bluuebunny/crossref_metadata_2025_split huggingface dataset:
HaloClass: Salt-Tolerant Protein Classification with Protein Language Models
Authors: Narang Kush , Nath Abhigyan , Hemstrom William , Chu Simon K. S. 
Published: October 2024

Abstract

Salt-tolerant proteins, also known as halophilic proteins, have unique adaptations to function in high-salinity environments. These proteins have naturally evolved in extremophilic organisms, and more recently, are being increasingly applied as enzymes in industrial processes. Due to an abundance of salt-tolerant sequences and a simultaneous lack of experimental structures, most computational methods to predict stability are sequence-based only. These approaches, however, are hindered by a lack of structural understanding of these proteins. Here, we present HaloClass, an SVM classifier that leverages ESM-2 protein language model embeddings to accurately identify salt-tolerant proteins. On a newer and larger test dataset, HaloClass outperforms existing approaches when predicting the stability of never-before-seen proteins that are distal to its training set. Finally, on a mutation study that evaluated changes in salt tolerance based on single- and multiple-point mutants, HaloClass outperforms existing approaches, suggesting applications in the guided design of salt-tolerant enzymes.
Genome-wide identification of the potato GGPS gene family and analysis of its response to abiotic stress
Authors: Man Quancai , LI Wei , Chen Xiaotian , Gao Shunjuan , Jia Mingfei , Zhang Shuqing , Cui Jianghui 
Published: October 2024

Abstract

Background: Geranylgeranyl pyrophosphate synthase (GGPS) plays a crucial role in terpene biosynthesis, contributing to the synthesis of carotenoids, chlorophylls, and various phytohormones. This study aims to identify and characterize the GGPS gene family in potato (Solanum tuberosum) to understand its role in carotenoid synthesis and response to abiotic stress.
Results: Eleven GGPS genes (StGGPSs) were identified across the potato genome, distributed unevenly on seven chromosomes. These genes were categorized into three subfamilies based on protein structure and phylogenetic analysis. Covariance analyses revealed one pair of replicated genes within the potato genome and several homologous pairs between potato and other species such as Arabidopsis and tomato. RNA-seq data and qPCR data indicated differential expression of StGGPS genes in potato patches of different colors, highlighting their role in response to abiotic stresses.
Conclusion: The study provides new insights into the evolution of the StGGPS gene family in potato, emphasizing its significance in regulating carotenoid synthesis and abiotic stress response. These findings lay the groundwork for future research on the genetic manipulation of GGPS genes to enhance stress tolerance in potatoes.
The Spatiotemporal Structure of Information Diffusion: A Study Based on the Growth Curve Model and Social Network Analysis
Authors: Zhu Panlong , Zhou Yunqian , Xia Yixue 
Published: October 2024

Abstract

Due to the rapid development of internet technology, it has provided convenient online channels for information diffusion, which has resulted in the formation of complex network structures during the process of information diffusion. In response to the previous studies that solely focused on the temporal or spatial aspects of information diffusion network structures, overlooking the combined characteristics of both discrete time points and continuous process accumulation within the diffusion process, we propose a novel approach from a dual-temporal and spatial perspective. This approach utilizes the growth curve model and social network analysis to analyze network structures of information diffusion. Firstly, leveraging the life cycle theory and employing the logistic model, we partition the process of information diffusion into three distinct phases - the latency period, the diffusion period, and the fading period - based on two characteristic time points, t1 and t2. This approach allows us to develop a dynamic evolutionary model for the social network structure of information diffusion. Secondly, incorporating temporal evolution into the spatial perspective, we conduct spatial structure analysis based on time-evolving data from three phases: (0,t1), (t1,t2), and (t2,tk). This comprehensive approach allows for the presentation of the network spatial structure characteristics of information diffusion throughout its temporal evolution. Lastly, taking the “Tangshan Assault Incident” as an example, we employ social network analysis theory to conduct empirical research from the perspectives of network spatial structure analysis with temporal evolution and network spatial structure analysis at a specific time point. Through this approach, we derive the characteristics of the information diffusion network structure under different perspectives. The results indicate that the research methodology of information diffusion based on the growth curve model and social network analysis, coupled with a temporal evolution perspective to examine network spatial structural characteristics, reveals the uneven distribution of information diffusion. Furthermore, under the accumulative effect of time, it enables better identification of key nodes and groups with enduring influence and potential for explosive impact.
New low-cost and compact experimental system for characterization of porous materials by quasi-equilibrated thermodesorption of nonane or water
Authors: Makowski Wacław , Yaremenko Nikita , Gryta Patrycja , Cieślik-Górna Monika , Korzeniowska Aleksandra , Majda Dorota 
Published: October 2024

Abstract

The new low-cost, simple and compact experimental system for characterization of porous materials by quasi-equilibrated temperature-programmed desorption and adsorption (QE-TPDA) based on the miniature microprocessor-controlled thermal conductivity sensor Sensirion STC31 has been described in detail. The performance of the new system has been tested in QE-TPDA measurements of nonane for high silica zeolites Y and ZSM-5, as well as for a series of ordered mesoporous silicas SBA-15. Although very good qualitative agreement of the QE-TPDA profiles measured in the new system with those observed in a standard one was found, slightly lower saturation sorption capacities based on the new profiles were obtained. The pores size distributions (PSDs) calculated from the new nonane QE-TPDA profiles for SBA-15 silicas showed very good agreement with those obtained from N2 adsorption isotherms using the NLDFT method. An excellent correlation between the pore size values based on both sets of PSDs was found. The new system was also applied in the QE-TPDA of water for selected metal-organic frameworks (MOFs). The QE-TPDA profiles of water observed for two fumarate containing MOFs Al-fum (aka Basolite A520) and MIL-88A were consistent with the adsorption-desorption isotherms obtained in a standard manometric apparatus. Hydrothermal stability tests of these MOFs, based on prolonged water QE-TPDA measurements, revealed the onset of structure degradation of Al-fum at 350°C and at 250°C for MIL-88A.
Single-step synthesis of high surface area activated carbon from polyethylene terephthalate plastic waste for environmental treatment applications
Authors: Lai Hoan Thi , Le Quoc Anh , Tran Nga Thuy , Tran Chinh , Ho Phuong Hien , Nguyen D. Duc , Thi Hoai Phuong Nguyen , La Duong Duc 
Published: October 2024

Abstract

The escalating environmental concerns regarding plastic waste necessitate innovative strategies for waste management and resource utilization. This study presented a novel approach for synthesizing high surface area activated carbon through a single-step process, using polyethylene terephthalate (PET) plastic waste as the precursor and potassium hydroxide (KOH) as the activating agent. The optimal activation conditions were established using a weight ratio of 1:1 of PET to KOH and annealing for 15 minutes at 700 oC. The conversion efficiency of PET plastic trash into activated carbon exceeded 20%. The materials underwent thorough characterization using scanning electron microscopy (SEM), X-ray diffraction (XRD), Brunauer-Emmett-Teller (BET) analysis, and Fourier transform infrared spectroscopy (FTIR). The activated carbon obtained has a mesoporous structure and a surface area of 1831.166 m2/g. The activated carbon-prepared plastic waste showed high removal efficiency for the organic dyes in an aqueous solution, with a maximum adsorption capacity of 131.58 mg/g. The successful transformation of plastic waste into a valuable resource underscores the importance of innovative approaches to mitigating environmental degradation. The synthesized activated carbon's efficacy in adsorption-based remediation strategies establishes its potential for addressing various pollution issues and opens new avenues for valuing plastic waste.
Assessment of Potentially Toxic and Rare Earth Elements in Surface Soils of Dong Nai, Vietnam
Authors: Vo Tran Quang-Thai , Tran Quang-Thien , Tran Tuan-Anh , Tuong Thi Thu-Huong , Nguyen Thi Huong-Lan , Chau Thi Nhu-Quynh , Le Nhu-Sieu , Vo Thi Mong-Tham , Le Xuan-Thang , Truong Duc-Toan , Phan Quang-Trung , Nguyen Huu-Nghia , Nguyen Minh-Dao 
Published: October 2024

Abstract

This study investigates the quantities of Rare Earth Elements (REEs) and Potentially Toxic Elements (PTEs) in Dong Nai Province's surface soils. Atomic Absorption Spectrometry (AAS) and Instrumental Neutron Activation Analysis (INAA) are used to determine element concentrations. To validate the concentration results, established reference materials (NIST 2711 and IAEA Soil-7) were used. Element concentrations followed a certain order, with Mn, Cr, V, and Zn dominating, except for Al, which was used to determine the enrichment factor. Arsenic (As) concentrations ranged from 0.8 to 37.5 mg/kg, exceeding global averages but below Vietnam quality standards. Cadmium (Cd) concentrations ranged from 0.03 to 0.16 mg/kg, below global averages and quality standards. Cobalt (Co) and chromium (Cr) concentrations ranged from 0.5 to 135.1 mg/kg and 18 to 844 mg/kg, respectively, with notable percentages of samples exceeding global averages. Copper (Cu) and lead (Pb) exhibited elevated concentrations, with varying proportions exceeding quality standards. Manganese (Mn) and antimony (Sb) exceeded global averages in a significant percentage of samples. Vanadium (V) concentrations surpassed the crustal average in over half of the sites. Zinc (Zn) concentrations were below reference values. REEs showed significantly higher concentrations than global soil averages, with a substantial proportion of samples exceeding reference values. Geo Accumulation Index (Igeo), Enrichment Factor (EF), and Pollution Load Index (PLI) analyses provided a detailed numerical assessment of contamination and soil quality. Statistical analysis showed correlations and clusters of toxic elements and highlighted the spatial distribution of samples based on elemental compositions.
PAR2 deletion in the osteoblast lineage affords long-term cartilage protection in experimental osteoarthritis
Authors: Huesa Carmen , McGrath Sarah , Dunning Lynette , Vieri Maria , McCulloch Kendal , McIntosh Kathryn , Brown Tatiana , Cole John , Plevin Robin , Rowan Drew , Hof Rob van ‘t , Ferrell William , Lockhart John , Goodyear Carl 
Published: October 2024

Abstract

Protease-activated receptor 2 (PAR2) plays a pivotal role in the early stages of surgery-induced murine osteoarthritis OA. It remains to be determined however, whether PAR2 contributes to later stages of disease pathology and which cellular compartments drive pathological changes. Thus, we characterised OA pathology in global, chondrocyte- or osteoblast-specific PAR2 knockout mice up to 12 months after OA induction. While wild-type mice display a gradual increase in cartilage damage/loss, PAR2 knockout mice had significantly reduced cartilage pathology. Notably, removing PAR2 specifically in osteoblasts, but not in chondrocytes, substantially improved cartilage health. Interrogation of the osteoblast compartment revealed that PAR2 has a divergent role during osteoblast development and maturation compared to its function in already differentiated cells. This suggests that PAR2 expression in the bone compartment promotes joint deterioration in later stages of OA, highlighting the important role of bone in OA and the therapeutic potential of targeting PAR2.
Discovery of Unconventional and Non-intuitive Self-assembling Peptide Materials using Experiment Driven Machine Learning
Authors: Batra Rohit , Talluri Y Nissi , Sankaranarayanan Subramanian , Fry H. Christopher 
Published: October 2024

Abstract

The synthesis of secondary structures such as β-sheet assembly in peptides poses significant challenges, as their formation is governed by complexity of molecular interactions, sequence-specific behavior, and influence of various environmental factors such as solvent, pH, and temperature. While rational design strategies have been attempted to predict peptide sequences that form desired nanostructures, these methods are often biased and ineffective, particularly when dealing with the complexities associated with β-sheet formation. Computational models also struggle to reliably predict β-peptide formation due to the limited understanding of the vast chemical space and the lack of comprehensive experimental data. Furthermore, existing models often fail to capture the diversity and non-intuitive nature of sequences capable of forming β-sheets, leading to a constrained discovery process. To address these issues, we developed an integrated high-throughput experimental workflow and an active learning-based AI framework to better predict the β-sheet formation propensity of peptide sequences. By focusing on sequences where ML predictions deviate from conventional design strategies, we synthesized and tested 268 pentapeptides, discovering 96 that successfully formed β-sheet assemblies. The ML models were found to surpass the commonly used β-sheet propensity table in identifying β-sheet forming sequences, especially for cases that do not contain valine, a high propensity β-sheet conformer. Furthermore, several diverse, non-intuitive and unusual β-sheet forming pentapeptides (for e.g., ILFSM, LMISI, MITIY, MISIW, and WKIYI) were identified by the ML models. Novel chemical trends were mined by analyzing the ML models and a user-friendly web-interface is provided to make these models accessible to the community. Overall, this work underscores the need for AI driven experimental exploration of diverse peptide chemistries and provides a robust strategy to overcome the biases and limitations inherent in current rational design methods to form secondary structures like β-sheets.
Rejuvenation driven reprograming in T lymphocytes
Authors: Lanna Alessio , D'Ambra Clara , Delpero Manuel , Capitani Melania , Chocarro Luisa , Rinaldi Federica , Karin Michael 
Published: October 2024

Abstract

Rejuvenation restores cellular function lost with age, but it is not known to confer properties the cell lacked in its younger past. We found that Disruptors of sestrin-MAPK interactions (DOS) reprogramed senescent T cells into new stem like T clones with different T cell receptors (TCRs). DOS targeted sestrin-MAPK complexes (sMAC) to ubiquitin-dependent proteasomal degradation, resulting in long-term sestrin transcriptional inhibition, increased T cell fitness, and generation of long-lived stem like memory clones. Strikingly, DOS reactivated juvenile related Rag re-expression, leading to antigen-specific TCR rearrangements in formerly senescent cells. As such, rejuvenated T cells, with stem features and new TCRs, combated multiple lethal challenges never previously encountered in their lifetime, with no need for vaccination. T cell rejuvenation confers new properties whilst preserving cellular state, which unravels an unknown rejuvenating principle in biological systems.
О некоторых источниках и проблемах перевода кантовского термина «Ding an sich»
Authors: Круглов А.Н 
Published: October 2024

В статье указывается на латинские и немецкие философские тексты как на терминологические источники для образования кантовского понятия «Ding an sich», а именно на «Немецкую метафизику» Хр. Вольфа, «Метафизику» А.Г. Баумгартена, «Архитектонику» И.Г. Ламберта и «Философские опыты о человеческой природе и ее развитии» И.Н. Тетенса. Отрицается терминологическое влияние понятия Дж. Локка «thing in itself» из «Опыта о человеческом разумении» на И. Канта. На основе сопоставительного изучения фрагментов «Критики чистого разума» и других печатных произведений Канта, черновых заметок и записей его лекций, а также всех русских переводов «Критики чистого разума» и «Пролегоменов» уточняется перевод ряда важных выражений первой «Критики» Канта, а также обсуждается проблема синонимии кантовских выражений «Ding an sich selbst» и «Sache an sich selbst».The paper deals with German and Latin philosophical texts, namely Chr. Wolff’s “German Metaphysics”, A.G. Baimgarten’s “Metaphysics”, J.H. Lam- bert’s “Architectonics” and J.N. Tetens’s “Philosophical essays on human nature and its development”, that have contributed to the problem of terminological sources of Kant’s “Ding an sich”. I deny the terminological influence of Lock’s “thing in itself” from his “An Essay Concerning Human Understanding” on I. Kant. Based on comparative analysis of some fragments that have been taken from “Critique of Pure Reason”, other published papers, reflections and lectures recordings, as well as all Russian translations of “Critique of Pure Reason” and “Prolegomena to Any Future Metaphysics”, I specify the translation of important terms from the first Kant’s “Critique” and, in addition, discuss the problem of synonymy of two Kant’s terms “Ding an sich selbst” and “Sache an sich selbst”.
Effect of ozone on Vibrio removal in a simulated earthen shrimp pond
Authors: Sitthi Sitthakarn , Mirutanaphai Mongkol , Satanwat Penpicha , Powtongsook Sorawit , Pungrasmi Wiboonluk 
Published: October 2024

ABSTRACT

This study investigated the efficacy of ozone treatment on Vibrio pathogen removal within a simulated earthen shrimp pond, conducted in three phases. First, physical and chemical properties of the soil, alongside the Vibrio pathogen, were assessed. Results indicated neutral pH levels, high organic matter, and organic carbon content, with a Vibrio pathogen load of 1.0 ± 0.0 × 103 CFU/mg. Second, ozone treatment was applied, comparing its effectiveness in Vibrio pathogen control between treated and untreated soil sets. The treated set exhibited a significantly lower Vibrio pathogen load (6.00 ± 1.41 × 103 CFU/mg) compared to the untreated control (2.00 ± 2.12 × 105 CFU/mg), resulting in a 97.23% eradication efficiency. Concurrently, ammonia rates decreased with ozone, indicating potential benefits for shrimp aquaculture. Finally, ozone application in a simulated earthen pond over 45 days effectively controlled Vibrio pathogens. In the untreated soil set, Vibrio pathogen levels rose to 9.48 ± 1.73 × 105 CFU/mg, while in the ozone-treated, they ranged from 6.5 ± 2.12 × 103 to 1.25 ± 0.29 × 105 CFU/mg. Shrimp growth parameters, including average daily gain, survival rates, and feed conversion ratio, were compared between groups, suggesting ozone treatment's feasibility without adverse effects on shrimp growth. Water quality parameters remained within suitable ranges for shrimp cultivation. These findings highlight ozone's potential as an effective method for Vibrio pathogen control in shrimp aquaculture, with implications for industry sustainability and productivity.
Dark Triad Traits and Workplace Performance on the Iowa Gambling Task (IGT)
Authors: Volkova Nataliia , Kurpatov Andrey 
Published: October 2024

Background
Psychologists have recently turned their focus to the “dark side” of workplace behavior, particularly negative traits that impact professional environments.

Methods
In this exploratory study, we examined the Dark Triad traits Machiavellianism, narcissism, and psychopathy among 3,112 bank employees. Additionally, we analyzed the Iowa Gambling Task (IGT) performance in a subset of 1,613 participants to explore correlations between Dark Triad traits and decision-making. We also investigated differences based on sex and job position.

Results
Our findings reveal that men scored higher on Dark Triad traits than women, reinforcing well-established findings. Furthermore, sales managers and premium client managers displayed the highest levels of Machiavellian strategies, though overall, bank employees showed significantly lower Machiavellianism scores compared to published Russian norms. While IGT performance showed no sex differences, it varied between managers and non-managers. A significant negative correlation emerged between Machiavellianism and psychopathy and good deck choices on the IGT, with a linear regression indicating that lower Dark Triad scores predicted better decision-making.

Conclusion
Further research is needed to explore the relationship between affective decision-making and dark personality traits.
Categorization of mHealth Coaching Technologies for Children or Adolescents With Type 1 Diabetes: Systematic Review
Authors: Trnka Pavel , Aldaghi Tahmineh , Muzik Jan 
Published: October 2024

Abstract

Background
Managing type 1 diabetes in children and adolescents can be difficult for parents, health care professionals, and even patients. However, over the last decades, the quality of services provided to patients with diabetes has increased due to advances in IT.

Objective
This study aims to comprehensively document the range of IT tools used in the management of diabetes among children and adolescents, with a focus on identifying the technologies most commonly used based on their frequency. In addition, the study aims to explore relevant methodologies for developing diabetes technology and provide valuable information to developers by delineating essential phases of the design process.

Methods
The literature search was focused on MEDLINE (PubMed), Web of Science, and Google Scholar for relevant studies. Keywords such as “type 1 diabetes,” “adolescents,” “kids,” “mHealth,” “children,” and “coaching” were combined using Boolean operators. The inclusion criteria were open access, English-language papers published between 2012 and 2023 focusing on patients younger than 18 years and aligned with our research goal. The exclusion criteria included irrelevant topics and papers older than 18 years. By applying the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) method, 2080 studies were recognized, and after selection, 33 papers were agreed upon between the researchers.

Results
Four primary categories were defined: types of IT, methodology identification, purpose identification, and feature determination. Among these, mobile health (mHealth) apps emerged as the predominant type of information, garnering 27 mentions. In particular, user-centered design was identified as the most prevalent methodology, cited 22 times. The primary purpose of self-monitoring blood glucose values was mentioned 20 times, while patient education was the highest among common characteristics, with 23 mentions.

Conclusions
Based on our research, we advocate for developers to focus on creating an mHealth app that integrates gamification techniques to develop innovative diabetes management solutions. This app should include vital functionalities such as blood glucose monitoring, strategies to improve hemoglobin A1c levels, carbohydrate tracking, and comprehensive educational materials for patients and caregivers. By prioritizing these features, developers can enhance the usability and effectiveness of the technology, thereby better supporting children or adolescents with diabetes in their daily management endeavors.