Nevin Manimala

JMIR Public Health Surveill. 2024 Jun 13. doi: 10.2196/53409. Online ahead of print.

ABSTRACT

BACKGROUND: This study updates the COVID-19 pandemic surveillance in Sub-Saharan Africa (SSA) we first conducted in 2020 by providing two additional years of data for the region.

OBJECTIVE: First, we aim to measure whether there was an expansion or contraction in the pandemic in SSA when the World Health Organization (WHO) declared the end of the public health emergency for the COVID-19 pandemic on May 5, 2023. Second, we use dynamic and genomic surveillance methods to describe the history of the pandemic in the region and situate the window of the WHO declaration within the broader history. Third, we aim to provide historical context for the course of the pandemic in SSA.

METHODS: In addition to updates of traditional surveillance data and dynamic panel estimates from the original study by Post et al. (2021), this study used data on sequenced SARS-CoV-2 variants from the Global Initiative on Sharing All Influenza Data (GISAID) to identify the appearance and duration of variants of concern. We used Nextclade nomenclature to collect clade designations from sequences and Pangolin nomenclature for lineage designations of SARS-CoV-2. Finally, we conducted a one-sided t-test for whether regional weekly speed was greater than an outbreak threshold of ten. We ran the test iteratively with a rolling, six month-window of data across the sample period.

RESULTS: Speed for the region remained well below the outbreak threshold before and after the WHO declaration. Acceleration and jerk were also low and stable. The 7-day persistence coefficient remained somewhat large (1.11) and statistically significant. However, both shift parameters for the weeks around the WHO declaration were negative, meaning the clustering effect of new COVID-19 cases had become recently smaller. From November 2021 onward, Omicron was the predominant variant of concern in sequenced viral samples. The rolling t-test of speed equal to ten was insignificant for the entire sample period.

CONCLUSIONS: While COVID-19 continues to circulate in SSA, the region never reached outbreak status, and the weekly transmission rate had remained below one case per 100,000 population for well over one year ahead of the WHO declaration. COVID-19 is endemic in the region and no longer reaches the threshold of a pandemic definition. Both standard and enhanced surveillance metrics confirm that the pandemic had ended in SSA by the time of the WHO declaration.

PMID:39013111 | DOI:10.2196/53409

Genetics. 2024 Jul 16:iyae100. doi: 10.1093/genetics/iyae100. Online ahead of print.

ABSTRACT

As a result of recombination, adjacent nucleotides can have different paths of genetic inheritance and therefore the genealogical trees for a sample of DNA sequences vary along the genome. The structure capturing the details of these intricately interwoven paths of inheritance is referred to as an ancestral recombination graph (ARG). Classical formalisms have focused on mapping coalescence and recombination events to the nodes in an ARG. However, this approach is out of step with some modern developments, which do not represent genetic inheritance in terms of these events or explicitly infer them. We present a simple formalism that defines an ARG in terms of specific genomes and their intervals of genetic inheritance, and show how it generalizes these classical treatments and encompasses the outputs of recent methods. We discuss nuances arising from this more general structure, and argue that it forms an appropriate basis for a software standard in this rapidly growing field.

PMID:39013109 | DOI:10.1093/genetics/iyae100

S D Med. 2024 Jun;77(6):252-256.

ABSTRACT

INTRODUCTION: Facial lacerations are a common reason for emergency department (ED) visits in the U.S. Proper laceration repair is imperative as poor wound management can lead to functional and aesthetic impairment and significantly impact patient quality of life. For the best outcomes and long-term scar reduction, treatment by and follow-up with a plastic surgeon or facial trauma specialist is recommended. The present study examines variations in facial trauma specialist consultation and referral by ED provider type for adult patients at hospitals within a large rural South Dakota health system.

METHODS: Records for patients above the age of 18 who received treatment for facial lacerations between January 1, 2017 and January 1, 2022 were retrospectively reviewed across multiple hospitals in South Dakota, spanning a large rural catchment area. Multivariable logistic regression and Fisher’s exact test were performed to examine the relationship between ED provider type and the probability of receiving specialty consult and/or referral.

RESULTS: One hundred fifty-four ED visits were included in the analysis. Among these patients, 53 received specialty consult and/or follow-up referral and 101 were treated without consult or referral. ED provider type was significantly associated with the probability of having a specialty consult (OR = 5.11, 95% CI [1.05, 24.96]). When the patients had a certified nurse practitioner (CNP) as their ED provider, they had a significantly higher chance (40%) of receiving specialist consultation.

CONCLUSION: For patients presenting to the ED with facial lacerations, facial trauma specialist consultation and referral for follow up varies based on provider type. CNPs placed specialist consultations more often than other ED provider types.

PMID:39013096

Magy Onkol. 2024 Jul 16;68(2):95-112. Epub 2024 Apr 30.

ABSTRACT

The objective of our study was to map county differences in incidence and mortality by cancers and examine their changes over time. Based on the database of National Cancer Registry and Central Statistical Office, age-standardized incidence and mortality rates per 100,000 person-years were calculated for each county for 15 cancer types and 3 time periods. East-West divide was apparent in incidence and mortality of lung cancer, with larger weight in East (Borsod-Abaúj-Zemplén, Heves, Jász-Nagykun-Szolnok, Békés counties). Concentration of lip and oral cavity malignancies was identified in the northeastern periphery (Borsod-Abaúj-Zemplén, Szabolcs-Szatmár-Bereg counties). Breast cancer incidence was the highest in Budapest. As a conclusion, changes in cancer incidence and mortality over time were similar to developed countries; however, values were higher. Differences in spatial distribution follow territorial pattern of social deprivation, which correspond to higher prevalence of health risk factors. Our study contributes to planning of public health programs by pinpointing regional inequalities in different cancer types.

PMID:39013084

Syst Biol Reprod Med. 2024 Dec;70(1):218-227. doi: 10.1080/19396368.2024.2375710. Epub 2024 Jul 16.

ABSTRACT

Sperm-derived genetic material contributes half of the genome to the embryo, hence it’s crucial to investigate which sperm parameter influences blastocyst formation in the intracytoplasmic sperm injection (ICSI) cycles with severe male infertility. The retrospective study analyzed 296 ICSI cycles with severe oligoasthenoteratozoospermia (OAT) and 99 ICSI cycles with preimplantation genetic testing for aneuploidy (PGT-A). Following the correlation analysis, data stratifications were performed in the OAT ICSI subgroup. The results showed that the matching blastocyst in the OAT ICSI cycles had inferior sperm parameters. DFI and sperm morphology had an influence on the blastocyst formation rate and the high-quality blastocysts formation rate on Day6, but no significant effect on the blastocyst development on Day 5. The high-quality blastocysts formation rate and ratio of high-quality blastocyst on Day 6 were demonstrably better in the subgroup of the teratozoospermic morphology when DFI was within the normal range. In the case of the normal sperm morphology, no statistically significant difference was found in blastocyst development, although there were numerical differences within different DFI subgroups. It was concluded that the blastocyst quality and development declined with the decreased sperm qualities.

PMID:39013025 | DOI:10.1080/19396368.2024.2375710

Sex Health. 2024 Jul;21:SH24049. doi: 10.1071/SH24049.

ABSTRACT

Background A growing number of men who have sex with men (MSM) utilise Grindr for seeking relationships and immediate/casual sexual encounters. Grindr and other mobile applications can be a valuable source of information on sociological predictors of health. One topic that is under reported is the use of Grindr by MSM with obesity. We described differences in Grindr use between MSM with and without obesity, and to use Grindr information to reveal trends which may serve as potential predictors of health. Methods Data was collected from 3744 Grindr users (mean age [s.d.], 32.3 years [9.1]) from the largest 50 metropolitan centres in the USA between February and May 2018. Users were divided into two cohorts based on BMI: (1) MSM with obesity (BMI>30), n =253; and (2) MSM without obesity, n =3491. Profile characteristics were compared. Results When evaluating potential predictors for obesity, we found that black/African-American and older MSM were significantly more likely to have obesity. Further, we found that obesity among MSM was significantly inversely associated with the population percent lesbian, gay, bisexual, and transgender (LGBT) within a city. Additionally, we found that MSM with obesity were significantly more likely to indicate interest in immediate sexual encounters. Conclusions These results highlight important trends that may serve as predictors of health in urban settings. Furthermore, our results suggest that MSM with obesity may be more likely to engage in risky sexual behaviours. These findings may be useful in informing providers and healthcare officials on when and how to provide outreach to this unique population.

PMID:39013024 | DOI:10.1071/SH24049

Brain. 2024 Jul 16:awae234. doi: 10.1093/brain/awae234. Online ahead of print.

ABSTRACT

Brain inflammation, with an increased density of microglia and macrophages, is an important component of Alzheimer’s disease (AD) and a potential therapeutic target. However, it is incompletely characterized, particularly in patients whose disease begins before the age of 65 years and, thus, have few co-pathologies. Inflammation has been usefully imaged with translocator protein (TSPO) positron emission tomography (PET), but most inflammation PET tracers cannot image subjects with a low-binder TSPO rs6971 genotype. In an important development, participants with any TSPO genotype can be imaged with a novel tracer, [11C]ER176, that has a high binding potential and a more favorable metabolite profile than other TSPO tracers currently available. We applied [11C]ER176 to detect brain inflammation in mild cognitive impairment (MCI) caused by early-onset AD. Furthermore, we sought to correlate the brain localization of inflammation, volume loss, elevated Aβ and tau. We studied brain inflammation in 25 patients with early-onset amnestic MCI (average age 59 ± 4.5 years, 10 women) and 23 healthy controls (average age 65 ± 6.0 years, 12 women), both groups with a similar proportion of all three TSPO-binding affinities. [11C]ER176 total distribution volume (VT), obtained with an arterial input function, was compared across patients and controls using voxel-wise and region-wise analyses. In addition to inflammation PET, most MCI patients had Aβ (n=23), and tau PET (n=21). For Aβ and tau tracers, standard uptake value ratios (SUVRs) were calculated using cerebellar grey matter as region of reference. Regional correlations among the three tracers were determined. Data were corrected for partial volume effect. Cognitive performance was studied with standard neuropsychological tools. In MCI caused by early-onset AD, there was inflammation in the default network, reaching statistical significance in precuneus and lateral temporal and parietal association cortex bilaterally, and in the right amygdala. Topographically, inflammation co-localized most strongly with tau (r= 0.63 ± 0.24). This correlation was higher than the co-localization of Aβ with tau (r= 0.55±0.25) and of inflammation with Aβ (0.43±0.22). Inflammation co-localized least with atrophy (-0.29±0.26). These regional correlations could be detected in participants with any of the three rs6971 TSPO polymorphisms. Inflammation in AD-related regions correlated with impaired cognitive scores. Our data highlight the importance of inflammation, a potential therapeutic target, in the AD process. Furthermore, they support the notion that, as shown in experimental tissue and animal models, the propagation of tau in humans is associated with brain inflammation.

PMID:39013020 | DOI:10.1093/brain/awae234

Genetics. 2024 Jul 16:iyae110. doi: 10.1093/genetics/iyae110. Online ahead of print.

ABSTRACT

Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches – firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes – and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We observe population differentiation is the primary factor driving qpAdm performance. Notably, whilst complex gene-flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible amongst a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations.

PMID:39013011 | DOI:10.1093/genetics/iyae110

Neurodiagn J. 2024 Jul 16:1-8. doi: 10.1080/21646821.2024.2375477. Online ahead of print.

ABSTRACT

Although real-time event detection during video EEG recording is required to ensure patients’ safety, it is limited by the technologists’ availability. We sought to explore the efficiency of real-time event detection by the EEG technologists in a single tertiary academic center. We retrospectively reviewed events from continuous inpatient video EEGs (cEEGs) and epilepsy monitoring unit (EMU) recordings in January 2017, when real-time surveillance was only available during the night shift, and June 2017, when a dedicated neurodiagnostic EEG technologist was available for real-time monitoring during all shifts. The events were categorized into those detected immediately (eyes-on), later in the same shift (delayed) or identified on the subsequent shift (missed). Chi-square and Fisher’s exact tests were used for statistical comparisons. In January 2017, there were 25 patients (117 days of monitoring) in the EMU and 54 inpatients (146 days of monitoring) on cEEG with 92 total events, (39% seizures). In June 2017, there were 30 patients (133 days of monitoring) in the EMU and 47 additional inpatients (80 days of monitoring) on cEEG with 110 total events, (39% seizures). The number of events identified in real time was low and did not significantly differ among shifts regardless of the availability of the monitoring technologist. Most events were identified at the time of subsequent EEG scanning by the EEG technologist. Partial staffing for continuous video EEG surveillance is insufficient to identify events in real time. EEG technologists are able to identify events during regular EEG scanning.

PMID:39012963 | DOI:10.1080/21646821.2024.2375477

Circ Cardiovasc Imaging. 2024 Jul;17(7):e016152. doi: 10.1161/CIRCIMAGING.123.016152. Epub 2024 Jul 16.

ABSTRACT

BACKGROUND: Elevated levels of lipoprotein(a) (Lp(a)) are independently associated with an increased risk of atherosclerotic cardiovascular disease events. However, the mechanisms driving this association are poorly understood. We aimed to evaluate the association between Lp(a) and coronary plaque characteristics in a contemporary US cohort without clinical atherosclerotic cardiovascular disease, undergoing coronary computed tomography angiography, the noninvasive gold standard for the assessment of coronary atherosclerosis.

METHODS: We used baseline data from the Miami Heart Study-a community-based, prospective cohort study-which included asymptomatic adults aged 40 to 65 years evaluated using coronary computed tomography angiography. Those taking any lipid-lowering therapies were excluded. Elevated Lp(a) was defined as ≥125 nmol/L. Outcomes included any plaque, coronary artery calcium score >0, maximal stenosis ≥50%, presence of any high-risk plaque feature (positive remodeling, spotty calcification, low-attenuation plaque, napkin ring), and the presence of ≥2 high-risk plaque features.

RESULTS: Among 1795 participants (median age, 52 years; 54.3% women; 49.6% Hispanic), 291 (16.2%) had Lp(a) ≥125 nmol/L. In unadjusted analyses, individuals with Lp(a) ≥125 nmol/L had a higher prevalence of all outcomes compared with Lp(a) <125 nmol/L, although differences were only statistically significant for the presence of any coronary plaque and ≥2 high-risk features. In multivariable models, elevated Lp(a) was independently associated with the presence of any coronary plaque (odds ratio, 1.40, [95% CI, 1.05-1.86]) and with ≥2 high-risk features (odds ratio, 3.94, [95% CI, 1.82-8.52]), although only 35 participants had this finding. Among participants with a coronary artery calcium score of 0 (n=1200), those with Lp(a) ≥125 nmol/L had a significantly higher percentage of any plaque compared with those with Lp(a) <125 nmol/L (24.2% versus 14.2%; P<0.001).

CONCLUSIONS: In this contemporary analysis, elevated Lp(a) was independently associated with the presence of coronary plaque. Larger studies are needed to confirm the strong association observed with the presence of multiple high-risk coronary plaque features.

PMID:39012945 | DOI:10.1161/CIRCIMAGING.123.016152