bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)
Authors: Ma Mengli , Meng Hengling , Lei En , Wang Tiantao , Zhang Wei , Lu Bingyue 
Published: September 2022

AbstractBackgroundAmomum tsaokois a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from differentA. tsaokotissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers.ResultsA total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism inA. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72A. tsaokoaccessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the sixA. tsaokopopulations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species.ConclusionsOur study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection inA. tsaoko.
Characteristics and comparison between e-scooters and bicycle-related trauma: a multicentre cross-sectional analysis of data from a road collision registry
Authors: Benhamed Axel , Gossiome Amaury , Ndiaye Amina , Tazarourte Karim 
Published: September 2022

Abstract
Background
Urban mobility has drastically evolved over the last decade and micromobility rapidly became an expanding segment of contemporary daily transportation routines. E-scooter riders and bicyclists may share similar trauma characteristics, but this has been little explored. The objective was to describe and compare the characteristics of e-scooter and bicycle-related trauma.

Methods
We conducted a cross-sectional analysis of data from the Rhône road collision registry (January 1, 2019 to December 31, 2019). We included all e-scooter or bicycle riders injured in traffic collisions during the study period; there were no exclusion criterion.

Results
A total of 2,779 patients were included; 825 (29.7%) were e-scooter riders and 1,954 (70.3%) were bicyclists. E-scooter riders were younger (median [IQR]: 24 [20–32] vs 29 [20–45] years, p < 0.001) and less frequently male (64.2% vs 73.4%, p < 0.001). Most e-scooter and bicycle road collisions were consequent to a fall or loss of vehicle control (74.2% vs 67.7%, p < 0.001). E-scooter riders were less frequently wearing a helmet at the time of the road collision (6.1% vs 30.7%, p < 0.001) and had more frequently head (24.2% vs 19.9%, p = 0.01) and face (30.6 vs 20.5%, p < 0.001) injuries compared to bicyclists. The median injury severity score was 2 [1–4] in both groups with no significant difference (p = 0.77).

Conclusions
E-scooter and bicycle-related trauma patients were mainly young males with minor injuries and most of them sustained a road collision with no third-party. However, they suffered from different injury patterns; e-scooter riders suffered more frequently face and head injuries than bicycle riders, which may be at least partly the consequence of less frequent helmet use among e-scooter riders compared to bicyclists. Hence the two groups of users should not be considered as a single trauma entity. This issue should be promptly addressed to bring down the incidence of preventable injuries and avoid healthcare costs.
Item response theory and differential test functioning analysis of the HBSC-Symptom-Checklist across 46 countries
Authors: Heinz Andreas , Sischka Philipp E. , Catunda Carolina , Cosma Alina , García-Moya Irene , Lyyra Nelli , Kaman Anne , Ravens-Sieberer Ulrike , Pickett William 
Published: September 2022

Abstract
Background
The Symptom Checklist (SCL) developed by the Health Behaviour in School-aged Children (HBSC) study is a non-clinical measure of psychosomatic complaints (e.g., headache and feeling low) that has been used in numerous studies. Several studies have investigated the psychometric characteristics of this scale; however, some psychometric properties remain unclear, among them especially a) dimensionality, b) adequacy of the Graded Response Model (GRM), and c) measurement invariance across countries.

Methods
Data from 229,906 adolescents aged 11, 13 and 15 from 46 countries that participated in the 2018 HBSC survey were analyzed. Adolescents were selected using representative sampling and surveyed by questionnaire in the classroom. Dimensionality was investigated using exploratory graph analysis. In addition, we investigated whether the GRM provided an adequate description of the data. Reliability over the latent variable continuum and differential test functioning across countries were also examined.

Results
Exploratory graph analyses showed that SCL can be considered as one-dimensional in 16 countries. However, a comparison of the unidimensional with a post-hoc bifactor GRM showed that deviation from a hypothesized one-dimensional structure was negligible in most countries. Multigroup invariance analyses supported configural and metric invariance, but not scalar invariance across 32 countries. Alignment analysis showed non-invariance especially for the items irritability, feeling nervous/bad temper and feeling low.

Conclusion
HBSC-SCL appears to represent a consistent and reliable unidimensional instrument across most countries. This bodes well for population health analyses that rely on this scale as an early indicator of mental health status.
Circulating miR-181a as a novel potential plasma biomarker for multimorbidity burden in the older population
Authors: Iannone Francesca , Crocco Paolina , Dato Serena , Passarino Giuseppe , Rose Giuseppina 
Published: September 2022

Abstract
Background
Chronic low-level inflammation is thought to play a role in many age-related diseases and to contribute to multimorbidity and to the disability related to this condition. In this framework, inflamma-miRs, an important subset of miRNA able to regulate inflammation molecules, appear to be key players. This study aimed to evaluate plasma levels of the inflamma-miR-181a in relation to age, parameters of health status (clinical, physical, and cognitive) and indices of multimorbidity in a cohort of 244 subjects aged 65- 97.

Methods
MiR-181a was isolated from plasma according to standardized procedures and its expression levels measured by qPCR. Correlation tests and multivariate regression analyses were applied on gender-stratified groups.

Results
MiR-181a levels resulted increased in old men, and significantly correlated with worsened blood parameters of inflammation (such as low levels of albumin and bilirubin and high lymphocyte content), particularly in females. Furthermore, we found miR-181a positively correlated with the overall multimorbidity burden, measured by CIRS Comorbidity Score, in both genders.

Conclusions
These data support a role of miR-181a in age-related chronic inflammation and in the development of multimorbidity in older adults and indicate that the routes by which this miRNA influence health status are likely to be gender specific. Based on our results, we suggest that miR-181a is a promising biomarker of health status of the older population.
Assessment of genotypes, endosymbionts and clinical characteristics of Acanthamoeba recovered from ocular infection
Authors: Rayamajhee Binod , Sharma Savitri , Willcox Mark , Henriquez Fiona L. , Rajagopal Raksheeth Nathan , Shrestha Gauri Shankar , Subedi Dinesh , Bagga Bhupesh , Carnt Nicole 
Published: September 2022

Abstract
Introduction
Acanthamoeba is an emerging pathogen, infamous for its resilience against antiprotozoal compounds, disinfectants and harsh environments. It is known to cause keratitis, a sight-threatening, painful and difficult to treat corneal infection which is often reported among contact lens wearers and patients with ocular trauma. Acanthamoeba comprises over 24 species and currently 23 genotypes (T1-T23) have been identified.

Aims
This retrospective study was designed to examine the Acanthamoeba species and genotypes recovered from patients with Acanthamoeba keratitis (AK), determine the presence of endosymbionts in ocular isolates of Acanthamoeba and review the clinical presentations.

Methodology
Thirteen culture-confirmed AK patients treated in a tertiary eye care facility in Hyderabad, India from February to October 2020 were included in this study. The clinical manifestations, medications and visual outcomes of all patients were obtained from medical records. The Acanthamoeba isolates were identified by sequencing the ribosomal nuclear subunit (rns) gene. Acanthamoeba isolates were assessed for the presence of bacterial or fungal endosymbionts using molecular assays, PCR and fluorescence in situ hybridization (FISH).

Results
The mean age of the patients was 33 years (SD ± 17.4; 95% CI 22.5 to 43.5 years). Six (46.2%) cases had AK associated risk factors; four patients had ocular trauma and two were contact lens wearers. A. culbertsoni (6/13, 46.2%) was the most common species, followed by A. polyphaga and A. triangularis. Most of the isolates (12/13) belonged to genotype T4 and one was a T12; three sub-clusters T4A, T4B, and T4F were identified within the T4 genotype. There was no significant association between Acanthamoeba types and clinical outcomes. Eight (61.5%) isolates harboured intracellular bacteria and one contained Malassezia restricta. The presence of intracellular microbes was associated with a higher proportion of stromal infiltrates (88.9%, 8/9), epithelial defect (55.6%, 5/9) and hypopyon (55.6%, 5/9) compared to 50% (2/4), 25% (1/4) and 25% (1/4) AK cases without intracellular microbes, respectively.

Conclusions
Genotype T4 was the predominant isolate in southern India. This is the second report of T12 genotype identified from AK patient in India, which is rarely reported worldwide. The majority of the Acanthamoeba clinical isolates in this study harboured intracellular microbes, which may impact clinical characteristics of AK.
Hemorrhagic fever with renal syndrome caused by destruction of residential area of rodent in a construction site: epidemiological investigation
Authors: Wei Xiao , Meng Biao , Peng Hong , Li Yan , Liu Min , Si Hairui , Wu Rui , Chen Hailong , Bai Ying , Li Yan , Feng Qunling , Wang Changjun , Zhao Xiangna 
Published: September 2022

Abstract
Background
An outbreak of hemorrhagic fever with renal syndrome (HFRS), caused by a Hantavirus, affected nine adult males in the southwest area of Xi’an in November 2020 was analyzed in this study.

Methods
Clinical and epidemiological data of HFRS patients in this outbreak were retrospectively analyzed. The whole genome of a hantavirus named 201120HV03xa (hv03xa for short) isolated from Apodemus agrarius captured in the construction site was sequenced and analyzed. In addition, nine HFRS patients were monitored for the IgG antibody against the HV N protein at 6 and 12 months, respectively.

Results
In this study, inhalation of aerosolized excreta and contaminated food may be the main source of infection. Genome analysis and phylogenetic analysis showed that hv03xa is a reassortment strain of HTNV, having an S segment related to A16 of HTN 4, an M segment related to Q37 and Q10 of HTN 4, and an L segment related to prototype strain 76–118 of HTN 7. Potential recombination was detected in the S segment of hv03xa strain. The anti-HV-IgG level of all the patients persist for at least one year after infection.

Conclusions
This report documented an HFRS outbreak in Xi’an, China, which provided the basic data for epidemiological surveillance of endemic HTNV infection and facilitated to predict disease risk and implement prevention measures.
Three-dimensional nuclear telomere architecture and differential expression of aurora kinase genes in chronic myeloid leukemia to measure cell transformation
Authors: de Oliveira Fábio Morato , Jamur Valderez Ravaglio , Merfort Lismeri Wuicik , Pozzo Aline Rangel , Mai Sabine 
Published: September 2022

AbstractBackgroundTelomere dysfunction results in aneuploidy, and ongoing chromosomal abnormalities. The three-dimensional (3D) nuclear organization of telomeres allows for a distinction between normal and tumor cells. On the other hand, aurora kinase genes (AURKAandAURKB) play an important role regulating the cell cycle. A correlation between overexpression of aurora kinase genes and clinical aggressiveness has been demonstrated in different types of neoplasias. To better understand cellular and molecular mechanisms of CML evolution, it was examined telomere dysfunction (alterations in the 3D nuclear telomere architecture), and the expression levels ofAURKAandAURKBgenes in two clinical distinct subgroups of CML samples, from the same patient.MethodsEighteen CML patients, in total, 36 bone marrow samples (18 patients,chronicvs.accelerated/blast phase) were eligible for 3D telomeric investigations. Quantitative 3D imaging, cytologic diagnosis and cytogenetic determination of additional chromosomal abnormalities were assessed according to standard protocols.ResultsUsing TeloView software, two CML subgroups were defined based on their 3D telomeric profiles, reflecting the different stages of the disease (chronicvs.accelerated/blast phase). Statistical analyses showed significant differences between the CML subgroups (p < 0.001). We also found thatAURKAandAURKBmRNA were expressed at significantly higher levels in both CML subgroups, when compared with healthy donors. Our findings suggest that the evolution of CML progresses from a low to a high level of telomere dysfunction, that is, from an early stage to a more aggressive stage, followed by disease transformation, as demonstrated by telomere, additional chromosomal abnormalities, and gene expression profile dynamics.ConclusionsThus, we demonstrated that 3D telomere organization, in accordance with the genomic instability observed in CML samples were able to distinguish subgroup CML patients. Classifying CML patients based on these characteristics might represent an important strategy to define better therapeutic strategies.
Identifying individuals with undiagnosed post-traumatic stress disorder in a large United States civilian population – a machine learning approach
Authors: Gagnon-Sanschagrin Patrick , Schein Jeff , Urganus Annette , Serra Elizabeth , Liang Yawen , Musingarimi Primrose , Cloutier Martin , Guérin Annie , Davis Lori L. 
Published: September 2022

Abstract
Background
The proportion of patients with post-traumatic stress disorder (PTSD) that remain undiagnosed may be substantial. Without an accurate diagnosis, these patients may lack PTSD-targeted treatments and experience adverse health outcomes. This study used a machine learning approach to identify and describe civilian patients likely to have undiagnosed PTSD in the US commercial population.

Methods
The IBM® MarketScan® Commercial Subset (10/01/2015–12/31/2018) was used. A random forest machine learning model was developed and trained to differentiate between patients with and without PTSD using non–trauma-based features. The model was applied to patients for whom PTSD status could not be confirmed to identify individuals likely and unlikely to have undiagnosed PTSD. Patient characteristics, symptoms and complications potentially related to PTSD, treatments received, healthcare costs, and healthcare resource utilization were described separately for patients with PTSD (Actual Positive PTSD cohort), patients likely to have PTSD (Likely PTSD cohort), and patients without PTSD (Without PTSD cohort).

Results
A total of 44,342 patients were classified in the Actual Positive PTSD cohort, 5683 in the Likely PTSD cohort, and 2,074,471 in the Without PTSD cohort. While several symptoms/comorbidities were similar between the Actual Positive and Likely PTSD cohorts, others, including depression and anxiety disorders, suicidal thoughts/actions, and substance use, were more common in the Likely PTSD cohort, suggesting that certain symptoms may be exacerbated among those without a formal diagnosis. Mean per-patient-per-6-month healthcare costs were similar between the Actual Positive and Likely PTSD cohorts ($11,156 and $11,723) and were higher than those of the Without PTSD cohort ($3616); however, cost drivers differed between cohorts, with the Likely PTSD cohort experiencing more inpatient admissions and less outpatient visits than the Actual Positive PTSD cohort.

Conclusions
These findings suggest that the lack of a PTSD diagnosis and targeted management of PTSD may result in a greater burden among undiagnosed patients and highlights the need for increased awareness of PTSD in clinical practice and among the civilian population.
The impact of human resources for health on the health outcomes of Chinese people
Authors: Cheng Jingjing , Kuang Xianming , Zeng Linghuang 
Published: September 2022

AbstractHuman resources for health (HRH) is a cornerstone in the medical system. This paper combined data envelopment analysis (DEA) with Tobit regression analysis to evaluate the efficiency of health care services in China over the years between 2007 and 2019. Efficiency was first estimated by using DEA with the choice of inputs and outputs being specific to health care services and residents’ health status. Malmquist index model was selected for estimating the changes in total factor productivity of provinces and exploring whether their performance had improved over the years. Tobit regression model was then employed in which the efficiency score obtained from the DEA computations used as the dependent variable, and HRH was chosen as the independent variables. The results showed that all kinds of health personnel had a significantly positive impact on the efficiency, and more importantly, pharmacists played a critical role in affecting both the provincial and national efficiency. Therefore, the health sector should pay more attention to optimizing allocation of HRH and focusing on professional training of clinical pharmacists.
LncRNA Airn maintains LSEC differentiation to alleviate liver fibrosis via the KLF2-eNOS-sGC pathway
Authors: Chen Ting , Shi Zhemin , Zhao Yanmian , Meng Xiaoxiang , Zhao Sicong , Zheng Lina , Han Xiaohui , Hu Zhimei , Yao Qingbin , Lin Huajiang , Du Xiaoxiao , Zhang Kun , Han Tao , Hong Wei 
Published: September 2022

Abstract
Background
Long noncoding RNAs (lncRNAs) have emerged as important regulators in a variety of human diseases. The dysregulation of liver sinusoidal endothelial cell (LSEC) phenotype is a critical early event in the fibrotic process. However, the biological function of lncRNAs in LSEC still remains unclear.

Methods
The expression level of lncRNA Airn was evaluated in both human fibrotic livers and serums, as well as mouse fibrotic livers. Gain- and loss-of-function experiments were performed to detect the effect of Airn on LSEC differentiation and hepatic stellate cell (HSC) activation in liver fibrosis. Furthermore, RIP, RNA pull-down-immunoblotting, and ChIP experiments were performed to explore the underlying mechanisms of Airn.

Results
We have identified Airn was significantly upregulated in liver tissues and LSEC of carbon tetrachloride (CCl4)-induced liver fibrosis mouse model. Moreover, the expression of AIRN in fibrotic human liver tissues and serums was remarkably increased compared with healthy controls. In vivo studies showed that Airn deficiency aggravated CCl4- and bile duct ligation (BDL)-induced liver fibrosis, while Airn over-expression by AAV8 alleviated CCl4-induced liver fibrosis. Furthermore, we revealed that Airn maintained LSEC differentiation in vivo and in vitro. Additionally, Airn inhibited HSC activation indirectly by regulating LSEC differentiation and promoted hepatocyte (HC) proliferation by increasing paracrine secretion of Wnt2a and HGF from LSEC. Mechanistically, Airn interacted with EZH2 to maintain LSEC differentiation through KLF2-eNOS-sGC pathway, thereby maintaining HSC quiescence and promoting HC proliferation.

Conclusions
Our work identified that Airn is beneficial to liver fibrosis by maintaining LSEC differentiation and might be a serum biomarker for liver fibrogenesis.
Clinical and genetic analyses of patients with lateralized overgrowth
Authors: Kim Yoon-Myung , Lee Yena , Choi Yunha , Choi In Hee , Heo Sun Hee , Choi Jung Min , Do Hyo-Sang , Jang Ja-Hyun , Yum Mi-Sun , Yoo Han-Wook , Lee Beom Hee 
Published: September 2022

Abstract
Background
The genetic features and treatment strategies of lateralized overgrowth have been elusive. We performed this study to analyze the genetic characteristics and treatment results of propranolol- or alpelisib-treated patients with lateralized overgrowth.

Methods
Fifteen patients with lateralized overgrowth were involved. Clinical characteristics and whole-body magnetic resonance imaging (WB-MRI) findings were evaluated. Targeted exome sequencing with a gene panel of affected tissue and peripheral white blood cells was performed. Propranolol was administered and treatment results were evaluated. The PIK3CA inhibitor alpelisib was prescribed via a managed access program.

Results
The identified mutations were PIK3CA (n = 7), KRAS (n = 2), PTEN (n = 1), MAP2K3 (n = 1), GNAQ (n = 1), TBC1D4 (n = 1), and TEK (n = 1). Propranolol was prescribed in 12 patients, and 7 experienced mild improvement of symptoms. Alpelisib was prescribed in two patients with a PIK3CA mutation, and the reduction of proliferated masses after 1 year of treatment was proved by WB-MRI.

Conclusions
Targeted exome sequencing identified various genetic features of lateralized overgrowth. Propranolol could be applied as an adjuvant therapy for reducing vascular symptoms, but a PIK3CA inhibitor would be the primary therapeutic strategy for PIK3CA-related overgrowth syndrome.