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Evaluation of the Roche MagNA Pure 96 nucleic acid extraction platform for the Seegene Anyplex II HPV28 detection assay

Atchison S, Shilling H, Balgovind P, Machalek DA, Hawkes D, Garland SM, et al.

J Appl Microbiol, 2021 Nov;131(5):2592-2599.
PMID: 33942451 DOI: 10.1111/jam.15126

AIM: Validate the Roche, MagNAPure96 (MP96) nucleic acid extraction platform for Seegene Anyplex II HPV28 (Anyplex28) detection of Human Papillomavirus.
METHODS AND RESULTS: Comparisons were made for Anyplex28 genotyping from 115 cervical samples extracted on the Hamilton, STARlet and the MP96. Two DNA concentrations were used for the MP96, one matched for sample input to the STARlet and another 5× concentration (laboratory standard). Agreement of HPV detection was 89·8% (κ = 0·798; P = 0·007), with HPV detected in 10 more samples for the MP96. There was a high concordance of detection for any oncogenic HPV genotype (κ = 0·77; P = 0·007) and for any low-risk HPV genotype (κ = 0·85; P = 0·008). DNA extracted at laboratory standard had a lower overall agreement 85·2% (κ = 0·708; P
Fulltext Evaluation of Seegene Anyplex II Performance for Detection of Human Papillomavirus Genotypes in Formalin-Fixed, Paraffin-Embedded Cervical Cancer Specimens

Haqshenas G, Molano M, Phillips S, Balgovind P, Garland SM, Hawkes D, et al.

Arch Pathol Lab Med, 2024 Mar 01;148(3):353-358.
PMID: 37226838 DOI: 10.5858/arpa.2022-0317-OA

CONTEXT.—: Detection of human papillomavirus (HPV) in formalin-fixed, paraffin-embedded (FFPE) tissues may identify the cause of lesions and has value for the development of new diagnostic assays and epidemiologic studies. Seegene Anyplex II assays are widely used for HPV screening, but their performance using FFPE samples has not been fully explored.
OBJECTIVE.—: To validate Anyplex II HPV HR Detection (Anyplex II, Seegene) using FFPE samples.
DESIGN.—: We used 248 stored DNA extracts from cervical cancer FFPE samples collected during 2005-2015 that tested HPV positive using the RHA kit HPV SPF10-LiPA25, v1 (SPF10, Labo Biomedical Products) HPV genotyping assay, manufacturer-validated for FFPE samples.
RESULTS.—: Of the selected 248 samples, 243 were used in our analysis. Consistent with SPF10 genotyping results, Anyplex II detected all 12 oncogenic types and had an overall HPV detection rate of 86.4% (210 of 243 samples). Anyplex II and SPF10 showed very high agreement for the detection of the 2 most important oncogenic genotypes: HPV 16 (219 of 226; 96.9%; 95% CI, 93.7-98.75) and HPV 18 (221 of 226; 97.8%; 95% CI, 94.9-99.3).
CONCLUSIONS.—: Overall results showed that both platforms produced comparable HPV genotyping results, indicating the suitability of Anyplex II for FFPE samples. The Anyplex II assay has the added convenience of being an efficient, single-well semiquantitative polymerase chain reaction assay. Further optimization of Anyplex II may enhance its performance using FFPE samples by improving the detection limit.
Fulltext Impacts of logging on density-dependent predation of dipterocarp seeds in a South East Asian rainforest

Bagchi R, Philipson CD, Slade EM, Hector A, Phillips S, Villanueva JF, et al.

Philos Trans R Soc Lond B Biol Sci, 2011 Nov 27;366(1582):3246-55.
PMID: 22006965 DOI: 10.1098/rstb.2011.0034

Much of the forest remaining in South East Asia has been selectively logged. The processes promoting species coexistence may be the key to the recovery and maintenance of diversity in these forests. One such process is the Janzen-Connell mechanism, where specialized natural enemies such as seed predators maintain diversity by inhibiting regeneration near conspecifics. In Neotropical forests, anthropogenic disturbance can disrupt the Janzen-Connell mechanism, but similar data are unavailable for South East Asia. We investigated the effects of conspecific density (two spatial scales) and distance from fruiting trees on seed and seedling survival of the canopy tree Parashorea malaanonan in unlogged and logged forests in Sabah, Malaysia. The production of mature seeds was higher in unlogged forest, perhaps because high adult densities facilitate pollination or satiate pre-dispersal predators. In both forest types, post-dispersal survival was reduced by small-scale (1 m(2)) conspecific density, but not by proximity to the nearest fruiting tree. Large-scale conspecific density (seeds per fruiting tree) reduced predation, probably by satiating predators. Higher seed production in unlogged forest, in combination with slightly higher survival, meant that recruitment was almost entirely limited to unlogged forest. Thus, while logging might not affect the Janzen-Connell mechanism at this site, it may influence the recruitment of particular species.
UEFA expert group statement on nutrition in elite football. Current evidence to inform practical recommendations and guide future research

Collins J, Maughan RJ, Gleeson M, Bilsborough J, Jeukendrup A, Morton JP, et al.

Br J Sports Med, 2021 Apr;55(8):416.
PMID: 33097528 DOI: 10.1136/bjsports-2019-101961

Football is a global game which is constantly evolving, showing substantial increases in physical and technical demands. Nutrition plays a valuable integrated role in optimising performance of elite players during training and match-play, and maintaining their overall health throughout the season. An evidence-based approach to nutrition emphasising, a 'food first' philosophy (ie, food over supplements), is fundamental to ensure effective player support. This requires relevant scientific evidence to be applied according to the constraints of what is practical and feasible in the football setting. The science underpinning sports nutrition is evolving fast, and practitioners must be alert to new developments. In response to these developments, the Union of European Football Associations (UEFA) has gathered experts in applied sports nutrition research as well as practitioners working with elite football clubs and national associations/federations to issue an expert statement on a range of topics relevant to elite football nutrition: (1) match day nutrition, (2) training day nutrition, (3) body composition, (4) stressful environments and travel, (5) cultural diversity and dietary considerations, (6) dietary supplements, (7) rehabilitation, (8) referees and (9) junior high-level players. The expert group provide a narrative synthesis of the scientific background relating to these topics based on their knowledge and experience of the scientific research literature, as well as practical experience of applying knowledge within an elite sports setting. Our intention is to provide readers with content to help drive their own practical recommendations. In addition, to provide guidance to applied researchers where to focus future efforts.
Erratum to: Methods for evaluating medical tests and biomarkers

Gopalakrishna G, Langendam M, Scholten R, Bossuyt P, Leeflang M, Noel-Storr A, et al.

Diagn Progn Res, 2017;1:11.
PMID: 31095132 DOI: 10.1186/s41512-017-0011-4

[This corrects the article DOI: 10.1186/s41512-016-0001-y.].