Reservoir Flooding Optimization by Control Polynomial Approximations

In this dissertation, we provide novel parametrization procedures for water-flooding production optimization problems, using polynomial approximation techniques. The methods project the original infinite dimensional controls space into a polynomial subspace. Our contribution includes new parameterization formulations using natural polynomials, orthogonal Chebyshev polynomials and Cubic spline interpolation. We show that the proposed methods are well suited for black-box approach with stochastic global-search method as they tend to produce smooth control trajectories, while reducing the solution space size. We demonstrate their efficiency on synthetic two-dimensional problems and on a realistic 3-dimensional problem. By contributing with a new adjoint method formulation for polynomial approximation, we implemented the methods also with gradient-based algorithms. In addition to fine-scale simulation, we also performed reduced order modeling, where we demonstrated a synergistic effect when combining polynomial approximation with model order reduction, that leads to faster optimization with higher gains in terms of Net Present Value. Finally, we performed gradient-based optimization under uncertainty. We proposed a new multi-objective function with three components, one that maximizes the expected value of all realizations, and two that maximize the averages of distribution tails from both sides. The new objective provides decision makers with the flexibility to choose the amount of risk they are willing to take, while deciding on production strategy or performing reserves estimation (P10;P50;P90)

Assessing the number of ancestral alternatively spliced exons in the human genome

BACKGROUND: It is estimated that between 35% and 74% of all human genes undergo alternative splicing. However, as a gene that undergoes alternative splicing can have between one and dozens of alternative exons, the number of alternatively spliced genes by itself is not informative enough. An additional parameter, which was not addressed so far, is therefore the number of human exons that undergo alternative splicing. We have previously described an accurate machine-learning method allowing the detection of conserved alternatively spliced exons without using ESTs, which relies on specific features of the exon and its genomic vicinity that distinguish alternatively spliced exons from constitutive ones. RESULTS: In this study we use the above-described approach to calculate that 7.2% (± 1.1%) of all human exons that are conserved in mouse are alternatively spliced in both species. CONCLUSION: This number is the first estimation for the extent of ancestral alternatively spliced exons in the human genome

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

The categorisation and structural analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) sequences from 195 microbial genomes show that repeats from diverse organisms can be grouped based on sequence similarity, and that some groups have pronounced secondary structures with compensatory base changes

DSCOVR-EPIC MAIAC AOD - A Proxy for Understanding Aerosol Diurnal Patterns from Space

The Deep Space Climate Observatory (DSCOVR) spacecraft was launched on 11 February 2015 and in June 2015 achieved its orbit at the first Lagrange point (L1), 1.5 million km from Earth toward the sun. The Earth Polychromatic Imaging Camera (EPIC) onboard DSCOVR views the entire sunlit Earth from sunrise to sunset, every 1-2 hours, at scattering angles between 168.5 and 175.5 with 10 narrowband filters in the range of 317-779 nm. NASA Multiangle Implementation of Atmospheric Correction (MAIAC) algorithm, originally developed for MODIS, has been applied to EPIC data with an Aerosol Optical Depth (AOD) product at 440nm with a 10km spatial resolution. This high temporal resolution product is a unique dataset for investigating diurnal patterns in aerosols from space. Our work analyzed the capability of the satellite-borne data to capture the aerosol diurnal variation by associating it with AERONET AOD at 440nm data over the contiguous US. We validated the DSCOVR MAIAC AOD data over 100 AERONET stations during 2015-2018, and examined the contribution of the surface reflectance and relevant acquisition angles, derived by the MAIAC algorithm, to the predicted error. We used over 180,000 hourly DSCOVR-EPIC MAIAC AOD observations with collocated with AERONET AOD observations averaged over +-30 minutes from the satellite overpass time. The AERONET and DSCOVR AOD temporal patterns show that the diurnal variation is different across US AERONET sites, with higher diurnal variation in the DSCOVR dataset in general

Clustered Spanning Tree - Conditions for Feasibility

International audienceLet H = be a hypergraph, where V is a set of vertices and S is a set of not necessarily disjoint clusters Si ⊆ V. The Clustered Spanning Tree problem is to find a spanning tree of G which satisfies that each cluster induces a subtree, when it exists. We provide an efficient and unique algorithm which finds a feasible solution tree for H when it exists, or states that no feasible solution exists. The paper also uses special structures of the intersection graph of H to construct a feasible solution more efficiently. For cases when the hypergraph does not have a feasible solution tree, we consider adding vertices to exactly one cluster in order to gain feasibility. We characterize when such addition can gain feasibility, find the appropriate cluster and a possible set of vertices to be added

Association between Sensory Processing by Children with High Functioning Autism Spectrum Disorder and their Daily Routines

Background: Children diagnosed with autism spectrum disorder exhibit persistent deficits in social communication and social interaction accompanied by restricted, repetitive patterns of behavior, interests, or activities. Those with normal intelligence are considered to have high functioning autism spectrum disorder (HFASD). Method: The study participants were 20 children with HFASD aged 5 to 7 years old attending mainstream educational programs and their parents (study group) and 30 typically-developing age-matched children from the same socio-economic background and their parents (control group). Parents from both groups completed the Short Sensory Profile to investigate their children’s sensory processing and the presence of Sensory Processing Disorder. Children and parents from both groups were administered the Make My Day (MMD) to obtain information regarding the children’s participation and performance in daily activities. Results: The study group had significantly more sensory difficulties, which correlated with restricted daily routines, compared with the control group. SPD significantly predicted the quality and independence of the performance of daily activities by children with HFASD as measured by the MMD. Conclusions: SPD may be a worthwhile therapeutic target for therapists seeking to improve participation in and performance of daily activities, as identified by the MMD, among children with HFASD

TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates

Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic insertions of TEs also led to creation and expression of new functional non-coding RNAs such as micro- RNAs. We have constructed the TranspoGene database, which covers TEs located inside proteincoding genes of seven species: human, mouse, chicken, zebrafish, fruit fly, nematode and sea squirt. TEs were classified according to location within the gene: proximal promoter TEs, exonized TEs (insertion within an intron that led to exon creation), exonic TEs (insertion into an existing exon) or intronic TEs. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. In addition, we created microTranspoGene: a database of human, mouse, zebrafish and nematode TEderived microRNAs. The TranspoGene and micro- TranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome

Memory and Identity The Land Day Monument

The establishment of monuments for commemorating the victims of violent confrontations constitutes a major element in the construction of modern national consciousness. The Arab-Palestinian citizens of Israel, approximately 19% of all Israeli citizens, have experienced in the last five years an accelerated process of 'monumentalization' of their identity as a national minority - many monuments that commemorate their victims in the Zionist-Palestinian conflict have been established in Arab villages and towns inside Israel

Draft Genome Sequence of the Iron-Oxidizing AcidophileLeptospirillum ferriphilum Type Strain DSM 14647

The genomic features of the Leptospirillum ferriphilum type strain DSM 14647 are described here. An analysis of the predicted genes enriches our knowledge of the molecular basis of iron oxidation, improves our understanding of its role in industrial bioleaching, and suggests how it is adapted to live at extremely low pH