Variants of constrained longest common subsequence

We consider a variant of the classical Longest Common Subsequence problem called Doubly-Constrained Longest Common Subsequence (DC-LCS). Given two strings s₁ and s₂ over an alphabet Σ, a set Cs of strings, and a function Co:Σ→N, the DC-LCS problem consists of finding the longest subsequence s of s₁ and s₂ such that s is a supersequence of all the strings in Cs and such that the number of occurrences in s of each symbol σ∈Σ is upper bounded by Co(σ). The DC-LCS problem provides a clear mathematical formulation of a sequence comparison problem in Computational Biology and generalizes two other constrained variants of the LCS problem that have been introduced previously in the literature: the Constrained LCS and the Repetition-Free LCS. We present two results for the DC-LCS problem. First, we illustrate a fixed-parameter algorithm where the parameter is the length of the solution which is also applicable to the more specialized problems. Second, we prove a parameterized hardness result for the Constrained LCS problem when the parameter is the number of the constraint strings (|Cs|) and the size of the alphabet Σ. This hardness result also implies the parameterized hardness of the DC-LCS problem (with the same parameters) and its NP-hardness when the size of the alphabet is constant.     

Benchmarking of the 3-D CAD-based Discrete Ordinates code “ATTILA” for dose rate calculations against experiments and Monte Carlo calculations

Shutdown dose rate (SDDR) inside and around the diagnostics ports of ITER is performed at PPPL/UCLA using the 3-D, FEM, Discrete Ordinates code, ATTILA, along with its updated FORNAX transmutation/decay gamma library. Other ITER partners assess SDDR using codes based on the Monte Carlo (MC) approach (e.g. MCNP code) for transport calculation and the radioactivity inventory code FISPACT or other equivalent decay data libraries for dose rate assessment. To reveal the range of discrepancies in the results obtained by various analysts, an extensive experimental and calculation benchmarking effort has been undertaken to validate the capability of ATTILA for dose rate assessment. On the experimental validation front, the comparison was performed using the measured data from two SDDR experiments performed at the FNG facility, Italy. Comparison was made to the experimental data and to MC results obtained by other analysts. On the calculation validation front, the ATTILA's predictions were compared to other results at key locations inside a calculation benchmark whose configuration duplicates an upper diagnostics port plug (UPP) in ITER. Both serial and parallel version of ATTILA-7.1.0 are used in the PPPL/UCLA analysis performed with FENDL-2.1/FORNAX databases. In the FNG 1st experimental, it was shown that ATTILA's dose rates are largely over estimated (by ～30–60%) with the ANSI/ANS-6.1.1 flux-to-dose factors whereas the ICRP-74 factors give better agreement (10–20%) with the experimental data and with the MC results at all cooling times. In the 2nd experiment, there is an under estimation in SDDR calculated by both MCNP and ATTILA based on ANSI/ANS-6.1.1 for cooling times up to ～4 days after irradiation. Thereafter, an over estimation is observed (～5–10% with MCNP and ～10–15% with ATTILA). As for the calculation benchmark, the agreement is much better based on ICRP-74 1996 data. The divergence among all dose rate results at ～11 days cooling time is no more than 15% among all participants.     

Online Coloring of Bipartite Graphs with and without Advice

In the online version of the well-known graph coloring problem, the vertices appear one after the other together with the edges to the already known vertices and have to be irrevocably colored immediately after their appearance. We consider this problem on bipartite, i.e., two-colorable graphs. We prove that at least ?1.13746?log₂(n)?0.49887? colors are necessary for any deterministic online algorithm to be able to color any given bipartite graph on n vertices, thus improving on the previously known lower bound of ?log₂ n?+1 for sufficiently large n. Recently, the advice complexity was introduced as a method for a fine-grained analysis of the hardness of online problems. We apply this method to the online coloring problem and prove (almost) tight linear upper and lower bounds on the advice complexity of coloring a bipartite graph online optimally or using 3 colors. Moreover, we prove that \(O(\sqrt{n})\) advice bits are sufficient for coloring any bipartite graph on n vertices with at most ?log₂ n? colors.     

Role of NEU3 Overexpression in the Prediction of Efficacy of EGFR-Targeted Therapies in Colon Cancer Cell Lines

The epidermal growth factor receptor (EGFR), through the MAP kinase and PI3K-Akt-mTOR axis, plays a pivotal role in colorectal cancer (CRC) pathogenesis. The membrane-associated NEU3 sialidase interacts with and desialylates EGFR by promoting its dimerization and downstream effectors’ activation. Among the targeted therapies against EGFR, the monoclonal antibody cetuximab is active only in a subgroup of patients not carrying mutations in the MAP kinase pathway. In order to better understand the EGFR-NEU3 interplay and the mechanisms of pharmacological resistance, we investigated the role of NEU3 deregulation in cetuximab-treated CRC cell lines transiently transfected with NEU3 using Western blot analysis. Our results indicate that NEU3 overexpression can enhance EGFR activation only if EGFR is overexpressed, indicating the existence of a threshold for NEU3-mediated EGFR activation. This enhancement mainly leads to the constitutive activation of the MAP kinase pathway. Consequently, we suggest that the evaluation of NEU3 expression cannot entirely substitute the evaluation of EGFR because EGFR-negative cases cannot be stimulated by NEU3. Furthermore, NEU3-mediated hyperactivation of EGFR is counterbalanced by the administration of cetuximab, hypothesizing that a combined treatment of NEU3- and EGFR-targeted therapies may represent a valid option for CRC patients, which must be investigated in the future.     

Net-Zero Energy Building Enhancement for a Leadership in Energy and Environmental Design Platinum Educational Facility

In the United States, university buildings use 17% of total non-residential building energy per year. According to the NREL （National Renewable Energy Laboratory）, the average lifecycle of a building in a university is 42 years with an EUI （energy use intensity） of 23 kWh/m^2/y. Current building and energy codes limit the EUI to 16 kWh/m^2/y for new school buildings; this benchmark can vary depending on climate, occupancy, and other contextual factors. Although the LEED （leadership in energy and environmental design） system provides a set of guidelines to rate sustainable buildings, studies have shown that 28%-35% of the educational LEED-rated buildings use more energy than their conventional counterparts. This paper examines the issues specific to a LEED-rated design addition to an existing university building. The forum, a lecture hall expansion of to an existing building at the University of Kansas, has been proposed as environmentally friendly and energy-efficient building addition. Comfort and health aspects have been considered in the design in order to obtain LEED platinum certificate. The forum＇s energy performance strategies include a double-skin facade to reduce energy consumption and PV （photovoltaic） panels to generate onsite energy. This study considers various scenarios to meet NZEB （net-zero energy building） criteria and maximize energy savings. The feasibility of NZE criteria is evaluated for： （a） seasonal comparison; （b） facility occupancy; （c） PV panels＇ addition in relation to double skin facade. The results of NZEB approach are compared to LEED platinum requirements, based on Rol （return on investment） and PV panel＇s efficiency for this specific educational building.     

In vitro hypoglycaemic and hypolipidemic potential of white tea polyphenols

The leaves at different processing stages of a single tea cultivar in order to obtain white (WT), green (GT) and black tea (BT) samples, were analysed. The capacities of tea polyphenolics to influence the glucose and lipid metabolism in HepG2 cell lines were evaluated. WT appeared the most active in reducing the glucose and cholesterol uptake (+17.7% and +32.4% in the glucose and cholesterol cell medium concentration, respectively). Incubation with WT enhanced LDL receptor binding activity by 40% (+20% for GT and +0% for BT) and led to an increase in HDL cell medium concentration of 33.3% (+20% for GT and +0% for BT). Finally, WT revealed the best inhibition capacity against lipase activity, and triglyceride levels in the cell medium increased by 400% (+382.6% for GT and +191.3% for BT). The present study intended to contribute to the little knowledge about the potential health benefits of white tea in individuals affected by metabolic syndrome.     

The role of tryptophan in protein fibrillogenesis: relevance of Trp7 and Trp14 to the amyloidogenic properties of myoglobin

In order to understand the role of tryptophan in the mechanisms of fibrils formation, the ability of a series of analogs of the residue 7-18 span of myoglobin to form amyloid-like fibrils was investigated. Alternatively one or both tryptophans were substituted with alanine and leucine, to determine the contribution of hydrophobicity and aromaticity. The scale of aggregation propensity of the peptides determined indicates that tryptophan is crucial for the amyloidogenic process. Since the rare tryptophan residue is generally engaged in structural roles in proteins, or when exposed serves as binding sites, we surmise that its exposure in the amyloidogenic fragments allows for intermolecular clustering with residues from other molecules leading to the formation of amyloid aggregates.