Biology subjects

Vaez, A.

Publications and source records attributed to Vaez, A..

4 recordsLinked to original sources

bioRxiv2026

User-driven development and evaluation of an agentic framework for analysis of large pathway diagrams

As biomedical knowledge keeps growing, resources storing available information multiply and grow in size and complexity. Such resources can be in the format of molecular interaction maps, which represent cellular and molecular processes under normal or pathological conditions. However, these maps can be complex and hard to navigate, especially to novice users. Large Language Models (LLMs), particularly in the form of agentic frameworks, have emerged as a promising technology to support this exploration. In this article, we describe a user-driven process of prototyping, development, and user testing of Llemy, an LLM-based system for exploring these molecular interaction maps. By involving domain experts from the very first prototyping in the form of a hackathon and collecting both fine-grained and general feedback on more refined versions, we were able to evaluate the perceived utility and quality of the developed system, in particular for summarising maps and pathways, as well as prioritise the development of future features. We recommend continued user-driven development and benchmarking to keep the community engaged. This will also facilitate the transition towards open-weight LLMs to support the needs of the open research environment in an ever-changing technology landscape.

bioinformatics↗

bioRxiv2020

Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.

Identifying genetic determinants of reproductive success may highlight mechanisms underlying fertility and also identify alleles under present-day selection. Using data in 785,604 individuals of European ancestry, we identify 43 genomic loci associated with either number of children ever born (NEB) or childlessness. These loci span diverse aspects of reproductive biology across the life course, including puberty timing, age at first birth, sex hormone regulation and age at menopause. Missense alleles in ARHGAP27 were associated with increased NEB but reduced reproductive lifespan, suggesting a trade-off between reproductive ageing and intensity. As NEB is one component of evolutionary fitness, our identified associations indicate loci under present-day natural selection. Accordingly, we find that NEB-increasing alleles have increased in frequency over the past two generations. Furthermore, integration with data from ancient selection scans identifies a unique example of an allele--FADS1/2 gene locus--that has been under selection for thousands of years and remains under selection today. Collectively, our findings demonstrate that diverse biological mechanisms contribute to reproductive success, implicating both neuro-endocrine and behavioural influences.

genetics↗

bioRxiv2020

Identification of 370 loci for age at onset of sexual and reproductive behaviour, highlighting common aetiology with reproductive biology, externalizing behaviour and longevity

Age at first sexual intercourse (AFS) and age at first birth (AFB) have implications for health and evolutionary fitness. In the largest genome-wide association study to date (AFS, N=387,338; AFB, N=542,901), we identify 370 independent signals, 11 sex-specific, with a 5-6% polygenic score (PGS) prediction. Heritability of AFB shifted from 9% [CI=4-14] for women born in 1940 to 22% [CI=19-25] in 1965. Signals are driven by the genetics of reproductive biology and externalising behaviour, with key genes related to follicle stimulating hormone (FSHB), implantation (ESR1), infertility, and spermatid differentiation. Polycystic Ovarian Syndrome leads to later AFB, linking with infertility. Late AFB is protective against later-life disease and associated with parental longevity. Higher childhood socioeconomic circumstances and those in the highest PGS decile (90%+) experience markedly later reproductive onset. Results are relevant for improving teenage and late-life health, for understanding longevity, and guiding experimentation into mechanisms of infertility.

genetics↗

bioRxiv2019

Electrospun cellulose acetate/gelatin nanofibrous wound dressing containing berberine for diabetic foot ulcer healing: in vitro and in vivo studies

Functional dressing with tailored physicochemical and biological properties is vital for diabetic foot ulcer (DFU) treatment. Our main objective in the current study was to fabricate Cellulose Acetate/Gelatin (CA/Gel) electrospun nanofibrous mat loaded with berberine (Beri) as the DFU dressing. The results demonstrated that the diameter of the nanofibers was around 502 nm, the tensile strength, contact angle, porosity, water vapor permeability, and water uptake ratio of CA/Gel nanofibers were around 2.83 MPa, 58.07, 78.17 %, 11.23 mg/cm2 hr, and 12.78 respectively, while these values for CA/Gel/Beri nanofibers were 2.69 {+/-} 0.05 MPa, 56.93 {+/-} 1, 76.17 {+/-} 0.76 %, 10.17 {+/-} 0.21 mg/cm2 hr, 14.37 {+/-} 0.42 respectively. The bacterial evaluations demonstrated that the dressings are an excellent barrier against bacterial penetration with potent antibacterial activity. The animal studies depicted that the collagen density and angiogenesis score in the CA/Gel/Beri treated group were 88.8{+/-}6.7 % and 19.8{+/-}3.8, respectively. These findings implied that the incorporation of berberine did not compromise the physical properties of dressing, while improving the biological activates. In conclusion, our findings implied that the prepared mat is a proper wound dressing for DFU management and treatment.

bioengineering↗