Approximate Quantum Fourier Transform and Decoherence

We discuss the advantages of using the approximate quantum Fourier transform (AQFT) in algorithms which involve periodicity estimations. We analyse quantum networks performing AQFT in the presence of decoherence and show that extensive approximations can be made before the accuracy of AQFT (as compared with regular quantum Fourier transform) is compromised. We show that for some computations an approximation may imply a better performance.Comment: 14 pages, 10 fig. (8 *.eps files). More information on http://eve.physics.ox.ac.uk/QChome.html http://www.physics.helsinki.fi/~kasuomin http://www.physics.helsinki.fi/~kira/group.htm

Effects of upper body eccentric versus concentric strength training and detraining on maximal force, muscle activation, hypertrophy and serum hormones in women

Effects of eccentric (ECC) versus concentric (CON) strength training of the upper body performed twice a week for 10 weeks followed by detraining for five weeks on maximal force, muscle activation, muscle mass and serum hormone concentrations were investigated in young women (n = 11 and n = 12). One-repetition bench press (1RM), maximal isometric force and surface electromyography (EMG) of triceps brachii (TB), anterior deltoid (AD) and pectoralis major (PM), cross-sectional area (CSA) of TB (Long (LoH) and Lateral Head (LaH)) and thickness of PM, as well as serum concentrations of free testosterone, cortisol, follicle-stimulating hormone, estradiol and sex hormone-binding globulin were measured. ECC and CON training led to increases of 17.2 ± 11.3% (p \u3c 0.001) and 13.1 ± 5.7% (p \u3c 0.001) in 1RM followed by decreases of-6.6 ± 3.6% (p \u3c 0.01) and-8.0 ± 4.5% (p \u3c 0.001) during detraining, respectively. Isometric force increased in ECC by 11.4 ± 9.6 % (p \u3c 0.05) from week 5 to 10, while the change in CON by 3.9±6.8% was not significant and a between group difference was noted (p \u3c 0.05). Maximal total integrated EMG of trained muscles increased only in the whole subject group (p \u3c 0.05). CSA of TB (LoH) increased in ECC by 8.7 ± 8.0% (p \u3c 0.001) and in CON by 3.4 ± 1.6% (p \u3c 0.01) and differed between groups (p \u3c 0.05), and CSA of TB (LaH) in ECC by 15.7 ± 8.0% (p \u3c 0.001) and CON by 9.7 ± 6.6% (p \u3c 0.001). PM thickness increased in ECC by 17.7 ± 10.9% (p \u3c 0.001) and CON by 14.0 ± 5.9% (p \u3c 0.001). Total muscle sum value (LoH + LaH + PM) increased in ECC by 12.4 ± 6.9% (p \u3c 0.001) and in CON by 7.1 ± 2.9% (p \u3c 0.001) differing between groups (p \u3c 0.05) and decreased during detraining in ECC by-6.5 ± 4.3% (p \u3c 0.001) and CON by-6.1 ± 2.8% (p \u3c 0.001). The post detraining combined sum value of CSA and thickness was in ECC higher (p \u3c 0.05) than at pre training. No changes were detected in serum hormone concentrations, but baseline free testosterone levels in the ECC and CON group combined correlated with changes in 1RM (r = 0.520, p \u3c 0.016) during training. Large neuromuscular adaptations of the upper body occurred in women during ECC, and CON training in 10 weeks. Isometric force increased only in response to ECC, and total muscle sum value increased more during ECC than CON training. However, no changes occurred in serum hormones, but individual serum-free testosterone baseline concentrations correlated with changes in 1RM during strength training in the entire group. Both groups showed significant decreases in neuromuscular performance and muscle mass during detraining, while post detraining muscle sum value was only in ECC significantly higher than at pre training

Vestiges of an Ancient Border in the Contemporary Genetic Diversity of North-Eastern Europe

It has previously been demonstrated that the advance of the Neolithic Revolution from the Near East through Europe was decelerated in the northernmost confines of the continent, possibly as a result of space and resource competition with lingering Mesolithic populations. Finland was among the last domains to adopt a farming lifestyle, and is characterized by substructuring in the form of a distinct genetic border dividing the northeastern and southwestern regions of the country. To explore the origins of this divergence, the geographical patterns of mitochondrial and Y-chromosomal haplogroups of Neolithic and Mesolithic ancestry were assessed in Finnish populations. The distribution of these uniparental markers revealed a northeastern bias for hunter-gatherer haplogroups, while haplogroups associated with the farming lifestyle clustered in the southwest. In addition, a correlation could be observed between more ancient mitochondrial haplogroup age and eastern concentration. These results coupled with prior archeological evidence suggest the genetic northeast/southwest division observed in contemporary Finland represents an ancient vestigial border between Mesolithic and Neolithic populations undetectable in most other regions of Europe.Peer reviewe

Global SUMOylation on active chromatin is an acute heat stress response restricting transcription

ArticleBackground Cells have developed many ways to cope with external stress. One distinctive feature in acute proteotoxic stresses, such as heat shock (HS), is rapid post-translational modification of proteins by SUMOs (small ubiquitin-like modifier proteins; SUMOylation). While many of the SUMO targets are chromatin proteins, there is scarce information on chromatin binding of SUMOylated proteins in HS and the role of chromatin SUMOylation in the regulation of transcription. Results We mapped HS-induced genome-wide changes in chromatin occupancy of SUMO-2/3-modified proteins in K562 and VCaP cells using ChIP-seq. Chromatin SUMOylation was further correlated with HS-induced global changes in transcription using GRO-seq and RNA polymerase II (Pol2) ChIP-seq along with ENCODE data for K562 cells. HS induced a rapid and massive rearrangement of chromatin SUMOylation pattern: SUMOylation was gained at active promoters and enhancers associated with multiple transcription factors, including heat shock factor 1. Concomitant loss of SUMOylation occurred at inactive intergenic chromatin regions that were associated with CTCF-cohesin complex and SETDB1 methyltransferase complex. In addition, HS triggered a dynamic chromatin binding of SUMO ligase PIAS1, especially onto promoters. The HS-induced SUMOylation on chromatin was most notable at promoters of transcribed genes where it positively correlated with active transcription and Pol2 promoter-proximal pausing. Furthermore, silencing of SUMOylation machinery either by depletion of UBC9 or PIAS1 enhanced expression of HS-induced genes. Conclusions HS-triggered SUMOylation targets promoters and enhancers of actively transcribed genes where it restricts the transcriptional activity of the HS-induced genes. PIAS1-mediated promoter SUMOylation is likely to regulate Pol2-associated factors in HS.Publisher’s pd

Aluminum fluoride-18 labeled folate enables in vivo detection of atherosclerotic plaque inflammation by positron emission tomography

Inflammation plays an important role in the development of atherosclerosis and its complications. Because the folate receptor beta (FR-beta) is selectively expressed on macrophages, an FR targeted imaging agent could be useful for assessment of atherosclerotic inflammation. We investigated aluminum fluoride-18-labeled 1,4,7-triazacyclononane-1,4,7-triacetic acid conjugated folate (F-18-FOL) for the detection of atherosclerotic plaque inflammation. We studied atherosclerotic plaques in mice, rabbits, and human tissue samples using F-18-FOL positron emission tomography/computed tomography (PET/CT). Compound 2-deoxy-2-[F-18]fluoro-D-glucose (F-1(8)-FDG) was used as a comparison. Firstly, we found that the in vitro binding of F-18-FOL co-localized with FR-beta-positive macrophages in carotid endarterectomy samples from patients with recent ischemic symptoms. We then demonstrated specific accumulation of intravenously administered F-18-FOL in atherosclerotic plaques in mice and rabbits using PET/CT. We noticed that the F-18-FOL uptake correlated with the density of macrophages in plaques and provided a target-to-background ratio as high as F-18-FDG, but with considerably lower myocardial uptake. Thus, F-18-FOL PET/CT targeting of FR-beta-positive macrophages presents a promising new tool for the in vivo imaging of atherosclerotic inflammation

Breast cancer risks associated with missense variants in breast cancer susceptibility genes

BACKGROUND: Protein truncating variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2 are associated with increased breast cancer risk, but risks associated with missense variants in these genes are uncertain. METHODS: We analyzed data on 59,639 breast cancer cases and 53,165 controls from studies participating in the Breast Cancer Association Consortium BRIDGES project. We sampled training (80%) and validation (20%) sets to analyze rare missense variants in ATM (1146 training variants), BRCA1 (644), BRCA2 (1425), CHEK2 (325), and PALB2 (472). We evaluated breast cancer risks according to five in silico prediction-of-deleteriousness algorithms, functional protein domain, and frequency, using logistic regression models and also mixture models in which a subset of variants was assumed to be risk-associated. RESULTS: The most predictive in silico algorithms were Helix (BRCA1, BRCA2 and CHEK2) and CADD (ATM). Increased risks appeared restricted to functional protein domains for ATM (FAT and PIK domains) and BRCA1 (RING and BRCT domains). For ATM, BRCA1, and BRCA2, data were compatible with small subsets (approximately 7%, 2%, and 0.6%, respectively) of rare missense variants giving similar risk to those of protein truncating variants in the same gene. For CHEK2, data were more consistent with a large fraction (approximately 60%) of rare missense variants giving a lower risk (OR 1.75, 95% CI (1.47-2.08)) than CHEK2 protein truncating variants. There was little evidence for an association with risk for missense variants in PALB2. The best fitting models were well calibrated in the validation set. CONCLUSIONS: These results will inform risk prediction models and the selection of candidate variants for functional assays and could contribute to the clinical reporting of gene panel testing for breast cancer susceptibility

The impact of coding germline variants on contralateral breast cancer risk and survival

Evidence linking coding germline variants in breast cancer (BC)-susceptibility genes other than BRCA1, BRCA2, and CHEK2 with contralateral breast cancer (CBC) risk and breast cancer-specific survival (BCSS) is scarce. The aim of this study was to assess the association of protein-truncating variants (PTVs) and rare missense variants (MSVs) in nine known (ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53) and 25 suspected BC-susceptibility genes with CBC risk and BCSS. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated with Cox regression models. Analyses included 34,401 women of European ancestry diagnosed with BC, including 676 CBCs and 3,449 BC deaths; the median follow-up was 10.9 years. Subtype analyses were based on estrogen receptor (ER) status of the first BC. Combined PTVs and pathogenic/likely pathogenic MSVs in BRCA1, BRCA2, and TP53 and PTVs in CHEK2 and PALB2 were associated with increased CBC risk [HRs (95% CIs): 2.88 (1.70–4.87), 2.31 (1.39–3.85), 8.29 (2.53–27.21), 2.25 (1.55–3.27), and 2.67 (1.33–5.35), respectively]. The strongest evidence of association with BCSS was for PTVs and pathogenic/likely pathogenic MSVs in BRCA2 (ER-positive BC) and TP53 and PTVs in CHEK2 [HRs (95% CIs): 1.53 (1.13–2.07), 2.08 (0.95–4.57), and 1.39 (1.13–1.72), respectively, after adjusting for tumor characteristics and treatment]. HRs were essentially unchanged when censoring for CBC, suggesting that these associations are not completely explained by increased CBC risk, tumor characteristics, or treatment. There was limited evidence of associations of PTVs and/or rare MSVs with CBC risk or BCSS for the 25 suspected BC genes. The CBC findings are relevant to treatment decisions, follow-up, and screening after BC diagnosis.</p

Effect of remdesivir post hospitalization for COVID-19 infection from the randomized SOLIDARITY Finland trial

We report the first long-term follow-up of a randomized trial (NCT04978259) addressing the effects of remdesivir on recovery (primary outcome) and other patient-important outcomes one year after hospitalization resulting from COVID-19. Of the 208 patients recruited from 11 Finnish hospitals, 198 survived, of whom 181 (92%) completed follow-up. At one year, self-reported recovery occurred in 85% in remdesivir and 86% in standard of care (SoC) (RR 0.94, 95% CI 0.47-1.90). We infer no convincing difference between remdesivir and SoC in quality of life or symptom outcomes (p > 0.05). Of the 21 potential long-COVID symptoms, patients reported moderate/major bother from fatigue (26%), joint pain (22%), and problems with memory (19%) and attention/concentration (18%). In conclusion, after a one-year follow-up of hospitalized patients, one in six reported they had not recovered well from COVID-19. Our results provide no convincing evidence of remdesivir benefit, but wide confidence intervals included possible benefit and harm.Peer reviewe