Category: Nevin Manimala

Brief Bioinform. 2021 Sep 8:bbab354. doi: 10.1093/bib/bbab354. Online ahead of print.

ABSTRACT

Feature selection is crucial for the analysis of high-dimensional data, but benchmark studies for data with a survival outcome are rare. We compare 14 filter methods for feature selection based on 11 high-dimensional gene expression survival data sets. The aim is to provide guidance on the choice of filter methods for other researchers and practitioners. We analyze the accuracy of predictive models that employ the features selected by the filter methods. Also, we consider the run time, the number of selected features for fitting models with high predictive accuracy as well as the feature selection stability. We conclude that the simple variance filter outperforms all other considered filter methods. This filter selects the features with the largest variance and does not take into account the survival outcome. Also, we identify the correlation-adjusted regression scores filter as a more elaborate alternative that allows fitting models with similar predictive accuracy. Additionally, we investigate the filter methods based on feature rankings, finding groups of similar filters.

PMID:34498681 | DOI:10.1093/bib/bbab354

Exp Clin Transplant. 2021 Sep 8. doi: 10.6002/ect.2021.0284. Online ahead of print.

ABSTRACT

OBJECTIVES: There is scarcity of data on reoccurrence of SARS-CoV-2 infections in kidney transplant recipients.

MATERIALS AND METHODS: We conducted a retrospective multicenter cohort study and identified 13 kidney transplant recipients (10 living and 3 deceased donors) with recurrent COVID-19, and here we report demographics, immunosuppression regimens, clinical profiles, treatments, and outcomes.

RESULTS: COVID-19 second infection rate was 0.9% (13/1350) in kidney transplant recipients with a median age of 46 years; median time interval from transplant to first episode of COVID-19 diagnosis was 9.2 months (interquartile range, 2.2-46.5 months). The most common comorbidities were hypertension (84%) and diabetes (23%). Fever was significantly less common with recurrent COVID-19. COVID-19 severity ranged from asymptomatic (23%), mild (31%), and moderate (46%) during the first infection and asymptomatic (8%), mild (46%), and severe (46%) in the second infection. All 6 kidney transplant recipients with severe second infections died. The median interval between the 2 episodes based upon reverse transcriptase polymerase chain reaction COVID-19- positive tests was 135 days (interquartile range, 71-274 days) without symptoms. Statistically signi – ficant risk factors for mortality were dyspnea (P = .04), disease severity (P = .004), allograft dysfunction (P < .05), higher levels of neutrophil-to-lymphocyte ratio (P = .05), and intensive care unit/ventilator requirement (P = .004). Although our limited resources did not allow for molecular diagnostics and typing, we suggest that these second episodes were reinfections with SARS-CoV-2.

CONCLUSIONS: To our knowledge, this is the largest study of kidney transplant recipients with reoccurring SARS-CoV-2 infection, and we observed 46% mortality.

PMID:34498549 | DOI:10.6002/ect.2021.0284

Anatol J Cardiol. 2021 Sep;25(9):646-652. doi: 10.5152/AnatolJCardiol.2021.51152.

ABSTRACT

OBJECTIVE: Although electrophysiological study (EPS) is one of the most useful diagnostic approaches to detect the cardiac origin of palpitations, there is no clear indication for EPS in patients with palpitation in the absence of documented supraventricular tachycardia (SVT). In this study, we aimed to create a new SVT score model to detect the requirement of EPS in patients with palpitation without documented tachycardia.

METHODS: A total of 154 patients with palpitation were included in this study. To create the SVT score, we considered four main criteria with their subunits. They were severity, frequency, duration, and termination of the symptoms. EPS was performed on all the patients after their scoring assessment.

RESULTS: Median SVT score of induced tachycardia and non-induced patients was determined as 10 and 6 points, respectively; and it was found to be statistically significant; p<0.001. The cut-off value for inducibility was found to be 7.5 points through receiver operating characteristic curve analysis, (94.9% sensitivity, 92.1% specificity), and the area under the curve was determined to be 97.2 (94.8-99.5, p<0.001).

CONCLUSION: According to our new SVT score model, ≥8 points strongly correlates with the inducibility of SVT during EPS.

PMID:34498596 | DOI:10.5152/AnatolJCardiol.2021.51152

N Z Vet J. 2021 Sep 9:1-23. doi: 10.1080/00480169.2021.1978896. Online ahead of print.

ABSTRACT

AIMS: To determine if milk composition, milk yield, live weight, live weight change, breed and heterosis are associated with reproductive performance in dairy cows from two dairy farms under New Zealand grazing conditions.

METHODS: Milk composition was determined in herd tests from 205 Holstein-Friesian (F), 77 Jersey (J) and 351 F×J crossbred cows from two Massey University dairy herds in the 2016 and 2017 production seasons. Mating occurred from October to December in each production season. The start of breeding to first service (SBFS), start of breeding to conception (SBCO), submission rate at 21 days (SR21), pregnancy rate at 21 (PR21) and 42 days (PR42) were calculated for each cow. These traits were analysed using mixed linear models that included fixed effects for herd, production season, regression coefficients of deviation from median calving date, lactation number, proportion of F, F×J heterosis, energy-corrected milk yield (ECMY), percentages of fat, protein and lactose, milk urea nitrogen (MUN), live weight and live weigh change, with random effects for cow and residual error. The variables with binomial distribution were analysed using logistic regression.

RESULTS: Deviation from the herd’s median calving date had a significant effect (p<0.05) on all reproductive traits. Proportion of F was significant (p=0.022) on PR21, and F×J heterosis effects were significant on PR21 (p=0.049) and PR42 (p=0.046). F cows had 17.8% higher PR21 than J cows, and F×J cows had higher reproductive performance than the mean of the two purebreeds. ECMY was negatively associated with SBFS (p=0.001) and SBCO (p=0.001) and positively associated with PR21 (p=0.002) and PR42 (p=0.001). Protein percentage was positively associated (p<0.05) with PR21 and PR42, whereas lactose percentage was negatively associated (p<0.05) with PR21 and PR42. Cows gaining live weight were more likely to become pregnant within 21 days of the start of breeding (p=0.020). Milk urea nitrogen was negatively associated (p=0.042) with SR21.

CONCLUSIONS AND CLINICAL RELEVANCE: This study confirms that breed, heterosis, ECMY, protein and lactose percentages, live weight change and calving date are associated with the reproductive performance of grazing cows. Results from this study contrast with the historical antagonism between milk production and reproductive performance in dairy cattle, demonstrating that well managed cows can achieve high levels of production and good reproductive performance. MUN was not associated with reproductive performance traits, except with SR21.

PMID:34498540 | DOI:10.1080/00480169.2021.1978896

J Sports Sci. 2021 Sep 9:1-9. doi: 10.1080/02640414.2021.1976488. Online ahead of print.

ABSTRACT

The aim of this study was to determine the association of playing style and efficacy variables with football success in a professional football league. Match statistics were obtained from 23 football teams competing in the 2017-2018 and 2018-2019 seasons of the Spanish national league(LaLiga). Offensive and defensive playing style and efficacy variables were calculated. Pearson’s correlation coefficient tests and principal component analysis (PCA) were applied to establish the influence of these variables on the number of points obtained at the end of the season and on the ranking position. In isolation, the efficacy of completion showed the highest association with ranking points and position. A two-dimension PCA explained 77.8% of the variance in the ranking position. In dimension-1 (58.5%), game initiative and attack building, and in dimension-2 (19.3%), efficacy of defensive containment and a lower rate of long passes were within the variables that explained more variance in the ranking position. Success in football, measured by ranking position at the end of the Spanish national league, was associated with several playing style and efficacy variables. Overall, a dominant game style with high efficacy to finish attacking plays, and an offensive game initiative, are most associated with successful football.

PMID:34498545 | DOI:10.1080/02640414.2021.1976488

Eur J Sport Sci. 2021 Sep 9:1-19. doi: 10.1080/17461391.2021.1979103. Online ahead of print.

ABSTRACT

Overhead throwing by cricketers when fielding with different approaches has been described using two-dimensional analysis. Currently, the three-dimensional kinematic and kinetic characteristics of an overhead throw performed by cricketers following a run-up is unknown. Fifteen South African cricketers performed six overhead throws, from a stationary position and with a run-up over 15-20 m prior to fielding a ball, respectively. Kinematic data and ground reaction forces were collected throughout the throwing trials. Joint kinetics were calculated using inverse dynamics. An independent t-test or Mann-Whitney U test was used to determine joint kinetic differences between throwing approaches. Differences between the kinematic waveforms for stationary and run-up throwing approaches were assessed using one-dimensional statistical parametric mapping ANOVA (P<0.05). The shoulder, elbow and thoraco-lumbar joints displayed similar kinematics between throwing approaches. The run-up approach displayed increased hip flexion between 0-34% and 57-100% (F(1, 28) = 6.726;P=0.01) of the throwing cycle; and lumbo-pelvic flexion between 57-65% (F(1, 28) = 6.823;P=0.02) of the throwing cycle; greater shoulder compression (F(1, 28) = 1.036;P=0.02) and posterior force (F(1, 28) = 1.052;P=0.009) at maximum external rotation; yet less superior shoulder force (F(1, 28) = 1.744;P=0.005) and elbow compression (F(1, 28) = 4.331;P=0.03), superior (F(1, 28) = 1.212;P=0.002) and medial (F(1, 28) = 1.370;P=0.03) elbow forces at ball release, when compared to a stationary position. Cricketers maintain similar upper limb kinematics between overhead throwing approaches. However, throwing with a run-up approximately doubles the forces exerted on the shoulder at maximum external rotation, which is most likely caused by the greater dominant hip and lumbo-pelvic flexion noted. This may amplify the potential risk for shoulder injury when throwing.

PMID:34498548 | DOI:10.1080/17461391.2021.1979103

Ann Med. 2021 Dec;53(1):1632-1641. doi: 10.1080/07853890.2021.1974082.

ABSTRACT

BACKGROUND: Disturbances in maternal lipid metabolism may increase the risk of developing pregnancy complications and adverse perinatal outcomes. However, there is no consensus as to what constitutes normal serum lipid ranges during pregnancy. Our study was aimed to establish trimester-specific serum lipid reference intervals (RIs) and investigate the associations between maternal dyslipidaemia and adverse outcomes in a population-based study.

METHODS: The first- and third-trimester lipid profiles were derived from 16,489 singlet pregnant women for regular antenatal check-ups between 2017 and 2019. The serum samples were assayed for total cholesterol (TC), triglycerides (TG), high-density lipoprotein-cholesterol (HDL-C), and low-density lipoprotein-cholesterol (LDL-C) in the institutional clinical laboratory. The trimester-specific lipid RIs were estimated with both of the direct observational and the indirect Hoffmann methods. The associations between maternal lipid profiling and pregnancy complications and perinatal outcomes were assessed statistically.

RESULTS: Serum levels of TC, TG, LDL-C and HDL-C were all increased significantly in the third trimester of pregnancy. There was no significant difference between the observed RIs established with healthy pregnant women and the calculated RIs derived from the Hoffmann method. A trend towards increased risks of gestational complications and adverse perinatal outcomes was observed in the subjects with elevated levels of TC, TG, and LDL-C or decreased level of HDL-C.

CONCLUSIONS: In pregnancy, increased serum levels of TC, TG and LDL-C, and a decreased level of HDL-C posed higher risks of developing pregnancy complications and adverse perinatal outcomes.Key messagesIt is necessary to establish trimester-specific reference intervals for serum lipids including TC, TG, LDL-C and HDL-C that were found significantly increased as the gestational age went up. More importantly, around the upper reference limits of TC, TG and LDL-C (or the lower reference limit of HDL-C), the higher the serum lipid levels were (or the lower the HDL-C level was), the higher risks of developing pregnancy complications and adverse perinatal outcomes were observed.

PMID:34498500 | DOI:10.1080/07853890.2021.1974082

Syst Biol Reprod Med. 2021 Sep 9:1-13. doi: 10.1080/19396368.2021.1965673. Online ahead of print.

ABSTRACT

Recurrent pregnancy loss (RPL) is the most common reproductive failure, reaching 1-5% of women throughout their lives, and having unknown etiology in 50% of the cases. In humans, EGF-CFC1 (Epidermal Growth Factors & Cripto/FRL-1/Cryptic) gene family is composed by TDGF1 and CFC1, two developmental genes. The aim of this study was to investigate the role of EGF-CFC on RPL. To this, multiple approaches were performed; we conducted an expression analysis of TDGF1 and CFC1 using publicly available data from Gene Omnibus Expression (GEO), systems biology analyses and functional prediction; and a molecular analysis carried out in a case-control study. Our GEO analysis showed a decrease in TDGF1 expression in the endometrium (p=0.049) and CFC1 expression in placenta (p=0.015) of women with RPL. Network analysis, gene ontology and literature pointed to a strong connection between EGF-CFC1 gene family to pathways that play key roles during pregnancy, including TGF-β, c-Src/MAPK/AKT, Notch, TNFα, IFNγ and IL-6. A pathogenicity score developed for this gene family showed that the c.-14+1429T>C (rs3806702) variant in the TDGF1 and the p.Arg47Gln (rs201431919) variant in CFC1 gene would be the ones with the highest deleterious effect for RPL. In the case-control study, which involved 149 women with RPL and 159 controls, no statistical difference was observed in the allele and genotype distributions of the variants studied in the two groups. In this study, we performed extensive bioinformatics analysis for biomarker prioritization followed by experimental validation of proposed selected markers. Although there is no statistical difference in the frequencies of these variants between RPL and controls, the expression analysis results suggest that TDGF1 and CFC1 genes might play a role in RPL. In addition, systems biology analyzes raise the hypothesis that genes in other signaling pathways that may be related to RPL as good candidates for future studies.Abbreviations RPL: recurrent pregnancy loss; EGF-CFC1: Epidermal Growth Factors – Cripto/FRL-1; GEO: Gene Omnibus Expression; KEGG: Kyoto Encyclopedia of Genes and Genomes.

PMID:34498535 | DOI:10.1080/19396368.2021.1965673

Ann Palliat Med. 2021 Aug 31:apm-21-1650. doi: 10.21037/apm-21-1650. Online ahead of print.

ABSTRACT

BACKGROUND: Weight gain during chemotherapy for breast cancer is quite common and has a major impact on the quality of life. Post-treatment weight gain can also impact on primary endpoints such as tumor recurrence and overall survival. Parameters thought to impact weight gain include menopausal status, age and chemotherapy regimen. Using meta-regression, we studied the effect of age on weight change by menopausal status and chemotherapy regimen.

METHODS: Twenty-four studies were identified, and extracted for weight change, mean/median age, menopausal status and chemotherapy regimen. A meta-regression was performed using a random-effects model for high heterogeneity and fixed-effects inverse-variance model for low heterogeneity. Subgroup analyses by menopausal status and chemotherapy regimen were conducted. P values <0.05 were considered statistically significant.

RESULTS: There exists no relationship between weight change and age (β=0.00; P=0.987). Stratifying by menopausal status (β=0.05 and P=0.150 for premenopausal patients; β=0.09 and P=0.588 for postmenopausal patients) and chemotherapy regimens (β=-0.07 and P=0.562 for patients receiving CMF alone; β=0.08 and P=0.707 for patients receiving CMF in addition to others; β=0.02 and P=0.807 for patients not receiving CMF), there likewise was no relationship between weight change and age.

CONCLUSIONS: Management of weight gain due to chemotherapy has been focused on relatively young women who are generally at higher risk of mortality and tumor recurrence. However, our results suggest that age should not be used for differential care.

PMID:34498483 | DOI:10.21037/apm-21-1650

Environ Health Perspect. 2021 Sep;129(9):97702. doi: 10.1289/EHP9131. Epub 2021 Sep 9.

NO ABSTRACT

PMID:34498494 | DOI:10.1289/EHP9131