bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metatranscriptomics unmasks Mollusca virome with a remarkable presence of rhabdovirus in cephalopods
Authors: Rey-Campos Magalí , González-Vázquez Luis Daniel , Novoa Beatriz , Figueras Antonio 
Published: June 2023

IntroductionMollusks play a significant role in marine ecosystems and have economic value for aquaculture. Sometimes, unexpected and unexplained mortalities among mollusks have been described. The role of potential pathogens such as viruses remains unknown due to the lack of molluscan cell cultures, which is one of the major drawbacks to determining the viral role in such mortalities. Several oceanographic studies have suggested a high abundance of viruses in the oceans. Virus identification and understanding of viral interaction with organisms in marine ecosystems are in their infancy. Metatranscriptomics could become a useful tool to identify viruses using a shotgun approach and the growing number of viral genomes and sequences deposited in public databases.MethodsIn this work, several bioinformatics approaches were set up to screen Mollusca RNA sequences to find and confirm viral traces in their transcriptomes. This meta-analysis included an extensive search of SRA datasets belonging to mollusks available in the NCBI database, selecting a total of 55 SRA datasets that were further analyzed searching for viral sequences.ResultsTwenty-two bivalves, 19 cephalopods and 16 gastropods from 16 geographical origins and 17 different tissues were considered. The domain search approach was the most productive method to find viral sequences. This virus search showed that Cephalopoda samples (Idiosepius notoides and Amphioctopus fangsiao) exhibited the highest number of virus identifications. Some of the detected viral sequences were similar or identical to others previously identified. However, 33 putative new viruses were identified and analyzed phylogenetically when the RdRp domain was available. Specifically, Cephalopoda samples showed a considerable number of viruses belonging to the Rhabdoviridae family.
Phenotyping cardiogenic shock that showed different clinical outcomes and responses to vasopressor use: a latent profile analysis from MIMIC-IV database
Authors: Yu Yue , Rao Jin , Xu Qiumeng , Xiao Jian , Cheng Pengchao , Wang Junnan , Xi Wang , Wang Pei , Zhang Yufeng , Wang Zhinong 
Published: June 2023

BackgroundCardiogenic shock (CS) is increasingly recognized as heterogeneous in its severity and response to therapies. This study aimed to identify CS phenotypes and their responses to the use of vasopressors.MethodThe current study included patients with CS complicating acute myocardial infarction (AMI) at the time of admission from the Medical Information Mart for Intensive Care IV (MIMIC-IV) database. Laboratory and clinical variables were collected and used to conduct latent profile (LPA) analysis. Furthermore, we used a multivariable logistic regression (LR) model to explore the independent association between the use of vasopressors and endpoints.ResultA total of 630 eligible patients with CS after AMI were enrolled in the study. The LPA identified three profiles of CS: profile 1 (n = 259, 37.5%) was considered as the baseline group; profile 2 (n = 261, 37.8%) was characterized by advanced age, more comorbidities, and worse renal function; and profile 3 (n = 170, 24.6%) was characterized by systemic inflammatory response syndrome (SIRS)-related indexes and acid–base balance disturbance. Profile 3 showed the highest all-cause in-hospital mortality rate (45.9%), followed by profile 2 (43.3%), and profile 1 (16.6%). The LR analyses showed that the phenotype of CS was an independent prognostic factor for outcomes, and profiles 2 and 3 were significantly associated with a higher risk of in-hospital mortality (profile 2: odds ratio [OR] 3.95, 95% confidence interval [CI] 2.61–5.97, p &lt; 0.001; profile 3: OR 3.90, 95%CI 2.48–6.13, p &lt; 0.001) compared with profile 1. Vasopressor use was associated with an improved risk of in-hospital mortality for profile 2 (OR: 2.03, 95% CI: 1.15–3.60, p = 0.015) and profile 3 (OR: 2.91, 95% CI: 1.02–8.32, p = 0.047), respectively. The results of vasopressor use showed no significance for profile 1.ConclusionThree phenotypes of CS were identified, which showed different outcomes and responses to vasopressor use.
Impact of Electronic Chronic Pain Questions on patient-reported outcomes and healthcare utilization, and attitudes toward eCPQ use among patients and physicians: prospective pragmatic study in a US general practice setting
Authors: Lamerato Lois , Shah Vinay , Abraham Lucy , Cappelleri Joseph C. , DeLor Bonnie , Ellsworth Stacy R. , Hegeman-Dingle Rozelle , Park Peter W. 
Published: June 2023

ObjectiveThe Electronic Chronic Pain Questions (eCPQ) has been developed to help healthcare providers systematically capture chronic pain data. This study evaluated the impact of using the eCPQ on patient-reported outcomes (PROs) and healthcare resource utilization (HCRU) in a primary care setting, and patient and physician perceptions regarding use of, and satisfaction with, the eCPQ.MethodsThis was a prospective pragmatic study conducted at the Internal Medicine clinic within the Henry Ford Health (HFH) Detroit campus between June 2017 and April 2020. Patients (aged ≥18 years) attending the clinic for chronic pain were allocated to an Intervention Group to complete the eCPQ in addition to regular care, or a control group to receive regular care only. The Patient Health Questionnaire-2 and a Patient Global Assessment were assessed at baseline, 6-months, and 12-months study visits. HCRU data were extracted from the HFH database. Telephone qualitative interviews were conducted with randomly selected patients and physicians who used the eCPQ.ResultsTwo hundred patients were enrolled, 79 in each treatment group completed all 3 study visits. No significant differences (p &gt; 0.05) were found in PROs and HCRU between the 2 groups. In qualitative interviews, physicians and patients reported the eCPQ as useful, and using the eCPQ improved patient-clinician interactions.ConclusionAdding the eCPQ to regular care for patients with chronic pain did not significantly impact the PROs assessed in this study. However, qualitative interviews suggested that the eCPQ was a well-accepted and potentially useful tool from a patient and physician perspective. By using the eCPQ, patients were better prepared when they attended a primary care visit for their chronic pain and the quality of patient-physician communication was increased.
Clinical characteristics and outcomes of infection with human T-lymphotropic virus in a non-endemic area: a single institution study
Authors: Gang Margery , Gao Feng , Poondru Sneha , Thomas Theodore , Ratner Lee 
Published: June 2023

IntroductionUnderstanding of human T-lymphotropic virus (HTLV) remains largely based on epidemiologic and clinical data from endemic areas. Globalization has resulted in migration of persons living with HTLV (PLHTLV) from endemic to non-endemic areas, and a rise of HTLV infection in the United States. Yet, due to the historical rarity of this disease, affected patients are often under- and mis-diagnosed. Thus, we sought to characterize the epidemiology, clinical features, comorbidities, and survival of HTLV-1- or HTLV-2-positive individuals identified in a non-endemic area.MethodsOur study was a single institution, retrospective case–control analysis of HTLV-1 or HTLV-2 patients between 1998 and 2020. We utilized two HTLV-negative controls, matched for age, sex, and ethnicity, for each HTLV-positive case. We evaluated associations between HTLV infection and several hematologic, neurologic, infectious, and rheumatologic covariates. Finally, clinical factors predictive of overall survival (OS) were assessed.ResultsWe identified 38 cases of HTLV infection, of whom 23 were HTLV-1 and 15 were HTLV-2 positive. The majority (~54%) of patients in our control group received HTLV testing for transplant evaluation, compared to ~24% of HTLV-seropositive patients. Co-morbidities associated with HTLV, hepatitis C seropositivity were higher in HTLV-seropositive patients compared to controls (OR 10.7, 95% CI = 3.2–59.0, p &lt; 0.001). Hepatitis C and HTLV co-infection resulted in decreased OS, compared to no infection, hepatitis C infection alone, or HTLV infection alone. Patients with any cancer diagnosis and HTLV infection had worse OS compared to patients with cancer or HTLV alone. HTLV-1 positive patients had lower median OS compared to HTLV-2 patients (47.7 months vs. 77.4 months). In univariate analysis, the hazard for 1-year all-cause mortality was increased among patients with HTLV-seropositivity, adult T-cell leukemia, acute myelogenous leukemia, and hepatitis C infection. When corrected, multivariate analysis showed that HTLV seropositivity was no longer associated with 1 year all-cause mortality; however association with AML and hepatitis C infection remained significant.ConclusionHTLV-seropositivity was not associated with increased 1 year mortality in multivariate analysis. However, our study is limited by our small patient sample size, as well as the biased patient control population due to selection factors for HTLV testing.
Physiological variations in hypovirus-infected wild and model long-term laboratory strains of Cryphonectria parasitica
Authors: Popović Maja , Nuskern Lucija , Peranić Karla , Vuković Rosemary , Katanić Zorana , Krstin Ljiljana , Ćurković-Perica Mirna , Leigh Deborah Marie , Poljak Igor , Idžojtić Marilena , Rigling Daniel , Ježić Marin 
Published: June 2023

IntroductionForest ecosystems are highly threatened by the simultaneous effects of climate change and invasive pathogens. Chestnut blight, caused by the invasive phytopathogenic fungus Cryphonectria parasitica, has caused severe damage to European chestnut groves and catastrophic dieback of American chestnut in North America. Within Europe, the impacts of the fungus are widely mitigated through biological control that utilizes the RNA mycovirus: Cryphonectria hypovirus 1 (CHV1). Viral infections, similarly to abiotic factors, can cause oxidative stress in their hosts leading to physiological attrition through stimulating ROS (reactive oxygen species) and NOx production.MethodsTo fully understand the interactions leading to the biocontrol of chestnut blight, it is vital to determine oxidative stress damage arising during CHV1 infection, especially considering that other abiotic factors, like long-term cultivation of model fungal strains, can also impact oxidative stress. Our study compared CHV1-infected C. parasitica isolates from two Croatian wild populations with CHV1-infected model strains (EP713, Euro7 and CR23) that have experienced long-term laboratory cultivation.Results and DiscussionWe determined the level of oxidative stress in the samples by measuring stress enzymes’ activity and oxidative stress biomarkers. Furthermore, for the wild populations, we studied the activity of fungal laccases, expression of the laccase gene lac1, and a possible effect of CHV1 intra-host diversity on the observed biochemical responses. Relative to the wild isolates, the long-term model strains had lower enzymatic activities of superoxide dismutase (SOD) and glutathione S-transferase (GST), and higher content of malondialdehyde (MDA) and total non-protein thiols. This indicated generally higher oxidative stress, likely arising from their decades-long history of subculturing and freeze–thaw cycles. When comparing the two wild populations, differences between them in stress resilience and levels of oxidative stress were also observed, as evident from the different MDA content. The intra-host genetic diversity of the CHV1 had no discernible effect on the stress levels of the virus-infected fungal cultures. Our research indicated that an important determinant modulating both lac1 expression and laccase enzyme activity is intrinsic to the fungus itself, possibly related to the vc type of the fungus, i.e., vegetative incompatibility genotype.
Prenatal lead exposure is negatively associated with the gut microbiome in childhood
Authors: Eggers Shoshannah , Midya Vishal , Bixby Moira , Gennings Chris , Torres-Olascoaga Libni A. , Walker Ryan W. , Wright Robert O. , Arora Manish , Téllez-Rojo Martha María 
Published: June 2023

BackgroundMetal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role of the GM in association with many adverse health outcomes, understanding the relationship between prenatal metal exposures and the GM is critically important. However, there is sparse knowledge of the association between prenatal metal exposure and GM later in childhood.ObjectivesThis analysis aims to identify associations between prenatal lead (Pb) exposure and GM composition and function in children 9–11 years old.MethodsData come from the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) cohort based in Mexico City, Mexico. Prenatal metal concentrations were measured in maternal whole blood drawn during the second and third trimesters of pregnancy. Stool samples collected at 9–11 years old underwent metagenomic sequencing to assess the GM. This analysis uses multiple statistical modeling approaches, including linear regression, permutational analysis of variance, weighted quantile sum regression (WQS), and individual taxa regressions, to estimate the association between maternal blood Pb during pregnancy and multiple aspects of the child GM at 9–11 years old, adjusting for relevant confounders.ResultsOf the 123 child participants in this pilot data analysis, 74 were male and 49 were female. Mean prenatal maternal blood Pb was 33.6 (SE = 2.1) ug/L and 34.9 (SE = 2.1) ug/L at second and third trimesters, respectively. Analysis suggests a consistent negative relationship between prenatal maternal blood Pb and the GM at age 9–11, including measures of alpha and beta diversity, microbiome mixture analysis, and individual taxa. The WQS analysis showed a negative association between prenatal Pb exposure and the gut microbiome, for both second and third trimester exposures (2Tβ = −0.17, 95%CI = [−0.46,0.11]; 3Tβ = −0.17, 95%CI = [−0.44,0.10]). Ruminococcus gnavus, Bifidobacterium longum, Alistipes indistinctus, Bacteroides caccae, and Bifidobacterium bifidum all had weights above the importance threshold from 80% or more of the WQS repeated holdouts in association with both second and third trimester Pb exposure.DiscussionPilot data analysis suggests a negative association between prenatal Pb exposure and the gut microbiome later in childhood; however, additional investigation is needed.
Genetic characterization and whole-genome sequencing-based genetic analysis of influenza virus in Jining City during 2021–2022
Authors: Li Libo , Liu Tiantian , Wang Qingchuan , Ding Yi , Jiang Yajuan , Wu Zengding , Wang Xiaoyu , Dou Huixin , Jia Yongjian , Jiao Boyan 
Published: June 2023

BackgroundThe influenza virus poses a significant threat to global public health due to its high mutation rate. Continuous surveillance, development of new vaccines, and public health measures are crucial in managing and mitigating the impact of influenza outbreaks.MethodsNasal swabs were collected from individuals with influenza-like symptoms in Jining City during 2021-2022. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect influenza A viruses, followed by isolation using MDCK cells. Additionally, nucleic acid detection was performed to identify influenza A H1N1, seasonal H3N2, B/Victoria, and B/Yamagata strains. Whole-genome sequencing was conducted on 24 influenza virus strains, and subsequent analyses included characterization, phylogenetic construction, mutation analysis, and assessment of nucleotide diversity.ResultsA total of 1,543 throat swab samples were collected. The study revealed the dominance of the B/Victoria influenza virus in Jining during 2021-2022. Whole-genome sequencing showed co-prevalence of B/Victoria influenza viruses in the branches of Victoria clade 1A.3a.1 and Victoria clade 1A.3a.2, with a higher incidence observed in winter and spring. Comparative analysis demonstrated lower similarity in the HA, MP, and PB2 gene segments of the 24 sequenced influenza virus strains compared to the Northern Hemisphere vaccine strain B/Washington/02/2019. Mutations were identified in all antigenic epitopes of the HA protein at R133G, N150K, and N197D, and the 17-sequence antigenic epitopes exhibited more than 4 amino acid variation sites, resulting in antigenic drift. Moreover, one sequence had a D197N mutation in the NA protein, while seven sequences had a K338R mutation in the PA protein.ConclusionThis study highlights the predominant presence of B/Victoria influenza strain in Jining from 2021 to 2022. The analysis also identified amino acid site variations in the antigenic epitopes, contributing to antigenic drift.
Modalities of sequential human robot collaboration trigger different modifications of trunk oscillations
Authors: Ranaldi Simone , Bibbo Daniele , Corvini Giovanni , Schmid Maurizio , Conforto Silvia 
Published: June 2023

IntroductionHuman robot collaboration is quickly gaining importance in the robotics and ergonomics fields due to its ability to reduce biomechanical risk on the human operator while increasing task efficiency. The performance of the collaboration is typically managed by the introduction of complex algorithms in the robot control schemes to ensure optimality of its behavior; however, a set of tools for characterizing the response of the human operator to the movement of the robot has yet to be developed.MethodsTrunk acceleration was measured and used to define descriptive metrics during various human robot collaboration strategies. Recurrence quantification analysis was used to build a compact description of trunk oscillations.Results and discussionThe results show that a thorough description can be easily developed using such methods; moreover, the obtained values highlight that, when designing strategies for human robot collaboration, ensuring that the subject maintains control of the rhythm of the task allows to maximize comfort in task execution, without affecting efficiency.
Characterizations of microRNAs involved in the molecular mechanisms underlying the therapeutic effects of noni (Morinda citrifolia L.) fruit juice on hyperuricemia in mice
Authors: Liu Yue , Liu Xianjun , Wang Mengyuan , Chen Changwu , Li Xiaohong , Liang Zhiyong , Shan Yaming , Yin Yuhe , Sun Fengjie , Li Zhandong , Li Hao 
Published: June 2023

BackgroundHyperuricemia is generally defined as the high level of serum uric acid and is well known as an important risk factor for the development of various medical disorders. However, the medicinal treatment of hyperuricemia is frequently associated with multiple side-effects.MethodsThe therapeutic effect of noni (Morinda citrifolia L.) fruit juice on hyperuricemia and the underlying molecular mechanisms were investigated in mouse model of hyperuricemia induced by potassium oxonate using biochemical and high-throughput RNA sequencing analyses.ResultsThe levels of serum uric acid (UA) and xanthine oxidase (XOD) in mice treated with noni fruit juice were significantly decreased, suggesting that the noni fruit juice could alleviate hyperuricemia by inhibiting the XOD activity and reducing the level of serum UA. The contents of both serum creatinine and blood urine nitrogen of the noni fruit juice group were significantly lower than those of the model group, suggesting that noni fruit juice promoted the excretion of UA without causing deleterious effect on the renal functions in mice. The differentially expressed microRNAs involved in the pathogenesis of hyperuricemia in mice were identified by RNA sequencing with their target genes further annotated based on both Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases to explore the metabolic pathways and molecular mechanisms underlying the therapeutic effect on hyperuricemia by noni fruit juice.ConclusionOur study provided strong experimental evidence to support the further investigations of the potential application of noni fruit juice in the treatment of hyperuricemia.
The causal relationship between metabolic factors, drinking, smoking and intrahepatic cholangiocarcinoma: a Mendelian randomization study
Authors: Qin Shan-shan , Pan Guo-qiang , Meng Qun-bo , Liu Jin-bo , Tian Zi-yu , Luan Shou-jing 
Published: June 2023

BackgroundIntrahepatic cholangiocarcinoma (iCCA) is the second most common primary liver cancer. While multiple risk factors for iCCA have been established, metabolic diseases (obesity, diabetes, NAFLD, dyslipidemia, and hypertension) and other risk factors, including smoking and drinking, are still controversial due to their potential confounders. Here, Mendelian randomization (MR) analysis was performed to identify the causal relationship between them.MethodIn this study, we obtained GWAS data related to exposures from corresponding large genome-wide association studies. Summary-level statistical data for iCCA were obtained from the UK Biobank (UKB). We performed a univariable MR analysis to identify whether genetic evidence of exposure was significantly associated with iCCA risk. A multivariable MR analysis was conducted to estimate the independent effects of exposures on iCCA.ResultsUnivariable and multivariable MR analysis based on the large GWAS data indicated that there is little evidence to support the genetic role of metabolic factors, smoking, drinking, and NAFLD in iCCA development (P &gt;0.05). In contrast to most current studies, their impact on iCCA development, if any, might be smaller than we thought. The previous positive results might be due to the comorbidities between diseases and potentially unavoidable confounding factors.ConclusionIn this MR study, we found no strong evidence to support causal associations between metabolic factors, NAFLD, smoking, drinking, and iCCA risk.
The long-term trend of uterine fibroid burden in China from 1990 to 2019: A Joinpoint and Age–Period–Cohort study
Authors: Liu Xingyu , Wang Bo , Zhang Qianyu , Zhang Jinjin , Wang Shixuan 
Published: June 2023

Purpose: Uterine fibroids occur in 40%–60% of women and are symptomatic in 30% of the patients by causing abnormal uterine bleeding, pelvic pressure, pain, and infertility. The study aims to evaluate the long-term trend of uterine fibroids mortality and disability-adjusted life years (DALYs) in China and the relative risks of age, period, and birth cohort effects.Methods: The mortality and DALYs of uterine fibroids from 1990 to 2019 were derived from the Global Burden of Disease 2019. The annual percentage change and average annual percent change (AAPC) were assessed using the Joinpoint regression. The effects of age, period, and birth cohort on death and DALYs were analyzed by the Age–Period–Cohort framework.Results: The age-standardized rates were all on the ascending trend, with the greatest increase in the age-standardized mortality rate (AAPC, 1.53; 95% CI, 1.04–2.02). The net drift was found to be 3.51% (95% CI, 2.25%–4.78%) per year for mortality and 0.34% (95% CI, 0.14%–0.53%) per year for DALYs. Significant age, period, and birth cohort effects were found for mortality and DALYs (p &lt; 0.001 for all). The mortality risk increased overall with age, but the DALYs risk increased first and then decreased with age. The period and birth cohort risks for mortality and DALYs showed different trends.Conclusion: These secular time trends and changes of mortality and DALYs reveal the socioeconomic alterations, reform of diagnosis and therapy, and changes in social lifestyles and behaviors. Uterine fibroids are still the most common benign gynecological tumors in women, and more epidemiological investigations and social health prevention and control should be applied.