A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets

Well-defined relationships between oligonucleotide properties and hybridization signal intensities (HSI) can aid chip design, data normalization and true biological knowledge discovery. We clarify these relationships using the data from two microarray experiments containing over three million probes from 48 high-density chips. We find that melting temperature (Tm) has the most significant effect on HSI while length for the long oligonucleotides studied has very little effect. Analysis of positional effect using a linear model provides evidence that the protruding ends of probes contribute more than tethered ends to HSI, which is further validated by specifically designed match fragment sliding and extension experiments. The impact of sequence similarity (SeqS) on HSI is not significant in comparison with other oligonucleotide properties. Using regression and regression tree analysis, we prioritize these oligonucleotide properties based on their effects on HSI. The implications of our discoveries for the design of unbiased oligonucleotides are discussed. We propose that isothermal probes designed by varying the length is a viable strategy to reduce sequence bias, though imposing selection constraints on other oligonucleotide properties is also essential

The Effect of a Division 1 Women’s Basketball Strength and Conditioning Protocol on Mental Toughness

International Journal of Exercise Science 16(5): 315-326, 2023. Mental toughness (MT) is a popularized term in sports since it has been found to be positively related to performance. Self-assessment is the most common method of MT data collection. In the strength and conditioning (S&C) context, MT research has focused on males with a notable lack of female participants. Division 1 NCAA strength and conditioning coaches (SCC) spend more hours with their athletes during offseason training than any other coach. The purpose of this study was to measure the perceived effectiveness of an off-season S&C training regimen on MT levels of female athletes while also examining the differences in these perceptions between athletes, teammates, and their SCC. Following a quasi-experimental, longitudinal design, 12 student-athletes assessed their own (n = 58) and one teammate’s (n = 58) levels of MT using the Mental Toughness Index five times over their off-season training S&C regimen. The SCC rated his players, as well (n = 60). MT levels increased significantly post-intervention [F (1, 23) = 7.27, p = .001]. The student-athletes perceived the effect of the intervention as more substantial compared to the SCC [F (1, 117) = 49.03, p \u3c .001]. A more compatible perception of MT was found between athlete and teammate; no statistical significance was observed [F (1, 115) = 1.51, p = .221]. Evidence to support that this off-season S&C program worked regarding increasing MT levels was found. Our findings indicate compatibility between athletes, but not between athletes and coach, in recognizing this construct