bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of food matrix and human gastrointestinal conditions on the in vitro protein hydrolysis of lentil proteins
Authors: Karakaya Sibel , Hassas Esra
Published: January 2025

This study aims to evaluate how food matrix, mechanical disintegration, and heat treatment can affect the protein hydrolysis of green lentils during three different in vitro gastrointestinal conditions (infant, late, and early phase adult). The hydrolysed proteins were characterised by sodium dodecyl sulphate–polyacrylamide gel electrophoresis and liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC/Q-TOF/MS). In all digestion protocols, protein hydrolysis was higher in the lentil protein isolate compared to lentil flour and cooked lentils. Apart from lentil protein isolate, proteolysis was more efficient in the late-phase intestinal digests of cooked lentils compared to digest of lentil flour. Peptides released during digestion were more frequent and had small molecular weights in cooked lentils and protein isolate. Low enzyme activity in infant digestion negatively affected proteolysis. Peptides released from len c 1.010, which is a well-known allergen during in vitro digestion, showed shared motifs with Pru p 3 from Prunus persica, Ara h 9 from Arachis hypogaea, and nonspecific lipid-transfer protein Cor a 8.0101 from Corylus avellana, which are food allergens.
Development of a cost-effective and protein-enhanced germinated cereal–legume–millet flour based multigrain cookie: a step towards sustainable goals
Authors: Rahman Shamsad , Dubey Praveen Kumar , Singh Harinder
Published: January 2025

Growing demand for better nutrition and health care is important due to modern lifestyles and behavioral shifts. This cereal-legume-millet-based study compares formulated germinated and ungerminated flour cookies prepared from the 3 different ratios (50:10:20:20, 50:20:10:20, and 50:20:20:10) of wheat, chickpea, and sorghum concerning control (refined wheat flour only). The results indicated that both the germinated and ungerminated flour cookies had a significant increase (p ≤ .05) in protein (11.41%–16.58%), ash (20.16%–22.78%), fat (0.99%–1.46%), DPPH (2,2-diphenyl-1-picrylhydrazyl) (27.17%–32.62%), and total phenolic content (71.03–97.95 mg gallic acid equivalent (GAE)/g) compared with the control cookies. Conversely, there was a decrease in carbohydrate content (53.83%–61.68%) in the formulated cookies. Furthermore, the hardness, fracturability, spread ratio, and lightness (L*) of the formulated cookies significantly decreased when compared with the control. Microstructural images revealed that control cookies had tightly bound starch granules, while the formulated cookies showed disrupted starch granules with pores. Fourier transform infrared spectroscopy (FTIR) analysis indicated an enhancement in peak patterns and intensity in the formulated germinated cookies compared to the control sample. Shelf-life determination showed that peroxide value, free fatty acid, moisture content, and microbial count were within acceptable limits over 28 days when stored in an aluminum pouch at a temperature of 28 ± 2 °C. These results suggest the potential for further research and scaling up the production of value-added, nutritionally enhanced, and functional multigrain cookies. Future studies could focus on commercial scale-up, optimising formulations, and addressing consumer preferences to facilitate broader market applications.
Techno-functional properties of soy, rice, and carioca bean protein blends
Authors: Santos Sarah da Costa , Kaspchak Elaine , Coelho Andriéli Aparício , Arbach Clara Takayama , Nabeshima Elizabeth Harumi , Pacheco Maria Teresa Bertoldo , Sadahira Mitie Sonia
Published: January 2025

This study investigated the impact of mixtures of soy protein isolate, pea protein concentrate, and carioca bean protein concentrate mixtures on techno-functional properties. Results showed a similar amino acid composition, with carioca bean presenting a higher content of hydrophobic amino acids compared to soy and pea proteins. Water retention index (WRI), solubility in water, emulsion and pasting properties of protein mixtures were successfully predicted by using special cubic and quadratic models derived from the simplex centroid design. A synergistic effect was observed for emulsion properties, suggesting protein mixtures are advantageous in applications involving both oily and aqueous phases. Conversely, an antagonistic effect was noted for WRI and final viscosity, which decreased compared to single proteins, making these mixtures suitable for liquid food applications, such as milk analogues. Overall, the study highlights the potential of protein mixtures to enhance functional properties according to the intended application.
Functional properties of betalains: binding of Hg2+ and Cu2+ ions, sensor capabilities, and antimicrobial activity
Authors: Şen Arslan Hülya , Yılmaz Altınok Bahar
Published: January 2025

In this study, betalain extracts were obtained from prickly pear (PPE), dragon fruit (DFE), and red beet (RBE). The total betalain content of the extracts was determined to be 335.5 mg/L for PPE, 372.38 mg/L for DFE, and 466.21 mg/L for RBE, respectively. Fluorescence titrations with metal cations revealed PPE’s highest intensity at 280 nm excitation, with DFE and RBE also responding, though less so. The fluorescence intensity for all extracts decreased significantly upon adding Hg2+ and Cu2+, indicating strong binding. PPE and DFE showed higher sensitivity and affinity for these ions than RBE. Absorption at 350 nm increased notably, along with visible color changes enabling potential ‘naked-eye’ detection. These extracts demonstrated high selectivity for Hg2+ and Cu2+, even with competing cations. Antibacterial tests showed significant inhibition against gram-positive and gram-negative bacteria. These findings, the extracts’ strong spectral responses and anti-interference properties support their use as selective, sensitive sensors for environmental monitoring and analytical applications. Due to their inherent fluorescence properties, betalains have significant potential as biosensors.
Healthy cereal bar enriched with probiotic bacillus: bromatological characterization, probiotic viability, consumers’ acceptance and gastrointestinal resistance in vitro
Authors: de Paula Antunes Daiana Júnia , de Almeida Costa Nataly , Martins Maurilio Lopes , do Nascimento Benevenuto Wellingta Cristina Almeida , Talma Simone Vilela , da Rocha Campos André Narvaes , Martins Eliane Maurício Furtado
Published: January 2025

The objective was to develop cereal bars enriched with Bacillus clausii and Bacillus coagulans and evaluate the bromatological characteristics, microbiological quality, and the viability of probiotics. The acceptability and resistance to the gastrointestinal tract (GIT) in vitro of B. clausii were evaluated. Regarding bromatological characteristics, there was no difference in pH, protein, lipids, carbohydrates, and ash between the bars and they were safe for consumption. B. clausii showed greater viability in cereal bars and maintained your count > 6.5 log CFU/g during 60 days. The sensory attributes presented scores between 8 and 9. After simulation of the GIT, in enteric phase II, it was found 6.82 log CFU/g. B. clausii presented a high survival rate, highlighting its excellent behavior in the product. The enrichment of products based on cereals with probiotics is an innovative alternative, expanding the possibilities of choice for healthy individuals and those with dietary restrictions.
‘Breaking the biofilm barrier: vitamin C as a novel strategy against multidrug-resistant salmonella Typhimurium’
Authors: Shivaprasad D P , Kaushik Abhishek , Taneja Neetu Kumra , Lakra Anupama , Bharadwaj Dinesh K , Juneja Vijay Kumar , Taneja Pankaj , Chauhan Komal , Oberoi Harinder Singh
Published: January 2025

The emergence of multidrug-resistant (MDR), biofilm-forming strains of Salmonella Typhimurium poses a significant threat to food safety due to their persistence on food surfaces and equipment, complicating eradication efforts and increasing the risk of contamination. This study explored the antibiofilm activity of Vitamin C (VC) against MDR biofilm-forming Salmonella Typhimurium. Vitamin C inhibited S. Typhimurium biofilms in a dose-dependent manner, with a minimum inhibitory concentration of 125 mM. Treatment with Vitamin C significantly disrupted the bacterial biofilm structure, creating cannonball-like pores in the cell wall as observed through electron microscopy. The antibiofilm mechanism of Vitamin C was mediated by reactive oxygen species (ROS) generation, leading to sugar and protein leakage, reduced exopolysaccharide (EPS) production, and decreased quorum sensing (QS) activity. Transcriptional analysis revealed that Vitamin C downregulated expression of biofilm-related genes responsible for initial cellular attachment and EPS production (fimA, adrA) and upregulated genes associated with adhesion and multidrug efflux pumps (csgA, ipfE, and arcA). Importantly, the application of Vitamin C on coated Paneer significantly extended its shelf life. These findings highlight the potential of Vitamin C in combating Salmonella biofilms, enhancing food safety, and providing a framework for the development of antibiotic-independent therapies to address MDR strains of Salmonella.
Multidisciplinary perspectives on cumulative impact assessment for vulnerable communities: expert elicitation using a Delphi method
Authors: Verwiel Ann , Rish William
Published: January 2025

Prompted by a series of executive orders, the U.S. Environmental Protection Agency (USEPA) is promoting cumulative impact assessment (CIA) to integrate numerous factors that have the potential to impact community health, which include nonchemical stressors such as socioeconomic conditions, pre-existing health conditions, and many others that historically have not been addressed by USEPA’s chemical risk assessment paradigm. Understanding the cumulative impact of all stressors on responses to environmental exposures requires multidisciplinary input from social scientists, economists, and others not traditionally involved in chemical risk assessments. To gather input from these disciplines, a group of 13 independent experts with perspectives on CIA as a social scientist, economist, public health expert, or decision analyst participated in a virtual workshop to obtain their perspectives regarding key aspects of CIA. The independent experts, who have decades of experience studying cumulative impacts in vulnerable population groups and environmental justice (EJ), responded anonymously to charge questions specific to their expertise and then were asked to review and comment on other’s responses within and outside their discipline. The questions and responses were organized by the authors into general topics (e.g., screening tools and indexes, role of nonchemical stressors in cumulative impacts, uncertainties), and discussions across and within the four disciplines were summarized by the authors. The expert’s opinions were used to frame a set of future research objectives to advance the development of CIA and improve its use in the EJ context. Specifically, the experts’ recommendations addressed the need for regulatory impact analysis, the appropriate use of screening tool information and indexes, the role and measurement of nonchemical stressors, relevance of a risk modifier approach to CIA, inclusion of uncertainty and causality, metrics to assess effectiveness of interventions, and methods for community communication.
Cancer immunotherapy in progress—an overview of the past 130 years
Authors: Ikeda Hiroaki
Published: January 2025

Since the first approval of an immune checkpoint inhibitor, we have witnessed the clinical success of cancer immunotherapy. Adoptive T-cell therapy with chimeric antigen receptor T (CAR-T) cells has shown remarkable efficacy in hematological malignancies. Concurrently with these successes, the cancer immunoediting concept that refined the cancer immunosurveillance concept underpinned the scientific mechanism and reason for past failures, as well as recent breakthroughs in cancer immunotherapy. Now, we face the next step of issues to be solved in this field, such as tumor heterogeneity, the tumor microenvironment, the metabolism of tumors and the immune system, and personalized approaches for patients, aiming to expand the population benefitted by the therapies.
The Violence We Unsee: Human Rights Erasures in Supply Chain Capitalism
Authors: Georgi F Richard
Published: January 2025

Violence caused by business practices along global value chains have inflicted myriad forms of massive harm and posed far-reaching regulatory challenges. The role that human rights could play in rendering corporate violence visible, remediable, and litigable remains quite contested. On the one hand, debates on business and human rights have driven a regulatory revolution over the last decade that is associated with the rise of the human rights due diligence (HRDD) norm. On the other hand, this revolution has been largely ignored by scholars in critical international political sociology; indeed, many critical scholars maintain that human rights are ineffective toward, or complicit in violent neoliberalism. This article bridges the scholarly divide by harnessing insights from the political, historical, and legal critique of rights to expose the inherent limitations of HRDD as the new hope for remedying corporate violence globally. Through a spectral lens, I explore foundational assumptions about the taxonomy of (un-)seeing corporate violence; business subjectivity and (ir-)responsibility for violence; and the epistemology of rendering knowledge on corporate violence (in-)admissible. This article contributes to multidisciplinary and pragmatic research on governing supply chain capitalism, understanding HRDD as a potentially powerful tool—provided it is accompanied by reforms tackling discourses, structures, and knowledges that condition corporate violence.
De Facto States and COVID-19: New Comparative Insights into Governmental Capacity to Act
Authors: Berg Eiki , Pegg Scott , Toomla Raul
Published: January 2025

This paper takes advantage of the exogenous shock of the COVID-19 pandemic to study de facto state agency. It builds upon previous scholarship on de facto states’ integration into international society by employing seven case studies while developing an independent capacity index. We argue that the COVID-19 pandemic is ideally suited to this task because it provided a powerful exogenous, non-conflict-related shock to all seven of our case studies, thus allowing for a valuable diagnostic tool from which to view how de facto states responded. We develop and test four specific theoretical hypotheses that offer different suggestions as to how well or how poorly individual de facto states might be expected to respond to the pandemic. Our empirical findings reveal Taiwan in a class by itself, followed by Northern Cyprus, Kosovo, and Transnistria with lesser agency, and finally, Abkhazia, Somaliland, and Nagorno-Karabakh with extremely limited agency.
Decrypting the phylogeny and metabolism of microbial dark matter in green and red Antarctic snow
Authors: Ren Ze , Luo Wei , Li Huirong , Ding Haitao , Zhang Yunlin
Published: January 2025

Antarctic snow harbors diverse microorganisms, including pigmented algae and bacteria, which create colored snow patches and influence global climate and biogeochemical cycles. However, the genomic diversity and metabolic potential of colored snow remain poorly understood. We conducted a genome-resolved study of microbiomes in colored snow from 13 patches (7 green and 6 red) on the Fildes Peninsula, Antarctica. Using metagenome assembly and binning, we reconstructed 223 metagenome-assembled genomes (MAGs), with 91% representing previously unexplored microbes. Green snow (GS) and red snow (RS) showed distinct MAGs profile, with Polaromonas and Ferruginibacter as the most abundant genera, respectively. GS exhibited higher alpha diversity with more unique and enriched MAGs, while RS showed greater variability with higher beta diversity. All MAGs contained genes encoding auxiliary activities (AAs), carbohydrate esterases (CEs), glycoside hydrolases (GHs), and glycosyl transferases (GTs), indicating microbial degradation of complex carbon substrates. The most abundant enzymes included GT2 (cellulose synthase), GT4 (sucrose synthase), CE1 (acetyl xylan esterase), GT41 (peptide beta-N-acetylglucosaminyltransferase), and CE10 (arylesterase). GS had a higher abundance of GTs, whereas RS was enriched in GHs. Furthermore, 56% of MAGs contained genes for inorganic nitrogen cycling, with 18 gene families involved in assimilatory nitrate reduction, dissimilatory nitrate reduction, and denitrification. Potential coupling of nitrogen cycling and carbohydrate metabolism was observed at both genome and community levels, suggesting close links between these pathways, particularly through nitrate reduction during carbohydrate degradation. This study enhances our understanding of microbial metabolic functions in polar ecosystems and highlights their roles in maintaining Antarctic ecological stability.
Effects of simvastatin on the mevalonate pathway and cell wall integrity of Staphylococcus aureus
Authors: Cortês Iago Torres , Silva Kátia de Pádua , Cogo-Müller Karina
Published: January 2025

Aims

To investigate the effects of simvastatin as an antimicrobial, considering its influence on the mevalonate pathway and the bacterial cell wall of S. aureus.

Methods and Results

S. aureus ATCC 29213 and 33591 were exposed to simvastatin in the presence of exogenous mevalonate to determine whether mevalonate could reverse the inhibition. S. aureus was also treated with simvastatin and gene expression analysis assays were performed to evaluate genes associated with the mevalonate pathway (mvaA, mvaS, mvaK1, and mvaK2), peptidoglycan synthesis (uppS, uppP, and murG), and cell wall stress (vraX, sgtB, and tcaA). Transmission electron microscopy was used to identify the presence of morphological changes. The data were compared using two-way ANOVA and Bonferroni post-test, or the Mann–Whitney test. Addition of exogenous mevalonate was able to partially or completely reverse the inhibition caused by simvastatin. A significant increase of the vraX gene and a reduction of the mvaA gene were observed, together with changes in bacterial morphology.

Conclusion

Simvastatin can exert its antimicrobial effect by means of changes in the cell wall associated with the mevalonate pathway.
Sprouty2/4 deficiency disrupts early signaling centers impacting chondrogenesis in the mouse forelimb
Authors: Dalecka Linda , Hruba Eva , Andrasova Marketa , Steklikova Klara , Pavlikova Zuzana , Kucerova Klara , Szotkowska Tereza , Bartos Martin , Buchtova Marcela , Tucker Abigail Saffron , Hovorakova Maria
Published: January 2025

The FGF signaling pathway plays an important role in the regulation of limb development, controlling cell migration, proliferation, differentiation, and apoptosis. Sprouty proteins act as antagonists of the FGF pathway and control the extent of FGF signaling as part of a negative feedback loop. Sprouty2/4 deficient mice evince defects in endochondral bone formation and digit patterning in their forelimbs, with pathogenesis recently related to ciliopathies. To understand the mechanisms behind these pathologies, the limb defects in Sprouty2+/−;Sprouty4−/− male and female mice were characterized and correlated to the dynamic expression patterns of Sprouty2 and Sprouty4, and the impact on the main signaling centers of the limb bud was assessed. Sprouty2 and Sprouty4 exhibited dynamic expressions during limb development. Interestingly, despite similar expression patterns in all limbs, the hindlimbs did not evince any obvious alterations in development, while the forelimbs showed consistent phenotypes of variable severity. Prenatally as well as postnatally, the left forelimb was significantly more severely affected than the right one. A broad variety of pathologies was present in the autopodium of the forelimb, including changes in digit number, size, shape, and number of bones, hand clefts, and digit fusions. Ectopic ossification of bones and abnormal bone fusions detected in micro-CT scans were frequently observed in the digital as well as in the carpal and metacarpal areas. Sprouty2+/−;Sprouty4−/− limb buds showed patchy loss of Fgf8 expression in the apical ectodermal ridge, and a loss of tissue underlying these regions. The zone of polarizing activity was also impacted, with lineage analysis highlighting a change in the contribution of Sonic hedgehog expressing cells. These findings support the link between Sproutys and Hedgehog signaling during limb development and highlight the importance of Sprouty2 and Sprouty4 in controlling early signaling centers in the limb.
Assessing hybridization between non-native Procambarus clarkii (Girard, 1852) and native Procambarus troglodytes (Le Conte, 1855) (Decapoda: Astacidea: Cambaridae) in Atlantic drainages of the southeastern USA
Authors: Kendrick Michael , Walker Matt , Darden Tanya
Published: January 2025

Crayfishes play important ecological and economic roles in the southeastern USA, with non-native crayfishes threatening many native species. While hybridization of crayfish species is observed in both wild and captive populations for some crayfishes, evidence for hybridization in the genus Procambarus Ortmann, 1905 is limited. The red swamp crayfish (Procambarus clarkii (Girard, 1852)) and the eastern red swamp crayfish (Procambarus troglodytes(Le Conte, 1855)) are two closely related crayfishes native to different basins in the southeastern USA. We used genetic markers to assess the potential for hybridization in these two crayfishes in the North Carolina and South Carolina, USA. A total of 292 specimens were collected with morphological identification distinguishing 134 P. clarkii and 158 P. troglodytes individuals from syntopic (i.e., co-occurring) and allopatric populations. Genetic microsatellite data was used to determine that no individuals were documented as hybrids in our collections and there was no indication of recent or rampant hybridization between P. clarkii and P. troglodytes at any of the sampling locations. A limited laboratory experiment showed successful mating and egg fertilization but failed to produce viable hybrid offspring. Although historical successful hybridization was not documented in our study, mating events between the two species resulting in inviable offspring may be having detrimental ecological consequences for populations of the native P. troglodytes that warrant additional exploration.
Multi-sample long-read nanopore sequencing of Agabus bipustulatus (Coleoptera: Dytiscidae: Agabinae) mitogenome produces effectively reliable data for downstream analyses
Authors: Bielikova Olena , Vargovčík Ondrej , Čiamporová-Zaťovičová Zuzana , Čiampor Fedor
Published: January 2025

Mitochondrial genomes are a rich source of data for various downstream analyses such as population genetics, phylogeny, and systematics. Today it is possible to assemble rapidly large numbers of mitogenomes, mainly employing next-generation sequencing and third-generation sequencing. However, verification of the correctness of the generated sequences is often lacking, especially for noncoding, length-variable parts. Here we have assembled the mitochondrial genome (mitogenome) from four specimens of Agabus bipustulatus (L.) using long-read nanopore sequence data. The use of the latest nanopore chemistry (V14) combined with a comprehensive error correction workflow enabled the generation of mitogenomes with high accuracy and reproducibility, as tested on four samples. The resulting mitogenome is 17,876 bp long, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Differences in the control region length between samples were minimal. The arrangement of protein-coding genes, transfer RNAs, and ribosomal RNAs is similar to that of the ancestral insect mitogenome. Finally, we used the assembled, well-supported mitogenomes in the phylogenetic analysis of a part of the Dytiscidae related to the studied species and confronted the results with previous hypotheses. Conflicting estimates of their phylogeny suggest that considerably more robust data are required for a plausible sketch of their evolutionary history. Our research has confirmed that readily available third-generation sequencing technologies, such as Oxford Nanopore Technologies, combined with long-read sequencing, offer a highly efficient, reliable, and cost-effective approach to generate complete mitogenomes and potentially other longer regions of the genome. The use of reliable data will ultimately contribute to a deeper understanding and improved conservation strategies for diving beetles and other organisms.
Application of machine learning for detecting high fall risk in middle-aged workers using video-based analysis of the first 3 steps
Authors: Sakane Naoki , Yamauchi Ken , Kutsuna Ippei , Suganuma Akiko , Domichi Masayuki , Hirano Kei , Wada Kengo , Ishimaru Masashi , Hosokawa Mitsuharu , Izawa Yosuke , Matsumura Yoshihiro , Hozumi Junichi
Published: January 2025

Objectives: Falls are among the most prevalent workplace accidents, necessitating thorough screening for susceptibility to falls and customization of individualized fall prevention programs. The aim of this study was to develop and validate a high fall risk prediction model using machine learning (ML) and video-based first 3 steps in middle-aged workers.

Methods: Participants to provide training data (n = 190, mean [SD] age = 54.5 [7.7] years, 48.9% male) and validation data (n = 28, age = 52.3 [6.0] years, 53.6% male) were enrolled in this study. Pose estimation was performed using a marker-free deep pose estimation method called MediaPipe Pose. The first 3 steps, including the movements of the arms, legs, trunk, and pelvis, were recorded using an RGB camera, and the gait features were identified. Using these gait features and fall histories, a stratified k-fold cross-validation method was used to ensure balanced training and test data, and the area under the curve (AUC) and 95% CI were calculated.

Results: Of 77 gait features in the first 3 steps, we found 3 gait features in men with an AUC of 0.909 (95% CI, 0.879-0.939) for fall risk, indicating an “excellent” (0.9-1.0) classification, whereas we determined 5 gait features in women with an AUC of 0.670 (95% CI, 0.621-0.719), indicating a “sufficient” (0.6-0.7) classification.

Conclusions: These findings suggest that fall risk prediction can be developed based on ML and the first 3 steps in men; however, the accuracy was only “sufficient” in women. Further development of the formula for women is required to improve its accuracy in the middle-aged working population.
Analytic natural gradient updates for Cholesky factor in Gaussian variational approximation
Authors: Tan Linda S L
Published: January 2025

Natural gradients can improve convergence in stochastic variational inference significantly but inverting the Fisher information matrix is daunting in high dimensions. Moreover, in Gaussian variational approximation, natural gradient updates of the precision matrix do not ensure positive definiteness. To tackle this issue, we derive analytic natural gradient updates of the Cholesky factor of the covariance or precision matrix and consider sparsity constraints representing different posterior correlation structures. Stochastic normalized natural gradient ascent with momentum is proposed for implementation in generalized linear mixed models and deep neural networks.
The role of mobile DNA elements in the dynamics of plant genome plasticity
Authors: Emmerson Robyn , Catoni Marco
Published: January 2025

Plants host a range of DNA elements capable of self-replication. These molecules, usually associated with the activity of transposable elements or viruses, are found integrated in the genome or in the form of extrachromosomal DNA. The activity of these elements can impact genome plasticity by a variety of mechanisms, including the generation of structural variants, the shuffling of regulatory or coding DNA sequences across the genome, and DNA endoduplication. This plasticity can dynamically alter gene expression and genome stability, ultimately affecting plant development or the response to environmental changes. While the activation of these elements is often considered deleterious to the genome, their role in creating variation is important in adaptation and evolution. Moreover, the mechanisms by which mobile DNA proliferates have been exploited for plant engineering, or contributed to understand how desirable traits can be generated in crops. In this review, we discuss the origins and the roles of mobile DNA element activity on genome plasticity and plant biology, as well as their potential function and current application in plant biotechnology.
Mapping dusty galaxy growth at z > 5 with FRESCO: detection of Hα in submm galaxy HDF850.1 and the surrounding overdense structures
Authors: Herard-Demanche Thomas , Bouwens Rychard J , Oesch Pascal A , Naidu Rohan P , Decarli Roberto , Nelson Erica J , Brammer Gabriel , Weibel Andrea , Xiao Mengyuan , Stefanon Mauro , Walter Fabian , Matthee Jorryt , Meyer Romain A , Wuyts Stijn , Reddy Naveen , Rowland Lucie , van Leeuwen Ivana , Haro Pablo Arrabal , Dannerbauer Helmut , Shapley Alice E , Chisholm John , van Dokkum Pieter , Labbe Ivo , Illingworth Garth , Schaerer Daniel , Shivaei Irene
Published: January 2025

We report the detection of a 13$\sigma$ H$\alpha$ emission line from HDF850.1 at $z=5.188\pm 0.001$ using the FRESCO (First Reionization Era Spectroscopically Complete Observations) NIRCam F444W grism observations. Detection of H$\alpha$ in HDF850.1 is noteworthy, given its high far-infrared (IR) luminosity, substantial dust obscuration, and the historical challenges in deriving its redshift. HDF850.1 shows a clear detection in the F444W imaging data, distributed between a northern and southern component, mirroring that seen in [C ii] from the Plateau de Bure Interferometer. Modelling the spectral energy distribution of each component separately, we find that the northern component has a higher mass, star formation rate (SFR), and dust extinction than the southern component. The observed H$\alpha$ emission appears to arise entirely from the less-obscured southern component and shows a similar $\Delta$v$\sim$ + 130 ${\rm{km\,s}}^{-1}$ velocity offset to that seen for [C ii] relative to the source systemic redshift. Leveraging H$\alpha$-derived redshifts from FRESCO observations, we find that HDF850.1 is forming in one of the richest environments identified to date at $z\gt 5$, with 100 $z=5.17$–5.20 galaxies distributed across 13 smaller structures and a $\sim$(15 cMpc)$^3$ volume. Based on the evolution of analogous structures in cosmological simulations, the $z=5.17$–5.20 structures seem likely to collapse into a single $\gt 10^{14}$${\rm M}_{\odot }$ cluster by $z\sim 0$. Comparing galaxy properties forming within this overdensity with those outside, we find the masses, SFRs, and $UV$ luminosities inside the overdensity to be clearly higher. The prominence of H$\alpha$ line emission from HDF850.1 and other known highly obscured $z\gt 5$ galaxies illustrates the potential of NIRCam-grism programs to map both the early build-up of IR-luminous galaxies and overdense structures.
Young onset chronic inflammatory back pain: A diagnostic dilemma between axial spondylitis and diffuse idiopathic skeletal hyperostosis
Authors: Namas Rajaie , Al Qassimi Sarah , Alameri Jawahir , Alawadhi Fatema , Memisoglu Esat , Almarzooqi Ahlam
Published: January 2025

Diffuse idiopathic skeletal hyperostosis (DISH) and axial spondyloarthritis (axSpA) share similarities in both clinical presentation and radiological findings, making the diagnostic process challenging. We report the case of a 30-year-old male with a long-standing history of back pain with an initial diagnosis of young-onset DISH. However, a diagnosis of axSpA was ultimately pursued based on his age and clinical presentation. This was further supported by improvement in both Ankylosing Spondylitis Disease Activity Score with Erythrocyte Sedimentation Rate (ASDAS-ESR) and Ankylosing Spondylitis Disease Activity Score with C-Reactive Protein (ASDAS-CRP) scores at his 6- and 12-month follow-ups on ixekizumab. Early and accurate diagnosis of axSpA, followed by appropriate treatment, is essential in preventing complications and improving patient outcomes.
(Un)Sustainable Science: Greening Practices in Research, Clinical Microbiology, and Veterinary Laboratories Locally and Globally
Authors: Bayrau Bethel Alebel , Buyukcangaz Esra , Sadarangani Sapna P , Ondigo Bartholomew N , Prinzi Andrea , LaBeaud A Desiree
Published: January 2025

Health care, veterinary, and research facilities produce tremendous amounts of waste and account for a significant proportion of their institutions’ energy and water use. The majority of municipal solid waste produced by these facilities gets unsustainably disposed of, including exportation to lower-income countries, and most of the plastic waste is nonrecyclable and nondegradable. The produced waste not only results in excessive carbon emissions harming planetary health but also poses direct harm to human health, broadens global inequities, and produces avoidable economic costs. Greening up laboratories by reducing waste production and water and energy use offers many benefits and does not have to be time or resource intensive. Sustainable practices to green up laboratories include reusing materials, decreasing energy use by choosing low-energy settings and shutting off equipment when not in use, installing low-flow faucets to decrease water use, proper sorting of waste, environmentally conscious purchases of supplies, and avoiding unnecessary medical and veterinary tests.
Chronic Hepatitis B and COVID-19 Clinical Outcomes in the United States: A Multisite Retrospective Cohort Study
Authors: Yendewa George A , Olasehinde Temitope , Mulindwa Frank , Salata Robert A , Mohareb Amir M , Jacobson Jeffrey M
Published: January 2025

Background

There is conflicting evidence regarding the impact of chronic hepatitis B virus (HBV) on SARS-CoV-2 outcomes. Additionally, the impact of SARS-CoV-2 vaccination and variant periods on outcomes in HBV/SARS-CoV-2 coinfection remain unexplored.

Methods

We utilized the TriNetX database to compare adults with HBV/SARS-CoV-2 (vs SARS-CoV-2 alone) across 97 US healthcare systems from 2020 to 2023. We assessed the odds of all inpatient hospitalizations, intensive care unit admissions, mechanical ventilation, 30-day, 90-day, and overall mortality. In sensitivity analyses, we excluded HIV, hepatitis C virus, and transplant cases and stratified the HBV/SARS-CoV-2 cohort by cirrhosis status. We applied propensity score matching to address confounding and reported odds ratios (OR) with 95% confidence intervals (CI).

Results

Of 4 206 774 individuals with SARS-CoV-2, about 0.2% (8293) were HBV/SARS-CoV-2. Individuals with HBV/SARS-CoV-2 (vs SARS-CoV-2 alone) had higher odds of intensive care unit admissions (OR, 1.18; 95% CI, 1.02–1.36), 90-day (OR, 1.22; 95% CI, 1.01–1.41) and overall mortality (OR, 1.18; 95% CI, 1.06–1.33). In sensitivity analyses, those with HBV/SARS-CoV-2 and cirrhosis had a 2.0- to 2.50-fold higher odds of adverse outcomes. Notably, even individuals with HBV/SARS-CoV-2 without cirrhosis had higher odds of mortality. Vaccinated (vs unvaccinated) individuals with HBV/SARS-CoV-2 had 57%, 54%, and 29% reduction in 30-day, 90-day, and overall mortality, respectively. The pre-Delta variant period was associated with higher odds of hospitalization compared to the Omicron but not the Delta period.

Conclusions

Chronic HBV was associated with worse SARS-CoV-2 outcomes, whereas SARS-CoV-2 vaccination reduced the likelihood of adverse outcomes.
MicroRNA analysis reveals 2 modules that antagonistically regulate xylem tracheary element development in Arabidopsis
Authors: Liu Chunhao , Li An , Guo Zhonglong , Chen Ningcong , Wang Yin , Tang Wenxiong , Wu Yuexin , Liu Jingyi , Wang Zihao , Li Lei , He Xin-Qiang
Published: January 2025

Tracheary elements (TEs) are vital in the transport of various substances and contribute to plant growth. The differentiation of TEs is complex and regulated by a variety of microRNAs (miRNAs). However, the dynamic changes in miRNAs during each stage of TE differentiation remain unclear, and the miRNA regulatory network is not yet complete. This study employed Vascular cell Induction culture System Using Arabidopsis Leaves to profile the miRNome during TE differentiation in Arabidopsis (Arabidopsis thaliana) and established comprehensive miRNA co-expression networks functioning at the different stages of TE differentiation. Two negatively correlated modules exist in the miRNA networks, each exhibiting strong intra-module positive correlation and strong inter-module negative correlation. Thus, the 2 modules may play opposite roles in TE differentiation and vascular development. Indeed, we found that miR408 promotes cambium formation and TE differentiation, consistent with miR408 as a key node in the networks of fate determination and the initiation of TE differentiation. Additionally, we found that miR163 inhibits secondary cell wall formation and TE differentiation, corresponding to miR163 as a key node in the TE maturation network. Moreover, we discovered that the miRNA co-expression network in poplar (Populus tomentosa) xylem development is also composed of 2 negatively correlated modules that contain miRNAs orthologous to those in Arabidopsis. Therefore, the 2 negatively correlated modules of the miRNA co-expression network are likely conserved and fundamental to xylem TE differentiation. These results provide insights into microRNA regulation in plant development.
Effectiveness of baricitinib versus sarilumab on disease activity in patients with RA: a propensity score matching study
Authors: Yukishima Toshitaka , Nakamura Yukio , Ohmura Shin-Ichiro , Kobayakawa Tomonori
Published: January 2025

Objectives

To evaluate the effects of baricitinib, a Janus kinase inhibitor, versus sarilumab, a human monoclonal antibody against the IL-6 receptor, on the disease activity of patients with RA.

Methods

At our hospital and cooperative facilities, we initiated treatment with baricitinib and sarilumab and observed patients with RA longitudinally for 52 weeks. Propensity score matching (age, sex, disease duration, MTX/glucocorticoid usage, RF/ACPA positivity and Disease Activity Score 28 with CRP level) was performed to address potential treatment selection bias, resulting in 46 patients in each group. The following data were collected: Disease Activity Score 28 with CRP, Clinical Disease Activity Index, Simplified Disease Activity Index, Boolean 2.0 and their component indices at weeks 24 and 52. A comparative analysis was conducted between the two groups.

Results

Compared with baricitinib, sarilumab induced a similar improvement in disease activity; however, baricitinib induced a significantly greater improvement in the Clinical Disease Activity Index at 24 weeks than sarilumab. At the component level, baricitinib significantly improved the number of swollen joints at 24 weeks, improving the Clinical Disease Activity Index; however, after 52 weeks, the difference between the two groups was no longer statistically significant.

Conclusion

Compared with sarilumab, baricitinib improved swollen joints and the Clinical Disease Activity Index at 24 weeks; however, by 52 weeks, no significant difference was observed between the two groups, indicating that both treatments are important for long-term use.
Extracellular microvesicles/exosomes - magic bullets in horizontal transfer between cells of mitochondria and molecules regulating mitochondria activity
Authors: Ratajczak Mariusz Z , Thetchinamoorthy Kannathasan , Wierzbicka Diana , Konopko Adrian , Ratajczak Janina , Kucia Magdalena
Published: January 2025

Extracellular microvesicles (ExMVs) were one of the first communication platforms between cells that emerged early in evolution. Evidence indicates that all types of cells secrete these small circular structures surrounded by a lipid membrane that plays an important role in cellular physiology and some pathological processes. ExMVs interact with target cells and may stimulate them by ligands expressed on their surface and/or transfer to the target cells their cargo comprising various RNA species, proteins, bioactive lipids, and signaling nucleotides. These small vesicles can also hijack some organelles from the cells and, in particular, transfer mitochondria, which are currently the focus of scientific interest for their potential application in clinical settings. Different mechanisms exist for transferring mitochondria between cells, including their encapsulation in ExMVs or their uptake in a “naked” form. It has also been demonstrated that mitochondria transfer may involve direct cell-cell connections by signaling nanotubules. In addition, evidence accumulated that ExMVs could be enriched for regulatory molecules, including some miRNA species and proteins that regulate the function of mitochondria in the target cells. Recently, a new beneficial effect of mitochondrial transfer has been reported based on inducing the mitophagy process, removing damaged mitochondria in the recipient cells to improve their energetic state. Based on this novel role of ExMVs in powering the energetic state of target cells, we present a current point of view on this topic and review some selected most recent discoveries and recently published most relevant papers.
The histone lactylation of AIM2 influences the suppression of ferroptosis by ACSL4 through STAT5B and promotes the progression of lung cancer
Authors: Wu Songze , Liu Man , Wang Xu , Wang Shan
Published: January 2025

Lung cancer progression is characterized by intricate epigenetic changes that impact critical metabolic processes and cell death pathways. In this study, we investigate the role of histone lactylation at the AIM2 locus and its downstream effects on ferroptosis regulation and lung cancer progression. We utilized a combination of biochemical assays, including chromatin immunoprecipitation (ChIP), quantitative real‐time PCR (qRT‐PCR), and western blotting to assess histone lactylation levels and gene expression. To evaluate the functional consequences, we employed gain‐ and loss‐of‐function approaches using shikonin treatment and siRNA knockdowns in lung cancer cell lines. Additionally, we assessed the impact of these interventions on ferroptosis markers and lung cancer cell viability. Our results reveal that increased histone lactylation at the AIM2 locus correlates with enhanced transcriptional activity of AIM2, leading to reduced ferroptosis through modulation of ACSL4 and STAT5B. Furthermore, we demonstrate that shikonin, a natural naphthoquinone derivative, effectively downregulates PKM2 and AIM2 expression, thereby inhibiting lung cancer progression by counteracting the effects of histone lactylation on AIM2 expression. These findings highlight the importance of histone lactylation in regulating AIM2 expression and ferroptosis in lung cancer cells. They also suggest that targeting PKM2 and AIM2, particularly through the use of shikonin, could be a promising strategy for developing novel therapies against lung cancer.
A multidimensional pan‐cancer analysis of NDUFA4L2 and verification of the oncogenic value in colon cancer
Authors: Yi Jianing , Gao Wenjie , Wu Cheng , Yang Ranzhiqiang , Yu Chunzhao
Published: January 2025

NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4‐like 2 (NDUFA4L2) protein is located in the mitochondria and can regulate cell proliferation. Some studies have shown that the high NDUFA4L2 expression is linked with poor prognosis and cancer progression in various patients with cancers. However, the correlation between NDUFA4L2 and pan‐cancer is unknown. In this study, we used the databases and investigated the expression and variation of NDUFA4L2 in many cancers in detail to determine its diagnostic and prognostic values. We also validated the oncogenic capability of NDUFA4L2 in colon cancer by experiments or tissue microarray. In most cancers, NDUFA4L2 expression levels are upregulated, and a high level of NDUFA4L2 expression is associated with poor OS. In addition, the results showed that 10 proteins and 30 genes were correlated to NDUFA4L2. An additional analysis demonstrated that these genes and proteins exhibited either negative or positive correlations with specific pathways. Moreover, we discovered that NDUFA4L2 expression was related to tumor stemness, MSI, TMB, immune cell infiltration and ROS production. Our results show that NDUFA4L2 affects the development and mitochondrial function of colon cancer cell lines. Finally, we identified that NDUFA4L2 was sensitive to 10 anticancer drugs. Our study suggest that NDUFA4L2 could serve as a prognostic and therapeutic biomarker for most cancer, including colon cancer.
Joint analysis of genome‐wide cross‐trait and multi‐omics reveals molecular mechanisms of inflammatory bowel disease and nominates its novel therapeutic genes
Authors: Zhu Zijun , Wei Rongxing , Li Hailong , Wang Xin , He Guanzhi , Du Meiyu , Tan Senwei , Cheng Liang
Published: January 2025

Inflammatory bowel disease (IBD) with the two predominant endophenotypes—Crohn's disease (CD) and ulcerative colitis (UC)—represents a group of chronic gastrointestinal inflammatory conditions. Since most genetic associations with IBD are often limited to independent subtypes, we reported a genome‐wide association study (GWAS) cross‐trait analysis combined with CD and UC to enhance statistical power. Initially, we detected 256 association signals at 54 genomic susceptibility loci and further characterized the functionality of variants within these regions. Subsequently, we revealed tissue and cell‐specific heritability enrichment, particularly in whole blood, small intestine terminal ileum, spleen, lung, and colon transverse. Leveraging multi‐omics datasets, we adopted a two‐pronged approach comprising summary data‐based Mendelian randomization (SMR) and transcriptome‐wide association study (TWAS) to pinpoint likely causal genes and variants. Further, RNA‐seq analysis facilitated the evaluation of differential expression and co‐expression in intestinal tissues. Through a multi‐stage prioritization strategy, compelling evidence for putative targets was nominated; notably highlighting several potential susceptibility genes such as IL27 and SBNO2. Finally, we utilized Mendelian randomization (MR) analysis with diverse datasets to verify the convergence of these two endophenotype‐driven genes. Our investigation yields valuable insights to inform genetic mechanisms in IBD and reveal potential causal gene targets.