bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the gut microbiome composition between Lawsonia intracellularis vaccinated and non-vaccinated pigs in a sub-clinically infected pig herd
Authors: Oh Yusik , Ha Donguk , Jang Hada , Park Chanyeong , Seo Hyunhee , Yu Hyunah , Moon Duwhan , Kim San , Lee Sungseok 
Published: September 2023

Abstract

Lawsonia intracellularis (LI) infection in pigs can cause several clinical manifestations such as retarded growth, hemorrhagic diarrhea and mortality. Despite decades since the first isolation of the causative agent, still the underlying pathogenesis and virulence of LI is not fully understood yet. For the control of LI infection in the field, the use of antibiotics and vaccination with live-attenuated strain of LI has been implemented. Several studies have been done to determine the effect of vaccination on the prevention of clinical onset and improvement of productivity and impact on microbiome composition under experimental challenge conditions. However, little is known about the impact of natural subclinical LI infection, the most common form of this disease, on the gut microbiome of pigs compared to the vaccinated pigs. In the current study, the composition of the gut microbiome between LI vaccinated and non-vaccinated pigs was investigated to determine the efficacy of the vaccine on the host and the gut microbiome in the pig herd with LI sub-clinical infection. The increased productivity of vaccinated pigs was observed, and taxa related with the digestion showed higher relative abundance in the vaccinated pigs significantly. The results of this study suggest that vaccination with an oral live LI vaccine successfully increased the productivity of pigs by leading to a gut microbiome enriched with digestion-related taxa.
Euboeus mimonti Boieldieu, 1865, the oldest record of an extant species of Tenebrionidae (Coleoptera) and notes on other species identified as darkling beetles from the Late Pliocene of Willershausen (Germany)
Authors: Nabozhenko Maxim V. , Shaw Josh Jenkins , Gehler Alexander , Kaulfuss Uwe 
Published: September 2023

Abstract
Several fossil beetles from the Late Pliocene (Piacenzian) of Willershausen (Lower Saxony, Germany) previously identified as Tenebrionidae and Staphylinidae are reviewed. One species, formerly determined as “Staphylinoidea” is identified as Euboeus mimonti Boieldieu, 1865 (Tenebrionidae: Helopini). This species is the oldest record of an extant species of darkling beetles, which occurs now in the Balkans and Anatolia. The discovery of Euboeus mimonti in the Late Pliocene of Germany indicates that the range of this species was much wider, and the climate in the Late Pliocene in the modern territory of Lower Saxony was much milder. One species formerly determined as “Alleculidae gen. sp.” belongs to the subfamily Alleculinae (Tenebrionidae) and it is identified here as Pseudocistela aff. cerambioides. Two species, misidentified by a previous author as Tenebrionidae belong to Elateridae and Cerambycidae respectively. Generic and species composition, as well as the ratio of extinct and extant beetle taxa in the Willershausen Fossil Lagerstätte are discussed.
Unravel the landscape of antibiotic resistance determinants in the nasopharynx and the impact of antibiotics: a longitudinal study of preterm infants
Authors: Petersen Fernanda Cristina , Dhariwal Achal , Rajar Polona , Salvadori Gabriela , Heidi  , Berild Dag , Saugstad Ola , Fugelseth Drude , Greisen Gorm , Dahle Ulf , Haaland Kirsti 
Published: September 2023

Abstract

Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. Utilizing shotgun metagenomics, we investigated the nasopharynx resistome development in preterm infants, assessed early antibiotic impact on its trajectory, and explored its association with clinical covariates. Our findings revealed widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persisted (at 8-10 months of age) for months following discharge, signifying hospitalization signature. The nasopharyngeal resistome strongly correlated with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. The collateral effects of antibiotics and hospitalization reported here highlights the importance of future studies focusing on this yet rather unexplored reservoir of pathogens and ARGs.
Spatial Functional Mapping of Hypoxia Inducible Factor Heterodimerisation and Immune checkpoint regulators in clear cell Renal Cell Carcinoma
Authors: Safrygina Elena , Applebee Christopher , McIntyre Alan , Padget Julian , Larijani Banafshé 
Published: September 2023

Abstract
Background:
Clear cell renal cell carcinoma (ccRCC) is a highly malignant subtype of kidney cancer. 90% of ccRCC have inactivating mutations of VHL that stablise transcription factors, HIF1α and HIF2α, only stabilised in hypoxia. The varied response to HIF2 inhibition, in the preclinical and clinical settings, suggests that assessment of HIF2αactivation state, not just expression levels is required as a biomarker of sensitivity to enable optimal clinical use.
Methods:
Two-site amplified time-resolved Förster Resonance Energy Transfer (aiFRET), with FRET-Efficiency, Ef, as its read out, provides functional proteomics quantification, a precise step forward from protein expression as a tool for patient stratification.
To enhance the clinical accessibility of Ef, we have devised a new computational approach, Functional Oncology map(FuncOmap).
Results:
FuncOmap directly maps functional states of oncoproteins and allows functional states quantification at an enhanced spatial resolution. The innovative contributions in FuncOmap are the means to co-analyse and map expressional and functional state images and the enhancement of spatial resolution to facilitate clinical application. We show the spatial interactive states HIF2α and HIF1b in ccRCC patient samples.
Conclusion:
FuncOmap can be used to quantify heterogeneity in patient response and improve accurate patient stratification, thus enhancing the power of precision.
Pharmacokinetic Parameters and Tissular Biodistribution of 1,3 β-glucans From Maitake Pro4x in Balbc Mice.
Authors: Aguilera-Braico Diego Maximo , Balogh Gabriela 
Published: September 2023

Abstract
The objective of this study was to examine the pharmacokinetic parameters of 1,3-beta-glucans from Maitake Pro4X in BALBc mice through oral and intravenous (IV) administration. The parameters of interest included Tmax (time to reach maximum concentration), Cmax (maximum concentration), t1/2 (half-life), ta1/2 (mean residence time), Ke (elimination rate constant), Ka (absorption rate constant), clearance, Vd (volume of distribution), Cp0 (initial plasma concentration), and AUC (area under the concentration-time curve). Additionally, the study aimed to investigate the tissular biodistribution of the 1,3-beta-glucans following both administration routes and identify the organs involved in absorption, elimination, and distribution. The comparison of the results revealed that some elimination constants (ke3 IV and ke2 oral) were similar for both routes. Additionally, Tmax was found to be approximately 10 hours for both routes, and the elimination t1/2 showed similarity between oral (12.93 h) and IV (12.81 h) administration. Similarities were also observed in total systemic clearance values. However, the IV route exhibited a higher volume of distribution while having a lower AUC Cp vs. time. The results indicated that the gastrointestinal tract (stomach, duodenum, and colon) exhibited the highest levels of uptake for both routes of administration. Conversely, the liver and kidney showed the lowest uptake for both routes. Comparatively, oral administration resulted in greater gastrointestinal accumulation. However, cerebral, pulmonary, renal, and hepatic uptake was higher following intravenous administration. Based on the in vivo pharmacokinetic studies in murine models, it can be concluded that oral and intravenous administration of Maitake Pro4X presented similar values for elimination speed, Tmax, t1/2, total systemic clearance, and bioavailability.
Development and validation of a model for predicting refracture in elderly patients with hip fracture
Authors: Zhang Linlin , Zhou Yanling , Gu Yanlin , Lin Shuqiu , Wang Wei , Xue Wenping 
Published: September 2023

Abstract
Purpose
The goal of our study was to determine the incidence of refractures within two years after hip fracture surgery in elderly patients. LASSO Cox was used to gather independent indicators. The nomogram model was developed to predict refractures.
Methods
In this retrospective analysis, 1254 participants were recruited between 2019 and 2021 at two general hospitals in China. Baseline variables were collected, including demographics, comorbidities, and living conditions. The primary outcome was refractures within two years. This model was developed using LASSO Cox and validated using bootstrapping methods. The calibration and discriminative ability were evaluated using C-index values, AUC values, calibration plots, and decision curves.
Results
A total of 119 patients with refractures were identified via telephone interview. Seven independent indicators were predictors for refractures, including age, Harris, anemia, neurologic disease, visual impairment, anti-osteoporosis, and exercise. Based on bootstrap resampling, the calibration curve value was 0.869 (95% CI: 0.795–0.987), and the AUC was 0.793 (95% CI 0.751–0.834).
Conclusion
This model shows potential as a prediction instrument that permits clinicians to precisely detect the high risk of refractures and further help patients make decisions.
Real-World Experience with Ruxolitinib Therapy for Steroid Refractory Acute Graft Versus Host Disease
Authors: Kim Dennis , Murray Alistair , Linn Swe Mar , Yu Benoit , Novitzky-Basso Igor , Mattsson Jonas , Elemary Mohamed , White Jennifer , Lemieux Christopher , Jamani Kareem , Kennah Michael 
Published: September 2023

Abstract
Acute graft versus host disease (aGVHD) is a complication of allogeneic hematopoietic stem cell transplant (HCT) and is associated with significant morbidity and mortality. Steroid refractory aGVHD (SR-aGVHD) carries a particularly grim prognosis. Ruxolitinib has shown promise for treatment of SR-aGVHD in a phase 3 trial; however, safety and efficacy data outside of the clinical trial setting is lacking. We performed a multicenter retrospective study to examine the response to ruxolitinib and its efficacy in patients with SR-aGVHD. We included 59 patients treated with ruxolitinib for SR-aGVHD between 2015 and 2022. Of these 59 patients, 36 patients (61.0%) achieved a complete (CR) or partial response (PR) at 28 days, while 31 patients (52.5%) obtained a CR/PR at day 56. Patients that achieved a CR or PR at day 28 had a higher rate of overall survival (OS; 69.2%), compared with patients that did not (31.6%; p=0.037). OS at 12 months was 41.5%, with a median OS duration of 5.3 months. Failure free survival (FFS) at 12 months was 29.1%, with a median FFS of 2.6 months. Overall, this real-world experience data support ruxolitinib as the standard of care for SR-aGVHD in a non-controlled trial population.
Molecular epidemiological investigation and genetic variation analysis of PPV5 in Mianyang, Sichuan Province from 2021 to 2022
Authors: Yin Miao , Chen Xi-wen , Xie Zuo-Jie , Deng YongTao 
Published: September 2023

Abstract
Background
Porcine Parvovirus type 5 (PPV5) is a novel porcine parvovirus first identified in the United States in 2013. Relevant studies found that PPV5 was co-infected with POS-PCV2 and NEG-PCV2, and the infection rate in serum samples was 13.5%[1]. PPV5, PPV4, and porcine circovirus are co-infected and can cause multiple system failure syndrome (PMWS) in weaned pigs after infection [2].
Objective
To investigate the prevalence and genetic variation of porcine parvovirus type 5 (PPV5) in Mianyang.
Results
296 whole blood samples were collected from large-scale pig farms in the Mianyang area of Sichuan Province for PCR detection and whole genome sequencing analysis. The results showed that the positive rate of PPV5 was 0.33% (1/296). A strain named MYSC-PPV5 was obtained by sequencing. The genetic variation results showed that the nucleotide homology of the whole gene of MYSC-PPV5 was 98.9%-99.6%, and the nucleotide homology of ORF1 and ORF2 genes was 98.9%-99.9% and 99.4%-99.7%, respectively. The results showed that PPV5 had high genetic stability. In addition, no amino acid mutation was found in ORF1, a total of 40 amino acid sites were replaced in ORF2, and one site had amino acid addition, indicating that the strain ORF1 in this study was more conserved than ORF2.
Conclusion
The epidemiological investigation and genetic variation analysis of PPV5 in Mianyang, Sichuan Province, not only enrich the epidemiological data of PPV5 but also provide a theoretical basis for subsequent vaccine research. At the same time, it also provides the basis for further research on the pathogenesis and virulence of PPV5 and provides certain theoretical support for reducing the loss of pig industry and disease prevention and control.
Regression modeling of subjective probability of river inundation with epistemic uncertainty: a short-term panel data analysis
Authors: Hidaka Ken , Ikegai Mirai , Masuda Satoki 
Published: September 2023

Abstract
Lack of sufficient knowledge about flood risk can lead to ''don't know'' responses or non-response in risk perception surveys, and incorrect treatment of these responses can bias results. In this study, we focus on the possibility that the ''50\%'' response option actually means ''fifty-fifty'' and thus reflects epistemic uncertainty in the subjective probability of river flooding; we conduct an analysis that introduces a concomitant-variable latent class model as a method to adjust for this. The results of the analysis accounting for epistemic uncertainty suggest that risk communication, such as simulated evacuation experiences and flood-related information distribution, has the effect of increasing subjective probability. Moreover, the proportion of latent classes with epistemic uncertainty decreased with each successive wave of the survey, thereby suggesting that knowledge acquisition and learning through the demonstration experiment led to a reduction in epistemic uncertainty. The analysis using the evacuation decision-making model also suggested that the introduction of subjective probability contributed to the improved likelihood of the model. These results suggest that knowledge acquisition through risk communication and short-term panel survey can lead to correct risk perception estimations and influence evacuation decisions.
Joint Loading and Muscle Activation of Upper-body in Different Incline/Decline Push-Up Variants by AnyBody Musculoskeletal Modeling
Authors: Zhang Jing , Dong Xianpeng , Zhao Shuaiyin , Hou Guohao , Chen Yixuan , Nie Jiachen , Ding Li 
Published: September 2023

Abstract
Background
Push-up exercises are known to effectively activate the upper body muscles, thereby enhancing core strength and endurance. The adaptability of push-ups, with different body inclinations, allows for easy implementation in various daily environments, offering a wide range of intensity options. This study aimed to investigate the muscle activation and joint loading effects resulting from different body inclination angles during push-ups.
Methods
Six distinct push-up movement models were established using AnyBody software, with body-to-ground angles set at -15°, 0°, 15°, 30°, 45°, and 60°. Eleven healthy adult males, who had undergone systematic training and mastered the push-up positions, performed the six push-up movements in a random order, and surface electromyography (sEMG) data was collected to validate the accuracy of the AnyBody push-up model. Based on the validated model, the muscle activity of six upper body muscles (pectoralis major, biceps, triceps, anterior deltoid, middle deltoid, and inferior trapezius) was analyzed, along with the joint forces in the three degrees of freedom at the shoulder and elbow joints. Additionally, the exercise effect assessment parameter RFM/JF was introduced.
Results
The results revealed greater muscle activation at body-to-ground angles of -15° and 0°, while less joint force was observed at 45° and 60°. Furthermore, push-ups performed at 0° and 30° demonstrated significant exercise effects, with reduced risk of joint strain for the six targeted muscles.
Conclusion
By approaching push-up exercises from a biomechanical standpoint and validating the AnyBody model, this study provided valuable insights for exercisers seeking a deeper understanding of the exercise and its potential to help them achieve diverse fitness goals.
Unveiling the Oral-Gut Connection: Chronic Periodontal Infection Accelerates Atherosclerosis via Gut Microbiota Dysbiosis and Altered Metabolites in apoE-/- Mice on a High-Fat Diet
Authors: Huang Xiaojing , Gan Guowu , Lin Shihan , Luo Yufang , Zeng Yu , Lu Beibei , Zhang Ren , Chen Shuai , Lei Huaxiang , Cai Zhiyu 
Published: September 2023

Abstract

This study aimed to explore the impact of chronic apical periodontitis (CAP) on atherosclerosis in apoE−/− mice subjected to a high-fat diet (HFD). The investigation focused on gut microbiota, metabolites, and intestinal barrier function to uncover potential links between oral health and cardiovascular disease. In this research, CAP was found to exacerbate atherosclerosis in HFD-fed apoE−/− mice, as evident from increased plaque size and volume in arterial walls by Oil Red-O staning. 16S rRNA sequence uncovered significant alterations in gut microbiota, with harmful bacterial species thriving while beneficial ones declined. Metabolomic profiling indicated disruptions in lipid metabolism and primary bile acid synthesis, leading to elevated levels of taurochenodeoxycholic acid (TCDCA), taurocholic acid (TCA), and tauroursodeoxycholic acid (TDCA). These metabolic shifts may contribute to atherosclerosis development. Furthermore, the study observed impairment in intestinal barrier function, characterized by reduced mucin expression and disrupted tight junction proteins. The increased intestinal permeability observed positively correlated with the extent of atherosclerotic lesions, emphasizing the significance of the intestinal barrier in cardiovascular health. In conclusion, this research underscores the intricate interplay between oral health, gut microbiota composition, metabolite profiles, and cardiovascular disease. It highlights the exacerbating effect of CAP on atherosclerosis in the context of a high-fat diet. These findings emphasize the importance of maintaining good oral hygiene as a potential preventive measure against cardiovascular issues, as well as the need for further investigations into the intricate mechanisms linking oral health, gut microbiota, and metabolic pathways in cardiovascular disease development.
A Revisit to Political Institutions and Inequality
Authors: DENIZ PINAR , Stengos Thanasis 
Published: September 2023

Abstract
This study revisits the drivers of income inequality with political institutions at the core. We take a multidimensional institutional approach by defining political institutions in terms of governance, political freedom, political fragmentation and political scale. The main contributions of our study are (i) presenting the most extensive analysis up-to-date of the role of political institutions by decomposing it into distinct elements and (ii) considering the difficulty and the lack of consensus and clarity regarding the choice of instruments in the literature we define an alternative methodology to deal with the potential endogeneity of political institutions. We combine an analysis of club convergence, a clustering mechanism according to the long term income trajectories of the countries under investigation with Bayesian Model Averaging (BMA) within each cluster to determine the most important variables that affect inequality out of a large set of potentially important variables. Our results show that the effectiveness of political institutions differ among country groups and that there is no "one size fits all" policy prescription that links institutional quality and income inequality.
Associations between deep venous thrombosis and thyroid diseases: A two-sample bidirectional Mendelian Randomization study
Authors: Zhang Lifeng , Li Kaibei , Yang Qifan , Lin Yao , Geng Caijuan , Huang Wei , Zeng Wei 
Published: September 2023

Abstract

Backgrounds:
In some previous observational studies, deep venous thrombosis (DVT) has been linked to thyroid diseases, but the findings are debatable. This study aimed to reveal whether some common thyroid diseases can causally result in DVT using the two-sample Mendelian Randomization (MR) approach.
Methods
We did a two-sample MR study that chose single nucleotide polymorphisms (SNPs) which are highly associated with some common thyroid diseases from the FinnGen datasets as our instruments, including autoimmune hyperthyroidism (962 cases and 172,976 controls), subacute thyroiditis (418 cases and 187,684 controls), hypothyroidism (26,342 cases and 59,827 controls) and malignant neoplasm of thyroid gland (989 cases and 217,803 controls). Outcomes datasets about deep venous thrombosis (6,767 cases and 330,392 controls) were obtained from the IEU open GWAS project. Inverse variance weighted (IVW), MR-Egger and weighted median were used to estimate the causal association between DVT and thyroid diseases. Cochran’s Q test was used to quantify the heterogeneity of instrumental variables. We also detected horizontal pleiotropy using MR-PRESSO. When the causal relationship was significant, a bidirectional Mendelian randomization analysis was performed to determine if there were reverse causal relationships between exposures and outcomes.
Results
The Mendelian Randomization analysis illustrated that autoimmune hyperthyroidism slightly raised the risk of DVT in IVW method[odds ratio (OR) = 1.000891; 95% confidence interval (CI):1.0001156–1.001667; p = 0.0243]. Weighted median showed a similar association[OR = 1.000984; 95%CI: 1.0000806–1.001888; p = 0.03278]. There was no evidence of heterogeneity in instrumental variables which Cochran’s Q test showed and MR-PRESSO didn’t assumed the presence of horizontal pleiotropy (p = 0.972). However, no evidence can point out that other thyroid diseases had relationship with DVT using the IVW method, weighted median method and MR-Egger regression.
Conclusion
Our research found that autoimmune hyperthyroidism may cause DVT. More evidences and lager samples are needed to draw more precise conclusions.