1% enrichment factors of 32.7 and 23.1 with the CASF2016 and DUD-E benchmark sets, respectively. The benchmark results using the LIT-PCBA set further confirmed its higher average enrichment factors, emphasizing the model’s efficiency and generalizability. The model’s efficiency was further validated by identifying 23 active compounds from 63 candidates in experimental screening for autotaxin inhibitors, demonstrating its practical applicability in hit discovery.Scientific contributionOur work introduces a novel training strategy for a protein–ligand binding affinity prediction model by integrating the outputs of three independent sub-models and utilizing expertly crafted decoy sets. The model showcases exceptional performance across multiple benchmarks. The high enrichment factors in the LIT-PCBA benchmark demonstrate its potential to accelerate hit discovery.
MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes
Authors: Cansdale Annabel , Chong James P. J. 
Published: November 2024

Abstract

Background
Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced and addressing variable dataset quality remain ongoing challenges. Another challenge arises from the number of assembly and binning strategies used across studies. Comparing datasets and analysis tools is complex as it requires the quantitative assessment of metagenome quality. The inherent limitations of metagenomic sequencing, which often involves sequencing complex communities, mean community members are challenging to interrogate with traditional culturing methods leading to many lacking reference sequences. MIMAG standards aim to provide a method to assess metagenome quality for comparison but have not been widely adopted.

Results
To address the need for simple and quick metagenome quality assignation, here we introduce the pipeline MAGqual (Metagenome-Assembled Genome qualifier) and demonstrate its effectiveness at determining metagenomic dataset quality in the context of the MIMAG standards.

Conclusions
The MAGqual pipeline offers an accessible way to evaluate metagenome quality and generate metadata on a large scale. MAGqual is built in Snakemake to ensure readability and scalability, and its open-source nature promotes accessibility, community development, and ease of updates. MAGqual is built in Snakemake, R, and Python and is available under the MIT license on GitHub at https://github.com/ac1513/MAGqual.
Detecting latent subpopulations in international large-scale assessments by fitting MixIRT models using NUTS
Authors: AlHakmani Rehab , Sheng Yanyan 
Published: November 2024

AbstractThe focus of this study is to use the mixture item response theory (MixIRT) model while implementing the no-U-turn sampler as a technique for investigating the presence of latent classes (i.e., subpopulations) among eighth-grade students who were administered TIMSS 2019 mathematics subtest in paper format from the gulf cooperation council (GCC) countries. One-, two-, and constrained three-parameter logistic MixIRT models with one to four classes were used to fit to the data, where the model data fit was assessed using Bayesian fit indices. The results indicate that multiple latent classes or subpopulations can better reflect the mathematical proficiency of eighth graders from the four GCC countries, and specifically the two-class constrained three-parameter MixIRT model provides a relatively better fit to the data. The results also indicate that when a mixture of several latent classes present, the conventional unidimensional IRT model is limited in providing information for multiple latent classes and shall be avoided. In addition to adding to the existing literature on MixIRT models for international large-scale assessments such as TIMSS on its heterogenous subpopulations from a fully Bayesian approach, this study sheds light on the limitation of conventional unidimensional IRT models and subsequently directs attention to the use of the more complex MixIRT model for such assessments.
Simulation of light environments inside lunar holes and their associated subsurface caverns
Authors: Ikeya Kodai , Haruyama Junichi , Miyake Wataru , Tanaka Makoto , Toyokawa Kosei , Nozawa Hitoshi 
Published: November 2024

AbstractVertical holes of several tens of meters in diameter and depth have been discovered on the Moon, potentially serving as skylights into subsurface volcanic caverns resembling lava tubes. Because of their scientific importance and potential for use as future lunar bases, these lunar holes and caverns are expected to be targets of intensive exploration in the near future. Using numerical simulations, this study investigates the light environment within a directly and/or indirectly sunlit subsurface cavern accessed through a skylight hole. We specifically analyze the Mare Tranquillitatis Hole (MTH), one of the largest lunar vertical holes, situated near the Moon's nearside meridian. The floor and walls of the hole, and the walls and ceiling of its associated subsurface cavern are lit by reflected sunlight from other parts of the hole and cavern, such as the floors, depending on the solar elevation angle. Furthermore, this paper presents estimation results for camera imaging for a case in which solar elevation angle is 45° in the morning, which is appropriate timing for exploration. Assuming reflectance of 0.1 for the lunar hole and cavern surfaces, we estimate the incident energy onto each pixel of a camera as it descends to the hole's floor. We specifically simulate conditions for a camera with a 12-bit dynamic range, similar to the wide-angle optical navigation camera (ONC-W) onboard the Hayabusa 2 spacecraft. The results suggest that a camera with a fixed gain would struggle to capture both directly and indirectly sunlit areas simultaneously, without saturating bright areas and ensuring minimum incident energy resolution (say, a 10 digital number) for darker areas. To overcome this challenge, adjusting the camera gain based on the hole's and cavern's illumination conditions is necessary.
Graphical abstract
Influence of political stability on the stock market returns and volatility: GARCH and EGARCH approach
Authors: Alim Wajid , Khan Naqib Ullah , Zhang Vince Wanhao , Cai Helen Huifen , Mikhaylov Alexey , Yuan Qiong 
Published: November 2024

AbstractPolitical instability has increased drastically in Pakistan during the last few decades. This may intensify the fear of investors and eventually affect investment decisions. Therefore, the stock market’s reaction to political stability must be explored and appropriate policy measures should be prescribed. This paper examines the effect of political stability on stock market returns and volatility using time series data from Pakistan for the period from January 02, 2004, to May 31, 2018. The study uses the Generalized Autoregressive Conditional Heteroskedastic (GARCH) and Exponential Generalized Autoregressive Conditional Heteroskedastic (EGARCH) models to achieve the main objectives. The findings of the GARCH and EGARCH models confirm that political stability has a positive and significant influence on both stock market returns and volatility in Pakistan. In addition, the EGARCH findings indicate that negative shock (political instability) creates more volatility in the stock market than positive shock (political stability). The results of this study reveal that financial market investors are affected more by political instability. In conclusion, this study suggests that political stability is an essential factor affecting financial market volatility, and it leads to stable financial markets. It also emphasizes that political instability needs to be resolved to achieve stable financial markets.
Thinking alike, acting alike? An assessment of organizational homophily and paradigmatic pragmatism in networks for local integration policies
Authors: Elien Diels , Stijn Oosterlynck 
Published: November 2024

AbstractAs migrant integration policies touch upon almost all spheres of citizens’ life, collaboration across policy levels as well as across policy domains is needed. Over time, a series of both policy and analytical paradigms on the integration of migrants emerged, going from the traditional ideas of differentialism and assimilation, over multiculturalism, interculturalism, integrationism, liberal egalitarianism and mainstreaming, up to superdiversity and intersectionality. While networks for integration policies are likely to be at least partly driven by these paradigms, recent studies seem to nuance this assumption based on so called paradigmatic pragmatism, meaning that cities draw on a variety of ideas and pragmatically combine them under the header of diversity policies. The need for multi-level and multi-actor governance on migrant integration, the theoretical knowledge about homophily in organizational networks, and the recent findings on paradigmatic pragmatism, raise the question to what extent collaboration between public and non-profit organizations active around migrant integration is based on a shared policy paradigm on the integration of migrants. This question is answered based on a multiple case study of four central cities in Flanders (Belgium), covering 1.403 organizations. In the quantitative and qualitative (social network) analyses, comparisons along both the axes of cities and policy domains are made. Findings contribute to literature on organizational homophily, showing that clustering of organizations is likely to be at least partly driven by policy paradigm on integration. This is however nuanced by the observation that policy paradigms appear to be ambiguous, which in turn reveals opportunities for more flexible collaborations between actors and for avoiding deadlocks in policy making.
Occurrence and exposure to polycyclic aromatic hydrocarbons (PAHs) in traditional dry-cured or smoked meat products from Brazil
Authors: da Silva Simone Alves , de Rossi Gustavo Zanetti , de Almeida Adriana Palma , Guizellini Glória Maria , Torres Elizabeth Aparecida Ferraz da Silva , Rogero Marcelo Macedo , Sampaio Geni Rodrigues 
Published: November 2024

AbstractPolycyclic aromatic hydrocarbons (PAHs) are classified as environmental and food contaminants, with several adverse health effects, especially genotoxic and carcinogenic actions. In processed meats, they are the major contaminants, especially those subjected to smoking processes. Considering that the population is exposed to PAHs through several routes, and that the ingestion of contaminated food is considered the main one, evaluating the concentrations of these contaminants in food becomes essential, as well as the exposure and risk to the population at different ages through ingestion of the evaluated products. In the current study, the levels of nine PAHs (PAH9) were measured in 205 processed meat products commercially available and with high consumption in Brazil. The methodology involved saponification, extraction with n-hexane, purification with solid-phase extraction (SPE) silica cartridges, and quantification by liquid chromatography with fluorescence detection. In general, 83% of all samples were contaminated with at least one of the studied PAHs, and the measured PAH9 levels ranged between < LOQ-108.24 µg/kg. The highest mean of total PAHs was found in smoked sausage (108.24 μg/kg), while the lowest content was found in ham (1.83 μg/kg). Benzo[a]pyrene (BaP) and PAH4 (benz[a]anthracene, chrysene, benzo[b]fluoranthene, and BaP) exceeded the maximum permissible limits of the European Union (EU) in three (1.5%) and 18 samples (8.7%), respectively. The results of margin of exposure results (MOE ≥ 10,000) and incremental lifetime cancer risk (ILCR) values (10 − 6 < ILCR < 10 − 4) in all ten types of meat indicated there were low significant potential health problems related to meat products consumption for the Brazilian population.
Graphical Abstract
Unlocking the sustainable role of melatonin in fruit production and stress tolerance: a review
Authors: Himanshu  , Sharma Sunny , Rana Vishal Singh , Ankit  , Thakur Vikanksha , Kumar Arun , Prachi  , Thakur Shivender , Sharma Neha 
Published: November 2024

Abstract
While melatonin, a vital player in plant physiology, initially attracted recognition due to its involvement in animal circadian rhythms, the molecule appears to be a multifunctional molecule requiring substantial attention for prospective applications in sustainable horticulture. It has been identified and recorded in numerous fruit crops, and its significance in physiological functions is critical for crop productivity. It is critical in safeguarding plants in response to reactive oxygen species in oxidative stress, one of the most damaging stressors to plant life in adverse conditions. Melatonin also cooperates with plants in boosting stress resistance, which concerns abiotic stress factors, e.g. low and high temperature, drought stress, toxicity of heavy metals, and biotic stress factors, including pests and pathogens. The anti-senescence properties of melatonin in aging leaves may be explained by its widespread antioxidant activity and its function in maintaining chlorophyll. The function of melatonin in controlling the production of genes linked to ethylene to modify postharvest fruit ripening has been the subject of an astounding amount of research. Additionally, recent research has shown that melatonin works with other phytohormones and well-known chemicals like nitric oxide and reactive oxygen species to assist plants in responding to biotic stress.The present review emphasizes a perspective that examining the role of melatonin in fruit crop physiology and stress responses may be a promising research direction in prospective fruit crop yield. In particular, this perspective is well supported by the following: melatonin is involved in the antioxidant response of fruit crops and can thus be used to mitigate the stressful impact of various environmental conditions; melatonin influences the development of plants and, consequently, affects fruit yield and quality; and applying melatonin is feasible for mitigating the impact of abiotic factors, such as cold, drought, heavy metals, and biotic factors, pests, and pathogens.
Severe Hypertriglyceridemia in a Patient Treated With Sirolimus for Graft-vs-Host Disease Prophylaxis
Authors: Criner Kristin , Student Jeffrey , Arkin Jacob , Carp Julia , Sokoloff Samantha 
Published: November 2024

Abstract
Hypertriglyceridemia is an important and well documented adverse effect caused by the immunosuppressive agent sirolimus. Patients treated with sirolimus require frequent monitoring of blood lipid panels and prompt treatment with appropriate triglyceride-lowering therapies. We report the case of an asymptomatic 65-year-old female stem cell transplant recipient who developed extreme hypertriglyceridemia with levels &gt; 19,000 mg/dL (214 mmol/L) (reference range, &lt; 150 mg/dL [&lt; 1.7 mmol/L]), secondary to sirolimus for prophylaxis of graft-vs-host disease. Acute treatment included admission to the intensive care unit for initiation of an intravenous insulin infusion, low-fat diet, and discontinuation of sirolimus. These measures, in addition to initiation of oral triglyceride-lowering agents and improved glycemic control, led to substantial improvement in triglyceride levels.
Pembrolizumab-induced Thyroiditis, Hypophysitis and Adrenalitis: A Case of Triple Endocrine Dysfunction
Authors: Rossi Silvia , Silvetti Francesca , Bordoni Monia , Ciarloni Alessandro , Salvio Gianmaria , Balercia Giancarlo 
Published: November 2024

Abstract
Immune checkpoint inhibitor drugs can trigger autoimmune endocrine reactions as a known side effect. Several cases of immunotherapy-induced autoimmune endocrinopathies have been described, but multiple sequential endocrine toxicities are a rare occurrence. A 39-year-old patient with metastatic melanoma started adjuvant therapy with pembrolizumab. One month later he presented with asymptomatic thyrotoxicosis and, within several weeks, overt hypothyroidism, for which he started levothyroxine therapy. Subsequently the patient developed central adrenal insufficiency due to probable hypophysitis, and steroid replacement therapy was started. Pembrolizumab therapy was then discontinued. After a few months, a full recovery of pituitary function was observed, but primary adrenal insufficiency occurred, requiring additional fludrocortisone therapy. The described clinical case is a very uncommon case of triple endocrinological toxicity from immunotherapy. The clinical and biochemical manifestations of immunotherapy-induced endocrinopathies can be variable and atypical; therefore, it is necessary to pay special attention to any clue of hormonal dysfunction.
Political communication strategies of local politicians in the political constellation of legislative elections at the Regency/City level
Authors: Nurhidayah Sitti , Fadillah Dani 
Published: November 2024

This research aims to determine how local politicians carry out the political communication strategy to win the political constellation of district/city-level legislative elections. This research uses a qualitative approach; in collecting data, researchers chose politicians from the Gerindra party named Muhasbih, who fought in the Polewali Mandar district legislative elections in the 2024 elections, as research subjects. Researchers conducted in-depth interviews with the politician and his success team, who actively participated in winning the 2024 election. The results of this study indicate that effective communication in winning political constellations in legislative elections at the district/city level requires understanding the audience and local political dynamics. Through in-depth interviews with politicians and their success teams, it was found that the success of political communication strategies lies in delivering relevant, measurable, and understandable messages to voters. In addition, it was found that the presence of politicians in the field and direct interaction with voters is very influential in building personal relationships and trust. This suggests that the human side and direct involvement in local politics play a crucial role in creating emotional bonds between politicians and voters, which can influence voters' decisions inside the voting booth. Furthermore, the results of this study also highlight the need for adopting strategies that are dynamic and responsive to political and technological developments. Although local politicians such as Muhasbih do not use social media in their campaigns, it is important to continuously monitor trends and adapt political communication strategies as needed as the political environment changes.
Prediction of humeral shaft fracture healing using the Radiographic Union Score for HUmeral Fractures (RUSHU)
Authors: Suter Cyrill , Mattila Henrik , Ibounig Thomas , Sumrein Bakir O. , Launonen Antti , Järvinen Teppo L. N. , Lähdeoja Tuomas , Rämö Lasse 
Published: November 2024

AimsThough most humeral shaft fractures heal nonoperatively, up to one-third may lead to nonunion with inferior outcomes. The Radiographic Union Score for HUmeral Fractures (RUSHU) was created to identify high-risk patients for nonunion. Our study evaluated the RUSHU’s prognostic performance at six and 12 weeks in discriminating nonunion within a significantly larger cohort than before.MethodsOur study included 226 nonoperatively treated humeral shaft fractures. We evaluated the interobserver reliability and intraobserver reproducibility of RUSHU scoring using intraclass correlation coefficients (ICCs). Additionally, we determined the optimal cut-off thresholds for predicting nonunion using the receiver operating characteristic (ROC) method.ResultsThe RUSHU demonstrated good interobserver reliability with an ICC of 0.78 (95% CI 0.72 to 0.83) at six weeks and 0.77 (95% CI 0.71 to 0.82) at 12 weeks. Intraobserver reproducibility was good or excellent for all analyses. Area under the curve in the ROC analysis was 0.83 (95% CI 0.77 to 0.88) at six weeks and 0.89 (95% CI 0.84 to 0.93) at 12 weeks, indicating excellent discrimination. The optimal cut-off values for predicting nonunion were ≤ eight points at six weeks and ≤ nine points at 12 weeks, providing the best specificity-sensitivity trade-off.ConclusionThe RUSHU proves to be a reliable and reproducible radiological scoring system that aids in identifying patients at risk of nonunion at both six and 12 weeks post-injury during non-surgical treatment of humeral shaft fractures. The statistically optimal cut-off values for predicting nonunion are ≤ eight at six weeks and ≤ nine points at 12 weeks post-injury.