Nevin Manimala

Mol Ecol Resour. 2021 Mar 7. doi: 10.1111/1755-0998.13371. Online ahead of print.

ABSTRACT

Strong selection can cause rapid evolutionary change, but temporal fluctuations in the form, direction and intensity of selection can limit net evolutionary change over longer time periods. Fluctuating selection could affect molecular diversity levels and the evolution of plasticity and ecological specialization. Nonetheless, this phenomenon remains understudied, in part because of analytical limitations and the general difficulty of detecting selection that does not occur in a consistent manner. Herein, I fill this analytical gap by presenting an approximate Bayesian computation (ABC) method to detect and quantify fluctuating selection on polygenic traits from population-genomic time-series data. I propose a model for environment dependent phenotypic selection. The evolutionary genetic consequences of selection are then modeled based on a genotype-phenotype map. Using simulations, I show that the proposed method generates accurate and precise estimates of selection when the generative model for the data is similar to the model assumed by the method. Performance of the method when applied to an evolve-and-resequence study of host adaptation in the cowpea seed beetle (Callosobruchus maculatus) was more idiosyncratic and depended on specific analytical choices. Despite some limitations, these results suggest the proposed method provides a powerful approach to connect causes of (variable) selection to traits and genome-wide patterns of evolution. Documentation and open source computer software (fsabc) implementing this method are available from GitHub (https://github.com/zgompert/fsabc.git).

PMID:33682340 | DOI:10.1111/1755-0998.13371

Mol Ecol Resour. 2021 Mar 8. doi: 10.1111/1755-0998.13355. Online ahead of print.

ABSTRACT

Inferring the frequency and mode of hybridization among closely related organisms is an important step for understanding the process of speciation and can help to uncover reticulated patterns of phylogeny more generally. Phylogenomic methods to test for the presence of hybridization come in many varieties and typically operate by leveraging expected patterns of genealogical discordance in the absence of hybridization. An important assumption made by these tests is that the data (genes or SNPs) are independent given the species tree. However, when the data are closely linked, it is especially important to consider their nonindependence. Recently, deep learning techniques such as convolutional neural networks (CNNs) have been used to perform population genetic inferences with linked SNPs coded as binary images. Here, we use CNNs for selecting among candidate hybridization scenarios using the tree topology (((P₁ , P₂ ), P₃ ), Out) and a matrix of pairwise nucleotide divergence (d_XY ) calculated in windows across the genome. Using coalescent simulations to train and independently test a neural network showed that our method, HyDe-CNN, was able to accurately perform model selection for hybridization scenarios across a wide breath of parameter space. We then used HyDe-CNN to test models of admixture in Heliconius butterflies, as well as comparing it to phylogeny-based introgression statistics. Given the flexibility of our approach, the dropping cost of long-read sequencing and the continued improvement of CNN architectures, we anticipate that inferences of hybridization using deep learning methods like ours will help researchers to better understand patterns of admixture in their study organisms.

PMID:33682305 | DOI:10.1111/1755-0998.13355

J Cosmet Dermatol. 2021 Mar 8. doi: 10.1111/jocd.14048. Online ahead of print.

ABSTRACT

AIM: Alopecia areata (AA) is an inflammatory condition that causes regional shedding without scarring on the hair or eyebrows, eyelashes and beard. In studies conducted, it has been concluded that platelet/lymphocyte ratio (PLR), neutrophil/lymphocyte ratio (NLR) and mean platelet volume (MPV) are significant indicators of systemic inflammation in various diseases. In the present study, our aim is to examine these parameters in AA patients and to investigate their relationship with the disease.

MATERIALS AND METHODS: 135 AA patients and 135 healthy controls who did not have any systemic, inflammatory, infectious or autoimmune diseases were included in this study. Demographic characteristics and complete blood count (CBC) results were analysed retrospectively and recorded and statistical analysis was performed.

RESULTS: PLR, NLR and MPV values were not differ between AA patients and the control group.

CONCLUSION: It can be concluded that PLR, NLR and MPV values are not convenient parameters to show inflammatory response in AA.

PMID:33682292 | DOI:10.1111/jocd.14048

J Cosmet Dermatol. 2021 Mar 8. doi: 10.1111/jocd.14044. Online ahead of print.

ABSTRACT

AIM: To investigate whether acne treatment agent systemic isotretinoin causes susceptibility to COVID-19 disease.

MATERIAL AND METHOD: Patients admitted to a single center due to acne between March 2020 and December 2020 were included. A retrospective analysis was conducted on the medical records of acne patients receiving systemic isotretinoin or topical treatments. The patients with PCR confirmed SARS-CoV-2 infection were recorded.

RESULTS: 302 patients who used isotretinoin and 329 patients who used topical treatment were included in the study. No statistically significant difference was found between the groups in terms of age (p=0,151). It was found that of the 302 patients who used isotretinoin, 33 had PCR test for SARS CoV-2 and 2 of these had PCR positivity, while of the 329 patients who received topical treatment, 45 had PCR test and 5 of these had PCR positivity. No statistically significant difference was found between the groups in terms of having SARS CoV-2 positivity with PCR (p=0,692).

CONCLUSION: Susceptibility to COVID-19 disease was not observed in patients using systemic isotretinoin.

PMID:33682290 | DOI:10.1111/jocd.14044

J Magn Reson Imaging. 2021 Mar 8. doi: 10.1002/jmri.27565. Online ahead of print.

ABSTRACT

BACKGROUND: It is feasible to use magnetic resonance (MR)-based radiomics to distinguish high-grade from low-grade prostate cancer (PCa), but radiomics model performance based on fully automated segmentation remains unknown.

PURPOSE: To develop and test radiomics models based on manually or automatically gained masks on apparent diffusion coefficient (ADC) maps to predict high-grade (Gleason score ≥ 4 + 3) PCa at radical prostatectomy (RP).

STUDY TYPE: Retrospective.

POPULATION: A total of 176 patients (94 high-grade PCa and 82 low-grade PCa) with complete RP, preoperative biopsy, and multiparametric magnetic resonance imaging (mpMRI) were retrospectively recruited and randomly divided into training (N = 123) and test (N = 53) cohorts.

FIELD STRENGTH/SEQUENCE: Using a 3.0-T MR scanner, ADC maps were calculated from diffusion-weighted imaging (b values = 0, 1400 s/mm² , echo planar imaging).

ASSESSMENT: Two radiologists segmented the whole prostate gland and the most index prostate lesion. Automatic segmentation of the prostate and the lesion were performed. Four radiomics models were constructed using four masks (manual/automatic prostate gland/PCa lesion segmentation). According to the standard reference of the RP histopathologic assessment, the performance of each radiomics models was compared with that of biopsy and Prostate Imaging Reporting and Data System version 2.1 (PI-RADS) assessment.

STATISTICAL TESTS: A receiver operating characteristic curve analysis was employed to estimate the area under the curve (AUC) values of the models. The AUCs of the four models, biopsy, and PI-RADS assessment were compared using the DeLong test.

RESULTS: The four radiomics models yielded AUCs of 0.710, 0.731, 0.726, and 0.709 in the test cohort, respectively; biopsy and PI-RADS assessment yielded AUCs of 0.793 and 0.680, respectively. No significant differences were found among model, biopsy, and PI-RADS assessment comparisons (P = 0.132-0.988).

DATA CONCLUSION: To distinguish high-grade from low-grade PCa, radiomics models based on automatic segmentation on ADC maps exhibit approximately the same diagnostic efficacy as manual segmentation and biopsy, highlighting the possibility of a fully automatic workflow combining automated segmentation with radiomics analysis.

EVIDENCE LEVEL: 4 TECHNICAL EFFICACY: Stage 2.

PMID:33682286 | DOI:10.1002/jmri.27565

Jpn J Nurs Sci. 2021 Mar 7:e12411. doi: 10.1111/jjns.12411. Online ahead of print.

ABSTRACT

AIM: This study aims to explore the effect of integrated traditional Chinese and Western medicine management mode on nursing care of patients with coronavirus disease 2019 (COVID-19).

METHODS: The study included 142 COVID-19 patients hospitalized in Huoshenshan Hospital from February to March 2020. Nursing measures in the treatment (n = 111) and control (n = 31) groups included integrated management care and usual care. The integrated management model had eight components: WeChat group management, early Traditional Chinese Medicine (TCM) treatment, emotional nursing, music therapy, observation of tongue coating and pulse, vital Qi strengthening, preventing recurrence after recovery, and an individualized follow-up scheme. The endpoints included clinical outcome, recovery time of clinical symptoms and signs, days of hospital stay, and survival without intensive care unit (ICU) admission.

RESULTS: Recovery time from clinical symptoms such as fever, cough, shortness of breath, muscle aches, and fatigue in the treatment group was shorter than that in the control group. Less time was required to show negative chest computed tomography findings in the treatment group than in the control group (13.0 ± 2.8 vs. 16.7 ± 3.9, p < .025). The lengths of hospital stay in the two groups were 16.4 ± 7.3 days (treatment group) and 24.4 ± 4.8 days (control group) (p < .001). Kaplan-Meier curves for survival without ICU transfer showed statistical difference between the two groups (χ² = 5.427, p = .020).

CONCLUSIONS: Our study shows that the integrated management mode can relieve the symptoms of patients faster, shorten hospital stay and disease course, and reduce the rate of ICU transfers.

PMID:33682284 | DOI:10.1111/jjns.12411

Aust Endod J. 2021 Mar 8. doi: 10.1111/aej.12482. Online ahead of print.

ABSTRACT

AIM: To compare the effectiveness of smear layer and debris removal in the final rinse of curved canals of permanent molars using different commercially available irrigant activation devices.

METHODS: The mesial roots of 74 extracted maxillary and mandibular molars were instrumented using the Mtwo nickel-titanium rotary system (VDW GmbH, Munich, Germany). They were then randomly assigned to one of three groups, varying in their final rinse protocol. Group 1 (n = 15) – conventional needle irrigation with 4% NaOCl; Group 2 (n = 19) – EndoActivator® (Dentsply Tulsa Dental Specialties, Tulsa, OK, USA) with 4% NaOCl; Group 3 (n = 17) – XP-endo® Finisher (FKG Dentaire SA, La Chaux-de-Fonds, Switzerland) with 4% NaOCl. After the final rinse, all canals were flushed with 1 mL 15% EDTA for 60 s and then flushed with saline. The roots were split longitudinally and prepared for scanning electron microscope imaging. ImageJ for Windows was utilised to assess the images for smear layer removal, while two blinded investigators assessed debris presence in the middle and apical thirds using a 5-point scale.

RESULTS: There was no significant difference in smear layer and debris removal between treatment and control groups in the same canal zones. A significant difference was noted across different canal zones both within and across the groups.

CONCLUSION: There is no statistically significant difference in effectiveness between activated irrigation techniques and manual activation. Further investigations are required to evaluate all methods available and determine the most efficient technique to irrigate successfully.

PMID:33682268 | DOI:10.1111/aej.12482

J Anim Breed Genet. 2021 Mar 8. doi: 10.1111/jbg.12542. Online ahead of print.

ABSTRACT

A total of 184 Djallonké (West African Dwarf) sheep of Burkina Faso were analysed for Copy Number Variations (CNV) using Ovine 50 K SNP BeadChip genotyping data and two different CNV calling platforms: PennCNV and QuantiSNP. Analyses allowed to identify a total of 63 candidate Copy Number Variations Regions (CNVR) on 11 different ovine chromosomes covering about 82.5 Mb of the sheep genome. Gene-annotation enrichment analysis allowed to identify a total of 751 potential candidate ovine genes located in the candidate CNVR bounds. Functional annotation allowed to identify five statistically significant Functional Clusters (FC; enrichment factor > 1.3) involving 61 candidate genes. All genes forming significantly enriched FC were located on ovine chromosome (OAR) 21. FC1 (22 genes including PAG4 and PAG6) and FC5 (three genes: CTSC, CTSW and CTSF), coding proteases (peptidases and cathepsins, respectively), were involved in reproductive performance and modulation of gestation. Both FC3 and FC4 were involved in inflammatory and immunologic response through coding serum amyloid A and B-box-type zinc finger proteins, respectively. Finally, FC2 consisted of 27 genes (including OR10G6 and OR8B8) involved in olfactory receptor activity, key for animals adapting to new food resources. CNVR identified on at least 15% of individuals were considered CNVR hotspots and further overlapped with previously reported quantitative trait loci (QTL). CNVR hotspots spanning genes putatively involved with lipid metabolism (SKP1, TCF7, JADE2, UBE2B and SAR1B) and differential expression in mammary gland (SEC24A and CDKN2AIPNL) on OAR5 and dairy traits (CCDC198 and SLC35F4) on OAR7 overlapped with QTL associated with lipid metabolism, milk protein yield and milk fat percentage. Information obtained from local sheep populations naturally adapted to harsh environments contributes to increase our understanding of the genomic importance of CNV.

PMID:33682236 | DOI:10.1111/jbg.12542

J Nurs Manag. 2021 Mar 7. doi: 10.1111/jonm.13302. Online ahead of print.

ABSTRACT

AIM: To understand the situational profiles of clinical nurse managers’ transformational leadership practices in Saudi hospitals.

BACKGROUND: Clinical nurse managers’ effective leadership may enable registered nurses to provide safe patient care.

METHODS: This included 29 clinical nurse managers and 318 registered nurses from three Saudi hospitals. Data were collected using the leadership practice inventory self-assessment and the leadership practice inventory-observer.

RESULTS: Significant difference between self and observer-assessed transformational leadership practices of clinical nurse managers was found. There was a significant difference in transformational leadership practice between Saudi and non-Saudi clinical nurse managers. Ward experience of clinical nurse managers was statistically positively associated with higher ratings of ‘enabling others to act’. Length of clinical nurse managers’ experience was associated with ‘enabling others to act’ and ‘encouraging the heart’ practices.

CONCLUSION: Clinical nurse managers rated their transformational leadership performance higher than that reported by registered nurses. Further, non-Saudi clinical nurse managers working in Saudi hospitals over-estimated the extent of their transformational leadership practices.

PMID:33682226 | DOI:10.1111/jonm.13302

J Cosmet Dermatol. 2021 Mar 8. doi: 10.1111/jocd.14049. Online ahead of print.

ABSTRACT

BACKGROUND: Low dose (<5mg) oral minoxidil (OM) seems a promising option for male androgenetic alopecia (MAGA).

AIM: To evaluate the role of oral minoxidil 1.25mg versus oral minoxidil 2.5mg along with platelet rich plasma in AGA METHODS: Group A consisted of fourty seven patients which included patients on OM 1.25mg daily and Platelet rich plasma therapy and Group B consisted of patients on OM 2.5 mg daily and Platelet rich plasma therapy. Photographs were taken before and after treatment along with trichoscopic evaluation. Selection of the dermoscopic variables was based on the published literature.

RESULTS: At 24 weeks, marked improvement on GCP were seen in 19 (19/47;40.4%) in Group A and 28 (28/48;58.3%) patients in Group B with P value of 0.058. The total increase in total hair/cm2 was around 24 and 36 in group A and B respectively with P>0.05. The percentage increase in mean total hair count/cm² after 6 month of treatment was 15.41% in group A and 22.15% in group B, but they were not statistically significant. The patient satisfaction score on a likert scale between both group were statistically significant.

CONCLUSION: This is a pilot study where OM along with PRP at different dosage has been compared, this can be used in patients who are a bit apprehensive on taking finasteride or dutasteride and are less responsive to topical minoxidil.

PMID:33682223 | DOI:10.1111/jocd.14049