TROM: A Testing-based Method for Finding Transcriptomic Similarity of Biological Samples

Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic data. An important question is to understand the conservation and differentiation of biological processes in different species. We propose a testing-based method TROM (Transcriptome Overlap Measure) for comparing transcriptomes within or between different species, and provide a different perspective to interpret transcriptomic similarity in contrast to traditional correlation analyses. Specifically, the TROM method focuses on identifying associated genes that capture molecular characteristics of biological samples, and subsequently comparing the biological samples by testing the overlap of their associated genes. We use simulation and real data studies to demonstrate that TROM is more powerful in identifying similar transcriptomes and more robust to stochastic gene expression noise than Pearson and Spearman correlations. We apply TROM to compare the developmental stages of six Drosophila species, C. elegans, S. purpuratus, D. rerio and mouse liver, and find interesting correspondence patterns that imply conserved gene expression programs in the development of these species. The TROM method is available as an R package on CRAN (http://cran.r-project.org/) with manuals and source codes available at http://www.stat.ucla.edu/ jingyi.li/software-and-data/trom.html

Relation of emissions to air quality for photochemical smog

Effective evaluation of air pollution control strategies requires the use of validated and reliable mathemtical models that can relate pollutant emissions to atmospheric air quality. The primary objective of this research program has been to develop a fundamental capability to assess the effectiveness of air pollution control measures in reducing photochemical air pollution. An important aspect of the development has been to simplify the preparation of input data and operational use of the resulting model. The system has been designed to be used by air pollution agencies with relatively little experience in atmospheric physics and chemistry. The assumptions commonly employed in model formulations have been evaluated to ensure a valid representation of the physical and chemical processes in the atmosphere. In the most recent phase of this research the comprehensive photochemical airshed model has been evaluated against data available in the South Coast Air Basin of Southern California. This task was undertaken in collaboration with the California Air Resources Board, Air Quality Modeling Section. A statistical analysis package has been used to evaluate the correspondence of predicted and observed concentrations for the days on which the model was evaluated. An assessment of the EPA ozone isopleth modeling technique has been initiated

Reconciliation between operational taxonomic units and species boundaries

The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into operational taxonomic units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for bacterial species. Our results show that the robustness of such a generalised cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene. It will lead to biases in diversity metrics and makes it hard to compare results obtained with amplicons derived with different primer sets. The method introduced within this work takes into account the differential evolutional rates of taxonomic lineages in order to define a dynamic and taxonomic-dependent OTU clustering cut-off score. For a taxonomic family consisting of species showing high evolutionary conservation in the amplified variable regions, the cut-off will be more stringent than 97%. By taking into consideration the amplified variable regions and the taxonomic family when defining this cut-off, such a threshold will lead to more robust results and closer correspondence between OTUs and species. This approach has been implemented in a publicly available software package called DynamiC

Tropical mirror symmetry for elliptic curves

Mirror symmetry relates Gromov-Witten invariants of an elliptic curve with certain integrals over Feynman graphs. We prove a tropical generalization of mirror symmetry for elliptic curves, i.e., a statement relating certain labeled Gromov-Witten invariants of a tropical elliptic curve to more refined Feynman integrals. This result easily implies the tropical analogue of the mirror symmetry statement mentioned above and, using the necessary Correspondence Theorem, also the mirror symmetry statement itself. In this way, our tropical generalization leads to an alternative proof of mirror symmetry for elliptic curves. We believe that our approach via tropical mirror symmetry naturally carries the potential of being generalized to more adventurous situations of mirror symmetry. Moreover, our tropical approach has the advantage that all involved invariants are easy to compute. Furthermore, we can use the techniques for computing Feynman integrals to prove that they are quasimodular forms. Also, as a side product, we can give a combinatorial characterization of Feynman graphs for which the corresponding integrals are zero. More generally, the tropical mirror symmetry theorem gives a natural interpretation of the A-model side (i.e., the generating function of Gromov-Witten invariants) in terms of a sum over Feynman graphs. Hence our quasimodularity result becomes meaningful on the A-model side as well. Our theoretical results are complemented by a Singular package including several procedures that can be used to compute Hurwitz numbers of the elliptic curve as integrals over Feynman graphs.Comment: comment on historical development adde

Analysis and prediction of city postal services in Albania. A case study

Postal service plays an important role in development of an effective and dynamic market. The role of postal services has changed in years. On one side, the demand for the delivery of letters, newspapers and other documments is reducing due to the use of electronic communication. On the other side, the demand for package services is increasing due to e-commerce development. Albanian postal service offers a very wide range of postal and financial services with quality and competitive prices. Postal services include: letters, small packages, telefax, correspondence, typography, telegrams, and subscribers of fixed and mobile telephony. In this article, we have done an analysis of postal services in Albania from 1993 to 2015 and a prediction for the next years. The most important services we have taken in consideration are: simple letters and parcels, registered letters and pasrcels, and insured parcels. We use statistical models for this prediction

Strategic Issues of Regional Development: Government Policy Evaluation of Papua

The five-year period of development as outlined in the document RPJMD (Medium-Term Regional Development Plan), has achieved significant success, although there are still conscious strategic issues that are unsolved optimally. It can be traced from a series of evaluation studies to ensure consistency between the programs organized in 5 years with defined policy agenda to achieve the vision of local government. This study was conducted in a pragmatic approach that emphasizes the evaluation of policies: First, Integratif. An evaluation of the program and its financial package on cross institutions (Ind: SKPD/regional work unit). Secondly, comparatively, the achievements of development program compared with: (a) the goals stated in the document of Medium-Term Regional Development Plan (RJPMD/Ind), (b) development of mean achievement average per year, (c) the achievements of other areas, including a national scale and the achievement of the MDG's (Millennium Development Goal's).Object of the study are: All the goals set out in the mission to realize its vision of regional development as well as development programs and activities to achieve the targets and affect from various sources of financial. This study covers the gains of development programs within 5 years, including: macro achievements and outcomes for each development field. In addition, it is also obtained a description of the degree of relevancy, coherence, and correspondence between the realization of programs and activities with targeted goals, as well as the achievement of the mission and the development agenda so it can be measured the degree of the medium-term vision achievement. The district/city as a target sample of the study is Jayapura District, Puncak Jaya, District, Mimika District, and Jayapura city

The development version of the CHEVIE package of GAP3

I describe the current state of the development version of the CHEVIE package, which deals with Coxeter groups, reductive algebraic groups, complex reflection groups, Hecke algebras, braid monoids, etc... Examples are given, showing the code to check some results of Lusztig.Comment: 24 pages. arXiv admin note: text overlap with arXiv:1003.492

Pola Pengembangan SIA Untuk Pemenuhan SDGs: Temuan Dari Rumah Sakit Muhammadiyah

The aim of this study is to describe the pattern of development of AIS in the hospital. There are three models of the development of AIS are: Waterfall, Iterative, and Spiral. Hospitals can use AIS package software that has been made and sold in the market but the software package does not allow to be developed in line with business development, organization, and technology. That is why many enterprises that designs and develops its own with the intention of AIS can meet the needs and desires of the company. This research was conducted with qualitative approach. The location of this research is in the hospital owned by Muhammadiyah in Lamongan and Ponorogo, East Java, Indonesia. Data were collected by in-depth interviews, outside observation, and documentation. The key informant involved a total of 56 people, consisting of 40 operators, 10 supervisors, and 6 managers. The data collected will be analyzed using content analysis. The research finding is a pattern of AIS development in accordance with the hospitals. Contributions from these research finding is the possibility of AIS development pattern can be used by other hospitals or other business entities when developing AIS. Keywords                   : Accounting Information System (AIS), AIS development, hospital, Muhammadiyah Correspondence to       :[email protected],[email protected], [email protected]