bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stress-induced changes in magnetite: insights from a numerical analysis of the Verwey transition
Authors: Fuchs Helena , Kontny Agnes , Schilling Frank R 
Published: June 2024

SUMMARY
Magnetic susceptibility behaviour around the Verwey transition of magnetite (≈125 K) is known to be sensitive to stress, composition and oxidation. From the isotropic point (≈130 K) to room temperature, decreasing magnetic susceptibility indicates an increase in magnetocrystalline anisotropy. In this study, we present a model which numerically analyses low-temperature magnetic susceptibility curves (80–280 K) of an experimentally shocked (up to 30 GPa) and later heated (973 K) magnetite ore. To quantify variations of the transition shape caused by both shock and heating, the model statistically describes local variations in the Verwey transition temperature within bulk magnetite. For the description, Voigt profiles are used, which indicate variations between a Gaussian and a Lorentzian character. These changes are generally interpreted as variations in the degree of correlation between observed events, that is between local transition temperatures in the model. Shock pressures exceeding the Hugoniot elastic limit of magnetite ($ \ge $5 GPa) cause an increase in transition width and Verwey transition temperature, which is partially recovered by heat treatment. Above the Verwey transition temperature, susceptibility variations related to the magnetocrystalline anisotropy are described with an exponential approach. The room temperature magnetic susceptibility relative to the maximum near the isotropic point is reduced after shock, which is related to grain size reduction. Since significant oxidation and cation substitution can be excluded for the studied samples, variations are only attributed to changes in elastic strain associated with shock-induced deformation and annealing due to heat treatment. The shocked magnetite shows a high correlation between local transition temperatures which is reduced by heat treatment. The model allows a quantitative description of low-temperature magnetic susceptibility curves of experimentally shocked and subsequently heat-treated polycrystalline magnetite around the Verwey transition temperature. The curves are accurately reproduced within the experimental uncertainties. Further applications for analysing magnetite-bearing rocks seem possible if model parameters, such as for oxidation are included into the model.
Dengue NS1 Antibodies Are Associated With Clearance of Viral Nonstructural Protein-1
Authors: Premazzi Papa Michelle , Mendoza-Torres Evelyn , Sun Peifang , Encinales Liliana , Goulet Joseph , Defang Gabriel , Vihasi Jani , Cheng Ying , Suchowiecki Karol , Rosales Wendy , Amdur Richard , Porras-Ramirez Alexandra , Rico-Mendoza Alejandro , Herrera Gomez Carlos , Nicholes Samuel , Zuluaga Ivan , Halstead Liam , Halstead Scott , Simon Gary , Porter Kevin , Lynch Rebecca M , Chang Aileen Y 
Published: June 2024

Abstract

Background
Dengue vascular permeability syndrome is the primary cause of death in severe dengue infections. The protective versus potentially pathogenic role of dengue nonstructural protein-1 (NS1) antibodies are not well understood. The main goal of this analysis was to characterize the relationship between free NS1 concentration and NS1 antibody titers in primary and secondary dengue infection to better understand the presence and duration of NS1 antibody complexes in clinical dengue infections.

Methods
Hospitalized participants with acute dengue infection were recruited from Northern Colombia between 2018 and 2020. Symptom assessment, including dengue signs and symptoms, chart review, and blood collection, was performed. Primary versus secondary dengue was assessed serologically. NS1 titers and anti-NS1 antibodies were measured daily.

Results
Patients with secondary infection had higher antibody titers than those in primary infection, and there was a negative correlation between anti-NS1 antibody titer and NS1 protein. We demonstrate that in a subset of secondary infection, there were indeed NS1 antigen-antibody complexes on the admission day during the febrile phase that were not detectable by the recovery phase. Furthermore, dengue infection status was associated with higher circulating sialidases.

Discussion
The negative correlation between antibody and protein suggests that antibodies may play a role in clearing this viral protein.
Frondoside A of Cucumaria frondosa (Gennerus, 1767): Chemistry, biosynthesis, medicinal applications, and mechanism of actions
Authors: Fagbohun Oladapo F , Rollins Amanda , Mattern Lindsey , Cipollini Kendra , Rupasinghe HP Vasantha 
Published: June 2024

Abstract
Cucumaria frondosa (Gennerus, 1767) or orange-footed sea cucumbers are traditional food and are used as natural sources of anti-diabetic, anti-inflammatory, antioxidant, anti-angiogenic, antimicrobial, and anticancer agents. Currently, the introduction of value-added sea cucumber products to the global market has inspired basic research on frondoside A and other saponins in sea cucumbers. These saponins serve as a means of their chemical defence. However, recent studies revealed that exposure to these saponins can lead to irritating symptoms from aerosolization of various holothurins. Moreover, extraction methods are critical to the bioavailability of various bioactive compounds found in sea cucumbers. Therefore, we have critically reviewed recent studies on the chemistry, biosynthesis, and pharmacological properties of frondoside A. Furthermore, the mechanism of actions of frondoside A was postulated and further studies are required for applications in functional foods, nutraceuticals, and pharmaceuticals. Frondoside A was first discovered from Cucumaria frondosa, and it is involved in protein kinase (PI3K/AKT/ERK1/2/p38 MAPK, RAC/CDC42 PAK1, NFκB/MAPK/JNK, and LXR-β) signalling pathways. It is also involved in the suppression of MYC oncogene transcriptional factors implicated and upregulated in over 70% of cancer types. Future research needs to be aimed at optimized green extraction techniques, efficient delivery methods, safety, and efficacy.
Ozone enhances the efficacy of radiation therapy in esophageal cancer
Authors: Guo Jiayou , Guo Jiayi , Cheng Beibei , Gong Mengxiao , Sun Xingbang , Zhang Hongwei , Ma Jianxin 
Published: June 2024

Abstract
Radioresistance is increasingly developed in esophageal cancer. Increasing radiation sensitivity can reduce the mortality of esophageal cancer. To investigate the effect and mechanism of ozone on the radiotherapy sensitization of esophageal carcinoma. KYSE150 cells were xenografted subcutaneously into nude mice and irradiated with 8 Gy radiation according to different subgroups (sham, radiation, ozone and radiation+ozone group (n = 10 per group)). Half of the mice were used to determine the body weight, tumor size and tumor weight. Half of the mice were used to collect peripheral blood. The serum was centrifuged to detect circulating cell-free DNA (cf-DNA), interleukin-6 (IL-6), interferon-γ (IFN-γ), myeloperoxidase (MPO)-DNA complexes, tumor necrosis factor-α (TNF-α), matrix metalloproteinase-9 (MMP-9) and hypoxia-inducible factor-1α (HIF-1α) using commercial kits. The levels of phosphorylation AMP-activated protein kinase (p-AMPK) and scavenger receptor-A (SR-A) were measured by immunocytochemistry and Western blotting in the tumor tissues of mice. Ozone alone or combined with radiation therapy significantly reduced the body weight, tumor volume and tumor weight of esophageal cancer compared to the sham group. The ELISA results showed that the levels of cf-DNA, IFN-γ, MPO-DNA complexes, TNF-α, IL-6, HIF-1α and MMP-9 in the peripheral blood of mice treated with ozone combined with radiation were significantly lower compared with the radiation group. Ozone, synergistically with radiation, significantly increased the protein expression of p-AMPK and SR-A. Ozone may increase the radiosensitivity of esophageal cancer by inhibiting neutrophil extracellular traps.
Adaptive modifications in plant sulfur metabolism over evolutionary time
Authors: Kopriva Stanislav , Rahimzadeh Karvansara Parisa , Takahashi Hideki 
Published: June 2024

Abstract
Sulfur (S) is an essential element for life on Earth. Plants are able to take up and utilize sulfate (SO42–), the most oxidized inorganic form of S compounds on Earth, through the reductive S assimilatory pathway that couples with photosynthetic energy conversion. Organic S compounds are subsequently synthesized in plants and made accessible to animals, primarily as the amino acid methionine. Thus, plant S metabolism clearly has nutritional importance in the global food chain. S metabolites may be part of redox regulation and drivers of essential metabolic pathways as cofactors and prosthetic groups, such as Fe–S centers, CoA, thiamine, and lipoic acid. The evolution of the S metabolic pathways and enzymes reflects the critical importance of functional innovation and diversifications. Here we review the major evolutionary alterations that took place in S metabolism across different scales and outline research directions that may take advantage of understanding the evolutionary adaptations.
Observations and detectability of young Suns’ flaring and CME activity in optical spectra
Authors: Leitzinger M , Odert P , Greimel R 
Published: June 2024

ABSTRACT
The Sun’s history is still a subject of interest to modern astrophysics. Observationally constrained rates of Coronal Mass Ejections (CMEs) of young solar analogues are still lacking, as those require dedicated monitoring. We present medium-resolution optical spectroscopic monitoring of a small sample of bright and prominent solar analogues over a period of 3 yr using the 0.5-m telescope at observatory Lustbühel Graz (OLG) of the University of Graz, Austria. The aim is the detection of flares and CMEs from those spectra. In more than 1700 h of spectroscopic monitoring, we found signatures of four flares and one filament eruption on EK Dra which has been reported in previous literature, but we complementarily extended the data to cover the latter phase. The other stars did not reveal detectable signatures of activity. For these non-detections, we derive upper limits of occurrence rates of very massive CMEs, which are detectable with our observational setup, ranging from 0.1 to 2.2 d−1, but these may be even smaller than the given rates considering observational biases. Furthermore, we investigate the detectability of flares/CMEs in OLG spectra by utilizing solar 2D Hα spectra from Mees Solar Observatory. We find that solar-sized events are not detectable within our observations. By scaling up the size of the solar event, we show that with a fractional active region area of 18 per cent in residual spectra and 24 per cent in equivalent width time series derived from the same residuals that solar events are detectable if they had hypothetically occurred on HN Peg.
Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function
Authors: Šoltysová Markéta , Škerlová Jana , Pachl Petr , Škubník Karel , Fábry Milan , Sieglová Irena , Farolfi Martina , Grishkovskaya Irina , Babiak Michal , Nováček Jiří , Krásný Libor , Řezáčová Pavlína 
Published: June 2024

Abstract
The SorC family of transcriptional regulators plays a crucial role in controlling the carbohydrate metabolism and quorum sensing. We employed an integrative approach combining X-ray crystallography and cryo-electron microscopy to investigate architecture and functional mechanism of two prototypical representatives of two sub-classes of the SorC family: DeoR and CggR from Bacillus subtilis. Despite possessing distinct DNA-binding domains, both proteins form similar tetrameric assemblies when bound to their respective DNA operators. Structural analysis elucidates the process by which the CggR-regulated gapA operon is derepressed through the action of two effectors: fructose-1,6-bisphosphate and newly confirmed dihydroxyacetone phosphate. Our findings provide the first comprehensive understanding of the DNA binding mechanism of the SorC-family proteins, shedding new light on their functional characteristics.
AlphaKnot 2.0: a web server for the visualization of proteins’ knotting and a database of knotted AlphaFold-predicted models
Authors: Rubach Pawel , Sikora Maciej , Jarmolinska Aleksandra I , Perlinska Agata P , Sulkowska Joanna I 
Published: June 2024

Abstract
The availability of 3D protein models is rapidly increasing with the development of structure prediction algorithms. With the expanding availability of data, new ways of analysis, especially topological analysis, of those predictions are becoming necessary. Here, we present the updated version of the AlphaKnot service that provides a straightforward way of analyzing structure topology. It was designed specifically to determine knot types of the predicted structure models, however, it can be used for all structures, including the ones solved experimentally. AlphaKnot 2.0 provides the user’s ability to obtain the knowledge necessary to assess the topological correctness of the model. Both probabilistic and deterministic knot detection methods are available, together with various visualizations (including a trajectory of simplification steps to highlight the topological complexities). Moreover, the web server provides a list of proteins similar to the queried model within AlphaKnot’s database and returns their knot types for direct comparison. We pre-calculated the topology of high-quality models from the AlphaFold Database (4th version) and there are now more than 680.000 knotted models available in the AlphaKnot database. AlphaKnot 2.0 is available at https://alphaknot.cent.uw.edu.pl/.
Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB
Authors: Chu Chen-Hsi , Wu Che-Ting , Lin Min-Guan , Yen Cheng-Yi , Wu Yi-Zhan , Hsiao Chwan-Deng , Sun Yuh-Ju 
Published: June 2024

Abstract
The ParABS system, composed of ParA (an ATPase), ParB (a DNA binding protein), and parS (a centromere-like DNA), regulates bacterial chromosome partition. The ParB-parS partition complex interacts with the nucleoid-bound ParA to form the nucleoid-adaptor complex (NAC). In Helicobacter pylori, ParA and ParB homologs are encoded as HpSoj and HpSpo0J (HpParA and HpParB), respectively. We determined the crystal structures of the ATP hydrolysis deficient mutant, HpParAD41A, and the HpParAD41A-DNA complex. We assayed the CTPase activity of HpParB and identified two potential DNA binding modes of HpParB regulated by CTP, one is the specific DNA binding by the DNA binding domain and the other is the non-specific DNA binding through the C-terminal domain under the regulation of CTP. We observed an interaction between HpParAD41A and the N-terminus fragment of HpParB (residue 1–10, HpParBN10) and determined the crystal structure of the ternary complex, HpParAD41A-DNA-HpParBN10 complex which mimics the NAC formation. HpParBN10 binds near the HpParAD41A dimer interface and is clamped by flexible loops, L23 and L34, through a specific cation-π interaction between Arg9 of HpParBN10 and Phe52 of HpParAD41A. We propose a molecular mechanism model of the ParABS system providing insight into chromosome partition in bacteria.
Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance
Authors: Bandyra Katarzyna J , Fröhlich Kathrin S , Vogel Jörg , Rodnina Marina , Goyal Akanksha , Luisi Ben F 
Published: June 2024

Abstract
The ompD transcript, encoding an outer membrane porin in Salmonella, harbors a controlling element in its coding region that base-pairs imperfectly with a ‘seed’ region of the small regulatory RNA (sRNA) MicC. When tagged with the sRNA, the ompD mRNA is cleaved downstream of the pairing site by the conserved endoribonuclease RNase E, leading to transcript destruction. We observe that the sRNA-induced cleavage site is accessible to RNase E in vitro upon recruitment of ompD into the 30S translation pre-initiation complex (PIC) in the presence of the degradosome components. Evaluation of substrate accessibility suggests that the paused 30S PIC presents the mRNA for targeted recognition and degradation. Ribonuclease activity on PIC-bound ompD is critically dependent on the recruitment of RNase E into the multi-enzyme RNA degradosome, and our data suggest a process of substrate capture and handover to catalytic sites within the degradosome, in which sequential steps of seed matching and duplex remodelling contribute to cleavage efficiency. Our findings support a putative mechanism of surveillance at translation that potentially terminates gene expression efficiently and rapidly in response to signals provided by regulatory RNA.
The Role of e-Cigarette Packaging as a Health Communications Tool: A Focus Group Study With Adolescents and Adults in England and Scotland
Authors: Jones Daniel , Morgan Amber , Moodie Crawford , Alexandrou Georgia , Ford Allison , Mitchell Danielle 
Published: June 2024

Abstract

Introduction
In the United Kingdom, e-cigarette and refill packaging must display a nicotine addiction warning. This study explored how this message is perceived, responses to alternative on-pack messages, and other options for using e-cigarette packaging to discourage youth and people who neither smoke nor use e-cigarettes while encouraging smokers to switch.

Aims and Methods
Between August and September 2022, 16 focus groups (n = 70) were conducted to explore these topics with adolescents (n = 31, aged 11–17 years) and adults (n = 39, nonsmokers, smokers that use e-cigarettes, smokers that do not use e-cigarettes) in England and Scotland.

Results
While several participants thought the current nicotine addiction warning could help increase awareness of nicotine addiction, most reported that it failed to capture attention and was not a deterrent. Alternative messages shown on packs (about harm, toxicity, wellness, litter, or relative risk) received mixed responses. Relative risk messages were perceived as most beneficial for smokers switching but also thought to potentially encourage uptake among nonsmokers. Some participants considered certain harm and toxicity messages to potentially dissuade uptake. Participants proposed several ideas to reduce the appeal of e-cigarette packaging and devices to deter youth uptake, including more prominent warnings, standardized packaging, and devices that are plain or include health messages.

Conclusions
Packaging can play a crucial role in communicating product and health messages to different consumer groups. Further consideration of how packaging and labeling can meet the needs of non-nicotine users while simultaneously reaching those who may benefit from using e-cigarettes to stop smoking is warranted.

Implications
While some viewed the nicotine addiction warning required on e-cigarettes and refill packaging in the United Kingdom as helpful in raising awareness of nicotine addiction, it did not resonate with most of our sample of adolescents and adults. The findings suggest that e-cigarette packaging could be better used to encourage smokers to switch to a less harmful alternative, with relative risk messages showing promise. Furthermore, strengthening on-pack messaging (eg increasing salience and rotating messages) and reducing the appeal of packaging (eg drab colors) and devices (eg including warnings) may help increase awareness of e-cigarette harms while deterring use among adolescents and nonsmokers.
Managing Fear Responses: A Qualitative Analysis of Pictorial Warning Labels Five Years Post-Plain Packaging
Authors: Ozarka Ellen , Teddy Lani , Blank Mei-Ling , Waa Andrew , Hoek Janet 
Published: June 2024

Abstract

Introduction
Although pictorial warning labels (PWLs) now dominate tobacco packages sold in many countries, few studies have probed how people who smoke respond to the threats presented several years post-plain packaging and larger PWLs. Understanding how people manage the fear and dissonance PWLs arouse, and the strategies they use to rationalize, diminish, and reject risk messages, could inform future PWL design.

Aims and Methods
We undertook 27 in-depth interviews with people aged 18 and over (16 female, 8 Māori, and 13 aged ≤35) who smoked roll-your-own tobacco and lived in Aotearoa New Zealand. We probed participants’ views on current PWLs and how they responded to these, then asked them to use alternative images and headlines to create new PWLs. We drew on the extended parallel processing model to interpret the data, which we analyzed using a reflexive thematic analysis approach.

Results
People who smoke dislike PWLs, which they think reduce them to diseased body parts. While a minority thought existing PWLs were believable and effective, most reported avoiding PWLs by hiding or cognitively blocking them. Participants used diverse counterarguments to diminish PWLs’ relevance and impact, and a minority displayed strong reactance. Several suggested developing PWLs that recognized them as whole people rather than patients in waiting, and recommended greater use of testimonials, particularly from people who had successfully become smoke free.

Conclusions
PWLs using more holistic and diverse messages could elicit greater engagement and responsiveness, and motivate cessation more effectively than existing health-oriented warnings.

Implications
Our findings suggest existing PWLs, which aim to arouse fear of ill health, could be complemented by warnings that emphasize the benefits of quitting. Continuing to use threat-based PWLs could stimulate greater rationalization and reactance. By contrast, PWLs that aim to illustrate how cessation could benefit people who smoke and their families, rather than instill a fear of disease, could avoid message rejection and counter-argument, and may prove a more powerful way of motivating cessation.
Genetic variability of aquaporin expression in maize: From eQTLs to a MITE insertion regulating PIP2;5 expression
Authors: Maistriaux Laurie C , Laurent Maxime J , Jeanguenin Linda , Prado Santiago Alvarez , Nader Joseph , Welcker Claude , Charcosset Alain , Tardieu François , Nicolas Stéphane D , Chaumont François 
Published: June 2024

Abstract
Plant aquaporins are involved in numerous physiological processes, such as cellular homeostasis, tissue hydraulics, transpiration, and nutrient supply, and are key players of the response to environmental cues. While varying expression patterns of aquaporin genes have been described across organs, developmental stages, and stress conditions, the underlying regulation mechanisms remain elusive. Hence, this work aimed to shed light on the expression variability of 4 plasma membrane intrinsic protein (PIP) genes in maize (Zea mays) leaves, and its genetic causes, through expression quantitative trait locus (eQTL) mapping across a 252-hybrid diversity panel. Significant genetic variability in PIP transcript abundance was observed to different extents depending on the isoforms. The genome-wide association study mapped numerous eQTLs, both local and distant, thus emphasizing the existing natural diversity of PIP gene expression across the studied panel and the potential to reveal regulatory actors and mechanisms. One eQTL associated with PIP2;5 expression variation was characterized. Genomic sequence comparison and in vivo reporter assay attributed, at least partly, the local eQTL to a transposon-containing polymorphism in the PIP2;5 promoter. This work paves the way to the molecular understanding of PIP gene regulation and its possible integration into larger networks regulating physiological and stress adaptation processes.