bluuebunny/crossref_metadata_2025 huggingface dataset:
Yoga and meditation for menopausal symptoms in breast cancer survivors: a qualitative study exploring participants’ experiences
Authors: Bilc Mirela , Pollmann Nina , Buchholz Analena , Lauche Romy , Cramer Holger
Published: June 2024

Purpose

Breast cancer survivors commonly experience menopausal symptoms, specifically when undergoing antihormonal therapy. Unfortunately, they often have a restricted range of treatment options available to alleviate menopausal symptoms. The objective of this qualitative study was to explore breast cancer survivors’ experiences and effects of a yoga and meditation intervention supplementing previously reported RCT outcomes.

Methods

The qualitative data included in this study were part of a larger randomized controlled trial which evaluated the efficacy and safety of a 12-week yoga and meditation intervention on menopausal symptoms in breast cancer survivors. All participants who underwent the yoga intervention (n = 19) were invited to take part in semi-structured interviews after all quantitative data collection had been completed. Interviews (n = 9) were recorded, transcribed, and then coded into superordinate themes using thematic analysis.

Results

Nine female participants were interviewed, and the following themes emerged: (1) representations and expectations from the yoga intervention; (2) course structure and implementation; (3) perceptions and effects of the intervention (at emotional, physical, behavioral, and spiritual level); (4) differences between the study yoga intervention and other physical activities.

Conclusions

In accordance with the accounts of participants, yoga might offer a promising intervention for breast cancer survivors. All those interviewed either currently attended a yoga class or expressed a desire to continue practicing yoga. Additionally, our findings inform future studies regarding aspects such as the importance of extending outcome measures beyond specific cancer-related complains, the advantages of addressing homogenous groups (i.e., breast cancer specific), or considering that different intervention components might need different assistance to encourage long-term use.
Restricting the level of the proteins essential for the regulation of the initiation step of replication extends the chronological lifespan and reproductive potential in budding yeast
Authors: Stępień Karolina , Enkhbaatar Tuguldur , Kula-Maximenko Monika , Jurczyk Łukasz , Skoneczna Adrianna , Mołoń Mateusz
Published: June 2024

Aging is defined as a progressive decline in physiological integrity, leading to impaired biological function, including fertility, and rising vulnerability to death. Disorders of DNA replication often lead to replication stress and are identified as factors influencing the aging rate. In this study, we aimed to reveal how the cells that lost strict control of the formation of crucial for replication initiation a pre-initiation complex impact the cells’ physiology and aging. As strains with the lower pre-IC control (lowPICC) we used, Saccharomyces cerevisiae heterozygous strains having only one functional copy of genes, encoding essential replication proteins such as Cdc6, Dbf4, Sld3, Sld7, Sld2, and Mcm10. The lowPICC strains exhibited a significant reduction in the respective genes’ mRNA levels, causing cell cycle aberrations and doubling time extensions. Additionally, the reduced expression of the lowPICC genes led to an aberrant DNA damage response, affected cellular and mitochondrial DNA content, extended the lifespan of post-mitotic cells, and increased the yeast’s reproductive potential. Importantly, we also demonstrated a strong negative correlation between the content of cellular macromolecules (RNA, proteins, lipids, polysaccharides) and aging. The data presented here will likely contribute to the future development of therapies for treating various human diseases.
Transcriptomics and metabolomics reveal hypothalamic metabolic characteristics and key genes after subarachnoid hemorrhage in rats
Authors: Liu Zongchi , Chai Zhaohui , Wu Fan , Zhang Luyuan , Wang Xiaoyi , Xu Zihan , Weng Yuxiang , Gong Jiangbiao , Shen Jian , Zhan Renya , Zhu Yu
Published: June 2024

Subarachnoid hemorrhage (SAH) is a serious hemorrhagic event with high mortality and morbidity. Multiple injurious events produced by SAH can lead to a series of pathophysiologic processes in the hypothalamus that can severely impact patients’ life. These pathophysiologic processes usually result in physiologic derangements and dysfunction of the brain and multiple organs. This dysfunction involved multiple dimensions of the genome and metabolome. In our study, we induced the SAH model in rats to obtain hypothalamic tissue and serum. The samples were subsequently analyzed by transcriptomics and metabolomics. Next, the functional enrichment analysis of the differentially expressed genes and metabolites were performed by GO and KEGG pathway analysis. Through transcriptomic analysis of hypothalamus samples, 263 up-regulated differential genes, and 207 down-regulated differential genes were identified in SAH groups compared to Sham groups. In the KEGG pathway analysis, a large number of differential genes were found to be enriched in IL-17 signaling pathway, PI3K-Akt signaling pathway, and bile secretion. Liquid chromatography-mass spectrometry metabolomics technology was conducted on the serum of SAH rats and identified 11 up-regulated and 26 down-regulated metabolites in positive ion model, and 1 up-regulated and 10 down-regulated metabolites in negative ion model. KEGG pathways analysis showed that differentially expressed metabolites were mainly enriched in pathways of bile secretion and primary bile acid biosynthesis. We systematically depicted the neuro- and metabolism-related biomolecular changes occurring in the hypothalamus after SAH by performing transcriptomics and metabolomics studies. These biomolecular changes may provide new insights into hypothalamus-induced metabolic changes and gene expression after SAH.
Shutdown-seeking AI
Authors: Goldstein Simon , Robinson Pamela
Published: June 2024

We propose developing AIs whose only final goal is being shut down. We argue that this approach to AI safety has three benefits: (i) it could potentially be implemented in reinforcement learning, (ii) it avoids some dangerous instrumental convergence dynamics, and (iii) it creates trip wires for monitoring dangerous capabilities. We also argue that the proposal can overcome a key challenge raised by Soares et al. (2015), that shutdown-seeking AIs will manipulate humans into shutting them down. We conclude by comparing our approach with Soares et al.'s corrigibility framework.
CRISPR/Cas9-mediated mutagenesis of FT/TFL1 in petunia improves plant architecture and early flowering
Authors: Abdulla Mohamed Farah , Mostafa Karam , Kavas Musa
Published: June 2024

Petunias are renowned ornamental species widely cultivated as pot plants for their aesthetic appeal both indoors and outdoors. The preference for pot plants depends on their compact growth habit and abundant flowering. While genome editing has gained significant popularity in many crop plants in addressing growth and development and abiotic and biotic stress factors, relatively less emphasis has been placed on its application in ornamental plant species. Genome editing in ornamental plants opens up possibilities for enhancing their aesthetic qualities, offering innovative opportunities for manipulating plant architecture and visual appeal through precise genetic modifications. In this study, we aimed to optimize the procedure for an efficient genome editing system in petunia plants using the highly efficient multiplexed CRISPR/Cas9 system. Specifically, we targeted a total of six genes in Petunia which are associated with plant architecture traits, two paralogous of FLOWERING LOCUS T (PhFT) and four TERMINAL FLOWER-LIKE1 (PhTFL1) paralogous genes separately in two constructs. We successfully induced homogeneous and heterogeneous indels in the targeted genes through precise genome editing, resulting in significant phenotypic alterations in petunia. Notably, the plants harboring edited PhTFL1 and PhFT exhibited a conspicuously early flowering time in comparison to the wild-type counterparts. Furthermore, mutants with alterations in the PhTFL1 demonstrated shorter internodes than wild-type, likely by downregulating the gibberellic acid pathway genes PhGAI, creating a more compact and aesthetically appealing phenotype. This study represents the first successful endeavor to produce compact petunia plants with increased flower abundance through genome editing. Our approach holds immense promise to improve economically important potting plants like petunia and serve as a potential foundation for further improvements in similar ornamental plant species.
An explainable content-based approach for recommender systems: a case study in journal recommendation for paper submission
Authors: de Campos Luis M. , Fernández-Luna Juan M. , Huete Juan F.
Published: June 2024

Explainable artificial intelligence is becoming increasingly important in new artificial intelligence developments since it enables users to understand and consequently trust system output. In the field of recommender systems, explanation is necessary not only for such understanding and trust but also because if users understand why the system is making certain suggestions, they are more likely to consume the recommended product. This paper proposes a novel approach for explaining content-based recommender systems by specifically focusing on publication venue recommendation. In this problem, the authors of a new research paper receive recommendations about possible journals (or other publication venues) to which they could submit their article based on content similarity, while the recommender system simultaneously explains its decisions. The proposed explanation ecosystem is based on various elements that support the explanation (topics, related articles, relevant terms, etc.) and is fully integrated with the underlying recommendation model. The proposed method is evaluated through a user study in the biomedical field, where transparency, satisfaction, trust, and scrutability are assessed. The obtained results suggest that the proposed approach is effective and useful for explaining the output of the recommender system to users.
Rotenone Induces a Neuropathological Phenotype in Cholinergic-like Neurons Resembling Parkinson’s Disease Dementia (PDD)
Authors: Giraldo-Berrio Daniela , Mendivil-Perez Miguel , Velez-Pardo Carlos , Jimenez-Del-Rio Marlene
Published: June 2024

Parkinson’s disease with dementia (PDD) is a neurological disorder that clinically and neuropathologically overlaps with Parkinson’s disease (PD) and Alzheimer’s disease (AD). Although it is assumed that alpha-synuclein ($$\mathrm{\alpha }$$
α
-Syn), amyloid beta (A$$\upbeta$$
β
), and the protein Tau might synergistically induce cholinergic neuronal degeneration, presently the pathological mechanism of PDD remains unclear. Therefore, it is essential to delve into the cellular and molecular aspects of this neurological entity to identify potential targets for prevention and treatment strategies. Cholinergic-like neurons (ChLNs) were exposed to rotenone (ROT, 10$$\upmu$$
μ
M) for 24 h. ROT provokes loss of $$\Delta \mathrm{\Psi m}$$

Δ

Ψ
m

, generation of reactive oxygen species (ROS), phosphorylation of leucine-rich repeated kinase 2 (LRRK2 at Ser935) concomitantly with phosphorylation of $$\mathrm{\alpha }$$
α
-synuclein ($$\mathrm{\alpha }$$
α
-Syn, Ser129), induces accumulation of intracellular A$$\upbeta$$
β
(iA$$\upbeta$$
β
), oxidized DJ-1 (Cys106), as well as phosphorylation of TAU (Ser202/Thr205), increases the phosphorylation of c-JUN (Ser63/Ser73), and increases expression of proapoptotic proteins TP53, PUMA, and cleaved caspase 3 (CC3) in ChLNs. These neuropathological features resemble those reproduced in presenilin 1 (PSEN1) E280A ChLNs. Interestingly, anti-oxidant and anti-amyloid cannabidiol (CBD), JNK inhibitor SP600125 (SP), TP53 inhibitor pifithrin-$$\mathrm{ \alpha }$$
α
(PFT), and LRRK2 kinase inhibitor PF-06447475 (PF475) significantly diminish ROT-induced oxidative stress (OS), proteinaceous, and cell death markers in ChLNs compared to naïve ChLNs. In conclusion, ROT induces p-$$\mathrm{ \alpha }$$
α
-Syn, iA$$\upbeta$$
β
, p-Tau, and cell death in ChLNs, recapitulating the neuropathology findings in PDD. Our report provides an excellent in vitro model to test for potential therapeutic strategies against PDD. Our data suggest that ROT induces a neuropathologic phenotype in ChLNs similar to that caused by the mutation PSEN1 E280A.
Raising undergraduate researchers’ interdisciplinary consciousness through dialogue
Authors: Imbruce Valerie , Jaeger Vanessa , Rinkus Marisa A. , Hua Jessica , O’Rourke Michael
Published: June 2024

The importance of interdisciplinary approaches for research and education in environmental studies and sciences is well known. Integration of the multiple disciplinary approaches taught in separate courses required within these undergraduate majors and minors, however, remains a challenge. Program faculty often come from different departments and do not have time or space to integrate their own approaches with each other, resulting in individual ways of understanding interdisciplinarity. Secondly, senior capstone, thesis, or other project-based degree requirements often come too late in an undergraduate education to design an integrative project. Students would benefit from prior training in identifying complementary or divergent approaches and insights among academic specializations—a skill built from raising interdisciplinary consciousness. We present a workshop designed to enhance undergraduates’ interdisciplinary consciousness that can be easily deployed within courses or co-curricular programs, specifically summer research programs that are focused on dedicated practice within a field of study. The central question of this project is: How do we facilitate interdisciplinary consciousness and assess its impact on our students? We propose a promising, dialogue-based intervention that can be easily replicated. This dialogue would benefit academic programs like environmental studies and sciences that require the interaction and integration of discipline-based norms. We found that our dialogue intervention opens students’ perspectives on the nature of research, who research is for, epistemological differences, and the importance of practicing the research process, a unique educational experience. These perspectives are crucial to becoming collaborative, twenty-first century professionals.
Novel Nafion nanocomposite membranes embedded with TiO2-decorated MWCNTs for high-temperature/low relative humidity fuel cell systems
Authors: Nicotera Isabella , Coppola Luigi , Simari Cataldo
Published: June 2024

Extending the operation of proton exchange membrane fuel cells (PEMFCs) at high temperature (i.e., 120 °C) and/or low relative humidity (< 50% RH) remains a significant challenge due to dehydration and subsequent performance failure of the Nafion electrolyte. We approached this problem by integrating the Nafion matrix with a novel hybrid nanofiller, created through direct growth of TiO2 nanoparticles on the surface of carbon nanotubes. This synthetic approach allowed to preserve an effective nanodispersion of Titania particles in the hosting matrix, thereby boosting dimensional stability, hydrophilicity, and physiochemical properties of the Nafion/MWCNTs-TiO2 (NMT-x) nanocomposites compared to parental Nafion. At optimal concentration (i.e., 3 wt% with respect to the polymer), the nanocomposite membrane exhibited high transport characteristics with impressive water retention capabilities, resulting in a proton conductivity of 8.3 mS cm− 1 at 80 °C and 20% RH. The Titania nanoparticles plays a key role in retaining water molecules even under dehydrating conditions, while also directly contributing to proton transport. Additionally, the long carbon nanotubes promote the formation of additional paths for proton conductivity. These combined features enabled the NMT-3 membrane to achieve a maximum power output of 307.7 mW/cm2 in a single H2/air fuel cell (5 cm2 active electrode area and 0.5 mg Pt/cm2 at both electrodes) under very challenging conditions, specifically at 120 °C and 30% RH. This represents a significant advancement towards overcoming the limitations of traditional Nafion membranes and opens up new possibilities for high-temperature, low-humidity H2/air fuel cell applications.
Non-syndromic tooth agenesis in Latvian adolescent dental patients: a retrospective study with relevant literature review
Authors: Meistere D. , Kronina L. , Karkle A. , Neimane L.
Published: June 2024

Aim

To investigate the prevalence of tooth agenesis and associated dental anomalies in Latvian adolescent dental patients and compare it to other European countries.

Design

Cross-sectional study of 2692 11-to-14-year-old patients (39.9% males and 60.1% females) attending Riga Stradins University Institute of Stomatology with panoramic radiographs taken between August 2020 and September 2021. Patients with any genetic syndromes were excluded. Data on tooth agenesis (excluding third molars) and other dental anomalies were recorded.

Results

The prevalence of tooth agenesis in Latvian adolescent dental patients was 9.3% with no statistically significant difference between genders (χ2 test, p = 0.472). The most commonly missing teeth were mandibular second premolars, followed by upper lateral incisors and upper second premolars. There was a statistically significant association with the presence of other dental anomalies in tooth agenesis patients (p < 0.001).

Conclusions

This study found that the prevalence of non-syndromic tooth agenesis in Latvian adolescent dental patients was 9.3% with no statistically significant differences between the genders. Patients with tooth agenesis have a statistically significant possibility of the presence of other dental anomalies (p < 0.001).
Predictive value of sarcopenia components for all-cause mortality: findings from population-based cohorts
Authors: Westbury Leo D. , Harvey Nicholas C. , Beaudart Charlotte , Bruyère Olivier , Cauley Jane A. , Cawthon Peggy , Cruz-Jentoft Alfonso J. , Curtis Elizabeth M. , Ensrud Kristine , Fielding Roger A. , Johansson Helena , Kanis John A. , Karlsson Magnus K. , Lane Nancy E. , Lengelé Laetitia , Lorentzon Mattias , McCloskey Eugene , Mellström Dan , Newman Anne B. , Ohlsson Claes , Orwoll Eric , Reginster Jean-Yves , Ribom Eva , Rosengren Björn E. , Schousboe John T. , Dennison Elaine M. , Cooper Cyrus ,   and the International Musculoskeletal Ageing Network
Published: June 2024

Background

Low grip strength and gait speed are associated with mortality. However, investigation of the additional mortality risk explained by these measures, over and above other factors, is limited.

Aim

We examined whether grip strength and gait speed improve discriminative capacity for mortality over and above more readily obtainable clinical risk factors.

Methods

Participants from the Health, Aging and Body Composition Study, Osteoporotic Fractures in Men Study, and the Hertfordshire Cohort Study were analysed. Appendicular lean mass (ALM) was ascertained using DXA; muscle strength by grip dynamometry; and usual gait speed over 2.4–6 m. Verified deaths were recorded. Associations between sarcopenia components and mortality were examined using Cox regression with cohort as a random effect; discriminative capacity was assessed using Harrell’s Concordance Index (C-index).

Results

Mean (SD) age of participants (n = 8362) was 73.8(5.1) years; 5231(62.6%) died during a median follow-up time of 13.3 years. Grip strength (hazard ratio (95% CI) per SD decrease: 1.14 (1.10,1.19)) and gait speed (1.21 (1.17,1.26)), but not ALM index (1.01 (0.95,1.06)), were associated with mortality in mutually-adjusted models after accounting for age, sex, BMI, smoking status, alcohol consumption, physical activity, ethnicity, education, history of fractures and falls, femoral neck bone mineral density (BMD), self-rated health, cognitive function and number of comorbidities. However, a model containing only age and sex as exposures gave a C-index (95% CI) of 0.65(0.64,0.66), which only increased to 0.67(0.67,0.68) after inclusion of grip strength and gait speed.

Conclusions

Grip strength and gait speed may generate only modest adjunctive risk information for mortality compared with other more readily obtainable risk factors.
Internet “piracy” and book sales: a field experiment
Authors: Hardy Wojciech , Krawczyk Michał , Tyrowicz Joanna
Published: June 2024

The widespread Internet “piracy” continues to fuel the debate about business models impervious to copyright infringement. We studied the displacement effects of “piracy” on sales in the book industry. We conducted a year-long large-scale field experiment: in the treatment group, we removed unauthorised copies appearing on the Internet and observed the sales data, whereas in the control group, we simply observed sales. We were able to substantially curb the unauthorised distribution, which resulted in a small, positive effect on sales. While using classical analysis we found it not to be significantly different from zero, a Bayesian approach using previous “piracy” studies to generate a prior led to the conclusion that protecting from piracy resulted in a significant sales boost of about 9 per cent.
Blockchain-based secure optimized traceable scheme for smart and sustainable food supply chain
Authors: Chunduri Venkata , Raparthi Mohan , Yellu Ramswaroop Reddy , Keshta Ismail , Byeon Haewon , Soni Mukesh , Bhatt Mohammed Wasim
Published: June 2024

A large number of nodes, and significant system overhead are among the challenges. To tackle these problems, a new PBFT technique known as trace-PBFT (t-PBFT) is being contemplated for adoption in the food supply chain. The PBFT algorithm, short for Practical Byzantine Fault Tolerance, serves as the fundamental algorithm. The linkages throughout the supply chain may be categorized into three primary groups. As a response to the continuing discussion over the amount of data, the status of each node is continuously updated in real time. This metric is utilized to evaluate the dependability of the principal node and to analyze the overall performance of the nodes. To minimize the amount of data transmitted between nodes, we optimized the consensus process of the first algorithm. The distinct attributes of offering collaborative food technology were considered throughout this procedure. Experimental evidence indicates that the t-PBFT approach outperforms the PBFT algorithm in terms of throughput, request delay, and information overhead. An architectural paradigm is proposed by integrating the t-PBFT algorithm with a federated network. This model was developed in response to the distinct demands of the food supply chain. This model effectively captures data at each stage of the food supply chain to ensure information tracking while preserving the safety of the food technology flow process.
Effectiveness of interventions to improve job-related wellbeing of employees working from home: a rapid review
Authors: Simpson Emma , Sutton Anthea , Cantrell Anna , Clowes Mark , Weich Scott , Bentley-Hollins Karen , Visintin Cristina , Axtell Carolyn
Published: June 2024

We conducted a rapid review examining the effectiveness of organisational interventions intended to improve job-related wellbeing of adult employees working from home. A systematic search was conducted on MEDLINE, PsycINFO, and Social Sciences Citation Index in June 2021. Studies were included of adult employees working from home, with wellbeing interventions implemented by organisations for all (or groups of) employees and study designs with any (or no) comparator group. Outcomes were quantitative/qualitative data related to employee psychological and subjective well-being. A total of 1906 unique records were retrieved, of which five studies with a total of 332 participants were included. All five studies included an online intervention, and each had a different type of intervention: well-being and performance coaching; positive psychology coaching; employee empowering sessions; corporate wellbeing programme; and yoga. Interventions showed a pattern of reducing stress levels and enhancing wellbeing. Review results should be interpreted with caution due to study small sample sizes, occurring during the pandemic and having inactive control or no control group, which may mean fluctuating levels of stress unrelated to interventions. The nature of the rapid review meant grey literature may have yielded more studies. This review was registered on Prospero (CRD42021262655).
How Soil Symbionts Could Unlock Climate-Smart Agriculture
Authors: Paszkowski Uta
Published: June 2024

By tracing the evolutionary history of beneficial soil microbes, scientists hope to unearth a sustainable solution for producing food to feed a growing global population.
High‐Frequency Tsunamis Excited Near Torishima Island, Japan, Observed by Distributed Acoustic Sensing
Authors: Tonegawa T. , Araki E.
Published: June 2024

Recent distributed acoustic sensing (DAS) experiments in ocean areas throughout the world have accumulated records for various wavefields. However, there are few tsunami records because tsunami observation depends on the DAS experimental period and its location. From continuous DAS records, we found tsunami signals at a frequency band of 5–30 mHz, which correspond to high‐frequency components of tsunamis and their propagation velocities differ from low‐frequency tsunamis. We estimated time series of the tsunami excitations at the source using the DAS records, which are consistent with those using records of ocean‐bottom absolute pressure gauges. Our study suggests that DAS records can be used for detecting tsunami propagations in the regions where other geophysical instruments are not available, and contribute to elucidating their excitation mechanisms.
What is the impact of the UK soft drinks industry levy on childhood tooth decay?
Authors: Watt Samantha
Published: June 2024

Design

Interrupted time series analysis.

Data analysis

An interrupted time series (ITS) analysis was conducted to determine if there was an association between the announcement and implementation of the soft drinks industry levy (SDIL) and rates of hospital admission for tooth extractions due to dental caries in children. Hospital Episode Statistics (HES) were used on hospital admissions for tooth extraction of one or more primary or permanent tooth due to a primary diagnosis of dental caries in children aged 0–18 years attending a National Health Service (NHS) hospital in England from January 2012 (pre-SDIL) to February 2020 (post-SDIL implementation). HES data were grouped and summarised by Index of Multiple Deprivation (IMD) and age group.

Results

There was an absolute reduction of 3.7% (95% CI 5.3% to 2.2%) per 100,000 population/month and a relative reduction of 12.1% (95% CI 17.0% to 7.2%) in hospital admissions for carious tooth extractions in all children (0–18 years) compared if there had been no announcement of the SDIL (counterfactual scenario). Reductions were observed in children living in most areas regardless of the level of deprivation and most notably in the youngest children (<10 years).

Conclusions

An ITS analysis of administrative data on hospital admissions found the announcement of the UK SDIL was associated with improvements (reduction) in the incidence of hospital admissions for tooth extractions due to dental caries. This study provides evidence of benefits of the UK SDIL to children’s oral health.
Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry
Authors: Engelbrecht Eric , Rodriguez Oscar L. , Shields Kaitlyn , Schultze Steven , Tieri David , Jana Uddalok , Yaari Gur , Lees William D. , Smith Melissa L. , Watson Corey T.
Published: June 2024

Immunoglobulins (IGs), critical components of the human immune system, are composed of heavy and light protein chains encoded at three genomic loci. The IG Kappa (IGK) chain locus consists of two large, inverted segmental duplications. The complexity of the IG loci has hindered use of standard high-throughput methods for characterizing genetic variation within these regions. To overcome these limitations, we use long-read sequencing to create haplotype-resolved IGK assemblies in an ancestrally diverse cohort (n = 36), representing the first comprehensive description of IGK haplotype variation. We identify extensive locus polymorphism, including novel single nucleotide variants (SNVs) and novel structural variants harboring functional IGKV genes. Among 47 functional IGKV genes, we identify 145 alleles, 67 of which were not previously curated. We report inter-population differences in allele frequencies for 10 IGKV genes, including alleles unique to specific populations within this dataset. We identify haplotypes carrying signatures of gene conversion that associate with SNV enrichment in the IGK distal region, and a haplotype with an inversion spanning the proximal and distal regions. These data provide a critical resource of curated genomic reference information from diverse ancestries, laying a foundation for advancing our understanding of population-level genetic variation in the IGK locus.
Folding the human proteome using BioNeMo: A fused dataset of structural models for machine learning purposes
Authors: Hetmann Michael , Parigger Lena , Sirelkhatim Hassan , Stern Abraham , Krassnigg Andreas , Gruber Karl , Steinkellner Georg , Ruau David , Gruber Christian C.
Published: June 2024

Human proteins are crucial players in both health and disease. Understanding their molecular landscape is a central topic in biological research. Here, we present an extensive dataset of predicted protein structures for 42,042 distinct human proteins, including splicing variants, derived from the UniProt reference proteome UP000005640. To ensure high quality and comparability, the dataset was generated by combining state-of-the-art modeling-tools AlphaFold 2, OpenFold, and ESMFold, provided within NVIDIA’s BioNeMo platform, as well as homology modeling using Innophore’s CavitomiX platform. Our dataset is offered in both unedited and edited formats for diverse research requirements. The unedited version contains structures as generated by the different prediction methods, whereas the edited version contains refinements, including a dataset of structures without low prediction-confidence regions and structures in complex with predicted ligands based on homologs in the PDB. We are confident that this dataset represents the most comprehensive collection of human protein structures available today, facilitating diverse applications such as structure-based drug design and the prediction of protein function and interactions.
Potential role of serum copeptin among smoker T2DM patients with emphasis to ACE I/D gene polymorphism predicting DN
Authors: Taha Mona Mohamed , Zakaria Mohamed Ahmed Yehia , Eisa Yasmine Hamdy , Rashed Maysa Hatem
Published: June 2024

Diabetic nephropathy represents one of the main long-term complications in T2DM patients. Cigarette smoking represents one of modifiable renal risk factors to kidney damage due to lead (Pb) exposure in these patients. Our goal is to investigate serum copeptin and Kidney injury molecule-1 (KIM-1) and urinary lead (UPb) in type 2 diabetes mellitus (T2DM) patients even smokers and non-smokers groups and compared to corresponding health controls and assess its associations with Angiotensin-Converting enzyme Insertion/Deletion polymorphism [ACE (I/D)] polymorphism in diabetic nephropathy progression in those patients. In present study, 106 T2DM patients and 102 healthy control individuals were enrolled. Serum glucose, copeptin, KIM-1, total cholesterol (TChol), triglycerides (TG), estimated glomerular filtration rate (eGFR) and UPb levels and ACE (I/D) polymorphisms were assessed in both groups. Results mentioned to significant variations in all parameters compared to in T2DM group compared to control group. Serum copeptin and UPb demonstrated significant difference in diabetic smokers (DS) and diabetic non-smokers (DNS) groups while KIM-1 exhibited significant change between DNS and healthy control non-smokers (CNS) groups. Positive relation was recorded between serum glucose and KIM-1 while negative one was found between serum copeptin and TChol. D allele was associated with significant variation in most parameters in T2DM, especially insertion/deletion (ID) polymorphism. ROC curve analysis (AUC) for serum copeptin was 0.8, p < 0.044 and for Kim-1 was 0.54, p = 0.13 while for uPb was 0.71, p < 0.033. Serum copeptin and UPb might be a prognostic biomarker for renal function decline in smoker T2DM patients while KIM-1 was potent marker in non-smoker T2DM with association with D allele of ACE I/D gene polymorphism.
Mandarin biochar-CO-TETA was utilized for Acid Red 73 dye adsorption from water, and its isotherm and kinetic studies were investigated
Authors: Eleryan Ahmed , Güner Eda Keleş , Hassaan Mohamed , El-Nemr Mohamed A. , Ragab Safaa , El Nemr Ahmed
Published: June 2024

Environmental pollution is a major issue today due to the release of dyestuff waste into the environment through industrial wastewater. There is a need for affordable and effective adsorbents to remove harmful dyes from industrial waste. In this study, Mandarin biochar-CO-TETA (MBCOT) adsorbent was prepared and used to remove Acid Red 73 (AR73) dye from aqueous solutions. The efficiency of dye removal was influenced by various factors such as solution pH, contact time, initial AR73 dye concentration, and MBCOT dosage. All experiments were conducted at 25 ± 2 °C, and the optimal pH was determined to be 1.5. The optimal conditions for dye removal were found to be an AR73 dye concentration of 100 mg/L, an MBCOT dosage of 1.5 g/L, and a contact time of 150 min, resulting in a 98.08% removal rate. Various models such as pseudo-first-order (PFO), pseudo-second-order (PSO), film diffusion (FD), and intraparticle diffusion (IPD) were used to determine the adsorption kinetics of AR73 dye onto MBCOT. The results showed that the PSO model best explains the AR73 dye adsorption. Furthermore, Langmuir and Freundlich's isotherm models were studied to explain the adsorption mechanism using experimental data. The adsorption capacities at equilibrium (qe) in eliminating AR73 dye varied from 92.05 to 32.15, 128.9 to 65.39, 129.25 to 91.69, 123.73 to 111.77, and 130.54 to 125.01 mg/g. The maximum adsorption capacity (Qm) was found to be 140.85 mg/g. In conclusion, this study demonstrates that biochar produced from mandarin peels has the potential to be an effective and promising adsorbent for removing AR73 dye from water.
Tsunami Squares: Leapfrog scheme implementation and benchmark study on wave–shore interaction of solitary waves
Authors: Zhang Yu , Yin Kunlong , Tang Yang , Xiao Lili
Published: June 2024

Impulse waves are generated by rapid subaerial mass movements including landslides, avalanches and glacier break-offs, which pose a potential risk to public facilities and residents along the shore of natural lakes or engineered reservoirs. Therefore, the prediction and assessment of impulse waves are of considerable importance to practical engineering. Tsunami Squares, as a meshless numerical method based on a hybrid Eulerian–Lagrangian algorithm, have focused on the simulation of landslide-generated impulse waves. An updated numerical scheme referred to as Tsunami Squares Leapfrog, was developed which contains a new smooth function able to achieve space and time convergence tests as well as the Leapfrog time integration method enabling second-order accuracy. The updated scheme shows improved performance due to a lower wave decay rate per unit propagation distance compared to the original implementation of Tsunami Squares. A systematic benchmark testing of the updated scheme was conducted by simulating the run-up, reflection and overland flow of solitary waves along a slope for various initial wave amplitudes, water depths and slope angles. For run-up, the updated scheme shows good performance when the initial relative wave amplitude is smaller than 0.4. Otherwise, the model tends to underestimate the run-up height for mild slopes, while an overestimation is observed for steeper slopes. With respect to overland flow, the prediction error of the maximum flow height can be limited to ± 50% within a 90% confidence interval. However, the prediction of the front propagation velocity can only be controlled to ± 100% within a 90% confidence interval. Furthermore, a sensitivity analysis of the dynamic friction coefficient of water was performed and a suggested range from 0.01 to 0.1 was given for reference.
Corona discharge plasma for green de-inking of inkjet printer ink
Authors: Priyanti Ika , Wongsawaeng Doonyapong , Ngaosuwan Kanokwan , Kiatkittipong Worapon , Hosemann Peter , Assabumrungrat Suttichai
Published: June 2024

This work features a new corona discharge plasma technology for de-inking yellow, blue, and red colors on various papers. This work was developed to minimize the chemical and environmental impacts of de-inking processes. A nonchemical contribution, operating at room temperature and atmospheric pressure, reduces the environmental impact of the process. The deinkability factor (DEMLab) values for all papers are determined with the optimal assessment results provided by a 36-mm variation gap at 2-min (blue) and 10-min (yellow and red) plasma exposure times, followed by applied voltages of 20 kV (yellow), 16 kV (blue), and 20 kV (red). The corona discharge plasma led to 48.58% (yellow printed paper), 64.11% (blue printed paper), and 41.11% (red printed paper) deinkability without altering the physical properties of the paper itself. The change in the tensile strength for the plasma-exposed paper was relatively little, less than 10%, compared to that of common recycling. The tensile strength of the untreated white paper was 5065 ± 487.44 N/mm2, and that of the plasma-treated printed paper was 4593 ± 248.47 N/mm2. It appears that there is little impact on the physicochemical properties of paper induced by the corona plasma treatment during the de-inking process.
Criticality and chaos in auditory and vestibular sensing
Authors: Faber Justin , Bozovic Dolores
Published: June 2024

The auditory and vestibular systems exhibit remarkable sensitivity of detection, responding to deflections on the order of angstroms, even in the presence of biological noise. The auditory system exhibits high temporal acuity and frequency selectivity, allowing us to make sense of the acoustic world around us. As the acoustic signals of interest span many orders of magnitude in both amplitude and frequency, this system relies heavily on nonlinearities and power-law scaling. The vestibular system, which detects ground-borne vibrations and creates the sense of balance, exhibits highly sensitive, broadband detection. It likewise requires high temporal acuity so as to allow us to maintain balance while in motion. The behavior of these sensory systems has been extensively studied in the context of dynamical systems theory, with many empirical phenomena described by critical dynamics. Other phenomena have been explained by systems in the chaotic regime, where weak perturbations drastically impact the future state of the system. Using a Hopf oscillator as a simple numerical model for a sensory element in these systems, we explore the intersection of the two types of dynamical phenomena. We identify the relative tradeoffs between different detection metrics, and propose that, for both types of sensory systems, the instabilities giving rise to chaotic dynamics improve signal detection.
Determination and health risk assessment of carbamate pesticide residues in date palm fruits (Phoenix dactylifera) using QuEChERS method and UHPLC-MS/MS
Authors: Morsi Rana , Ghoudi Kilani , Meetani Mohammed A.
Published: June 2024

This study aimed to investigate carbamate pesticide residues in different varieties of date palm fruits in the UAE, utilizing UHPLC-MS/MS. For sample preparation and clean-up, the efficiency and performance of different QuEChERS dispersive solid-phase extraction kits were compared. Precision and recovery were assessed at 10 μg kg−1 for the three kits, revealing that Kit 2 demonstrated the best performance. The selected QuEChERS method was validated to detect 14 carbamate residues in 55 date samples. The method exhibited strong linearity with R2 > 0.999 and low LOD (0.01–0.005 μg kg−1) and LOQ (0.003–0.04 μg kg−1). Excellent accuracy (recovery: 88–106%) and precision (RSD: 1–11%) were observed, with negligible matrix effect (− 4.98–13.26%). All samples contained at least one carbamate residue. While most detected residues were below their MRLs, carbosulfan was found in 21 samples, propoxur in 2 samples, and carbofuran in 1 sample above their MRLs. The hazard index (HI) was calculated for carbosulfan, phenmedipham, carbaryl, propoxur, carbofuran, and methomyl to assess potential health risks for date consumers. All HI values were below the safety limit of 1.0, indicating that the consumption of dates does not pose a non-carcinogenic health risk for adults and children.
Nonlinear ion-acoustic waves with Landau damping in non-Maxwellian space plasmas
Authors: Mushtaq Hadia , Singh Kuldeep , Zaheer Sadia , Kourakis Ioannis
Published: June 2024

The dynamics of nonlinear ion-acoustic solitary waves in the presence of kinetic (Landau type) damping have been investigated in a collisionless, non-magnetized electron-ion plasma. A cold ion fluid model, coupled to a Vlasov-type kinetic equation for the electron dynamics, has been adopted as a starting point. The electron population was assumed to be in a kappa-distributed state, in account of the non-Maxwellian behavior of energetic (suprathermal) electrons often observed in Space. A multiscale perturbation technique has led to an evolution equation for the electrostatic potential, in the form of a modified Korteweg-de Vries (KdV) equation, incorporating a non-local term accounting for Landau damping (associated with the electron statistics). Exact analytical solutions have been obtained, representing solitary waves undergoing amplitude decay over time. The combined effect of Landau damping and non-Maxwellian electron statistics (via the kappa parameter) on the characteristics of IASWs has been examined. Numerical integration of the evolution equation has been undertaken, to elucidate the importance of kinetic Landau damping on a shock-shaped initial condition. The results of this investigation aim to improve our understanding of the dynamics of nonlinear electrostatic waves under the influence of Landau damping in various space plasma environments.
A comprehensive study of the novel 4D hyperchaotic system with self-exited multistability and application in the voice encryption
Authors: Benkouider Khaled , Sambas Aceng , Bonny Talal , Al Nassan Wafaa , Moghrabi Issam A. R. , Sulaiman Ibrahim Mohammed , Hassan Basim A. , Mamat Mustafa
Published: June 2024

This paper describes a novel 4-D hyperchaotic system with a high level of complexity. It can produce chaotic, hyperchaotic, periodic, and quasi-periodic behaviors by adjusting its parameters. The study showed that the new system experienced the famous dynamical property of multistability. It can exhibit different coexisting attractors for the same parameter values. Furthermore, by using Lyapunov exponents, bifurcation diagram, equilibrium points’ stability, dissipativity, and phase plots, the study was able to investigate the dynamical features of the proposed system. The mathematical model’s feasibility is proved by applying the corresponding electronic circuit using Multisim software. The study also reveals an interesting and special feature of the system’s offset boosting control. Therefore, the new 4D system is very desirable to use in Chaos-based applications due to its hyperchaotic behavior, multistability, offset boosting property, and easily implementable electronic circuit. Then, the study presents a voice encryption scheme that employs the characteristics of the proposed hyperchaotic system to encrypt a voice signal. The new encryption system is implemented on MATLAB (R2023) to simulate the research findings. Numerous tests are used to measure the efficiency of the developed encryption system against attacks, such as histogram analysis, percent residual deviation (PRD), signal-to-noise ratio (SNR), correlation coefficient (cc), key sensitivity, and NIST randomness test. The simulation findings show how effective our proposed encryption system is and how resilient it is to different cryptographic assaults.
Loss of the proteasomal deubiquitinase USP14 induces growth defects and a senescence phenotype in colorectal cancer cells
Authors: Gubat Johannes , Sjöstrand Linda , Selvaraju Karthik , Telli Kübra , D’Arcy Pádraig
Published: June 2024

The proteasome-associated deubiquitinase USP14 is a potential drug target. Using an inducible USP14 knockout system in colon cancer cells, we found that USP14 depletion impedes cellular proliferation, induces cell cycle arrest, and leads to a senescence-like phenotype. Transcriptomic analysis revealed altered gene expression related to cell division and cellular differentiation. USP14 knockout cells also exhibited changes in morphology, actin distribution, and expression of actin cytoskeletal components. Increased ubiquitin turnover was observed, offset by upregulation of polyubiquitin genes UBB and UBC. Pharmacological inhibition of USP14 with IU1 increased ubiquitin turnover but did not affect cellular growth or morphology. BioGRID data identified USP14 interactors linked to actin cytoskeleton remodeling, DNA damage repair, mRNA splicing, and translation. In conclusion, USP14 loss in colon cancer cells induces a transient quiescent cancer phenotype not replicated by pharmacologic inhibition of its deubiquitinating activity.
Computational approach to grain boundary segregation engineering of nickel-base superalloys
Authors: Uruchida Haruna , Tsukada Yuhki , Matsuoka Yusuke , Koyama Toshiyuki
Published: June 2024

Grain boundary (GB) strengthening elements, such as B, C, and Zr have been added in small amounts to nickel-base superalloys. However, their strengthening effects have not been quantified and no specific design principles for GB chemistry have been reported. In this study, we propose a practical computational approach for the GB segregation engineering of nickel-base superalloys. Considering the partitioning of alloying elements into coexisting phases (strengthening phases, carbides, etc.), the equilibrium composition of a high-angle GB was computed for several nickel-base superalloys using a calculation of phase diagrams database. The computational results showed that B and Mo were enriched at the GB in most of the investigated alloys. The creep rupture strengths of the investigated alloys were predicted using the computed GB composition as a regression model feature. The regression coefficients for the features confirm that B segregation at the GB has a non-negligible strengthening effect on nickel-base superalloys.