PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology

PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented, accelerated Smith–Waterman and ParAlign. The ParAlign algorithm is similar to Smith–Waterman in sensitivity, while as quick as BLAST for protein searches. A form of parallel computing technology known as multimedia technology that is available in modern processors, but rarely used by other bioinformatics software, has been exploited to achieve the high speed. The software is also designed to run efficiently on computer clusters using the message-passing interface standard. A public search service powered by a large computer cluster has been set-up and is freely available at , where the major public databases can be searched. The software can also be downloaded free of charge for academic use

Diabetes and Breast Cancer Subtypes

Background Women with diabetes have a worse survival after breast cancer diagnosis compared to women without diabetes. This may be due to a different etiological profile, leading to the development of more aggressive breast cancer subtypes. Our aim was to investigate whether insulin and non-insulin treated women with diabetes develop specific clinicopathological breast cancer subtypes compared to women without diabetes. Methods and Findings This cross-sectional study included randomly selected patients with invasive breast cancer diagnosed in 2000-2010. Stratified by age at breast cancer diagnosis (50 years), women with diabetes were 2:1 frequency-matched on year of birth and age at breast cancer diagnosis (both in 10-year categories) to women without diabetes, to select similar to 300 patients with tumor tissue available. Tumor MicroArrays were stained by immunohistochemistry for estrogen and progesterone receptor (ER, PR), HER2, Ki67, CK5/6, CK14, and p63. A pathologist scored all stains and revised morphology and grade. Associations between diabetes/insulin treatment and clinicopathological subtypes were analyzed using multivariable logistic regression. Morphology and grade were not significantly different between women with diabetes (n = 211) and women without diabetes (n = 101), irrespective of menopausal status. Premenopausal women with diabetes tended to have more often PR-negative (OR = 2.44(95%C1:1.07-5.55)), HER2-negative (OR = 2.84(95%C1:1.11-7.22)), and basal-like (OR = 3.14(95%C1:1.03-9.60) tumors than the women without diabetes, with non-significantly increased frequencies of ER-negative (OR = 2.48(95`)/X1:0.95-6.45)) and triple negative (OR = 2.60(95%CI:0.88-7.67) tumors. After adjustment for age and BMI, the associations remained similar in size but less significant. We observed no evidence for associations of clinicopathological subtypes with diabetes in postmenopausal women, or with insulin treatment in general. Conclusions We found no compelling evidence that women with diabetes, treated with or without insulin, develop different breast cancer subtypes than women without diabetes. However, premenopausal women with diabetes tended to develop breast tumors that do not express hormonal receptors, which are typically associated with poor prognosis.Peer reviewe

Danger zone assessment in small-sided recreational football: Providing data for consideration in relation to COVID-19 transmission

Abstract - During the COVID-19 pandemic, physical inactivity has increased, and a wide range of sporting activities locked down, with possible long-term implications for public health. Football is the most popular sport worldwide, and recreational football training leads to broad-spectrum health effects. Football is, however, deemed a contact sport with frequent close contact important to consider during COVID-19 pandemic. Objectives - This study investigated time spent with close contact (danger zone (DZ) within 1.5 m), number of contacts and time per contact, and compared game formats in recreational small-sided football games for young and adult male football players. Methods - Movement analyses were performed on 10 Hz Global Positioning System (GPS) data collected during various small-sided football games prior to the COVID-19 outbreak. Results - Time spent in the DZ was 4.3–7.9 s/h per per cent infected players, corresponding to 34.3–114.8 s/h if one player was infected. Number of contacts with one infected player was 23.5–87.7 per hour, with an average contact time of 1.1–1.4 s, and a total number of contacts of 311–691 per hour with all players. 53%–65% of all contacts were shorter than 1 s and 77%–85% shorter than 2 s. Trivial to small effects were found for number of participants and area per player, whereas standard of play and playing with/without boards had no effect. Conclusion - This study demonstrated that during small-sided football limited time is spent within DZ and that player contacts are brief. Recreational football may therefore more appropriately be deemed as sporting activity with brief, sporadic contact

The Faroe Islands COVID-19 Recreational Football Study: Player-to-Player Distance, Body-to-Body Contact, Body-to-Ball Contact and Exercise Intensity during Various Types of Football Training for Both Genders and Various Age Groups

We determined player-to-player distance, body-to-ball contact, and exercise intensity during three training modalities in various football populations. 213 participants were recruited, ranging from 9-year-old boys to young men and 11-year-old girls to middleaged women. All groups were analysed with video-filming and GPS-based Polar Pro monitors during three types of football training for 20 min, i.e., COVID-19-modified training (CMT) with >2-metre player-to-player distance, small-sided games (SSG), and simulated match-play with normal rules (SMP), in randomised order. Time spent in a danger zone (1.5 m) perpercent-infected-player (DZ PPIP) ranged from 0.015 to 0.279% of playing time. DZ PPIP for SSG was higher (P < 0:05) than CMT and SMP. The average number of contacts (within 1.5 m) with a potentially infected player ranged from 12 to 73 contacts/hour. SSG had more (P < 0:05) contacts than CMT and SMP, with SMP having a higher (P < 0:05) number of contacts than CMT. Time/contact ranged from 0.87 to 3.00 seconds for the groups. No player-to-player and body-to-ball touches were registered for CMT. Total player-to-player contacts were 264% higher (P < 0:05) in SSG than SMP, ranging from 80 to 170 and 25 to 56 touches, respectively. In all groups, a greater total distance was covered during SMP compared to CMT (38–114%; P < 0:05). All groups performed more high-intensity running (33–54%; P < 0:05) and had higher heart rates during SMP compared to CMT. Different types of football training all appear to exert a minor COVID-19 infection risk; however, COVID-19-modified training may be safer than small-sided game training, but also match-play. In contrast, exercise intensity is lower during COVID-19-modified training than match-play

Strut chordal-sparing mitral valve replacement preserves long-term left ventricular shape and function in pigs

ObjectiveMitral valve replacement with preservation of the entire subvalvular apparatus entails superior postoperative left ventricular function compared with other techniques. However, this option is often not possible because of valve pathology. We hypothesized that preservation of only 4 mitral valve secondary (“strut”) chordae would be functionally and geometrically equivalent to total valve preservation in the long-term setting. In a porcine mitral valve replacement model we investigated the long-term effects of 3 surgical techniques on left ventricular function and geometry: (1) total preservation of the native valve, (2) strut chordal preservation, and (3) total excision of the subvalvular apparatus.MethodsForty 60-kg pigs were randomized to 1 of the 3 techniques. Global and regional left ventricular function and dimensions were assessed with cardiovascular magnetic resonance and conductance catheter 90 days after mitral valve replacement. Groups were compared by multivariate analysis of variance.ResultsThere was no overall difference between groups 1 and 2. Group 3 animals had (1) greater base-apex diastolic and systolic lengths, and smaller short-axis diameters, and (2) lower sphericity indices, and greater base-apex and short-axis fractional shortening than groups 1 and 2. Regional analysis showed slimming and elongation to occur primarily in the basal left ventricular segments. Left ventricular contractility and hemodynamic parameters did not differ between groups.ConclusionsStrut chordal preservation was equivalent to total valve preservation during mitral valve replacement, whereas total chordal resection caused significant left ventricular slimming with compensatory increases in fractional shortening. Therefore, to preserve left ventricular geometry, special attention must be paid to maintain the valvular–ventricular continuity through the strut chordae during mitral valve replacement. This concept may have important therapeutic implications for chordal-sparing mitral valve replacement

Complex multi-block analysis identifies new immunologic and genetic disease progression patterns associated with the residual β-cell function 1 year after diagnosis of type 1 diabetes

The purpose of the present study is to explore the progression of type 1 diabetes (T1D) in Danish children 12 months after diagnosis using Latent Factor Modelling. We include three data blocks of dynamic paraclinical biomarkers, baseline clinical characteristics and genetic profiles of diabetes related SNPs in the analyses. This method identified a model explaining 21.6% of the total variation in the data set. The model consists of two components: (1) A pattern of declining residual β-cell function positively associated with young age, presence of diabetic ketoacidosis and long duration of disease symptoms (P = 0.0004), and with risk alleles of WFS1, CDKN2A/2B and RNLS (P = 0.006). (2) A second pattern of high ZnT8 autoantibody levels and low postprandial glucagon levels associated with risk alleles of IFIH1, TCF2, TAF5L, IL2RA and PTPN2 and protective alleles of ERBB3 gene (P = 0.0005). These results demonstrate that Latent Factor Modelling can identify associating patterns in clinical prospective data--future functional studies will be needed to clarify the relevance of these patterns