Huffman source coding

Abstract. In this work, A Huffman source coding system is studied and implemented. The work will go through the basics of the source coding theorem, standard Huffman code is introduced, its weaknesses in a practical system are presented, and finally, methods and algorithms are introduced to overcome these weaknesses. In Particular, the preset dictionaries and Vitter algorithm are introduced. Then, the implementation is presented and the performance is studied by compressing text files.Huffman lähteenkoodaus. Tiivistelmä. Tässä työssä tutkitaan ja toteutetaan Huffman lähteenkoodaus järjestelmä. Työssä käydään läpi lähteenkoodauksen teoriaa, standardi Huffman koodaus, sen heikkoudet käytännön järjestelmässä, ja lopuksi keinoja näiden heikkouksien yli pääsemiseksi. Erityisesti huomioidaan etukäteen lasketut lähdekoodit ja dynaaminen Vitter algoritmi. Lopuksi työ toteutetaan ohjelmistona ja eri koodaustapoja verrataan keskenään kompressoimalla tekstitiedostoja

A family of thermostable fungal cellulases created by structure-guided recombination

SCHEMA structure-guided recombination of 3 fungal class II cellobiohydrolases (CBH II cellulases) has yielded a collection of highly thermostable CBH II chimeras. Twenty-three of 48 genes sampled from the 6,561 possible chimeric sequences were secreted by the Saccharomyces cerevisiae heterologous host in catalytically active form. Five of these chimeras have half-lives of thermal inactivation at 63°C that are greater than the most stable parent, CBH II enzyme from the thermophilic fungus Humicola insolens, which suggests that this chimera collection contains hundreds of highly stable cellulases. Twenty-five new sequences were designed based on mathematical modeling of the thermostabilities for the first set of chimeras. Ten of these sequences were expressed in active form; all 10 retained more activity than H. insolens CBH II after incubation at 63°C. The total of 15 validated thermostable CBH II enzymes have high sequence diversity, differing from their closest natural homologs at up to 63 amino acid positions. Selected purified thermostable chimeras hydrolyzed phosphoric acid swollen cellulose at temperatures 7 to 15°C higher than the parent enzymes. These chimeras also hydrolyzed as much or more cellulose than the parent CBH II enzymes in long-time cellulose hydrolysis assays and had pH/activity profiles as broad, or broader than, the parent enzymes. Generating this group of diverse, thermostable fungal CBH II chimeras is the first step in building an inventory of stable cellulases from which optimized enzyme mixtures for biomass conversion can be formulated

Can number and size of offspring increase simultaneously? - a central life-history trade-off reconsidered

Background: To maximize their fitness, parents are assumed to allocate their resources optimally between number and size of offspring. Although this fundamental life-history trade-off has been subject to long standing interest, its genetic basis, especially in wild mammals, still remains unresolved. One important reason for this problem is that a large multigenerational pedigree is required to conduct a reliable analysis of this trade-off. Results: We used the REML-animal model to estimate genetic parameters for litter size and individual birth size for a common Palearctic small mammal, the bank vole (Myodes glareolus). Even though a phenotypic trade-off between offspring number and size was evident, it was not explained by a genetic trade-off, but rather by negative correlations in permanent and temporary environmental effects. In fact, even positive genetic correlations were estimated between direct genetic effects for offspring number and size indicating that genetic variation in these two traits is not necessarily antagonistic in mammals. Conclusions: Our results have notable implications for the study of the life-history trade-off between offspring number and size in mammals. The estimated genetic correlations suggest that evolution of offspring number and size in polytocous mammals is not constrained by the trade-off caused by antagonistic selection responses per se, but rather by the opposing correlative selection responses in direct and maternal genetic effects for birth size.peerReviewe

Cavitation inception of a van der Waals fluid at a sack-wall obstacle

Cavitation in a liquid moving past a constraint is numerically investigated by means of a free-energy lattice Boltzmann simulation based on the van der Waals equation of state. The fluid is streamed past an obstacle and, depending on the pressure drop between inlet and outlet, vapor formation underneath the corner of the sack-wall is observed. The circumstances of cavitation formation are investigated and it is found that the local bulk pressure and mean stress are insufficient to explain the phenomenon. Results obtained in this study strongly suggest that the viscous stress, interfacial contributions to the local pressure, and the Laplace pressure are relevant to the opening of a vapor cavity. This can be described by a generalization of Joseph's criterion that includes these contributions. A macroscopic investigation measuring mass flow rate behavior and discharge coefficient was also performed. As theoretically predicted, mass flow rate increases linearly with the square root of the pressure drop. However, when cavitation occurs, the mass flow growth rate is reduced and eventually it collapses into a choked flow state. In the cavitating regime, as theoretically predicted and experimentally verified, the discharge coefficient grows with the Nurick cavitation number

SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation That Contributes Markedly to Stability

A quantitative linear model accurately (R^2 = 0.88) describes the thermostabilities of 54 characterized members of a family of fungal cellobiohydrolase class II (CBH II) cellulase chimeras made by SCHEMA recombination of three fungal enzymes, demonstrating that the contributions of SCHEMA sequence blocks to stability are predominantly additive. Thirty-one of 31 predicted thermostable CBH II chimeras have thermal inactivation temperatures higher than the most thermostable parent CBH II, from Humicola insolens, and the model predicts that hundreds more CBH II chimeras share this superior thermostability. Eight of eight thermostable chimeras assayed hydrolyze the solid cellulosic substrate Avicel at temperatures at least 5 °C above the most stable parent, and seven of these showed superior activity in 16-h Avicel hydrolysis assays. The sequence-stability model identified a single block of sequence that adds 8.5 °C to chimera thermostability. Mutating individual residues in this block identified the C313S substitution as responsible for the entire thermostabilizing effect. Introducing this mutation into the two recombination parent CBH IIs not featuring it (Hypocrea jecorina and H. insolens) decreased inactivation, increased maximum Avicel hydrolysis temperature, and improved long time hydrolysis performance. This mutation also stabilized and improved Avicel hydrolysis by Phanerochaete chrysosporium CBH II, which is only 55–56% identical to recombination parent CBH IIs. Furthermore, the C313S mutation increased total H. jecorina CBH II activity secreted by the Saccharomyces cerevisiae expression host more than 10-fold. Our results show that SCHEMA structure-guided recombination enables quantitative prediction of cellulase chimera thermostability and efficient identification of stabilizing mutations

Single-step genomic BLUP with many metafounders

Single-step genomic BLUP (ssGBLUP) model for routine genomic prediction of breeding values is developed intensively for many dairy cattle populations. Compatibility between the genomic (G) and the pedigree (A) relationship matrices remains an important challenge required in ssGBLUP. The compatibility relates to the amount of missing pedigree information. There are two prevailing approaches to account for the incomplete pedigree information: unknown parent groups (UPG) and metafounders (MF). unknown parent groups have been used routinely in pedigree-based evaluations to account for the differences in genetic level between groups of animals with missing parents. The MF approach is an extension of the UPG approach. The MF approach defines MF which are related pseudo-individuals. The MF approach needs a Γ matrix of the size number of MF to describe relationships between MF. The UPG and MF can be the same. However, the challenge in the MF approach is the estimation of Γ having many MF, typically needed in dairy cattle. In our study, we present an approach to fit the same amount of MF as UPG in ssGBLUP with Woodbury matrix identity (ssGTBLUP). We used 305-day milk, protein, and fat yield data from the DFS (Denmark, Finland, Sweden) Red Dairy cattle population. The pedigree had more than 6 million animals of which 207,475 were genotyped. We constructed the preliminary gamma matrix (Γpre) with 29 MF which was expanded to 148 MF by a covariance function (Γ148). The quality of the extrapolation of the Γpre matrix was studied by comparing average off-diagonal elements between breed groups. On average relationships among MF in Γ148 were 1.8% higher than in Γpre. The use of Γ148 increased the correlation between the G and A matrices by 0.13 and 0.11 for the diagonal and off-diagonal elements, respectively. [G]EBV were predicted using the ssGTBLUP and Pedigree-BLUP models with the MF and UPG. The prediction reliabilities were slightly higher for the ssGTBLUP model using MF than UPG. The ssGBLUP MF model showed less overprediction compared to other models

Intensity-based dual model method for generation of synthetic CT images from standard T2-weighted MR images - Generalized technique for four different MR scanners

Background and purpose: Recent studies have shown that it is possible to conduct entire radiotherapy treatment planning (RTP) workflow using only MR images. This study aims to develop a generalized intensity-based method to generate synthetic CT (sCT) images from standard T2-weighted (T2(W)) MR images of the pelvis. Materials and methods: This study developed a generalized dual model HU conversion method to convert standard T2(W) MR image intensity values to synthetic HU values, separately inside and outside of atlas-segmented bone volume contour. The method was developed and evaluated with 20 and 35 prostate cancer patients, respectively. MR images with scanning sequences in clinical use were acquired with four different MR scanners of three vendors. Results: For the generated synthetic CT (sCT) images of the 35 prostate patients, the mean (and maximal) HU differences in soft and bony tissue volumes were 16 +/- 6 HUs (34 HUs) and -46 +/- 56 HUs (181 HUs), respectively, against the true CT images. The average of the PTV mean dose difference in sCTs compared to those in true CTs was -0.6 +/- 0.4% (-1.3%). Conclusions: The study provides a generalized method for sCT creation from standard T2(W) images of the pelvis. The method produced clinically acceptable dose calculation results for all the included scanners and MR sequences. (c) 2017 Elsevier B.V. All rights reserved.Peer reviewe

Genetic Determinants of Long-Term Changes in Blood Lipid Concentrations: 10-Year Follow-Up of the GLACIER Study

Recent genome-wide meta-analyses identified 157 loci associated with cross-sectional lipid traits. Here we tested whether these loci associate (singly and in trait-specific genetic risk scores [GRS]) with longitudinal changes in total cholesterol (TC) and triglyceride (TG) levels in a population-based prospective cohort from Northern Sweden (the GLACIER Study). We sought replication in a southern Swedish cohort (the MDC Study; N = 2,943). GLACIER Study participants (N = 6,064) were genotyped with the MetaboChip array. Up to 3,495 participants had 10-yr follow-up data available in the GLACIER Study. The TC- and TG-specific GRSs were strongly associated with change in lipid levels (β = 0.02 mmol/l per effect allele per decade follow-up, P = 2.0×10−11 for TC; β = 0.02 mmol/l per effect allele per decade follow-up, P = 5.0×10−5 for TG). In individual SNP analysis, one TC locus, apolipoprotein E (APOE) rs4420638 (β = 0.12 mmol/l per effect allele per decade follow-up, P = 2.0×10−5), and two TG loci, tribbles pseudokinase 1 (TRIB1) rs2954029 (β = 0.09 mmol/l per effect allele per decade follow-up, P = 5.1×10−4) and apolipoprotein A-I (APOA1) rs6589564 (β = 0.31 mmol/l per effect allele per decade follow-up, P = 1.4×10−8), remained significantly associated with longitudinal changes for the respective traits after correction for multiple testing. An additional 12 loci were nominally associated with TC or TG changes. In replication analyses, the APOE rs4420638, TRIB1 rs2954029, and APOA1 rs6589564 associations were confirmed (P≤0.001). In summary, trait-specific GRSs are robustly associated with 10-yr changes in lipid levels and three individual SNPs were strongly associated with 10-yr changes in lipid levels