A Decision Support System for Construction Project Risk Assessment

This paper presents an integrated system in which a computer-based decision support system (DSS) for construction project risks assessment at stage of contracting and construction. The Analytic Hierarchy Process (AHP) method is used to determine the weightings of risk factors from subjective judgment of experts and practitioners, and Fuzzy Multiple Criteria Decision Making (FMCDM) is used to assess the synthetic judgment of risk degree for the main activities of a construction project in different phase. A simple case study illustrates the effectiveness of the proposed approach and developed system

Galaxy Occupation Statistics of Dark Matter Haloes: Observational Results

We study the occupation statistics of galaxies in dark matter haloes using galaxy groups identified from the 2-degree Field Galaxy Redshift Survey with the halo-based group finder of Yang et al. The occupation distribution is considered separately for early and late type galaxies, as well as in terms of central and satellite galaxies. The mean luminosity of the central galaxies scales with halo mass approximately as $L_c\propto M^{2/3}$ for haloes with masses M<10^{13}h^{-1}\msun, and as $L_c\propto M^{1/4}$ for more massive haloes. The characteristic mass of 10^{13} h^{-1} \Msun is consistent with the mass scale where galaxy formation models suggest a transition from efficient to inefficient cooling. Another characteristic halo mass scale, M\sim 10^{11} h^{-1}\msun, which cannot be probed directly by our groups, is inferred from the conditional luminosity function (CLF) that matches the observed galaxy luminosity function and clustering. For a halo of given mass, the distribution of $L_c$ is rather narrow. The satellite galaxies are found to follow a Poissonian number distribution. The central galaxies in low-mass haloes are mostly late type galaxies, while those in massive haloes are almost all early types. We also measure the CLF of galaxies in haloes of given mass. Over the mass range that can be reliably probed with the present data (13.3 \lta {\rm log}[M/(h^{-1}\Msun)] \lta 14.7), the CLF is reasonably well fit by a Schechter function. Contrary to recent claims based on semi-analytical models of galaxy formation, the presence of central galaxies does not show up as a strong peak at the bright end of the CLF. (Abridged)Comment: 17 pages, 11 figures, revised version. Two figures added. A few small changes. Main conclusions remain unchange

Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities

Diatoms (Bacillariophyceae) are characterized by silicified cell walls that favor their long-term preservation in sediments, therefore widely used as bioindicators of present and past water conditions. Alongside with traditional morphological analyses, metabarcoding has become a valuable tool to study the community structures of various organisms, including diatoms. Here, we test whether the quantity of sediment sample used for DNA extraction affects the results obtained from high-throughput sequencing (metabarcoding) of the diatom rbcL region by isolating DNA from 10 g and 0.5 g (wet weight) of lake surface sediment samples. Because bioinformatics processing of metabarcoding data may affect the outcome, we also tested the consistency of the results from three different pipelines: 1) ESVs (exact sequence variants) pipeline; 2) clustering sequences at 95% sequence identity to form OTUs (operational taxonomic units; 95% OTUs); and 3) 97% OTUs pipeline. Additionally, the agreement between metabarcoding data and morphological inventories of corresponding samples were compared. Our results demonstrate highly uniform patterns between the diatom rbcL amplicons from 10 g and 0.5 g of sedimentary DNA (sedDNA) extracts (HTS 10 and HTS 0.5, respectively). Furthermore, after the careful curation of the sequencing data, metabarcoding results were highly consistent among the data sets produced by different bioinformatics pipelines. Comparing results from metabarcoding and microscopy, we identified some taxonomic mismatches: morphological analyses identified 59 diatom genera, whereas metabarcoding 49 to 54 genera. These mismatches are related to incompleteness of the sequence databases, but also to inconsistencies in diatom taxonomy in general and potential dissolution effects of diatom valves caused by high alkalinity of the investigated lake waters. Nevertheless, multivariate community analysis revealed consistent results between data sets identified by microscopy and metabarcoding – water depth and conductivity as the most significant variables in driving diatom communities in Lake Nam Co – further confirming that metabarcoding is a viable method for identifying diatom-environment relationships

Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows

We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing

Global Network Alignment

Motivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment. Analogous to sequence alignment, efficient and reliable network alignment methods will improve our understanding of biological systems. Network alignment is computationally hard. Hence, devising efficient network alignment heuristics is currently one of the foremost challenges in computational biology. &#xd;&#xa;&#xd;&#xa;Results: We present a superior heuristic network alignment algorithm, called Matching-based GRAph ALigner (M-GRAAL), which can process and integrate any number and type of similarity measures between network nodes (e.g., proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity, and structural similarity. This is efficient in resolving ties in similarity measures and in finding a combination of similarity measures yielding the largest biologically sound alignments. When used to align protein-protein interaction (PPI) networks of various species, M-GRAAL exposes the largest known functional and contiguous regions of network similarity. Hence, we use M-GRAAL&#x2019;s alignments to predict functions of un-annotated proteins in yeast, human, and bacteria _C. jejuni_ and _E. coli_. Furthermore, using M-GRAAL to compare PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship and our phylogenetic tree is the same as sequenced-based one

Competition and well-being

We study the effects of competition in a context in which people's actions can not be contractually fixed. We find that in such an environment the very presence of competition does neither increase efficiency nor does it yield any payoff gains for the short side of the market. We also find that competition has a strong negative impact on social well-being, the disposition towards others, and individually experienced well-being, the emotional state, of those on the long side of the market. We conjecture that this limits the possibilities of satisfactory interaction in the future and, hence, has negative implications for efficiency in the longer-ru

Towards Semantically Enriched Embeddings for Knowledge Graph Completion

Embedding based Knowledge Graph (KG) Completion has gained much attention over the past few years. Most of the current algorithms consider a KG as a multidirectional labeled graph and lack the ability to capture the semantics underlying the schematic information. In a separate development, a vast amount of information has been captured within the Large Language Models (LLMs) which has revolutionized the field of Artificial Intelligence. KGs could benefit from these LLMs and vice versa. This vision paper discusses the existing algorithms for KG completion based on the variations for generating KG embeddings. It starts with discussing various KG completion algorithms such as transductive and inductive link prediction and entity type prediction algorithms. It then moves on to the algorithms utilizing type information within the KGs, LLMs, and finally to algorithms capturing the semantics represented in different description logic axioms. We conclude the paper with a critical reflection on the current state of work in the community and give recommendations for future directions