bluuebunny/crossref_metadata_2025 huggingface dataset:
Supervised and unsupervised mapping of binary variables: a proximity perspective
Authors: de Rooij Mark , Woestenburg Dion , Busing Frank
Published: January 2025

We propose a new mapping tool for supervised and unsupervised analysis of multivariate binary data with multiple items, questions, or response variables. The mapping assumes an underlying proximity response function, where participants can have multiple reasons to disagree or say “no” to a question. The probability to endorse, or to agree with an item depends on an item specific parameter and the distance in a joint space between a point representing the item and a point representing the participant. The item specific parameter defines a circle in the joint space around the location of the item such that for participants positioned within the circle the endorsement probability is larger than 0.5. For map estimation, we develop and test an MM-algorithm in which the negative log-likelihood function is majorized with a weighted least squares function. The weighted least squares function can be minimized with standard algorithms for multidimensional unfolding. To illustrate the new mapping, two empirical data sets are analyzed. The mappings are interpreted in detail and the unsupervised map is compared to a visualization based on correspondence analysis. In a Monte Carlo study, we test the performance of the algorithm in terms of recovery of population parameters and conclude that this recovery is adequate. A second Monte Carlo study investigates the predictive performance of the new mapping compared to a similar mapping with a monotone response function.
drSMALL: Database for disease resistance-shaping small molecules derived from the plant microbiome
Authors: Cheng Rui , Ke Tingli , Gui Fangze , Li Junnan , Zhang Xiaoyan , Vílchez Juan Ignacio , Matsumoto Haruna
Published: January 2025

Recent evidence highlights the potential of the plant microbiota to increase host plant disease resistance through the production of bioactive small molecules. However, the absence of comprehensive platforms for rapid access to this information hampers progress in the field. To address this gap, we developed the Disease Resistance-Shaping Small Molecules Database (drSMALL), a freely accessible and continuously updated resource that compiles profiles of microbial small molecules, which were experimentally evidenced to be associated with host disease resistance. drSMALL interlinks detailed information on microbial species, the small molecules they produce, host plants, and targeted pathogens, facilitating streamlined access to essential data. This initiative aims to advance the understanding of small molecules in disease resistance, filling a critical gap in data accessibility while fostering deeper exploration of sustainable agricultural practices. By leveraging the natural capabilities of plant microbiomes, drSMALL seeks to support innovative strategies for enhancing crop health and resilience against diseases.
A NOTE ON CONTINUOUS FUNCTIONS ON METRIC SPACES
Authors: SANDERS SAM
Published: January 2025

Continuous functions on the unit interval are relatively tame from the logical and computational point of view. A similar behaviour is exhibited by continuous functions on compact metric spaces equipped with a countable dense subset. It is then a natural question what happens if we omit the latter ‘extra data’, i.e., work with ‘unrepresented’ compact metric spaces. In this paper, we study basic third-order statements about continuous functions on such unrepresented compact metric spaces in Kohlenbach’s higher-order Reverse Mathematics. We establish that some (very specific) statements are classified in the (second-order) Big Five of Reverse Mathematics, while most variations/generalisations are not provable from the latter, and much stronger systems. Thus, continuous functions on unrepresented metric spaces are ‘wild’, though ‘more tame’ than (slightly) discontinuous functions on the reals.
Evaluating translational science knowledge gains following an online short course for a general scientific audience
Authors: Vogel Amanda L. , Hussain Shadab F. , Faupel-Badger Jessica M.
Published: January 2025

Purpose:

The translational science workforce requires preparation in both core skills for biomedical research and competencies for advancing progress along the translational pipeline. Delivering this content in a highly accessible manner will help expand and diversify the workforce.

Methods:

The NCATS Education Branch offers online case study-based courses in translational science for a general scientific audience. The branch updated its course in preclinical translational science with additional content aligned with the NCATS Translational Science Principles, which characterize effective approaches to advance translation. The updated course was offered in 2021 and 2022. The branch also revised the course evaluation to capture knowledge change aligned with the NCATS Translational Science Principles.

Results:

Of 106 students, 88 completed baseline or endpoint surveys, with 48 completing both. Most found the online format (n = 48; 91%) and case study approach (n = 48; 91%) effective. There was a statistically significant increase in knowledge related to the Translational Science Principles (p < 0.001). Survey items with the highest endpoint scores reflected the principles on creativity and innovation, efficiency, cross-disciplinary team science, and boundary-crossing collaborations. Findings highlighted the effectiveness of pairing a case study with lectures that offer generalizable strategies aligned with the translational science principles. Students reported the course helped them learn about the trajectory of a drug discovery and development initiative, where their own work fit in, and scientific and operational approaches to apply in their own work.

Conclusions:

This online case study-based course was effective in teaching generalizable principles for translational science to students with varied scientific backgrounds.
The party politics of diplomatic engagements: evidence from Italy
Authors: Corda Tiziana , Casiraghi Matteo C.M.
Published: January 2025

Leaders decide to engage diplomatically with their foreign peers for various reasons but, given their limited time and resources, they have to choose which peers to prioritize. As such, the study of international diplomatic visits helps shed light on a government's foreign policy approach and better understand its priorities in how it conceives and builds foreign relations. While the literature on diplomatic engagements has largely debated its drivers and effects, the role of domestic influences, in particular of party politics, has remained understudied. We address this gap and investigate the party politics of diplomatic engagements leveraging a new dataset on Italy's high-level international bilateral diplomatic visits in 2000–2023. Our findings show that partisan differences influence not only the overall frequency of such engagements, following curvilinear left–right patterns, but also the political regimes that left- and right-wing governments prioritize in such endeavours, exposing the lower importance right-wing parties assign to democratic principles when managing their countries' foreign relations, as these governments are systematically more likely to interact with authoritarian regimes than with democracies.
A conceptual replication of an implicit test of grammatical gender effects on inanimate concepts
Authors: Mahajan Devyani , Durgin Frank H.
Published: January 2025

It has been argued that the incidental and arbitrary use of gender markings for inanimate concepts in language may affect the conceptualization or semantics of those inanimate concepts. The present article sought to replicate the findings of a classic paper that made this argument. Konishi used the potency dimension of the semantic differential method as an implicit measure of perceived gender. He reported that words for inanimate concepts of masculine grammatical gender were rated as higher in potency than words for the same concepts that had feminine grammatical gender. Two preregistered replication studies are reported here. The first was a conceptual replication of Konishi’s study that was conducted with 240 bilingual native speakers of either German or Spanish. Included in the study was a follow-up with 120 monolingual native English speakers. This data was used to test whether the grammatical gender in the native languages of German and Spanish speakers affected their sense of the potency of common inanimate categories when tested in a second language (English) in which they were fluent and the nouns had no grammatical gender. A second version of the study was conducted in the native languages of Spanish and German speakers, as a closer attempt at a replication of Konishi’s original study. The results of both studies provided evidence against the grammatical-gender hypothesis. Bayesian tests of both studies strongly favored the null hypothesis that there were no grammatical gender effects on implicit measures of perceived potency.
Death on “live broadcast”—fish mortichnia from the Upper Cretaceous plattenkalk of Lebanon
Authors: Pokorný Richard , Nohra Roy , Abi Saad Pierre , Vallon Lothar H.
Published: January 2025

Proper identification of behavioral patterns is an important prerequisite for the identification of any trace fossil and even more so for its interpretation. For the last 70 yr, the continually advancing state of ichnological knowledge has led to a gradual recognition of recurrent patterns of organismal behavior documented in the fossil record, which in turn gave rise to the ethological categories. “Mortichnia” was proposed for traces created during a death struggle of the tracemaker but has been reported only in a few cases. Fish mortichnia so far have only been reported in one specimen recovered from the Upper Jurassic Plattenkalk of Nusplingen (SW Germany). The category mortichnia is refined herein, but remains ambiguous. Eight newly discovered unique specimens of mortichnia from Upper Cretaceous marine sediments in central Lebanon (Haqil, En Nammoura) are preserved together with their tracemakers and described herein. In addition, 14 further incomplete specimens were collected where no tracemakers are present. However, morphology and close provenance allow them to be assigned to the same ichnotaxon.

The Lebanese mortichnia originate from fish that were subjected to significant environmental or individual stress leading to their deaths. During death convulsions, their bodies created sedimentary structures with a specific recurring morphology. The ichnogenus Pinnichnus n. igen. with ichnospecies P. haqilensis and P. emmae n. ispp. is proposed for these specimens.
Sinistroporomonorchis bolini n. sp. (Trematoda: Monorchiidae) from the Ocellated killifish, Floridichthys polyommus (Cyprinodontidae) in the Yucatán Peninsula, Mexico based on an integrative taxonomy analysis
Authors: Andrade-Gómez Leopoldo , Espínola-Novelo Juan F. , Solórzano-García Brenda , Pérez-Ponce de León Gerardo
Published: January 2025

Members of Sinistroporomonorchis Wee, Cutmore, Pérez-del-Olmo & Cribb, 2020 represent a small group of trematodes belonging to the Monorchiidae Odhner, 1911 with 5 species described from mugilid hosts. Specimens consistent with the generic concept of Sinistroporomonorchis were obtained from Floridichthys polyommus (Cyprinodontidae); most of them were juveniles from 4 localities within the Yucatán Peninsula. After a detailed morphological examination including scanning electron microscopy images and a principal component analysis, the specimens collected represented a new species, Sinistroporomonorchis bolini n. sp. The new species can be differentiated by the presence of an overall large pharynx including the proportion of pharynx width to oral sucker width, a uterus arranged in 2 main lateral fields, and by presenting robust caeca. In addition, sequences of the 28S of large subunit of nuclear ribosomal RNA and cox1 of the mitochondrial DNA were obtained. Phylogenetic trees inferred from each dataset, placed all the specimens in a monophyletic clade, confirming that the isolates belonged to the same species. The new species is the sixth described for the genus Sinistroporomonorchis, the fifth described from the Yucatán Peninsula and the first described from a non-mugilid host.
How Much Does Suffering Matter?
Authors: Kious Brent M.
Published: January 2025

Ethicists frequently suppose that suffering has special moral significance. It is often claimed that a main goal of medicine—perhaps its primary goal—is the alleviation of human suffering. Following Eric Cassell and others, this essay considers suffering understood as the experience of distress—negative emotions—in response to threats to something that one cares about. It examines whether, on this value-based account of suffering, we should accept the claim that suffering has special moral significance. It argues that we should not: suffering does not add significantly to the value of other human interests and rarely changes our moral obligations itself; it merely seems to have strong moral relevance because it often attends to interests that matter. This is because negative emotions themselves have only limited moral significance, which is due to the fact that their primary mental role is to indicate to us the relative importance of non-emotional goods.
Assessment of psychometric properties of the Persian version of the spiritual care competency self-assessment tool
Authors: Jalali Amir , Merati Fashi Fatemeh , Karami Mohammad , Kalhory Parnia , Mardani Taghvostani Nazanin , Moradi Khalil
Published: January 2025

Background

Spiritual care is essential for the health and well-being of patients and their families, so nursing and midwifery students should have professional competency in this field.

Objectives

The present study aimed to translate the Spiritual Care Competency Self-Assessment Tool for nursing and midwifery students into Persian and evaluate its psychometric properties.

Methods

This study has a methodological study design.

Methods measures

The present study was conducted from July 4 to November 19, 2023, at the Faculty of Nursing and Midwifery in west of Iran. The tool was translated into Persian using the forward-backward translation method. The construct validity was examined using exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) with a total of 536 nursing and midwifery students. The internal consistency was assessed using Cronbach’s alpha coefficient. Also, the reliability of the tool was evaluated using the test–retest method. SPSS version 26 and Lisrel version 8 software were used in this study.

Results

Face and content validity was confirmed quantitatively and qualitatively. The results of EFA and CFA confirmed the tool with 4 factors and 28 items. CFA results indicated a well-fitting model (comparative fit index [CFI] = .97, Non-Normed Fit Index (NNFI) = .92, goodness of fit index [GFI] = .91, root mean square error of approximation [RMSEA] = .05, Standardized Root Mean Square Residual (SRMR) = .046). Pearson’s correlation coefficient confirmed a significant relationship between items, subscales, and the main scale. Also, Cronbach’s alpha coefficient (.968) and test–retest (.867) confirmed the reliability of the Persian version of the tool.

Conclusion

The present study showed that the Persian version of the EPICC Spiritual Care, with 4 factors and 28 items, was suitable for validation and that its psychometric properties were acceptable according to COSMIN criteria. In general, the results showed that the Persian version of the EPICC Spiritual Care is a valid and reliable tool that students, preceptors, and educators can use in clinical settings as a practical way of discussing and evaluating spiritual care competency in Iran.
Cosmology of belonging: The role of community in the therapeutic use of psychedelics
Authors: Dorsen Caroline , Noero Lola , Knapp Michelle , Arden Kristin , Rosa William E
Published: January 2025

Background

The recent wave of clinical trials of psychedelic substances among patients with life-limiting illness has largely focused on individual healing. This most often translates to a single patient receiving an intervention with researchers guiding them. As social isolation and lack of connection are major drivers of current mental health crises and group work is expected to be an important aspect of psychedelic assisted psychotherapy, it is essential that we understand the role of community in psychedelic healing.

Objectives

To explore how psychedelic guides in the United States discuss the role of “community” in naturalistic psychedelic groups.

Methods

This is a secondary qualitative data study of data from a larger modified ethnographic study of psychedelic plant medicine use in the US. Fifteen facilitators of naturalistic psychedelic groups were recruited via snowball sampling. Content analysis was used to identify themes.

Results

Participants viewed the concept of community as essential to every aspect of psychedelic work, from the motivation to use psychedelics, to the psychedelic dosing experience and the integration of lessons learned during psychedelic experiences into everyday life. Themes and subthemes were identified. Theme 1: The arc of healing through community (Subthemes: Community as intention, the group psychedelic journey experience, community and integration); Theme 2: Naturally occurring psychedelic communities as group therapy (Subthemes [as described in Table 2]: Belonging, authenticity, corrective experience, trust, touch).

Significance

Results suggest that existing knowledge about therapeutic group processes may be helpful in structuring and optimizing group psychedelic work. More research is needed on how to leverage the benefit of community connection in the therapeutic psychedelic context, including size and composition of groups, selection and dosing of psychedelic substances in group settings, facilitator training, and role of community integration. Psychedelic groups may provide benefits that individual work does not support.
Temperature Anomalies During Late Boreal Winters With and Without Sudden Stratospheric Warming
Authors: Vokhmyanin Mikhail , Asikainen Timo , Salminen Antti , Mursula Kalevi
Published: January 2025

The polar stratosphere in the Northern Hemisphere influences wintertime surface weather across Northern Eurasia, Eastern Canada, the Middle East, and the Eastern United States. This influence is pronounced following sudden stratospheric warmings (SSWs), during which the polar vortex is displaced from the pole or collapses. The surface impacts vary considerably and are challenging to predict. Here, we study the extratropical surface temperature anomalies in winters with and without SSW. Our analysis reveals a statistically significant surface impact of SSWs is observed in February and March, particularly when the Quasi‐Biennial Oscillation (QBO) is in the easterly phase. During the westerly QBO phases, the SSW surface impact is less systematic. Surface anomalies in winters without SSW are also more pronounced in the late phase of eQBO winters. We further demonstrate that seasonal forecasts of SSW probability can be used to predict regional temperature anomalies especially in Northern Europe.
Storm‐Time Ring Current Plasma Pressure Prediction Based on the Multi‐Output Convolutional Neural Network Model
Authors: Yan Yun , Xie Zi‐Kang , Yue Chao , Zhao Jiu‐Tong , Yang Fan , Xie Lun , Zong Qiu‐Gang , Zhou Xu‐Zhi , Wang Shan
Published: January 2025

The terrestrial ring current consists of particles with energy from several keV to 100 s of keV, and its enhancement will result in magnetic field depression, known as geomagnetic storms. The ring current is mainly composed of H+, O+, He+, and electrons, and there has been a longstanding debate regarding their relative contributions. In this study, we employed a multi‐output convolutional neural network to predict the storm‐time ring current plasma pressures of these particles. Taking solar wind parameters, interplanetary magnetic field (IMF) data, and geomagnetic indices with a time history of 3 days as input parameters, the model shows good performances for electron plasma pressure, H+ plasma pressure, He+ plasma pressure, and O+ plasma pressure in both quiet‐time and storm‐time periods, with high correlation coefficients and small root mean square errors between the measured and the predicted values. Our model successfully captures ring current enhancement during the storm main phase and species‐dependent decay during the recovery phase. Moreover, the model's ability to predict plasma pressures of different species simultaneously facilitates a comparative analysis of their respective contributions to the ring current. The storm event where our model was applied demonstrates that during the storm, the contribution of H+ decreases but still dominates, while the contribution of O+ increases dramatically, and electrons and He+ also play roles in some localized regions. The application of this model is in line with previous observations and simulations, which can be utilized for quantitative analysis of storm‐time ring current dynamics.
GnIH secreted by green light exposure, regulates bone mass through the activation of Gpr147
Authors: You Yu , Huo Konglin , He Liang , Wang Tongyue , Zhao Lei , Li Rong , Cheng Xiaoqing , Ma Xuebin , Yue Zhiying , Siwko Stefan , Wang Ning , Liao Lujian , Liu Mingyao , Luo Jian
Published: January 2025

Reproductive hormones associated with the hypothalamic-pituitary-gonadal (HPG) axis are closely linked to bone homeostasis. In this study, we demonstrate that Gonadotropin inhibitory hormone (GnIH, one of the key reproductive hormones upstream of the HPG axis) plays an indispensable role in regulating bone homeostasis and maintaining bone mass. We find that deficiency of GnIH or its receptor Gpr147 leads to a significant reduction in bone mineral density (BMD) in mice primarily by enhancement of osteoclast activation in vivo and in vitro. Mechanistically, GnIH/Gpr147 inhibits osteoclastogenesis by the PI3K/AKT, MAPK, NF-κB and Nfatc1 signaling pathways. Furthermore, GnIH treatment was able to alleviate bone loss in aging, ovariectomy (OVX) or LPS-induced mice. Moreover, the therapy using green light promotes the release of GnIH and rescues OVX-induced bone loss. In humans, serum GnIH increases and bone resorption markers decrease after green light exposure. Therefore, our study elucidates that GnIH plays an important role in maintaining bone homeostasis via modulating osteoclast differentiation and demonstrates the potential of GnIH therapy or green light therapy in preventing osteoporosis.
TRAF2 and RIPK1 redundantly mediate classical NFκB signaling by TNFR1 and CD95-type death receptors
Authors: Wagner Jennifer , Vredevoogd David , Yu Xin , Lu Dong , Peeper Daniel S. , Hermanns Heike M. , Wang Jin , Wajant Harald , Siegmund Daniela
Published: January 2025

This study suggests a modified model of TNFR1-induced complex I-mediated NFκB signaling. Evaluation of a panel of five tumor cell lines (HCT116-PIK3CAmut, SK-MEL-23, HeLa-RIPK3, HT29, D10) with TRAF2 knockout revealed in two cell lines (HT29, HeLa-RIPK3) a sensitizing effect for death receptor-induced necroptosis and in one cell line (D10) a mild sensitization for TNFR1-induced apoptosis. TRAF2 deficiency inhibited death receptor-induced classical NFκB-mediated production of IL-8 only in a subset of cell lines and only partly. TRAF5, furthermore, failed to improve DR-induced NFκB signaling in HCT116-PIK3CAmut and HCT116-PIK3CAmut-TRAF2KO cells. These findings argue for a non-obligatory role of TRAF2 in death receptor-induced classical NFκB signaling. Similar as in TRAF2-deficient cells, TNF- and CD95L-induced NFκB signaling was found to be only poorly affected in RIPK1KO cells and in cells treated with the RIPK1-specific PROTAC LD4172. Intriguingly, however, death receptor-induced NFκB signaling was completely inhibited in HCT116-PIK3CAmut cells double deficient for TRAF2 and RIPK1 and in TRAF2-deficient cells treated with LD4172. Moreover, with exception of recruitment of TRADD, acting upstream to TRAF2 and parallel to RIPK1, TNFR1 signaling complex formation was abrogated in TRAF2-RIPK1 DKO cells. Based on our findings, two distinguishable types of TNFR1-interacting complexes promote TNF-induced NFκB signaling: First, a TRADD-TRAF2/cIAP utilizing complex Ia which becomes evident in RIPK1-deficient cells. Second, a non-modified RIPK1 utilizing complex Ib which acts in TRADD- or TRAF2-deficient cells. Complex Ia and Ib may furthermore interact and cooperate to ubiquitinate RIPK1 resulting in a modified complex Ia/b preventing complex Ia and Ib to convert to the established TNFR1-induced cytotoxic complexes IIa and IIb.
Role of the androgen receptor in melanoma aggressiveness
Authors: Di Donato Marzia , Cristiani Costanza Maria , Capone Mariaelena , Garofalo Cinzia , Madonna Gabriele , Passacatini Lucia Carmela , Ottaviano Margaret , Ascierto Paolo Antonio , Auricchio Ferdinando , Carbone Ennio , Migliaccio Antimo , Castoria Gabriella
Published: January 2025

Malignant melanoma represents the fifth most common cancer in the world and its incidence is rising. Novel therapies targeting receptor tyrosine kinases, kinases and immune checkpoints have been employed with a significant improvement of the overall survival and long-term disease containment. Nevertheless, the disease often progresses and becomes resistant to the therapies. As such, the discovery of new targets and drugs for advanced melanoma still remains a difficult task. Gender disparities, with a female advantage in melanoma incidence and outcome, have been reported. Although emerging studies support the pro-tumorigenic role of androgen/androgen receptor axis in melanoma, the molecular bases of such evidence are still under intense investigation. We now report that ligand activation of the androgen receptor drives melanoma invasiveness and its escape from natural killer-mediated cytotoxic effect. By combining different experimental approaches, we observe that melanoma escape is mediated by the androgen-triggered shedding of the surface molecule MICA. Specific blockade of ADAM10 or androgen receptor impairs the androgen-induced MICA shedding and melanoma immune-escape. Further, the increase in MICA serum levels correlates with a poor outcome in melanoma patients treated with the anti-PD-1 monoclonal antibody, pembrolizumab. At last, melanoma cells depleted of the androgen receptor become more responsive to the most commonly used immunocheckpoint inhibitors, suggesting that the receptor dampens the immunotherapy efficacy. Taken together, our findings identify the androgen receptor as a diagnostic guidance in melanoma and support the repositioning of AR blockers in clinical management of patients.
Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics
Authors: Wu Honggui , Wang Maoxu , Zheng Yinghui , Xie X. Sunney
Published: January 2025

Single-cell three-dimensional (3D) genome techniques have advanced our understanding of cell-type-specific chromatin structures in complex tissues, yet current methodologies are limited in cell throughput. Here we introduce a high-throughput single-cell Hi-C (dscHi-C) approach and its transcriptome co-assay (dscHi-C-multiome) using droplet microfluidics. Using dscHi-C, we investigate chromatin structural changes during mouse brain aging by profiling 32,777 single cells across three developmental stages (3 months, 12 months, and 23 months), yielding a median of 78,220 unique contacts. Our results show that genes with significant structural changes are enriched in pathways related to metabolic process and morphology change in neurons, and innate immune response in glial cells, highlighting the role of 3D genome organization in physiological brain aging. Furthermore, our multi-omics joint assay, dscHi-C-multiome, enables precise cell type identification in the adult mouse brain and uncovers the intricate relationship between genome architecture and gene expression. Collectively, we developed the sensitive, high-throughput dscHi-C and its multi-omics derivative, dscHi-C-multiome, demonstrating their potential for large-scale cell atlas studies in development and disease.
OGG1 and MUTYH repair activities promote telomeric 8-oxoguanine induced senescence in human fibroblasts
Authors: De Rosa Mariarosaria , Barnes Ryan P. , Detwiler Ariana C. , Nyalapatla Prasanth R. , Wipf Peter , Opresko Patricia L.
Published: January 2025

Telomeres are hypersensitive to the formation of the common oxidative lesion 8-oxoguanine (8oxoG), which impacts telomere stability and function. OGG1 and MUTYH glycosylases initiate base excision repair (BER) to remove 8oxoG or prevent mutation. Here, we show OGG1 loss or inhibition, or MUTYH loss, partially rescues telomeric 8oxoG-induced premature senescence and associated proinflammatory responses, while loss of both glycosylases causes a near complete rescue in human fibroblasts. Glycosylase deficiency also suppresses 8oxoG-induced telomere fragility and dysfunction, indicating that downstream single-stranded break (SSB) repair intermediates impair telomere replication. Preventing BER initiation suppresses PARylation and confers resistance to the synergistic effects of PARP inhibitors on 8oxoG-induced senescence. However, OGG1 activity is essential for preserving cell growth after chronic telomeric 8oxoG formation, whereas MUTYH promotes senescence to prevent chromosomal instability from unrepaired damage. Our studies reveal that inefficient completion of 8oxoG BER at telomeres triggers cellular senescence via SSB intermediates which disrupt telomere function.
Taming large-scale genomic analyses via sparsified genomics
Authors: Alser Mohammed , Eudine Julien , Mutlu Onur
Published: January 2025

Searching for similar genomic sequences is an essential and fundamental step in biomedical research. State-of-the-art computational methods performing such comparisons fail to cope with the exponential growth of genomic sequencing data. We introduce the concept of sparsified genomics where we systematically exclude a large number of bases from genomic sequences and enable faster and memory-efficient processing of the sparsified, shorter genomic sequences, while providing comparable accuracy to processing non-sparsified sequences. Sparsified genomics provides benefits to many genomic analyses and has broad applicability. Sparsifying genomic sequences accelerates the state-of-the-art read mapper (minimap2) by 2.57-5.38x, 1.13-2.78x, and 3.52-6.28x using real Illumina, HiFi, and ONT reads, respectively, while providing comparable memory footprint, 2x smaller index size, and more correctly detected variations compared to minimap2. Sparsifying genomic sequences makes containment search through very large genomes and large databases 72.7-75.88x (1.62-1.9x when indexing is preprocessed) faster and 723.3x more storage-efficient than searching through non-sparsified genomic sequences (with CMash and KMC3). Sparsifying genomic sequences enables robust microbiome discovery by providing 54.15-61.88x (1.58-1.71x when indexing is preprocessed) faster and 720x more storage-efficient taxonomic profiling of metagenomic samples over the state-of-the-art tool (Metalign).
A comparative petrophysical evaluation of the Abu Roash, Bahariya, and Kharita reservoirs using well-logging data, East El-Fayoum, Egypt
Authors: Ebraheem Mohamed Osman , Ibrahim Hamza Ahmed , Senosy Ahmed Hosny
Published: January 2025

The exploration and development of hydrocarbon resources in the Western Desert require more continuous activities. The Silah is a newly discovered field in this region. Therefore, this study emphasizes the application of petrophysical evaluation to sandstone and carbonate reservoirs from the late and early Cretaceous. These formations are the most potential hydrocarbon reservoirs in the studied area as a part of the western desert. Additionally, this study involves a comparative evaluation of the Abu Roash, Bahariya, and Kharita reservoirs using well-logging data by applying different cross-plots that are used for determining different petrophysical parameters such as shale volume, porosity, fluid saturation, permeability, and net-to-gross ratio. These logs are gamma-ray (GR), calliper, resistivity (RLA5, RLA3, and RXOZ), photoelectric effect (PEFZ), neutron (APLC), and density (RHOZ). These plots agree with the results deduced from the interpretation of lithologic logs. Fourteen hydrocarbon-bearing zones are identified in the Silah field. Only two zones, namely, Zone 2 in Silah-15 and Zone 1 in South Silah-1X, are considered the best for hydrocarbon generation. These zones are characterized by low to moderate shale volume, moderate to high total porosity, good effective porosity, low water saturation, and high net-to-gross ratio. These zones lie in the Abu Roash/F member. These deduced points prove that the Abu Roash/F member can be an abundant hydrocarbon reservoir. This member in the Silah field appears to be a promising hydrocarbon reservoir because it matches the petrophysical parameters of the investigated zones and others in the northwestern Desert. This suggests that there may be reservoir continuity and similarity.
Monascus red pigment influence on hydroxyapatite nanoparticles-mediated renal toxicity in rats
Authors: Alqurashy Nasser N. , Yousef Mokhtar I. , Hussein Ahmed A. , Kamel Maher A. , El Wakil Abeer
Published: January 2025

Hydroxyapatite nanoparticles (HANPs) have been applied in several biomedical fields. However, its interaction with biological systems is less exploited. This study aimed to characterize HANPs, examine their influence on kidneys, and explore the potential protective effects of naturally extracted red pigment (RP) from Monascus purpureus against HANPs-induced renal toxicity. To this aim, forty eight adult male rats were randomly divided into 8 equal groups: a control group receiving 4% dimethyl sulfoxide (the solvent for HANPs), three groups receiving extracted RP at different doses of 10, 20, and 40 mg/kg, a group receiving HANPs at a dose of 88.3 mg/kg, and three more groups receiving a double treatment of HANPs associated with RP. The respective treatment was given daily by oral gavage to animals for 50 days which is the duration of the whole experiment. The renal toxicity caused by HANPs was manifested by aberrations in kidney function parameters, intensification of oxidative stress markers, and a decrease in the activity of antioxidant enzymes. Moreover, an increase in inflammatory (TNF-α and TGF-β) and apoptotic (caspace-3) markers, an elevation in gene-based kidney injuries markers (Kim-1 and lipocalin-2), and pathological tissue changes were determined. Meanwhile, co-treatment with different doses of biopigment and HANPs have reduced oxidative stress via their potent antioxidant effect. This was confirmed by pronounced improvement in the measured parameters along with the histological structural enhancement in a dose dependent manner compared to controls. To sum up, RP from M. purpureus has potential protective benefits in mitigating the adverse effects of HANPs.
Thrush nightingales adjust the peak frequency and structure of their songs in response to different types of experimental noise
Authors: Budka Michał
Published: January 2025

Animals employ various strategies to minimize the overlap of their vocalizations with other sounds, thereby enhancing the effectiveness of their communication. However, little attention has been given to experimentally examining how the structure of the acoustic signal changes in response to various kinds of disturbances in the soundscape. In this study, I experimentally investigated whether male thrush nightingales (Luscinia luscinia) adjust their singing rate, song frequency, and song type in response to different types of artificial sounds. While males did not reduce the intensity of their singing in noise, they did adjust the peak frequency of their songs—raising it in the presence of low-frequency noise and lowering it in response to high-frequency noise. These bidirectional changes were associated with selective use of phrases from their repertoire. The proportion of low- to high-frequency phrases was significantly reduced under low-frequency noise and increased under high-frequency noise. The results suggest that disturbing sounds can modify the peak frequency and structure of songbird vocalizations, at least in the short term. Birds may enhance the signal-to-noise ratio by selecting phrases from their repertoire that are less affected by noise. For species with a large repertoire, new sounds transmitted within a species-specific frequency range may play an important role in the process of cultural song transmission.
Identifying impairments and compensatory strategies for temporal gait asymmetry in post-stroke persons
Authors: Mizuta Naomichi , Hasui Naruhito , Higa Yasutaka , Matsunaga Ayaka , Ohnishi Sora , Sato Yuki , Nakatani Tomoki , Taguchi Junji , Morioka Shu
Published: January 2025

In post-stroke persons, temporal gait asymmetry (TGA) during comfortable gait involves a combination of pure impairments and compensatory strategies. In this study, we aimed to differentiate between pure impairments and compensatory strategies underlying TGA in post-stroke individuals and identify associated clinical factors. We examined 39 post-stroke individuals who participated in comfortable walking speed (CWS) and rhythmic auditory cueing (RAC). Gait evaluation included spatiotemporal parameters and trunk acceleration, while clinical evaluation comprised motor paralysis severity, sensory disturbances, spasticity, balance ability, and gait efficacy. The participants were classified by clustering based on the symmetry index during CWS and RAC. TGA during CWS or RAC gait showed no association (ρ = 0.062, p = 0.707). Clustering yielded four optimal clusters. Cluster 1 was asymmetric during CWS but symmetric during RAC condition (over-compensatory strategies); these participants had a poor score on the modified gait efficacy scale, and despite mild functional impairments, they lacked the confidence to walk safely. Cluster 2 showed impairment-driven asymmetry during CWS and RAC, with severe impairments and instability. Participants showing improved TGA under auditory cueing compared with comfortable speed demonstrate strong compensatory strategies associated with low gait efficacy. This suggests a need for targeted interventions to enhance gait self-efficacy and maximize residual function.
Characterization of some selected macroalgae extracts and assessment of their insecticidal and genotoxicity in Culex pipiens L. mosquito larvae
Authors: Refaay Dina A. , El-Sheekh Mostafa M. , Heikal Yasmin M. , Rashed Ahmed A.
Published: January 2025

The continual use of synthetic insecticides to control mosquito larvae has severe implications for human health and the ecosystem, highlighting the need for alternative natural insecticides. Macroalgae may be a good alternative because of their biologically active metabolites with distinctive chemical structures that have been reported for their insecticidal properties. The study aimed to investigate the potential of different extracts from Jania rubens (Linnaeus) J.V.Lamouroux and Colpomenia sinuosa (Mertens ex Roth) Derbès & Solier as genotoxic and larvicidal agents against Culex pipiens Linnaeus larvae. The algae thallus was subjected to extraction using methanol, acetone, and methylene chloride. The phytochemical composition was quantified. The larvicidal activity of the different algae extracts was assessed against the third instar larvae of Culex pipiens. Genotoxic evaluation through comet assays and compound characterization by GC/MS was done. The results demonstrated that J. rubens methylene chloride extract exhibited the highest contents of phenolics, alkaloids, flavonoids, terpenoids, and tannins while C. sinuosa methanol extract demonstrated the highest levels of flavonoids, alkaloids, phenolics, and saponins. The larvicidal activity results revealed that J. rubens methylene chloride extract was the most toxic for C. pipiens larvae with LC50 = 9.30 ppm followed by C. sinuosa acetone extract with LC50 = 82.58 ppm after 72 h of exposure. At 50 and 250 ppm, J. rubens methylene chloride and C. sinuosa acetone extracts maintained 100 and 93.33% larval mortality rates, respectively. Comet assay results demonstrated the genotoxicity of both algae extracts in C. pipiens larvae. This study would be a beginning towards replacing chemical insecticides with algae-based bioinsecticides against C. pipiens mosquitos.
Improving ocean reanalyses of observationally sparse regions with transfer learning
Authors: Lentz Simon , Brune Sebastian , Kadow Christopher , Baehr Johanna
Published: January 2025

Oceanic subsurface observations are sparse and lead to large uncertainties in any model-based estimate. We investigate the applicability of transfer learning based neural networks to reconstruct North Atlantic temperatures in times with sparse observations. Our network is trained on a time period with abundant observations to learn realistic physical behavior. Evaluating it within a consistent data assimilation framework, this network learns and reproduces its training data’s physical patterns. Additionally, the network is able to transfer these patterns towards a historical ocean heat content estimate in times with sparse observations. Consequently, with infrequent input data, machine learning reconstructions exhibit similar physical structures, while correcting for known errors compared to state-of-the-art data assimilation products. In this manner, transfer learning can impact the initialization and evaluation of climate hindcasts. Furthermore, by exhibiting the capability to accurately transfer results from high to low-frequencies, transfer learning based neural networks showcase their relevance in mixed-frequency measurements beyond climate science.
Association between extracellular DNA levels, markers of inflammation and left ventricular mass index in children with chronic kidney disease
Authors: Lindblad Ylva Tranæus , Tóthová Ľubomíra , Celec Peter , Kublickiene Karolina , Bárány Peter , Chromek Milan
Published: January 2025

Chronic kidney disease (CKD) is associated with chronic low-grade inflammation, but the primary factors triggering this inflammation remain unclear. Extracellular or cell-free DNA (exDNA) originates from virtually all tissues, being released during cell death, and stimulates the innate immune system. Our study was designed as an observational, cross-sectional cohort study of children with CKD (both before and after kidney transplantation) and controls to analyze associations between exDNA, markers of inflammation, and cardiovascular health. Extracellular DNA (total, nuclear, and mitochondrial) was analyzed in plasma using fluorometry and real-time PCR. We found that children with CKD after kidney transplantation had higher concentrations of total and nuclear extracellular DNA (total exDNA and nc_exDNA) in plasma compared to controls. In univariate analysis, levels of interleukin-6 (IL-6), antimicrobial peptide cathelicidin (LL-37), soluble vascular cell adhesion molecule-1 (VCAM-1) and left ventricular mass index (LVMI) were positively correlated with total exDNA and nc_exDNA concentrations. Multivariate analysis revealed LVMI as the only independent variable associated with high levels of both total exDNA and nc_exDNA. We believe that our results contribute new knowledge to the pathogenesis of CKD and its complications and may help identify new treatment targets.
A multi-modal deep learning model for prediction of Ki-67 for meningiomas using pretreatment MR images
Authors: Chen Chaoyue , Zhao Yanjie , Cai Linrui , Jiang Haoze , Teng Yuen , Zhang Yang , Zhang Shuangyi , Zheng Junkai , Zhao Fumin , Huang Zhouyang , Xu Xiaolong , Zan Xin , Xu Jianfeng , Zhang Lei , Xu Jianguo
Published: January 2025

This study developed and validated a deep learning network using baseline magnetic resonance imaging (MRI) to predict Ki-67 status in meningioma patients. A total of 1239 patients were retrospectively recruited from three hospitals between January 2010 and December 2023, forming training, internal validation, and two external validation cohorts. A representation learning framework was utilized for modeling, and performance was assessed against existing methods. Furthermore, Kaplan–Meier survival analysis was conducted to investigate whether the model could be used for tumor growth prediction. The model achieved superior results, with areas under the curve (AUCs) of 0.797 for internal testing and 0.808 for generalization, alongside 0.756 and 0.727 for 3- and 5-year tumor growth predictions, respectively. The prediction was significantly associated with the growth of asymptomatic small meningiomas. Overall, the model provides an effective tool for early prediction of Ki-67 and tumor volume growth, aiding in individualized patient management.
Determination of 36 non-phthalate plasticizers with the QuEChERS method in milk powder by gas chromatography coupled with quadrupole/orbitrap high-resolution mass spectrometry
Authors: Li Jia-Jia , Kou Lu , Li Jun , Shi Pei-Yu , Guo Tian-Rong , Xiao Quan-Wei , Wang Yi , Zhang Min , Wu Wen-Lin
Published: January 2025

A method involving gas chromatography coupled with quadrupole/orbitrap high-resolution mass spectrometry (GC-Q/Orbitrap HRMS) with the QuEChERS method was developed to analyze 36 non-phthalate plasticizers in milk powder products.
Rational design of a donor–acceptor structure in covalent heptazine frameworks to boost photocatalytic nitrogen fixation
Authors: Deng Yuhang , Sun Tao , Zhou Shi , Jiang Wei , Liu Chunbo , Ma Chunhong , Che Guangbo
Published: January 2025

Designing a D–A structure within a covalent heptazine framework can significantly enhance the photogenerated carrier migration efficiency, leading to effective photocatalytic reduction for N2 fixation.
A 3D rigid Mn-MOF heterogeneous catalyst for thioether oxidation, cyanosilylation and Knoevenagel condensation
Authors: Liu Han-Fu , Hu Zhi-Rong , Wu Tai-Xue , Hao Hong-Mei , Li Hai-Ye , Huang Fu-Ping
Published: January 2025

A robust Mn(ii) MOF with high thermal stability and chemical stability was prepared as an effective catalyst for thioether oxidation, cyanosilylation and Knoevenagel condensation with recycling runs.
Enhanced NH3 and NO sensing performance of Ti3C2O2 MXene by biaxial strain: insights from first-principles calculations
Authors: Khammuang Satchakorn , Wongphen Kantaphong , Hussain Tanveer , Kotmool Komsilp
Published: January 2025

Ti3C2O2 MXene was studied via DFT for CO, NH3, and NO gas adsorption under biaxial strain (−2% to 4%). The results show that NH3 and NO exhibit stronger interactions, with strain enhancing sensitivity and recovery time.
Densimeter-on-chip (DoC): measuring a single-cell mass density by sedimentation in microchannel flows
Authors: Dannhauser David , Maremonti Maria Isabella , Netti Paolo Antonio , Causa Filippo
Published: January 2025

Label-free in-flow identification of blood cell types by biophysical and morphological cell features.
Microfluidic-based redesign of a humidity-driven energy harvester
Authors: Hirama Hirotada , Komazaki Yusuke
Published: January 2025

We redesigned a humidity-driven energy harvester into a microfluidic device fabricated via photolithography and printing to achieve a self-powered microfluidic system.
Modulating charge transfer pathway via halide tuning of layered Bi-oxyhalides on an MOF-derived CuO nanorod photocathode
Authors: Joseph Sneha , Kumar Mohit , Chalamalasetty Suryansh , Meena Bhagatram , Challapalli Subrahmanyam
Published: January 2025

Modulation of charge transfer pathways by varying halides in bismuth oxyhalides over 1D CuO nanorods derived from 3D metal–organic framework.
Adhesive, biocompatible, and conductive reduced graphene oxide hydrogel-based bioelectrodes for epidermal electrophysiological signal monitoring
Authors: Kim Deukhee , Lee Hyun Joo , Oh Jiwon , Yang Hee Yeon , Park Hyung Ju , Huh Chul , Ha Dong Han , Jun Yongseok , Yun Yong Ju
Published: January 2025

Adhesive, biocompatible, and conductive epidermal bioelectrodes based on reduced graphene oxide hydrogels were designed to monitor multiple electrophysiological biosignals during human physical/chemical activities.