bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed
Authors: Fang Lin , Xu Xin , Li Ji , Zheng Feng , Li Mingzhi , Yan Jingwei , Li Yuan , Zhang Xinhua , Li Lin , Ma Guohua , Zhang Aying , Lv Fubing , Wu Kunlin , Zeng Songjun 
Published: July 2020

Abstract
Backgrounds
Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts their germplasm conservation and commercial production. The factors inhibiting germination are largely unknown.

Results
In this study, large amounts of non-methylated lignin accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. The transcriptome profiles of P. armeniacum seed at different development stages were compared to explore the molecular clues for non-methylated lignin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism during seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathway displayed different expression patterns during the lignification process. PAL, 4CL, HCT, and CSE upregulation was associated with C and H lignin accumulation. The expression of CCoAOMT, F5H, and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes in seeds and vegetative tissues.

Conclusions
This work demonstrated the plasticity of natural lignin polymer assembly in seed and provided a better understanding of the molecular mechanism of seed-specific lignification process.
Polyploidization and pseudogenization in allotetraploid frog Xenopus laevis promote the evolution of aquaporin family in higher vertebrates
Authors: Jia Yanglei , Liu Xiao 
Published: July 2020

Abstract
Background
Aquaporins (AQPs), as members of the major intrinsic protein (MIP) superfamily, facilitated the permeation of water and other solutes and are involved in multiple biological processes. AQP family exists in almost all living organisms and is highly diversified in vertebrates in both classification and function due to genome wide duplication. While some AQP orthologs have been lost in higher vertebrates through evolution.

Result
Genome-wide comparative analyses of the AQP family between allotetraploid frog Xenopus laevis (Xla) and diploid frog Xenopus tropicalis (Xtr), based on the genome assemblies, revealed that the number of AQPs in Xla genome nearly doubled that in Xtr (32 vs. 19). Synteny analysis indicated that the distribution of the retained AQPs in Xla subgenomes (17 in Xla. L, the longer homeolog of Xla genome and 15 in Xla. S, the shorter homeolog of Xla genome) were highly symmetrical when compared with that in Xtr genome. Remarkably, two members in Xla. L and four members in Xla. S were lost through evolution. Blast analysis revealed that the lost AQPs in Xla are pseudogenized via either the deletion of some exons or some single nucleotide insertions or deletions that lead the reading frame shift. Additionally, comparative genomic analyses suggested that the orthologs of AQPs that with one copy absence in Xla are also prone to be lost in higher vertebrates.

Conclusion
This study revealed that polyploidization and subsequent pseudogenization and deletion in Xla genome promote the evolution of AQP family in higher vertebrates. Besides, our results would also contribute to understanding the evolution of AQP family.
Changes in the vaginal microbiota associated with primary ovarian failure
Authors: Wang Juan , Xu Jieying , Han Qixin , Chu Weiwei , Lu Gang , Chan Wai-Yee , Qin Yingying , Du Yanzhi 
Published: July 2020

Abstract
Background
Primary ovarian failure (POF) is defined as follicular failure in women of reproductive age. Although many factors are speculated to contribute to the occurrence of POF, the exact aetiology remains unclear. Moreover, alterations in the microbiome of patients with POF are poorly studied.

Results
This study investigated the vaginal microbiota of 22 patients with POF and 29 healthy individuals. High-throughput Illumina MiSeq sequencing targeting the V3-V4 region of the 16S ribosomal RNA (rRNA) gene was used to evaluate the relationships between the vaginal flora and clinical characteristics of POF. Different from results of previous studies, we found that the diversity and richness of the vaginal flora of patients with POF was significantly different from those of healthy controls. Comparison of the vaginal flora of patients with POF with that of menopausal women revealed that the relative abundance of Lactobacillus was significantly reduced in the latter. A reduced abundance of Lactobacillus was furthermore associated with a lower pregnancy success rate. Of particular interest is that L. gallinarum especially appeared to be beneficially associated with reproductive-related indicators (FSH, E2, AMH, PRL) whilst L. iners appeared to have a detrimental effect. The result of the present study may enable the identification of microbiota associated with POF, however, further investigations of differences in the microbiota in the context of POF will enable a deeper understanding of the disease pathogenesis that involves modification of the vaginal microbiota.

Conclusions
The present study identified the microbiota associated with POF. Further investigations on the differences in the microbiota in the context of POF will improve our understanding of the pathogenesis of the disease which involves modification of the vaginal microbiota.
Integrated metabolomics and transcriptome analysis on flavonoid biosynthesis in safflower (Carthamus tinctorius L.) under MeJA treatment
Authors: Chen Jiang , Wang Jie , Wang Rui , Xian Bin , Ren Chaoxiang , Liu Qianqian , Wu Qinghua , Pei Jin 
Published: July 2020

Abstract
Background
Safflower (Carthamus tinctorius L.) is an important cash crop, of which the dried tube flower is not only an important raw material for dyes and cosmetics but also an important herb widely used in traditional Chinese medicine. The pigment and bioactive compounds are composed of flavonoids (mainly quinone chalcones), and studies have reported that MeJA can promote the biosynthesis of quinone chalcones, but the mechanism underlying the effect of MeJA in safflower remains unclear. Here, we attempt to use metabolomics and transcriptome technologies to analyse the molecular mechanism of flavonoid biosynthesis under MeJA treatment in safflower.

Results
Based on a UHPLC-ESI-MS/MS detection platform and a self-built database (including hydroxysafflor yellow A, HSYA), a total of 209 flavonoid metabolites were detected, and 35 metabolites were significantly different after treatment with MeJA. Among them, 24 metabolites were upregulated upon MeJA treatment, especially HSYA. Eleven metabolites were downregulated after MeJA treatment. Integrated metabolomics and transcriptome analysis showed that MeJA might upregulate the expression of upstream genes in the flavonoid biosynthesis pathway (such as CHSs, CHIs and HCTs) and downregulate the expression of downstream genes (such as F3Ms, ANRs and ANSs), thus promoting the biosynthesis of quinone chalcones, such as HSYA. The transcription expressions of these genes were validated by real-time PCR. In addition, the promoters of two genes (CtCHI and CtHCT) that were significantly upregulated under MeJA treatment were cloned and analysed. 7 and 3 MeJA response elements were found in the promoters, respectively.

Conclusions
MeJA might upregulate the expression of the upstream genes in the flavonoid biosynthesis pathway and downregulate the expression of the downstream genes, thus promoting the biosynthesis of quinone chalcones. Our results provide insights and basic data for the molecular mechanism analysis of flavonoid synthesis in safflower under MeJA treatment.
De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics
Authors: Vu Dinh Duy , Shah Syed Noor Muhammad , Pham Mai Phuong , Bui Van Thang , Nguyen Minh Tam , Nguyen Thi Phuong Trang 
Published: July 2020

AbstractBackgroundUnderstanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management.Panax vietnamensisHa et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers.ResultsIn this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes ofP. vietnamensis(roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances.ConclusionOur study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.
Prognostic value of heart failure echocardiography index in HF patients with preserved, mid-ranged and reduced ejection fraction
Authors: Chen Jian-Shu , Pei Ying , Li Cai-e , Li Ning-yin , Guo Tao , Yu Jing 
Published: July 2020

Abstract
Background
To investigate the clinical value of heart failure echocardiography index (HFEI) in evaluating the cardiac function and predicting the prognosis of patients with different types of heart failure (HF).

Methods
Four hundred eighty-nine consecutively admitted HF patients were divided into three groups: HF with reduced ejection (HFrEF), HF with mid-range ejection fraction (HFmrEF), and HF with preserved ejection fraction (HFpEF). The baseline characteristics and ultrasound indexes were compared between the three groups. The correlation between HFEI and one-year risk of adverse events was compared by multivariate logistic regression. The clinical value of HFEI and plasma level of NT-proBNP in assessing the prognosis of patients with chronic heart failure (CHF) was analyzed by the receiver operating characteristic (ROC) curve.

Results
HFEI in HFrEF was significantly higher than that in HFmrEF and HFpEF. Multivariate regression analysis indicated that HFEI and plasma level of NT-proBNP were independent risk factors for predicting the short-time prognosis of HF patients. The ROC curve indicated that the HFEI cutoff level of 3.5 and the plasma NT-proBNP level of 3000 pg/ml predicted a poor prognosis of CHF patients with a sensitivity of 64% and a specificity of 75% vs. 68 and 65%.

Conclusion
HFEI can comprehensively evaluate the overall cardiac function of patients with various types of HF, and may prove to be an important index of assessing the prognosis of HF patients.
Measuring psychological safety in healthcare teams: developing an observational measure to complement survey methods
Authors: O’Donovan Róisín , Van Dun Desirée , McAuliffe Eilish 
Published: July 2020

Abstract
Background
Psychological safety is a dynamic team-level phenomenon which exists when team members believe that it is safe to take interpersonal risks. In healthcare teams, the presence of psychological safety is critical to delivering safe care. Scholars have highlighted a need for alternative measures which compliment survey-based measures of psychological safety in healthcare teams.

Methods
The exploratory phase of this study raised concerns about whether current survey measures could provide a sufficient understanding of psychological safety within healthcare teams to inform strategies to improve it. Thus, previously validated psychological safety surveys and a meeting observation measure were adapted for use in healthcare teams. First, two group feedback sessions were held with 22 healthcare professionals, as well as a systematic literature review. Then, the members of eleven healthcare teams in Ireland and The Netherlands (n = 135) took part in the pilot test of the adapted composite measure.

Results
The final composite measure has two parts: a team meeting observation measure and an adapted survey. The observation measure has 31 observable behaviours fitting seven categories: voice, defensive voice, silence behaviours, supportive, unsupportive, learning or improvement-oriented and familiarity type behaviours. The survey part consists of 19 items in three sub-dimensions related to; the team leader, other team members and the team as a whole. Three additional items capture the perceived representativeness of the observed team meeting compared to other similar meetings. Final adaptations were made in order to integrate the observation and survey measure.

Conclusions
The resulting composite measure combines the strengths of observational and survey measures and is tailored for use in healthcare teams. It is uniquely co-developed with healthcare professionals and grounded in the psychological safety and healthcare literature. This composite measure can enable longitudinal research on psychological safety and inform future research to develop and test interventions to improve psychological safety.
Informing retention in longitudinal cohort studies through a social marketing lens: Raine Study Generation 2 participants’ perspectives on benefits and barriers to participation
Authors: Costello Leesa , Dare Julie , Dontje Manon , Straker Leon 
Published: July 2020

AbstractBackgroundLongitudinal cohort studies have made significant contributions to medical discoveries and provide the impetus for health interventions which reduce the risk of disease. Establishing and maintaining these cohorts is challenging and costly. While some attrition is unavoidable, maintaining a sufficient number of participants ensures that results remain representative and free from bias. Numerous studies have investigated ways to reduce attrition but few studies have sought to understand the experience of participants, and none have examined this through a social marketing framework. This first paper in a two part-series describes participants’ experiences according to: benefits, barriers, motivators and influencers. The second paper uses this understanding to address issues relating to the 4Ps (product, price, place, promotion) of social marketing.MethodsParticipants were recruited from the Raine Study, a pregnancy cohort study that has been running in Western Australia since 1989. Qualitative interviews were conducted with 29 active and inactive participants from the Generation 2 cohort, who were originally enrolled in the Raine Study at birth by their parents (Generation 1). ‘Active’ participants (n = 17) were defined as those who agreed to attend their 27 year follow-up, while ‘inactive’ (n = 12) participants were defined as those who had not attended either of the past two follow-ups (at 22 and 27 years).ResultsThere were considerable differences between active and inactive participants, with active participants perceiving far more personal and collective benefits from their participation. Inactive participants described being constrained by structural barriers around work and life, whereas active participants were able to overcome them to attend follow-ups. Inactive participants also described the value of extrinsic incentives which might motivate their attendance, and active participants described the role of their parents as significant influencers in their propensity to remain in the study.ConclusionsThis paper provides rich descriptions of what participation in a long-running study means to participants. Use of a social marketing framework ensured that participants were constructed as ‘human consumers’ who are influenced by individual and broader social systems. Understanding participants in this way means that differentiated strategies can be tailored to enhance retention.
Clinical and genomic characteristics of mucosal signet-ring cell carcinoma in Helicobacter pylori-uninfected stomach
Authors: Kiso Mariko , Urabe Yuji , Ito Masanori , Masuda Kazuhiko , Boda Tomoyuki , Kotachi Takahiro , Hata Kosaku , Yorita Naoki , Nagasaki Naoko , Abduwali Madina , Hiyama Yuich , Oka Shiro , Tanaka Shinji , Chayama Kazuaki 
Published: July 2020

Abstract
Background
Gastric cancer develops even in Helicobacter pylori(H. pylori)-uninfected patients and its typical histological feature is signet ring cell carcinoma (SRCC) within the mucosal layer. However, the biological characteristics of SRCC remain unclear. We aimed to clarify the pathological and genetic features of SRCC in H. pylori-uninfected patients.

Methods
Seventeen H. pylori-uninfected patients with mucosal SRCCs were enrolled and their clinicopathological characteristics were compared with those of H. pylori-infected patients with mucosal SRCCs. Seven SRCCs without H. pylori-infected, including two invasive SRCCs, and seven H. pylori-infected SRCCs were subjected to a genetic analysis using next-generation sequencing.

Results
H. pylori-uninfected patients with mucosal SRCCs revealed male dominancy and a significantly higher prevalence of smokers among them as compared with the H. pylori-infected patients with SRCC. A CDH1 mutation (frame shift indel) was detected in one H. pylori-uninfected cancer not only in the mucosal SRCC but also in the invasive portion. A TP53 mutation was detected in one SRCC without H. pylori-infected. In the control group, ARID1A and TP53 mutations were detected in one SRCC each. The C to A mutation, which is a characteristic smoking-induced mutation, was not found in any of the samples.

Conclusions
Some SRCCs in H. pylori-uninfected patients may have a malignant potential similar to that of SRCCs in H. pylori-infected patients. Smoking may not be the main carcinogenic factor for the development of SRCCs among the H. pylori-uninfected patients.
Racial disparities of Black Americans hospitalized for decompensated liver cirrhosis
Authors: Spiewak Ted , Taefi Amir , Patel Shruti , Li Chin-Shang , Chak Eric 
Published: July 2020

Abstract
Background
Racial disparities have been reported in liver transplantation and chronic hepatitis C treatment outcomes. Determining causes of these disparities is important given the racially diverse American population and the economic burden associated with chronic liver disease.

Methods
A retrospective study was performed among 463 patients diagnosed with cirrhosis admitted from (January 1, 2013 to January 1, 2018) to a tertiary care academic medical center. Patients were identified based on the International Classification of Diseases (ICD-10) for cirrhosis or its complications. Demographic information, laboratory data, medical comorbidities, insurance and adherence to cirrhosis quality care indicators were recorded to determine their relationship to readmission rates and other healthcare outcomes.

Results
A total of 463 individual patients with cirrhosis were identified including Whites (n = 241), Hispanics (n = 106), Blacks (n = 50), Asian and Pacific Islander Americans (API, n = 27) and Other (n = 39). A significantly higher proportion of Blacks had Medicaid insurance compared to Whites (40% versus 20%, p = 0.0002) and Blacks had lower median income than Whites ($45,710 versus $54,844, p = 0.01). All groups received high quality cirrhosis care. Regarding healthcare outcomes, Black patients had the highest mean total hospital admissions (6.1 ± 6.3, p = 0.01) and the highest mean number of 30-day re-admissions (2.1 ± 3.7, p = 0.05) compared to all other racial groups. Multivariable proportional odds regression analysis showed that race was a statistically significant predictor of 90-day readmission (p = 0.03).

Conclusions
Black Americans hospitalized for complications of cirrhosis may experience significant disparities in healthcare outcomes compared to Whites despite high quality cirrhosis care. Socioeconomic factors may contribute to these disparities.
Use of BioFire FilmArray gastrointestinal PCR panel associated with reductions in antibiotic use, time to optimal antibiotics, and length of stay
Authors: Torres-Miranda Daisy , Akselrod Hana , Karsner Ryan , Secco Alessandra , Silva-Cantillo Diana , Siegel Marc O. , Roberts Afsoon D. , Simon Gary L. 
Published: July 2020

Abstract
Background
Rapid and accurate diagnostic tools are needed for appropriate management of infectious diarrhea.

Methods
We evaluated the impact of the introduction of rapid multiplex PCR testing using the FilmArray gastrointestinal (GI) panel (BioFire Diagnostics, LLC, Salt Lake City, UT) at our institution, and compared the results to those of standard stool cultures.

Results
The most common pathogens detected by the FilmArray GI panel were Clostridium difficile (55.0%), Campylobacter species (20.9%), Salmonella species (12.4%), and Shigella/EIEC species (12.4%). Rates of reproducibility in stool culture for these pathogens ranged from 56.3 to 77.8%. Co-detection of two or more organisms was common (24.2%), most commonly involving EPEC, EAEC, ETEC, and STEC. The time from arrival in the Emergency Department to discharge or admission to the hospital was unchanged after the introduction of FilmArray GI panel, but length of hospital stay was shorter (3 vs. 7.5 days, p = 0.0002) for the FilmArray group. The time to empiric antibiotics did not differ significantly, but optimal antibiotics were started earlier after introduction of the FilmArray GI panel (hospital day 1 vs. 2, p < 0.0001). More patients were discharged without antibiotics after introduction of the FilmArray GI panel (14.0% vs. 4.5%; p < 0.001).

Conclusion
Our results demonstrate that the FilmArray GI panel is an important tool for improving both patient care and antibiotic stewardship, despite the tendency for positive results with multiple pathogens.