Tag: pubmed

Bioinformatics. 2022 Feb 21:btac110. doi: 10.1093/bioinformatics/btac110. Online ahead of print.

ABSTRACT

MOTIVATION: microRNAs are important post-transcriptional regulators of gene expression, but the identification of functionally relevant targets is still challenging. Recent research has shown improved prediction of microRNA-mediated repression using a biochemical model combined with empirically-derived k-mer affinity predictions, however these findings are not easily applicable.

RESULTS: We translate this approach into a flexible and user-friendly bioconductor package, scanMiR, also available through a web interface. Using lightweight linear models, scanMiR efficiently scans for binding sites, estimates their affinity, and predicts aggregated transcript repression. Moreover, flexible 3′-supplementary alignment enables the prediction of unconventional interactions, such as bindings potentially leading to target-directed microRNA degradation or slicing. We showcase scanMiR through a systematic scan for such unconventional sites on neuronal transcripts, including lncRNAs and circRNAs. Finally, in addition to the main bioconductor package implementing these functions, we provide a user-friendly web application enabling the scanning of sequences, the visualization of predicted bindings, and the browsing of predicted target repression.

AVAILABILITY: scanMiR and companion packages are implemented in R, released under the GPL-3 and accessible on Bioconductor (https://bioconductor.org/packages/release/bioc/html/scanMiR.html) as well as through a shiny web server (https://ethz-ins.org/scanMiR/).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:35188178 | DOI:10.1093/bioinformatics/btac110

Elife. 2022 Feb 21;11:e72707. doi: 10.7554/eLife.72707.

ABSTRACT

The prevalence of multicellular organisms is due in part to their ability to form complex structures. How cells pack in these structures is a fundamental biophysical issue, underlying their functional properties. However, much remains unknown about how cell packing geometries arise, and how they are affected by random noise during growth – especially absent developmental programs. Here, we quantify the statistics of cellular neighborhoods of two different multicellular eukaryotes: lab-evolved ‘snowflake’ yeast and the green alga Volvox carteri. We find that despite large differences in cellular organization, the free space associated with individual cells in both organisms closely fits a modified gamma distribution, consistent with maximum entropy predictions originally developed for granular materials. This ‘entropic’ cellular packing ensures a degree of predictability despite noise, facilitating parent-offspring fidelity even in the absence of developmental regulation. Together with simulations of diverse growth morphologies, these results suggest that gamma-distributed cell neighborhood sizes are a general feature of multicellularity, arising from conserved statistics of cellular packing.

PMID:35188101 | DOI:10.7554/eLife.72707

Clin Exp Optom. 2022 Feb 20:1-11. doi: 10.1080/08164622.2022.2033603. Online ahead of print.

ABSTRACT

CLINICAL RELEVANCE: This paper provides eye care practitioners with important information about the potential side effects of 0.01% atropine.

BACKGROUND: Eye care practitioners routinely administer 0.01% atropine eye drops nightly to slow the progression of myopia, but nobody has assessed accommodative lag or facility, near phoria, intraocular pressure or comfort of drop administration.

METHODS: All 21- to 30-year-old adults with no history of accommodative issues or therapy were eligible. During the baseline visit, participants underwent testing related to potential side effects. Participants then administered one drop of 0.01% atropine nightly to both eyes, and all tests were repeated 1 week later.

RESULTS: The average ± standard deviation age of the 31 participants was 23.9 ± 1.6 years, 71% were female, and 81% were Caucasian. The only significant changes were an increase in photopic pupil size from 4.9 ± 0.8 at baseline to 5.1 ± 0.6 mm after 1 week (paired sample t-test, p = 0.002) and an increase of the average intraocular pressure of the two eyes from 15.6 ± 2.7 to 16.7 ± 3.1 mmHg (paired-sample t-test, p = 0.003), but neither of these changes was clinically meaningful. There were no other statistically significant differences before and after 1-week administration of 0.01% atropine for any of the vision, accommodation, reading speed or subjective side effects. When asked how likely they would be to take the atropine drops to delay the onset of myopia on a scale from 1 (definitely not) to 10 (definitely would), participants replied with an average of 8.2 ± 2.0 after taking atropine eye drops for 1 week (paired-sample t-test, p = 0.81).

CONCLUSION: Nightly administration of 0.01% atropine did not result in any clinically meaningful symptoms, so patients would be very likely to take the drops to delay the onset of myopia.

PMID:35188076 | DOI:10.1080/08164622.2022.2033603

J Int Neuropsychol Soc. 2022 Feb 21:1-11. doi: 10.1017/S1355617722000091. Online ahead of print.

ABSTRACT

OBJECTIVE: To determine whether the DCTclock can detect differences across groups of patients seen in the memory clinic for suspected dementia.

METHOD: Patients (n = 123) were classified into the following groups: cognitively normal (CN), subtle cognitive impairment (SbCI), amnestic cognitive impairment (aMCI), and mixed/dysexecutive cognitive impairment (mx/dysMCI). Nine outcome variables included a combined command/copy total score and four command and four copy indices measuring drawing efficiency, simple/complex motor operations, information processing speed, and spatial reasoning.

RESULTS: Total combined command/copy score distinguished between groups in all comparisons with medium to large effects. The mx/dysMCI group had the lowest total combined command/copy scores out of all groups. The mx/dysMCI group scored lower than the CN group on all command indices (p < .050, all analyses); and lower than the SbCI group on drawing efficiency (p = .011). The aMCI group scored lower than the CN group on spatial reasoning (p = .019). Smaller effect sizes were obtained for the four copy indices.

CONCLUSIONS: These results suggest that DCTclock command/copy parameters can dissociate CN, SbCI, and MCI subtypes. The larger effect sizes for command clock indices suggest these metrics are sensitive in detecting early cognitive decline. Additional research with a larger sample is warranted.

PMID:35188095 | DOI:10.1017/S1355617722000091

J Matern Fetal Neonatal Med. 2022 Feb 20:1-8. doi: 10.1080/14767058.2022.2040475. Online ahead of print.

ABSTRACT

PURPOSE: Vitamin D deficiency is common during pregnancy and may cause complications such as preterm labor (PTL). This study was aimed to investigate the effect of the vitamin D-binding protein (VDBP) rs7041 genotype, which has a significant effect on vitamin D metabolism and PTL.

METHODS: This cross-sectional study was conducted with 32 pregnant women who had spontaneous PTL and 54 pregnant women who had no specific findings as a control group. Serum total vitamin D 25-hydroxy vitamin D (25(OH)D) levels were measured using the Elecsys Vitamin D Total Kit. VDBP was measured using a VDBP Quantikine ELISA Kit. The levels of bioavailable 25(OH)D were calculated based on the total 25(OH)D and VDBP concentrations. DNA was extracted using the DNeasy Blood and Tissue Kit. Single nucleotide polymorphisms (rs7041) in GC were analyzed using a TaqMan SNP Genotyping Assay Kit. The unpaired t-test, Chi-squared, and ANCOVA tests were performed. Firth’s penalized logistic regression was applied. The area under the curve (AUC) was calculated and the cutoff value was determined. All statistical analyses were performed using R version 4.0.3 (R Foundation for Statistical Computing, Vienna, Austria).

RESULTS: Total 25(OH)D levels were not significantly different between the two groups. Bioavailable 25(OH)D was significantly decreased in PTL women (p= .011), and VDBP was significantly increased in PTL women (p= .004) compared to the controls. Bioavailable 25(OH)D was lower in women with GT/TG and TT rs7041 genotypes than in those with GG, with statistical significance in women with the TT allele (p= .048). VDBP was higher in women with GT/TG and TT than those with GG, but there was no statistical significance. In PTL prevalence, bioavailable 25(OH)D and VDBP, the odds ratio increased by 1.463 times in GT/TG (p= .728) and increased by 1.675 times in TT compared to the GG allele (p= .640). In receiver operating characteristic (ROC) analysis for bioavailable 25(OH)D and VDBP, the AUC was 0.665 and 0685, respectively. The optimum cutoff of bioavailable 25(OH)D and VDBP levels for the diagnosis of PTL was calculated as 0.6 ng/mL and 523 µg/mL, respectively.

CONCLUSIONS: Pregnant women with the VDBP rs7041(c.1296 T > G) T allele genotype had reduced serum levels of bioavailable 25(OH)D and were more likely to develop PTL. Therefore, if the T allele is found in the VDBP rs7041 SNP genotyping test before or during pregnancy, more careful prenatal care may be required because of the increased risk of PTL.

PMID:35188037 | DOI:10.1080/14767058.2022.2040475

Gynecol Endocrinol. 2022 Feb 21:1-5. doi: 10.1080/09513590.2022.2040474. Online ahead of print.

ABSTRACT

OBJECTIVE: To explore the influence of the one-day diabetes mellitus (DM) clinic management model on blood glucose control and prognosis in patients with gestational diabetes mellitus (GDM).

METHODS: A total of 930 patients diagnosed with GDM by oral glucose tolerance test screening at 24-28 weeks of gestation were selected from those who underwent outpatient prenatal checkups at our hospital and were randomly divided into one-day DM clinic group (n = 509) and control group (n = 421). A one-day DM clinic intervention was conducted in the one-day DM clinic group, and individualized dietary interventions and exercise instruction were given in the control group.

RESULTS: The compliance rates of fasting blood glucose and two-hour postprandial blood glucose (2-h PPBG) were higher in the one-day DM clinic group than in the control group (p < .05). The compliance rates of the oral glucose tolerance test and insulin release test were higher in the one-day DM clinic group than in the control group (p < .05). There existed statistically significant differences in fasting blood glucose before delivery, together with the difference between fasting blood glucose at enrollment and before delivery and the difference between glycated hemoglobin at enrollment and before delivery (p < .05).

CONCLUSION: The one-day diabetes mellitus clinic management model is more conducive to blood glucose control in patients with GDM and more conducive to the recovery of blood glucose and islet function in patients with GDM after delivery and to reduce the occurrence of adverse pregnancy outcomes.

PMID:35188053 | DOI:10.1080/09513590.2022.2040474

Nutr Cancer. 2022 Feb 21:1-14. doi: 10.1080/01635581.2021.2019284. Online ahead of print.

ABSTRACT

The aim of this systematic review and meta-analysis was to investigate the effects of resistant starch (RS) on inflammation and oxidative stress related indicators. PubMed, Embase and The Cochrane library were systematically searched to find randomized controlled trials (RCTs) of RS intervention up to February 2020. We used from the effect size, as estimated by the standardized mean difference (SMD) with 95% confidence intervals (95%CI) to perform the random method meta-analysis, with P value ≦0.05 as statistically significant. The 16 included trials with 17 effect sizes included a total of 739 participants in this paper. The intervention duration was from 2 weeks to 3 months. The analysis indicated that RS decreases the levels of tumor necrosis factor-α (TNF-α) (SMD = -0.711; 95%CI: -1.227, -0.194; P = 0.007) and interleukin 6 (IL-6) (SMD = -0.609; 95%CI: -0.924, -0.294; P < 0.001), increases total antioxidant capacity (TAC) (SMD = 2.543, 95% CI: 0.069: 5.017, P = 0.044). No significant effects on C-reactive protein (CRP) (SMD = -0.583; 95%CI: -1.270, 0.104; P = 0.096), superoxide dismutase (SOD) (SMD = 0.091; 95%CI: -0.156, 0.338; P = 0.471), and malondialdehyde (MDA) (SMD = -0.320; 95%CI: -0.907, 0.266; P = 0.285). Subgroup analysis shown that CRP level significant reduced in subjects from the east (SMD = -1.501; 95%CI: -2.662, -0.340; P = 0.011) or suffering from diseases (SMD: -1.057; 95%CI: -1.999, -0.115; P = 0.028).Supplemental data for this article is available online at https://doi.org/10.1080/01635581.2021.2019284.

PMID:35188032 | DOI:10.1080/01635581.2021.2019284

Ear Nose Throat J. 2022 Feb 21:1455613221076786. doi: 10.1177/01455613221076786. Online ahead of print.

ABSTRACT

OBJECTIVE: This study aims to explore the effects of laryngopharyngeal reflux disease (LPRD) and proton pump inhibitor (PPI) treatment on Eustachian tube function in patients with obstructive sleep apnea (OSA).

METHODS: The Eustachian tube score-7 (ETS-7) was observed before and after PPI treatment in the control group, OSA only group, and OSA + LPRD group.

RESULTS: Age, sex, smoking history, and drinking history showed no differences among 3 groups (P > .05). The body mass index (BMI) in the control group was lower than that in other groups (P < .017). Before PPI treatment, the abnormality rate of ETS-7 in the OSA + LPRD group statistically differed from that in the control group and the OSA only group (P < .017). After PPI treatment, the abnormality rate of ETS-7 in the OSA + LPRD group exhibited no significant differences compared with that in the control group and the OSA only group (P > .017), and it declined remarkably compared with that before PPI treatment (75% vs 35%, χ² = 13.334, P = .001). Moreover, the multivariate analysis revealed that only LPRD had an independent correlation with the abnormality of ETS-7 (OR = 1.245, 95% CI: 1.759-6.861, P = .000).

CONCLUSION: In view of its high incidence in OSA patients, LPRD may be a considerable factor for the high incidence of abnormality rate of ETS-7 in OSA patients, and PPI therapy is of significant value in improving Eustachian tube function in OSA patients with LPRD.

PMID:35187968 | DOI:10.1177/01455613221076786

Urologia. 2022 Feb 21:3915603221078263. doi: 10.1177/03915603221078263. Online ahead of print.

ABSTRACT

PURPOSE: To investigate the prevalence of overactive bladder (OAB) in patients with obstructive sleep apnea syndrome (OSAS) and the factors affecting it.

MATERIALS AND METHODS: A total of 255 patients were included in this prospectively designed study. Among all patients, 166 were male, 89 were female; 213 patients were married and 42 were single. All patients underwent polysomnography. All patients completed the OAB-V8 form. OSAS was diagnosed via polysomnography. OAB was diagnosed via OABV8. The participants were evaluated as patients with and without OAB and those with and without OSAS. SPSS for Windows version 18.0 software was used for the statistical analysis and the level of significance was set at α = 0.05.

RESULTS: The prevalence of OAB was high among the OSAS patients (66.3%, n = 136). Age, body mass index, waist circumference, marital status, oxygen desaturation index (ODI4) ⩾4%, apneahypopnea index (AHI), the number and duration of decreases in O₂ saturation below 90%, wake after sleep onset (WASO) duration, and groups, and OSAS severity were different in the OAB group (p < 0.05). Duration and number of O₂ saturation <90%, and ODI4 are higher in the OSAS group and OAB group (p < 0.05). In multivariate logistic regression analysis, AHI, WASO, age, and marital status were the factors influencing OAB.

CONCLUSION: OAB is seen at a high rate in OSAS patients. Hypoxia is the main basis for both diseases and probably it is the common pathway. AHI, WASO, age, and marital status can provide valuable information to physicians for predicting OAB.

PMID:35188003 | DOI:10.1177/03915603221078263

Eur J Ophthalmol. 2022 Feb 21:11206721221080818. doi: 10.1177/11206721221080818. Online ahead of print.

ABSTRACT

BACKGROUND: To assess the benefit of macular spectral-domain optical coherence tomography (SD-OCT) as a part of the routinary preoperative study of patients undergoing cataract surgery.

METHODS: A prospective single-center study study was performed. Consecutive patients with normal biomicroscopic funduscopy, moderate cataract and no history of ophthalmological pathologies were enrolled. All patients underwent macular SD-OCT. The obtained images were analysed by a general ophthalmologist and two retina specialists. Incidence of macular pathology and its relation to age and comorbidities were assessed.

RESULTS: Eight-hundred and thirty-six eyes of 419 patients were enrolled in this study. All images were analysed telematically by a general ophthalmologist. Forty-nine eyes were excluded due to insufficient quality of the obtained images. Abnormal images were observed in 156 eyes (18.6%), including age-related macular degeneration in 68 (8.2%), epiretinal membrane (ERM) in 67 (8.0%), cystoid macular edema in 3 eyes (0.4%), among others. Diagnostics with severe impact on patient visual prognosis were observed in 16 eyes (3.82%) from 12 patients. The relationship between incidence of macular pathologies and age or comorbidities was not statistically significant. To assess accuracy of the first observer, images were subsequently analysed by two retinologists. The kappa index of concordance was 0.80 and 0.85.

CONCLUSIONS: Implementing a systematic macular SD-OCT as a preoperative test prior to cataract surgery would improve quality of postoperative visual prognosis information. A general ophthalmologist would be suitable to screen for pathology through macular OCT images.

PMID:35187961 | DOI:10.1177/11206721221080818