bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a major-effect QTL associated with pre-harvest sprouting in cucumber (Cucumis sativus L.) using the QTL-seq method
Authors: Cao Mingming , Li Shuju , Deng Qiang , Wang Huizhe , Yang Ruihuan 
Published: April 2021

Abstract
Background
Cucumber (Cucumis sativus L.) is cultivated worldwide, and it is essential to produce enough high-quality seeds to meet demand. Pre-harvest sprouting (PHS) in cucumber is a critical problem and causes serious damage to seed production and quality. Nevertheless, the genetic basis and molecular mechanisms underlying cucumber PHS remain unclear. QTL-seq is an efficient approach for rapid quantitative trait loci (QTL) identification that simultaneously takes advantage of bulked-segregant analysis (BSA) and whole-genome resequencing. In the present research, QTL-seq analysis was performed to identify QTLs associated with PHS in cucumber using an F2 segregating population.

Results
Two QTLs that spanned 7.3 Mb on Chromosome 4 and 0.15 Mb on Chromosome 5 were identified by QTL-seq and named qPHS4.1 and qPHS5.1, respectively. Subsequently, SNP and InDel markers selected from the candidate regions were used to refine the intervals using the extended F2 populations grown in the 2016 and 2017 seasons. Finally, qPHS4.1 was narrowed to 0.53 Mb on chromosome 4 flanked by the markers SNP-16 and SNP-24 and was found to explain 19–22% of the phenotypic variation in cucumber PHS. These results reveal that qPHS4.1 is a major-effect QTL associated with PHS in cucumber. Based on gene annotations and qRT-PCR expression analyses, Csa4G622760 and Csa4G622800 were proposed as the candidate genes.

Conclusions
These results provide novel insights into the genetic mechanism controlling PHS in cucumber and highlight the potential for marker-assisted selection of PHS resistance breeding.
Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues
Authors: Franzo Giovanni , Tucciarone Claudia Maria , Legnardi Matteo , Cecchinato Mattia 
Published: April 2021

Abstract
Background
Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues.

Results
The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle.

Conclusions
The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.
Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls
Authors: Howard Nicholas P. , Troggio Michela , Durel Charles-Eric , Muranty Hélène , Denancé Caroline , Bianco Luca , Tillman John , van de Weg Eric 
Published: April 2021

Abstract
Background
Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20 K and Affymetrix Axiom® 480 K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n = 3141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls.

Results
Concordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3′ end of the probe.

Conclusions
The Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in the literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development.
Removal of beneficial insertion effects prevent the long-term persistence of transposable elements within simulated asexual populations
Authors: Butler Christopher L. , Bell Ellen A. , Taylor Martin I. 
Published: April 2021

Abstract
Background
Transposable elements are significant components of most organism’s genomes, yet the reasons why their abundances vary significantly among species is poorly understood. A recent study has suggested that even in the absence of traditional molecular evolutionary explanations, transposon proliferation may occur through a process known as ‘transposon engineering’. However, their model used a fixed beneficial transposon insertion frequency of 20%, which we believe to be unrealistically high.

Results
Reducing this beneficial insertion frequency, while keeping all other parameters identical, prevented transposon proliferation.

Conclusions
We conclude that the author’s original findings are better explained through the action of positive selection rather than ‘transposon engineering’, with beneficial insertion effects remaining important during transposon proliferation events.
Experience of using video support by prehospital emergency care physician in ambulance care - an interview study with prehospital emergency nurses in Sweden
Authors: Vicente Veronica , Johansson Anders , Selling Magnus , Johansson Johnny , Möller Sebastian , Todorova Lizbet 
Published: April 2021

Abstract
Introduction
When in need of emergency care and ambulance services, the ambulance nurse is often the first point of contact for the patient with healthcare. This role requires comprehensive knowledge of the ambulance nurse to be able to assign the right level of care and, if necessary, to provide self-care advice for patients with no further conveyance to hospital. Recently, an application was developed for transmitting real-time video to facilitate consultation between ambulance nurses and prehospital physicians in the role of regional medical support (RMS) for ambulance care. The use of video communication as a complement of medical support when referring to self-care is still an unexplored method in a prehospital setting.
Our study aimed to elucidate ambulance nurses’ experience of video consultation with RMS physician during the assessment of patients considered to be triaged to self-care.

Method
We conducted a qualitative design study using semi-structured interviews with open questions. Twelve ambulance nurses were included in the study. To explore the ambulance nurses’ experience of performing video consultation with RMS physician, in cases when a patient was assessed and triaged to self-care, a content analysis was performed.

Results
A main category emerged from the results: “ Video consultation as decision support in the ambulance care promotes increased patient participation and for the ambulance nurses, it creates a feeling of increased patient safety “. The main category was based and formed on the following categories: “ Simultaneous presence of ambulance nurse and a physician increases patient participation during the assessment resulting in a confident care decision “. “Interprofessional collaboration strengthens the medical assessment”. “Video technology promotes accessibility for patients needs in the ambulance care regardless of emergency level”.

Conclusions
Ambulance nurses experienced that the use of video consultation increases patient involvement and confidence in healthcare when both the ambulance nurse and the physician were present when deciding on self-care advice. The live imaging allowed the ambulance nurse and prehospital physician to reach a consensus on the patient’s current medical care needs, which in turn led to a feeling of increased patient safety for the ambulance nurses.
Palliative care in general practice; a questionnaire study on the GPs role and guideline implementation in Norway
Authors: Fasting Anne , Hetlevik Irene , Mjølstad Bente Prytz 
Published: April 2021

AbstractBackgroundPatients in need of palliative care often want to reside at home. Providing palliative care requires resources and a high level of competence in primary care. The Norwegian guideline for palliative care points to the central role of the regular general practitioner (RGP), specifying a high expected level of competence. Guideline implementation is known to be challenging in primary care. This study investigates adherence to the guideline, the RGPs experience with, and view of their role in palliative care.MethodsA questionnaire was distributed, by post, to all 246 RGPs in a Norwegian county. Themes of the questionnaire focused on experience with palliative and terminal care, the use of recommended work methods from the guideline, communication with partners, self-reported role in palliative care and confidence in providing palliative care. Data were analyzed descriptively, using SPSS.ResultsEach RGP had few patients needing palliative care, and limited experience with terminal care at home. Limited experience challenged RGPs possibilities to maintain knowledge about palliative care. Their clinical approach was not in agreement with the guideline, but most of them saw themselves as central, and were confident in the provision of palliative care. Rural RGPs saw themselves as more central in this work than their urban colleagues.ConclusionsThis study demonstrated low adherence of the RGPs, to the Norwegian guideline for palliative care. Guideline requirements may not correspond with the methods of general practice, making them difficult to adopt. The RGPs seemed to have too few clinical cases over time to maintain skills at a complex and specialized level. Yet, there seems to be a great potential for the RGP, with the inherent specialist skills of the general practitioner, to be a key worker in the palliative care trajectory.
Differentiation of small (≤ 3 cm) hepatocellular carcinomas from benign nodules in cirrhotic liver: the added additive value of MRI-based radiomics analysis to LI-RADS version 2018 algorithm
Authors: Zhong Xi , Guan Tianpei , Tang Danrui , Li Jiansheng , Lu Bingui , Cui Shuzhong , Tang Hongsheng 
Published: April 2021

Abstract
Background
Accurate characterization of small nodules in a cirrhotic liver is challenging. We aimed to determine the additive value of MRI-based radiomics analysis to Liver Imaging Reporting and Data System version 2018 (LI-RADS v 2018) algorithm in differentiating small (≤ 3 cm) hepatocellular carcinomas (HCCs) from benign nodules in cirrhotic liver.

Methods
In this retrospective study, 150 cirrhosis patients with histopathologically confirmed small liver nodules (HCC, 112; benign nodules, 44) were evaluated from January 2013 to October 2018. Based on the LI-RADS algorithm, a LI-RADS category was assigned for each lesion. A radiomics signature was generated based on texture features extracted from T1-weighted, T2W, and apparent diffusion coefficient (ADC) images by using the least absolute shrinkage and selection operator regression model. A nomogram model was developed for the combined diagnosis. Diagnostic performance was assessed using receiver operating characteristic curve (ROC) analysis.

Results
A radiomics signature consisting of eight features was significantly associated with the differentiation of HCCs from benign nodules. Both LI-RADS algorithm (area under ROC [Az] = 0.898) and the MRI-Based radiomics signature (Az = 0.917) demonstrated good discrimination, and the nomogram model showed a superior classification performance (Az = 0.975). Compared with LI-RADS alone, the combined approach significantly improved the specificity (97.7% vs 81.8%, p = 0.030) and positive predictive value (99.1% vs 92.9%, p = 0.031) and afforded comparable sensitivity (97.3% vs 93.8%, p = 0.215) and negative predictive value (93.5% vs 83.7%, p = 0.188).

Conclusions
MRI-based radiomics analysis showed additive value to the LI-RADS v 2018 algorithm for differentiating small HCCs from benign nodules in the cirrhotic liver.
Mobility in community-dwelling older adults; what are its determinants?
Authors: Zijlstra Wiebren , Giannouli Eleftheria 
Published: April 2021

Abstract
Background
Based on a conceptual framework, Kuspinar and colleagues analysed life-space mobility in community-dwelling older adults. However, a number of earlier mobility studies that used the same framework remained undiscussed. This correspondence article addresses similarities and differences between these studies, as well as highlight issues that need to be addressed to improve our understanding of mobility determinants in older adults.

Findings
Despite differences in methodological approach as well as in detailed results, the studies share one important outcome: regardless of the specific choice of potential mobility determinants, only a low to moderate proportion of mobility could be explained.

Conclusions
Our present understanding of the determinants of mobility in community-dwelling older adults is limited. A consistent terminology that takes into account the different aspects of mobility; the use of objective methods to assess real-life mobility; and monitoring changes in real-life mobility in response to interventions will contribute to furthering our understanding of mobility determinants.
Caregiving, care burden and awareness of caregivers and patients with dementia in Asian locations: a secondary analysis
Authors: Shim Yong S. , Park Kee Hyung , Chen Christopher , Dominguez Jacqueline C. , Kang Kyunghun , Kim Hee-Jin , Hong Zhen , Lin Yu-Te , Chu Leung-Wing , Jung San , Kim SangYun 
Published: April 2021

Abstract
Background
This study investigated the differences in caregiver activity, caregiver burden, and awareness of both caregivers and patients with Alzheimer’s disease (AD) across different Asian locations.

Methods
This was a secondary analysis of a multi-national cohort study that aimed to assess caregiver activity and caregiver burden using the Caregiver Activity Scale (CAS) and Zarit Burden Interview (ZBI), respectively. Patients’ awareness of their dementia diagnosis was assessed by asking the following yes/no question: “Do you have dementia?” Caregivers’ awareness of the patient’s dementia diagnosis was assessed by asking the following yes/no question: “Does your patient have dementia?”

Results
In total, 524 caregivers of patients with AD from China, Hong Kong, South Korea, the Philippines, Singapore, Thailand, and Taiwan participated. The CAS and ZBI score were significantly different across most locations (p < 0.001 and p = 0.033, respectively). Overall, 56.6% of caregivers and 37.5% of patients had awareness of the dementia diagnosis, and the proportion of patients and caregivers with awareness were also different between each location (all, p < 0.001).

Conclusions
Caregiving, caregiver burden, and the awareness of caregivers and patients were different across many Asian locations. With understanding of cultural differences, further public education on dementia could help increase the awareness of patients and caregivers and reduce caregiver burden.

Trial registration
ClinicalTrials.gov, NCT02262975. Registered 13 October 2014,
Polypharmacy and severe potential drug-drug interactions among older adults with cardiovascular disease in the United States
Authors: Sheikh-Taha Marwan , Asmar Myriam 
Published: April 2021

Abstract
Background
Polypharmacy continues to be a topic of concern among older adults and puts patients at increased risk of potential drug-drug interactions (DDIs) and negative health outcomes. The objective of this study was to assess the prevalence of polypharmacy among older adults with cardiovascular disease (CVD) and to identify severe potential DDIs.

Methods
A retrospective chart review was conducted in a tertiary care center over a three-month period where we reviewed home medications of older adults upon hospital admission. Inclusion criteria were age ≥ 65 years, history of CVD, and admission to the cardiology service. Polypharmacy was defined as 5 or more medications taken concomitantly, hyper-polypharmacy was defined as 10 or more medications taken concomitantly, and severe potential DDIs were considered to be those belonging to category D or X using Lexicomp® Drug Information Handbook. Category D interaction states that modification of therapy should be considered while category X states that the combination should be absolutely avoided.

Results
A total of 404 patients with a mean age of 76.6 ± 7.4 years were included. Patients were taking an average of 11.6 ± 4.5 medications at home and 385 (95%) received polypharmacy, 278 (69%) received hyper-polypharmacy, and 313 (77.5%) had at least one severe potential DDI. Under category D, the most common potential DDIs were drugs with additive central nervous system (CNS) depressant effect and drugs that increase the risk of QT prolongation. Under category X, the most common potential DDIs were non-selective β-blockers that may diminish the bronchodilator effect of β2 agonists and drugs with anticholinergic properties that enhance the ulcerogenic effect of oral solid potassium.

Conclusions
Polypharmacy, hyper-polypharmacy, and severe potential DDIs are very common in older adults with CVD. Clinicians should vigilantly review patients’ drug records and adjust therapy accordingly to prevent adverse drug reactions and negative health outcomes.
The associations of serum S100A9 with the severity and prognosis in patients with community-acquired pneumonia: a prospective cohort study
Authors: Liu Hong-Yan , Xiang Hui-Xian , Xiang Ying , Xu Zheng , Feng Chun-Mei , Fei Jun , Fu Lin , Zhao Hui 
Published: April 2021

Abstract
Background
Previous studies found that S100A9 may involve in the pathophysiology of community-acquired pneumonia (CAP). However, the role of S100A9 was unclear in the CAP. The goal was to explore the correlations of serum S100A9 with the severity and prognosis of CAP patients based on a prospective cohort study.

Methods
A total of 220 CAP patients and 110 control subjects were recruited. Demographic and clinical data were collected. Serum S100A9 and inflammatory cytokines were measured.

Results
Serum S100A9 was elevated in CAP patients on admission. Serum S100A9 was gradually elevated parallelly with CAP severity scores. Additionally, inflammatory cytokines were increased and blood routine parameters were changed in CAP patients compared with control subjects. Correlation analysis found that serum S100A9 was positively associated with CAP severity scores, blood routine parameters (WBC, NLR and MON) and inflammatory cytokines. Further, logistic regression analysis demonstrated that there were positive associations between serum S100A9 and CAP severity scores. Besides, the prognosis of CAP was tracked. Serum higher S100A9 on the early stage elevated the death of risk and hospital stay among CAP patients.

Conclusion
Serum S100A9 is positively correlated with the severity of CAP. On admission, serum higher S100A9 elevates the risk of death and hospital stay in CAP patients, suggesting that S100A9 may exert a certain role in the pathophysiology of CAP and regard as a serum diagnostic and managing biomarker for CAP.