A TQFT associated to the LMO invariant of three-dimensional manifolds

We construct a Topological Quantum Field Theory (in the sense of Atiyah) associated to the universal finite-type invariant of 3-dimensional manifolds, as a functor from the category of 3-dimensional manifolds with parametrized boundary, satisfying some additional conditions, to an algebraic-combinatorial category. It is built together with its truncations with respect to a natural grading, and we prove that these TQFTs are non-degenerate and anomaly-free. The TQFT(s) induce(s) a (series of) representation(s) of a subgroup ${\cal L}_g$ of the Mapping Class Group that contains the Torelli group. The N=1 truncation produces a TQFT for the Casson-Walker-Lescop invariant.Comment: 28 pages, 13 postscript figures. Version 2 (Section 1 has been considerably shorten, and section 3 has been slightly shorten, since they will constitute a separate paper. Section 4, which contained only announce of results, has been suprimated; it will appear in detail elsewhere. Consequently some statements have been re-numbered. No mathematical changes have been made.

Methodology for the comparative assessment of the Satellite Power System (SPS) and alternative technologies

The energy systems concerned are the satellite power system, several coal technologies, geothermal energy, fission, fusion, terrestrial solar systems, and ocean thermal energy conversion. Guidelines are suggested for the characterization of these systems, side-by-side analysis, alternative futures analysis, and integration and aggregation of data. A description of the methods for assessing the technical, economic, environmental, societal, and institutional issues surrounding the development of the selected energy technologies is presented

Accidental Hypothermia in a Swiss Alpine Trauma Centre-Not an Alpine Problem.

BACKGROUND Research in accidental hypothermia focuses on trauma patients, patients exposed to cold environments or patients after drowning but rarely on hypothermia in combination with intoxications or on medical or neurological issues. The aim of this retrospective single-centre cohort study was to define the aetiologies, severity and relative incidences of accidental hypothermia, methods of measuring temperature and in-hospital mortality. METHODS The study included patients ≥18 years with a documented body temperature ≤35 °C who were admitted to the emergency department (ED) of the University Hospital in Bern between 2000 and 2019. RESULTS 439 cases were included, corresponding to 0.32 per 1000 ED visits. Median age was 55 years (IQR 39-70). A total of 167 patients (38.0%) were female. Furthermore, 63.3% of the patients suffered from mild, 24.8% from moderate and 11.9% from severe hypothermia. Exposure as a single cause for accidental hypothermia accounted for 12 cases. The majority were combinations of hypothermia with trauma (32.6%), medical conditions (34.2%), neurological conditions (5.2%), intoxications (20.3%) or drowning (12.0%). Overall mortality was 22.3% and depended on the underlying causes, severity of hypothermia, age and sex

A Computational Framework Discovers New Copy Number Variants with Functional Importance

Structural variants which cause changes in copy numbers constitute an important component of genomic variability. They account for 0.7% of genomic differences in two individual genomes, of which copy number variants (CNVs) are the largest component. A recent population-based CNV study revealed the need of better characterization of CNVs, especially the small ones (<500 bp).We propose a three step computational framework (Identification of germline Changes in Copy Number or IgC2N) to discover and genotype germline CNVs. First, we detect candidate CNV loci by combining information across multiple samples without imposing restrictions to the number of coverage markers or to the variant size. Secondly, we fine tune the detection of rare variants and infer the putative copy number classes for each locus. Last, for each variant we combine the relative distance between consecutive copy number classes with genetic information in a novel attempt to estimate the reference model bias. This computational approach is applied to genome-wide data from 1250 HapMap individuals. Novel variants were discovered and characterized in terms of size, minor allele frequency, type of polymorphism (gains, losses or both), and mechanism of formation. Using data generated for a subset of individuals by a 42 million marker platform, we validated the majority of the variants with the highest validation rate (66.7%) was for variants of size larger than 1 kb. Finally, we queried transcriptomic data from 129 individuals determined by RNA-sequencing as further validation and to assess the functional role of the new variants. We investigated the possible enrichment for variant's regulatory effect and found that smaller variants (<1 Kb) are more likely to regulate gene transcript than larger variants (p-value = 2.04e-08). Our results support the validity of the computational framework to detect novel variants relevant to disease susceptibility studies and provide evidence of the importance of genetic variants in regulatory network studies

Phase transition in Random Circuit Sampling

Quantum computers hold the promise of executing tasks beyond the capability of classical computers. Noise competes with coherent evolution and destroys long-range correlations, making it an outstanding challenge to fully leverage the computation power of near-term quantum processors. We report Random Circuit Sampling (RCS) experiments where we identify distinct phases driven by the interplay between quantum dynamics and noise. Using cross-entropy benchmarking, we observe phase boundaries which can define the computational complexity of noisy quantum evolution. We conclude by presenting an RCS experiment with 70 qubits at 24 cycles. We estimate the computational cost against improved classical methods and demonstrate that our experiment is beyond the capabilities of existing classical supercomputers

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements

Metabolically protective cytokines adiponectin and fibroblast growth factor-21 are increased by acute overfeeding in healthy humans

Context: Circulating levels of metabolically protective and adverse cytokines are altered in obese humans and rodent models. However, it is not clear whether these cytokines are altered rapidly in response to over-nutrition, or as a later consequence of the obese state. Methods: Forty sedentary healthy individuals were examined prior to and at 3 and 28 days of high fat overfeeding (+1250 kCal/day, 45% fat). Insulin sensitivity (hyperinsulinaemic-euglycaemic clamp), adiposity, serum levels of adiponectin and fibroblast growth factor-21 (FGF21), fatty acid binding protein-4 (FABP4), lipocalin-2 and plasminogen activator factor-1 (PAI1) were assessed. Statistics were performed by repeated measures ANOVA. Results: Overfeeding increased weight, body fat and liver fat, fasting glucose, insulin and reduced insulin sensitivity by clamp (all P <0.05). Metabolically protective cytokines, adiponectin and FGF21 were increased at day 3 of overfeeding (P ≤0.001) and adiponectin was also elevated at day 28 (P=0.001). FABP4, lipocalin-2 and PAI-1 were not changed by overfeeding at either time point. Conclusion: Metabolically protective cytokines, adiponectin and FGF-21, were increased by over nutrition and weight gain in healthy humans, despite increases in insulin resistance. We speculate that this was in attempt to maintain glucose homeostasis in a state of nutritional excess. PAI-I, FABP4 and lipocalin 2 were not altered by overfeeding suggesting that changes in these cytokines may be a later consequence of the obese state.Leonie K. Heilbronn, Lesley V. Campbell, Aimin Xu, Dorit Samocha-Bone

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure

Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies