bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep eutectic solvents for next-generation cyclodextrin science
Authors: Komiyama Makoto 
Published: November 2024

Abstract
In cyclodextrin science, water is employed as a solvent almost exclusively, and this imposes non-negligible limitations to the scope of applications. Accordingly, deep eutectic solvents, constructed from hydrogen-bonding donors and acceptors, have been attracting much interest as important substitutes for water. This review comprehensively covers chemical and physicochemical features of cyclodextrins in these eco-friendly solvents. In one category, cyclodextrins or their derivatives are dissolved as solutes in conventional deep eutectic solvents. All of α-, β-, and γ-cyclodextrins efficiently form inclusion complexes with various guest molecules, exactly as observed in water. Notably, chemically modified cyclodextrins (e.g. 2-hydroxypropyl-cyclodextrins) form even more stable inclusion complexes than native cyclodextrins. Alternatively, deep eutectic solvents are prepared by combining cyclodextrins with other hydrogen-bonding components. The cyclodextrin units in these mixtures also form inclusion complexes with guest molecules. It has been proposed that enhanced flexibility of cylindrical structures of cyclodextrins allows effective induced-fit to stabilize inclusion complexes. The applications of these systems range widely, from catalysis for organic synthesis to extraction, analysis, pharmaceutics, and many other fields. High solubilities of cyclodextrins and various chemicals in these solvents guarantee high productivity in target transformations. These unique systems promise further innovation.
Dexmedetomidine regulates exosomal miR-29b-3p from macrophages and alleviates septic myocardial injury by promoting autophagy in cardiomyocytes via targeting glycogen synthase kinase 3β
Authors: Yu Tianyi , Liu Hsinying , Gao Min , Liu Dan , Wang JiaQiang , Zhang Jie , Wang Jizhuang , Yang Peilang , Zhang Xiong , Liu Yan 
Published: November 2024

Abstract

Background
Our previous research suggested that dexmedetomidine (Dex) promotes autophagy in cardiomyocytes, thus safeguarding them against apoptosis during sepsis. However, the underlying mechanisms of Dex-regulated autophagy have remained elusive. This study aimed to explore the role of exosomes and how they participate in Dex-induced cardioprotection in sepsis. The underlying microRNA (miRNA) mechanisms and possible therapeutic targets for septic myocardial injury were identified.

Methods
We first collected plasma exosomes from rats with sepsis induced by caecal ligation and puncture (CLP) with or without Dex treatment, and then incubated them with H9c2 cells to observe the effect on cardiomyocytes. Subsequently, the differential expression of miRNAs in plasma exosomes from each group of rats was identified through miRNA sequencing. miR-29b-3p expression in circulating exosomes of septic or non-septic patients, as well as in lipopolysaccharide-induced macrophages after Dex treatment, was analysed by quantitative real-time polymerase chain reaction (qRT–PCR). The autophagy level of cardiomyocytes after macrophage-derived exosome treatment was assessed by an exosome tracing assay, western blotting, and an autophagic flux assay. Specific miRNA mimics and inhibitors or small interfering RNAs were used to predict and evaluate the function of candidate miRNA and its target genes by qRT-PCR, annexin V/propyl iodide staining, autophagy flux analysis, and western blotting.

Results
We found that plasma-derived exosomes from Dex-treated rats promoted cardiomyocyte autophagy and exerted antiapoptotic effects. Additionally, they exhibited a high expression of miRNA, including miR-29b-3p. Conversely, a significant decrease in miR-29b-3p was observed in circulating exosomes from CLP rats, as well as in plasma exosomes from sepsis patients. Furthermore, Dex upregulated the lipopolysaccharide-induced decrease in miR-29b-3p expression in macrophage-derived exosomes. Exosomal miR-29b-3p from macrophages is thought to be transferred to cardiomyocytes, thus leading to the promotion of autophagy in cardiomyocytes. Database predictions, luciferase reporter assays, and small interfering RNA intervention confirmed that glycogen synthase kinase 3β (GSK-3β) is a target of miR-29b-3p. miR-29b-3p promotes cardiomyocyte autophagy by inhibiting GSK-3β expression and activation.

Conclusions
These findings demonstrate that Dex attenuates sepsis-associated myocardial injury by modulating exosome-mediated macrophage–cardiomyocyte crosstalk and that the miR-29b-3p/GSK-3β signaling pathway represents a hopeful target for the treatment of septic myocardial injury.
From communities to interpretable network and word embedding: an unified approach
Authors: Prouteau Thibault , Dugué Nicolas , Guillot Simon 
Published: November 2024

Abstract
Modelling information from complex systems such as humans social interaction or words co-occurrences in our languages can help to understand how these systems are organized and function. Such systems can be modelled by networks, and network theory provides a useful set of methods to analyze them. Among these methods, graph embedding is a powerful tool to summarize the interactions and topology of a network in a vectorized feature space. When used in input of machine learning algorithms, embedding vectors help with common graph problems such as link prediction, graph matching, etc In Natural Language Processing (NLP), such a vectorization process is also employed. Word embedding has the goal of representing the sense of words, extracting it from large text corpora. Despite differences in the structure of information in input of embedding algorithms, many graph embedding approaches are adapted and inspired from methods in NLP. Limits of these methods are observed in both domains. Most of these methods require long and resource greedy training. Another downside to most methods is that they are black-box, from which understanding how the information is structured is rather complex. Interpretability of a model allows understanding how the vector space is structured without the need for external information, and thus can be audited more easily. With both these limitations in mind, we propose a novel framework to efficiently embed network vertices in an interpretable vector space. Our Lower Dimension Bipartite Framework (LDBGF) leverages the bipartite projection of a network using cliques to reduce dimensionality. Along with LDBGF, we introduce two implementations of this framework that rely on communities instead of cliques: SINr-NR and SINr-MF. We show that SINr-MF can perform well on classical graphs and SINr-NR can produce high-quality graph and word embeddings that are interpretable and stable across runs.
Device–device interference triggered by an abandoned pacemaker: a case report
Authors: Wang Dong , Mueller-Leisse Johanna , Hillmann Henrike A K , Eiringhaus Jörg , Duncker David 
Published: November 2024

Abstract

Background
Cardiac implantable electronic devices (CIEDs) are prone to electromagnetic interference. Common sources include household electronics and industrial machinery. However, medical equipment can also trigger interferences and cause CIED malfunction.

Case summary
We report on a 79-year-old male with sudden onset of presyncope. He has a long history of device therapy, including an active VVI leadless pacemaker and an abandoned abdominal pacemaker with epicardial leads. Automatic reactivation of the abandoned pacemaker due to reaching end-of-life mode led to interaction with the active pacemaker, inhibiting it in its function. Due to elevated capture threshold and insufficient output, pacing by the reactivated pacemaker was accompanied by intermittent loss of myocardial capture and patient symptoms. By changing the mode to VOO and increasing the pacing rate of the active pacemaker, the interaction was prevented as an intermittent solution. The final therapy consisted of explanting the pulse generator of the abdominal pacemaker.

Discussion
We present a patient with a deactivated abandoned cardiac pacemaker, which self-activated after reaching end-of-life mode and triggered an interaction with his active pacemaker. This case emphasizes the importance of explanting old devices to avoid potential interaction.
Shared genetic associations and aetiology between obstructive sleep apnoea and cardiovascular diseases: a genome-wide cross-trait analysis and bidirectional Mendelian randomization analysis
Authors: Feng Kun , Yang Jinyue , Liu Kai 
Published: November 2024

Abstract

Aims
Study aimed to investigate the genetic correlations and potential causal relationships between obstructive sleep apnoea (OSA) and various cardiovascular diseases (CVDs), aiming to enhance understanding of shared genetic mechanisms and improve recognition and treatment of OSA in patients with CVDs.

Methods and results
Utilizing genome-wide association study (GWAS) data, we analysed shared genetics between OSA and CVDs using linkage disequilibrium score regression, multi-trait analysis of GWAS (MTAG), and genotype–tissue expression analysis. We further investigated causal relationships using Bayesian co-localization tests, bidirectional Mendelian randomization, and latent causal variable analysis. We found strong associations between OSA and multiple CVDs: coronary artery disease (CAD), heart failure (HF), myocardial infarction (MI), stroke, and atrial fibrillation (AF). Novel single-nucleotide polymorphisms related to CVDs were identified during single-trait MTAG analysis. By applying cross-trait MTAG, we identified 15 shared loci between OSA and CAD, 25 shared loci between OSA and MI, and 7 shared loci between OSA and HF. Shared genes are primarily expressed in the blood, heart, kidney, liver, muscle, and pancreas. Mendelian randomization analysis indicated a significant causal effect of OSA on HF and AF as a causal factor for OSA. Latent causal variable analysis suggested that AF was causally associated with OSA, while HF showed partial causality.

Conclusion
Our study suggests strong genetic correlations between OSA and several CVDs. Further research is needed on the associations between OSA and CVDs, as well as the mechanisms of the identified loci.
Ventricular arrhythmias in association with athletic cardiac remodelling
Authors: D’Ambrosio Paolo , Claessen Guido , Kistler Peter M , Heidbuchel Hein , Kalman Jonathan M , La Gerche André 
Published: November 2024

Abstract
Athletes are predisposed to atrial arrhythmias but the association between intense endurance exercise training, ventricular arrhythmias (VAs), and sudden cardiac death is less well established. Thus, it is unclear whether the ‘athlete’s heart’ promotes specific arrhythmias or whether it represents a more general pro-arrhythmogenic phenotype. Whilst direct causality has not been established, it appears possible that repeated exposure to high-intensity endurance exercise in some athletes contributes to formation of pro-arrhythmic cardiac phenotypes that underlie VAs. Theories regarding potential mechanisms for exercise-induced VAs include repeated bouts of myocardial inflammation and stretch-induced cellular remodelling. Small animal models provide some insights, but larger animal and human data are sparse.
The current clinical approach to VAs in athletes is to differentiate those with and without structural or electrical heart disease. However, if the athlete’s heart involves a degree of pro-arrhythmogenic remodelling, then this may not be such a simple dichotomy. Questions are posed by athletes with VAs in combination with extreme remodelling. Some markers, such as scar on magnetic resonance imaging, may point towards a less benign phenotype but are also quite common in ostensibly healthy athletes. Other clinical and invasive electrophysiology features may be helpful in identifying the at-risk athlete.
This review seeks to discuss the association between athletic training and VAs. We will discuss the potential mechanisms, clinical significance, and approach to the management of athletes with VAs.
A review of multimodal deep learning methods for genomic-enabled prediction in plant breeding
Authors: Montesinos-López Osval A , Chavira-Flores Moises , Kiasmiantini  , Crespo-Herrera Leo , Saint Piere Carolina , Li HuiHui , Fritsche-Neto Roberto , Al-Nowibet Khalid , Montesinos-López Abelardo , Crossa José 
Published: November 2024

Abstract
Deep learning methods have been applied when working to enhance the prediction accuracy of traditional statistical methods in the field of plant breeding. Although deep learning seems to be a promising approach for genomic prediction, it has proven to have some limitations, since its conventional methods fail to leverage all available information. Multimodal deep learning methods aim to improve the predictive power of their unimodal counterparts by introducing several modalities (sources) of input information. In this review, we introduce some theoretical basic concepts of multimodal deep learning and provide a list of the most widely used neural network architectures in deep learning, as well as the available strategies to fuse data from different modalities. We mention some of the available computational resources for the practical implementation of multimodal deep learning problems. We finally performed a review of applications of multimodal deep learning to genomic selection in plant breeding and other related fields. We present a meta-picture of the practical performance of multimodal deep learning methods to highlight how these tools can help address complex problems in the field of plant breeding. We discussed some relevant considerations that researchers should keep in mind when applying multimodal deep learning methods. Multimodal deep learning holds significant potential for various fields, including genomic selection. While multimodal deep learning displays enhanced prediction capabilities over unimodal deep learning and other machine learning methods, it demands more computational resources. Multimodal deep learning effectively captures intermodal interactions, especially when integrating data from different sources. To apply multimodal deep learning in genomic selection, suitable architectures and fusion strategies must be chosen. It is relevant to keep in mind that multimodal deep learning, like unimodal deep learning, is a powerful tool but should be carefully applied. Given its predictive edge over traditional methods, multimodal deep learning is valuable in addressing challenges in plant breeding and food security amid a growing global population.
FOXO3 Longevity Genotype Mitigates Risk Posed by Hypertension on Incident Coronary Artery Disease in Middle-Aged Men: Kuakini Honolulu Heart Program
Authors: Chen Randi , Morris Brian J , Donlon Timothy A , Nakagawa Kazuma , Allsopp Richard C , Willcox Bradley J , Masaki Kamal H 
Published: November 2024

Abstract

Background
This study tested whether the carriage of the longevity-associated G-allele of FOXO3 SNP rs2802292 (TG/GG) protects against incident coronary artery disease (CAD) in men with hypertension.

Methods
Subjects were American men residing on Oahu having Japanese (n = 5415) or Okinawan (n = 897) ancestry and free of CAD at baseline (1965–1968) when aged 45–68 years.

Results
During the follow-up, there were 1 629 incident CAD cases. Adjusting for age and cardiovascular disease risk factors, the main effect Cox model showed that in men of Japanese ancestry, hypertension was a strong predictor of CAD (hazard ratio [HR] 1.61; 95% confidence interval [CI] 1.44–1.80), p &lt; .0001), but TG/GG genotype was not associated with CAD (HR 0.92; 95% CI = 0.82–1.02; p = .11). A full Cox model showed the interaction of TG/GG with hypertension was significant (β = –0.23, p = .038). Stratified by hypertension status, TG/GG genotype TG/GG had a protective effect against CAD in each group (HR 0.83; 95% CI 0.71–0.96; p = .021 in men of Japanese heritage, and HR 0.66; 95% CI 0.43–1.01; p = .054 in men of Okinawan heritage). No association with CAD was seen in normotensive men having either Japanese (HR 1.04; 95% CI 0.89–1.22; p = .61) or Okinawan (HR 0.95; 95% CI 0.66–1.38; p = .79) heritage.

Conclusions
The present prospective study found that longevity-associated FOXO3 genotype did not independently affect the risk of CAD in all men. Rather, it was associated with protection against incident CAD in men with hypertension. Hypertensive middle-aged men with FOXO3TT genotype may merit particular attention in CAD prevention programs.
In-plane dynamic analysis of supershear rupture transition due to poroelastic pressurization
Authors: Mu Changqing , Song Yongjia , Hu Hengshan 
Published: November 2024

SUMMARY
Although pore fluid has received increased attention in the problems of earthquake rupture, its effects on coseismic rupture are not fully understood. In this paper, we numerically simulate dynamic rupture in saturated poroelastic media to study the interplay between poroelastic pressurization and rupture evolution. Particular attention is paid to the physical process of the supershear transition. The spontaneous rupture is assumed to be governed by slip weakening law and the fault is treated as a leaky interface where pore pressure equilibrium is delayed. Results show that the pore pressure induced by coseismic mechanical deformation can strengthen the fault on the extensional side but weaken the fault on the compressional side. As a result, the poroelastic pressurization on the compressional side can promote the occurrence of the transition to supershear rupture while its strengthening effect on the extensional side can suppress this transition even in the state of high-initial shear stress. Meanwhile, it is found that the permeability distribution along the fault plane also affects rupture evolution. Faults with nucleation zones located in low-permeability regions are more likely to undergo a supershear rupture.
Evolution of Plant Genome Size and Composition
Authors: He Bing , Liu Wanfei , Li Jianyang , Xiong Siwei , Jia Jing , Lin Qiang , Liu Hailin , Cui Peng 
Published: November 2024

Abstract
The rapid development of sequencing technology has led to an explosion of plant genome data, opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes. In this review, we focus on changes in plant genome size and composition, examining the effects of polyploidy, whole-genome duplication, and alternations in transposable elements on plant genome architecture and evolution, respectively. In addition, to address gaps in the available information, we also collected and analyzed 234 representative plant genome data as a supplement. We aim to provide a comprehensive, up-to-date summary of information on plant genome architecture and evolution in this review.
Right ventricular outlet tract reconstruction for tetralogy of Fallot: systematic review and network meta-analysis
Authors: Yamaguchi Akira , Shimoda Tomonari , Kinami Hiroo , Yasuhara Jun , Takagi Hisato , Fukuhara Shinichi , Kuno Toshiki 
Published: November 2024

Abstract

OBJECTIVES
Concerns persist regarding pulmonary regurgitation after transannular patch repair (TAP) for tetralogy of Fallot. Despite the introduction of various architectural preservation techniques, the optimal strategy remains controversial. Our goal was to compare different right ventricular outlet tract reconstruction techniques.

METHODS
PubMed, EMBASE and Cochrane Central were searched through March 2024 to identify comparative studies on right ventricular outlet tract reconstruction techniques (PROSPERO ID: CRD42024519404). The primary outcome was mid-term pulmonary regurgitation, with secondary outcomes including postoperative mortality, postoperative pulmonary regurgitation, length of intensive care unit stays, postoperative right ventricular outlet tract pressure gradient and mid-term mortality. We performed a network meta-analysis to compare outcomes among TAP, valve-repairing (VR), TAP with neo-valve creation (TAPN) and valve-sparing (VS).

RESULTS
Two randomized controlled studies and 32 observational studies were identified with 8890 patients. TAP carried a higher risk of mid-term pulmonary regurgitation compared to TAPN [hazard ratio, 0.53; 95% confidence interval (CI) (0.33; 0.85)] and VS [hazard ratio, 0.27; 95% CI (0.19; 0.39)], with no significant difference compared to VR. VS was also associated with reduced postoperative mortality compared to TAP [risk ratio, 0.31; 95% CI (0.18; 0.56)], in addition to reduced ventilation time. TAP also carried an increased risk of postoperative pulmonary regurgitation compared to the other groups. The groups were comparable in terms of length of intensive care unit stay, right ventricular outlet tract pressure gradient and mid-term mortality.

CONCLUSIONS
VR was associated with a reduced risk of postoperative pulmonary regurgitation, whereas TAPN was associated with reduced risks of both postoperative and mid-term pulmonary regurgitation.
Global Well-Posedness for the Derivative Nonlinear Schrödinger Equation with Periodic Boundary Condition
Authors: Bahouri Hajer , Perelman Galina 
Published: November 2024

Abstract
We prove global well-posedness for the derivative nonlinear Schrödinger equation on the torus in the Sobolev space $H^{1}(\mathbb{T})$ provided that the mass of initial data is strictly less than $8\pi $.
Sheaths are diverse and abundant cell surface layers in archaea
Authors: Medvedeva Sofia , Borrel Guillaume , Gribaldo Simonetta 
Published: November 2024

Abstract
Prokaryotic cells employ multiple protective layers crucial for defense, structural integrity, and cellular interactions in the environment. Archaea often feature an S-layer, with some species possessing additional and remarkably resistant sheaths. The archaeal sheath has been studied in Methanothrix and Methanospirillum, revealing a complex structure consisting of amyloid proteins organized into rings. Here, we conducted a comprehensive survey of sheath-forming proteins (SH proteins) across archaeal genomes. Structural modeling reveals a rich diversity of SH proteins, indicating the presence of a sheath in members of the TACK superphylum (Thermoprotei), as well as in the methanotrophic ANME-1. SH proteins are present in up to 40 copies per genome and display diverse domain arrangements suggesting multifunctional roles within the sheath, and potential involvement in cell–cell interaction with syntrophic partners. We uncover a complex evolutionary dynamic, indicating active exchange of SH proteins in archaeal communities. We find that viruses infecting sheathed archaea encode a diversity of SH-like proteins and we use them as markers to identify 580 vOTUs potentially associated with sheathed archaea. Structural modeling suggests that viral SH proteins can form complexes with the host SH proteins. We propose a previously unreported egress strategy where the expression of viral SH-like proteins may disrupt the integrity of the host sheath and facilitate viral exit during lysis. Together, our results significantly expand knowledge of the diversity and evolution of the archaeal sheath, which has been largely understudied but might have an important role in shaping microbial communities.