Category: Statistics

PLoS One. 2021 Jul 27;16(7):e0255290. doi: 10.1371/journal.pone.0255290. eCollection 2021.

ABSTRACT

Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower’s genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.

PMID:34314448 | DOI:10.1371/journal.pone.0255290

PLoS One. 2021 Jul 27;16(7):e0255203. doi: 10.1371/journal.pone.0255203. eCollection 2021.

ABSTRACT

BACKGROUND: Behavioural patterns are typically derived using unsupervised multivariate methods such as principal component analysis (PCA), latent profile analysis (LPA) and cluster analysis (CA). Comparability and congruence between the patterns derived from these methods has not been previously investigated, thus it’s unclear whether patterns from studies using different methods are directly comparable. This study aimed to compare behavioural patterns derived across diet, physical activity, sedentary behaviour and sleep domains, using PCA, LPA and CA in a single dataset.

METHODS: Parent-report and accelerometry data from the second wave (2011/12; child age 6-8y, n = 432) of the HAPPY cohort study (Melbourne, Australia) were used to derive behavioural patterns using PCA, LPA and CA. Standardized variables assessing diet (intake of fruit, vegetable, sweet, and savoury discretionary items), physical activity (moderate- to vigorous-intensity physical activity [MVPA] from accelerometry, organised sport duration and outdoor playtime from parent report), sedentary behaviour (sedentary time from accelerometry, screen time, videogames and quiet playtime from parent report) and sleep (daily sleep duration) were included in the analyses. For each method, commonly used criteria for pattern retention were applied.

RESULTS: PCA produced four patterns whereas LPA and CA each generated three patterns. Despite the number and characterisation of the behavioural patterns derived being non-identical, each method identified a healthy, unhealthy and a mixed pattern. Three common underlying themes emerged across the methods for each type of pattern: (i) High fruit and vegetable intake and high outdoor play (“healthy”); (ii) poor diet (either low fruit and vegetable intake or high discretionary food intake) and high sedentary behaviour (“unhealthy”); and (iii) high MVPA, poor diet (as defined above) and low sedentary time (“mixed”).

CONCLUSION: Within this sample, despite differences in the number of patterns derived by each method, a good degree of concordance across pattern characteristics was seen between the methods. Differences between patterns could be attributable to the underpinning statistical technique of each method. Therefore, acknowledging the differences between the methods and ensuring thorough documentation of the pattern derivation analyses is essential to inform comparison of patterns derived through a range of approaches across studies.

PMID:34314443 | DOI:10.1371/journal.pone.0255203

PLoS One. 2021 Jul 27;16(7):e0255026. doi: 10.1371/journal.pone.0255026. eCollection 2021.

ABSTRACT

Building capacity for developing skills as leadership, teamwork, and continuous academic support has become essential for fulfilling a successful pharmacy career. This study aims to assess Jordanian pharmacists’ views on professional development, namely: the continuous education infrastructure, strategies and programs for personal development, leadership skills, incentive schemes, drug information resources and digital services. As well as exploring options for better academic support delivered to pharmacists. To capture participant’s views, an online validated and reliable survey was developed. Non-probability sampling design was used. Participants were qualified pharmacists working at Royal Medical Services (RMS) and Community Pharmacists (CP). Comparison and descriptive statistics were used to report the results. A total of 271 pharmacists participated, 144 from RMS (8% more than the needed sample) and 127 CP (7% more than the needed sample). There was a strong desire amongst both RMS and PC groups for continuous educational training particularly in the following areas, first: Advanced counselling and communication skills (means = 8.99±0.145, CI 95% = 3.70-4.28 and 9.37±0.096, CI 95% = 4.18-4.56). Second: Personal development skills (mean = 8.92±0.142, CI 95% = 3.64-4.20 and 9.02±0.145, CI 95% = 3.73-4.30). Third, Pharmaceutical health promotion (mean = 8.05±0.180, CI 95% = 2.70-3.41 and 8.57±0.159, CI 95% = 3.26-3.89). Only 19.4% and 18.1% of the RMS and CPs respectively reported the presence of a written policy for personal development and leadership in their workplace. There were few incentives for pharmacists to participate in research. Few pharmacists used the available drug information and toxicology centers. The professional and continuous personal development of pharmacists support an evolving healthcare system. This study emphasizes the need for a tailored and documented postgraduate educational strategy, personal development, and leadership skills training in Jordan. Implementing a well-defined scheme of incentives should be encouraged to engage pharmacists in continuous professional development programs and pharmaceutical research. Such strategy and training should enhance both professional and personal performance.

PMID:34314444 | DOI:10.1371/journal.pone.0255026

PLoS One. 2021 Jul 27;16(7):e0255379. doi: 10.1371/journal.pone.0255379. eCollection 2021.

ABSTRACT

BACKGROUND: The hematological abnormalities are assumed to be involved in the disease progression of COVID-19. However, the actual associations between specific blood parameters and COVID-19 are not well understood. Here we aimed to assess the correlations between hematological parameters and the severity of COVID-19.

METHODS: We included COVID-19 patients who were admitted to Evercare Hospital Ltd, Dhaka, Bangladesh, between November 10, 2020, to April 12, 2021, with a confirmed case of RT-PCR test. We recorded demographic information, clinical data, and routine hematological examination results of all COVID-19 patients. We performed statistical analyses and interpretation of data to compare severe COVID-19 patients (SCP) and non-severe COVID-19 patients (NSCP).

RESULTS: The age and BMI of the admitted COVID-19 patients were 48.79±8.53 years and 25.82±3.75 kg/m2. This study included a total of 306 hospitalized COVID-19 patients. Among them, NSCP and SCP were 198 and 108, respectively. And we recorded 12 deaths from SCP. We observed the alterations of several hematological parameters between SCP and NSCP. Among them, we noticed the increased levels of C-reactive protein (CRP), d-dimer, and ferritin showed good indicative value to evaluate the severity of COVID-19. Also, there were positive correlations among these parameters. Moreover, we found correlations between the outcomes of COVID-19 patients with patient’s demographics and comorbid diseases.

CONCLUSION: Based on our results, CRP, d-dimer, and ferritin levels at admission to hospitals represent simple assessment factors for COVID-19 severity and the treatment decisions at the hospital setup. These blood parameters could serve as indicators for the prognosis and severity of COVID-19. Therefore, our study findings might help to develop a treatment protocol for COVID-19 patients at the hospital setup.

PMID:34314447 | DOI:10.1371/journal.pone.0255379

PLoS Genet. 2021 Jul 27;17(7):e1009684. doi: 10.1371/journal.pgen.1009684. Online ahead of print.

ABSTRACT

Functional mechanisms remain unknown for most genetic loci associated to complex human traits and diseases. In this study, we first mapped trans-eQTLs in a data set of primary monocytes stimulated with LPS, and discovered that a risk variant for autoimmune disease, rs17622517 in an intron of C5ORF56, affects the expression of the transcription factor IRF1 20 kb away. The cis-regulatory effect specific to IRF1 is active under early immune stimulus, with a large number of trans-eQTL effects across the genome under late LPS response. Using CRISPRi silencing, we showed that perturbation of the SNP locus downregulates IRF1 and causes widespread transcriptional effects. Genome editing by CRISPR had suggestive recapitulation of the LPS-specific trans-eQTL signal and lent support for the rs17622517 site being functional. Our results suggest that this common genetic variant affects inter-individual response to immune stimuli via regulation of IRF1. For this autoimmune GWAS locus, our work provides evidence of the functional variant, demonstrates a condition-specific enhancer effect, identifies IRF1 as the likely causal gene in cis, and indicates that overactivation of the downstream immune-related pathway may be the cellular mechanism increasing disease risk. This work not only provides rare experimental validation of a master-regulatory trans-eQTL, but also demonstrates the power of eQTL mapping to build mechanistic hypotheses amenable for experimental follow-up using the CRISPR toolkit.

PMID:34314424 | DOI:10.1371/journal.pgen.1009684

PLoS Negl Trop Dis. 2021 Jul 27;15(7):e0009647. doi: 10.1371/journal.pntd.0009647. Online ahead of print.

ABSTRACT

BACKGROUND: The sand fly Phlebotomus perniciosus is the main vector of Leishmania infantum, etiological agent of zoonotic visceral leishmaniasis in the Western Mediterranean basin. Dogs are the main reservoir host of this disease. The main objective of this study was to determine, under both laboratory and field conditions, if dogs infected with L. infantum, were more attractive to female P. perniciosus than uninfected dogs.

METHODOLOGY/PRINCIPAL FINDINGS: We carried out a series of host choice experiments and found that infected dogs were significantly more attractive to P. perniciosus than uninfected dogs in the laboratory as well as in the field. Significantly more P. perniciosus fed on infected dogs than on uninfected dogs. However, the fecundity of P. perniciosus fed on infected dogs was adversely impacted compared to uninfected dogs by lowering the number of laid eggs. Phlebotomus perfiliewi, the second most abundant sand fly species in the field site and a competent vector of L. infantum had similar trends of attractivity as P. perniciosus toward infected dogs under field conditions.

CONCLUSIONS: The results strongly suggest that L. infantum causes physiological changes in the reservoir host which lead to the host becoming more attractive to both male and female P. perniciosus. These changes are likely to improve the chance of successful transmission because of increased contact with infected hosts and therefore, infected dogs should be particularly targeted in the control of zoonotic visceral leishmaniasis in North Africa.

PMID:34314425 | DOI:10.1371/journal.pntd.0009647

Anesth Analg. 2021 Jul 27. doi: 10.1213/ANE.0000000000005673. Online ahead of print.

ABSTRACT

BACKGROUND: We recently reported that a 6-day continuous peripheral nerve block reduced established postamputation phantom pain 3 weeks after treatment ended. However, the immediate effects of perineural infusion (secondary outcomes) have yet to be reported.

METHODS: Participants from 5 enrolling academic centers with an upper or lower limb amputation and established phantom pain received a single-injection ropivacaine peripheral nerve block(s) and perineural catheter insertion(s). They were subsequently randomized to receive a 6-day ambulatory perineural infusion of either ropivacaine 0.5% or normal saline in a double-masked fashion. Participants were contacted by telephone 1, 7, 14, 21, and 28 days after the infusion started, with pain measured using the Numeric Rating Scale. Treatment effects were assessed using the Wilcoxon rank-sum test at each time point. Adjusting for 4 time points (days 1, 7, 14, and 21), P < .0125 was deemed statistically significant. Significance at 28 days was reported using methods from the original, previously published article.

RESULTS: Pretreatment average phantom and residual pain scores were balanced between the groups. The day after infusion initiation (day 1), average phantom, and residual limb pain intensity was lower in patients receiving local anesthetic (n = 71) versus placebo (n = 73): median [quartiles] of 0 [0-2.5] vs 3.3 [0-5.0], median difference (98.75% confidence interval [CI]) of -1.0 (-3.0 to 0) for phantom pain (P = .001) and 0 [0-0] vs 0 [0-4.3], and median difference 0.0 (-2.0 to 0.0) for residual limb pain (P < .001). Pain’s interference with physical and emotional functioning as measured with the interference domain of the Brief Pain Inventory improved during the infusion on day 1 for patients receiving local anesthetic versus placebo: 0 [0-10] vs 10 [0-40], median difference (98.75% CI) of 0.0 (-16.0 to 0.0), P = .002. Following infusion discontinuation (day 6), a few differences were found between the active and placebo treatment groups between days 7 and 21. In general, sample medians for average phantom and residual limb pain scores gradually increased after catheter removal for both treatments, but to a greater degree in the control group until day 28, at which time the differences between the groups returned to statistical significance.

CONCLUSIONS: This secondary analysis suggests that a continuous peripheral nerve block decreases phantom and residual limb pain during the infusion, although few improvements were again detected until day 28, 3 weeks following catheter removal.

PMID:34314392 | DOI:10.1213/ANE.0000000000005673

J Clin Sleep Med. 2021 Jul 27. doi: 10.5664/jcsm.9566. Online ahead of print.

ABSTRACT

STUDY OBJECTIVES: The aim of this study is to determine the extent of agreement between self-reported measurements of total sleep time (TST) and actigraphy in the fire and emergency services occupation.

METHODS: Twenty-four firefighters participated in an 18-day study. Four measurements were used to assess TST: PSQI, a newly developed habitual Extended Sleep Survey, a newly developed daily Emergency Services Sleep Diary (ESSD), and actigraphy. The Extended Sleep Survey and ESSD were constructed to address the specific job-related characteristics of fire and emergency services that other measurements cannot achieve (e.g., multiple sleep bouts in a single night).

RESULTS: The PSQI TST is least accurate compared to actigraphy. The Extended Sleep Survey TST shows improvement over PSQI TST, but was statistically different from actigraphy TST. No difference in mean TST was found between ESSD TST and Actigraphy TST. Furthermore, ESSD TST and Actigraphy TST correlated strongly together.

CONCLUSIONS: Without modification, traditional self-reported measures may not be appropriate in the fire and emergency service occupation. This study suggests that the ESSD may serve as a useful alternative to actigraphy to measure TST.

PMID:34314350 | DOI:10.5664/jcsm.9566

Scand J Gastroenterol. 2021 Jul 27:1-6. doi: 10.1080/00365521.2021.1955965. Online ahead of print.

ABSTRACT

BACKGROUND AND AIMS: Fecal calprotectin (fCP) has been shown to correlate with endoscopic disease activity in Crohn’s disease (CD). The aim of this study was to evaluate its role in predicting early endoscopic recurrence in postoperative CD.

METHODS: Patients who underwent CD-related intestinal resection with ileocolonic anastomosis were prospectively followed up until ileocolonoscopy was performed around 12 months post-surgery. Endoscopic recurrence (ER) was defined as modified Rutgeerts score i2b or higher. Endoscopic still images were reviewed by 2 independent reviewers blinded to fCP results. Stool specimens were collected 6 months post-surgery and a multivariate logistic regression model was established to explore the predictive value of fCP for ER.

RESULTS: 79 patients were included. FCP was significantly associated with endoscopic recurrence (p = .036). A cut-off value of fCP of 267 µg/g at 6 months post-surgery predicted ER with a sensitivity of 61.8% and a specificity of 72.7% (AUC 0.669). A prediction model subsuming age at diagnosis and fCP 6 months post-surgery were significantly associated with ER (fCP at 6 months [p = .007] and age at diagnosis [p = .004], multivariate analysis).

CONCLUSIONS: FCP 6 months after surgery and age at diagnosis predict early ER at 1 year postoperatively. However, the low sensitivity of fCP still suggests the necessity of endoscopy as a gold standard for the assessment of postoperative recurrence of CD.KEY SUMMARYWhat is already known? Fecal calprotectin (fCP) correlates with endoscopic disease activity. Endoscopic recurrence occurs in up to 70% of patients after intestinal resection within 1 year.What are the significant and/or new findings of this study? Fecal calprotectin 6 months post-surgery and age at diagnosis significantly predict endoscopic recurrence at 1 year. Due to low sensitivity fCP cannot replace the necessity of endoscopy for accurate assessment of postoperative recurrence.

PMID:34314308 | DOI:10.1080/00365521.2021.1955965

J Clin Sleep Med. 2021 Jul 27. doi: 10.5664/jcsm.9564. Online ahead of print.

ABSTRACT

STUDY OBJECTIVES: We determined the relationship of cardiovascular risk factors (CRF), cardiovascular diseases (CVD), nocturnal blood pressure (NBP) and nocturnal blood pressure fluctuations (NBPFs) with the severity of obstructive sleep apnea (OSA). We also investigated the effect of short-term continuous positive airway pressure (CPAP) therapy on NBP parameters.

METHODS: This retrospective study included 548 patients from our cardiac clinic with suspected OSA. Patients underwent polysomnography and continuous NBP measurement using the pulse transit time (PTT). According to their apnea-hypopnea index (AHI), patients were subclassified: Controls (AHI < 5/h), mild (AHI 5 – < 15/h), moderate (AHI 15 – < 30/h) and severe OSA (AHI ≥ 30/h). 294 patients received CPAP therapy.

RESULTS: Analysis of covariance (ANCOVA) showed that NBP and the frequency of NBPFs were the highest in severe followed by moderate and mild OSA (all p < 0.001). Multivariable regression analysis revealed a significant association of NBPFs with AHI, BMI, systolic NBP and lowest SpO₂. The severity of OSA is also associated with the frequency of obesity, hypertension, diabetes mellitus, atrial fibrillation, heart failure (all p < 0.001) and coronary artery disease (p = 0.035). Short-term CPAP decreased the frequency of NBPFs in all OSA groups and the systolic NBP in severe and moderate but not in mild OSA.

CONCLUSIONS: The severity of OSA is associated with an increase in NBP and NBPFs. CPAP reduces NBP parameters already after the first night. In addition to BP, the diagnosis and therapy of NBPFs should be considered in patients with OSA.

CLINICAL TRIAL REGISTRATION: Registry: German Clinical Trials Register; Title: Nocturnal blood pressure and nocturnal blood pressure fluctuations associated with the severity of obstructive sleep apnea; Identifier: DRKS00024087; URL: https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00024087.

PMID:34314347 | DOI:10.5664/jcsm.9564