bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae
Authors: Alzahrani Dhafer A. , Yaradua Samaila S. , Albokhari Enas J. , Abba Abidina 
Published: June 2020

Abstract
Background
The plastome of medicinal and endangered species in Kingdom of Saudi Arabia, Barleria prionitis was sequenced. The plastome was compared with that of seven Acanthoideae species in order to describe the plastome, spot the microsatellite, assess the dissimilarities within the sampled plastomes and to infer their phylogenetic relationships.

Results
The plastome of B. prionitis was 152,217 bp in length with Guanine-Cytosine and Adenine-Thymine content of 38.3 and 61.7% respectively. It is circular and quadripartite in structure and constitute of a large single copy (LSC, 83, 772 bp), small single copy (SSC, 17, 803 bp) and a pair of inverted repeat (IRa and IRb 25, 321 bp each). 131 genes were identified in the plastome out of which 113 are unique and 18 were repeated in IR region. The genome consists of 4 rRNA, 30 tRNA and 80 protein-coding genes. The analysis of long repeat showed all types of repeats were present in the plastome and palindromic has the highest frequency. A total number of 98 SSR were also identified of which mostly were mononucleotide Adenine-Thymine and are located at the non coding regions. Comparative genomic analysis among the plastomes revealed that the pair of the inverted repeat is more conserved than the single copy region. In addition high variation is observed in the intergenic spacer region than the coding region. The genes, ycf1and ndhF and are located at the border junction of the small single copy region and IRb region of all the plastome. The analysis of sequence divergence in the protein coding genes indicates that the following genes undergo positive selection (atpF, petD, psbZ, rpl20, petB, rpl16, rps16, rpoC, rps7, rpl32 and ycf3). Phylogenetic analysis indicated sister relationship between Ruellieae and Justcieae. In addition, Barleria, Justicia and Ruellia are paraphyletic, suggesting that Justiceae, Ruellieae, Andrographideae and Barlerieae should be treated as tribes.

Conclusions
This study sequenced and assembled the first plastome of the taxon Barleria and reported the basics resources for evolutionary studies of B. prionitis and tools for phylogenetic relationship studies within the core Acanthaceae.
Genomic variation between PRSV resistant transgenic SunUp and its progenitor cultivar Sunset
Authors: Fang Jingping , Wood Andrew Michael , Chen Youqiang , Yue Jingjing , Ming Ray 
Published: June 2020

Abstract
Background
The safety of genetically transformed plants remains a subject of scrutiny. Genomic variants in PRSV resistant transgenic papaya will provide evidence to rationally address such concerns.

Results
In this study, a total of more than 74 million Illumina reads for progenitor ‘Sunset’ were mapped onto transgenic papaya ‘SunUp’ reference genome. 310,364 single nucleotide polymorphisms (SNPs) and 34,071 small Inserts/deletions (InDels) were detected between ‘Sunset’ and ‘SunUp’. Those variations have an uneven distribution across nine chromosomes in papaya. Only 0.27% of mutations were predicted to be high-impact mutations. ATP-related categories were highly enriched among these high-impact genes. The SNP mutation rate was about 8.4 × 10− 4 per site, comparable with the rate induced by spontaneous mutation over numerous generations. The transition-to-transversion ratio was 1.439 and the predominant mutations were C/G to T/A transitions. A total of 3430 nuclear plastid DNA (NUPT) and 2764 nuclear mitochondrial DNA (NUMT) junction sites have been found in ‘SunUp’, which is proportionally higher than the predicted total NUPT and NUMT junction sites in ‘Sunset’ (3346 and 2745, respectively). Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by ‘SunUp’ and ‘Sunset’. The average identity between ‘SunUp’ specific norgDNA and corresponding organelle genomes was higher than that of norgDNA shared by ‘SunUp’ and ‘Sunset’. Six ‘SunUp’ organelle-like borders of transgenic insertions were nearly identical to corresponding sequences in organelle genomes (98.18 ~ 100%). None of the paired-end spans of mapped ‘Sunset’ reads were elongated by any ‘SunUp’ transformation plasmid derived inserts. Significant amounts of DNA were transferred from organelles to the nuclear genome during bombardment, including the six flanking sequences of the three transgenic insertions.

Conclusions
Comparative whole-genome analyses between ‘SunUp’ and ‘Sunset’ provide a reliable estimate of genome-wide variations and evidence of organelle-to-nucleus transfer of DNA associated with biolistic transformation.
Oak displays common local but specific distant gene regulation responses to different mycorrhizal fungi
Authors: Bouffaud Marie-Lara , Herrmann Sylvie , Tarkka Mika T. , Bönn Markus , Feldhahn Lasse , Buscot François 
Published: June 2020

Abstract
Background
Associations of tree roots with diverse symbiotic mycorrhizal fungi have distinct effects on whole plant functioning. An untested explanation might be that such effect variability is associated with distinct impacts of different fungi on gene expression in local and distant plant organs. Using a large scale transcriptome sequencing approach, we compared the impact of three ectomycorrhizal (EMF) and one orchid mycorrhizal fungi (OMF) on gene regulation in colonized roots (local), non-colonized roots (short distance) and leaves (long distance) of the Quercus robur clone DF159 with reference to the recently published oak genome. Since different mycorrhizal fungi form symbiosis in a different time span and variable extents of apposition structure development, we sampled inoculated but non-mycorrhizal plants, for which however markedly symbiotic effects have been reported. Local root colonization by the fungi was assessed by fungal transcript analysis.

Results
The EMF induced marked and species specific effects on plant development in the analysed association stage, but the OMF did not. At local level, a common set of plant differentially expressed genes (DEG) was identified with similar patterns of responses to the three EMF, but not to the OMF. Most of these core DEG were down-regulated and correspond to already described but also new functions related to establishment of EMF symbiosis. Analysis of the fungal transcripts of two EMF in highly colonized roots also revealed onset of a symbiosis establishment. In contrast, in the OMF, the DEG were mainly related to plant defence. Already at short distances, high specificities in transcriptomic responses to the four fungi were detected, which were further enhanced at long distance in leaves, where almost no common DEG were found between the treatments. Notably, no correlation between phylogeny of the EMF and gene expression patterns was observed.

Conclusions
Use of clonal oaks allowed us to identify a core transcriptional program in roots colonized by three different EMF, supporting the existence of a common EMF symbiotic pathway. Conversely, the specific responses in non-colonized organs were more closely related to the specific impacts of the different of EMF on plant performance.
Piloting data linkage in a prospective cohort study of a GP referral scheme to avoid unnecessary emergency department conveyance
Authors: Blodgett Joanna M. , Robertson Duncan J. , Ratcliffe David , Rockwood Kenneth 
Published: June 2020

Abstract
Background
UK Ambulance services are under pressure to safely stream appropriate patients away from the Emergency Department (ED). Even so, there has been little evaluation of patient outcomes. We investigated differences between patients who are conveyed directly to ED after calling 999 and those referred by an ambulance crew to a novel GP referral scheme.

Methods
This was a prospective study comparing patients from two cohorts, one conveyed directly to the ED (n = 4219) and the other referred to a GP by the on-scene paramedic (n = 321). To compare differences in patient outcomes, we include follow-up data of a smaller subset of each cohort (up to n = 150 in each) including hospital admission, history of long-term illness, previous ED attendance, length of stay, hospital investigations, internal transfers, 30-day re-admission and 10-month mortality.

Results
Older individuals, females, and those with minor incidents were more likely to be referred to a GP than conveyed directly to ED. Of those patients referred to the GP, only 22.4% presented at ED within 30 days. These patients were more likely to be admitted then than were those initially conveyed directly to ED (59% vs 31%). Those conveyed to ED had a higher risk of death compared to those who were referred to the GP (HR: 2.59; 95% CI 1.14–5.89), however when analyses were restricted to those who presented at ED within 30 days, there was no difference in mortality risk (HR: 1.45; 95% CI 0.58–3.65).

Conclusions
Despite limited data and a small sample size, there were differences between patients conveyed directly to ED and those who were referred into GP care. Initial evidence suggests that referring individuals to a GP may provide an appropriate and safe alternative path of care. This pilot study demonstrated a need for larger scale, methodologically rigorous study to demonstrate the benefits of alternative conveyance schemes and recommend changes to the current system of urgent and emergency care.
Developing strategies to improve fidelity of delivery of, and engagement with, a complex intervention to improve independence in dementia: a mixed methods study
Authors: Walton Holly , Spector Aimee , Roberts Anna , Williamson Morgan , Bhatt Jem , Tombor Ildiko , Michie Susan 
Published: June 2020

Abstract
Background
It is important to evaluate fidelity of delivery and engagement during feasibility trials. However, there is little guidance on how to systematically develop strategies to improve implementation if problems arise. We aimed to: 1) Assess fidelity of delivery and engagement, 2) Identify factors influencing fidelity of delivery and engagement, and 3) Develop strategies to improve fidelity of delivery of, and engagement with, a complex intervention to improve independence in dementia, within a feasibility trial.

Methods
A mixed methods evaluation of an intervention that aimed to improve independence in dementia. To assess fidelity of delivery and engagement, observation and self-report methods were used: 60% of audio-recorded intervention sessions were transcribed and reliably rated for fidelity. Providers (n = 12) and people with dementia/supporters (n = 34) were asked to complete checklists after each session. Descriptive statistics were used to analyse the data. To identify factors influencing fidelity and engagement, one-to-one semi-structured interviews were conducted with providers (n = 8), people with dementia (n = 7) and supporters (n = 7). Thematic analysis and content analysis were used to analyse data. To develop strategies, we followed four steps proposed by the authors of the Behaviour Change Wheel (1. Understanding the behaviour, 2. Identifying intervention functions, 3. Specifying intervention content, 4. Identifying mode of delivery).

Results
Researcher ratings indicated moderate fidelity and provider/participant ratings indicated high fidelity of delivery. Knowledge, providers’ attributes, ease of adaptation of the intervention in relation to participants’ needs and logistical considerations influenced fidelity. We developed four strategies to improve fidelity of delivery of PRIDE: 1) showing a video, 2) giving an instruction sheet, 3) giving time to practice and 4) providing continued support. Participants reported high levels of engagement. Participants’ attributes, capability and opportunity influenced engagement. We developed four strategies to improve engagement with PRIDE: 1) a session summary document, 2) clear instructions, 3) time to practice activity and 4) providing regular compulsory telephone support.

Conclusion
Fidelity of delivery and engagement are complex behaviours. This manuscript provides an example of how the Behaviour Change Wheel can be used during a feasibility trial to systematically develop strategies to improve implementation of complex interventions.
Using multiple agreement methods for continuous repeated measures data: a tutorial for practitioners
Authors: Parker Richard A. , Scott Charles , Inácio Vanda , Stevens Nathaniel T. 
Published: June 2020

AbstractBackgroundStudies of agreement examine the distance between readings made by different devices or observers measuring the same quantity. If the values generated by each device are close together most of the time then we conclude that the devices agree. Several different agreement methods have been described in the literature, in the linear mixed modelling framework, for use when there are time-matched repeated measurements within subjects.MethodsWe provide a tutorial to help guide practitioners when choosing among different methods of assessing agreement based on a linear mixed model assumption. We illustrate the use of five methods in a head-to-head comparison using real data from a study involving Chronic Obstructive Pulmonary Disease (COPD) patients and matched repeated respiratory rate observations. The methods used were the concordance correlation coefficient, limits of agreement, total deviation index, coverage probability, and coefficient of individual agreement.ResultsThe five methods generated similar conclusions about the agreement between devices in the COPD example; however, some methods emphasized different aspects of the between-device comparison, and the interpretation was clearer for some methods compared to others.ConclusionsFive different methods used to assess agreement have been compared in the same setting to facilitate understanding and encourage the use of multiple agreement methods in practice. Although there are similarities between the methods, each method has its own strengths and weaknesses which are important for researchers to be aware of. We suggest that researchers consider using the coverage probability method alongside a graphical display of the raw data in method comparison studies. In the case of disagreement between devices, it is important to look beyond the overall summary agreement indices and consider the underlying causes. Summarising the data graphically and examining model parameters can both help with this.
Using the Drug Burden Index to identify older adults at highest risk for medication-related falls
Authors: Blalock Susan J. , Renfro Chelsea P. , Robinson Jessica M. , Farley Joel F. , Busby-Whitehead Jan , Ferreri Stefanie P. 
Published: June 2020

Abstract
Background
The Drug Burden Index (DBI) was developed to assess patient exposure to medications associated with an increased risk of falling. The objective of this study was to examine the association between the DBI and medication-related fall risk.

Methods
The study used a retrospective cohort design, with a 1-year observation period. Participants (n = 1562) were identified from 31 community pharmacies. We examined the association between DBI scores and four outcomes. Our primary outcome, which was limited to participants who received a medication review, indexed whether the review resulted in at least one medication-related recommendation (e.g., discontinue medication) being communicated to the participant’s health care provider. Secondary outcomes indexed whether participants in the full sample: (1) screened positive for fall risk, (2) reported 1+ falls in the past year, and (3) reported 1+ injurious falls in the past year. All outcome variables were dichotomous (yes/no).

Results
Among those who received a medication review (n = 387), the percentage of patients receiving at least one medication-related recommendation ranged from 10.2% among those with DBI scores of 0 compared to 60.2% among those with DBI scores ≥1.0 (Chi-square (4)=42.4, p < 0.0001). Among those screened for fall risk (n = 1058), DBI scores were higher among those who screened positive compared to those who did not (Means = 0.98 (SD = 1.00) versus 0.59 (SD = 0.74), respectively, p < 0.0001).

Conclusion
Our findings suggest that the DBI is a useful tool that could be used to improve future research and practice by focusing limited resources on those individuals at greatest risk of medication-related falls.
Multiple subcutaneous tuberculous abscesses in a dermatomyositis patient without pulmonary tuberculosis: a case report and literature review
Authors: Gao Weiwei , Zeng Yi , Chen Wei 
Published: June 2020

Abstract
Background
Even though remarkable progress for diagnostics of pulmonary TB has been made, it is still a challenge to establish a definitive diagnosis for extrapulmonary TB (EPTB) in clinical practice. Among all the presentations of EPTB, cold abscesses are unusual and deceptive, which are often reported in the chest wall and spine. Subcutaneous abscess in the connective tissue of limbs is extremely rare.

Case presentation
A 48-year-old man with dermatomyositis was hospitalized because of multiple subcutaneous tuberculous abscesses in his limbs, but without pulmonary tuberculosis. Particularly, one insidious abscess appeared during anti-TB treatment due to “paradoxical reaction”. After routine anti-TB therapy, local puncture drainage and surgical resection, the patient was cured and discharged.

Conclusions
Tuberculous infection should be kept in mind for the subcutaneous abscess of immunocompromised patients, even without previous TB history. Treatment strategy depends on the suppurating progress of abscess lesions. Meanwhile, complication of newly-developed insidious abscess during treatment should be vigilant.
Diagnosis of foetal vein of galen aneurysmal malformation by ultrasound combined with magnetic resonance imaging: a case series
Authors: Li Tian-gang , Zhang Yao-yue , Nie Fang , Peng Mei-juan , Li Yun-Zhi , Li Pei-long 
Published: June 2020

Abstract
Background
Foetal vein of Galen aneurysmal malformation (VGAM) is a very rare congenital malformation of the cerebral blood vessels. We sought to evaluate the diagnostic value of ultrasound in combination with magnetic resonance imaging (MRI) in foetal VGAM.

Case presentation
Prenatal ultrasound combined with MRI diagnosed five cases of VGAM. Two dimensional ultrasound images were used to find the echo-free cystic structure below the thalamus and above the cerebellum with five cases. Colour blood flow showed dilated VGAM in five cases, while the arteriovenous spectrum was explored in two cases and foetal heart failure was found in other three cases. MRI was manifested as a dilated VGAM found at the midline of the brain, demonstrating widening or dilation of the straight sinus in four cases, ventricular dilatation in one case, brain parenchyma bleeding in two cases, and grey matter softening in one case. One infant died on the day of its birth, while the other four infants died within one month to six months after birth.

Conclusions
Ultrasound combined with MRI can more accurately and comprehensively observe the pathological characteristics of VGAM, diagnose related complications early and determine its prognosis.
Chronically reduced IL-10 plasma levels are associated with hippocampal sclerosis in temporal lobe epilepsy patients
Authors: Basnyat Pabitra , Pesu Marko , Söderqvist Mikael , Grönholm Anna , Liimatainen Suvi , Peltola Maria , Raitanen Jani , Peltola Jukka 
Published: June 2020

AbstractBackgroundIncreasing evidence supports the role of soluble inflammatory mediators in the pathogenesis of refractory temporal lobe epilepsy (TLE). Hippocampal sclerosis (HS) is a well-described pathohistological abnormality in TLE. The association of proinflammatory cytokines with epileptic disease profiles is well established; however, the potential significance of circulating interleukin 10 (IL-10), particularly in TLE-associated HS, is still poorly understood. Therefore, taking into consideration the neuroprotective and anticonvulsive effects of IL-10, we performed this study to examine the role of the plasma levels of IL-10 in patients with TLE with HS (TLE + HS), TLE without HS (TLE-HS) and with other types of epilepsy.MethodsThis study included 270 patients with refractory epilepsy who were classified into four groups: i) 34 patients with TLE + HS, ii) 105 patients with TLE-HS, iii) 95 patients with extra-TLE (XLE) and iv) 36 patients with idiopathic generalized epilepsy (IGE). The plasma IL-10 levels were quantified using a commercially available enzyme-linked immunosorbent assay (ELISA).ResultsIL-10 levels were significantly lower in TLE + HS than in TLE-HS (p = 0.013). In a subgroup of TLE-HS patients who had seizures 1 month before sampling, patients with seizures had significantly higher IL-10 levels than patients who were seizure-free (p = 0.039). Among a small group (n = 15) of non-refractory TLE-HS patients, IL-10 levels showed a moderate negative correlation with the duration of epilepsy (r = − 0.585,p = 0.023).ConclusionsThis study demonstrated that chronically reduced levels of plasma IL-10 were associated with HS in TLE patients, suggesting that there was an inadequate systemic anti-inflammatory immune response. These results could provide new biological insights into the pathophysiology of HS in TLE. We also found that the production of IL-10 could be affected by the seizure frequency and declined concomitantly with increased disease durations. Therefore, the measurement of plasma IL-10 may have diagnostic value as a biomarker for stratifying TLE + HS from other epilepsy types or as a marker of disease progression towards a progressive form of epilepsy.
Correlation study between flash dual source CT perfusion imaging and regional lymph node metastasis of non-small cell lung cancer
Authors: Huang Tingting , Sun Hui , Luo Xianli , Zhang Xuemei , Jin Kaiyuan , Wang Feng , Sun Lv , Cheng Nianlan , Wu Shuo , Lou Qin , Li Bangguo 
Published: June 2020

Abstract
Background
To explore the correlation of flash dual source computed tomography perfusion imaging (CTPI) and regional lymph node metastasis of non-small cell lung cancer (NSCLC), and to evaluate the value of CT perfusion parameters in predicting regional lymph node metastasis of NSCLC.

Methods
120 consecutive patients with NSCLC confirmed by postoperative histopathology were underwent flash dual source CT perfusion imaging in pre-operation. The CT perfusion parameters of NSCLC, such as blood flow (BF), blood volume (BV), mean transit time (MTT) and permeability (PMB) were obtained by the image post-processing. Then microvessel density (MVD), luminal vascular number (LVN), luminal vascular area (LVA) and luminal vascular perimeter (LVP) of NSCLC were counted by immunohistochemistry. These cases were divided into group A (patients with lymph node metastasis, 58 cases) and group B (patients without lymph node metastasis, 62 cases) according to their pathological results. The CT perfusion parameters and the microvessel parameters were contrastively analysed between the two groups. Receiver operating characteristic (ROC) curve was used to assess the diagnostic efficiency of CT perfusion parameters in predicting regional lymph node metastasis of NSCLC in pre-operation.

Results
Group A presented significantly lower LVA, BF and higher MTT, PMB than Group B (P < 0.05), while BV, LVN, LVP and MVD were no significant difference (P > 0.05). Correlation analysis showed that BF was correlated with LVA and LVP (P < 0.05), while BV, MTT and PMB were not correlated with LVN, LVA and LVP (P > 0.05). All the perfusion parameters were not correlated with MVD. According to the ROC curve analysis, when BF < 85.16 ml/100 ml/min as a cutoff point to predict regional lymph node metastasis of NSCLC, the sensitivity, specificity, accuracy, positive predictive value and negative predictive value were 60.8, 81.7, 71.5, 75.6 and 69.5% respectively.

Conclusion
Flash dual source CT perfusion imaging can non-invasively indicate the luminal vascular structure of tumor and BF can be used as one of the important indexes in predicting regional lymph node metastasis of NSCLC in pre-operation.