Category: Statistics

BMC Bioinformatics. 2022 Oct 7;23(1):415. doi: 10.1186/s12859-022-04972-9.

ABSTRACT

BACKGROUND: Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological experiments, in whole organisms, tissues, and at the single cell level. Collectively, this is a vast comparative dataset on transcriptional processes across organisms. Yet, due to technical differences between the studies (sequencing, experimental design, and analysis) extracting usable comparative information and conducting meta-analyses remains challenging.

RESULTS: We introduce Comparative RNA-Seq Metadata Analysis Pipeline (CoRMAP), a meta-analysis tool to retrieve comparative gene expression data from any RNA-Seq dataset using de novo assembly, standardized gene expression tools and the implementation of OrthoMCL, a gene orthology search algorithm. It employs the use of orthogroup assignments to ensure the accurate comparison of gene expression levels between experiments and species. Here we demonstrate the use of CoRMAP on two mouse brain transcriptomes with similar scope, that were collected several years from each other using different sequencing technologies and analysis methods. We also compare the performance of CoRMAP with a functional mapping tool, previously published.

CONCLUSION: CoRMAP provides a framework for the meta-analysis of RNA-Seq data from divergent taxonomic groups. This method facilitates the retrieval and comparison of gene expression levels from published data sets using standardized assembly and analysis. CoRMAP does not rely on reference genomes and consequently facilitates direct comparison between diverse studies on a range of organisms.

PMID:36207678 | DOI:10.1186/s12859-022-04972-9

BMC Med Res Methodol. 2022 Oct 7;22(1):263. doi: 10.1186/s12874-022-01740-4.

ABSTRACT

BACKGROUND: Biotechnology in genomics, such as sequencing devices and gene quantification software, has proliferated and been applied to clinical settings. However, the lack of standards applicable to it poses practical problems in interoperability and reusability of the technology across various application domains. This study aims to visualize and identify the standard trends in clinical genomics and to suggest areas on which standardization efforts must focus.

METHODS: Of 16,538 articles retrieved from PubMed, published from 1975 to 2020, using search keywords “genomics and standard” and “clinical genomic sequence and standard”, terms were extracted from the abstracts and titles of 15,855 articles. Our analysis includes (1) network analysis of full phases (2) period analysis with five phases; (3) statistical analysis; (4) content analysis.

RESULTS: Our research trend showed an increasing trend from 2003, years marked by the completion of the human genome project (2003). The content analysis showed that keywords related to such concepts as gene types for analysis, and analysis techniques were increased in phase 3 when US-FDA first approved the next-generation sequencer. During 2017-2019, oncology-relevant terms were clustered and contributed to the increasing trend in phase 4 of the content analysis. In the statistical analysis, all the categories showed high regression values (R² > 0.586) throughout the whole analysis period and phase-based statistical analysis showed significance only in the Genetics terminology category (P = .039^*) at phase 4.

CONCLUSIONS: Through comprehensive trend analysis from our study, we provided the trend shifts and high-demand items in standardization for clinical genetics.

PMID:36207671 | DOI:10.1186/s12874-022-01740-4

BMC Ophthalmol. 2022 Oct 7;22(1):401. doi: 10.1186/s12886-022-02622-5.

ABSTRACT

BACKGROUND: High-intensity focused ultrasound cyclo-plasty (UCP) is a recently developed glaucoma surgery. This study collected and analysed the clinical data of patients who underwent UCP to observe the efficacy and safety of this surgery in Chinese glaucoma patients.

METHODS: This was a retrospective study. The clinical data of all the patients who underwent UCP at Affiliated Foshan Hospital, Southern Medical University, were collected and analysed to evaluate the efficacy and safety of UCP. The main outcome measure was intraocular pressure, and the secondary outcome measures were best corrected visual acuity (logMAR) and complications.

RESULTS: Fifty-eight patients (61 eyes) were recruited for this study. IOP was dramatically decreased during the 12 months after UCP (p<0.05). The median IOP reduction during the 18 months post-procedure was more than 30%. The greatest reduction was at 1 month post-UCP (60.86%). The qualified success rate was more than 60% during the 18-month follow-up (Fig. 1). Poor follow up was found after 6-month post-UCP. The highest success rate was obtained at 7 days post-UCP (94.55%). No statistically significant decrease in BCVA in the vison group was observed at the follow-up visits, except for 1 day post-UCP. There was a statistically significant reduction in the use of IOP lowering medications during the 6 months post-UCP. No severe complications occurred.

CONCLUSION: UCP is a safe and effective procedure for primary and refractive glaucoma at least during the 6 months post-UCP procedure. Studies with longer follow-up time and better follow up are needed to further confirm the long-term efficacy and safety of UCP in Chinese glaucoma patients.

PMID:36207670 | DOI:10.1186/s12886-022-02622-5

Atten Percept Psychophys. 2022 Oct 7. doi: 10.3758/s13414-022-02573-5. Online ahead of print.

ABSTRACT

In dynamic environments, statistical learning of spatial and temporal regularities guides visual attention in space and time. In the current study, we explored whether and how combined spatiotemporal regularities regarding target events guide visual attention. In three experiments, participants performed the additional singleton task. They were asked to search for a target stimulus with a unique shape among five non-target distractors and respond to the orientation of a line inside the target. Unbeknownst to the participants, the moment in time that the search display was presented was predictive of the target location. Specifically, the target was more likely to be presented at one high-probability location after a short interval and at another high-probability location after a long interval. The results showed that participants’ performance was better for high-probability locations than for low-probability locations. Moreover, visual search efficiency was greater when the target appeared at the high-probability location after its associated interval than when it occurred there after its nonassociated interval, regardless of whether the distribution of intervals was uniform (Experiment 1), exponential (Experiment 2), or anti-exponential (Experiment 3). Taken together, the results indicate that implicitly learned spatiotemporal regularities dynamically guide visual attention towards the probable target location.

PMID:36207663 | DOI:10.3758/s13414-022-02573-5

Breast Cancer Res Treat. 2022 Oct 7. doi: 10.1007/s10549-022-06746-6. Online ahead of print.

ABSTRACT

PURPOSE: Findings from randomized clinical trials have shown that survival in patients with sentinel lymph node (SLN)-negative breast cancer is noninferior with SLN biopsy (SLNB) alone versus further axillary lymph node dissection (ALND). However, the long-term outcome of these two surgical approaches in pN0 breast cancer patients in real-world setting remains uncertain.

METHODS: We included patients diagnosed with pathologically staged T1-2N0M0 breast cancer between 2000 and 2015 in surveillance, epidemiology, and end results 18-registry database. Patients were considered to have undergone SLNB alone if they had ≤ 5 examined lymph nodes (ELNs), and ALND if they had ≥ 10 ELNs. The outcomes included overall survival (OS) and breast cancer-specific survival. Propensity score analyses by weighting and matching and multivariable Cox regression analysis were performed to minimize treatment selection bias.

RESULTS: We included 309,430 patients (253,501 SLNB and 55,929 ALND). In the weighted cohort, ALND was associated with significantly lower OS (hazard ratio [HR] 1.13; 95% confidence interval [CI] 1.10-1.16) and BCSS (HR 1.16; 95% CI 1.10-1.22) compared with SLNB alone. Both the propensity score-matching model and multivariable Cox model demonstrated a survival benefit for SLNB when compared with ALND. Subgroup analyses for key variables did not change these findings.

CONCLUSION: We found statistically significant differences in OS and BCSS between SLNB and ALND, though the magnitude of these differences was small. Our findings further support that SLNB alone should be the standard of care for patients who do not have metastatic lymph nodes identified during breast cancer surgery.

PMID:36207619 | DOI:10.1007/s10549-022-06746-6

Sci Rep. 2022 Oct 7;12(1):16879. doi: 10.1038/s41598-022-21438-3.

ABSTRACT

The infant mortality rate remains unacceptably high in sub-Saharan African countries. Ethiopia has one of the highest rates of infant death. This study aimed to identify individual-and community-level factors associated with infant death in the rural part of Ethiopia. The data for the study was obtained from the 2016 Ethiopian Demographic and Health Survey. A total of 8667 newborn children were included in the analysis. The multilevel logistic regression model was considered to identify the individual and community-level factors associated with new born mortality. The random effect model found that 87.68% of the variation in infant mortality was accounted for by individual and community level variables. Multiple births (AOR = 4.35; 95%CI: 2.18, 8.69), small birth size (AOR = 1.29; 95%CI: 1.10, 1.52), unvaccinated infants (AOR = 2.03; 95%CI: 1.75, 2.37), unprotected source of water (AOR = 1.40; 95%CI: 1.09, 1.80), and non-latrine facilities (AOR = 1.62; 95%CI: 1.20) were associated with a higher risk of infant mortality. While delivery in a health facility (AOR = 0.25; 95%CI: 0.19, 0.32), maternal age 35-49 years (AOR = 0.65; 95%CI: 0.49, 0.86), mothers receiving four or more TT injections during pregnancy (AOR = 0.043, 95% CI: 0.026, 0.071), and current breast feeders (AOR = 0.33; 95% CI: 0.26, 0.42) were associated with a lower risk of infant mortality. Furthermore, Infant mortality rates were also higher in Afar, Amhara, Oromia, Somalia, and Harari than in Tigray. Infant mortality in rural Ethiopia is higher than the national average. The government and other concerned bodies should mainly focus on multiple births, unimproved breastfeeding culture, and the spacing between the orders of birth to reduce infant mortality. Furthermore, community-based outreach activities and public health interventions focused on improving the latrine facility and source of drinking water as well as the importance of health facility delivery and received TT injections during the pregnancy.

PMID:36207579 | DOI:10.1038/s41598-022-21438-3

J Behav Health Serv Res. 2022 Oct 7. doi: 10.1007/s11414-022-09813-4. Online ahead of print.

ABSTRACT

To inform the potential use of patient-reported depression symptom outcomes as measures of care quality, this study collected and analyzed longitudinal Patient Health Questionnaire (PHQ9) scores among 1,638 patients who screened positive for major depression according to a PHQ9 ≥ 10 across 29 Department of Veterans Affairs facilities. The study found baseline PHQ9, prior mental health visits, physical functioning, and treatment expectancy were consistently associated with subsequent PHQ9 outcomes. No facilities outperformed any others on PHQ9 scores at the 6-month primary endpoint, and the corresponding intra-class coefficient was ≤ .01 for the entire sample (n = 1,214) and 0.03 for the subgroup of patients with new depression episodes (n = 629). Measures of antidepressant receipt, psychotherapy, or treatment intensification were not associated with 6-month PHQ9 scores. PHQ9 outcomes are therefore unlikely to be useful as quality indicators for VA healthcare facilities due to low inter-facility variation, and new care process measures are needed to inform care for patients with chronic depression prevalent in this sample.

PMID:36207569 | DOI:10.1007/s11414-022-09813-4

J Neurovirol. 2022 Oct 7. doi: 10.1007/s13365-022-01051-w. Online ahead of print.

ABSTRACT

Human immunodeficiency virus-associated distal sensory polyneuropathy (HIV-DSP) affects up to 50% of people with HIV and is associated with depression, unemployment, and generally worsened quality of life. Previous work on the cortical mechanism of HIV neuropathy found decreased gray matter volume in the bilateral midbrain, thalamus, and posterior cingulate cortex, but structural connectivity in this context remains under-studied. Here we examine alterations in white matter microstructure using diffusion imaging, hypothesizing that cortical white matter degeneration would be observed in continuation of the peripheral white matter atrophy previously observed in HIV-DSP. Male HIV seropositive patients (n = 57) experiencing varying degrees of HIV neuropathy underwent single-shell diffusion tensor imaging with 51 sampling directions. The scans were pooled using tractography and connectometry to create a quantitative map of white matter tract integrity, measured in generalized fractional anisotropy (GFA). The relationship between GFA and neuropathy severity was evaluated with linear regression. Correction for multiple comparisons was done using false discovery rate (FDR), a statistical method commonly used in genomics and imaging to minimize false positives when thousands of individual comparisons are made. Neuropathy severity was associated with decreased GFA along thalamocortical radiations leading along the lateral thalamus to sensorimotor cortex, with r = -0.405 (p < 0.001; FDR), as well as with the superior bilateral cingulum (r = -0.346 (p < 0.05; FDR)). Among a population of HIV neuropathy patients, greater neuropathy severity was correlated with lower white matter integrity running from midbrain to somatosensory cortex. This suggests ascending deafferentation extending from damaged peripheral nerves further downstream than seen previously, into the axons of third-order neurons. There is also evidence of cingulum degeneration, implying some more complex mechanism beyond the ascending atrophy observed here.

PMID:36207560 | DOI:10.1007/s13365-022-01051-w

S D Med. 2022 Jun;75(6):263-267.

ABSTRACT

INTRODUCTION: The coronavirus pandemic has posed many challenges for healthcare facilities. One patient population particularly affected was pregnant women who delivered during the 2020 year. Many antenatal and postpartum services normally available were altered during the pandemic, including the number of available lactation consultants. This change in the availability of lactation consultants led to a decrease in face-to-face breastfeeding education and support for postpartum women. This study aimed to identify if the coronavirus pandemic had a negative effect on breastfeeding prevalence in a single tertiary healthcare center.

METHOD: This study was a retrospective chart review with data collected from March 1, 2019-March 1, 2021. The study population was defined as pregnant women age 18 and older who delivered at a single hospital. The prevalence of women who stated they intended to exclusively breastfeed during the pandemic (March 1, 2020-March 1, 2021) was compared to the pre-pandemic year (March 1, 2019-Feb. 29, 2020) as a control. This breastfeeding prevalence was also compared to monthly county-specific coronavirus cases from the South Dakota Department of Health.

RESULTS: The prevalence of women who stated they intended to exclusively breastfeed at the time of delivery during the study population was statistically less when compared to the previous pre-pandemic year.

CONCLUSIONS: The coronavirus pandemic has posed many challenges for healthcare facilities. One patient populationThe exclusive breastfeeding prevalence was negatively affected during the coronavirus pandemic in this single tertiary health center. Knowledge of this demonstrates patient fears regarding breastfeeding during a pandemic and the importance of lactation education and consultation.

PMID:36206567

Ultrasound Obstet Gynecol. 2022 Oct 7. doi: 10.1002/uog.26093. Online ahead of print.

ABSTRACT

OBJECTIVE: To evaluate national preterm birth (PTB) prevalence (delivery before 37 weeks) rates in relation to local professional guidelines recommending second trimester ultrasound cervical length measurement.

METHODS: The 2012 guidelines specified cervical length be measured transabdominally, or if not visible transvaginally, at the 19-25 weeks ultrasound anomaly scan; < 25 mm would indicate further work-up and treatment, although the type was unspecified. In 2000, the Israel Ministry of Health issued a legal requirement for the submission of delivery records to a national registry. These data were used to compare PTB prevalence before and after the guidelines, as well as trends within each time period. Information was available on multiple pregnancies, maternal age, and parity, as well as low birth-weight. During 2000-2020 there were 3,403,976 live born infants; 1,797,657 before and 1,606,319 after the guidelines.

RESULTS: PTB prevalence was 7.64% [95% CI 7.52-7.77] before the guidelines and 6.84% [6.43-7.24] afterwards (P<0.0002, 2-tail). Annual PTB prevalence was static in the first period, but declined by 0.18% per annum during the second period. The proportional reduction in PTB prevalence between the periods was 9%, 18% and 24% at 33-36, 28-32 and <28 weeks, respectively. Reduced prevalence was observed among singletons (5.49% vs. 4.83%, P<0.0001), but not among infants in twin or grand multiple pregnancies. This reduction was statistically significant in the 19-39 years age group, and in both primiparous and multiparous women. Even though reductions were also noted in high risk groups (<19 years and over 40 years of age), these did not reach statistical significance. There was a similar reduction in the prevalence of birth-weight under 2,500 g.

CONCLUSIONS: National guidelines on routine cervical length screening were associated with a fall in PTB prevalence. Whilst direct evidence linking screening with prevalence is lacking, considering the alternatives, this is the most likely explanation. Screening can be readily incorporated into the second trimester anomaly scan. This article is protected by copyright. All rights reserved.

PMID:36206549 | DOI:10.1002/uog.26093