bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers
Authors: Clerissi Camille , Guillou Laure , Escoubas Jean-Michel , Toulza Eve 
Published: July 2020

Abstract
Background
Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far.

Results
To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities were sequenced using metabarcoding. Alveolata, Stramenopiles and Archaeplastida were the main protist phyla associated with oysters. In particular, Codonellopsis, Cyclotella, Gymnodinium, Polarella, Trichodina, and Woloszynskia were the dominant genera. The potential pathogen Alexandrium was also found in high abundances within some samples.

Conclusions
Our study revealed the main protist taxa within oysters as well as the occurrence of potential oyster pathogens. These new primer sets are promising tools to better understand oyster homeostasis and disease development, such as the Pacific Oyster Mortality Syndrome (POMS) targeting juveniles.
Novel multiplex real-time PCR assays reveal a high prevalence of diarrhoeagenic Escherichia coli pathotypes in healthy and diarrhoeal children in the south of Vietnam
Authors: Duong Vu Thuy , Tu Le Thi Phuong , Tuyen Ha Thanh , Nhi Le Thi Quynh , Campbell James I. , Van Minh Pham , Le Phuc Hoang , Chau Tran Thi Hong , Ngoc Nguyen Minh , Vi Lu Lan , Jenkins Claire , Okeke Iruka , Higginson Ellen , Baker Stephen 
Published: July 2020

Abstract
Background
Diarrhoeagenic Escherichia coli (DEC) infections are common in children in low-middle income countries (LMICs). However, detecting the various DEC pathotypes is complex as they cannot be differentiated by classical microbiology. We developed four multiplex real-time PCR assays were to detect virulence markers of six DEC pathotypes; specificity was tested using DEC controls and other enteric pathogens. PCR amplicons from the six E. coli pathotypes were purified and amplified to be used to optimize PCR reactions and to calculate reproducibility. After validation, these assays were applied to clinical samples from healthy and diarrhoeal Vietnamese children and associated with clinical data.

Results
The multiplex real-time PCRs were found to be reproducible, and specific. At least one DEC variant was detected in 34.7% (978/2815) of the faecal samples from diarrhoeal children; EAEC, EIEC and atypical EPEC were most frequent Notably, 41.2% (205/498) of samples from non-diarrhoeal children was positive with a DEC pathotype. In this population, only EIEC, which was detected in 34.3% (99/289) of diarrhoeal samples vs. 0.8% (4/498) non-diarrhoeal samples (p < 0.001), was significantly associated with diarrhoea. Multiplex real-time PCR when applied to clinical samples is an efficient and high-throughput approach to DEC pathotypes.

Conclusions
This approach revealed high carriage rates of DEC pathotypes among Vietnamese children. We describe a novel diagnostic approach for DEC, which provides baseline data for future surveillance studies assessing DEC burden in LMICs.
Transcriptome analysis of salt-responsive and wood-associated NACs in Populus simonii × Populus nigra
Authors: Yao Wenjing , Li Chuanzhe , Lin Shuyan , Wang Jianping , Zhou Boru , Jiang Tingbo 
Published: July 2020

AbstractBackgroundNAC (NAM, ATAF1–2, and CUC2) family is one of the largest plant-specific transcription factor families known to play significant roles in plant development processes and stress responses.ResultsIn the study, a total of 112 NACs were identified to be differentially expressed in the comparisons of leaves and stems, leaves and roots, roots and stems ofPopulus simonii×P. nigraamong 289 members by RNA-Seq. And 148, 144 and 134 NACs were detected to be salt-responsive in the roots, stems and leaves under 150 mM NaCl stress, respectively. Among them, a total of 53 salt-responsive NACs were shared across the three tissues. Under salt stress, 41/37 NACs were identified to be up/down-regulated in the leaves ofPopulus simonii × P.nigraamong 170 non-redundant NACs by RT-qPCR, which was similar with RNA-Seq results. The expression pattern analysis of 6 NACs including four randomly up-regulated genes (NAC86,NAC105,NAC139andNAC163) and two down-regulated genes (NAC15andNAC149) indicated a few NACs showed specific temporal and spatial expression patterns in the three tissues ofPopulus simonii×P.nigra. Based on transcriptome screening and phylogenic analysis of differentially expressed NACs in different tissues under salt stress, 18 potential NACs associated with wood formation and 20 involved in stress responses were identified inPopulus simonii×P.nigra.ConclusionsThe study further gains an understanding of the connection of tissue specificity and gene function in poplar, and lays the foundation of functional analysis of poplar NACs in stress responses.
Agreement between original and Rasch-approved neck disability index
Authors: Lu Ze , MacDermid Joy C. , Nazari Goris 
Published: July 2020

Abstract
Background
Given the high prevalence of neck pain, the neck disability index (NDI) has been used to evaluate patient status and treatment outcomes. Modified versions were proposed as solutions to measurement deficits in the NDI. However, the original 10-item NDI was scored out of 50 and is still the most frequently administered version. Examining the extent of agreement between traditional and Rasch-based versions using Bland-Altman (B&A) plots will inform our understanding of score differences that might rise from using different versions. Therefore, the objective of current study was to describe the extent of agreement between different versions of NDI.

Methods
The current study was a secondary data analysis. The study data was compiled from two prospectively collected data sources. We performed a comprehensive literature search to identify Rasch approved NDI within four databases including Embase, Medline, PubMed, and Google Scholar. Alternate forms and scorings were compared to each other and to the standard NDI. We graphed B&A plots and calculated the mean difference and the 95% limits of agreement (LoA; ±1.96 times the standard deviation).

Results
Two Rasch approved alternative versions (8 vs 5 items) were identified from 303 screened publications. We analyzed data from 201 (43 males and 158 females) patients attending community clinics for neck pain. We found that the mean difference was approximately 10% of the total score between the 10-item and 5-item (− 4.6 points), whereas the 10-item versus 8-item and 8-item versus 5-item had smaller mean differences (− 2.3 points). The B&A plots displayed wider 95% LoA for the agreement between 10-item and 8-item (LoA: − 12.0, 7.4) and 5-item (LoA: − 14.9, 5.8) compared with the LoA for the 8-item and 5-item (LoA: − 7.8, 3.3).

Conclusion
Two Rasch-based NDI solutions (8 vs 5 items) which differ in number of items and conceptual construction are available to provide interval level scoring. They both provide scores that are substantially different from the ordinal NDI, which does not provide interval level scoring. Smaller differences between the two Rasch solutions exist and may relate to the items included. Due to the size and unpredictable nature of the bias between measures, they should not be used interchangeably.
Seasonal Bordetella pertussis pattern in the period from 2008 to 2018 in Germany
Authors: Hitz Daniel Allermann , Tewald Friedemann , Eggers Maren 
Published: July 2020

Abstract
Background
After the introduction of a vaccine against B. pertussis the seasonal pattern with the highest number of infections in the spring to summer months changed. Recent studies from around the world suggest that B. pertussis infections again follow a seasonal pattern with increased incidence in summer.The aim of this study was to investigate whether respiratory infections caused by B. pertussis in the period from January 2008 to December 2018 also seasonally spread in Germany and if so, when the B. pertussis activity peaked.

Methods
We tested 19,031 samples, mainly from Southern Germany, collected in the period from January 2008 to December 2018 using a Multiplex PCR assay. We assessed the number and proportion of samples positive for B. pertussis, stratified by patient’s age and month. The seasonal distribution was investigated by plotting the average proportion of positive samples for each month.

Results
We observed a B. pertussis seasonality with the highest number of positive samples in the months from June until September. In contrast, testing of samples for B. pertussis was requested most frequently in the period from October until March. The proportion of positive samples increased earlier in adolescents (age 10 to 19) than in other age groups.

Conclusions
We found a seasonality of B. pertussis infections in Germany, which differs from the time when most samples are sent in for testing of B. pertussis. Our study suggests that clinicians should be more aware of B. pertussis infections in the months from June until September to prevent further transmission to vulnerable family members.
Incidence, prevalence, mortality, and causes of death in Waldenström macroglobulinemia: a nationwide, population-based cohort study
Authors: Jeong Seri , Kong Seom Gim , Kim Da Jung , Lee Sangjin , Lee Ho Sup 
Published: July 2020

Abstract
Background
The epidemiological features of Waldenström macroglobulinemia (WM) have seldom been investigated at a national level, particularly in East Asia. The goal of our study is to present the incidence, prevalence, mortality, survival with competing risks, and causes of death of patients with WM.

Methods
We used a national population-based database, operated by the Health Insurance Review and Assessment Service of the Korean government. This data includes information on all WM patients diagnosed according to uniform criteria, between 2003 and 2016.

Results
The total number of patients newly diagnosed with WM during the study period was 427, with a male-to-female ratio of 3.2:1. The incidence increased from 0.03 to 0.10 per 105 between 2003 and 2016, and the prevalence was 0.42 per 105 in 2016. A total of 217 patients with WM died during the study period (standardized mortality ratio = 7.57), and the overall survival (OS) of WM patients was 47.5%. On multivariate analysis, older age was associated with worse OS (P <  0.0001). WM was the most common cause of death (n = 102, 48.6%), followed by other malignant neoplasms (n = 82, 39.0%).

Conclusions
The national incidence of WM in Korea, a racially homogeneous country in Asia, was lower than that in previous reports from other countries, reflecting ethnic disparities. However, the incidence increased, and mortality was the highest ever reported. The main cause of death was WM in itself. This study reflects the need for greater awareness of WM, particularly in Asian countries.
Understanding cartilage protection in OA and injury: a spectrum of possibilities
Authors: Masson Anand O. , Krawetz Roman J. 
Published: July 2020

Abstract
Background
Osteoarthritis (OA) is a prevalent musculoskeletal disease resulting in progressive degeneration of the hyaline articular cartilage within synovial joints. Current repair treatments for OA often result in poor quality tissue that is functionally ineffective compared to the hyaline cartilage and demonstrates increased failure rates post-treatment. Complicating efforts to improve clinical outcomes, animal models used in pre-clinical research show significant heterogeneity in their regenerative and degenerative responses associated with their species, age, genetic/epigenetic traits, and context of cartilage injury or disease. These can lead to variable outcomes when testing and validating novel therapeutic approaches for OA. Furthermore, it remains unclear whether protection against OA among different model systems is driven by inhibition of cartilage degeneration, enhancement of cartilage regeneration, or any combination thereof.

Main text
Understanding the mechanistic basis underlying this context-dependent duality is essential for the rational design of targeted cartilage repair and OA therapies. Here, we discuss some of the critical variables related to the cross-species paradigm of degenerative and regenerative abilities found in pre-clinical animal models, to highlight that a gradient of regenerative competence within cartilage may exist across species and even in the greater human population, and likely influences clinical outcomes.

Conclusions
A more complete understanding of the endogenous regenerative potential of cartilage in a species specific context may facilitate the development of effective therapeutic approaches for cartilage injury and/or OA.
Salivary parameters and oral health status amongst adolescents in Mexico
Authors: González-Aragón Pineda A. E. , García Pérez A. , García-Godoy F. 
Published: July 2020

AbstractBackgroundIn the last years an increased interest in the use of salivary parameters in connection with caries experience and caries prediction has been shown. In schoolchildren investigations are known, where the relationship between caries prevalence and salivary parameters has been assessed, but in the adolescent population studies are scarce. The aim of the study was evaluate of the association among salivary parameters, oral health status and caries experience in adolescents in Mexico.MethodsA cross-sectional study was conducted on 256 (DMFT≥5) and 165 (DMFT< 5) 12-to- 14-year-old adolescents. From all the adolescents, unstimulated mid-morning saliva samples were collected, after which the salivary flow rate was calculated, and the salivary pH and buffer capacity was measured. The caries was evaluated via the application of the DMFT score. Clinical variables such as oral hygiene and dental calculus were examined in the adolescent’s oral cavity. The adolescents provided data on their personal characteristics by completing a questionnaire, while socioeconomic data were collected from their parents. Descriptive, bivariate and logistic regression model analyses were performed.ResultsThe prevalence of caries was 61.1% (DMFT≥5) in permanent dentition, with 72.7% of subjects presenting poor oral hygiene. The mean levels of salivary flow rate, pH, and buffer capacity was significantly lower (p < 0.05) in adolescents with caries score of DMFT≥5 than in those with caries score of DMFT < 5. Salivary flow and buffer capacity were higher in boys than in girls. The logistic regression model applied showed that adolescents with a salivary flow rate < 1 ml per min were more likely to present caries [OR = 1.58 (CI95% 1.04–2.40);p = 0.033] than adolescents with a flow rate ≥ 1 ml per-min, and that, for each unit of increased pH, the probability of presenting caries reduced by 76% [OR = 0.24 (CI95% 0.10–0.55);p = 0.001].ConclusionSignificant association was found in salivary flow rate, pH and buffer capacity in adolescents with caries (DMFT≥5). In addition to differences of these parameters by sex, the results suggest saliva parameters may act as indicators of caries in adolescents.
Weighted correlation network bioinformatics uncovers a key molecular biosignature driving the left-sided heart failure
Authors: Zhou Jiamin , Zhang Wei , Wei Chunying , Zhang Zhiliang , Yi Dasong , Peng Xiaoping , Peng Jingtian , Yin Ran , Zheng Zeqi , Qi Hongmei , Wei Yunfeng , Wen Tong 
Published: July 2020

AbstractBackgroundLeft-sided heart failure (HF) is documented as a key prognostic factor in HF. However, the relative molecular mechanisms underlying left-sided HF is unknown. The purpose of this study is to unearth significant modules, pivotal genes and candidate regulatory components governing the progression of left-sided HF by bioinformatical analysis.MethodsA total of 319 samples in GSE57345 dataset were used for weighted gene correlation network analysis (WGCNA). ClusterProfiler package in R was used to conduct functional enrichment for genes uncovered from the modules of interest. Regulatory networks of genes were built using Cytoscape while Enrichr database was used for identification of transcription factors (TFs). The MCODE plugin was used for identifying hub genes in the modules of interest and their validation was performed based on GSE1869 dataset.ResultsA total of six significant modules were identified. Notably, the blue module was confirmed as the most crucially associated with left-sided HF, ischemic heart disease (ISCH) and dilated cardiomyopathy (CMP). Functional enrichment conveyed that genes belonging to this module were mainly those driving the extracellular matrix-associated processes such as extracellular matrix structural constituent and collagen binding. A total of seven transcriptional factors, including Suppressor of Zeste 12 Protein Homolog (SUZ12) and nuclear factor erythroid 2 like 2 (NFE2L2), adrenergic receptor (AR), were identified as possible regulators of coexpression genes identified in the blue module. A total of three key genes (OGN, HTRA1 and MXRA5) were retained after validation of their prognostic value in left-sided HF. The results of functional enrichment confirmed that these key genes were primarily involved in response to transforming growth factor beta and extracellular matrix.ConclusionWe uncovered a candidate gene signature correlated with HF, ISCH and CMP in the left ventricle, which may help provide better prognosis and therapeutic decisions and in HF, ISCH and CMP patients.
Dynamic changes of D-dimer and neutrophil-lymphocyte count ratio as prognostic biomarkers in COVID-19
Authors: Ye Wenjing , Chen Guoxi , Li Xiaopan , Lan Xing , Ji Chen , Hou Min , Zhang Di , Zeng Guangwang , Wang Yaling , Xu Cheng , Lu Weiwei , Cui Ruolin , Cai Yuyang , Huang Hai , Yang Ling 
Published: July 2020

Abstract
Background
Since December 2019, the outbreak of COVID-19 caused a large number of hospital admissions in China. Many patients with COVID-19 have symptoms of acute respiratory distress syndrome, even are in danger of death. This is the first study to evaluate dynamic changes of D-Dimer and Neutrophil-Lymphocyte Count Ratio (NLR) as a prognostic utility in patients with COVID-19 for clinical use.

Methods
In a retrospective study, we collected data from 349 hospitalized patients who diagnosed as the infection of the COVID-19 in Wuhan Pulmonary Hospital. We used ROC curves and Cox regression analysis to explore critical value (optimal cut-off point associated with Youden index) and prognostic role of dynamic changes of D-Dimer and NLR.

Results
Three hundred forty-nine participants were enrolled in this study and the mortality rate of the patients with laboratory diagnosed COVID-19 was 14.9%. The initial and peak value of D-Dimer and NLR in deceased patients were higher statistically compared with survivors (P < 0.001). There was a more significant upward trend of D-Dimer and NLR during hospitalization in the deceased patients, initial D-Dimer and NLR were lower than the peak tests (MD) -25.23, 95% CI: − 31.81- -18.64, P < 0.001; (MD) -43.73, 95% CI:-59.28- -31.17, P < 0.001. The test showed a stronger correlation between hospitalization days, PCT and peak D-Dimer than initial D-Dimer. The areas under the ROC curves of peak D-Dimer and peak NLR tests were higher than the initial tests (0.94(95%CI: 0.90–0.98) vs. 0.80 (95% CI: 0.73–0.87); 0.93 (95%CI:0.90–0.96) vs. 0.86 (95%CI:0.82–0.91). The critical value of initial D-Dimer, peak D-Dimer, initial NLR and peak NLR was 0.73 mg/L, 3.78 mg/L,7.13 and 14.31 respectively. 35 (10.03%) patients were intubated. In the intubated patients, initial and peak D-Dimer and NLR were much higher than non-intubated patients (P < 0.001). The critical value of initial D-Dimer, peak D-Dimer, initial NLR and peak NLR in prognosticate of intubation was 0.73 mg/L, 12.75 mg/L,7.28 and 27.55. The multivariable Cox regression analysis showed that age (HR 1.04, 95% CI 1.00–1.07, P = 0.01), the peak D-Dimer (HR 1.03, 95% CI 1.01–1.04, P < 0.001) were prognostic factors for COVID-19 patients’ death.

Conclusions
To dynamically observe the ratio of D-Dimer and NLR was more valuable during the prognosis of COVID-19. The rising trend in D-Dimer and NLR, or the test results higher than the critical values may indicate a risk of death for participants with COVID-19.
A longitudinal study on the relationship between mother’s personality trait and eating behaviors, food intake, maternal weight gain during pregnancy and neonatal birth weight
Authors: Shakeri Mahboobeh , Jafarirad Sima , Amani Reza , Cheraghian Bahman , Najafian Mahin 
Published: July 2020

Abstract
Background
Many factors such as social and behavioral are related to appropriate weight gain during pregnancy, and there is much of importance to find them. The aim of the study was to explore the association of personality traits, with eating behaviors, food intake, maternal weight gain during pregnancy as well as the neonatal birth weight.

Methods
This is a longitudinal and cross-sectional study. Eating behaviors were assessed using the Dutch Eating Behavior Questionnaire (DEBQ), and the NEO personality inventory was used to assess personality in pregnant subjects. A validated food frequency questionnaire was used to determine food intake. Three hundred and sixty pregnant subjects from Ahvaz (the capital city of Khuzestan province, Iran) were followed from the 20th week of pregnancy until delivery.

Results
High neuroticism was associated with higher consumption of highly energetic foods (p < 0.05) and less consumption of vegetables (p < 0.01), also was related with lower weight gain during pregnancy and neonatal birth weight (p < 0.05). Openness to experience, extraversion and agreeableness were linked with higher consumption of vegetables (p < 0.05). Conscientiousness predicted lower neonatal weight (odds ratio: 1.20, confidence interval: 1.07–1.34, p < 0.01).

Conclusions
Identification of personality traits would help to change the lifestyle and improve management guidelines.