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Nevin Manimala Statistics

Spatiotemporal analysis of bubonic plague in Pernambuco, northeast of Brazil: Case study in the municipality of Exu

PLoS One. 2021 Apr 2;16(4):e0249464. doi: 10.1371/journal.pone.0249464. eCollection 2021.

ABSTRACT

Along with other countries in America, plague reached Brazil through the sea routes during the third pandemic. A brief ports phase was followed by an urban phase that took place in smaller inland cities and finally, it attained the rural area and established several foci where the ecological conditions were suitable for its continued existence. However, the geographic dispersion of plague in Brazil is still poorly studied. To better understand the disease dynamics, we accessed satellite-based data to trace the spatial occurrence and distribution of human plague cases in Pernambuco, Northeastern Brazil and using the municipality of Exu as study case area. Along with the satellite data, a historical survey using the Plague Control Program files was applied to characterize the spatial and temporal dispersion of cases in the period of 1945-1976. Kernel density estimation, spatial and temporal clusters with statistical significance and maximum entropy modeling were used for spatial data analysis, by means of the spatial analysis software packages. The use of geostatistical tools allowed evidencing the shift of the infection from the urban to the wild-sylvatic areas and the reemergence of cases after a period of quiescence, independent of the reintroduction from other plague areas.

PMID:33798208 | DOI:10.1371/journal.pone.0249464

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Nevin Manimala Statistics

Choice of CTO scores to predict procedural success in clinical practice. A comparison of 4 different CTO PCI scores in a comprehensive national registry including expert and learning CTO operators

PLoS One. 2021 Apr 2;16(4):e0245898. doi: 10.1371/journal.pone.0245898. eCollection 2021.

ABSTRACT

BACKGROUND: We aimed to compare the performance of the recent CASTLE score to J-CTO, CL and PROGRESS CTO scores in a comprehensive database of percutaneous coronary intervention of chronic total occlusion procedures.

METHODS: Scores were calculated using raw data from 1,342 chronic total occlusion procedures included in REBECO Registry that includes learning and expert operators. Calibration, discrimination and reclassification were evaluated and compared.

RESULTS: Mean score values were: CASTLE 1.60±1.10, J-CTO 2.15±1.24, PROGRESS 1.68±0.94 and CL 2.52±1.52 points. The overall percutaneous coronary intervention success rate was 77.8%. Calibration was good for CASTLE and CL, but not for J-CTO or PROGRESS scores. Discrimination: the area under the curve (AUC) of CASTLE (0.633) was significantly higher than PROGRESS (0.557) and similar to J-CTO (0.628) and CL (0.652). Reclassification: CASTLE, as assessed by integrated discrimination improvement, was superior to PROGRESS (integrated discrimination improvement +0.036, p<0.001), similar to J-CTO and slightly inferior to CL score (- 0.011, p = 0.004). Regarding net reclassification improvement, CASTLE reclassified better than PROGRESS (overall continuous net reclassification improvement 0.379, p<0.001) in roughly 20% of cases.

CONCLUSION: Procedural percutaneous coronary intervention difficulty is not consistently depicted by available chronic total occlusion scores and is influenced by the characteristics of each chronic total occlusion cohort. In our study population, including expert and learning operators, the CASTLE score had slightly better overall performance along with CL score. However, we found only intermediate performance in the c-statistic predicting chronic total occlusion success among all scores.

PMID:33798205 | DOI:10.1371/journal.pone.0245898

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Nevin Manimala Statistics

Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor

PLoS Comput Biol. 2021 Apr 2;17(4):e1008890. doi: 10.1371/journal.pcbi.1008890. Online ahead of print.

ABSTRACT

Protein-protein interaction networks are one of the most effective representations of cellular behavior. In order to build these models, high-throughput techniques are required. Next-generation interaction screening (NGIS) protocols that combine yeast two-hybrid (Y2H) with deep sequencing are promising approaches to generate interactome networks in any organism. However, challenges remain to mining reliable information from these screens and thus, limit its broader implementation. Here, we present a computational framework, designated Y2H-SCORES, for analyzing high-throughput Y2H screens. Y2H-SCORES considers key aspects of NGIS experimental design and important characteristics of the resulting data that distinguish it from RNA-seq expression datasets. Three quantitative ranking scores were implemented to identify interacting partners, comprising: 1) significant enrichment under selection for positive interactions, 2) degree of interaction specificity among multi-bait comparisons, and 3) selection of in-frame interactors. Using simulation and an empirical dataset, we provide a quantitative assessment to predict interacting partners under a wide range of experimental scenarios, facilitating independent confirmation by one-to-one bait-prey tests. Simulation of Y2H-NGIS enabled us to identify conditions that maximize detection of true interactors, which can be achieved with protocols such as prey library normalization, maintenance of larger culture volumes and replication of experimental treatments. Y2H-SCORES can be implemented in different yeast-based interaction screenings, with an equivalent or superior performance than existing methods. Proof-of-concept was demonstrated by discovery and validation of novel interactions between the barley nucleotide-binding leucine-rich repeat (NLR) immune receptor MLA6, and fourteen proteins, including those that function in signaling, transcriptional regulation, and intracellular trafficking.

PMID:33798202 | DOI:10.1371/journal.pcbi.1008890

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Nevin Manimala Statistics

Association between dental diseases and history of stroke in the United States

Clin Exp Dent Res. 2021 Apr 2. doi: 10.1002/cre2.416. Online ahead of print.

ABSTRACT

OBJECTIVE: This study aimed to determine the potential association between the dental diseases and self-reported history of stroke in the United States based on data from the Third National Health and Nutrition Examination Survey (NHANES III).

METHODS: Data were extracted from NHANES III. Dental variables were carious tooth surfaces, number of missing teeth, gingival bleeding, and periodontal pockets. Multiple logistic regression modeling was used to estimate the effect of these dental diseases on the self-reported history of stroke with intent to adjust for the other potential determinants: age, sex, race, marital status, health insurance, education, exercise, body mass index, smoking, alcohol, hypertension, high serum cholesterol, and diabetes.

RESULTS: Number of missing teeth was found to be significantly associated with the self-reported history of stroke. Associations between the self-reported history of stroke and caries, gingival bleeding, or periodontal pockets were not statistically significant.

CONCLUSIONS: Number of missing teeth was an independent determinant of the self-reported history of stroke.

PMID:33797859 | DOI:10.1002/cre2.416

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Nevin Manimala Statistics

Treatment of oral fungal infections using photodynamic therapy: Systematic review and meta-analysis

Clin Exp Dent Res. 2021 Apr 2. doi: 10.1002/cre2.408. Online ahead of print.

ABSTRACT

OBJECTIVES: This systematic review evaluated the evidence for the effectiveness of Photodynamic therapy (PDT) in treating oral fungal infections, as an alternative to conventional antifungal medications.

METHODS: Five randomized control trials (168 participants) comparing the treatment of oral fungal infections using met with our inclusion criteria. Clinical and microbiological improvement was assessed by random-effects meta-analysis. Methodological quality assessment and heterogeneity were performed using peer-reviewed criteria. PROSPERO registration: CRD42017076.

RESULTS: PDT showed statistically non-significant increased clinical efficacy (risk ratio (RR) = 1.47 [95% confidence interval (CI), 0.68; 3.17]; three studies, n = 108 participants, I2 = 50%) and mycological efficacy (mean difference (MD) = 0.54 [95%CI, -0.71; 1.79]; three studies, n = 100; I2 = 39%) at 30 days, as compared with conventional antifungal therapy. Lack of standardization of treatment parameters and variability in the assessment of outcomes was observed across the studies. All included studies had a moderate to low risk of bias.

CONCLUSIONS: PDT showed comparable effectiveness at treating oral fungal infections, particularly denture stomatitis. The small number of studies in this review, small sample size and variability of methods and outcome measures across studies, highlight the need for more standardized studies with longer follow-up periods to enable recommendation of PDT as an alternative to conventional antifungal therapy.

PMID:33797857 | DOI:10.1002/cre2.408

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Nevin Manimala Statistics

The impact of primary tumor sidedness on survival in early-onset colorectal cancer by stage: A National Veterans Affairs retrospective analysis

Cancer Med. 2021 Apr 2. doi: 10.1002/cam4.3757. Online ahead of print.

ABSTRACT

BACKGROUND: The incidence of early-onset colorectal cancer (EOCRC) is rising. Left-sided colorectal cancer (LCC) is associated with better survival compared to right-sided colon cancer (RCC) in metastatic disease. NCCN guidelines recommend the addition of EGFR inhibitors to KRAS/NRAS WT metastatic CRC originating from the left only. Whether laterality impacts survival in locoregional disease and EOCRC is of interest.

METHODS: 65,940 CRC cases from the National VA Cancer Cube Registry (2001-2015) were studied. EOCRC (2096 cases) was defined as CRC diagnosed at <50 years. Using ICD codes, RCC was defined from the cecum to the hepatic flexure (C18.0-C18.3), and LCC from the splenic flexure to the rectum (C18.5-18.7; C19 and C20).

RESULTS: EOCRC is more likely to originate from the left side (66.65% LCC in EOCRC vs. 58.77% in CRC). Overall, LCC has better 5-year Overall Survival (OS) than RCC in stages I (61.67% vs. 58.01%) and III (46.1% vs. 42.1%) and better 1-year OS in stage IV (57.79% vs. 49.49%). Stage II RCC has better 5-year OS than LCC (53.39% vs. 49.28%). In EOCRC, there is no statistically significant difference between LCC and RCC in stages I-III. Stage IV EOCRC patients with LCC and RCC have a 1-year OS of 73.23% and 59.84%, respectively.

CONCLUSION: In EOCRC, LCC is associated with better OS than RCC only stage IV. In the overall population, LCC is associated with better OS in all stages except stage II. The better prognosis of stage II RCC might be due to the high incidence of mismatch repair deficient tumors in this subpopulation.

PMID:33797856 | DOI:10.1002/cam4.3757

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Nevin Manimala Statistics

HLA-G in Mayas from Yucatan: An evolutionary approach

Int J Immunogenet. 2021 Apr 2. doi: 10.1111/iji.12537. Online ahead of print.

ABSTRACT

HLA-G allele frequencies were studied in Yucatán (Mexico) Maya Amerindians by a direct exon DNA sequencing technique. It is described that Mayas are probably one of the first populations together with Olmecs that populated Meso America and that important HLA genetic differences between Mexican and Guatemalan Mayas support that Maya languages were imposed to several neighbouring Amerindian groups. HLA-G*01:01:02, HLA-G*01:01:01 and HLA-G*01:04:01 are the most frequent alleles in this population. It is remarkable that HLA-G*01:05N allele was not found in the population in accordance with similar results found in another Amerindians. Also, protein allele HLA-G*01:04 frequency is found not to differ to those found in another far or close living Amerindians in contrast to other World populations. It seems that while high HLA-G*01:05N frequency is found in Iran and Middle East populations, probably where this allele appeared within an ancestral HLA-A*19 group of alleles haplotype and it is maintained by unknown evolutionary forces, Amerindians do not have a high frequency because a founder effect or because required natural evolutionary forces do not exist in America. Finally, we believe useful to study HLA-G evolution for its physiopathology understanding in addition to the many papers on statistics on HLA-G and in vitro models that are yearly published.

PMID:33797843 | DOI:10.1111/iji.12537

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Nevin Manimala Statistics

Neurophysiological and functional neuroanatomical coding of statistical and deterministic rule information during sequence learning

Hum Brain Mapp. 2021 Apr 2. doi: 10.1002/hbm.25427. Online ahead of print.

ABSTRACT

Humans are capable of acquiring multiple types of information presented in the same information stream. It has been suggested that at least two parallel learning processes are important during learning of sequential patterns-statistical learning and rule-based learning. Yet, the neurophysiological underpinnings of these parallel learning processes are not fully understood. To differentiate between the simultaneous mechanisms at the single trial level, we apply a temporal EEG signal decomposition approach together with sLORETA source localization method to delineate whether distinct statistical and rule-based learning codes can be distinguished in EEG data and can be related to distinct functional neuroanatomical structures. We demonstrate that concomitant but distinct aspects of information coded in the N2 time window play a role in these mechanisms: mismatch detection and response control underlie statistical learning and rule-based learning, respectively, albeit with different levels of time-sensitivity. Moreover, the effects of the two learning mechanisms in the different temporally decomposed clusters of neural activity also differed from each other in neural sources. Importantly, the right inferior frontal cortex (BA44) was specifically implicated in visuomotor statistical learning, confirming its role in the acquisition of transitional probabilities. In contrast, visuomotor rule-based learning was associated with the prefrontal gyrus (BA6). The results show how simultaneous learning mechanisms operate at the neurophysiological level and are orchestrated by distinct prefrontal cortical areas. The current findings deepen our understanding on the mechanisms of how humans are capable of learning multiple types of information from the same stimulus stream in a parallel fashion.

PMID:33797825 | DOI:10.1002/hbm.25427

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Nevin Manimala Statistics

Opioid Prescribing and Risks among Commercially Insured Women Undergoing Pelvic Organ Prolapse Repair

Pharmacoepidemiol Drug Saf. 2021 Apr 2. doi: 10.1002/pds.5239. Online ahead of print.

ABSTRACT

PURPOSE: Opioid use after surgical repair for pelvic organ prolapse (POP) is intended for short-term post-operative pain. This study compared the incidence of opioid prescribing in women undergoing POP transabdominal repair with mesh and transvaginal native tissue repair.

METHODS: A retrospective cohort of women undergoing POP transabdominal repair with mesh or transvaginal native tissue repair, was derived from a 10% random sample of enrollees from 2007-2015 within the IQVIA PharMetrics® Plus Database. Primary outcomes were any prescription of opioids and cumulative days of opioids prescribed in the 14 to 180 days following surgical intervention. Inverse probability of treatment weights controlled for observed baseline confounders. Any opioid prescription was estimated using logistic regression and generalized linear regression for cumulative days of opioids prescribed.

RESULTS: The cohort of 49 052 women who underwent POP surgical repair included 46 813 women with transvaginal native tissue repair and 2239 women with transabdominal repair with mesh. Women with a transabdominal repair with mesh had a 1.19(95%CI:1.09-1.31) significantly higher odds of receiving an opioid prescription than women with transvaginal native tissue repair. Post-operatively, over 29% of women received opioid prescriptions. Mean cumulative days of post-surgical opioid prescribing was 32.2(SD = 43.1), and was not statistically different between groups. Thirteen percent of women were prescribed opioids for 90 days or more.

CONCLUSIONS: Women undergoing POP with transabdominal mesh are more likely to receive prescriptions for opioids after surgery compared to transvaginal native tissue repair. Treatment plans that address pain while mitigating the risks associated with prolonged opioid prescribing should be employed. This article is protected by copyright. All rights reserved.

PMID:33797822 | DOI:10.1002/pds.5239

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Nevin Manimala Statistics

Surgical procedures for coronary arteries in pediatric cardiac surgery: Risk factors and outcomes

J Card Surg. 2021 Apr 2. doi: 10.1111/jocs.15547. Online ahead of print.

ABSTRACT

BACKGROUND: Limited data exist regarding the coronary revascularization procedures needed during the repair of several congenital and pediatric cardiac malformations. We aimed to determine risk factors for in-hospital mortality and long-term outcomes of various pediatric coronary revascularization procedures.

METHODS: We retrospectively reviewed the records of 32 consecutive pediatric patients who underwent coronary revascularization procedures at our institution between May 1995 and June 2020. In-hospital mortality, risk factors, surgical indications, revascularization patency, and mid- and long-term follow-up data were investigated. Patients were categorized into the coronary artery bypass grafting (n = 11) and other coronary artery procedure (n = 21) groups.

RESULTS: The median age and weight of patients at the time of surgery were 9 months and 4.8 kg, respectively. There were five in-hospital deaths (5/32, 15.6%). The mortality rates were 27.2% (3/11) in the coronary artery bypass grafting group and 9.5% (2/21) in the other coronary artery procedure group (p = .206; 95% confidence interval: 0.496-25.563). The mortality rates for planned and rescue procedures were 8.3% (2/24) and 37.5% (3/8) (p = .06), respectively. The median follow-up time was 12.5 years. Control imaging studies for coronary patency were performed in 70.3% (19/27) of surviving patients. The overall coronary patency rate was 94.7% (18/19).

CONCLUSIONS: Pediatric coronary revascularization procedures with elective-planned indications can be performed with good outcomes. Young age and rescue and emergency procedures may carry an increased risk of in-hospital mortality, although not found to be statistically significant. Surviving patients require lifelong follow-up regarding the patency of reperfused coronary arteries.

PMID:33797801 | DOI:10.1111/jocs.15547