bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues
Authors: Marczyk Michal , Fu Chunxiao , Lau Rosanna , Du Lili , Trevarton Alexander J. , Sinn Bruno V. , Gould Rebekah E. , Pusztai Lajos , Hatzis Christos , Symmans W. Fraser 
Published: December 2019

Abstract
Background
Utilization of RNA sequencing methods to measure gene expression from archival formalin-fixed paraffin-embedded (FFPE) tumor samples in translational research and clinical trials requires reliable interpretation of the impact of pre-analytical variables on the data obtained, particularly the methods used to preserve samples and to purify RNA.

Methods
Matched tissue samples from 12 breast cancers were fresh frozen (FF) and preserved in RNAlater or fixed in formalin and processed as FFPE tissue. Total RNA was extracted and purified from FF samples using the Qiagen RNeasy kit, and in duplicate from FFPE tissue sections using three different kits (Norgen, Qiagen and Roche). All RNA samples underwent whole transcriptome RNA sequencing (wtRNAseq) and targeted RNA sequencing for 31 transcripts included in a signature of sensitivity to endocrine therapy. We assessed the effect of RNA extraction kit on the reliability of gene expression levels using linear mixed-effects model analysis, concordance correlation coefficient (CCC) and differential analysis. All protein-coding genes in the wtRNAseq and three gene expression signatures for breast cancer were assessed for concordance.

Results
Despite variable quality of the RNA extracted from FFPE samples by different kits, all had similar concordance of overall gene expression from wtRNAseq between matched FF and FFPE samples (median CCC 0.63–0.66) and between technical replicates (median expression difference 0.13–0.22). More than half of genes were differentially expressed between FF and FFPE, but with low fold change (median |LFC| 0.31–0.34). Two out of three breast cancer signatures studied were highly robust in all samples using any kit, whereas the third signature was similarly discordant irrespective of the kit used. The targeted RNAseq assay was concordant between FFPE and FF samples using any of the kits (CCC 0.91–0.96).

Conclusions
The selection of kit to purify RNA from FFPE did not influence the overall quality of results from wtRNAseq, thus variable reproducibility of gene signatures probably relates to the reliability of individual gene selected and possibly to the algorithm. Targeted RNAseq showed promising performance for clinical deployment of quantitative assays in breast cancer from FFPE samples, although numerical scores were not identical to those from wtRNAseq and would require calibration.
Ages of hepatocellular carcinoma occurrence and life expectancy are associated with a UGT2B28 genomic variation
Authors: Le Puo-Hsien , Kuo Chia-Jung , Hsieh Yi-Chung , Chen Tsung-Hsing , Lin Chih-Lang , Yeh Chau-Ting , Liang Kung-Hao 
Published: December 2019

Abstract
Background
Hepatocellular carcinoma (HCC) is an aggressive solid tumor. HCC occurred at younger and elder ages were considered driven by different oncogenic mechanisms, and they demonstrated distinct clinical courses.

Methods
A total of 382 HCC patients treated by surgical resections was analyzed.

Results
A univariate-multivariate analysis showed that viral etiology (chronic hepatitis B, C) and the UDP glucuronosyltransferase family 2 member B28 (UGT2B28) genomic variant rs2132039 were independently associated with the age at presentation of HCC (all adjusted P < 0.05). An extensive evaluations of clinicalpathological factors showed that the age (Odds ratio [OR], 1.016; 95% confidence interval [CI], 1.001–1.032; adjusted P = 0.037) and ascites (OR, 3.505; CI, 1.358–9.048; adjusted P = 0.010) were two independent factors associated with this genomic variant. The age was 54.1 ± 14.6 years for patients with the “TT” variant type, and 58.2 ± 13.7 years for those with the “Non-TT” variant type. The age disparity was most prominent in alcoholic patients (OR, 1.079; CI, 1.035–1.125; P < 0.001, age of “TT”, 49.6 ± 12.2; age of “non-TT”, 59.3 ± 10.7). This genomic variant was also associated with age of recurrence (P = 0.025), distant metastasis (P = 0.024) and HCC-related death (P = 0.008) in non-censored patients.

Conclusions
An UGT2B28 genomic variant was indicative of the age of HCC presentation, recurrence, distant metastasis and death.
Could aspirin be a lifesaver for prostate cancer patients in prostate cancer-specific mortality?: an update systematic review and meta-analysis
Authors: Zhou Jiatong , Xia Shuai , Li Tao , Liu Ranlu 
Published: December 2019

Abstract
Background
Currently, clinical studies on the prognosis of prostate cancer (PC) taking aspirin were developing, but the precise mechanism of aspirin on tumor cells was still unclear. In addition, the conclusion that aspirin can improve the prognosis of PC patients continues to be controversial. Therefore, we collected comprehensive literatures and performed our study to explore the prognostic effect of aspirin on PC.

Methods
A comprehensive literature search was performed in April 2019 based on PUBMED. EMBASE. Hazard Ratio (HR) as well as its 95% confidence interval (CIs) for prostate cancer specific mortality (PCSM) was extracted from eligible studies.

Result
A total of 10 eligible articles were used in our study. The pooled results showed that PC patients who used aspirin or taking aspirin did not have lower PCSM than those who had not used (HR =0.89, 95% CI: 0.73–1.08, P>0.05). In subgroup analysis, we found that taking aspirin before diagnosis of prostate cancer and taking aspirin after diagnosis of prostate cancer did not have significant association with PCSM. (pre-diagnostic use, HR = 0.88, 95% CI: 0.72–1.06; post-diagnosis use, HR = 0.88, 95% CI: 0.67–1.17). In addition, we found no significant association between aspirin use or its duration and the risk of PCSM. Another important result demonstrated that aspirin use was not associated with risk of PSCM in either high risk (T ≥ 3 and/or Gleason score ≥ 8) or low risk PC patients(low-risk PC, HR = 1.05, 95% CI: 0.81–1.35; high-risk PC, HR = 0.97, 95% CI: 0.75–1.24).

Conclusion
Our results demonstrated that there was no significant association between aspirin use and the risk of PCSM. At the same time, the dosage and duration of aspirin use had no statistical influence on the risk of PCSM in high/low risk PC. Further studies are needed to confirm the findings.
Identification of food insecurity factors in French-speaking Belgium: a qualitative study
Authors: Huberland Vincent , Semaille Pascal , Kacenelenbogen Nadine 
Published: December 2019

Abstract
Background
Diet is an essential determinant of health. Among the health determinants, we find access problems that are summarized as food insecurity. While such food insecurity has been studied in other countries and correlated to several health problems, it has been scarcely assessed in Belgium. The purpose of this work was to determine the factors of food insecurity existing within the Belgian population.

Method
From November 2016 to February 2017, a qualitative study using semi-structured interviews with 19 adults present attending the waiting rooms of six Public Social Action Centers in French-speaking Belgium, analyzed by grounded theory.

Results
In Belgium, for given food preferences and needs, food insecurity could be summarized as inadequacy between necessary and available resources within two dimensions: at the access level, for financial, temporal, informational, and freedom of action, and at the food use level, for temporal factors, material, knowledge, and skills. In these situations of inadequacy, participants reported finding either strategies to restore balance, or being forced to alter the quality or quantity of their diet.

Conclusion
While several factors of food insecurity may exist in Belgium, it appears essential that the first line of care these factors into consideration, since they could interfere with care and health, and because the first line of care is ideally placed to inform and refer the patients in question. Several courses of action are proposed in this work, which must still be confirmed by other studies.
The relationship between social capital and self-rated health: a multilevel analysis based on a poverty alleviation program in the Philippines
Authors: Hung Natalee , Lau Lincoln Leehang 
Published: December 2019

AbstractBackgroundPoor health is both a cause and consequence of poverty, and there is a growing body of evidence suggesting that social capital is an important factor for improving health in resource-poor settings. International Care Ministries (ICM) is a non-governmental organization in the Philippines that provides a poverty alleviation program calledTransform. A core aim of the program is to foster social connectedness and to create a network of support within each community, primarily through consistent community-led small group discussions. The purpose of this research was to investigate the relationship between social capital and self-rated health and how ICM’sTransformprogram may have facilitated changes in those relationships.MethodsThree types of social capital were explored: bonding-structural, bridging-structural and cognitive. Using cross-sectional data collected before and afterTransform, multilevel modelling was used to examine their effects on self-rated health between the two time points.ResultsThe analyses showed that while social capital had minimal effects on self-rated health beforeTransform, a series of associations were identified after the program. Evidence of interdependence between the different types of social capital was also observed: bonding social capital only had a beneficial effect on self-rated healthin the presenceof bridging social capital, but we found that there was a 17 percentage point increase in self-rated health when individuals possessed all possible bridging and bonding relationships. At the same time, our estimates showed that maximising all forms of social capital is not necessarily constructive, as the positive effect of cognitive social capital on self-rated health was weaker at higher levels of bridging social capital.ConclusionsThe results from this study has shown that building social capitalcaninfluence the way people perceive their own health, which can be facilitated by intervention programs which seek to create bonding and bridging relationships.Transform’sintentional design to learn in community could be relevant to program planners as they develop and evaluate community-based programs, making adaptations as necessary to achieve organisation-specific goals while acknowledging the potential for varied effects when applied in different contexts or circumstances.
Accuracy of planar anteversion measurements using anteroposterior radiographs
Authors: Lee Gwang Chul , Lee Sang Hong , Kang Sin Wook , Park Hyung Seok , Jo Suenghwan 
Published: December 2019

AbstractBackgroundSeveral methods using simple anteroposterior (AP) radiographs have been suggested for the measurement of anteversion of the cup component after total hip arthroplasty. Herein, we compared six widely used anteversion measurement methods using two different types of AP radiograph, the conventional pelvis AP and hip-centered AP radiographs, to identify the measurement method and the type of radiograph that would provide the highest accuracy and reliability.MethodsWe developed two custom-made bi-planar anteversion measurement models for the validation test. The models were designed for pelvis AP and hip-centered AP radiographs, respectively. The radiographs were acquired using the inclination angles of both models, changing from 10° to 70° at 10° increments. For each inclination angle, anteversion was changed from 0° to 30° at 5° increments. The measurements were obtained independently by two orthopedic surgeons blinded from each other’s measurements, using the methods of 1) Pradhan et al., 2) Lewinnek et al., 3) Widmer et al., 4) Liaw et al., 5) Hassan et al., and 6) Ackland et al. The measurements were repeated after 2 months. The accuracy, compared with that of the reference angle, and intra-observer and inter-observer reliabilities of each method were calculated.ResultsThe highest accuracy was found when the method of Liaw et al. was used with hip-centered AP radiographs, which showed a difference of 1.37° ± 1.73 from the reference angle. Moreover, regardless of the type of radiograph, the methods by Pradhan et al., Lewinnek et al., and Liaw et al. showed excellent correlations with the reference anteversion. However, substantial differences were found when the methods by Widmer et al., Hassan et al., and Ackland et al. were used, regardless of the type of radiograph used. When anteversion was measured in an inclination between 30° and 50°, the method of Pradhan et al., when used with pelvis AP radiographs, showed the highest accuracy (1.23° ± 0.92°). We also found no significant difference in anteversions between the measurements made on pelvic and hip-centered AP radiographs. Both interobserver and intraobserver reliabilities were high for all the measurements tested.ConclusionsThe methods by Pradhan et al., Liaw et al., and Lewinnek et al. may provide relatively accurate anteversion measurements with high reliability, regardless of the type of radiograph.
Paramedic information needs in end-of-life care: a qualitative interview study exploring access to a shared electronic record as a potential solution
Authors: Patterson Rebecca , Standing Holly , Lee Mark , Dalkin Sonia , Lhussier Monique , Exley Catherine , Brittain Katie 
Published: December 2019

AbstractBackgroundLimited access to, understanding of, and trust in paper-based patient information is a key factor influencing paramedic decisions to transfer patients nearing end-of-life to hospital. Practical solutions to this problem are rarely examined in research. This paper explores the extent to which access to, and quality of, patient information affects the care paramedics provide to patients nearing end-of-life, and their views on a shared electronic record as a means of accessing up-to-date patient information.MethodSemi-structured interviews with paramedics (n = 10) based in the north of England, drawn from a group of health and social care professionals (n = 61) participating in a study exploring data recording and sharing practices in end-of-life care. Data were analysed using thematic analysis.ResultsTwo key themes were identified regarding paramedic views of patient information: 1) access to information on patients nearing end-of-life, and 2) views on the proposed EPaCCS. Paramedics reported they are typically unable to access up-to-date patient information, particularly advance care planning documents, and consequently often feel they have little option but to actively treat and transport patients to hospital – a decision not always appropriate for, or desired by, the patient. While paramedics acknowledged a shared electronic record (such as EPaCCs) could support them to provide community-based care where desired and appropriate, numerous practical and technical issues must be overcome to ensure the successful implementation of such a record.ConclusionsAccess to up-to-date patient information is a barrier to paramedics delivering appropriate end-of-life care. Current approaches to information recording are often inconsistent, inaccurate, and inaccessible to paramedics. Whilst a shared electronic record may provide paramedics with greater and timelier access to patient information, meaning they are better able to facilitate community-based care, this is only one of a series of improvements required to enable this to become routine practice.
Preferred problem solving and decision-making role in fertility treatment among women following an unsuccessful in vitro fertilization cycle
Authors: Chan Celia Hoi Yan , Lau Bobo Hi Po , Tam Michelle Yi Jun , Ng Ernest Hung Yu 
Published: December 2019

Abstract
Background
While the literature on healthcare decision-making has long focused on doctor-patient interaction, fertility treatment is an exception, characterized by a triangular interplay between the doctor, the woman and her partner. This study examined treatment decision-making preferences of women undergoing in vitro fertilization (IVF) treatment, following an unsuccessful IVF cycle, especially their preferred level of doctor and spousal involvement.

Methods
A cross-sectional survey was conducted with 246 Chinese women undergoing IVF recruited from an assisted reproduction clinic of a university-affiliated hospital in Hong Kong. Data collection was conducted between January 2014 and August 2015.

Results
Most participants preferred sharing the decision-making tasks with their doctors (92%). In the doctor-patient relationship, passive roles were associated with higher marital satisfaction, presence of religious affiliation and secondary infertility, while autonomous roles were related to female-factor infertility. Fifty-two percent of participants anticipated sharing decision-making, while 46% preferred handing over the decision to their husbands. Preference for a passive rather than a shared role in the spousal relationship was related to a higher husband’s age, greater marital satisfaction and higher anxiety.

Conclusions
In brief, women tended to prefer sharing decision-making tasks with their doctor as well as actively engaging their partner in making decisions about fertility treatment. This study adds to our understanding of women’s role preference and level of involvement in infertility treatment decision-making by providing quantitative evidence from women’s experience. It highlights the importance of healthcare professionals in facilitating shared decision-making among couples.
Systems pharmacology based approach to investigate the in-vivo therapeutic efficacy of Albizia lebbeck (L.) in experimental model of Parkinson’s disease
Authors: Saleem Uzma , Raza Zohaib , Anwar Fareeha , Chaudary Zunera , Ahmad Bashir 
Published: December 2019

Abstract
Background
Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by loss of dopaminergic neurons in substantia nigra pars compacta and clinically manifested mainly with motor dysfunctions. Plants are rich source of medicinally important bioactive compounds and inhabitants of underdeveloped countries used plants for treatment of various ailments. Albizia lebbeck has been reported to possess antioxidant and neuroprotective properties that suggest the evaluation of its traditional therapeutic potential in neurodegenerative diseases.
The aim of present study was to validate the traditional use of Albizia lebbeck (L.) and delineate its mechanism of action in PD. The systems pharmacology approach was employed to explain the Albizia lebbeck (L.) mechanism of action in PD.

Methods
The haloperidol-induced catalepsy was adopted as experimental model of PD for in-vivo studies in wistar albino rats. The systems pharmacology approach was employed to explain the Albizia lebbeck (L.) mechanism of action in PD.

Results
In-vivo studies revealed that Albizia lebbeck improved the motor functions and endurance as demonstrated in behavioral studies which were further supported by the rescue of endogenous antioxidant defense and reversal of ultrastructural damages in histological studies. System pharmacology approach identified 25 drug like compounds interacting with 132 targets in a bipartite graph that revealed the synergistic mechanism of action at system level. Kaemferol, phytosterol and okanin were found to be the important compounds nodes with prominent target nodes of TDP1 and MAPT.

Conclusion
The therapeutic efficiency of Albizia lebbeck in PD was effectively delineated in our experimental and systems pharmacology approach. Moreover, this approach further facilitates the drug discovery from Albizia lebbeck for PD.
Evaluation of the undergraduate family medicine programme of Faculty of Medicine, University of Kelaniya: quantitative and qualitative student feedback
Authors: Perera D. P. , Withana S. S. , Mendis K. , Kasunjith D. V. T. , Jayathilaka W. T. S. , Wickramasuriya S. 
Published: December 2019

Abstract
Background
Worldwide there is an increasing emphasis on the importance of primary care. The ministry of health Sri Lanka issued a directive in 2016 that training of doctors in primary care should be strengthened.
Medical students of the Faculty of Medicine, University of Kelaniya follow a 1 month long clinical appointment in family medicine in their fourth year of study.

Methods
Feedback is taken from students on completion of the appointment. Half the students from each group complete a pre tested structured feedback questionnaire that consists of answers to questions based on a likert scale with a space for free comments. The other half provide qualitative feedback.
In this evaluation data were gathered from 185 (98%) students from all eight clinical groups throughout the year 2016.
Quantitative data were analysed using SPSS version 22. Inductive thematic analysis was used to analyse the qualitative data from the Round Robin activity and free comments from the questionnaire.

Results
The qualitative feedback provided a richer indepth overview of student ideas on the appointment compared to the quantitative data.
In reflection of a desire for learning to be of relevance students wanted clinically oriented teaching focused on management. They preferred active teaching learning methods such as the opportunity to conduct consultations and receive immediate feedback. Students had a high regard for the teaching sessions by general practitioners at their clinics.
The appointment had created an interest in the discipline of family medicine which could have an impact on future choice of career. There were indications to suggest that student attitudes towards patients may have evolved to be more patient centred.
Students appreciated the inclusive and low stress ambience of the learning environment.

Conclusions and recommendations
Regular evaluation of teaching programmes helps maintain accountability of faculty and paves the way for more student centred teaching through the incorporation of students’ views in devising teaching methods. This evaluation found that qualitative feedback provided more descriptive material to reflect on and therefore improve teaching on the programme. It is recommended that more use should be made of qualitative methodologies in programme evaluations.