Automating microsatellite screening and primer design from multi-individual libraries using Micro-Primers

Analysis of intra- and inter-population diversity has become important for defining the genetic status and distribution patterns of a species and a powerful tool for conservation programs, as high levels of inbreeding could lead into whole population extinction in few generations. Microsatellites (SSR) are commonly used in population studies but discovering highly variable regions across species’ genomes requires demanding computation and laboratorial optimization. In this work, we combine next generation sequencing (NGS) with automatic computing to develop a genomic-oriented tool for characterizing SSRs at the population level. Herein, we describe a new Python pipeline, named Micro-Primers, designed to identify, and design PCR primers for amplification of SSR loci from a multi-individual microsatellite library. By combining commonly used programs for data cleaning and microsatellite mining, this pipeline easily generates, from a fastq file produced by high-throughput sequencing, standard information about the selected microsatellite loci, including the number of alleles in the population subset, and the melting temperature and respective PCR product of each primer set. Additionally, potential polymorphic loci can be identified based on the allele ranges observed in the population, to easily guide the selection of optimal markers for the species. Experimental results show that Micro-Primers significantly reduces processing time in comparison to manual analysis while keeping the same quality of the results. The elapsed times at each step can be longer depending on the number of sequences to analyze and, if not assisted, the selection of polymorphic loci from multiple individuals can represent a major bottleneck in population studies.

What Is the Evidence on Natural Recovery Over the Year Following Sports-Related and Non-sports-Related Mild Traumatic Brain Injury: A Scoping Review

Background: Treatment approaches often differ dependent upon whether a person experiences a sports-related or a non-sports-related mild traumatic brain injury. It remains unclear if recovery from these injuries is comparable or unique to context of the injury.Objective: To identify knowledge gaps on self-reported outcomes and trajectories between sports- and non-sports-related mild traumatic brain injuries and how they are assessed in adults.Methods: This scoping review used a systematic search of key electronic databases, including PubMed, SPORTDiscus, Embase, MEDLINE, and CINAHL for articles published in 1937 until March 10, 2021. Articles were included if they were available in English; full text published in a peer-reviewed journal; had a prospective or retrospective study design; reported data on mild TBI cases >16 years of age, and included data from at least two time points on self-reported outcomes within 12 months post-injury. A standardized data extraction spreadsheet was used to determine the participant characteristics, definitions, assessment methods, outcomes, and recovery time frames.Results: Following removal of duplicates, the search strategy elicited 6,974 abstracts. Following abstract review, 174 were retained for full text review. Of the 42 articles that met inclusion criteria, 18 were sports related (15 in the USA and three in Canada) and 24 were general population studies (six in USA, three in Canada, three in Australasia, nine in Europe, two in Taiwan, and one in Morocco). Direct comparison in recovery trajectories between the sport and general population studies was difficult, given notable differences in methodology, definitions, types of outcome measures, and timing of follow-up assessments. Only one article reported on both sports-related and non-sports-related traumatic brain injuries separately at comparable timepoints. This study revealed no differences in recovery time frames or overall symptom burden.Discussion: Whilst there is a clear benefit in researching specific subpopulations in detail, standardized outcome measures and follow-up time frames are needed across contexts to facilitate understanding of similarities and differences between sports- and non-sports-related mild traumatic brain injuries to inform clinical treatment.

On the Safety of the COVID-19 Convalescent Plasma Treatment: Thrombotic and Thromboembolic Concerns

Recently, it was reported that near-sourced COVID-19 convalescent plasma (CP) is more efficient than distantly sourced CP. What was left behind in this analysis is the investigation of the possible causes of mortality associated with the CP transfusion itself. Knowing this information is important for determining whether not receiving CP of near source is the main cause of high rate of death in the group of patients who received distantly sourced CP. We argue that the thrombotic and thromboembolic events may act as risk factors for adverse complications and death associated with CP transfusion. Therefore, they have to be considered and carefully accounted for in population studies as they can affect the CP safety profiles and change the interpretation of the cause of death in the studied groups.

Single M-Line Is as Reliable as Multiple M-Line Ultrasound for Carotid Artery Screening

Purpose: Carotid artery properties can be evaluated with high accuracy and reproducibility using multiple M-line ultrasound. However, the cost of multiple M-line-based imaging modalities and the extensive operator expertise requirements hamper the large-scale application for arterial properties assessment, particularly in resource-constrained settings. This study is aimed to assess the performance of a single M-line approach as an affordable and easy-to-use alternative to multiple M-line imaging for screening purposes.Methods: We used triplicate longitudinal common carotid artery (CCA) ultrasound recordings (17 M-lines covering about 16 mm, at 500 frames per second) of 500 subjects from The Maastricht Study to assess the validity and reproducibility of a single against multiple M-line approach. The multiple M-line measures were obtained by averaging over all available 17 lines, whereas the middle M-line was used as a proxy for the single M-line approach.Results: Diameter, intima-media thickness (IMT), and Young's elastic modulus (YEM) were not significantly different between the single and multiple M-line approaches (p > 0.07). Distension and distensibility coefficient (DC) did differ significantly (p < 0.001), however, differences were technically irrelevant. Similarly, Bland-Altman analysis revealed good agreement between the two approaches. The single M-line approach, compared to multiple M-line, exhibited an acceptable reproducibility coefficient of variation (CV) for diameter (2.5 vs. 2.2%), IMT (11.9 vs. 7.9%), distension (10 vs. 9.4%), DC (10.9 vs. 10.2%), and YEM (26.5 vs. 20.5%). Furthermore, in our study population, both methods showed a similar capability to detect age-related differences in arterial stiffness.Conclusion: Single M-line ultrasound appears to be a promising tool to estimate anatomical and functional CCA properties with very acceptable validity and reproducibility. Based on our results, we might infer that image-free, single M-line tools could be suited for screening and for performing population studies in low-resource settings worldwide. Whether the comparison between single and multiple M-line devices will yield similar findings requires further study.

Transmission of SARS-CoV-2 by children and young people in households and schools: a meta-analysis of population-based and contact-tracing studies

Background The role of children and young people (CYP) in transmission of SARS-CoV-2 in household and educational settings remains unclear. We undertook a systematic review and meta-analysis of contact-tracing and population-based studies at low risk of bias. Methods We searched 4 electronic databases on 28 July 2021 for contact-tracing studies and population-based studies informative about transmission of SARS-CoV-2 from 0-19 year olds in household or educational settings. We excluded studies at high risk of bias, including from under-ascertainment of asymptomatic infections. We undertook multilevel random effects meta-analyses of secondary attack rates (SAR: contact-tracing studies) and school infection prevalence, and used meta-regression to examine the impact of community SARS-CoV-2 incidence on school infection prevalence. Findings 4529 abstracts were reviewed, resulting in 37 included studies (16 contact-tracing; 19 population studies; 2 mixed studies). The pooled relative transmissibility of CYP compared with adults was 0.92 (0.68, 1.26) in adjusted household studies. The pooled SAR from CYP was lower (p=0.002) in school studies 0.7% (0.2, 2.7) than household studies (7.6% (3.6, 15.9) . There was no difference in SAR from CYP to child or adult contacts. School population studies showed some evidence of clustering in classes within schools. School infection prevalence was associated with contemporary community 14-day incidence (OR 1.003 (1.001, 1.004), p<0.001). Interpretation We found no difference in transmission of SARS-CoV-2 from CYP compared with adults within household settings. SAR were markedly lower in school compared with household settings, suggesting that household transmission is more important than school transmission in this pandemic. School infection prevalence was associated with community infection incidence, supporting hypotheses that school infections broadly reflect community infections. These findings are important for guiding policy decisions on shielding, vaccination school and operations during the pandemic.

Preeclampsia—an immune disease? An epidemiologic narrative

The maternal syndrome preeclampsia is triggered by syncytiotrophoblast (STB) stress; the heterogeneity of the syndrome is caused by the different pathways leading to this STB stress. Inflammation plays a pivotal role in the pathogenesis of preeclampsia. While, the immune system at large is therefore intimately involved in the causation of this heterogeneous syndrome, the role of the adaptive immune system is more controversial. The classic paradigm placed preeclampsia as the disease of the nulliparous pregnant women. Up to the later part of the 20th century, human reproduction, particularly in Western societies, was characterised by a low rate of pre-marital sex, and the great majority of children being born within one stable sexual relationship. More prolonged periods of regular sexual intercourse within a stable relationship have been demonstrated to reduce the risk of preeclampsia and fetal growth restriction. Primarily animal studies have indeed shown that repetitive sperm exposure leads to partner specific mucosal tolerance. Societal changes made partner change over the reproductive period of individual women extremely common. For the adaptive immune system of multiparous women, being pregnant in a new sexual relationship (primipaternity) would represent being faced with a new “hemi-allograft”. In these pregnancies, potential couple-specific immune “maladaptation” could lead to the superficial cytotrophoblast invasion of the spiral arteries, known to be associated with early-onset preeclampsia. Having a new pregnancy in a different relationship does indeed increase the risk for this type of preeclampsia. Large epidemiologic population studies identified prolonged birth interval but not “primipaternity” as a risk factor for preeclampsia in multiparous women. This apparent contradiction is explained by the fact that the great majority of preeclampsia cases in these population studies involve term preeclampsia. In late-onset preeclampsia, the far more common phenotype of the syndrome, STB stress is not caused by lack of proper spiral artery modification, but involves maternal genetic predisposition to cardiovascular and metabolic disease, with in particular obesity/metabolic syndrome representing major players. Partner or couple specific issues are not detectable in this disease phenotype.