Nevin Manimala

BMC Public Health. 2023 Jan 26;23(1):177. doi: 10.1186/s12889-022-14909-9.

ABSTRACT

BACKGROUND: Given the nature of the spread of SARS-CoV-2, strong regional patterns in the fatal consequences of the COVID-19 pandemic related to local characteristics such as population and health care infrastructures were to be expected. In this paper we conduct a detailed examination of the spatial correlation of deaths in the first year of the pandemic in two neighbouring countries – Germany and Poland, which, among high income countries, seem particularly different in terms of the death toll associated with the COVID-19 pandemic. The analysis aims to yield evidence that spatial patterns of mortality can provide important clues as to the reasons behind significant differences in the consequences of the COVID-19 pandemic in these two countries.

METHODS: Based on official health and population statistics on the level of counties, we explore the spatial nature of mortality in 2020 in the two countries – which, as we show, reflects important contextual differences. We investigate three different measures of deaths: the officially recorded COVID-19 deaths, the total values of excessive deaths and the difference between the two. We link them to important pre-pandemic regional characteristics such as population, health care and economic conditions in multivariate spatial autoregressive models. From the point of view of pandemic related fatalities we stress the distinction between direct and indirect consequences of COVID-19, separating the latter further into two types, the spatial nature of which is likely to differ.

RESULTS: The COVID-19 pandemic led to much more excess deaths in Poland than in Germany. Detailed spatial analysis of deaths at the regional level shows a consistent pattern of deaths officially registered as related to COVID-19. For excess deaths, however, we find strong spatial correlation in Germany but little such evidence in Poland.

CONCLUSIONS: In contrast to Germany, for Poland we do not observe the expected spatial pattern of total excess deaths and the excess deaths over and above the official COVID-19 deaths. This difference cannot be explained by pre-pandemic regional factors such as economic and population structures or by healthcare infrastructure. The findings point to the need for alternative explanations related to the Polish policy reaction to the pandemic and failures in the areas of healthcare and public health, which resulted in a massive loss of life.

PMID:36703167 | DOI:10.1186/s12889-022-14909-9

Genome Med. 2023 Jan 26;15(1):7. doi: 10.1186/s13073-022-01152-5.

ABSTRACT

BACKGROUND: Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes.

METHODS: We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes’ coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry.

RESULTS: In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 × 10^-6) and AC058822.1 (P = 1.47 × 10^-4), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C.

CONCLUSIONS: Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 × 10^-5), demonstrating the importance of diversifying study cohorts.

PMID:36703164 | DOI:10.1186/s13073-022-01152-5

BMC Med Educ. 2023 Jan 26;23(1):65. doi: 10.1186/s12909-023-04027-4.

ABSTRACT

BACKGROUND: The Recorded Consultation Assessment (RCA) was developed rapidly during the COVID-19 pandemic to replace the Clinical Skills Assessment (CSA) for UK general practice licensing. Our aim was to evaluate examiner perceptions of the RCA.

METHODS: We employed a cross-sectional design using a questionnaire survey of RCA examiners with attitudinal (relating to examiners thoughts and perceptions of the RCA) and free text response options. We conducted statistical descriptive and factor analysis of quantitative data with qualitative thematic analysis of free text responses.

RESULTS: Overall, 182 of 260 (70%) examiners completed the questionnaire. Responders felt that consultations submitted were representative of the work of a typical GP during the pandemic and provided a good sample across the curriculum. They were also generally positive about the logistic, advisory and other support provided as well as the digital platform. Despite responders generally agreeing there was sufficient information available in video or audio consultations to judge candidates’ data gathering, clinical management, and interpersonal skills, they were less confident about their ability to make judgments of candidates’ performance compared with the CSA. The qualitative analysis of free text responses detailed the problems of case selection and content, explained examiners’ difficulties when making judgments, and detailed the generally positive views about support, training and information technology. Responders also provided helpful recommendations for improving the assessment.

CONCLUSION: The RCA was considered by examiners to be feasible and broadly acceptable, although they experienced challenges from candidate case selection, case content and judgments leading to suggested areas for improvement.

PMID:36703159 | DOI:10.1186/s12909-023-04027-4

Parasit Vectors. 2023 Jan 26;16(1):36. doi: 10.1186/s13071-023-05658-8.

ABSTRACT

BACKGROUND: The invasive tick species, Haemaphysalis longicornis, is becoming established in the USA, presenting a growing threat to dogs and cats. Two 90-day studies were initiated, the same protocol in each, to confirm the efficacy of a single application of two fluralaner formulations against H. longicornis infestations of cats.

METHODS: Cats were randomized among three groups in a 1:1:1 ratio (10 cats/group). Group 1 cats were untreated controls; Group 2 cats were treated with a topical fluralaner formulation (Bravecto®); Group 3 cats received a topical formulation containing fluralaner and moxidectin (Bravecto® Plus). Treatments were administered once (Day 0) at the label dose rates. Each cat was infested with 50 H. longicornis ticks on Day 7 for study qualification and also infested with 50 ticks on Days 2, 28, 58 and 88. Tick counts were completed on Days 5, 2, 30, 60 and 90. The primary objective was based on percentage reductions in arithmetic mean tick counts.

RESULTS: Pre-study infestations showed all study cats were susceptible to tick challenge. Except for Day 2 in one study, at least six control cats retained ≥ 25% of each challenge, demonstrating an adequate infestation for efficacy assessments. Across studies on Days 2, 30, 60 and 90, the mean live tick infestation rate (number of ticks recovered from each cat/infesting challenge to each cat) of Group 1 cats ranged from 25.0 to 69.6%. Efficacy of each formulation, based on live tick counts, was 100% on Day 2 and > 95 to 100% at each subsequent assessment. Between-group differences were statistically significant (P < 0.0001) for each treatment versus control comparison.

CONCLUSION: At the label dose rate, both topical fluralaner formulations were 100% effective in eliminating H. longicornis ticks from cats infested at the time of treatment. Efficacy of > 95 to 100% was then maintained through 90 days following a single application. Fluralaner is therefore a treatment of choice for protecting cats against this invasive tick species.

PMID:36703156 | DOI:10.1186/s13071-023-05658-8

BMC Surg. 2023 Jan 27;23(1):21. doi: 10.1186/s12893-022-01897-1.

ABSTRACT

BACKGROUND: The number of older patients with multiple comorbidities in the emergency service is increasingly frequent, which implies the risk of incurring in futile surgical interventions. Some interventions generate false expectations of survival or quality of life in patients and families and represent a negligible therapeutic benefit in patients whose chances of survival are minimal. In order to address this dilemma, we describe mortality in a cohort of patients undergoing emergency laparotomy with a risk ≥ 75% per the ACS NSQIP Surgical Risk Calculator.

METHODS: A retrospective observational study was designed to analyze postoperative mortality and factors associated with postoperative mortality in a cohort of patients undergoing emergency laparotomy between January 2018 and December 2021 in a high-complexity hospital who had a mortality risk ≥ 75% per the ACS NSQIP Surgical Risk Calculator.

RESULTS: A total of 890 emergency laparotomies were performed during the study period, and 50 patients were included for the analysis. Patient median age was 82.5 (IQR: 18.25) years old and 33 (66.00%) were male. The most frequent diagnoses were mesenteric ischemia 21 (42%) and secondary peritonitis 18 (36%). Mortality in the series was 92%. Twenty-four (54.34%) died within the first 24 h of the postoperative period; 11 (23.91%) within 72 h and 10 (21.73%) within 30 days. APACHE II and SOFA scores were statistically significantly higher in patients who died.

CONCLUSIONS: All available tools should be used to make decisions, with the most reliable and objective information possible, and be particularly vigilant in patients at extreme risk (mortality risk greater than 75% according to ACS NSQIP Surgical Risk Calculator) to avoid futility and its consequences. The available information should be shared with the patient, the family, or their guardians through an assertive and empathetic communication strategy. It is necessary to insist on a culture of surgical ethics based on reflection and continuous improvement in patient care and to know how to accompany them in order to have a proper death.

PMID:36703155 | DOI:10.1186/s12893-022-01897-1

BMC Med Inform Decis Mak. 2023 Jan 26;23(1):19. doi: 10.1186/s12911-023-02098-3.

ABSTRACT

The coronavirus disease 2019 (COVID-19) has developed into a pandemic. Data-driven techniques can be used to inform and guide public health decision- and policy-makers. In generalizing the spread of a virus over a large area, such as a province, it must be assumed that the transmission occurs as a stochastic process. It is therefore very difficult for policy and decision makers to understand and visualize the location specific dynamics of the virus on a more granular level. A primary concern is exposing local virus hot-spots, in order to inform and implement non-pharmaceutical interventions. A hot-spot is defined as an area experiencing exponential growth relative to the generalised growth of the pandemic. This paper uses the first and second waves of the COVID-19 epidemic in Gauteng Province, South Africa, as a case study. The study aims provide a data-driven methodology and comprehensive case study to expose location specific virus dynamics within a given area. The methodology uses an unsupervised Gaussian Mixture model to cluster cases at a desired granularity. This is combined with an epidemiological analysis to quantify each cluster’s severity, progression and whether it can be defined as a hot-spot.

PMID:36703133 | DOI:10.1186/s12911-023-02098-3

BMC Musculoskelet Disord. 2023 Jan 26;24(1):70. doi: 10.1186/s12891-023-06140-3.

ABSTRACT

BACKGROUND: The fractures of femoral neck account for 50% among hip fractures with around 3%-10% occurring in younger population of below 65 years. The newly introduced FNS as management approach appears to be a potential alternative to the traditional CCS. The aim of this study was to compare the clinical efficacy and outcome of the femoral neck system (FNS) and the cannulated cancellous screw (CCS) in the treatment of femoral neck fractures in adult below 65 years of age.

METHODS: Data of 114 patients between 18-65 years, admitted in our department for femoral neck fracture from January 2019 to March 2021 were retrospectively studied and ranged into two groups based on the surgical methods: FNS group (56 patients) and CCS group (58 patients). The variables of interest including demographic and clinical variables (age, gender, fracture mechanism, injury side and classification), perioperative parameters(operation time, intraoperative bleeding, incision length and hospitalization time), postoperative outcomes and complications (fracture healing time, nonunion rate, femoral neck avascular necrosis, aseptic screw loosening and the Harris Hip Score), were analyzed and compared between the two groups.

RESULTS: All 114 patients presented satisfactory reduction and were followed-up for a period of 12 to 36 months (mean 27 ± 2.07 months); there were no significant differences between both groups in terms of age, gender, fracture classification, side of injury, mechanism of injury, the operative time, intraoperative blood loss and the hospital length of stay. However, the fracture healing time between FNS group and CCS group was statistically significant (p < 0.05), respectively 2.86 ± 0.77 and 5.10 ± 0.81 months. The significant differences were also found in terms of numbers of fluoroscopies 8.34 ± 1.38 Vs 17.72 ± 2.19, the HHS 87.80 ± 1.92 Vs 84.28 ± 2.24, postoperative complications 8 (14.28%) Vs 26 (44.82) respectively in FNS and CCS group.

CONCLUSION: FNS presented satisfactory outcomes had significantly lower complications rate, therefore, can be one of the alternatives for internal implantation devices in treatment of femoral neck fracture in non-geriatric population.

PMID:36703126 | DOI:10.1186/s12891-023-06140-3

BMC Surg. 2023 Jan 26;23(1):19. doi: 10.1186/s12893-023-01901-2.

ABSTRACT

INTRODUCTION: Radical gastrectomy has traditionally been the pillar treatment with curative intent for malignant tumors of the stomach. The safety of the laparoscopic approach for advanced gastric cancer (AGC) is still under debate. In our institution, laparoscopic gastrectomy is the most performed approach.

OBJECTIVE: Our aim is to describe the experience of a high-volume center in the treatment of AGC in Colombia and to analyze the short-term results and the overall survival rate at 1, 3, and 5 years comparing the open and laparoscopic approaches.

METHODS: A cross-sectional retrospective study of patients who underwent gastrectomy for advanced gastric cancer by open or laparoscopic approaches were performed. A Will-Coxon Mann Whitney test was performed in terms of lymph node status and surgical approach. Survival analysis was performed using the Kaplan-Meier method for overall survival at 1, 3, and 5 years. An initial log-rank test was performed to test the relationships between the operative variables and overall survival, the statistical value was accepted if p < 0.20. Data with an initial statistical relationship in the log-rank test were included in a secondary analysis using multivariate Cox proportional regression, variables with a value of p < 0.05 were considered statistically significant.

RESULTS: 310 patients met the inclusion criteria. 89% underwent laparoscopic gastrectomy and 10.9% open gastrectomy. The resection margins were negative at 93.5% and the In terms of lymph node dissection, the median lymph nodes extracted was 20 (12;37), with statistically significant differences between the approaches in favor of the laparoscopic approach (Median 21 vs 12; z = – 2.19, p = 0.02). The survival rate was at 1, 3, and 5 years of 84.04%, 66.9%, and 65.47% respectively. The presence of complications and the ICU requirement have a negative impact on survival at 1 year (p 0.00).

CONCLUSION: A laparoscopic approach is safe with acceptable morbidity and mortality rates for treating gastric cancer. D2 Lymphadenectomy could be performed successfully in a laparoscopic approach in a high-volume center and a properly standardized technique. Major postoperative morbidity with intensive care unit requirement seems to influence overall survival rates.

PMID:36703124 | DOI:10.1186/s12893-023-01901-2

BMC Geriatr. 2023 Jan 26;23(1):48. doi: 10.1186/s12877-022-03646-8.

ABSTRACT

BACKGROUND: Physical activity (PA) has beneficial effects on physical and mental health outcomes in older adults. However, a consistent decline in PA participation has been noted with increasing age, with older adults consistently being reported as the least physically active population. Previous evidence showed that dance is an appropriate form of PA in older adults as it integrates the body’s movement with physical, cognitive, and social elements. This study investigated the feasibility and efficacy of a weekly dance programme over a 12-month period on PA levels and wellbeing.

METHODS: A mixed-method intervention design was used. Community-dwelling older adults aged 55 + years were recruited from local community groups in Yorkshire (UK). The programme comprised of a 60-min mixed genre dance class per week. Changes with carried forward data in self-reported measures of PA (min/week) and wellbeing with EuroQol visual analogue scale (EQ VAS) across four different time points (baseline, 3, 6 and 12 months) were assessed using the Friedman test. Feasibility was also assessed through class attendance and focus groups (N = 6-9) with participants. A thematic analysis of qualitative data was conducted.

RESULTS: A total of 685 participants (589-89.1% females and 72-10.9% males) took part in the study. The mean age was 75 ± 10 years, and 38% of the participants were classed as highly deprived as per the index of multiple deprivation. There was a statistically significant increase in both PA (X2(3) = 192.42, P < 0.001) and EQ VAS scores across the four time points (X²(3) = 19.66, P < 0.001). The mean adherence rate was consistent across the 12-month period of intervention (70%). Themes from the focus groups included reasons for participating in the programme, perceptions of how the dance programme affected the participants, and facilitators to participation in the programme.

CONCLUSIONS: The good adherence and favourability indicate that the dance programme is feasible as an intervention in community-dwelling participants from socially economically diverse communities. The dance intervention showed a positive effect on PA levels and wellbeing. A randomised-controlled trial with a control group is required to test this intervention further.

PMID:36703116 | DOI:10.1186/s12877-022-03646-8

BMC Bioinformatics. 2023 Jan 26;24(1):28. doi: 10.1186/s12859-022-05111-0.

ABSTRACT

BACKGROUND: In individuals or animals suffering from genetic or acquired diseases, it is important to identify which clinical or phenotypic variables can be used to discriminate between disease and non-disease states, the response to treatments or sexual dimorphism. However, the data often suffers from low number of samples, high number of variables or unbalanced experimental designs. Moreover, several parameters can be recorded in the same test. Thus, correlations should be assessed, and a more complex statistical framework is necessary for the analysis. Packages already exist that provide analysis tools, but they are not found together, rendering the decision method and implementation difficult for non-statisticians.

RESULT: We present Gdaphen, a fast joint-pipeline allowing the identification of most important qualitative and quantitative predictor variables to discriminate between genotypes, treatments, or sex. Gdaphen takes as input behavioral/clinical data and uses a Multiple Factor Analysis (MFA) to deal with groups of variables recorded from the same individuals or anonymize genotype-based recordings. Gdaphen uses as optimized input the non-correlated variables with 30% correlation or higher on the MFA-Principal Component Analysis (PCA), increasing the discriminative power and the classifier’s predictive model efficiency. Gdaphen can determine the strongest variables that predict gene dosage effects thanks to the General Linear Model (GLM)-based classifiers or determine the most discriminative not linear distributed variables thanks to Random Forest (RF) implementation. Moreover, Gdaphen provides the efficacy of each classifier and several visualization options to fully understand and support the results as easily readable plots ready to be included in publications. We demonstrate Gdaphen capabilities on several datasets and provide easily followable vignettes.

CONCLUSIONS: Gdaphen makes the analysis of phenotypic data much easier for medical or preclinical behavioral researchers, providing an integrated framework to perform: (1) pre-processing steps as data imputation or anonymization; (2) a full statistical assessment to identify which variables are the most important discriminators; and (3) state of the art visualizations ready for publication to support the conclusions of the analyses. Gdaphen is open-source and freely available at https://github.com/munizmom/gdaphen , together with vignettes, documentation for the functions and examples to guide you in each own implementation.

PMID:36703114 | DOI:10.1186/s12859-022-05111-0