bluuebunny/crossref_metadata_2025 huggingface dataset:
Wijsman Deferred Invariant Statistical and Strong $p$-Deferred Invariant Equivalence of Order $\alpha$
Authors: GÜLLE Esra , ULUSU Uğur
Published: November 2023

With this work, we present the asymptotical strongly $p$-deferred invariant and asymptotical deferred invariant statistical equivalence of order $\alpha$ ($0<\alpha\leq 1$) for sequences of sets in the Wijsman sense. Furthermore, we investigate the connections between these concepts and conduct their properties.
Modeling grazer-mediated effects of demographic and material connectivity on giant kelp metapopulation dynamics
Authors: Detmer AR
Published: November 2023

From dispersal-based metapopulations to meta-ecosystems that arise from flows of non-living materials, spatial connectivity is a major driver of population dynamics. One potentially important process is material transport between populations also linked by individual dispersal. Here, I explored material and demographic connectivity in metapopulations of giant kelp Macrocystis pyrifera, a foundation species that produces both detritus and reproductive spores. Kelp detritus (drift) subsidizes grazers, helping maintain the kelp forest ecosystem state. Drift could potentially be exchanged among kelp patches, but this is less studied than spore dispersal. Therefore, I built an ordinary differential equation (ODE) model to investigate conditions under which drift and/or spore connectivity promotes the kelp forest state. I fit statistical models (generalized linear mixed models, GLMMs) to observational data and used the GLMM’s predictions to validate the ODE model. My results suggest kelp patch dynamics are best explained by connectivity of both drift and spores, and that the impacts of these forms of connectivity depend on local grazer (urchin) abundance. Both models predicted greater kelp persistence in well-connected patches across a range of urchin densities. These effects were largely driven by drift, which reduced grazing in recipient patches and thereby enhanced spore recruitment. While testing these predictions will require greater empirical quantification of interpatch drift transport, my findings indicate drift connectivity may be an important spatial process in kelp forest systems. More broadly, this work highlights the role of meta-ecosystem dynamics within a single ecosystem type, reinforcing the need to expand traditional metapopulation perspectives to consider multiple forms of spatial connectivity.
The Influence of Media Exposure, Company Size, Profitability, and Leverage on Carbon Emission Disclosure
Authors: Utari Tri Maya , Aprilina Vita
Published: November 2023

The purpose of this study is to analyze the effect of media exposure, company size, profitability, and leverage on carbon emission disclosures. This research is research using descriptive methods with quantitative analysis using secondary data. The sample for this research is non-cyclical consumer sector companies listed on the Indonesia Stock Exchange (IDX) for the 2019-2021 period. The sampling technique in this study was purposive sampling. The independent variables used in this study are the Effect of Media Exposure, Firm Size, Profitability, and Leverage. The dependent variable used in this study is Carbon Emission Disclosure. The data analysis technique used is multiple linear analysis. By processing data using Eviews 9. Based on the test results, media exposure and leverage have a positive effect on carbon emission disclosure. While company size and profitability have no effect on carbon emission disclosure. So with this, it is hoped that the next researcher can add other independent variables that are not used in this research.
Keywords: Media Exposure, Company Size, Profitability, Leverage, Carbon Emission Disclosure.
The structuralist tradition meets empirical data: Corpus data enhancing the Czech Internet Language Reference Book
Authors: Kováříková Dominika , Beneš Martin , Smejkalová Kamila , Kovářík Oleg
Published: November 2023

This paper demonstrates how the corpus grammar tool GramatiKat can be used to improve and refine morphological information in the Internet Language Reference Book (ILRB), which presents complete declension paradigms for 45,632 standard Czech nouns. The paradigm tables are based mainly on morphological types, following structuralist conceptions of language as a fully articulated system. The paper discusses how to update the ILRB and provide users with empirically based grammatical information for individual word forms in each cell of the paradigm. All noun lemmas have been investigated using the GramatiKat tool for research into grammatical categories in Czech. The tool observes the distribution of word forms of a particular lexeme in comparison with the standard distribution across the whole word class. It is capable of identifying nouns that have an unusually high occurrence of a certain word form, as well as nouns with unattested word forms. GramatiKat is based on the data from two corpora of Czech written texts, SYN2015 and SYN2020 (200 million word tokens). The paper investigates the relationship between defectiveness and overabundance on one side and language variability and potentiality on the other. Based on the unique combination of data from the ILRB and GramatiKat, the paper suggests how information about unusually frequent or overabundant word forms as well as unattested ones should be pointed out, so that ILRB provides the user with accurate, empirically based data.
Language Preservation through ASR
Authors: O'Neill Alexander , Meelen Marieke , Coto-Solano Rolando , Phuntsog Sonam , Ramble Charles
Published: November 2023

By the end of the century, over half of the 6500 languages spoken in the world will die out (Turin, 2007). Nepal's situation is particularly dire: of the 120+ distinct languages identified in the 2011 census, 60 are endangered due to globalisation, socio-political unrest, and environmental challenges. The loss of these languages also means the loss of unique cultural and religious identifiers. Given this, there is a need for methods and tools to preserve linguistic diversity. A major challenge in language preservation, however, is the transcription bottleneck (Shi et al., 2021): transcribing one minute of audio requires an average of 40+ minutes (Durantin et al., 2017). This becomes even more complicated for endangered languages with no (standardised) orthographies or documentation. While advanced automatic speech-recognition (ASR) tools are available, they are often ineffective for these extremely low-resource languages (Foley et al., 2018). This poster presents the preliminary results to address these issues for the Newar and Dzardzongke (both representing different branches of the Sino-Tibetan language family, spoken in Nepal) using Wav2Vec2 models fine-tuned for low-resource languages (Coto-Solano 2021, 2022). We show that endangered languages benefit from a specific set of optimisation procedures through tests with Kaldi vs Wav2Vec2; different types of data augmentation, and the development of a new or standardisation of orthography.
Exploring co-research interviews with older adults:
Authors: Hoppania Hanna-Kaisa , Vilkko Anni , Topo Päivi
Published: November 2023

Previous research has not only shown the potential of co-research with older adults but also pointed out the need for further study, for example on evaluation and how connections are forged between participants. To this end, this paper (1) describes and reflects on the development and implementation of a co-research interview methodology in the NGO sector and (2) analyses the experiences of the participants and the role of shared age group and locality. The results show that the structure of having several interviews and training and reflection sessions was the strength of the method. The co-researchers found the project interesting and even empowering. Expressions of shared age group and local knowledge were common in the interviews and helped build connections. The intervieweesvalued their participation in knowledge-production on issues related to ageing. Recruitment, resourcing and support for co-researchers when faced with difficult situations are some of the themes that require further attention.
Completeness of Immunization in Infants Aged 0-9 Months: The Role of Mother's Knowledge and Belief
Authors: Irnawati Irnawati , Kadek Sukmawati Niluh
Published: November 2023

Introduction: Over 1.4 million children have died from Immunization-Preventable Diseases (PD3I). The lack of socialization provided by health workers has an impact on the lack of understanding, admonition, and understanding of mothers when participating in immunization programs. Purpose: to determine the relationship between the knowledge and confidence of mothers on the completeness of immunization in infants aged 0-9 months. Method: using a cross-sectional research design, with a population of 216 infants, sampling using purposive sampling techniques totaling 54 respondents with inclusion criteria: infants aged 0-9 months and residing in the study area, while the exclusion criteria were babies who were sick during the study. The research was conducted in Kombo. Using questionnaires and using chi-square tests of vaccine availability. Results: there were 83.3% of respondents who had good knowledge and had complete immunization 75.9% and there were 16.6% who had less knowledge, had complete immunization of 9.1% with a value of ρ=0.006. Conclusion: there is a relationship between knowledge and maternal confidence in the completeness of immunization in infants aged 0 – 9 months. Parents should pay attention to their children's basic immunizations and public health guarantees the availability of vaccines
Difference Between Breastfeeding and Complementary food with Nutritional Status in Infants Aged 6-24 Months in the Working Area of the Pare Health Center
Authors: Fitriyadi Junianto , Yunita Astri , Alfonsa Alfonsa
Published: November 2023

Background: The problem of malnutrition in toddlers is the impact of low exclusive breastfeeding for up to 6 months and improper breastfeeding because it is given too early or too late, the amount is not enough to meet the needs of growth and development of babies at each age stage. Objective: to determine the difference between breastfeeding and MP-ASI with nutritional status in infants aged 6-24 months. Method: This study used a cross-sectional design. The study sample was mothers who had babies aged 6-24 months as many as 30 respondents with 2 groups of breastfeeding and MP-ASI (15 respondents per group) using quota sampling. The research was placed in the working area of the Pare Health Center for 2 weeks with questionnaire instruments according to the experience of breastfeeding and MP-ASI, as well as Z score measurement. Analysis of paired sample t-test. Results: The results of this study showed that most of the 15 respondents breastfeeding had less nutritional status as many as 9 respondents (60%), while of the 15 respondents of MP-ASI most had good nutritional status as many as 10 respondents (66.7%). Conclusion: Families must be more careful in understanding the nutritional needs of infants with a combination of nutritional content needed by the body in accordance with the stage of development and nutritional needs in infants aged 6-24 months.
Knowledge and Role of Cadres in Early Detection Stunting in Toddlers
Authors: Siregar Nilda Yulita , Hakim Fitrayani , Ramadhan Kadar
Published: November 2023

Background: Stunting is a condition of failure to thrive in children under five due to chronic malnutrition. Indonesia has a fairly high prevalence of stunting. The role of Posyandu cadres in preventing stunting through monitoring toddler growth requires knowledge so that they are good at early detection of stunting. Objective: knowledge and role of cadres in early detection of toddler stunting. Method: Descriptive research was conducted in the Lawanga Community Health Center Working Area from April to July 2020. The population of all cadres in the Lawanga Community Health Center Working Area with a sample of 35 people used simple random sampling. Results: There are 4 cadres with good knowledge and a role in early detection of stunting (100%). Cadres have sufficient knowledge and play a role in early detection of stunting, numbering 7 people (77.8%). There are 21 cadres who lack knowledge and play a role in early detection of stunting (95.5%). Conclusion: The role of cadres with less knowledge is greatest in early detection of stunting in toddlers. It is recommended that community health centers provide more information and motivation to cadres to take part in stunting early detection training programs.
Nanomedicine and regulatory science: the challenges in Africa
Authors: Nyazema N. Z. , Chanyandura J. T. , Kumar P. O.
Published: November 2023

The integrated approach in the development of nanotechnology is allowing its introduction into multiple fields, including pharmaceutical research, in which there are now several medicines containing nanomaterials or at least making nano-based claims. As a result of increasing research in nanotechnology, pre-existing medicines have been reformulated, and new medicines have been developed. This has brought challenges to the current regulatory frameworks in Europe and the United States. These regulatory agencies are known to be stringent because they have both the human capacity and skills and conducive policies and the landscape to manage new technology, unlike the agencies in most African countries. Because the European Medicines Agency (EMA) and the US Food and Drug Administration (FDA) have embraced regulatory science (RS) as a means of proactive analysis of regulatory principles, those agencies will be able to address nanomedicine challenges in a straightforward manner. African countries currently do not have a harmonized regulatory framework because different national regulatory authorities are at different levels of development. The pharmaceutical sector in Africa is facing many challenges, including the non-existence of research and development partnerships between industry, universities, and research institutions that foster nanomedicine development. Now that the African Medicine Agency (AMA) is in place, Africa should see the rapid implementation of the AU Model Law on Medical Products Regulation that will assist in putting in place capacity-building programs in nanomedicine RS.
Hybrid modeling of drop breakage in pulsed sieve tray extraction columns
Authors: Palmtag Andreas , Rousselli Johannes , Gröschl Henning , Jupke Andreas
Published: November 2023

Accurate models for pulsed sieve tray extraction columns (PSEs) depend on the correct prediction of the drop diameter to estimate extractive mass transfer across the phase boundary. Phenomenologically, the drop diameter is determined by a balance of drop breakage and coalescence. While for most industrial solvent systems, coalescence plays a minor role; breakage is mostly the dominant phenomenon determining the drop diameter. However, most modeling approaches for drop breakage in PSEs are characterized by a trade-off between a broad validity range and good prediction accuracy. To overcome this limitation, we developed a hybrid breakage model for drop breakage in PSEs in which a physical-empirical model basis is enhanced by data-driven parameter estimator models (PEMs). The hybrid model is based on a revised form of Garthe’s breakage model, for which we developed a linear PEM for the model parameters and two data-driven PEMs for dstab and d100, respectively. The hybrid breakage model was validated on 743 experimental data sets and evaluated based on the pull metric. In a sensitivity analysis, the model correctly predicted the breakage probability over a wide range of solvent properties, operating conditions, and sieve tray geometries. In future studies, the hybrid breakage model can be incorporated into extraction column models without an initial parametrization.
Decoding the mechanism of Eleutheroside E in treating osteoporosis via network pharmacological analysis and molecular docking of osteoclast-related genes and gut microbiota
Authors: Zhou Tianyu , Zhou Yilin , Ge Dongdong , Xie Youhong , Wang Jiangyan , Tang Lin , Dong Qunwei , Sun Ping
Published: November 2023

Objective

Eleutheroside E (EE) is an anti-inflammatory natural compound derived from the edible medicinal herb Acanthopanax senticosus. This study aims to investigate the underlying mechanism of the anti-osteoporosis action of EE through network pharmacology, molecular docking and gut microbiota.

Materials and methods

Network pharmacology was used to explore the potential core targets and main pathways mediated by EE in osteoporosis (OP) treatment. Molecular docking was exploited to investigate the interactions between the active anti-OP compounds in EE and the potential downstream targets. Following the multi-approach bioinformatics analysis, ovariectomy (OVX) model was also established to investigate the in vivo anti-OP effects of EE.

Results

The top 10 core targets in PPI network were TP53, AKT1, JUN, CTNNB1, STAT3, HIF1A, EP300, CREB1, IL1B and ESR1. Molecular docking results that the binding energy of target proteins and the active compounds was approximately between −5.0 and −7.0 kcal/mol, which EE has the lowest docking binding energy with HIF1A. Enrichment analysis of GO and KEGG pathways of target proteins indicated that EE treatment could potentially alter numerous biological processes and cellular pathways. In vivo experiments demonstrated the protective effect of EE treatment against accelerated bone loss, where reduced serum levels of TRAP, CTX, TNF-α, LPS, and IL-6 and increased bone volume and serum levels of P1NP were observed in EE-treated mice. In addition, changes in gut microbiota were spotted by 16S rRNA gene sequencing, showing that EE treatment increased the relative abundance of Lactobacillus and decreased the relative abundance of Clostridiaceae.

Conclusion

In summary, these findings suggested that the characteristics of multi-target and multi-pathway of EE against OP. In vivo, EE prevents the onset of OP by regulating gut microbiota and inflammatory response and is therefore a potential OP drug.
Modulatory effect of pomegranate peel extract on key regulators of ovarian cellular processes in vitro
Authors: Kolesarova Adriana , Baldovska Simona , Kohut Ladislav , Vasicek Jaromir , Ivanisova Eva , Arvay Julius , Duracka Michal , Roychoudhury Shubhadeep
Published: November 2023

In this study, response of ovarian cells (human granulosa cell line HGL5, and human adenocarcinoma cell line OVCAR-3) to short-term pomegranate peel extract (PPE) treatment (for 24 hours in cell culture) was evaluated in vitro. Quantitative and qualitative screening of polyphenols revealed punicalagins α and β as major polyphenolic components. Total phenolic content (TPC) was 93.76 mg GAE/g d.w. with a high antioxidant activity of 95.30 mg TEAC/g d.w. In OVCAR-3, PPE treatment inhibited the metabolic activity, and increased cyclin-dependent kinase 1 (CDKN1A, p21) level at the highest dose, but not in HGL5. Flow cytometry analysis could not detect any significant difference between proportions of live, dead, and apoptotic cells in both cell lines. Reactive oxygen species (ROS) revealed an antioxidant effect on HGL5, and a prooxidant effect by stimulating ROS generation in OVCAR-3 cells at the higher doses of PPE. However, in contrast to HGL5, PPE treatment decreased release of growth factors – TGF-β2 and EGF at the highest dose, as well as their receptors TGFBR2 and EGFR in OVCAR-3 cells. PPE also influenced steroidogenesis in granulosa cells HGL5 by stimulating 17β-estradiol secretion at higher doses. In conclusion, the present study highlighted the bioactive compounds in pomegranate peels and the possible mechanisms of action of PPE, shedding light on its promising role in ovarian cancer (chemo)prevention and/or management.
A deep learning technique Alexnet to detect electricity theft in smart grids
Authors: Khan Nitasha , Amir Raza Muhammad , Ara Darakhshan , Mirsaeidi Sohrab , Ali Aamir , Abbas Ghulam , Shahid Muhammad , Touti Ezzeddine , Yousef Amr , Bouzguenda Mounir
Published: November 2023

Electricity theft (ET), which endangers public safety, creates a problem with the regular operation of grid infrastructure and increases revenue losses. Numerous machine learning, deep learning, and mathematical-based algorithms are available to find ET. Still, these models do not produce the best results due to problems like the dimensionality curse, class imbalance, improper hyper-parameter tuning of machine learning and deep learning models, etc. We present a hybrid deep learning model for effectively detecting electricity thieves in smart grids while considering the abovementioned concerns. Pre-processing techniques are first employed to clean up the data from the smart meters. Then, the feature extraction technique, like AlexNet, addresses the curse of dimensionality. The effectiveness of the proposed method is evaluated through simulations using a real dataset of Chinese intelligent meters. To conduct a comparative analysis, various benchmark models are implemented as well. Our proposed model achieves accuracy, precision, recall, and F1, up to 86%, 89%, 86%, and 84%, respectively.
Metal mobility in an anaerobic-digestate-amended soil: the role of two bioenergy crop plants and their metal phytoremediation potential
Authors: Bonet-Garcia Neus , Baldasso Veronica , Robin Valentin , Gomes Carlos R. , Guibaud Gilles , Alves Maria João , Castro Ricardo , Mucha Ana Paula , Almeida C. Marisa R.
Published: November 2023

Panicum virgatum and Pennisetum alopecuroides, two non-food bioenergy crops, were evaluated for their capacity to phyto-manage trace metals (Pb, Zn, Ni, Fe, Mn, Co, Cr, and Cu) from municipal solid waste digestate after its application to a marginal soil. For that, 90-day vertical soil column mesocosm (columns with 0.6 × 0.2 m) experiments were carried out to assess 1) the impact of digestate application on the health of marginal soil, 2) plant effect on digestate-borne trace metals’ mobility along the soil profile (measuring total metal levels and fractionation in different soil layers by atomic absorption spectroscopy, and 3) plant growth performance and trace metal (Pb, Zn, and Cu) uptake capacity. The results showed that trace metals were mostly confined in the 0–0.2 m soil horizon over the course of the experimental period, migrating from the digestate-amended soil layer (0–0.1 m) to the layer underneath (0.1–0.2 m) within the first 21 days and remaining stable afterward. No evidence of the trace metals’ mobility to deeper soil layers was detected. Migration of trace metals was reduced in the presence of P. virgatum and P. alopecuroides, suggesting a phytoremediation (phytostabilization) effect. For both plant species, no trace metal accumulation in the roots was observed (bioconcentration factor <1), although both plants showed a potential for Zn translocation for aboveground tissues (translocation factor >1). The growth of both plants was positively affected by municipal solid waste digestate application, which also improved soil quality (increased concentration of total organic carbon and available phosphorus, as well as cation exchange capacity and water holding capacity).
Coral trophic pathways impact the allocation of carbon and nitrogen for egg development after bleaching
Authors: Jaffe Melissa D. , Padilla-Gamiño Jacqueline L. , Nunn Brook L. , Rodrigues Lisa J.
Published: November 2023

The persistence of coral reefs requires the survival of adult coral colonies and their continued sexual reproduction despite thermal stress. To assess the trophic pathway (i.e., autotrophy and/or heterotrophy) used to develop gametes following bleaching, we thermally stressed Montipora capitata for one month at a time when corals in Hawai’i typically experience elevated seawater temperatures. After six and nine months of recovery, we pulse-chased non-bleached and previously bleached colonies using a dual-label design to compare the allocation of carbon and nitrogen at significant stages of gamete development. Dissolved inorganic carbon- (DI13C) and nitrogen- (DI15N) labelled seawater or 13C- and 15N-labelled rotifers were used to assess the autotrophic and heterotrophic pathways, respectively. At multiple time points for up to two years later, we collected adult coral fragments and isolated host tissue, Symbiodiniaceae cells, and developing eggs and captured gamete bundles to analyze their carbon (δ13C) and nitrogen (δ15N) stable isotopes. We found that the presence of Symbiodiniaceae was important for gametogenesis in both non-bleached and previously bleached colonies in two main ways. First, autotrophically-acquired carbon and nitrogen were both allocated to gametes during development, suggesting that recovery of photosynthesis after bleaching is critical for gametogenesis. Second, only heterotrophically-acquired nitrogen, not carbon, was incorporated into gametes and was readily recycled between host tissues and Symbiodiniaceae cells. This suggests that one of the purposes of heterotrophy following coral bleaching for M. capitata may be to supplement the nitrogen pool, providing available nutrients for endosymbiotic algal growth. Allocation of carbon and nitrogen to eggs coincided with the period when vertical transmission of symbionts to gametes occurs, further supporting the important relationship between gametogenesis and availability of Symbiodiniaceae for M. capitata.
Using essential biodiversity variables to assess forest ecosystem integrity
Authors: Dias Arildo , Van Houdt Shaya , Meschin Katrin , Von Stackelberg Katherine , Bago Mari-Liis , Baldarelli Lauren , Gonzalez Downs Karen , Luuk Mariel , Delubac Timothée , Bottagisio Elio , Kasak Kuno , Kebabci Atilcan , Levers Oliver , Miilvee Igor , Paju-Hamburg Jana , Poncet Rémy , Sanfilippo Massimiliano , Sildam Jüri , Stepanov Dmitri , Karnauskaite Donalda
Published: November 2023

Introduction

An unprecedented amount of Earth Observations and in-situ data has become available in recent decades, opening up the possibility of developing scalable and practical solutions to assess and monitor ecosystems across the globe. Essential Biodiversity Variables are an example of the integration between Earth Observations and in-situ data for monitoring biodiversity and ecosystem integrity, with applicability to assess and monitor ecosystem structure, function, and composition. However, studies have yet to explore how such metrics can be organized in an effective workflow to create a composite Ecosystem Integrity Index and differentiate between local plots at the global scale.

Methods

Using available Essential Biodiversity Variables, we present and test a framework to assess and monitor forest ecosystem integrity at the global scale. We first defined the theoretical framework used to develop the workflow. We then measured ecosystem integrity across 333 forest plots of 5 km2. We classified the plots across the globe using two main categories of ecosystem integrity (Top and Down) defined using different Essential Biodiversity Variables.

Results and discussion:

We found that ecosystem integrity was significantly higher in forest plots located in more intact areas than in forest plots with higher disturbance. On average, intact forests had an Ecosystem Integrity Index score of 5.88 (CI: 5.53–6.23), whereas higher disturbance lowered the average to 4.97 (CI: 4.67–5.26). Knowing the state and changes in forest ecosystem integrity may help to deliver funding to priority areas that would benefit from mitigation strategies targeting climate change and biodiversity loss. This study may further provide decision- and policymakers with relevant information about the effectiveness of forest management and policies concerning forests. Our proposed method provides a flexible and scalable solution that facilitates the integration of essential biodiversity variables to monitor forest ecosystems.
Computational single cell oncology: state of the art
Authors: Paas-Oliveros Ernesto , Hernández-Lemus Enrique , de Anda-Jáuregui Guillermo
Published: November 2023

Single cell computational analysis has emerged as a powerful tool in the field of oncology, enabling researchers to decipher the complex cellular heterogeneity that characterizes cancer. By leveraging computational algorithms and bioinformatics approaches, this methodology provides insights into the underlying genetic, epigenetic and transcriptomic variations among individual cancer cells. In this paper, we present a comprehensive overview of single cell computational analysis in oncology, discussing the key computational techniques employed for data processing, analysis, and interpretation. We explore the challenges associated with single cell data, including data quality control, normalization, dimensionality reduction, clustering, and trajectory inference. Furthermore, we highlight the applications of single cell computational analysis, including the identification of novel cell states, the characterization of tumor subtypes, the discovery of biomarkers, and the prediction of therapy response. Finally, we address the future directions and potential advancements in the field, including the development of machine learning and deep learning approaches for single cell analysis. Overall, this paper aims to provide a roadmap for researchers interested in leveraging computational methods to unlock the full potential of single cell analysis in understanding cancer biology with the goal of advancing precision oncology. For this purpose, we also include a notebook that instructs on how to apply the recommended tools in the Preprocessing and Quality Control section.
Profound N-glycan remodelling accompanies MHC-II immunopeptide presentation
Authors: Goodson Hayley , Kawahara Rebeca , Chatterjee Sayantani , Goncalves Gabriel , Fehring Joshua , Purcell Anthony W. , Croft Nathan P. , Thaysen-Andersen Morten
Published: November 2023

Immunopeptidomics, the study of peptide antigens presented on the cell surface by the major histocompatibility complex (MHC), offers insights into how our immune system recognises self/non-self in health and disease. We recently discovered that hyper-processed (remodelled) N-glycans are dominant features decorating viral spike immunopeptides presented via MHC-class II (MHC-II) molecules by dendritic cells pulsed with SARS-CoV-2 spike protein, but it remains unknown if endogenous immunopeptides also undergo N-glycan remodelling. Taking a multi-omics approach, we here interrogate published MHC-II immunopeptidomics datasets of cultured monocyte-like (THP-1) and breast cancer-derived (MDA-MB-231) cell lines for overlooked N-glycosylated peptide antigens, which we compare to their source proteins in the cellular glycoproteome using proteomics and N-glycomics data from matching cell lines. Hyper-processed chitobiose core and paucimannosidic N-glycans alongside under-processed oligomannosidic N-glycans were found to prevalently modify MHC-II-bound immunopeptides isolated from both THP-1 and MDA-MB-231, while complex/hybrid-type N-glycans were (near-)absent in the immunopeptidome as supported further by new N-glycomics data generated from isolated MHC-II-bound peptides derived from MDA-MB-231 cells. Contrastingly, the cellular proteomics and N-glycomics data from both cell lines revealed conventional N-glycosylation rich in complex/hybrid-type N-glycans, which, together with the identification of key lysosomal glycosidases, suggest that MHC-II peptide antigen processing is accompanied by extensive N-glycan trimming. N-glycan remodelling appeared particularly dramatic for cell surface-located glycoproteins while less remodelling was observed for lysosomal-resident glycoproteins. Collectively, our findings indicate that both under- and hyper-processed N-glycans are prevalent features of endogenous MHC-II immunopeptides, an observation that demands further investigation to enable a better molecular-level understanding of immune surveillance.
The impact of aging and oxidative stress in metabolic and nervous system disorders: programmed cell death and molecular signal transduction crosstalk
Authors: Maiese Kenneth
Published: November 2023

Life expectancy is increasing throughout the world and coincides with a rise in non-communicable diseases (NCDs), especially for metabolic disease that includes diabetes mellitus (DM) and neurodegenerative disorders. The debilitating effects of metabolic disorders influence the entire body and significantly affect the nervous system impacting greater than one billion people with disability in the peripheral nervous system as well as with cognitive loss, now the seventh leading cause of death worldwide. Metabolic disorders, such as DM, and neurologic disease remain a significant challenge for the treatment and care of individuals since present therapies may limit symptoms but do not halt overall disease progression. These clinical challenges to address the interplay between metabolic and neurodegenerative disorders warrant innovative strategies that can focus upon the underlying mechanisms of aging-related disorders, oxidative stress, cell senescence, and cell death. Programmed cell death pathways that involve autophagy, apoptosis, ferroptosis, and pyroptosis can play a critical role in metabolic and neurodegenerative disorders and oversee processes that include insulin resistance, β-cell function, mitochondrial integrity, reactive oxygen species release, and inflammatory cell activation. The silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1), AMP activated protein kinase (AMPK), and Wnt1 inducible signaling pathway protein 1 (WISP1) are novel targets that can oversee programmed cell death pathways tied to β-nicotinamide adenine dinucleotide (NAD+), nicotinamide, apolipoprotein E (APOE), severe acute respiratory syndrome (SARS-CoV-2) exposure with coronavirus disease 2019 (COVID-19), and trophic factors, such as erythropoietin (EPO). The pathways of programmed cell death, SIRT1, AMPK, and WISP1 offer exciting prospects for maintaining metabolic homeostasis and nervous system function that can be compromised during aging-related disorders and lead to cognitive impairment, but these pathways have dual roles in determining the ultimate fate of cells and organ systems that warrant thoughtful insight into complex autofeedback mechanisms.
The microneme adhesive repeat domain of MIC3 protein determined the site specificity of Eimeria acervulina, Eimeria maxima, and Eimeria mitis
Authors: Zhang Yang , Lu Mingmin , Zhang Zhenchao , Huang Xinmei , Huang Jingwei , Liu Jiabin , Huang Jianmei , Song Xiaokai , Xu Lixin , Yan Ruofeng , Li Xiangrui
Published: November 2023

Understanding the determinants of host and tissue tropisms among parasites of veterinary and medical importance has long posed a substantial challenge. Among the seven species of Eimeria known to parasitize the chicken intestine, a wide variation in tissue tropisms has been observed. Prior research suggested that microneme protein (MIC) composed of microneme adhesive repeat (MAR) domain responsible for initial host cell recognition and attachment likely dictated the tissue tropism of Eimeria parasites. This study aimed to explore the roles of MICs and their associated MARs in conferring site-specific development of E. acervuline, E. maxima, and E. mitis within the host. Immunofluorescence assays revealed that MIC3 of E. acervuline (EaMIC3), MIC3 of E. maxima (EmMIC3), MIC3 of E. mitis (EmiMIC3), MAR3 of EaMIC3 (EaMIC3-MAR3), MAR2 of EmMIC3 (EmMIC3-MAR2), and MAR4 of EmiMIC3 (EmiMIC3-MAR4), exhibited binding capabilities to the specific intestinal tract where these parasites infect. In contrast, the invasion of sporozoites into host intestinal cells could be significantly inhibited by antibodies targeting EaMIC3, EmMIC3, EmiMIC3, EaMIC3-MAR3, EmMIC3-MAR2, and EmiMIC3-MAR4. Substitution experiments involving MAR domains highlighted the crucial roles of EaMIC3-MAR3, EmMIC3-MAR2, and EmiMIC3-MAR4 in governing interactions with host ligands. Furthermore, animal experiments substantiated the significant contribution of EmiMIC3, EmiMIC3-MAR4, and their polyclonal antibodies in conferring protective immunity to Eimeria-affiliated birds. In summary, EaMIC3, EmMIC3, and EmiMIC3 are the underlying factors behind the diverse tissue tropisms exhibited by E. acervuline, E. maxima, and E. mitis, and EaMIC3-MAR3, EmMIC3-MAR2, and EmiMIC3-MAR4 are the major determinants of MIC-mediated tissue tropism of each parasite. The results illuminated the molecular basis of the modes of action of Eimeria MICs, thereby facilitating an understanding and rationalization of the marked differences in tissue tropisms among E. acervuline, E. maxima, and E. mitis.
Metabolic scaling variation as a constitutive adaptation to tide level in Mytilus galloprovincialis
Authors: Pérez-Cebrecos Maitane , Berrojalbiz Xabier , Izagirre Urtzi , Ibarrola Irrintzi
Published: November 2023

Understanding how allometric exponents vary in the different biologically determined patterns turns out to be fundamental for the development of a unifying hypothesis that intends to explain most of the variation among taxa and physiological states. The aims of this study were (i) to analyze the scaling exponents of oxygen consumption at different metabolic rates in Mytilus galloprovincialis according to different seasons, habitat, and acclimation to laboratory conditions and (ii) to examine the variation in shell morphology depending on habitat or seasonal environmental hazards. The allometric exponent for standard metabolic rate (b value) did not vary across seasons or tide level, presenting a consistent value of 0.644. However, the mass-specific standard oxygen consumption (a value), i.e. metabolic level, was lower in intertidal mussels (subtidal mussels: a = - 1.364; intertidal mussels: a = - 1.634). The allometric exponent for routine metabolic rate changed significantly with tide level: lower allometric exponents for intertidal mussels (b = 0.673) than for subtidal mussels (b = 0.871). This differential response did not change for at least two months after the environmental cue was removed. We suggest that this is the result of intertidal mussels investing fundamentally in surface-dependent organs (gill and shell), with the exception of the slightly higher values obtained in May as a likely consequence of gonadal tissue development. Subtidal mussels, on the contrary, are probably in constant demand for volume-related resources, which makes them consistently obtain an allometric exponent of around 0.87.
Polyimide aerogel/aramid fiber composite with high mechanical strength and thermal insulation for thermal protective clothing
Authors: Liu Yuhang , Wang Donglin , Li Jie
Published: November 2023

Polyimide (PI) aerogel, as a new organic aerogel material, has the excellent thermal properties of polyimide and the characteristic of high thermal insulation of aerogels, and has gained increasing attention. In this work, using PI aerogel as the matrix material and aramid fiber as the reinforcement material, controllable flexible PI aerogel/aramid fiber composite insulation materials were successfully prepared by freeze-drying and soft treatment. This study sought to determine how the mass percentage of PI aerogel affected the microstructure, mechanical characteristics, thermal insulation capabilities, and thermal comfort of clothes in PI aerogel/aramid fiber composites. To achieve this, the preparation process of PI aerogel was optimized, and the effects of different mass fractions of PI aerogel on the properties of the composite material were evaluated. The results demonstrated that increasing the mass fraction of PI aerogel led to improvements in the mechanical properties, flexibility, and heat insulation properties of the composite material. Furthermore, the PI aerogel/aramid fiber composite offered enhanced thermal comfort to the wearer in hot and humid environments, indicating that the composite material is particularly suited for thermal insulation applications.
Diversity recovery and probiotic shift of gastric microbiota in functional dyspepsia patients after Helicobacter pylori eradication therapy
Authors: Wang Wenxue , Liu Zhongjian , Zhang Yu , Guo Zhiping , Liu Jieyu , Li Siyun , Huang Jihua , Geng Jiawei , Zhang Fan , Guo Qiang
Published: November 2023

The effects of Helicobacter pylori eradication on gastric mucosa-colonizing microbes in patients with functional dyspepsia (FD) remain unclear. Here, we explored microbial variation induced by H. pylori infection and eradication treatment in FD patients. Gastric microbial abundance and diversity were significantly reduced in the H. pylori-infected FD patients. Eradication treatment increased alpha and beta diversity of gastric mucosa-colonizing microbes, and promoted the expansion of several probiotic microbes, such as Leuconostoc mesenteroides, which exhibited a matched antagonistic performance against H. pylori. Significant variation was observed in gastric mucosa-colonizing microbes between H. pylori-positive and H. pylori-negative FD patients. Eradication treatment induced microbial diversity recovery and may provide sufficient nutrition and space for probiotic microbes, such as Leuconostoc mesenteroides.
Increased cranio-caudal spinal cord oscillations are the cardinal pathophysiological change in degenerative cervical myelopathy
Authors: Pfender Nikolai , Rosner Jan , Zipser Carl M. , Friedl Susanne , Schubert Martin , Sutter Reto , Klarhoefer Markus , Spirig José M. , Betz Michael , Freund Patrick , Farshad Mazda , Curt Armin , Hupp Markus
Published: November 2023

Introduction

Degenerative cervical myelopathy (DCM) is the most common cause of non-traumatic incomplete spinal cord injury, but its pathophysiology is poorly understood. As spinal cord compression observed in standard MRI often fails to explain a patient's status, new diagnostic techniques to assess DCM are one of the research priorities. Minor cardiac-related cranio-caudal oscillations of the cervical spinal cord are observed by phase-contrast MRI (PC-MRI) in healthy controls (HCs), while they become pathologically increased in patients suffering from degenerative cervical myelopathy. Whether transversal oscillations (i.e., anterior–posterior and right–left) also change in DCM patients is not known.

Methods

We assessed spinal cord motion simultaneously in all three spatial directions (i.e., cranio-caudal, anterior–posterior, and right–left) using sagittal PC-MRI and compared physiological oscillations in 18 HCs to pathological changes in 72 DCM patients with spinal canal stenosis. The parameter of interest was the amplitude of the velocity signal (i.e., maximum positive to maximum negative peak) during the cardiac cycle.

Results

Most patients suffered from mild DCM (mJOA score 16 (14–18) points), and the majority (68.1%) presented with multisegmental stenosis. The spinal canal was considerably constricted in DCM patients in all segments compared to HCs. Under physiological conditions in HCs, the cervical spinal cord oscillates in the cranio-caudal and anterior–posterior directions, while right–left motion was marginal [e.g., segment C5 amplitudes: cranio-caudal: 0.40 (0.27–0.48) cm/s; anterior–posterior: 0.18 (0.16–0.29) cm/s; right–left: 0.10 (0.08–0.13) cm/s]. Compared to HCs, DCM patients presented with considerably increased cranio-caudal oscillations due to the cardinal pathophysiologic change in non-stenotic [e.g., segment C5 amplitudes: 0.79 (0.49–1.32) cm/s] and stenotic segments [.g., segment C5 amplitudes: 0.99 (0.69–1.42) cm/s]). In contrast, right–left [e.g., segment C5 amplitudes: non-stenotic segment: 0.20 (0.13–0.32) cm/s; stenotic segment: 0.11 (0.09–0.18) cm/s] and anterior–posterior oscillations [e.g., segment C5 amplitudes: non-stenotic segment: 0.26 (0.15–0.45) cm/s; stenotic segment: 0.11 (0.09–0.18) cm/s] remained on low magnitudes comparable to HCs.

Conclusion

Increased cranio-caudal oscillations of the cervical cord are the cardinal pathophysiologic change and can be quantified using PC-MRI in DCM patients. This study addresses spinal cord oscillations as a relevant biomarker reflecting dynamic mechanical cord stress in DCM patients, potentially contributing to a loss of function.
Predicting short-term outcomes in atrial-fibrillation-related stroke using machine learning
Authors: Jeon Eun-Tae , Jung Seung Jin , Yeo Tae Young , Seo Woo-Keun , Jung Jin-Man
Published: November 2023

Background

Prognostic prediction and the identification of prognostic factors are critical during the early period of atrial-fibrillation (AF)-related strokes as AF is associated with poor outcomes in stroke patients.

Methods

Two independent datasets, namely, the Korean Atrial Fibrillation Evaluation Registry in Ischemic Stroke Patients (K-ATTENTION) and the Korea University Stroke Registry (KUSR), were used for internal and external validation, respectively. These datasets include common variables such as demographic, laboratory, and imaging findings during early hospitalization. Outcomes were unfavorable functional status with modified Rankin scores of 3 or higher and mortality at 3 months. We developed two machine learning models, namely, a tree-based model and a multi-layer perceptron (MLP), along with a baseline logistic regression model. The area under the receiver operating characteristic curve (AUROC) was used as the outcome metric. The Shapley additive explanation (SHAP) method was used to evaluate the contributions of variables.

Results

Machine learning models outperformed logistic regression in predicting both outcomes. For 3-month unfavorable outcomes, MLP exhibited significantly higher AUROC values of 0.890 and 0.859 in internal and external validation sets, respectively, than those of logistic regression. For 3-month mortality, both machine learning models exhibited significantly higher AUROC values than the logistic regression for internal validation but not for external validation. The most significant predictor for both outcomes was the initial National Institute of Health and Stroke Scale.

Conclusion

The explainable machine learning model can reliably predict short-term outcomes and identify high-risk patients with AF-related strokes.