title: Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?

authors: McGaughran, Angela

subjects: Science & Technology

abstract: Background: Next-generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wet lab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and several indicators of library quality following targeted NGS sequencing of ~1300 loci using 271 samples of pinned moth specimens (Helicoverpa armigera) ranging in age from 5 to 117 years.

Results: I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing.

Conclusions: Sample age has a significant, measurable impact on the quality of NGS data following targeted enrichment. However, incorporating an uracil-removing enzyme into the blunt-end repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.

text: Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time? Background: Next-generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wet lab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and several indicators of library quality following targeted NGS sequencing of ~1300 loci using 271 samples of pinned moth specimens (Helicoverpa armigera) ranging in age from 5 to 117 years.

Results: I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing.

Conclusions: Sample age has a significant, measurable impact on the quality of NGS data following targeted enrichment. However, incorporating an uracil-removing enzyme into the blunt-end repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.

year: 2020-02-28

title: Clinical Implications of Landing Distance on Landing Error Scoring System Scores

authors: Hanzlíková, Ivana

subjects: Science & Technology

abstract: Context: The Landing Error Scoring System (LESS) screens for the risk of non-contact anterior cruciate ligament injury. The LESS requires individuals to jump forward from a 30-cm box to a distance of 50% of their body height. However, different landing distances have been cited in the scientific literature.

Objective: To examine whether landing distance influences LESS outcomes.

Design: Cross-sectional study.

Setting: Laboratory.

Participants or Other Participants: Seventy young active individuals (34 males, 36 females).

Intervention(s): Participants performed 33 30-cm jump landing tasks under 2 landing conditions in randomized order: (1) 50% of body height (d50%), (2) self-selected distance (dss).

Main Outcome Measure(s): Mean LESS scores, proportions of individuals categorized at high (LESS: 5 errors) and low (LESS: <5 errors) injury risk, and landing distances were compared between conditions using generalized estimating equations. Consistency of risk categorization was examined using odds ratios (ORs) and McNemar tests. McNemar and Wilcoxon signed rank tests were used to compare the occurrence of specific LESS errors.

Results: Participants landed closer to the box under the dss condition (difference = 23.28 [95% CI = 20.73, 25.81]%, P < .001). Group mean LESS scores (difference = 0.01 [95% CI = 0.59, 0.57] error, P = .969) and risk categorization (OR = 0.94 [95% CI = 0.47, 1.88], P = .859) were similar between conditions. However, individual-level risk categorization was inconsistent in 33% of participants, as was the occurrence of specific errors.

Conclusions: Using dss during the LESS might lead to different LESS errors and risk categorizations at an individual level than using d50%. Given that individual LESS scores are of primary interest in clinical and sport settings and the injury-risk threshold has not been validated for dss, we recommend the use of the original LESS protocol. When only group mean LESS scores or proportions of at-risk individuals are of interest, using dss is feasible to facilitate the testing of large cohorts.

text: Clinical Implications of Landing Distance on Landing Error Scoring System Scores Context: The Landing Error Scoring System (LESS) screens for the risk of non-contact anterior cruciate ligament injury. The LESS requires individuals to jump forward from a 30-cm box to a distance of 50% of their body height. However, different landing distances have been cited in the scientific literature.

Objective: To examine whether landing distance influences LESS outcomes.

Design: Cross-sectional study.

Setting: Laboratory.

Participants or Other Participants: Seventy young active individuals (34 males, 36 females).

Intervention(s): Participants performed 33 30-cm jump landing tasks under 2 landing conditions in randomized order: (1) 50% of body height (d50%), (2) self-selected distance (dss).

Main Outcome Measure(s): Mean LESS scores, proportions of individuals categorized at high (LESS: 5 errors) and low (LESS: <5 errors) injury risk, and landing distances were compared between conditions using generalized estimating equations. Consistency of risk categorization was examined using odds ratios (ORs) and McNemar tests. McNemar and Wilcoxon signed rank tests were used to compare the occurrence of specific LESS errors.

Results: Participants landed closer to the box under the dss condition (difference = 23.28 [95% CI = 20.73, 25.81]%, P < .001). Group mean LESS scores (difference = 0.01 [95% CI = 0.59, 0.57] error, P = .969) and risk categorization (OR = 0.94 [95% CI = 0.47, 1.88], P = .859) were similar between conditions. However, individual-level risk categorization was inconsistent in 33% of participants, as was the occurrence of specific errors.

Conclusions: Using dss during the LESS might lead to different LESS errors and risk categorizations at an individual level than using d50%. Given that individual LESS scores are of primary interest in clinical and sport settings and the injury-risk threshold has not been validated for dss, we recommend the use of the original LESS protocol. When only group mean LESS scores or proportions of at-risk individuals are of interest, using dss is feasible to facilitate the testing of large cohorts.

year: 2021-06-01

title: Academic success amongst a cohort of gifted and talented Māori and Pasifika secondary school boys: Elements that have contributed to their achievement

authors: Miller, Graeme Oliver

subjects: Māori

abstract: In recent years Māori and Pasifika students have been the focus of much discussion and a significant amount of research relating to underachievement. Despite this, many Māori and Pasifika secondary school boys are achieving highly in the academic sphere within the context of mainstream boys’ state secondary schools in New Zealand. Achievement aside, evidence shows that Māori and Pasifika secondary school boys are seriously under-represented in programmes for the gifted and talented. This enquiry examines factors in relation to identifying gifted and talented students, and investigates how their abilities are forged and nurtured. The reasons for student success merit serious investigation because of how the multiple elements contributing to their achievement are likely to be applicable to others, and are a pressing concern for academic attainment in the New Zealand education system. 
 
This qualitative study examines why 30 academically successful Māori and Pasifika secondary school boys achieved highly in the mainstream education system. The boys ranged from 13 to 19 years, the youngest being in his first year at high school as a Year 9 student, and the oldest being in his second year at university. The thesis argues their academic success was due to the complex interplay of home and school environmental elements, and the boys’ intrapersonal characteristics. The study explored the boys’ and parents’ narratives to explain why students had achieved highly, and examined both the parents’ and boys’ perceptions of how well the schools had provided for their intellectual, emotional and cultural needs. Sociocultural learning theory is the main theoretical lens through which the findings are viewed. The methodology is primarily built upon narrative inquiry. The main method of data collection was by semi-structured interview, both individually and in focus groups. Supplementary methods utilised were questionnaires and observation.  
  
An issue in the research was the disparity between the cultural and ethnic background of the participants and myself as the researcher. However, an endeavour was made to mitigate this by consulting with Māori and Pasifika educators, a kaumatua (elder) and iwi (tribal) representative prior to the research commencing. In addition, models developed through this study were submitted to Māori and Pasifika educators for their comment and approval prior to being included. 
 
With its focus specifically on highly-achieving Māori and Pasifika secondary school boys, this thesis makes an original contribution to the national and international discussion about raising student achievement. It provides a platform for further research to 	address the particular concerns around the underachievement of Māori and Pasifika secondary school boys. 
 
While there are several implications arising from the research, all are linked to the need for policy makers and educators to address the issue of the underrepresentation of Māori and Pasifika students in programmes for the gifted and talented. Policies, practices and relationships need to be examined to evaluate how effectively they contribute to gifted and talented Māori and Pasifika students receiving the academic opportunities they deserve. A key part of this examination will need to include consultation with students and their whānau.

text: Academic success amongst a cohort of gifted and talented Māori and Pasifika secondary school boys: Elements that have contributed to their achievement In recent years Māori and Pasifika students have been the focus of much discussion and a significant amount of research relating to underachievement. Despite this, many Māori and Pasifika secondary school boys are achieving highly in the academic sphere within the context of mainstream boys’ state secondary schools in New Zealand. Achievement aside, evidence shows that Māori and Pasifika secondary school boys are seriously under-represented in programmes for the gifted and talented. This enquiry examines factors in relation to identifying gifted and talented students, and investigates how their abilities are forged and nurtured. The reasons for student success merit serious investigation because of how the multiple elements contributing to their achievement are likely to be applicable to others, and are a pressing concern for academic attainment in the New Zealand education system. 
 
This qualitative study examines why 30 academically successful Māori and Pasifika secondary school boys achieved highly in the mainstream education system. The boys ranged from 13 to 19 years, the youngest being in his first year at high school as a Year 9 student, and the oldest being in his second year at university. The thesis argues their academic success was due to the complex interplay of home and school environmental elements, and the boys’ intrapersonal characteristics. The study explored the boys’ and parents’ narratives to explain why students had achieved highly, and examined both the parents’ and boys’ perceptions of how well the schools had provided for their intellectual, emotional and cultural needs. Sociocultural learning theory is the main theoretical lens through which the findings are viewed. The methodology is primarily built upon narrative inquiry. The main method of data collection was by semi-structured interview, both individually and in focus groups. Supplementary methods utilised were questionnaires and observation.  
  
An issue in the research was the disparity between the cultural and ethnic background of the participants and myself as the researcher. However, an endeavour was made to mitigate this by consulting with Māori and Pasifika educators, a kaumatua (elder) and iwi (tribal) representative prior to the research commencing. In addition, models developed through this study were submitted to Māori and Pasifika educators for their comment and approval prior to being included. 
 
With its focus specifically on highly-achieving Māori and Pasifika secondary school boys, this thesis makes an original contribution to the national and international discussion about raising student achievement. It provides a platform for further research to 	address the particular concerns around the underachievement of Māori and Pasifika secondary school boys. 
 
While there are several implications arising from the research, all are linked to the need for policy makers and educators to address the issue of the underrepresentation of Māori and Pasifika students in programmes for the gifted and talented. Policies, practices and relationships need to be examined to evaluate how effectively they contribute to gifted and talented Māori and Pasifika students receiving the academic opportunities they deserve. A key part of this examination will need to include consultation with students and their whānau.

year: 2015