bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial quality control via organelle and protein degradation
Authors: Yamano Koji , Kinefuchi Hiroki , Kojima Waka 
Published: December 2023

Abstract
Mitochondria are essential eukaryotic organelles that produce ATP as well as synthesize various macromolecules. They also participate in signalling pathways such as the innate immune response and apoptosis. These diverse functions are performed by &gt;1,000 different mitochondrial proteins. Although mitochondria are continuously exposed to potentially damaging conditions such as reactive oxygen species, proteases/peptidases localized in different mitochondrial subcompartments, termed mitoproteases, maintain mitochondrial quality and integrity. In addition to processing incoming precursors and degrading damaged proteins, mitoproteases also regulate metabolic reactions, mitochondrial protein half-lives and gene transcription. Impaired mitoprotease function is associated with various pathologies. In this review, we highlight recent advances in our understanding of mitochondrial quality control regulated by autophagy, ubiquitin–proteasomes and mitoproteases.
NRIP1 regulates cell proliferation in lung adenocarcinoma cells
Authors: Watanabe Fumihiko , Sato Shigemitsu , Hirose Takuo , Endo Moe , Endo Akari , Ito Hiroki , Ohba Koji , Mori Takefumi , Takahashi Kazuhiro 
Published: December 2023

Abstract
Nuclear receptor interacting protein 1 (NRIP1) is a transcription cofactor that regulates the activity of nuclear receptors and transcription factors. Functional expression of NRIP1 has been identified in multiple cancers. However, the expression and function of NRIP1 in lung adenocarcinoma have remained unclear. Thus, we aimed to clarify the NRIP1 expression and its functions in lung adenocarcinoma cells. NRIP1 and Ki-67 were immunostained in the tissue microarray section consisting of 64 lung adenocarcinoma cases, and the association of NRIP1 immunoreactivity with clinical phenotypes was examined. Survival analysis was performed in lung adenocarcinoma data from The Cancer Genome Atlas (TCGA). Human A549 lung adenocarcinoma cell line with an NRIP1-silencing technique was used in vitro study. Forty-three of 64 cases were immunostained with NRIP1. Ki-67–positive cases were more frequent in NRIP1-positive cases as opposed to NRIP1-negative cases. Higher NRIP1 mRNA expression was associated with poor prognosis in the TCGA lung adenocarcinoma data. NRIP1 was mainly located in the nucleus of A549 cells. NRIP1 silencing significantly reduced the number of living cells, suppressed cell proliferation, and induced apoptosis. These results suggest that NRIP1 participates in the progression and development of lung adenocarcinoma. Targeting NRIP1 may be a possible therapeutic strategy against lung adenocarcinoma.
Exploring protein lipidation by mass spectrometry-based proteomics
Authors: Tsumagari Kazuya , Isobe Yosuke , Imami Koshi , Arita Makoto 
Published: December 2023

Abstract
Protein lipidation is a common co- or post-translational modification that plays a crucial role in regulating the localization, interaction and function of cellular proteins. Dysregulation of lipid modifications can lead to various diseases, including cancer, neurodegenerative diseases and infectious diseases. Therefore, the identification of proteins undergoing lipidation and their lipidation sites should provide insights into many aspects of lipid biology, as well as providing potential targets for therapeutic strategies. Bottom-up proteomics using liquid chromatography/tandem mass spectrometry is a powerful technique for the global analysis of protein lipidation. Here, we review proteomic methods for profiling protein lipidation, focusing on the two major approaches: the use of chemical probes, such as lipid alkyne probes, and the use of enrichment techniques for endogenous lipid-modified peptides. The challenges facing these methods and the prospects for developing them further to achieve a comprehensive analysis of lipid modifications are discussed.
Genome-wide analysis and characterization of HSP gene families (HSP20, HSP40, HSP60, HSP70, HSP90) in the yellow fever mosquito (Aedes aegypti) (Diptera: Culicidae)
Authors: Turan Murat 
Published: December 2023

Abstract
The heat shock protein (HSP) gene families, present across prokaryotes to eukaryotes, play vital roles in growth, development, and heat resistance processes. While HSP proteins have been identified and characterized in various species, this study achieved the first genome-wide identification and characterization of HSP proteins in the Aedes aegypti genome. This study identified and assessed 80 potential HSP genes in Ae. aegypti. The phylogenetic relationships of HSP genes were investigated in Ae. aegypti, Anopheles stephensi, and Drosophila melanogaster. Additionally, the structural features, chromosomal locations, protein characteristics, 3D structure, protein–protein interactions, and microsatellites associated with HSP proteins were examined in Ae. aegypti. The phylogenetic analysis of HSP gene families revealed distinct intra-group relationships for each HSP group. Each family exhibited relatively conserved genetic structures and motif components. In the expression analysis of growth and development, high expression was observed in certain HSP20 and HSP70 genes, while others exhibited low expression. Notably, sex-dependent expression differences were observed, particularly in HSP20 genes. These findings, the relationships, evolution, and modification of HSP gene families are illuminated by these comprehensive findings, and a better understanding of the mechanisms underlying growth, development, and heat resistance in vector organisms is facilitated.
Firmicutes and Bacteroidetes contribute to mass gain variation in female obligate hibernators
Authors: Degregori Samuel , Johnson Gina C , Barber Paul H , Blumstein Daniel T 
Published: December 2023

Abstract
Obtaining body condition is an important life history challenge that directly impacts individual fitness and is particularly important for hibernating animals, whose maintenance of adequate body fat and mass is essential for survival. It is well-documented that host-associated microorganisms play a vital role in animal physiology and behavior. Recent work demonstrates that gut microbes are associated with fat accumulation and obesity, particularly the phyla Firmicutes and Bacteroidetes. The focus of most microbiome studies has been on human health or involved lab-reared animals used as a model system. However, these microbes likely are important for individual fitness in wild populations and provide potential mechanistic insights into the adaptability and survival of wildlife. Here we tested whether symbiotic microorganisms within the phyla of Firmicutes and Bacteroidetes were associated with summer mass gain in an exceptionally well-studied wild population of yellow-bellied marmots (Marmota flaviventer) by analyzing 207 fecal samples collected over 5 summer active seasons. Results showed that marmots with higher mass gain rates had a greater relative abundance of Firmicutes. In contrast, a higher relative abundance of Bacteroidetes was associated with lower mass gain rates, but only for marmots living in harsher environments. Similar patterns were found at the family level where Ruminococcaceae, a member of Firmicutes, was associated with higher mass gain rates, and Muribaculaceae, a member of Bacteroidetes, was associated with lower mass gain rates in harsher environments. Although correlative, these results highlight the potential importance of symbiotic gut microbiota to mass gain in the wild—a trait associated with survival and fitness in many taxonomic groups.
A new extinct desert rodent from the Holocene of South America and its bearing on the diversity of Octodontidae (Hystricognathi)
Authors: Verzi Diego H , Olivares A Itatí , De Santi Nahuel A , Morgan Cecilia C , López José Manuel , Chiavazza Horacio 
Published: December 2023

Abstract
A Late Holocene (ca. 3,100 to 380 BP) sample of the viscacha rat genus Octomys (Octodontidae) from the Vaquerías Gruta 1 site (VQ-G1) in western Argentina is reported. Phylogenetic and morphometric comparative analyses with living octodontids support that the VQ-G1 sample is related to the desert specialists Tympanoctomys and Octomys, and is sister to the only living species of the latter, O. mimax. The estimated morphological distance to O. mimax is greater than that between pairs of congeneric octodontid species, and even greater than that between some species belonging to different genera. This suggests that the sample represents a new species, whose young age prevents interpreting it as an anagenetic ancestor of O. mimax. If the new species is the result of cladogenesis, its absence in the current fauna represents actual extinction, which among caviomorphs is added to those of †Clyomys riograndensis, †Dicolpomys fossor, †Ctenomys viarapaensis, and †Galea tixiensis—also extinct in the Late Holocene. Thus, the VQ-G1 sample provides evidence of changes in diversity and distribution undergone by small mammals in southern South America during that time. The potential contribution of the Holocene record may be key to elucidate this issue from both an evolutionary and a conservation perspective. This requires a detailed systematic approach to determine whether the taxa under study are truly independent evolutionary units, as well as geographically broad sampling efforts to distinguish the changes affecting distribution from those producing irreversible changes in diversity.
Optical microscopic imaging, manipulation, and analysis methods for morphogenesis research
Authors: Katoh Takanobu A , Fukai Yohsuke T , Ishibashi Tomoki 
Published: December 2023

Abstract
Morphogenesis is a developmental process of organisms being shaped through complex and cooperative cellular movements. To understand the interplay between genetic programs and the resulting multicellular morphogenesis, it is essential to characterize the morphologies and dynamics at the single-cell level and to understand how physical forces serve as both signaling components and driving forces of tissue deformations. In recent years, advances in microscopy techniques have led to improvements in imaging speed, resolution and depth. Concurrently, the development of various software packages has supported large-scale, analyses of challenging images at the single-cell resolution. While these tools have enhanced our ability to examine dynamics of cells and mechanical processes during morphogenesis, their effective integration requires specialized expertise. With this background, this review provides a practical overview of those techniques. First, we introduce microscopic techniques for multicellular imaging and image analysis software tools with a focus on cell segmentation and tracking. Second, we provide an overview of cutting-edge techniques for mechanical manipulation of cells and tissues. Finally, we introduce recent findings on morphogenetic mechanisms and mechanosensations that have been achieved by effectively combining microscopy, image analysis tools and mechanical manipulation techniques.
THE SOLACE OF PILGRIMS: MOVEMENT, REST, AND SLEEP IN THE PILGRIM’S PROGRESS
Authors: Christner Sharon Rose 
Published: December 2023

Abstract
Scholars of John Bunyan have understandably emphasised the progress of The Pilgrim’s Progress. However, the description of the places of rest along Christian’s journey call into question the role of the pause in the pilgrim’s journey, as well as the exclusive ‘futureness’ of the peace and rest of God as depicted by Bunyan. The encounter with Simple, Sloth, and Presumption, the Arbour on the Hill Difficulty, and the temptation of the Enchanted Ground are shown as moments of illusory or disobedient rest, where falling asleep is equated with spiritual drowsiness. The House Beautiful, the Delectable Mountains, and Beulah prove places that challenge the idea of unrelenting progress as ideal for the faithful pilgrim.
LEONTES’ ORIGINAL SIN: GENESIS 3 AND THE WINTER’S TALE
Authors: Kanary Jonathan 
Published: December 2023

Abstract
Scholars have often noted the presence of language about penance and repentance in The Winter’s Tale, but less attention has been paid to the way Shakespeare portrays sinfulness itself. This article argues that, especially in the first three acts, the playwright uses repeated allusions to Genesis 3, along with a theological interpretation of evil as privation, to reveal the nature, development, and consequences of Leontes’ sin. This biblically-inflected portrait of sin and evil, in turn, significantly shapes the themes of penitence and forgiveness in the latter half of the play, as Leontes’ repentant sinfulness is transfigured by grace.
Scientific preparation for CSST: classification of galaxy and nebula/star cluster based on deep learning
Authors: Zhang Yuquan , Cao Zhong , Wang Feng , Lam Man I , Deng Hui , Mei Ying , Tan Lei 
Published: December 2023

ABSTRACT
The Chinese Space Station Telescope (abbreviated as CSST) is a future advanced space telescope. Real-time identification of galaxy and nebula/star cluster (abbreviated as NSC) images is of great value during CSST survey. While recent research on celestial object recognition has progressed, the rapid and efficient identification of high-resolution local celestial images remains challenging. In this study, we conducted galaxy and NSC image classification research using deep learning methods based on data from the Hubble Space Telescope. We built a local celestial image data set and designed a deep learning model named HR-CelestialNet for classifying images of the galaxy and NSC. HR-CelestialNet achieved an accuracy of 89.09 per cent on the testing set, outperforming models such as AlexNet, VGGNet, and ResNet, while demonstrating faster recognition speeds. Furthermore, we investigated the factors influencing CSST image quality and evaluated the generalization ability of HR-CelestialNet on the blurry image data set, demonstrating its robustness to low image quality. The proposed method can enable real-time identification of celestial images during CSST survey mission.
Therapeutic effects and mechanisms of action of ginger and its bioactive components on inflammatory response, oxidative stress, the immune system, and organ failure in sepsis: a comprehensive systematic review
Authors: Velayati Aynaz , Vafa Mohamad Reza , Sani'ee Nadia , Darabi Zahra 
Published: December 2023

Abstract

Context
Sepsis refers to a usually lethal medical condition that results from an extreme, uncontrolled, and multifaceted immune system response to infection. Ginger (Zingiber officinale Roscoe; Zingiberaceae) is 1 of the most popular spice. It is widely used as a traditional herb and as medicine in the treatment of some inflammatory conditions, such as vomiting, pain, cancer, diabetes, and cardiovascular diseases, because of its varied medical characteristics, including anti-inflammatory, antioxidant, antimicrobial, and antitumor effects.

Objective
The aim of this study was to demonstrate the potential roles of ginger and its elements in sepsis.

Data Sources
This systematic review article was conducted and reported by following the guideline of the Preferred Reporting for Systematic Reviews (PRISMA). Electronic databases, including Web of Sciences, Google Scholar, PubMed, Scopus, and ProQuest, were searched using related key words up to January 2023.

Data Extraction
Among 141 found articles, 48 eligible articles were included and reviewed for their details. Data were extracted, including the first author's name, year of publication, name of origin country, study design, number and type of subject, dosage and type of intervention, study duration, assay, and main results.

Data Analysis
The data from the included articles showed that ginger and its bioactive elements, such as gingerol (1–300 µg/mL or 1–100 mg/kg for 24 hours to 14 days), shogaol (0.2–100 µg/mL or 10–40 mg/kg body weight for 24 hours to 8 days), gingerdione (1–100 µg/mL for 20–48 hours), and zingerone (2–20 µM for 4 hours to 8 days), can be effective in sepsis via suppressing the gene expression and production of pro-inflammatory cytokines and oxidant agents, downregulating immune response, and protecting against sepsis-induced organ failures in experimental and animal models.

Conclusion
Ginger has potential therapeutic effects in sepsis. Human clinical trials are recommended.

Systematic Review Registration
PROSPERO registration no. CRD42023373613.
Effect of breakfast protein intake on muscle mass and strength in adults: a scoping review
Authors: Khaing Inn-Kynn , Tahara Yu , Chimed-Ochir Odgerel , Shibata Shigenobu , Kubo Tatsuhiko 
Published: December 2023

Abstract

Background
The distribution of protein intake throughout the day is frequently skewed, with breakfast having the lowest protein intake across all age groups. There is no review that addresses the association between breakfast protein intake and muscle mass and strength.

Objective
This scoping review aims to summarize the literature on the relationship between protein intake during breakfast and muscle mass and strength in adults.

Methods
This review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews. Two independent reviewers screened and appraised the articles identified from 3 electronic databases (Medline, Web of Science, and Scopus) that focused on protein intake per meal and its impact on muscle-related outcomes.

Results
A total of 14 763 articles were retrieved from 3 databases, and after the screening process, 15 articles were included for analysis. Approximately 58.8% of findings from 11 studies examining the association between high protein intake during breakfast and muscle mass indicated an increase in muscle mass among participants. Half of 6 studies (50.0%) exploring the relationship between high protein intake at breakfast and muscle strength demonstrated an increase in muscle strength. Consuming high amounts of protein at breakfast or more protein in the morning than in the evening was associated with an increase in the skeletal muscle index and lean body mass.

Conclusion
Protein consumption at breakfast revealed potential benefits in increasing muscle mass across 5 studies involving an elderly population and 2 studies encompassing middle-aged women and young men in our review. However, the relationship between protein intake at breakfast and muscle strength remains unclear. Further high-quality randomized controlled trials are required to examine whether adults can preserve skeletal muscle health outcomes by consuming higher amounts of protein at breakfast.
Effects of intermittent dieting with break periods on body composition and metabolic adaptation: a systematic review and meta-analysis
Authors: Poon Eric Tsz-Chun , Tsang Jaclyn Hei , Sun Fenghua , Zheng Chen , Wong Stephen Heung-Sang 
Published: December 2023

Abstract

Context
Intermittent dieting incorporated with break periods (INT-B) has recently been promoted as an alternative dietary approach for optimal weight management.

Objective
This study assessed the effectiveness of INT-B compared with that of conventional continuous energy restriction (CER) for improving body composition and attenuating metabolic adaptation.

Data Sources
A systematic search was conducted on 6 databases using all available records until July 2023.

Data Extraction
The extracted data included the lead author, year of publication, population characteristics, intervention protocols, duration, and adherence.

Data Analysis
Random-effects meta-analyses were conducted for within-group and between-group comparisons of anthropometric and metabolic outcomes. Subgroup moderator analysis was performed for the types of INT-B, intervention duration, and population characteristics.

Results
Of the 1469 records, 12 randomized trials (with 881 participants) were included. Within-group analyses demonstrated significant improvements in body mass, fat mass, body mass index, body fat percentage, and waist circumference following both INT-B and CER, with no significant group differences. However, resting metabolic rate (RMR) was significantly reduced following CER only. The compensatory reduction in RMR was significantly smaller following INT-B compared with CER, suggesting a lesser degree of metabolic adaptation. INT-B had a more significant effect on RMR retention in individuals with overweight/obesity compared with resistance-trained individuals.

Conclusion
This review provides up-to-date evidence for INT-B as a viable dietary strategy to improve body composition and attenuate metabolic adaptation.

Systematic Review Registration
PROSPERO registration no. CRD42023448959.
Growing ecosystem of deep learning methods for modeling protein–protein interactions
Authors: Rogers Julia R , Nikolényi Gergő , AlQuraishi Mohammed 
Published: December 2023

Abstract
Numerous cellular functions rely on protein–protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep learning has emerged as a promising approach for tackling this problem by exploiting both experimental data and basic biophysical knowledge about protein interactions. Here, we review the growing ecosystem of deep learning methods for modeling protein interactions, highlighting the diversity of these biophysically informed models and their respective trade-offs. We discuss recent successes in using representation learning to capture complex features pertinent to predicting protein interactions and interaction sites, geometric deep learning to reason over protein structures and predict complex structures, and generative modeling to design de novo protein assemblies. We also outline some of the outstanding challenges and promising new directions. Opportunities abound to discover novel interactions, elucidate their physical mechanisms, and engineer binders to modulate their functions using deep learning and, ultimately, unravel how protein interactions orchestrate complex cellular behaviors.
Telehealth technologies in care homes: a gap for dentistry?
Authors: Bhamra Ishmyne B , Gallagher Jennifer E , Patel Rakhee 
Published: December 2023

Abstract

Background
Telehealth technologies are playing an increasing role in healthcare. This study aimed to review the literature relating to the use of telehealth technologies in care homes with a focus on teledentistry.

Methods
Khangura et al.’s (Evidence summaries: the evolution of a rapid review approach. Syst Rev 2012;1:10) rapid review method included an electronic database search on Embase, PubMed, Web of Science and OpenGrey. Out of 1525 papers, 1108 titles and abstracts were screened, and 75 full texts assessed for eligibility. Risk of bias was assessed using the Mixed Methods Assessment Tool 2018.

Results
Forty-seven papers (40 studies) from 10 countries, published 1997–2021, were included in the review, four studies related to teledentistry. Whilst some preferred in-person consultations, perceived benefits by stakeholders included reduced hospitalization rates (n = 14), cost-savings (n = 8) and high diagnostic accuracy (n = 7). Studies investigating teledentistry using intra-oral cameras reported that teleconsultations were feasible with potentially high diagnostic accuracy (n = 2), cost-savings (n = 1) and patient acceptability (n = 1).

Conclusion
There is limited published research on teledentistry, but wider telehealth research is applicable to teledentistry, with findings suggesting that telehealth technologies play a role in care homes consultations that are acceptable, cost-saving and with potential diagnostic accuracy. Further research is needed on the mode, utility and acceptability of teledentistry in care homes.