bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing core microbiota and regulatory functions of the pig gut microbiome
Authors: Hu Jun , Chen Jianwei , Ma Libao , Hou Qiliang , Zhang Yong , Kong Xiangfeng , Huang Xingguo , Tang Zhonglin , Wei Hong , Wang Xiangru , Yan Xianghua 
Published: January 2024

Abstract
Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host–microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes. We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as “steroid hormone biosynthesis,” “primary bile acid biosynthesis,” “phenylalanine, tyrosine and tryptophan biosynthesis,” and “phenylalanine metabolism”) in germ-free mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.
Doubts and certainties about the Duke of Urbino’s diplomatic gifts to Prince Philip of Spain in 1593
Authors: Campos-Perales Àngel 
Published: January 2024

Abstract
In 1593 Francesco Maria II della Rovere, Duke of Urbino, sent a number of diplomatic gifts to Philip II of Spain, intended for the crown prince, the future Philip III. The gifts included a silver model of a citadel accompanied by a set of compasses, the whereabouts of which are currently unknown; a small gilt-bronze sculptural group which has been identified with Giovanni Bandini’s The Hunt, today in the Prado Museum; and an illuminated manuscript recounting glorious episodes from the reign of the Emperor Charles V, Philip III’s grandfather, identified with British Library, Add. ms 33733, which contains miniatures possibly by Simonzio Lupi. A study of some of the inventories made in Madrid at the beginning of the seventeenth century has revealed that The Hunt and the illuminated manuscript might subsequently have belonged to persons close to the Duke of Lerma, Philip III’s prime minister – namely, Juan de Borja, the duke’s uncle, and Jerónimo Funes, the son-in-law of the secretary of state, Count of Villalonga, respectively.
Causes and consequences of pre-hibernation body mass in golden-mantled ground squirrels (Callospermophilus lateralis)
Authors: Howland Summer , Wells Caitlin P , Van Vuren Dirk H 
Published: January 2024

Abstract
Mammals that cope with harsh environmental conditions by hibernating show seasonal variation in body mass, as fat reserves are accumulated during summer and depleted during winter. In hibernating species, pre-hibernation mass is often considered a key phenotypic trait that can influence future survival and reproductive success—yet we know little about how variation in environmental conditions and seasonality affect pre-hibernation mass. We used 30 years of demographic data from a high-elevation population of golden-mantled ground squirrels (Callospermophilus lateralis) to identify life history and environmental variables that influenced pre-hibernation mass in females. Additionally, we determined if pre-hibernation mass influenced overwinter survival or subsequent reproduction. Growth curves revealed female-biased size dimorphism in body mass; adult mass was not attained until age 2 years, so we considered 3 age classes of females: juveniles, yearlings, and adults (≥2 years). We found that earlier snow melt during spring is associated with higher subsequent pre-hibernation body mass for yearlings and adults, and that juveniles emerging earlier from their natal burrows had higher pre-hibernation masses than later-emerging juveniles. Estimates of food quantity or quality did not affect pre-hibernation mass for any age class, nor was there an effect of reproductive status. Juvenile females with greater pre-hibernation mass were more likely to survive overwinter and reproduce as yearlings, but we found no such effect for yearlings or adult females. We did not find an effect of snow depth or winter duration on either survival or reproduction. Our results indicate that time appears to be the key variable for golden-mantled ground squirrels to acquire sufficient body mass to survive and reproduce, but the effects vary by age class.
Association of denosumab with serum cytokines, chemokines, and bone-related factors in patients with rheumatoid arthritis: A post hoc analysis of a multicentre, open-label, randomised, parallel-group study
Authors: Iwamoto Naoki , Sato Shuntaro , Furukawa Kaori , Michitsuji Toru , Shiraishi Kazuteru , Watanabe Kounosuke , Chiba Ko , Osaki Makoto , Kawakami Atsushi 
Published: January 2024

ABSTRACT

Objectives
To clarify changes in serum cytokines, chemokines, and bone-related factors during denosumab treatment in rheumatoid arthritis (RA) patients.

Methods
This was a post hoc analysis of a multicentre, open-label, randomised, parallel-group study. Patients were randomly assigned to continue treatment with conventional synthetic disease-modifying anti-rheumatic drugs (csDMARDs) plus receive treatment with denosumab (csDMARDs plus denosumab group) or to continue treatment with csDMARD therapy alone for 12 months. Serum biomarker levels were measured at baseline and at 6 and 12 months.

Results
Baseline and 6-month data from the csDMARDs plus denosumab (n = 22) and csDMARD therapy alone (n = 22) groups were analysed. Statistically significant changes from baseline were seen: Dickkopf-related protein 1 decreased at 6 and 12 months (both groups); osteopontin decreased at 6 months in the csDMARDs plus denosumab group; osteopontin and soluble CD40 ligand increased at 6 and 12 months in the csDMARD therapy alone group; osteocalcin decreased at 6 and 12 months, epidermal growth factor decreased at 12 months, and macrophage-derived chemokine decreased at 6 months in the csDMARDs plus denosumab group; and interferon gamma-induced protein-10 increased at 12 months in the csDMARD therapy alone group.

Conclusions
Denosumab may inhibit bone destruction by suppressing bone-related factors/chemokines.
NAC and Zuotin/Hsp70 chaperone systems coexist at the ribosome tunnel exit in vivo
Authors: Ziegelhoffer Thomas , Verma Amit K , Delewski Wojciech , Schilke Brenda A , Hill Paige M , Pitek Marcin , Marszalek Jaroslaw , Craig Elizabeth A 
Published: January 2024

Abstract
The area surrounding the tunnel exit of the 60S ribosomal subunit is a hub for proteins involved in maturation and folding of emerging nascent polypeptide chains. How different factors vie for positioning at the tunnel exit in the complex cellular environment is not well understood. We used in vivo site-specific cross-linking to approach this question, focusing on two abundant factors—the nascent chain-associated complex (NAC) and the Hsp70 chaperone system that includes the J-domain protein co-chaperone Zuotin. We found that NAC and Zuotin can cross-link to each other at the ribosome, even when translation initiation is inhibited. Positions yielding NAC–Zuotin cross-links indicate that when both are present the central globular domain of NAC is modestly shifted from the mutually exclusive position observed in cryogenic electron microscopy analysis. Cross-linking results also suggest that, even in NAC’s presence, Hsp70 can situate in a manner conducive for productive nascent chain interaction—with the peptide binding site at the tunnel exit and the J-domain of Zuotin appropriately positioned to drive stabilization of nascent chain binding. Overall, our results are consistent with the idea that, in vivo, the NAC and Hsp70 systems can productively position on the ribosome simultaneously.
Single-cell evidence for plasmid addiction mediated by toxin–antitoxin systems
Authors: Fraikin Nathan , Van Melderen Laurence 
Published: January 2024

Abstract
Toxin–antitoxin (TA) systems are small selfish genetic modules that increase vertical stability of their replicons. They have long been thought to stabilize plasmids by killing cells that fail to inherit a plasmid copy through a phenomenon called post-segregational killing (PSK) or addiction. While this model has been widely accepted, no direct observation of PSK was reported in the literature. Here, we devised a system that enables visualization of plasmid loss and PSK at the single-cell level using meganuclease-driven plasmid curing. Using the ccd system, we show that cells deprived of a ccd-encoding plasmid show hallmarks of DNA damage, i.e. filamentation and induction of the SOS response. Activation of ccd triggered cell death in most plasmid-free segregants, although some intoxicated cells were able to resume growth, showing that PSK-induced damage can be repaired in a SOS-dependent manner. Damage induced by ccd activates resident lambdoid prophages, which potentiate the killing effect of ccd. The loss of a model plasmid containing TA systems encoding toxins presenting various molecular mechanisms induced different morphological changes, growth arrest and loss of viability. Our experimental setup enables further studies of TA-induced phenotypes and suggests that PSK is a general mechanism for plasmid stabilization by TA systems.
Plumage coloration differs between offspring raised in natural cavities and nestboxes
Authors: Janas Katarzyna , Di Lecce Irene , Szulkin Marta , Sudyka Joanna 
Published: January 2024

Abstract
Most of our knowledge of secondary hole-nesting birds comes from populations breeding in human-provided nestboxes, yet these might differ from natural cavities in a number of parameters, including internal dimensions or microclimate, leading to differences in reproductive ecology. Here, we demonstrate differences in plumage coloration, an important visual signal of individual quality, in Blue Tit (Cyanistes caeruleus) and Great Tit (Parus major) nestlings raised in natural cavities and nestboxes. For this study, we collected feather samples over two breeding seasons and applied reflectance spectrophotometry to calculate color metrics. Carotenoid chroma was higher in nestbox-reared Blue Tits, whereas brightness was higher in nestbox-reared Great Tits (with a similar tendency for Blue Tits). The latter result might be explained by the better nutritional condition of Great Tit nestlings raised in nestboxes. Furthermore, we found no evidence for preference of adults expressing more elaborate plumage towards a specific cavity type in either species. Consequently, we assume that differences in nestling plumage reported here are driven by rearing conditions (nestboxes vs. natural cavities) and not by differences in plumage-based parental quality. Our study adds to the growing body of evidence confirming that anthropogenic environmental modifiers, such as nestboxes, might influence avian physiology and the resulting phenotype.
A commitment forlife:Decades of unraveling the molecular mechanisms behind seed dormancy and germination
Authors: Sajeev Nikita , Koornneef Maarten , Bentsink Leónie 
Published: January 2024

AbstractSeeds are unique time capsules that can switch between 2 complex and highly interlinked stages: seed dormancy and germination. Dormancy contributes to the survival of plants because it allows to delay germination to optimal conditions. The switch between dormancy and germination occurs in response to developmental and environmental cues. In this review we provide a comprehensive overview of studies that have helped to unravel the molecular mechanisms underlying dormancy and germination over the last decades. Genetic and physiological studies provided a strong foundation for this field of research and revealed the critical role of the plant hormones abscisic acid and gibberellins in the regulation of dormancy and germination, and later natural variation studies together with quantitative genetics identified previously unknown genetic components that control these processes. Omics technologies like transcriptome, proteome, and translatomics analysis allowed us to mechanistically dissect these processes and identify new components in the regulation of seed dormancy and germination.
Assessment of radioactivity in sand samples from eastern Nepal in perspective of radiological hazards
Authors: Shrestha Arun Kumar , Shrestha Ganesh Kumar , Shah Buddha Ram , Koirala Ram Prasad 
Published: January 2024

Abstract
This study was conducted to investigate the activity concentrations of 226Ra, 232Th and 40K in the sand samples and the health hazards associated with them utilizing a NaI (Tl) gamma spectrometer. The average activity concentrations of 226Ra, 232Th and 40K were found to be 24.8 ± 10.1, 39.8 ± 16.4 and 531.3 ± 52.8 Bq kg−1, respectively. The calculated radiological hazard parameters, including radium equivalent activity, absorbed gamma dose and effective dose rate, were found to be 122.7 ± 34.0 Bq kg−1, 57.7 ± 14.9 nGy h−1 and 0.3 ± 0.1 mSv y−1, respectively. Notably, these results were observed to be below the recommended thresholds. Other measured hazard indices were also lower than the prescribed values. From a radiological perspective, the present study concludes that the sand samples do not pose any threat to human health when utilized as a building material.
Skill Specificity on High-Skill Online Gig Platforms: Same as in Traditional Labour Markets?
Authors: van Slageren Jaap , Herrmann Andrea M 
Published: January 2024

Abstract
Political economists and labour sociologists alike have studied how the skill specificity of workers can be explained, as it significantly affects workers’ performance. However, the emergence of the gig economy may substantially change skill hiring and specificity in online labour markets because gig workers do not need formal educational credentials to offer their services. Instead, skills are “unbundled” from occupations, and platforms provide alternative ways to signal competencies, for example, via their rating and review systems. To shed light on the applicability of existing theories to explain the skill profiles of gig workers, we examine what predicts the skills hired in the online gig economy. Based on multilevel ordinal logistic regression analyses of 2336 gig worker profiles, we show that—as in traditional labour markets—gig workers with a vocational degree and longer online work experience are hired for more specific skills. However, national labour market institutions and educational systems affect the gig workers’ skill specificity in the opposite direction than in traditional labour markets. Our findings thus suggest that online gig platforms allow workers to overcome restrictions imposed by national institutions as they are hired for those skills in the online gig economy that are institutionally less facilitated in their home labour markets.
No Place Like Home
Authors: Toole Cheryl , DeGrazia Michele , Andrews Theresa M. , Bouve Mary Ellen , Pezanowski Regina , Cole Alexandra , Kourembanas Stella , Hickey Patricia A. 
Published: January 2024

Background:
Boston Children's Hospital's Level IV Neonatal Intensive Care Unit (NICU) discharges about a third of its medically complex infants home. Parental feedback indicated a need for more education and training in discharge preparation.

Purpose:
The NICU to Nursery (N2N) program was created to better prepare parents to care for their medically complex infants following Level IV NICU discharge. The goals were to (1) mitigate safety risks, (2) assess parent satisfaction, (3) assess pediatric primary care providers' (PCPs') satisfaction, (4) assess community visiting nurses' and PCPs' knowledge deficits, and (5) develop educational materials.

Methods:
The N2N program provided parents with pre- and postdischarge assessments with an experienced nurse. Parents completed a survey following assessments to measure satisfaction. To enhance PCPs' knowledge, they were sent summary reports and asked for feedback. PCP feedback, along with a needs assessment of community visiting nurses, guided the development of free Web-based educational videos.

Results:
One hundred and fifty-five parents participated in the N2N program. Parents' educational needs included medication education, safe sleep, and well-infant care, with some requiring significant nursing interventions for safety risk mitigation. Most PCPs found the home visit reports helpful. Knowledge deficits identified among PCPs and community visiting nurses included management of tubes and drains, growth and nutrition, and emergency response. More than 100,000 providers viewed the 3 Web-based educational videos developed.

Implications for Practice and Research:
The N2N program fills a crucial gap in the transition of medically complex infants discharged home. The next steps are developing best practices for virtual in-home assessments.
Performance of ChatGPT on NASS Clinical Guidelines for the Diagnosis and Treatment of Low Back Pain
Authors: Shrestha Nancy , Shen Zekun , Zaidat Bashar , Duey Akiro H. , Tang Justin E. , Ahmed Wasil , Hoang Timothy , Restrepo Mejia Mateo , Rajjoub Rami , Markowitz Jonathan S. , Kim Jun S. , Cho Samuel K. 
Published: January 2024

Study Design.
Comparative analysis.

Objective.
To evaluate Chat Generative Pre-trained Transformer (ChatGPT’s) ability to predict appropriate clinical recommendations based on the most recent clinical guidelines for the diagnosis and treatment of low back pain.

Background.
Low back pain is a very common and often debilitating condition that affects many people globally. ChatGPT is an artificial intelligence model that may be able to generate recommendations for low back pain.

Materials and Methods.
Using the North American Spine Society Evidence-Based Clinical Guidelines as the gold standard, 82 clinical questions relating to low back pain were entered into ChatGPT (GPT-3.5) independently. For each question, we recorded ChatGPT’s answer, then used a point-answer system—the point being the guideline recommendation and the answer being ChatGPT’s response—and asked ChatGPT if the point was mentioned in the answer to assess for accuracy. This response accuracy was repeated with one caveat—a prior prompt is given in ChatGPT to answer as an experienced orthopedic surgeon—for each question by guideline category. A two-sample proportion z test was used to assess any differences between the preprompt and postprompt scenarios with alpha=0.05.

Results.
ChatGPT’s response was accurate 65% (72% postprompt, P=0.41) for guidelines with clinical recommendations, 46% (58% postprompt, P=0.11) for guidelines with insufficient or conflicting data, and 49% (16% postprompt, P=0.003*) for guidelines with no adequate study to address the clinical question. For guidelines with insufficient or conflicting data, 44% (25% postprompt, P=0.01*) of ChatGPT responses wrongly suggested that sufficient evidence existed.

Conclusion.
ChatGPT was able to produce a sufficient clinical guideline recommendation for low back pain, with overall improvements if initially prompted. However, it tended to wrongly suggest evidence and often failed to mention, especially postprompt, when there is not enough evidence to adequately give an accurate recommendation.
Tryptophan intake and pancreatic cancer: findings from a case-control study
Authors: Luu Hung N. , Pham Yen Thi-Hai , Yuan Jian-Min , Brand Randall E. , Pham Tuyen Van , Dao Hang Viet , Le Chung Kim Thi , Huynh Nhi Yen Ngoc , Nguyen Hai Minh , Le Ngoan Tran 
Published: January 2024

Background
Pancreatic cancer is a leading cause of cancer-related death worldwide. Tryptophan plays a vital role in cell growth and maintenance as a building block of protein and coordination of organismal responses to environmental and dietary cues. Animal model study showed that dietary tryptophan improved treatment response in those who received chemotherapy or immune checkpoint inhibitors. Limited data are available assessing the association between tryptophan intake and risk of pancreatic cancer. We aimed to evaluate this association in a case-control study in Vietnam.

Methods
We analyzed data from a case-control study, including 3759 cancer cases and 2995 control subjects of whom 37 with pancreatic cancer cases. Tryptophan intake was derived from food frequency questionnaire. Unconditional logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for different levels of tryptophan intake with pancreatic cancer risk.

Results
Overall, tryptophan intake was inversely associated with pancreatic cancer risk in a dose-dependent manner. The ORs and 95% CIs of pancreatic cancer were 0.51 (0.29–0.92) for continuous scale, 0.27 (0.10–0.73) for tertile 2 and 0.34 (0.11–1.06) for tertile 3, compared with tertile 1 (the lowest intake) (P

trend
= 0.02). In stratified analysis, this inverse association pattern was present among those with BMI < 23 kg/m2 and ever drinkers.

Conclusion
A diet with a higher intake of tryptophan was significantly associated with a lower incidence of pancreatic cancer among Vietnamese population. These suggest that dietary modification may be an effective strategy for primary prevention of pancreatic cancer development.
Efficiency and Safety of Tocilizumab for the Treatment of Thyroid Eye Disease: A Systematic Review
Authors: Duarte Ana F. , Xavier Naiara F. , Sales Sanz Marco , Cruz Antonio A. V. 
Published: January 2024

Purpose:
To review existing literature concerning the effectiveness and safety of tocilizumab (TCZ) for managing thyroid eye disease.

Methods:
A systematic search was conducted across the PubMed and Embase databases to identify studies on TCZ therapy, from inception to May 2023. The search included the keywords “Graves orbitopathy,” “thyroid ophthalmopathy,” “thyroid eye disease,” “thyroid-associated orbitopathy,” “thyroid-associated ophthalmopathy,” “Graves ophthalmopathy,” “endocrine ophthalmopathy,” and “Tocilizumab.” Only articles written in English, Spanish, or French were considered.

Results:
Among the 1,013 articles initially screened, a total of 29 fulfilled the eligibility criteria and were selected. Most studies were case reports or case series, and only one randomized clinical trial was found. TCZ has been used mainly in glucocorticoid-resistant or relapsing cases, with a dosage ranging from 4 or 8 mg/kg every 4 weeks when intravenous or a weekly subcutaneous dose of 162 mg. Treatment duration is usually adjusted to the clinical response. TCZ is mostly effective in reducing inflammatory signs during the active phase of thyroid eye disease, with an improvement of at least 3 points in clinical activity score and an overall relapsing rate of 8.2%. Numerous studies have shown marked reductions in proptosis; although the only available randomized controlled trial reported a nonstatistically significant improvement 6 months after treatment, a recent meta-analysis indicated that TCZ seems to be the most effective treatment for reducing proptosis. No severe side effects related to intravenous or subcutaneous TCZ administration were reported.

Discussion:
Despite these promising findings, randomized clinical trials to directly compare the efficacy and safety of TCZ and other currently available therapeutic options are needed.