bluuebunny/crossref_metadata_2025 huggingface dataset:
2D electrophoresis image brightness correction based on gradient interval histogram
Authors: Ou Qiaofeng , Xiao Jiabing , Yu Lei , Wu Kaizhi , Xiong Bangshu
Published: March 2020

Background

Two-dimensional electrophoresis (2DE) is one of the most widely applied techniques in comparative proteomics. The basic task of 2DE is to identify differential protein expression by quantitative analysis of 2DE images. To reduce the errors of spot quantification in 2DE images, a novel brightness correction method based on gradient interval histogram (GIH) is proposed in this paper.

Results

First, GIH equalization is proposed to enhance the protein spot edges, especially the weak protein spots in the 2DE image. Second, to eliminate the overall brightness shift, GIH matching is applied to the 2DE images that need to be compared. Finally, the proposed method is verified by subjective quality evaluation and quantitative analysis of protein spots in real 2DE images.

Conclusions

The experimental results show that the average error of the quantification of corresponding protein spots in the resulting image pairs is less than 3%, which is significantly superior to that of the existing methods.
Comparison of RNA isolation methods on RNA-Seq: implications for differential expression and meta-analyses
Authors: Scholes Amanda N. , Lewis Jeffrey A.
Published: March 2020

Background

The increasing number of transcriptomic datasets has allowed for meta-analyses, which can be valuable due to their increased statistical power. However, meta-analyses can be confounded by so-called “batch effects,” where technical variation across different batches of RNA-seq experiments can clearly produce spurious signals of differential expression and reduce our power to detect true differences. While batch effects can sometimes be accounted for, albeit with caveats, a better strategy is to understand their sources to better avoid them. In this study, we examined the effects of RNA isolation method as a possible source of batch effects in RNA-seq design.

Results

Based on the different chemistries of “classic” hot phenol extraction of RNA compared to common commercial RNA isolation kits, we hypothesized that specific mRNAs may be preferentially extracted depending upon method, which could masquerade as differential expression in downstream RNA-seq analyses. We tested this hypothesis using the Saccharomyces cerevisiae heat shock response as a well-validated environmental response. Comparing technical replicates that only differed in RNA isolation method, we found over one thousand transcripts that appeared “differentially” expressed when comparing hot phenol extraction with the two kits. Strikingly, transcripts with higher abundance in the phenol-extracted samples were enriched for membrane proteins, suggesting that indeed the chemistry of hot phenol extraction better solubilizes those species of mRNA.

Conclusions

Within a self-contained experimental batch (e.g. control versus treatment), the method of RNA isolation had little effect on the ability to identify differentially expressed transcripts. However, we suggest that researchers performing meta-analyses across different experimental batches strongly consider the RNA isolation methods for each experiment.
Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates
Authors: Li Yuxiang , Xia Chongjing , Wang Meinan , Yin Chuntao , Chen Xianming
Published: March 2020

Background

The stripe rust pathogen,Puccinia striiformisf. sp.tritici(Pst), threats world wheat production. Resistance toPstis often overcome by pathogen virulence changes, but the mechanisms of variation are not clearly understood. To determine the role of mutation inPstvirulence changes, in previous studies 30 mutant isolates were developed from a least virulent isolate using ethyl methanesulfonate (EMS) mutagenesis and phenotyped for virulence changes. The progenitor isolate was sequenced, assembled and annotated for establishing a high-quality reference genome. In the present study, the 30 mutant isolates were sequenced and compared to the wide-type isolate to determine the genomic variation and identify candidates for avirulence (Avr) genes.

Results

The sequence reads of the 30 mutant isolates were mapped to the wild-type reference genome to identify genomic changes. After selecting EMS preferred mutations, 264,630 and 118,913 single nucleotide polymorphism (SNP) sites and 89,078 and 72,513 Indels (Insertion/deletion) were detected among the 30 mutant isolates compared to the primary scaffolds and haplotigs of the wild-type isolate, respectively. Deleterious variants including SNPs and Indels occurred in 1866 genes. Genome wide association analysis identified 754 genes associated with avirulence phenotypes. A total of 62 genes were found significantly associated to 16 avirulence genes after selection through six criteria for putative effectors and degree of association, including 48 genes encoding secreted proteins (SPs) and 14 non-SP genes but with high levels of association (P ≤ 0.001) to avirulence phenotypes. Eight of the SP genes were identified as avirulence-associated effectors with high-confidence as they met five or six criteria used to determine effectors.

Conclusions

Genome sequence comparison of the mutant isolates with the progenitor isolate unraveled a large number of mutation sites along the genome and identified high-confidence effector genes as candidates for avirulence genes inPst.Since the avirulence gene candidates were identified from associated SNPs and Indels caused by artificial mutagenesis, these avirulence gene candidates are valuable resources for elucidating the mechanisms of the pathogen pathogenicity, and will be studied to determine their functions in the interactions between the wheat host and thePstpathogen.
A combination of the activation marker CD86 and the immune checkpoint marker B and T lymphocyte attenuator (BTLA) indicates a putative permissive activation state of B cell subtypes in healthy blood donors independent of age and sex
Authors: Axelsson Susanne , Magnuson Anders , Lange Anna , Alshamari Aseel , Hörnquist Elisabeth Hultgren , Hultgren Olof
Published: March 2020

Background

The use of anti-B cell based therapies in immune-mediated diseases targeting general B cell markers or molecules important for B cell function has increased the clinical needs of monitoring B cell subpopulations.

Results

We analyzed the expression profile of cell surface markers CD86 and B and T lymphocyte attenuator (BTLA) in B cell subtypes using flow cytometry, including naïve, transitional, switched memory, non-switched memory and double-negative memory B cells and plasmablasts, and investigated the dependence of age and sex in a healthy adult blood donor population. The switched memory B cell subtype displayed a divergent expression of the markers, with increased CD86 and decreased BTLA as compared to non-switched and double negative memory cells, as well as compared to naïve B cells. Plasmablasts expressed highly increased CD86 compared to all other subtypes and a decreased expression of BTLA compared to naïve cells, but still higher compared to the memory cell populations. Transitional B cells had CD86 and BTLA expression similar to the other naïve cells.

Conclusions

We show divergent expression of CD86 and BTLA in memory cells and plasmablasts compared to naïve B cells independent of age and sex. Furthermore, a similarly divergent difference of expression pattern was seen between the memory cell subtypes, altogether indicating that the combination of CD86 and BTLA might be markers for a permissive activation state. We suggest the combination of CD86 and BTLA expression on B cell subtypes as a potentially important tool in monitoring the status of B cell subtypes before and after treatments influencing the B cell compartment.
Phosphate transporters, PnPht1;1 and PnPht1;2 from Panax notoginseng enhance phosphate and arsenate acquisition
Authors: Cao Guan-Hua , Li Ze-Dong , Wang Xi-Fu , Zhang Xue , Zhao Rong-Hua , Gu Wen , Chen Di , Yu Jie , He Sen
Published: March 2020

Background

Panax notoginseng is a medicinally important Chinese herb with a long history of cultivation and clinical application. The planting area is mainly distributed in Wenshan Prefecture, where the quality and safety of P. notoginseng have been threatened by high concentration of arsenic (As) from the soil. The roles of phosphate (Pi) transporters involved in Pi acquisition and arsenate (AsV) tolerance were still unclear in this species.

Results

In this study, two open reading frames (ORFs) of PnPht1;1 and PnPht1;2 separated from P. notoginseng were cloned based on RNA-seq, which encoded 527 and 541 amino acids, respectively. The results of relative expression levels showed that both genes responded to the Pi deficiency or As exposure, and were highly upregulated. Heterologous expression in Saccharomyces cerevisiae MB192 revealed that PnPht1;1 and PnPht1;2 performed optimally in complementing the yeast Pi-transport defect, particularly in PnPht1;2. Cells expressing PnPht1;2 had a stronger AsV tolerance than PnPht1;1-expressing cells, and accumulated less As in cells under a high-Pi concentration. Combining with the result of plasma membrane localization, these data confirmed that transporters PnPht1;1 and PnPht1;2 were putative high-affinity H+/H2PO4− symporters, mediating the uptake of Pi and AsV.

Conclusion

PnPht1;1 and PnPht1;2 encoded functional plasma membrane-localized transporter proteins that mediated a putative high-affinity Pi/H+ symport activity. Expression of PnPht1;1 or PnPht1;2 in mutant strains could enhance the uptake of Pi and AsV, that is probably responsible for the As accumulation in the roots of P. notoginseng.
Anemia risk factors among people living with HIV across the United States in the current treatment era: a clinical cohort study
Authors: Harding B. N. , Whitney B. M. , Nance R. M. , Ruderman S. A. , Crane H. M. , Burkholder G. , Moore R. D. , Mathews W. C. , Eron J. J. , Hunt P. W. , Volberding P. , Rodriguez B. , Mayer K. H. , Saag M. S. , Kitahata M. M. , Heckbert S. R. , Delaney J. A. C.
Published: March 2020

Background

Anemia is common among people living with HIV infection (PLWH) and is associated with adverse health outcomes. Information on risk factors for anemia incidence in the current antiretroviral therapy (ART) era is lacking.

Methods

Within a prospective clinical cohort of adult PLWH receiving care at eight sites across the United States between 1/2010–3/2018, Cox proportional hazards regression analyses were conducted among a) PLWH free of anemia at baseline and b) PLWH free of severe anemia at baseline to determine associations between time-updated patient characteristics and development of anemia (hemoglobin < 10 g/dL), or severe anemia (hemoglobin < 7.5 g/dL). Linear mixed effects models were used to examine relationships between patient characteristics and hemoglobin levels during follow-up. Hemoglobin levels were ascertained using laboratory data from routine clinical care. Potential risk factors included: age, sex, race/ethnicity, body mass index, smoking status, hazardous alcohol use, illicit drug use, hepatitis C virus (HCV) coinfection, estimated glomerular filtration rate (eGFR), CD4 cell count, viral load, ART use and time in care at CNICS site.

Results

This retrospective cohort study included 15,126 PLWH. During a median follow-up of 6.6 (interquartile range [IQR] 4.3–7.6) years, 1086 participants developed anemia and 465 participants developed severe anemia. Factors that were associated with incident anemia included: older age, female sex, black race, HCV coinfection, lower CD4 cell counts, VL ≥400 copies/ml and lower eGFR.

Conclusion

Because anemia is a treatable condition associated with increased morbidity and mortality among PLWH, hemoglobin levels should be monitored routinely, especially among PLWH who have one or more risk factors for anemia.
Prognostic value of the bone scan index in patients with metastatic castration-resistant prostate cancer: a systematic review and meta-analysis
Authors: Song Hualin , Jin Song , Xiang Peng , Hu Shuai , Jin Jie
Published: March 2020

Background

Many studies have reported the prognostic significance of the bone scan index (BSI) for metastatic castration-resistant prostate cancer (mCRPC); however, these reports are controversial. This study investigated the BSI in mCRPC and its relationship with prognosis.

Methods

The PubMed, Cochrane, and Embase databases were searched systematically for relevant articles published before September 1, 2019. Hazard ratios (HRs) were used to investigate the prognostic value.

Results

This study finally identified 9 eligible studies. The results suggested that high baseline BSI predicted poor OS (HR = 1.331, 95% CI: 1.081–1.640) and that elevated ΔBSI also predicted poor OS (HR = 1.220, 95% CI: 1.015–1.467). The subgroup analysis stratified by ethnicity showed that the baseline BSI and ΔBSI predicted poor OS in the Asian population but not in the Caucasian population. We also performed a subgroup analysis based on the different cut-off values of baseline BSI. The subgroup of ≤1 showed a significant association with OS in mCRPC patients.

Conclusion

Our study demonstrated that high baseline BSI and elevated ΔBSI predicted poor OS in patients with mCRPC. Hence, the BSI can serve as a prognostic indicator for mCRPC patients and may therefore guide clinical treatment in the future.
Neck lymph node metastasis detection in patients with differentiated thyroid carcinoma (DTC) in long-term follow-up: a 131I-SPECT/CT study
Authors: Spanu Angela , Nuvoli Susanna , Marongiu Andrea , Gelo Ilaria , Mele Luciana , Piras Bastiana , Madeddu Giuseppe
Published: March 2020

Background

The identification of neck lymph node (LN) metastases represents a very important issue in the management of patients with differentiated thyroid carcinoma (DTC). To this purpose, in the present study, we used 131I-SPECT/CT as a diagnostic imaging procedure.

Methods

A consecutive series of 224 DTC patients with ascertained neck radioiodine-avid foci at131I-SPECT/CT during long-term follow-up was evaluated. All patients had already undergone total thyroidectomy and radioiodine therapy and had been classified as follows: 62 at high risk (H), 64 at low risk (L) and 98 at very low risk (VL).131I-Whole body scan (WBS) followed by SPECT/CT was performed in all cases.

Results

In the 224 patients, 449 neck iodine avid foci were ascertained at SPECT/CT, while 322 were evidenced at WBS in 165/224 patients. WBS classified as residues 263/322 foci and as unclear 59/322 foci; among the former foci SPECT/CT correctly characterized 8 LN metastases and 3 physiologic uptakes and among the latter, it pinpointed 26 LN metastases, 18 residues, and 15 physiologic uptakes. SPECT/CT also classified 127 foci occult at WBS as 59 LN metastases and 68 residues. Globally, SPECT/CT identified 93 LN metastases in 59 patients (26 H, 20 L, 13 VL), while WBS evidenced 34 in 25 cases. All 13 VL patients, T1aN0M0, 5 of whom with LN near sub-mandibular glands, had thyroglobulin undetectable or < 2.5 ng/ml. Globally, SPECT/CT obtained an incremental value than WBS in 45.5% of patients, a more correct patient classification changing therapeutic approach in 30.3% of cases and identified WBS false-positive findings in 8% of cases.

Conclusions

131I-SPECT/CT proved to correctly detect and characterize neck LN metastases in DTC patients in long-term follow-up, improving the performance of planar WBS. SPECT/CT routine use is thus suggested; its role is particularly relevant in patients with WBS inconclusive, VL, T1aN0M0 and with undetectable or very low thyroglobulin levels.
Inequalities in the utilisation of maternal health Care in Rural India: Evidences from National Family Health Survey III & IV
Authors: Ali Balhasan , Chauhan Shekhar
Published: March 2020

Background

Since the implementation of National Rural Health Mission (NRHM) in 2005, Maternal Mortality Ratio has significantly declined in India through a noticeable improvement in maternal health care services. However, India did not succeed to achieve the target of millennium development goal to reduced maternal mortality ratio by 2015. Also, there is substantial inequality exist at the regional, geographic, economic, and social level, and various socioeconomic factors contribute to the significantly large share in inequality in utilisation of maternal health care in India.

Methods

Using data from the National Family Health Survey (2005 and 2015), this study examined the degree of inequality exist in maternal health care namely full antenatal care (full ANC), skilled attendants at birth (SBA), and postnatal care (PNC) in rural India. Descriptive statistics, concentration index (CI), and Wagstaff decomposition method have been performed to understand the pattern of maternal health care utilisation, and to explain the extent of inequality in maternal health care utilisation.

Results

The study revealed that a substantial gap across socioeconomic groups exist in utilisation of maternal health care has significantly reduced in rural India during 2005–16. The results found a noticeable improvement in maternal health care utilisation, especially in utilisation of skilled attendants at birth (SBA). During this decade, the concentration index for SBA showed a significant decline from 0.28 in 2005–06 to 0.09 in 2015–16, while that of full ANC declined from 0.47 to 0.32 over the same period, and reduction of inequality in full ANC was least. Further, the results of decomposition analysis suggested that secondary and higher education, mass media exposure, and scheduled tribe contributed a significant share to the inequality.

Conclusion

The exposure to mass media is the most significant contributor to inequality, and hence, there is a need for broad dissemination of awareness regarding maternal health care schemes in rural parts of country. Based on findings of study, it is suggested that health scheme related to maternal and child health care under NRHM be continued and focused for lower socioeconomic groups and marginalized mothers to reduce maternal health services inequality, particularly in the component of full ANC.
Associations of self-reported physical activity and anxiety symptoms and status among 7,874 Irish adults across harmonised datasets: a DEDIPAC-study
Authors: Mc Dowell Cillian P. , Carlin Angela , Capranica Laura , Dillon Christina , Harrington Janas M. , Lakerveld Jeroen , Loyen Anne , Ling Fiona Chun Man , Brug Johannes , MacDonncha Ciaran , Herring Matthew P.
Published: March 2020

Background

Anxiety is an adaptive response to an objective or perceived threat; however, when symptoms become severe and chronic it that can become a maladaptive anxiety disorder. Limited evidence suggests that physical activity may be associated with prevention against anxiety. This study uses data from The Irish Longitudinal Study on Ageing (TILDA) and The Mitchelstown Cohort Study to investigate cross-sectional associations between physical activity and anxiety symptoms and status among Irish adults.

Methods

Both datasets were harmonized (n = 7874). The short form International Physical Activity Questionnaire measured physical activity. Participants were classified as meeting World Health Organization physical activity guidelines (≥150 min weekly of moderate intensity physical activity, ≥75 min weekly of vigorous intensity physical activity, or ≥ 600 MET-minutes) or not. They were also divided into three groups based on weekly MET-minutes of moderate-to-vigorous physical activity (Low: 0–599; Moderate: 600–1199; High: ≥1200), and three groups based on weekly minutes of walking (Low: 0–209; Moderate: 210–419; High: 420+). Anxiety symptoms were measured by the Hospital Anxiety and Depression Scale with a score of ≥8 indicating anxiety. Binomial logistic regression, adjusted for relevant confounders examined physical activity–anxiety associations.

Results

Females had higher rates of anxiety than males (28.0% vs 20.0%; p < 0.001). Following adjustment for relevant covariates, meeting physical activity guidelines was associated with 13.5% (95% CI: 2.0–23.7; p = 0.023) lower odds of anxiety. Moderate and High physical activity were associated with 13.5% (− 11.0–32.6; p = 0.254) and 13.6% (1.4–4.2; p = 0.030) lower odds of anxiety compared to Low physical activity, respectively. Moderate and High walking were associated with 2.1% (− 14.5–16.3; p = 0.789) and 5.1% (− 9.3–17.6; p = 0.467) lower odds of anxiety compared to Low walking, respectively.

Conclusion

Meeting physical activity guidelines is associated with lower odds of anxiety, but the strength of associations did not increase considerably with increased physical activity levels.
Impact of sleep problems on daytime function in school life: a cross-sectional study involving Japanese university students
Authors: Kayaba Momoko , Matsushita Toshiko , Enomoto Minori , Kanai Chieko , Katayama Noriko , Inoue Yuichi , Sasai-Sakuma Taeko
Published: March 2020

Background

The aims of this study were 1) to clarify the prevalence of sleep problems (insomnia, insufficient sleep, and delayed sleep-wake phase) among Japanese university students; 2) to examine sociodemographic characteristics, lifestyle, and sleep-related symptoms in each sleep problem; and 3) to evaluate the association between the above-mentioned sleep problems and daytime dysfunction in school life.

Methods

Self-report questionnaire surveys were conducted at eight universities in Japan, and we received 1034 valid answers (78% female). The questionnaire consisted of socio-demographic characteristics, information on lifestyle, sleep pattern, sleep-related symptoms, and daytime dysfunction in school life. Groups with insomnia, behaviorally induced insufficient sleep syndrome (BIISS), delayed sleep-wake phase (DSWP), and BIISS + DSWP were defined. To identify the association between sleep problems and daytime dysfunction in school life, the generalized linear mixed effect model was conducted.

Results

Sleep duration on weekdays was 5.9 ± 1.2 h, and 38.2% of the students had a sleep duration < 6.0 h. About 16% of the students were categorized as evening-type individuals. More than half of the students (56.1%) had excessive daytime sleepiness. Insomnia was associated with tardiness (aOR: 0.8, 95%CI: 0.7–0.9) and falling asleep during class (aOR: 1.6: 95%CI: 1.4–2.0). BIISS was associated with tardiness (aOR: 1.5, 95%CI: 1.1–2.2) and interference with academic achievement (aOR: 1.9, 95%CI: 1.3–2.6). DSWP and BIISS + DSWP were associated with absence (aOR: 3.4, 95%CI: 2.2–5.1 / aOR: 4.2, 95%CI: 3.2–5.6), tardiness (aOR: 2.7, 95%CI: 1.8–4.1 / aOR: 2.2, 95%CI: 1.6–2.8), falling asleep during class (aOR: 2.6, 95%CI: 1.4–4.8 / aOR: 7.6, 95%CI: 3.3–17.2), and interference with academic achievement (aOR: 2.6, 95%CI: 1.7–3.9 / aOR: 2.1, 95%CI: 1.6–2.8).

Conclusions

Students with DSWP and BIISS + DSWP were significantly associated with daytime dysfunction in school life, i.e. absence, tardiness, falling asleep during class and interference with academic achievement. Students displaying BIISS + DSWP were considered to have a relatively more serious condition compared with those with only insomnia, DSWP, or BIISS. It is therefore of utmost importance that university students aim to prevent DSWP and BIISS which were associated with daytime function in school life.
Gender disparities in the education gradient in self-reported health across birth cohorts in China
Authors: Zhu Bowen , Ye Yiwan
Published: March 2020

Background

Variation in the relationship between education and health has been studied intensely over the past few decades. Although there is research on gender disparity and cohort variations in educational effect on health using samples from the U.S. and Europe, research about China’s is limited. Given the specific social changes in China, our study is designed to analyze the gender and cohort patterns in the education-health gradient.

Method

The latent growth-curve modeling was used to analyze the gender and cohort variations in the education gradient in self-rated health among Chinese respondents. The study employed longitudinal and nationally representative data from the Chinese Family Panel Studies from the years 2010 to 2016. Each cohort is specified according to their distinct periods of social change in China. Following the analysis, we used latent growth-curve model to illustrate gender and cohort differences in the age-graded education and health trajectories.

Results

Although Chinese men have reported to have better health than women in general, women reported 1.6 percentage points higher in self-reported health for each additional year of schooling compared to that of men (P < 0.001). The latent growth curve model showed women’s extra education benefits were persistent overtime. Compared to the people born during the “Old China” (1908–1938), the education gradient in self-rated health did not change for cohorts born before 1955 and after 1977, but the education-health gap changed significantly in the 1956–1960 (O.R. = 1.038, P < 0.05), 1967–1976 (O.R. = 1.058, P < 0.001), and 1977–1983 (O.R. = 1.063, P < 0.001) cohorts. There was a gender difference for the cohort variations in the education-health gradient. For women, the education effect in the 1956–1960 (O.R. = 1.063, P < 0.05), 1967–1976 (O.R. = 1.088, P < 0.001) and 1977–1983 (O.R. = 1.102, P < 0.001) cohorts was significantly higher than that of the 1908–1938 cohort. On the contrary, the education-health gradient remained the same across all cohorts for men.

Conclusion

Our study suggests that the education-health gradient varies across cohorts for women, but the size of education effect remains consistent for men across cohorts. The findings support the resource-substitution hypothesis and not the rising-importance hypothesis in China. We discussed the potential influences of the unique, social transformation and educational expansion in China.
Analyzing big tobacco’s global youth marketing strategies and factors influencing smoking initiation by Nigeria youths using the theory of triadic influence
Authors: Isip Ukoabasi , Calvert John
Published: March 2020

Background

Major transnational tobacco companies (TTCs) have identified Nigeria, the seventh most populous country in the world, as a market with a significant revenue potential, given its high youth population and growing gross domestic product (GDP). This research analyses tobacco industry-related strategies and activities targeting youth (aged 15 to 24 years) in Nigeria involving existing, but most importantly, future tobacco users. Nigeria is the focus of this study because the tobacco industry has viewed it as a major emerging market since the 1990s. Successful marketing in Nigeria could provide the industry with a template for similar initiatives in other emerging markets in low- and middle-income countries.

Methods

The research began with a systematic review of secondary literature to determine how the tobacco industry has targeted youth globally and factors contributing to youth smoking initiation. It then used the theory of triadic influence as a heuristic framework to categorize the various factors influencing youth smoking initiation and industry strategies related to increasing tobacco use among youths. Quotations from internal tobacco industry documents were organized into the three streams of the theory of triadic influence: biology/personality, social and cultural/environmental streams. A total of 12 interviews were conducted with 6 policymakers and governmental officials, 2 civil society organization representatives, a high school principal, a journalist and 2 researchers to investigate how the tobacco industry had targeted youth in Nigeria.

Results

The findings indicate that TTCs have actively targeted youth in Nigeria since the 1990s, focusing on changing behaviour through the biology/personality, social and environmental/ cultural streams.

Conclusion

The study suggests that Nigeria implement and vigorously enforce its 2015 National Tobacco Control Bill as well as a package of other measures to prevent tobacco companies targeting youth.
A new simple score of chronic cough: cough evaluation test
Authors: Zhan Wenzhi , Zhang Liting , Jiang Mei , Chen Meihua , Yuan Xiaoling , Sun Jianxin , Xu Pusheng , Wu Feng , Zhang Chunlai , Luo Wei , Chen Xiaomei , Li Hu , Lai Kefang
Published: March 2020

Background

Chronic cough has an important impact on physical, social and psychological aspects. A simple and effective method to assess different aspects of chronic cough severity is required. We aimed to develop a simple, self-completed test, Cough Evaluation Test (CET), to evaluate cough severity and its impact on health.

Method

The items of preliminary CET were generated based on literature review and clinical practice. Items reduction was conducted by modified Delphi method. Patients with chronic cough were recruited to complete CET, Cough Visual Analog Scales (VAS), Mandarin Chinese version of the Leicester Cough Questionnaire (LCQ-MC), and Cough Symptom Score (CSS). Reassessments were performed at 1 week apart before treatment, and after more than 2 weeks treatments. Concurrent validation, internal consistency, repeatability, responsiveness and the minimal important difference (MID) were determined.

Results

CET consists of five items with a 5-point Likert scale (1–5 scaling of items, 5–25 score range). The Cronbach’s alpha values for CET was 0.80. CET showed a stronger correlation with LCQ-MC (r = − 0.74) compared to that between LCQ-MC with VAS (r = − 0.61). CET also showed a stronger correlation with VAS (r = 0.70) compared to that between VAS with other measures. Intraclass correlation coefficients for CET was 0.84. In patients undergoing treatment, CET scores significantly changed (p < 0.0001). The MID of CET was 2.

Conclusion

Cough Evaluate Test is a reliable, valid and responsive tool to simply evaluate impact of cough on physical, social and psychological aspects.
Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome
Authors: Ji Yingjie , Liang Xiao , Lu Hong
Published: March 2020

Abstracts

Background

There have been reports of Helicobacter pylori (H. pylori) in the oral cavity and it has been suggested that the oral cavity may be a reservoir for H. pylori reflux from the stomach. High-throughput sequencing was used to assess the structure and composition of oral microbiota communities in individuals with or without confirmed H. pylori infection.

Methods

Saliva samples were obtained from 34 H. pylori infected and 24 H. pylori uninfected subjects. Bacterial genomic DNA was extracted and examined by sequencing by amplification of the 16S rDNA V3-V4 hypervariable regions followed by bioinformatics analysis. Saliva sampling was repeated from 22 of the 34 H. pylori infected subjects 2 months after H. pylori eradication.

Results

High-quality sequences (2,812,659) clustered into 95,812 operational taxonomic units (OTUs; 97% identity). H. pylori was detected in the oral cavity in infected (12/34), uninfected (11/24) and eradicated (15/22) subjects by technique of high-throughput sequencing, occupying 0.0139% of the total sequences. Alpha diversity of H. pylori infected subjects was similar to that of uninfected subjects (Shannon: 1417.58 vs. 1393.60, p > 0.05, ACE: 1491.22 vs. 1465.97, p > 0.05, Chao 1: 1417.58 vs. 1393.60, p > 0.05, t-test). Eradication treatment decreased salivary bacterial diversity (Shannon, p = 0.015, ACE, p = 0.003, Chao 1, p = 0.002, t-test). Beta diversity analysis based on unweighted UniFrac distances showed that the salivary microbial community structure differed between H. pylori infected and uninfected subjects (PERMANOVAR, pseudo-F: 1.49, p = 0.033), as well as before and after H. pylori eradication (PERMANOVAR, pseudo-F: 3.34, p = 0.001). Using LEfSe analysis, 16 differentially abundant genera were defined between infected and uninfected subjects, 12 of which had a further alteration after successful eradication.

Conclusions

Our study using high-throughput sequencing showed that H. pylori was present commonly in the oral cavity with no clear relation to H. pylori infection of the stomach. Both H. pylori infection and eradication therapy caused alterations in community and structure of the oral microbiota.

Trial registration

clinicaltrials.gov, NCT03730766. Registered 2 Nov 2018 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/ NCT03730766.
A phenomenological study of nurses experience about their palliative approach and their use of mobile palliative care teams in medical and surgical care units in France
Authors: Engberink Agnès Oude , Mailly Maryse , Marco Valerie , Bourrie Daniele , Benezech Jean-Pierre , Chevallier Josyane , Vanderhoeven Sandrine , Crosnier Remy , Bourrel Gérard , Lognos Béatrice
Published: March 2020

Background

Despite a broad consensus and recommendations, numerous international reports or studies have shown the difficulties of implementing palliative care within healthcare services. The objective of this study was to understand the palliative approach of registered nurses in hospital medical and surgical care units and their use of mobile palliative care teams.

Methods

Qualitative study using individual in depth semi-structured interviews and focus group of registered nurses. Data were analyzed using a semiopragmatic phenomenological analysis.

Expert nurses of mobile palliative care team carried out this study. 20 registered nurses from three different hospitals in France agreed to participate.

Results

Nurses recognize their role as being witnesses to the patient’s experience through their constant presence. This is in line with their professional values and gives them an “alert role” that can anticipate a patient-centered palliative approach. The physician’s positioning on palliative care plays a key role in its implementation. The lack of recognition of the individual role of the nurse leads to a questioning of her/his professional values, causing inappropriate behavior and distress.

According to nurses, “rethinking care within a team environment” allows for the anticipation of a patient-centered palliative approach. Mobile Palliative Care Team highlights the major role of physicians-nurses “balance” while providing personal and professional support.

Conclusions

The Physician’s positioning and attitude toward palliative approach sets the tone for its early implementation and determines the behavior of different staff members within healthcare service. “Recognition at work”, specifically “recognition of the individual role of nurse” is an essential concept for understanding what causes the delay in the implementation of a palliative approach. Interprofessional training (physicians and nurses) could optimize sharing expertise. Registered nurses consider MPCT as a “facilitating intermediary” within the healthcare service improving communication. Restoring a balance in sharing care and decision between physicians and other caregivers lead care teams to an anticipated and patient-centered palliative approach according to guidelines.
Clarifying how to deploy the public interest criterion in consent waivers for health data and tissue research
Authors: Schaefer G. Owen , Laurie Graeme , Menon Sumytra , Campbell Alastair V. , Voo Teck Chuan
Published: March 2020

Background

Several jurisdictions, including Singapore, Australia, New Zealand and most recently Ireland, have a public interest or public good criterion for granting waivers of consent in biomedical research using secondary health data or tissue. However, the concept of the public interest is not well defined in this context, which creates difficulties for institutions, institutional review boards (IRBs) and regulators trying to implement the criterion.

Main text

This paper clarifies how the public interest criterion can be defensibly deployed. We first explain the ethical basis for requiring waivers to only be granted to studies meeting the public interest criterion, then explore how further criteria may be set to determine the extent to which a given study can legitimately claim to be in the public interest. We propose an approach that does not attempt to measure magnitude of benefit directly, but rather takes into account metrics that are more straightforward to apply. To ensure consistent and justifiable interpretation, research institutions and IRBs should also incorporate procedural features such as transparency and public engagement in determining which studies satisfy the public interest requirement.

Conclusion

The requirement of public interest for consent waivers in secondary biomedical research should be guided by well-defined criteria for systematic evaluation. Such a criteria and its application need to be periodically subject to intra-committee and intra-institution review, reflection, deliberation and amendment.
Public health nursing education viewed through the lens of superdiversity: a resource for global health
Authors: Dupin Cécile-Marie , Pinon Mélanie , Jaggi Karine , Teixera Celina , Sagne Aurèle , Delicado Noelia
Published: March 2020

Background

Nurses are increasingly confronted with the challenge of globalization and the acceleration of migratory flows. This reality affects the notion of culture and its influence on health-related behaviors. The state of health of the population in the Canton of Geneva, where there is a wide diversity of origins, is characterized by significant differences. The term “superdiversity” is used to describe the increasing complexity in ethnic diversity due to migration and social stratification. Nursing education in Geneva, influenced by the Bologna Process, appears appropriate for superdiverse contexts of care, with the development of dedicated competencies.

Aim

This discussion paper aims to examine the academic curricula implemented in Geneva in the light of the concept of superdiversity.

Main text

In Geneva, nursing education and curricula in public health are based on a competence framework for nursing care divided into 7 roles and educational tracks. Bachelor’s-level nurses know how to assess a care problem quickly and solve it effectively by setting relevant priorities, and do so based on evidence. The curricula aim to teach nurses to design population and individual interventions in their superdiverse context.

Discussion

Education should enable students to develop their role as health promoters for the well-being of patients and communities, taking into account cultural complexity.

Conclusions

Superdiverse contexts highlight the role of nurse educators in preparing future generations of public health nurses.
Systematic review of statistical methods for safety data in malaria chemoprevention in pregnancy trials
Authors: Patson Noel , Mukaka Mavuto , Otwombe Kennedy N. , Kazembe Lawrence , Mathanga Don P. , Mwapasa Victor , Kabaghe Alinune N. , Eijkemans Marinus J. C. , Laufer Miriam K. , Chirwa Tobias
Published: March 2020

Background

Drug safety assessments in clinical trials present unique analytical challenges. Some of these include adjusting for individual follow-up time, repeated measurements of multiple outcomes and missing data among others. Furthermore, pre-specifying appropriate analysis becomes difficult as some safety endpoints are unexpected. Although existing guidelines such as CONSORT encourage thorough reporting of adverse events (AEs) in clinical trials, they provide limited details for safety data analysis. The limited guidelines may influence suboptimal analysis by failing to account for some analysis challenges above. A typical example where such challenges exist are trials of anti-malarial drugs for malaria prevention during pregnancy. Lack of proper standardized evaluation of the safety of antimalarial drugs has limited the ability to draw conclusions about safety. Therefore, a systematic review was conducted to establish the current practice in statistical analysis for preventive antimalarial drug safety in pregnancy.

Methods

The search included five databases (PubMed, Embase, Scopus, Malaria in Pregnancy Library and Cochrane Central Register of Controlled Trials) to identify original English articles reporting Phase III randomized controlled trials (RCTs) on anti-malarial drugs for malaria prevention in pregnancy published from January 2010 to July 2019.

Results

Eighteen trials were included in this review that collected multiple longitudinal safety outcomes including AEs. Statistical analysis and reporting of the safety outcomes in all the trials used descriptive statistics; proportions/counts (n = 18, 100%) and mean/median (n = 2, 11.1%). Results presentation included tabular (n = 16, 88.9%) and text description (n = 2, 11.1%). Univariate inferential methods were reported in most trials (n = 16, 88.9%); including Chi square/Fisher’s exact test (n = 12, 66.7%), t test (n = 2, 11.1%) and Mann–Whitney/Wilcoxon test (n = 1, 5.6%). Multivariable methods, including Poisson and negative binomial were reported in few trials (n = 3, 16.7%). Assessment of a potential link between missing efficacy data and safety outcomes was not reported in any of the trials that reported efficacy missing data (n = 7, 38.9%).

Conclusion

The review demonstrated that statistical analysis of safety data in anti-malarial drugs for malarial chemoprevention in pregnancy RCTs is inadequate. The analyses insufficiently account for multiple safety outcomes potential dependence, follow-up time and informative missing data which can compromise anti-malarial drug safety evidence development, based on the available data.
Economic valuation of health benefits from using geologic data to communicate radon risk potential
Authors: Chiavacci Scott J. , Shapiro Carl D. , Pindilli Emily J. , Casey Clyde F. , Rayens Mary Kay , Wiggins Amanda T. , Andrews William M. , Hahn Ellen J.
Published: March 2020

Background

Radon exposure is the second leading cause of lung cancer worldwide and represents a major health concern within and outside the United States. Mitigating exposure to radon is especially critical in places with high rates of tobacco smoking (e.g., Kentucky, USA), as radon-induced lung cancer is markedly greater among people exposed to tobacco smoke. Despite homes being a common source of radon exposure, convincing homeowners to test and mitigate for radon remains a challenge. A new communication strategy to increase radon testing among Kentucky homeowners utilizes fine-scale geologic map data to create detailed radon risk potential maps. We assessed the health benefits of this strategy via avoided lung cancer and associated premature mortality and quantified the economic value of these benefits to indicate the potential utility of using geologic map data in radon communication strategies.

Methods

We estimated the change in radon testing among all 120 counties in Kentucky following a new communication strategy reliant on geologic maps. We approximated the resultant potential change in radon mitigation rates and subsequent expected lung cancer cases and mortality avoided among smokers and non-smokers exposed to 4 pCi/L of radon in the home. We then applied the value of a statistical life to derive the economic value of the expected avoided mortality.

Results

The new communication strategy is estimated to help 75 Kentucky residents in 1 year avoid exposure to harmful radon levels via increased testing and mitigation rates. This equated to the potential avoidance of approximately one premature death due to lung cancer, with a net present value of $3.4 to $8.5 million (2016 USD).

Conclusions

Our analysis illustrates the potential economic value of health benefits associated with geologic map data used as part of a communication strategy conveying radon risk to the public. Geologic map data are freely available in varying resolutions throughout the United States, suggesting Kentucky’s radon communication strategy using geologic maps can be employed in other states to educate the public about radon. As this is only a single application, in a single state, the economic and health benefits of geologic map data in educating the public about radon are likely to exceed our estimates.
Recent changes in the Dutch foodscape: socioeconomic and urban-rural differences
Authors: Pinho Maria Gabriela M. , Mackenbach Joreintje D. , den Braver Nicole R. , Beulens Joline J. W. , Brug Johannes , Lakerveld Jeroen
Published: March 2020

Background

Obesogenic food environments may influence dietary behaviours and contribute to obesity. Few countries quantified changes in their foodscape. We explored how the availability of different types of food retailers has changed in the Netherlands across levels of neighbourhood socioeconomic status (SES) and urbanisation.

Methods

This longitudinal ecological study conducted in the Netherlands had as unit of analysis administrative neighbourhoods. From 2004 to 2018, the geographic location and type of each food retailer were objectively assessed by a commercial company. Food retailers were categorised as local food shops, fast food restaurants, food delivery, restaurants, supermarkets, and convenience stores. Information on neighbourhood SES and urbanisation was obtained from Central Bureau of Statistics (CBS). To test the change in the counts of food retailers we used negative binomial generalized estimating equations (GEE), with neighbourhoods as the group variable, time as the independent variable and the counts of each type of food retailer as outcome. To account for changes in population density, analyses were adjusted for the number of inhabitants per neighbourhood. We tested effect modification by adding an interaction term for neighbourhood SES and urbanisation to the models.

Results

In Dutch neighbourhoods between 2004 and 2018, a 120 and 35% increase was found in the count of food delivery outlets and restaurants, respectively, and a 24% decrease in count of local food shops. Stratified analyses showed an increase in the availability of supermarkets and convenience stores in the more urbanised and lower SES neighbourhoods, while a decrease was observed in the less urbanised and higher SES neighbourhoods.

Conclusions

We observed considerable changes in the Dutch foodscape. Over a 14 years period, the foodscape changed towards a higher availability of food retailers offering convenience and ready-to-eat foods. These findings can help policy makers aiming to promote a healthier food environment and obesity prevention.
The self-organization model reveals systematic characteristics of aging
Authors: Wang Yin , Huang Tao , Li Yixue , Sha Xianzheng
Published: March 2020

Background

Aging is a fundamental biological process, where key bio-markers interact with each other and synergistically regulate the aging process. Thus aging dysfunction will induce many disorders. Finding aging markers and re-constructing networks based on multi-omics data (i.e. methylation, transcriptional and so on) are informative to study the aging process. However, optimizing the model to predict aging have not been performed systemically, although it is critical to identify potential molecular mechanism of aging related diseases.

Methods

This paper aims to model the aging self-organization system using a series of supervised learning methods, and study complex molecular mechanisms of aging at system level: i.e. optimizing the aging network; summarizing interactions between aging markers; accumulating patterns of aging markers within module; finding order-parameters in the aging self-organization system.

Results

In this work, the normal aging process is modeled based on multi-omics profiles across different tissues. In addition, the computational pipeline aims to model aging self-organizing systems and study the relationship between aging and related diseases (i.e. cancers), thus provide useful indicators of aging related diseases and could help to improve prediction abilities of diagnostics.

Conclusions

The aging process could be studied thoroughly by modelling the self-organization system, where key functions and the crosstalk between aging and cancers were identified.