Nevin Manimala

Adv Med Sci. 2021 Mar 30;66(2):237-245. doi: 10.1016/j.advms.2021.03.005. Online ahead of print.

ABSTRACT

PURPOSE: We analyzed the SARS-CoV-2 genome using our integrated genome analysis system and present the concept of a comprehensive approach to monitoring and surveillance of emerging variants.

MATERIAL/METHODS: A total of 69 SARS-CoV-2 positive samples (with Ct value ​≤ ​28) were tested. Samples included in this study were selected from 7 areas of eastern Poland. All samples were sequenced on an Illumina MiSeq platform using a 300-cycle MiSeq Reagent Kit v2. BWA was used for reads mapping on the reference SARS-CoV-2 sequence. SAMTools were used for post-processing of reads to genome assembly. Pango lineage and Nexstrain were used to identify variants and amino acid mutations. Statistical analysis was performed with R 4.0.2.

RESULTS: This study shows the first confirmed case of SARS-CoV-2 in Poland with the lineage B.1.351 (known as 501Y.V2 South African variant), as well as another 18 cases with epidemiologically relevant lineage B.1.1.7, known as British variant. Supplementary analysis of SARS-CoV-2 sequences deposited in GISAID shows that the share of a new variant can change rapidly within one month. In addition, we show a complete, integrated concept of a networked system for analyzing the variability of the SARS-CoV-2 genome, which, used in the present study, generated data and a variant report within 6 days.

CONCLUSION: The analyzed viral genomes showed considerable variability with simultaneous clear distinction of local clusters of genomes showing high similarity. Implementing real-time monitoring of new SARS-CoV-2 variants in Poland is urgently needed, and our developed system is available to be implemented on a large scale.

PMID:33827042 | DOI:10.1016/j.advms.2021.03.005

J Environ Manage. 2021 Mar 31;288:112456. doi: 10.1016/j.jenvman.2021.112456. Online ahead of print.

ABSTRACT

The present study describes the development of a web-based flood risk information system ‘WebFRIS’ for Jagatsinghpur district, a severely flood-prone region in Eastern India. The WebFRIS is designed by using various readily available open-source web tools and packages such as Google Map, PHP, MySQL, and JSON. Special emphasis is directed towards designing the layout and architecture, to be easily accessible by any end-user irrespective of any technical know-how. The WebFRIS illustrates spatial maps of flood hazard, socio-economic vulnerability, and flood risk at the village level for two-time scenarios. While analyzing a set of graphical statistics depicting the changes in flood risk components, a significant increase in high and very-high categories of both flood hazard (~140%) and socio-economically vulnerable villages (~68%) is noticed during Scenario-I. The number of villages facing compound risk (contributed equally by flood hazard and socio-economic vulnerability) nearly doubled in Scenario-I. A spatial analysis of diametric changes in flood risk shows that a large proportion of villages in Balikuda, Ersama, and Tirtol tehsils have undergone radical changes. Following these observations, a set of possible engineering, social, and policy measures are proposed, whose implementation in the near future is expected to reinforce flood management in the study area. The WebFRIS architecture is flexible, easy-to-use; it is expected to provide crucial lessons to the local bodies, town-planners, water professionals, flood experts, and also the citizens, a precious knowledge on flood risk management. The WebFRIS may be considered as a precious cartographic product for environmental management. The proposed web platform is generic, as it can be applied to study other inter-related systems such as environmental protection, land-use planning, coastal habitat restoration, and community resilience building.

PMID:33827018 | DOI:10.1016/j.jenvman.2021.112456

J Contam Hydrol. 2021 Mar 2;240:103792. doi: 10.1016/j.jconhyd.2021.103792. Online ahead of print.

ABSTRACT

Groundwater samples from 61 randomly selected tube-wells in densely residential (DR) and sparse residential (SR) parts of Aba, Nigeria were analysed to elucidate the influence of urban land-use on the quality and characterize the hydrochemistry of the groundwater. Twelve water quality indicators: temperature, pH, EC, and TDS (physicochemical), as well as HCO₃, Cl, SO₄, NO₃, Na, K, Ca, and Mg (major ions) were analysed for each well. The results of the analyses were grouped based on the influence of land-use on the wells. The descriptive statistics, Piper, Chadha’s, and bivariate scattered plots, as well as index of base ion-exchange, and Friedman nonparametric statistical test were used to delineate and ascertain the significance of the urban impact on the quality of the groundwater wells. The results showed that the groundwater pH is acidic (3.7-5.6), and the mineralization low, with TDS ranging between 6.5 mg/l – 365 mg/l. The statistical mean and standard deviation (x¯±S.D) of the remaining quality indicators were found within the limits set by WHO in all the wells. The Piper and Chadha’s plots revealed four dominant water-types with spatial differentiation in the area. Though there are several mixed water-types in the SR area, the Na-HCO₃ water-type is dominant and represents the background hydrochemistry of the groundwater in the area. Whereas, Mg, Ca-Cl, water-types predominates in the DR wells. Other dominant water-types found between the SR and DR areas are Na-Cl and Ca-HCO₃ types. The rapid compositional change and local alteration in the hydrochemistry of the groundwater were impacted by some identified urban land-use practices, which introduce additional major ions in the groundwater solution. The mixed water-types found in the SR wells were influenced by factors such as the direction of flow and mixing of the groundwater reservoirs impacted by the hydrochemistry of the DR groundwater, which were upstream to the SR wells. The results of indicators such as EC, TDS, Cl, and NO₃, when compared showed observable local deterioration moving from wells in the SR to wells in the DR area. This was supported by the Friedman statistical test which revealed statistical significance of some urban practices on the quality of the groundwater. These results highlight the current quality status and harmonize the reports of previous studies which have characterized the hydrochemistry of the groundwater in the study area.

PMID:33827000 | DOI:10.1016/j.jconhyd.2021.103792

Int Immunopharmacol. 2021 Apr 4;96:107606. doi: 10.1016/j.intimp.2021.107606. Online ahead of print.

ABSTRACT

Patients with Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis (EBV-HLH) have a poor prognosis. This study investigated the efficacy of rituximab-containing immuno-chemotherapy regimens for EBV-HLH. In this study, 15 patients were treated with rituximab-containing regimens. The treatment efficacy and adverse events were evaluated. In 10 patients, EBV DNA became negative after the first course of treatment. The lymphocyte types infected by EBV in the 10 patients were only infected with B cells and mainly infected with B cells. In the other 5 patients, the EBV DNA of peripheral blood mononuclear cells (PBMC) before and after treatment with the regimens had no statistical difference (P = 0.111). In addition, in these 5 patients, EBV mainly infected T and NK cells. Among the 5 patients without a significant decline in EBV DNA of PBMC, 2 patients received allogeneic hematopoietic stem cell transplantation and turned negative for EBV DNA. This study suggests that rituximab-containing regimens are effective therapy for EBV-HLH with only and mainly B lymphocytes infected by EBV, especially for eliminating EBV.

PMID:33826999 | DOI:10.1016/j.intimp.2021.107606

Addict Behav. 2021 Mar 26;119:106923. doi: 10.1016/j.addbeh.2021.106923. Online ahead of print.

ABSTRACT

BACKGROUND: Adolescent cigarette smoking has continued to decline, whereas electronic cigarette (e-cigarette) use has increased dramatically among youth. Nicotine use in any form, even at low levels, during adolescence can have adverse consequences, particularly for low-income individuals. To elucidate potential early intervention targets, this study examined childhood executive control (EC), a set of cognitive processes for directing attention and behavior, in relation to adolescent cigarette and e-cigarette onset, testing for differential prediction by poverty level.

METHOD: Participants were 313 children (51% female, 64% European American) recruited in a small city in the Midwestern United States beginning in 2006 and then followed into adolescence between ages 14 and 16 years. EC was measured in the laboratory with performance-based tasks when children were age 5 years, 3 months. Self-reports of cigarette onset and e-cigarette onset were obtained in adolescence (M^age = 15.65 years). Overall, 24% of the sample was at or below the poverty line.

RESULTS: Cigarette onset was higher in the poverty group (17%) than in the non-poverty (8%) group, but e-cigarette onset did not differ by poverty level (36% poverty versus 38% non-poverty). Multiple group structural equation modeling revealed a statistically significant group difference such that EC ability was a significant negative predictor of e-cigarette onset for poverty but not for non-poverty youth. A similar group difference was evident as a trend for cigarette onset.

CONCLUSIONS: Because EC has been shown to be modifiable, early interventions to improve EC for children living in poverty might help prevent adolescent e-cigarette onset.

PMID:33826966 | DOI:10.1016/j.addbeh.2021.106923

Ann Vasc Surg. 2021 Apr 4:S0890-5096(21)00251-X. doi: 10.1016/j.avsg.2021.02.032. Online ahead of print.

ABSTRACT

OBJECTIVE: Inferior vena cava (IVC) injuries have a high mortality rate that may be related to the location of injury and type of repair. Previous studies have been either single center series or database studies lacking granular detail. These have reported conflicting results. We aimed to perform a systematic review and meta-analysis of published literature evaluating ligation versus repair.

METHODS: Studies published in English on MEDLINE or EMBASE from 1946 through October 2018 were examined to evaluate mortality among patients treated with ligation versus repair of IVC injuries. Studies were included if they provided mortality associated with ligation versus repair and reported IVC injury by level. Risk of bias was assessed regarding incomplete and selective outcome reporting with Newcastle-Ottawa score of 7 or higher to evaluate study quality. We used a random-effects model with restricted maximum likelihood estimation method in R using the Metafor package to evaluate outcomes.

RESULTS: Our systematic review identified 26 studies, of which 14 studies, including 855 patients, met our inclusion criteria for meta-analysis. IVC ligation was associated with higher mortality than IVC repair (OR: 3.12, p<0.01, I²=49%). Ligation of infrarenal IVC injuries was not statistically associated with mortality (OR: 3.13, p=0.09). Suprarenal injury location compared to infrarenal (OR 3.11, p<0.01, I²=28%) and blunt mechanism compared to penetrating (OR: 1.91, p=0.02, I²=0%) were also associated with higher mortality.

CONCLUSIONS: In this meta-analysis, ligation of IVC injuries was associated with increased mortality compared to repair, but not specifically for infrarenal IVC injuries. Suprarenal IVC injury, and blunt mechanism was associated with increased mortality compared to infrarenal IVC injury and penetrating mechanism, respectively. Data are limited regarding acute renal injury and venous thromboembolic events after IVC ligation and may warrant multicenter studies. Standardized reporting of IVC injury data has not been well established and is needed in order to enable comparison of outcomes across institutions. In particular, reporting of injury location, severity, and repair type should be standardized. A contemporary prospective, multicenter study is needed in order to definitively compare surgical technique.

PMID:33826960 | DOI:10.1016/j.avsg.2021.02.032

Ann Vasc Surg. 2021 Apr 4:S0890-5096(21)00279-X. doi: 10.1016/j.avsg.2021.02.048. Online ahead of print.

ABSTRACT

INTRODUCTION: . Metformin is a commonly used drug in diabetes mellitus treatment. Recently it has been suggested that the use of metformin on diabetes mellitus patients may lower the prevalence and slow the progression of AAA (abdominal aortic aneurysm) as well as the risk of rupture related mortality. The aim of this study was to investigate the impact of metformin treatment on the risk of AAA repair related mortality and surgical complications.

METHODS: . In this retrospective study, the clinical data of 306 patients, including 77 patients with diabetes mellitus, who underwent abdominal aortic aneurysm repair has been analysed. Treatment outcomes have been investigated. The diabetes and metformin prescription status has been obtained from the medical history. Patients were divided into three groups: diabetes-free individuals, diabetics treated with metformin and diabetics treated with other glucose lowering drugs. The association between metformin treatment and AAA diameter, surgical complications and mortality were assessed using chi-square independence test and odds ratio analysis. In order to assess which factors are influencing AAA repair related complications and mortality a multi-variables analysis has been performed.

RESULTS: . A significant protective effect of metformin treatment towards AAA repair related mortality (p=0.019) and complications (p=0.032) among patients suffering from diabetes mellitus was revealed. These findings were statistically insignificant when considering all groups of patients (diabetes-free individuals, diabetics treated with metformin and diabetics treated with other glucose lowering drugs).

CONCLUSION: . Metformin may lower the risk of AAA repair related mortality and surgical complications among patients with diabetes.

PMID:33826959 | DOI:10.1016/j.avsg.2021.02.048

Cell Rep. 2021 Apr 6;35(1):108954. doi: 10.1016/j.celrep.2021.108954.

ABSTRACT

The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising tool for this purpose, and recent developments have achieved a high signal-to-noise ratio in vivo with 1-photon fluorescence imaging. However, these recordings exhibit several sources of noise and signal extraction remains a challenge. We present an improved signal extraction pipeline, spike-guided penalized matrix decomposition-nonnegative matrix factorization (SGPMD-NMF), which resolves supra- and subthreshold voltages in vivo. The method incorporates biophysical and optical constraints. We validate the pipeline with simultaneous patch-clamp and optical recordings from mouse layer 1 in vivo and with simulated and composite datasets with realistic noise. We demonstrate applications to mouse hippocampus expressing paQuasAr3-s or SomArchon1, mouse cortex expressing SomArchon1 or Voltron, and zebrafish spines expressing zArchon1.

PMID:33826882 | DOI:10.1016/j.celrep.2021.108954

J Womens Health (Larchmt). 2021 Apr 7. doi: 10.1089/jwh.2020.8610. Online ahead of print.

ABSTRACT

Background: Women bear a heavier burden of the consequences related to prescription opioid use compared to their male counterparts; however, there has been little attention in the literature regarding prescription opioid use among women. We aimed to examine risk factors for prescription opioid use among women. Methods: Demographics, health status, and substance use data, including prescription opioid use, were collected through a community engagement program, HealthStreet, during a health needs assessment. Women older than 18 years were classified by opioid use: past 30-day, lifetime, but not past 30-day, or no lifetime prescription opioid use. Descriptive statistics and chi-square tests were calculated, and multinomial logistic regression was used to calculate adjusted odds ratios (aORs; confidence interval [CI]). Results: Among 5,549 women assessed, 15% reported past 30-day use and 41% reported lifetime use of prescription opioids. While prescription sedative use was the strongest risk factor for past 30-day use among younger women (aOR = 4.84; 95% CI, 3.59-6.51), past 6-month doctor visits was the strongest risk factor for past 30-day use among older women (aOR = 4.15; 95% CI, 2.62-6.60). Conclusions: We found higher rates of prescription opioid use in this community sample of women compared to national rates. Risk factors for recent prescription opioid use (past 30-day use) differed among older and younger women. Clinicians should be more vigilant about prescribing opioids as the medical profile for women may change through age, especially the co-prescribing of opioids and sedatives.

PMID:33826866 | DOI:10.1089/jwh.2020.8610

J Womens Health (Larchmt). 2021 Apr 7. doi: 10.1089/jwh.2020.8733. Online ahead of print.

ABSTRACT

Background: Breast arterial calcification (BAC), which may be detected during screening mammography, is hypothesized to be a noninvasive imaging marker that may enhance cardiovascular risk assessment. Materials and Methods: In this systematic review and meta-analysis, we sought to assess the association between BAC and coronary artery disease (CAD) by conducting a meta-analysis. We conducted a literature search of PubMed, Scopus, Cochrane library, ClinicalTrials.gov, and conference proceedings, from inception through December 24, 2019. The outcome of interest was the presence of CAD in patients with BAC. This was reported as crude and adjusted odds ratio (OR). Results: A total of 18 studies comprising 33,494 women (mean age of 60.8 ± 3.7 years, 25% with diabetes, 57% with hypertension, and 21% with history of tobacco smoking) were included in the current meta-analysis. The prevalence of BAC among study participants was 10%. There was a statistically significant association between BAC and CAD (unadjusted OR 2.14; 95% confidence interval [CI] 1.63-2.81, p < 0.001, I² = 76.5%). Moreover, adjusted estimates were available from 10 studies and BAC was an independent predictor of CAD (OR 2.39; 95% CI 1.68-3.41, p < 0.001, I² = 61.7%). In the meta-regression analysis, covariates included year of publication, age, hypertension, diabetes mellitus, and history of tobacco smoking. None of these study covariates explained the heterogeneity across studies. Conclusions: BAC detected as part of screening mammography is a promising noninvasive imaging marker that may enhance CAD risk prediction in women. The clinical value of BAC for cardiovascular risk stratification merits further evaluation in large prospective studies.

PMID:33826862 | DOI:10.1089/jwh.2020.8733