Tag: statistics

Cytopathology. 2021 Sep 15. doi: 10.1111/cyt.13058. Online ahead of print.

ABSTRACT

Accurate and thorough data analysis and reporting are essential to ensure the interpretation of the findings is appropriate. A detailed methods section in a manuscript contains enough information to permit a researcher with access to the study components, including the data, to replicate the findings. This descriptive study of 2.5 years of Cytopathology articles uncovers opportunities to elevate the quality of methods and data reporting. The findings include approximately 4 out of 5 articles (79%) identified the calculations or statistical test, nearly 3 out of 4 articles (74%) that involved significance testing included the threshold for significance in the methods section, 7 out of 10 (70%) articles defined the abbreviations and/or symbols used, and roughly half (51%) of the articles documented the software used for analysis. Omission of any of these areas of reporting (calculations or statistics performed, significance level utilized, abbreviations and/or symbols applied, and software used) could lead to a misinterpretation in the reported study or the inability to replicate findings in similar research. This study identified that there is an opportunity to elevate the quality of data reporting in this journal.

PMID:34525237 | DOI:10.1111/cyt.13058

Head Neck. 2021 Sep 15. doi: 10.1002/hed.26868. Online ahead of print.

ABSTRACT

BACKGROUND: This systematic review and meta-analysis sought to assess the extent to which pretreatment depression or depressive symptoms are related to prognosis in patients with head and neck cancer (HNC).

METHODS: Medline, EMbase, Scopus, and The Cochrane Library databases were searched. A meta-analysis was done to generate a forest plot and pooled hazard ratio (HR) with 95% CI for overall survival (OS). RevMan 5.3 and Meta Essentials were used for statistical analysis.

RESULTS: Based on seven studies involving 1743 patients, the results showed that HNC patients with pretreatment depression or depressive symptoms had worse OS than patients without depression or depressive symptoms, with an HR of 1.33, 95% CI 1.16-1.52, p = <0.0001. There is heterogeneity in the pooled summary effect (I² = 80%, p < 0.0001).

CONCLUSIONS: Pretreatment depression or depressive symptoms may indicate worse OS in patients with HNC. The pooled analysis demonstrated a statistically significant effect. These results were limited by mild heterogeneity.

PMID:34525238 | DOI:10.1002/hed.26868

Crim Behav Ment Health. 2021 Sep 15. doi: 10.1002/cbm.2216. Online ahead of print.

ABSTRACT

BACKGROUND: While the presence or absence of previous healthcare and criminal justice system (CJS) contacts in the histories of mentally ill offenders has been well-studied, the frequency of these contacts and when they occur in the period leading up to an index criminal event has received less research attention.

AIMS: To explore patterns of healthcare and CJS use in the year prior to a criminal act leading to a Not Criminally Responsible on Account of Mental Disorder (NCRMD) finding in Canada.

METHODS: In this 3-year retrospective records study, the case files of all patients newly admitted to the British Columbia forensic psychiatric system after a finding of NCRMD between 1st July 2012 and 31st July 2015 were reviewed. Data were extracted on healthcare and CJS use for the 12 months before the act leading to the NCRMD finding. Time-based descriptive statistics and two-step cluster analysis were used to investigate service use patterns.

RESULTS: Among 94 eligible patients, only four had no service contacts in the year leading up to the index event, leaving 90 in the cohort for further analysis. On average, these 90 patients had seven contacts with health or criminal justice services in the year prior to the index offence. Cluster analysis revealed a high healthcare pathway group who had had many healthcare and few CJS contacts; a limited service user group who had had few contacts of any kind and a heavy service user group who had had a high volume of contacts with both types of service providers.

CONCLUSIONS: The different patterns of patient contact prior to the index event imply that each practitioner-type has distinct and temporally relevant opportunities to provide preventative interventions to their patients or user groups.

PMID:34525231 | DOI:10.1002/cbm.2216

J Food Prot. 2021 Sep 15. doi: 10.4315/JFP-21-287. Online ahead of print.

ABSTRACT

Salmonella spp. is one of the primary pathogens that cause foodborne diseases worldwide. In the present study, we deeply characterized Salmonella spp. originated from foods related to human salmonellosis outbreaks in Minas Gerais – Brazil, from 2003 to 2017. In this regard, the serotyping, antimicrobial susceptibility, virulence genes and genetic polymorphism determined by rep-PCR were performed in 70 Salmonella spp. isolates. Thirteen serotypes of Salmonella spp. were identified, and S. Enteritidis and S. Typhimurium were the most prevalent, both corresponding to 74.3% (52/70) of all isolates. Sixty-five (92.8%) isolates demonstrated to be resistant to at least one of the 15 antimicrobials tested. Ten isolates (14.2%) showed a multidrug-resistant phenotype. Sixteen virulence genes were screened and detection ranged from 75.7 to 100% of all isolates. There was a statistical difference among Salmonella spp. serotypes in detecting the sipB , sopE , lfpA , sefA and spvC genes. Forty isolates of S. Enteritidis from 16 outbreaks were grouped into 14 fingerprints, while 12 S. Typhimurium retrieved six fingerprints. The bacteria presented a serological pattern like those reported by main public health centers worldwide. One major concern of our findings is the high levels of both detection of virulence genes and resistance to antimicrobials, especially to critically important drugs. In this concern, especial attention should be given to the serotype S. Enteritidis. Although the isolates of Salmonella spp. have presented a relatively variable genome, high genetic similarity was observed among them, with some of them sharing identical fingerprints. These results corroborate the hypothesis of clonal circulation of Salmonella spp. in human infections in Minas Gerais.

PMID:34525206 | DOI:10.4315/JFP-21-287

Soft Matter. 2021 Sep 15;17(35):8068-8077. doi: 10.1039/d1sm00941a.

ABSTRACT

The encapsulation of particles in droplets using microfluidic devices finds application across several fields ranging from biomedical engineering to materials science. The encapsulation process, however, is often affected by poor single encapsulation efficiency, quantified by the Poisson statistics, with droplets containing more than one particle or with several empty droplets. We here demonstrate that viscoelastic aqueous solutions of xanthan gum enable controlled single particle encapsulation in microfluidic devices with a single encapsulation efficiency up to 2-fold larger than the one predicted by the Poisson statistics. We achieved such a result by identifying viscoelastic xanthan gum aqueous solutions that could drive particle ordering before approaching the encapsulation area and simultaneously form uniform droplets. This is the first experimental evidence of viscoelastic encapsulation in microfluidic devices, the existing literature on the subject being focused on Newtonian suspending liquids. We first studied the process of viscoelastic droplet formation, and found that the droplet length normalised by the channel diameter scaled as predicted for Newtonian solutions. At variance with Newtonian solutions, we observed that the droplet formation mechanism became unstable above critical values of the Weissenberg number, which quantifies the elasticity of the xanthan gum solutions carrying the particles. In terms of controlled encapsulation, we discovered that the single encapsulation efficiency was larger than the Poisson values in a specific range of xanthan gum mass concentrations. Finally, we introduced an empirical formula that can help the design of controlled viscoelastic encapsulation systems.

PMID:34525163 | DOI:10.1039/d1sm00941a

Anesthesiology. 2021 Sep 15. doi: 10.1097/ALN.0000000000003962. Online ahead of print.

ABSTRACT

BACKGROUND: There is need to identify perioperative interventions that decrease chronic opioid use. The authors hypothesized that receipt of a peripheral nerve block would be associated with a lower incidence of persistent postoperative opioid prescription fulfillment.

METHODS: This was a retrospective population-based cohort study examining ambulatory shoulder surgery patients in Ontario, Canada. The main outcome measure was persistent postoperative opioid prescription fulfillment. In opioid-naive patients (no opioid prescription fulfillment in 90 days preoperatively), this was present if an individual fulfilled an opioid prescription of at least a 60-day supply during postoperative days 90 to 365. In opioid-exposed (less than 60 mg oral morphine equivalent dose per day within 90 days preoperatively) or opioid-tolerant (60 mg oral morphine equivalent dose per day or above within 90 days preoperatively) patients, this was classified as present if an individual experienced any increase in opioid prescription fulfillment from postoperative day 90 to 365 relative to their baseline use before surgery. The authors’ exposure was the receipt of a peripheral nerve block.

RESULTS: The authors identified 48,523 people who underwent elective shoulder surgery from July 1, 2012, to December 31, 2017, at one of 118 Ontario hospitals. There were 8,229 (17%) patients who had persistent postoperative opioid prescription fulfillment. Of those who received a peripheral nerve block, 5,008 (16%) went on to persistent postoperative opioid prescription fulfillment compared to 3,221 (18%) patients who did not (adjusted odds ratio, 0.90; 95% CI, 0.83 to 0.97; P = 0.007). This statistically significant observation was not reproduced in a coarsened exact matching sensitivity analysis (adjusted odds ratio, 0.85; 95% CI, 0.71 to 1.02; P = 0.087) or several other subgroup and sensitivity analyses.

CONCLUSIONS: This retrospective analysis found no association between receipt of a peripheral nerve block and a lower incidence of persistent postoperative opioid prescription fulfillment in ambulatory shoulder surgery patients.

PMID:34525173 | DOI:10.1097/ALN.0000000000003962

PLoS One. 2021 Sep 15;16(9):e0257091. doi: 10.1371/journal.pone.0257091. eCollection 2021.

ABSTRACT

What makes written text appealing? In this registered report protocol, we propose to study the linguistic characteristics of news headline success using a large-scale dataset of field experiments (A/B tests) conducted on the popular website Upworthy comparing multiple headline variants for the same news articles. This unique setup allows us to control for factors that can have crucial confounding effects on headline success. Based on prior literature and a pilot partition of the data, we formulate hypotheses about the linguistic features that are associated with statistically superior headlines. We will test our hypotheses on a much larger partition of the data that will become available after the publication of this registered report protocol. Our results will contribute to resolving competing hypotheses about the linguistic features that affect the success of text and will provide avenues for research into the psychological mechanisms that are activated by those features.

PMID:34525115 | DOI:10.1371/journal.pone.0257091

PLoS One. 2021 Sep 15;16(9):e0255017. doi: 10.1371/journal.pone.0255017. eCollection 2021.

ABSTRACT

PURPOSE: Observational studies using routinely collected data are faced with a number of potential shortcomings that can bias their results. Many methods rely on controlling for measured and unmeasured confounders. In this work, we investigate the use of instrumental variables (IV) and quasi-trial analysis to control for unmeasured confounders in the context of a study based on the retrospective Epidemiological Strategy and Medical Economics (ESME) database, which compared overall survival (OS) with paclitaxel plus bevacizumab or paclitaxel alone as first-line treatment in patients with HER2-negative metastatic breast cancer (MBC).

PATIENTS AND METHODS: Causal interpretations and estimates can be made from observation data using IV and quasi-trial analysis. Quasi-trial analysis has the same conceptual basis as IV, however, instead of using IV in the analysis, a “superficial” or “pseudo” randomized trial is used in a Cox model. For instance, in a multicenter trial, instead of using the treatment variable, quasi-trial analysis can consider the treatment preference in each center, which can be informative, and then comparisons of results between centers or clinicians can be informative.

RESULTS: In the original analysis, the OS adjusted for major factors was significantly longer with paclitaxel and bevacizumab than with paclitaxel alone. Using the center-treatment preference as an instrument yielded to concordant results. For the quasi-trial analysis, a Cox model was used, adjusted on all factors initially used. The results consolidate those obtained with a conventional multivariate Cox model.

CONCLUSION: Unmeasured confounding is a major concern in observational studies, and IV or quasi-trial analysis can be helpful to complement analysis of studies of this nature.

PMID:34525119 | DOI:10.1371/journal.pone.0255017

PLoS One. 2021 Sep 15;16(9):e0257472. doi: 10.1371/journal.pone.0257472. eCollection 2021.

ABSTRACT

In a balanced design, researchers allocate the same number of units across all treatment groups. It has been believed as a rule of thumb among some researchers in agriculture. Sometimes, an unbalanced design outperforms a balanced design. Given a specific parameter of interest, researchers can design an experiment by unevenly distributing experimental units to increase statistical information about the parameter of interest. An additional way of improving an experiment is an adaptive design (e.g., spending the total sample size in multiple steps). It is helpful to have some knowledge about the parameter of interest to design an experiment. In the initial phase of an experiment, a researcher may spend a portion of the total sample size to learn about the parameter of interest. In the later phase, the remaining portion of the sample size can be distributed in order to gain more information about the parameter of interest. Though such ideas have existed in statistical literature, they have not been applied broadly in agricultural studies. In this article, we used simulations to demonstrate the superiority of the experimental designs over the balanced designs under three practical situations: comparing two groups, studying a dose-response relationship with right-censored data, and studying a synergetic effect of two treatments. The simulations showed that an objective-specific design provides smaller error in parameter estimation and higher statistical power in hypothesis testing when compared to a balanced design. We also conducted an adaptive experimental design applied to a dose-response study with right-censored data to quantify the effect of ethanol on weed control. Retrospective simulations supported the benefit of this adaptive design as well. All researchers face different practical situations, and appropriate experimental designs will help utilize available resources efficiently.

PMID:34525126 | DOI:10.1371/journal.pone.0257472

PLoS Comput Biol. 2021 Sep 15;17(9):e1009375. doi: 10.1371/journal.pcbi.1009375. Online ahead of print.

ABSTRACT

Interactions within a population shape the spread of infectious diseases but contact patterns between individuals are difficult to access. We hypothesised that key properties of these patterns can be inferred from multiple infection data in longitudinal follow-ups. We developed a simulator for epidemics with multiple infections on networks and analysed the resulting individual infection time series by introducing similarity metrics between hosts based on their multiple infection histories. We find that, depending on infection multiplicity and network sampling, multiple infection summary statistics can recover network properties such as degree distribution. Furthermore, we show that by mining simulation outputs for multiple infection patterns, one can detect immunological interference between pathogens (i.e. the fact that past infections in a host condition future probability of infection). The combination of individual-based simulations and analysis of multiple infection histories opens promising perspectives to infer and validate transmission networks and immunological interference for infectious diseases from longitudinal cohort data.

PMID:34525092 | DOI:10.1371/journal.pcbi.1009375