Decoding of Repeated-Root Cyclic Codes up to New Bounds on Their Minimum Distance

The well-known approach of Bose, Ray-Chaudhuri and Hocquenghem and its generalization by Hartmann and Tzeng are lower bounds on the minimum distance of simple-root cyclic codes. We generalize these two bounds to the case of repeated-root cyclic codes and present a syndrome-based burst error decoding algorithm with guaranteed decoding radius based on an associated folded cyclic code. Furthermore, we present a third technique for bounding the minimum Hamming distance based on the embedding of a given repeated-root cyclic code into a repeated-root cyclic product code. A second quadratic-time probabilistic burst error decoding procedure based on the third bound is outlined. Index Terms Bound on the minimum distance, burst error, efficient decoding, folded code, repeated-root cyclic code, repeated-root cyclic product cod

Convolutional Codes in Rank Metric with Application to Random Network Coding

Random network coding recently attracts attention as a technique to disseminate information in a network. This paper considers a non-coherent multi-shot network, where the unknown and time-variant network is used several times. In order to create dependencies between the different shots, particular convolutional codes in rank metric are used. These codes are so-called (partial) unit memory ((P)UM) codes, i.e., convolutional codes with memory one. First, distance measures for convolutional codes in rank metric are shown and two constructions of (P)UM codes in rank metric based on the generator matrices of maximum rank distance codes are presented. Second, an efficient error-erasure decoding algorithm for these codes is presented. Its guaranteed decoding radius is derived and its complexity is bounded. Finally, it is shown how to apply these codes for error correction in random linear and affine network coding.Comment: presented in part at Netcod 2012, submitted to IEEE Transactions on Information Theor

Temporary collapse of the Daphnia population in turbid and ultra-oligotrophic Lake Brienz

Abstract.: The cyclical parthenogen Daphnia is a key species in aquatic food webs. Its abundance is influenced by environmental factors like food quantity and quality, predation, diseases, temperature and washout by discharge. In ultra-oligotrophic Lake Brienz (Switzerland), which is turbid from suspended glacial material, Daphnia density has continuously decreased since the 1990 s. In spring and summer 1999, during and after a severe flood, Daphnia density was below detection level, but the population recovered the following year. Simultaneously, a drastic two-year decline occurred in the yield of whitefish (Coregonus sp.), which mainly feed on Daphnia. Several hypotheses were tested to explain the collapse of the Daphnia population: a negative effect of the suspended particles, a covering of the diapausing eggs by sediment, and a combined washout/temperature effect. A direct negative effect of the particles and covering of diapausing eggs could be excluded. According to model calculations, the spring growth of the Daphnia population could not compensate the washout losses, as it was limited by poor food conditions due to re-oligotrophication and reduced by extraordinarily low water temperatures. Moreover, ephippia abundance analysed from sediment cores was consistent with the process of eutrophication and re-oligotrophication and indicated that daphnids did not persist in the lake in the period before eutrophication (until 1955). Like most peri-alpine lakes in Europe, Lake Brienz has returned to its natural ultra-oligotrophic state and is now unable to support a large Daphnia population and fishing yiel

Effects of upstream hydropower operation and oligotrophication on the light regime of a turbid peri-alpine lake

Abstract.: Anthropogenic activities in catchments can alter the light regimes in downstream natural waters, affecting light attenuation and the perceived optical properties of the waters. We analyzed the effects of upstream hydropower operation and oligotrophication on light attenuation and reflectance in Lake Brienz (Switzerland). For this purpose, we reconstructed its light regime for the pre-dam condition and for periods of 4-fold increased primary productivity, based on direct observations of light and beam attenuation as well as concentrations of optically active compounds, especially observed and simulated mineral particle concentrations. Based on our assessment, light attenuation before the construction of upstream dams was double the current value during summer and nearly half in winter. This result is consistent with pre-dam measurements of Secchi depths in the early 1920s. Using a simple optical model, a significant increase in reflectance since the 1970s was estimated, assuming a 4-fold decrease of optical active organic compounds within the lake. As reflectance is perceived by human eyes as turbidity, this may explain subjective reports by local residents of increasing turbidity in recent year

Effects of alpine hydropower operations on primary production in a downstream lake

Abstract.: During the past century, the construction of hydropower dams in the watershed of Lake Brienz has significantly altered the dynamics of turbidity, which has important implications for lake productivity. To assess these effects, we measured in situ carbon assimilation rates and ambient light intensities over 18months. Based on experimental data, a numerical model was developed to assess gross primary production under present light conditions and those under a hypothetical case without upstream dams. Light conditions for the hypothetical ‘no-dam' situation were estimated from pre-dam Secchi depths and simulated ‘no-dam' particle concentrations. Current gross primary production is low (~66 gC m−2 yr−1), and could increase ~44% if the lake was less turbid. Disregarding nutrient retention in reservoirs, we estimate gross primary production would be ~35% lower in summer and ~23% higher in winter in the absence of reservoirs. The annual primary production (~58 gC m−2 yr−1) would decrease ~12% compared to the current primary production with dams. According to model calculations, hydropower operations have significantly altered the seasonal dynamics, but have little effect on annual primary production in Lake Brien

Outcomes and risk score for distal pancreatectomy with celiac axis resection (DP-CAR) : an international multicenter analysis

Background: Distal pancreatectomy with celiac axis resection (DP-CAR) is a treatment option for selected patients with pancreatic cancer involving the celiac axis. A recent multicenter European study reported a 90-day mortality rate of 16%, highlighting the importance of patient selection. The authors constructed a risk score to predict 90-day mortality and assessed oncologic outcomes. Methods: This multicenter retrospective cohort study investigated patients undergoing DP-CAR at 20 European centers from 12 countries (model design 2000-2016) and three very-high-volume international centers in the United States and Japan (model validation 2004-2017). The area under receiver operator curve (AUC) and calibration plots were used for validation of the 90-day mortality risk model. Secondary outcomes included resection margin status, adjuvant therapy, and survival. Results: For 191 DP-CAR patients, the 90-day mortality rate was 5.5% (95 confidence interval [CI], 2.2-11%) at 5 high-volume (1 DP-CAR/year) and 18% (95 CI, 9-30%) at 18 low-volume DP-CAR centers (P=0.015). A risk score with age, sex, body mass index (BMI), American Society of Anesthesiologists (ASA) score, multivisceral resection, open versus minimally invasive surgery, and low- versus high-volume center performed well in both the design and validation cohorts (AUC, 0.79 vs 0.74; P=0.642). For 174 patients with pancreatic ductal adenocarcinoma, the R0 resection rate was 60%, neoadjuvant and adjuvant therapies were applied for respectively 69% and 67% of the patients, and the median overall survival period was 19months (95 CI, 15-25months). Conclusions: When performed for selected patients at high-volume centers, DP-CAR is associated with acceptable 90-day mortality and overall survival. The authors propose a 90-day mortality risk score to improve patient selection and outcomes, with DP-CAR volume as the dominant predictor

SAM levels, gene expression of SAM synthetase, methionine synthase and ACC oxidase, and ethylene emission from N. suaveolens flowers

S′adenosyl-l-methionine (SAM) is a ubiquitous methyl donor and a precursor in the biosynthesis of ethylene, polyamines, biotin, and nicotianamine in plants. Only limited information is available regarding its synthesis (SAM cycle) and its concentrations in plant tissues. The SAM concentrations in flowers of Nicotiana suaveolens were determined during day/night cycles and found to fluctuate rhythmically between 10 and 50 nmol g−1 fresh weight. Troughs of SAM levels were measured in the evening and night, which corresponds to the time when the major floral scent compound, methyl benzoate, is synthesized by a SAM dependent methyltransferase (NsBSMT) and when this enzyme possesses its highest activity. The SAM synthetase (NsSAMS1) and methionine synthase (NsMS1) are enzymes, among others, which are involved in the synthesis and regeneration of SAM. Respective genes were isolated from a N. suaveolens petal cDNA library. Transcript accumulation patterns of both SAM regenerating enzymes matched perfectly those of the bifunctional NsBSMT; maximum mRNA accumulations of NsMS1 and NsSAMS1 were attained in the evening. Ethylene, which is synthesized from SAM, reached only low levels of 1–2 ppbv in N. suaveolens flowers. It is emitted in a burst at the end of the life span of the flowers, which correlates with the increased expression of the 1-aminocyclopropane-1-carboxylate oxidase (NsACO)

Transgenerational Effects of Parental Larval Diet on Offspring Development Time, Adult Body Size and Pathogen Resistance in Drosophila melanogaster

Environmental conditions experienced by parents are increasingly recognized to affect offspring performance. We set out to investigate the effect of parental larval diet on offspring development time, adult body size and adult resistance to the bacterium Serratia marcescens in Drosophila melanogaster. Flies for the parental generation were raised on either poor or standard diet and then mated in the four possible sex-by-parental diet crosses. Females that were raised on poor food produced larger offspring than females that were raised on standard food. Furthermore, male progeny sired by fathers that were raised on poor food were larger than male progeny sired by males raised on standard food. Development times were shortest for offspring whose one parent (mother or the father) was raised on standard and the other parent on poor food and longest for offspring whose parents both were raised on poor food. No evidence for transgenerational effects of parental diet on offspring disease resistance was found. Although paternal effects have been previously demonstrated in D. melanogaster, no earlier studies have investigated male-mediated transgenerational effects of diet in this species. The results highlight the importance of not only considering the relative contribution each parental sex has on progeny performance but also the combined effects that the two sexes may have on offspring performance

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival