Identifying the favored mutation in a positive selective sweep.

Most approaches that capture signatures of selective sweeps in population genomics data do not identify the specific mutation favored by selection. We present iSAFE (for "integrated selection of allele favored by evolution"), a method that enables researchers to accurately pinpoint the favored mutation in a large region (∼5 Mbp) by using a statistic derived solely from population genetics signals. iSAFE does not require knowledge of demography, the phenotype under selection, or functional annotations of mutations

Evaluation of sperm chromatin integrity using aniline blue and toluidine blue staining in infertile and normozoospermic men

Background: Male infertility is defined as a man lost his ability to fertilize a fertile female naturally. Diagnosis of male infertility cannot be made just according to basic semen analysis. It is necessity to have specific tests for evaluation of chromatin integrity. In this study, an attempt was made to evaluate the sperm chromatin quality in fertile men and infertile subgroup. Methods: Among 1386 couples, 342 men were categorized into normospermia and 1044 were infertile and they were referred to Yazd Research and Clinical Center for infertility treatment. Standard semen analysis and sperm nuclear maturity tests including aniline blue (AB) and toluidine blue (TB) staining were done. Data were analyzed by SPSS software. The p=0.05 was considered statistically significant. Results: The mean value of TB staining was significantly higher in infertile group compared to normospermic group (p=0.005). Mean of sperm normal morphology was lower in idiopathic infertile men in comparison with normozoospermic men (p= 0.001). The highest negative correlation was obtained between sperm count and AB staining. Progressive motility was negatively correlated with AB and TB staining in both groups but there was no significant difference between AB staining and progressive motility in men normospermia group. Conclusion: Sperm chromatin staining using AB and TB showed a negative association between sperm chromatin condensation with sperm count, normal morphology and progressive motility. It seems that the AB and TB test may be useful for the assessment of male fertility potential. © 2019 Avicenna Research Institute. All rights reserved

Containing the spread of mumps on college campuses

College campuses are vulnerable to infectious disease outbreaks, and there is an urgent need to develop better strategies to mitigate their size and duration, particularly as educational institutions around the world adapt to in-person instruction during the COVID-19 pandemic. Towards addressing this need, we applied a stochastic compartmental model to quantify the impact of university-level responses to contain a mumps outbreak at Harvard University in 2016. We used our model to determine which containment interventions were most effective and study alternative scenarios without and with earlier interventions. This model allows for stochastic variation in small populations, missing or unobserved case data and changes in disease transmission rates post-intervention. The results suggest that control measures implemented by the University\u27s Health Services, including rapid isolation of suspected cases, were very effective at containing the outbreak. Without those measures, the outbreak could have been four times larger. More generally, we conclude that universities should apply (i) diagnostic protocols that address false negatives from molecular tests and (ii) strict quarantine policies to contain the spread of easily transmissible infectious diseases such as mumps among their students. This modelling approach could be applied to data from other outbreaks in college campuses and similar small population settings

Containing the Spread of Infectious Disease on College Campuses [preprint]

College campuses are highly vulnerable to infectious disease outbreaks, and there is a pressing need to develop better strategies to mitigate their size and duration, particularly as educational institutions around the world reopen to in-person instruction in the midst of the COVID-19 pandemic. Towards addressing this need, we applied a stochastic compartmental model to quantify the impact of university-level responses to past mumps outbreaks in college campuses and used it to determine which control interventions are most effective. Mumps is a very relevant disease in such settings, given its airborne mode of transmission, high infectivity, and recurrence of outbreaks despite availability of a vaccine. Our model aims to simultaneously overcome three crucial issues: stochastic variation in small populations, missing or unobserved case data, and changes in disease transmission rates post-intervention. We tested the model and assessed various interventions using data from the 2014 and 2016 mumps outbreaks at Ohio State University and Harvard University, respectively. Our results suggest that in order to decrease infectious disease incidence on their campuses, universities should apply diagnostic protocols that address false negatives from molecular tests, stricter quarantine policies, and effective awareness campaigns among their students and staff. Our model can be applied to data from other outbreaks in college campuses and similar small-population settings

The experience of visual art for people living with mild-to-moderate vision loss

Background: Visual art can enhance wellbeing and quality-of-life; however, the experience of visual art for people with mild-to-moderate vision loss has not been examined. Methods: Eight participants (6 females, 2 males; Mean age = 81 years, SD = 7.9, range 70–91 years; 4 with mild vision loss and 4 with moderate vision loss based on binocular visual acuity) completed a mixed-methods study comprising: a semi-structured interview on visual art experience; an eye examination; and questionnaires about visual functioning and quality-of-life. Results: Various themes were identified: visual perception of art (e.g. altered colours, visual distortions, etc.), viewing conditions, elements of art, personal preference, deriving meaning, appreciation of art, impact of impaired visual perception, and social aspects of art. Conclusions: The overall experience of art is influenced by how an individual sees, perceives, and makes meaning from art. Even mild vision loss can impair this experience and impact emotional and social wellbeing.</p

Discriminating early-stage diabetic retinopathy with subjective and objective perimetry

Introduction: To prevent progression of early-stage diabetic retinopathy, we need functional tests that can distinguish multiple levels of neural damage before classical vasculopathy. To that end, we compared multifocal pupillographic objective perimetry (mfPOP), and two types of subjective automated perimetry (SAP), in persons with type 2 diabetes (PwT2D) with either no retinopathy (noDR) or mild to-moderate non-proliferative retinopathy (mmDR). Methods: Both eyes were assessed by two mfPOP test methods that present stimuli within either the central ±15° (OFA15) or ±30° (OFA30), each producing per-region sensitivities and response delays. The SAP tests were 24-2 Short Wavelength Automated Perimetry and 24-2 Matrix perimetry. Results: Five of eight mfPOP global indices were significantly different between noDR and mmDR eyes, but none of the equivalent measures differed for SAP. Per-region mfPOP identified significant hypersensitivity and longer delays in the peripheral visual field, verifying earlier findings. Diagnostic power for discrimination of noDR vs. mmDR, and normal controls vs. PwT2D, was much higher for mfPOP than SAP. The mfPOP per-region delays provided the best discrimination. The presence of localized rather than global changes in delay ruled out iris neuropathy as a major factor. Discussion: mfPOP response delays may provide new surrogate endpoints for studies of interventions for early-stage diabetic eye damage.</p

Gene Expression Levels Are a Target of Recent Natural Selection in the Human Genome

Changes in gene expression may represent an important mode of human adaptation. However, to date, there are relatively few known examples in which selection has been shown to act directly on levels or patterns of gene expression. In order to test whether single nucleotide polymorphisms (SNPs) that affect gene expression in cis are frequently targets of positive natural selection in humans, we analyzed genome-wide SNP and expression data from cell lines associated with the International HapMap Project. Using a haplotype-based test for selection that was designed to detect incomplete selective sweeps, we found that SNPs showing signals of selection are more likely than random SNPs to be associated with gene expression levels in cis. This signal is significant in the Yoruba (which is the population that shows the strongest signals of selection overall) and shows a trend in the same direction in the other HapMap populations. Our results argue that selection on gene expression levels is an important type of human adaptation. Finally, our work provides an analytical framework for tackling a more general problem that will become increasingly important: namely, testing whether selection signals overlap significantly with SNPs that are associated with phenotypes of interest

Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever

Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural selection in West African populations where Lassa haemorrhagic fever is endemic. In this study, we provide further evidence for this notion. By applying tests for selection to genome-wide data from the International Haplotype Map Consortium and the 1000 Genomes Consortium, we demonstrate evidence for positive selection in LARGE and interleukin 21 (IL21), two genes implicated in LASV infectivity and immunity. We further localized the signals of selection, using the recently developed composite of multiple signals method, to introns and putative regulatory regions of those genes. Our results suggest that natural selection may have targeted variants giving rise to alternative splicing or differential gene expression of LARGE and IL21. Overall, our study supports the hypothesis that selective pressures imposed by LASV may have led to the emergence of particular alleles conferring resistance to Lassa fever, and opens up new avenues of research pursuit

Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome

<p>Abstract</p> <p>Background</p> <p>The creation of a coherent genomic map of recent selection is one of the greatest challenges towards a better understanding of human evolution and the identification of functional genetic variants. Several methods have been proposed to detect linkage disequilibrium (LD), which is indicative of natural selection, from genome-wide profiles of common genetic variations but are designed for large regions.</p> <p>Results</p> <p>To find population-specific LD within small regions, we have devised an entropy-based method that utilizes differences in haplotype frequency between populations. The method has the advantages of incorporating multilocus association, conciliation with low allele frequencies, and independence from allele polarity, which are ideal for short haplotype analysis. The comparison of HapMap SNPs data from African and Caucasian populations with a median resolution size of ~23 kb gave us novel candidates as well as known selection targets. Enrichment analysis for the yielded genes showed associations with diverse diseases such as cardiovascular, immunological, neurological, and skeletal and muscular diseases. A possible scenario for a selective force is discussed. In addition, we have developed a web interface (ENIGMA, available at <url>http://gibk21.bse.kyutech.ac.jp/ENIGMA/index.html</url>), which allows researchers to query their regions of interest for population-specific LD.</p> <p>Conclusion</p> <p>The haplotype entropy method is powerful for detecting population-specific LD embedded in short regions and should contribute to further studies aiming to decipher the evolutionary histories of modern humans.</p