bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide screening of the RNase T2 gene family and functional analyses in jujube (Ziziphus jujuba Mill.)
Authors: Luo Zhi , Zhang Yu , Tian Chunjiao , Wang Lihu , Zhao Xuan , Liu Zhiguo , Wang Lili , Wang Lixin , Zhao Jin , Wang Jiurui , Liu Mengjun 
Published: February 2023

Abstract
Background
Ribonuclease (RNase T2) plays crucial roles in plant evolution and breeding. However, there have been few studies on the RNase T2 gene family in Ziziphus jujuba Mill., one of important dried fruit tree species. Recently, the released sequences of the reference genome of jujube provide a good chance to perform genome-wide identification and characterization of ZjRNase gene family in the jujube.

Results
In this study, we identified four members of RNase T2 in jujube distributed on three chromosomes and unassembled chromosomes. They all contained two conserved sites (CASI and CASII). Analysis of the phylogenetic relationships revealed that the RNase T2 genes in jujube could be divided into two groups: ZjRNase1 and ZjRNase2 belonged to class I, while ZjRNase3 and ZjRNase4 belonged to class II. Only ZjRNase1 and ZjRNase2 expression were shown by the jujube fruit transcriptome analysis. So ZjRNase1 and ZjRNase2 were selected functional verification by overexpression transformation of Arabidopsis. The overexpression of these two genes led to an approximately 50% reduction in seed number, which deserve further attention. Moreover, the leaves of the ZjRNase1 overexpression transgenic lines were curled and twisted. Overexpression of ZjRNase2 resulted in shortened and crisp siliques and the production of trichomes, and no seeds were produced.

Conclusion
In summary, these findings will provide new insights into the molecular mechanisms of low number of hybrid seeds in jujube and a reference for the future molecular breeding of jujube.
Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors
Authors: Bovio-Winkler Patricia , Guerrero Leandro D. , Erijman Leonardo , Oyarzúa Pía , Suárez-Ojeda María Eugenia , Cabezas Angela , Etchebehere Claudia 
Published: February 2023

Abstract
Background
The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor.

Results
Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus ‘Ca. Villigracilis’. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization.

Conclusion
Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.
Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization
Authors: Mao Jiuyang , Liang Yuze , Wang Xue , Zhang Dequan 
Published: February 2023

AbstractBackgroundGentiana rigescensFranchet is an endangered medicinal herb from the family Gentianaceae with medicinal values.Gentiana cephalanthaFranchet is a sister species toG. rigescenspossessing similar morphology and wider distribution. To explore the phylogeny of the two species and reveal potential hybridization, we adopted next-generation sequencing technology to acquire their complete chloroplast genomes from sympatric and allopatric distributions, as along with Sanger sequencing to produce the nrDNA ITS sequences.ResultsThe plastid genomes were highly similar betweenG. rigescensandG. cephalantha. The lengths of the genomes ranged from 146,795 to 147,001 bp inG. rigescensand from 146,856 to 147,016 bp inG. cephalantha. All genomes consisted of 116 genes, including 78 protein-coding genes, 30 tRNA genes, four rRNA genes and four pseudogenes. The total length of the ITS sequence was 626 bp, including six informative sites. Heterozygotes occurred intensively in individuals from sympatric distribution. Phylogenetic analysis was performed based on chloroplast genomes, coding sequences (CDS), hypervariable sequences (HVR), and nrDNA ITS. Analysis based on all the datasets showed thatG. rigescensandG. cephalanthaformed a monophyly. The two species were well separated in phylogenetic trees using ITS, except for potential hybrids, but were mixed based on plastid genomes. This study supports thatG. rigescensandG. cephalanthaare closely related, but independent species. However, hybridization was confirmed to occur frequently betweenG. rigescensandG. cephalanthain sympatric distribution owing to the lack of stable reproductive barriers. Asymmetric introgression, along with hybridization and backcrossing, may probably lead to genetic swamping and even extinction ofG. rigescens.ConclusionG. rigescensandG. cephalanthaare recently diverged species which might not have undergone stable post-zygotic isolation. Though plastid genome shows obvious advantage in exploring phylogenetic relationships of some complicated genera, the intrinsic phylogeny was not revealed because of matrilineal inheritance here; nuclear genomes or regions are hence crucial for uncovering the truth. As an endangered species,G. rigescensfaces serious threats from both natural hybridization and human activities; therefore, a balance between conservation and utilization of the species is extremely critical in formulating conservation strategies.
Stress of emergency physicians during helicopter operations: impact of patients’ diagnoses, severity of diagnoses, and physicians’ work experience
Authors: Petrowski Katja , Malkewitz Camila Paola , Schöniger Christian , Frank Mark , Theiler Lorenz 
Published: February 2023

Abstract
Purpose
Emergency physicians are in danger of developing illnesses due to stress in their demanding work environment. Until today, scholars have not identified stressors or resilience factors that qualify to promote the preservation of emergency physicians’ well-being. Therefore, potential influencing variables such as patients’ diagnoses, the severity of diagnoses, as well as physicians’ work experience have to be considered. The present study aims at investigating emergency physicians in the Helicopter Emergency Medical Service (HEMS)’ autonomic nervous system activity during emergency operations in one shift with respect to patients’ diagnoses, severity of diagnoses, and physicians’ work experience.

Methods
Measurement of HRV (employing the parameters RMSSD and LF/HF) for 59 EPs (age: M = 39.69, SD = 6.19) was performed during two complete air-rescue-days, the alarm and landing phase being investigated in particular. Besides patients’ diagnoses, the National Advisory Committee for Aeronautics Score (NACA) was included as an indicator for severity. Diagnoses’ and NACA’s effect on HRV were examined using a linear mixed model.

Results
Both HRV parameters indicate a significant decrease of the parasympathetic nervous system as a function of the diagnoses. Furthermore, high NACA scores (≥ V) predicted a significantly lower HRV. In addition, a lower HRV/RMSSD with increasing work experience was observed as well as a positive association between physicians’ work experience and sympathetic activation (LF/HF).

Conclusion
The present study showed that pediatric diagnoses as well as time-critical diagnoses are most stressful and have the highest impact on the physicians’ ANS. This knowledge allows the development of specific training to reduce stress.
Concordance of neonatal critical condition data between secondary databases: Florida and Texas birth certificate Linkage with medicaid analytic extract
Authors: Albogami Yasser , Zhu Yanmin , Wang Xi , Winterstein Almut G 
Published: February 2023

Abstract
Background
Limited information is available about neonates’ critical conditions data quality. The study aim was to measure the agreement regarding presence of neonatal critical conditions between Medicaid Analytic eXtract claims data and Birth Certificate (BC) records.

Methods
Claims data files of neonates born between 1999–2010 and their mothers were linked to birth certificates in the states of Texas and Florida. In claims data, neonatal critical conditions were identified using medical encounter claims records within the first 30 days postpartum, while in birth certificates, the conditions were identified based on predetermined variables. We calculated the prevalence of cases within each data source that were identified by its comparator, in addition to calculating overall agreement and kappa statistics.

Results
The sample included 558,224 and 981,120 neonates in Florida and Texas, respectively. Kappa values show poor agreement (< 20%) for all critical conditions except neonatal intensive care unit (NICU) admission, which showed moderate (> 50%) and substantial (> 60%) agreement in Florida and Texas, respectively. claims data resulted in higher prevalences and capture of a larger proportion of cases than the BC, except for assisted ventilation.

Conclusions
Claims data and BC showed low agreement on neonatal critical conditions except for NICU admission. Each data source identified cases most of which the comparator failed to capture, with higher prevalences estimated within claims data except for assisted ventilation.
A clinical indicator-based prognostic model predicting treatment outcomes of pulmonary tuberculosis: a prospective cohort study
Authors: Zhan Mengyao , Xue Hao , Wang Yuting , Wu Zhuchao , Wen Qin , Shi Xinling , Wang Jianming 
Published: February 2023

Abstract
Objectives
Identifying prognostic factors helps optimize the treatment regimen and promote favorable outcomes. We conducted a prospective cohort study on patients with pulmonary tuberculosis to construct a clinical indicator-based model and estimate its performance.

Methods
We performed a two-stage study by recruiting 346 pulmonary tuberculosis patients diagnosed between 2016 and 2018 in Dafeng city as the training cohort and 132 patients diagnosed between 2018 and 2019 in Nanjing city as the external validation population. We generated a risk score based on blood and biochemistry examination indicators by the least absolute shrinkage and selection operator (LASSO) Cox regression. Univariate and multivariate Cox regression models were used to assess the risk score, and the strength of association was expressed as the hazard ratio (HR) and 95% confidence interval (CI). We plotted the receiver operating characteristic (ROC) curve and calculated the area under the curve (AUC). Internal validation was conducted by 10-fold cross-validation.

Results
Ten significant indicators (PLT, PCV, LYMPH, MONO%, NEUT, NEUT%, TBTL, ALT, UA, and Cys-C) were selected to generate the risk score. Clinical indicator-based score (HR: 10.018, 95% CI: 4.904–20.468, P < 0.001), symptom-based score (HR: 1.356, 95% CI: 1.079–1.704, P = 0.009), pulmonary cavity (HR: 0.242, 95% CI: 0.087–0.674, P = 0.007), treatment history (HR: 2.810, 95% CI: 1.137–6.948, P = 0.025), and tobacco smoking (HR: 2.499, 95% CI: 1.097–5.691, P = 0.029) were significantly related to the treatment outcomes. The AUC was 0.766 (95% CI: 0.649–0.863) in the training cohort and 0.796 (95% CI: 0.630–0.928) in the validation dataset.

Conclusion
In addition to the traditional predictive factors, the clinical indicator-based risk score determined in this study has a good prediction effect on the prognosis of tuberculosis.
Reducing urinary catheter use in geriatric patients - results of a single-center champion-led intervention
Authors: Mrziglod L , Saydan S , Schwab F , Zohlnhöfer-Momm D , Gastmeier P , Hansen S 
Published: February 2023

Abstract
Background
Indwelling urinary tract catheters (UTC) are a well-known risk factor for urinary tract infections (UTI). Because geriatric patients are at high risk of infection, an intervention with a focus on appropriate and minimal UTC use was introduced in 4 acute care geriatric wards.

Methods
Between 11/2018 and 1/2020, unit-based data on UTC use and nosocomial UTI was collected in accordance with the methods of the German national surveillance system KISS. From 6/2019 to 1/2020, a champion-led intervention was implemented which focused on: (i) feedback of surveillance data, (ii) education and training in aseptic UTC insertion and maintenance, (iii) HCW’s daily assessment of UTC necessity based on a checklist and (iv) timely removal of unnecessary UTCs. UTC use, incidence, and incidence densities for catheter-associated UTI (CAUTI) were calculated before and during the intervention. In addition, we analyzed adherence to a scheduled daily assessment of UTC necessity. Rate ratios (RR) with 95% confidence intervals (95%CI) were calculated. Differences based on the quality of checklist completion were evaluated using the Kruskal Wallis test.

Results
We analyzed the data of 3,564 patients with a total 53,954 patient days, 9,208 UTC days, and 61 CAUTI. Surveillance data showed a significant decrease in the pooled UTC utilization rate from 19.1/100 patient days to 15.2/100 patient days (RR = 0.80, 95%CI 0.77–0.83, p < 0.001). CAUTI per 100 patients dropped from 2.07 to 1.40 (RR = 0.68, 95%CI 0.41–1.12, p = 0.1279). Overall, 373 patients received a UTC during the intervention. Of those patients 351 patients had an UTC ≥ 2 days. The analysis of these patients showed that 186 patients (53%) received a checklist as part of their chart for daily evaluation of UTC necessity. 43 (23.1%) of the completed checklists were of good quality; 143 (76.9%) were of poor quality. Patients in the group whose checklists were of good quality had fewer UTC days (median 7 UTC days IQR (3–11)) than patients whose checklists were of poor quality (11 UTC days IQR (6–16), p = 0.001).

Conclusion
We conclude that a champion-led, surveillance-based intervention reduces the use of UTC among geriatric patients. Further research is needed to determine to what extent the use of checklists in daily medical UTC assessment affects the prevention of CAUTI. The fact that patients whose checklists were completed well had fewer UTC days should encourage a conscientious and thorough daily review of the need for UTC.
Perinatal and pediatric outcomes associated with the use of fertility treatment: a population-based retrospective cohort study in Ontario, Canada
Authors: Dimanlig-Cruz Sheryll , Corsi Daniel J. , Lanes Andrea , Meng Lynn , Miao Qun , Walker Mark , Fell Deshayne B. 
Published: February 2023

Abstract
Background
Around 2% of births in Ontario, Canada involve the use of assisted reproductive technology (ART), and it is rising due to the implementation of a publicly funded ART program in 2016. To better understand the impact of fertility treatments, we assessed perinatal and pediatric health outcomes associated with ART, hormonal treatments, and artificial insemination compared with spontaneously conceived births.

Methods
This population-based retrospective cohort study was conducted using provincial birth registry data linked with fertility registry and health administrative databases in Ontario, Canada. Live births and stillbirths from January 2013 to July 2016 were included and followed to age one. The risks of adverse pregnancy, birth and infant health outcomes were assessed by conception method (spontaneous conception, ART – in vitro fertilization and non-ART – ovulation induction, intra-uterine or vaginal insemination) using risk ratios and incidence rate ratios with 95% confidence intervals (CI). Propensity score weighting using a generalized boosted model was applied to adjust for confounding.

Result(s)
Of 177,901 births with a median gestation age of 39 weeks (IQR 38.0–40.0), 3,457 (1.9%) were conceived via ART, and 3,511 (2.0%) via non-ART treatments. There were increased risks (adjusted risk ratio [95% CI]) of cesarean delivery (ART: 1.44 [1.42–1.47]; non-ART: 1.09 [1.07–1.11]), preterm birth (ART: 2.06 [1.98–2.14]; non-ART: 1.85 [1.79–1.91]), very preterm birth (ART: 2.99 [2.75–3.25]; non-ART: 1.89 [1.67–2.13]), 5-min Apgar < 7 (ART: 1.28 [1.16–1.42]; non-ART: 1.62 [1.45–1.81]), and composite neonatal adverse outcome indicator (ART: 1.61 [1.55–1.68]; non-ART: 1.29 [1.25–1.34]). Infants born after fertility treatments had increased risk of admission to neonatal intensive care unit (ART: 1.98 [1.84–2.13]; non-ART: 1.59 [1.51–1.67]) and prolonged birth admission (≥ 3 days) (ART: 1.60 [1.54–1.65]; non-ART: 1.42 [1.39–1.45]). The rate of emergency and in-hospital health services use within the first year was significantly increased for both exposure groups and remained elevated when limiting analyses to term singletons.

Conclusion(s)
Fertility treatments were associated with increased risks of adverse outcomes; however, the overall magnitude of risks was lower for infants conceived via non-ART treatments.
Cytoplasmic poly(A)-binding protein 1 (PABPC1) is a prognostic biomarker to predict survival in nasopharyngeal carcinoma regardless of chemoradiotherapy
Authors: Ling Feng , Xu Shengen , Li Xiaochen , Sun Xingwang , Long Wenbo 
Published: February 2023

AbstractBackgroundNasopharyngeal carcinoma (NPC), especially the nonkeratinizing type, is a malignant tumor primarily occurring in southern China and Southeast Asia. Chemotherapy (CT) and combined radiotherapy (RT) is used to treat NPC. However, the mortality rate is high in recurrent and metastatic NPC. We developed a molecular marker, analyzed its correlation with clinical characteristics, and assessed the prognostic value among NPC patients with or without chemoradiotherapy.MethodsA total of 157 NPC patients were included in this study, with 120 undergoing treatment and 37 without treatment. EBER1/2 expression was investigated using in situ hybridization (ISH). Expression of PABPC1, Ki-67, and p53 was detected with immunohistochemistry. The correlations of EBER1/2 and the expression of the three proteins having clinical features and prognosis were evaluated.ResultsThe expression of PABPC1 was associated with age, recurrence, and treatment but not with gender, TNM classification, or the expression of Ki-67, p53, or EBER. High expression of PABPC1 was associated with poor overall survival (OS) and disease-free survival (DFS) and was an independent predictor depending on multivariate analysis. Comparatively, no significant correlation was observed between the expression of p53, Ki-67, and EBER and survival. In this study, 120 patients received treatments and revealed significantly better OS and DFS than the untreated 37 patients. PABPC1 high expression was an independent predictor of shorter OS in the treated (HR = 4.012 (1.238–13.522), 95% CI,p = 0.021) and the untreated groups (HR = 5.473 (1.051–28.508), 95% CI,p = 0.044). However, it was not an independent predictor of shorter DFS in either the treated or the untreated groups. No significant survival difference was observed between patients with docetaxel-based induction chemotherapy (IC) + concurrent chemoradiotherapy (CCRT) and those with paclitaxel-based IC + CCRT. However, when combined with treatment and PABPC1 expression, patients with paclitaxel-added chemoradiotherapy plus PABPC1 low expression had significantly better OS than those who underwent chemoradiotherapy (p = 0.036).ConclusionsHigh expression of PABPC1 is associated with poorer OS and DFS among NPC patients. Patients with PABPC1 having low expression revealed good survival irrespective of the treatment received, indicating that PABPC1 could be a potential biomarker for triaging NPC patients.
Season of birth and atopic dermatitis in early infancy: results from the Japan Environment and Children’s Study
Authors: Tsuchida Akiko , Itazawa Toshiko , Matsumura Kenta , Yokomichi Hiroshi , Yamagata Zentaro , Adachi Yuichi , Inadera Hidekuni ,   on behalf of the Japan Environment and Children’s Study Group, Kamijima Michihiro , Yamazaki Shin , Ohya Yukihiro , Kishi Reiko , Yaegashi Nobuo , Hashimoto Koichi , Mori Chisato , Ito Shuichi , Nakayama Takeo , Sobue Tomotaka , Shima Masayuki , Nakamura Hiroshige , Suganuma Narufumi , Kusuhara Koichi , Katoh Takahiko 
Published: February 2023

AbstractBackgroundAtopic dermatitis (AD) is reported to be more prevalent in children who were born in autumn than in spring. Here, we investigated how early the association between season of birth and eczema or AD can be observed in the postnatal period. We also examined whether specific prevalence outcomes for infant eczema and AD differed according to sex and maternal history of allergic disease in a large Japanese cohort.MethodsUsing data of 81,615 infants from the Japan Environment and Children’s Study, we examined the associations of birth month or season with four different outcomes—eczema at 1 month, 6 months, and 1 year of age and physician-diagnosed AD up to 1 year of age—using multiple logistic regression analysis. We also analyzed the effect of maternal history of allergic disease on these outcomes stratified by infant sex.ResultsThe risk of eczema at 1 month was highest in infants born in July. In contrast, infants born in autumn had higher risks of eczema at 6 months (adjusted odds ratio [aOR], 2.19; 95% confidence interval [CI], 2.10–2.30) and at 1 year (aOR, 1.08; 95% CI, 1.02–1.14) and of physician-diagnosed AD up to 1 year of age (aOR, 1.33; 95% CI, 1.20–1.47) compared with infants born in spring. Eczema and AD were more prevalent in infants with a maternal history of allergic disease, particularly boys.ConclusionsOur findings suggest that the prevalence of AD is associated with the season of observation. Eczema is prevalent in infants born in autumn, and this phenomenon was observed in infants as young as 6 months old. The risk associated with being born in autumn was particularly clear in boys with a maternal history of allergic disease.Trial registrationUMIN000030786