dataesr/scientific-paragraphs-categorization huggingface dataset:
The heterogeneity is strongest in Fungi, where some pairs of branches are predicted to have undergone more than 150 gene transfers, or even 300 transfers on tree B (Fig. 7 ). These transfers do not seem to be due to hybridization, as most of them are not replacement transfers, whereby a gene in a species is replaced by another gene coming from another species (the median branch-wise fraction of gene transfers that are compensated by loss on the same branch, i. e. replacement transfers, is 31% for Fungi on tree A , 34% on tree B and 49% for Cyanobacteria). For the same reason, these transfers cannot be misinterpreted events of incomplete lineage sorting. In fact, among genes that have only one The cyanobacterial and fungal datasets we considered differ both in the number of genomes (40 vs. 28) and in their age (nearly 3 billion years vs.
Figure5: Similar rate of transfers in Fungi and Cyanobacteria. The cyanobacterial and fungal datasets we considered differ both in the number of genomes(40 vs. 28)  and in their age (nearly 3 billion years vs. less than three quarters of a billion years). (A) In order to account for differences in age we consider the ratio T /(T + D), i. e. the fraction of transfer events among all gene birth events (duplications plus transfers) and L/(T + D + L) the ratio of loss events to all events. (B) To ascertain the effect of the differences in the number of genomes we constructed replicates with random subsamples of genomes of varying numbers. Extrapolation of the results suggests that T /((D + T ) for Fungi is as large or larger than for Cyanobacteria (for details see text). Fungi are shown with squares for tree A (red online), and circles for tree B (orange online) and Cyanobacteria with triangles (green online).
Since the beginning of the 21st century, straw-bale buildings are reappearing in the world; however, their thermal performances were not thoroughly investigated up to now. The purpose of this study is to analyze thermal behavior and energy performance of a straw-bale building in Switzerland. Using Pleiades+Comfie Software, building designs have been studied to understand the best way to mitigate overheating risks due to the low heat capacity of straw. Thermal-dynamic results and Life Cycle Assessment conclude that straw bale buildings can be a sustainable alternative in the energy evolution of building construction, due to its low embodied energy and excellent thermal performance.
In this context, the Municipality of Lausanne in Switzerland has decided to make an administrative straw-bale building in 2011 -that is to say without any structure but only straw -on the site of the service Parks and Areas of La Bourdonnette. An overall energy assessment of the construction was required to compare its consumption with the Swiss energy labels and the standard solutions. Straw is rarely used and data on that is quite scattered, which requires some effort for gathering information before modelling the building. This study will present thermal characteristics of straw as a construction material and uses them in the thermal model of the building, using Pleiades+Comfie Software. Results are used to assess the energy performance of the building ECO46 against some common Swiss administrative buildings.
To estimate the heating average energy consumed by ECO46, the calibrated model was subjected to the weather file proposed by the Meteonorm software for Lausanne, representing the average climatic conditions from 1996 to 2005. The results given by the model have a consumption of 3800 kWh of final energy, therefore, a consumption of 12,7 kWh. m -2. an -  of final energy or of 8,9 kWh. m -2 per year of primary energy as ECO46 has a surface area of 300 m 2 and the factor for wood primary/final energy is 0,7 in Switzerland in 2014. First, it is possible to compare this result to the value 111 kWh. m -2 per year of primary energy for existing administrative Swiss buildings  [10]. The study shows that ECO46 consumes less than 10% energy consumed by standard office building. Electricity efficiency assessment of the building shows that the annual mechanical ventilation, Domestic Hot Water and lighting consumption (around 2080 kWh per year) is offset by 19 m 2 of the mono-crystalline solar panels.
Evolution of buildings consumption sectors since 1975 until today This section focuses on the evolution of total energy consumption of a building during its life from 1975 to today. The objective was to compare the importance of embodied energy with the energy consumed during the life and destruction of the building and compare straw bale building with standard solution. This Life Cycle Analysis (LCA) was conducted using SIMAPRO software that uses the database EcoInvent v2 and permits to calculate construction and destruction energy consumption. First of all, it is considered that resources are available in the environment. Only the necessary energy that has been expended to extract the raw material and transform it to create building materials is taken into account. The transport of materials to their site of production to the construction site is also taken into account.
Finally, scenario 5 presents ECO46 building with the same performance of ECO46 but constructed in concrete and 35 cm of polystyrene insulation meeting Minergie-P ® requirements (triple glazing and energy saving bulb). Scenario 6 presents ECO46 building built with straw. A seventh variant is proposed with the incineration of waste at ECO46 end of life replacing conventional fuel consumption as the recycled straw is used in a district heating system. Each scenario has been modelled with Pleiades Software to determine the energy consumption for heating during the life of the building using the same Meteonorm file for Swiss climate. The lighting, ventilation and hot water are taken into account in computing the electricity consumption. The lifespan of the building is 60 years. Results of Fig. 2.
Besides selection for translational efficiency and accuracy, the choice of synonymous codons may also be under the selective pressure for optimal translation kinetics, to ensure correct messenger RNA (mRNA) structure and protein folding  (Plotkin and Kudla 2011). Inappropriate CUPrefs may impair translation kinetics, thus leading to fitness costs associated to low quantity of functional protein, but also to waste of cellular resources incurred through accumulation of erroneous and misfolded protein, increased toxicity, and cleaning costs  (Gingold and Pilpel 2011). Codon usage in viruses seems to be shaped both by selection and mutation. On one side, all viruses depend on host translational machinery, in particular viruses that do not encode their own tRNAs (as it is the case for human viruses), and CUPrefs in viral genes tend to match protein-specific requirements  (Akashi and Eyre-Walker 1998) : proteins required in large amount are usually encoded by genes optimized to the host CUPrefs, while maladaptation of CUPrefs results in reduced protein production  (Bahir et al.
Human PVs Gene Sequences The ORFs of all human PVs available at the Papillomavirus Episteme Database (http://pave. niaid. nih. gov ) were collected between March and April 2013. Using an in-house PERL script, the ORFs were examined by checking the start codon, stop codon, and internal stop codons to guarantee that only true ORFs were used. The final data set included 156 HPV types: 63 AlphaPVs, 45 BetaPVs, 45 GammaPVs, 2 MuPVs, and 1 NuPV. Names, accession numbers, and other information are detailed in supplementary table S1, Supplementary Material online.
The E5 gene was excluded from the analysis because it is absent in most human PVs. The relative frequency (RF) distribution of 59 codons (excluding Met, Trp, and stop codons) was calculated using an inhouse PERL script. The abundance of each codon in a gene was calculated and pondered by a factor corresponding to the sum of all synonymous codons: RF ac ¼ n ac X ta c¼1 n ac where n ac is the number of events in which the c-th codon for the a-th amino acid is used, and t a the total number of synonymous codons that encode the ath amino acid. The final representation of the codon usage data for each gene is thus a vector of 59 positions with values between 0 and 1. We calculated the pairwise CUPrefs distances as the Euclidean distances between the RF vectors of the corresponding human PVs.
Codon Adaptation Index To analyze the relationship of CUPrefs between human PVs and humans, we employed the codon adaptation index (CAI)  (Sharp and Li 1987). This index evaluates the match between the CUPrefs of a particular gene and those in a reference set. In our case, the reference values were the average CUPrefs in the human genome, as retrieved from the Kazusa codon usage database, under http://www. kazusa. or. jp/codon/cgi-bin/showcodon. cgi?species=9606, last accessed April 2013)  (Nakamura et al. 2000). CAI values were calculated for all human PV genes. CAI values were also calculated for the subset of human genes differentially expressed in the epithelium. Epithelial genes were retrieved from the UCSC browser in May 2015  (Kent et al. 2002)  filtering skin genes by their expression (log 2 (tissue/reference) with a maximum value of 5 and minimum of À5).
ICA, which is basically a double within-between-CA, has been found to be the best method in generating axes that reflect variations in synonymous codon usage  (Suzuki et al. 2008). This method further allows distinguishing within and between group variability with respect to genotype, gene, or clinical manifestations. ICA was run in R-3. 0. 1 with package ade4-1. 5. 2 and cross-checked with the implementations in vegan-2. 0. 9 and FactoMineR-1. 25. We additionally used seqinr-3. 0. 7 for computing codon usage counts and boot1. 3-11 for bootstrapping to assess the variance in each codon's contribution to the first principal axis under sampling from a sequence population. Here, we sampled with replacement from the population of all PVs, performed the ICA, and obtained the projections of codons on the first axis of the ICA.
Statistical Analysis The Huber's M-estimator calculated with R was used as robust central estimator for CAI values. The significance of the differences in CAI values between PV genes and human genes was tested with a Wilcoxon and Mann-Whitney (WMW) test, implemented in R package stats. The effect of clinical presentation and gene (and their interaction) on CAI values was tested through a two-way analysis of variance (ANOVA) followed by Tukey post hoc test (SPSS Statistics; IBM). Pearson's correlations (implemented in R) were used to determine if there was a relationship between evolutionary and codon usage-based distances. Moreover, in order to identify major sources of variation among human PVs on the axes generated by ICA, we tested for the correlation between projections to the first principal axis with CAI and average GC content at the third position in 4-fold family codons and also for the 4-fold component in the 6-fold family codons, for each gene separately.
Genes in Human PVs Do Not Follow Human Codon Usage Preferences We first evaluated the global adaptation of CUPrefs in human PV genes to the human CUPrefs, by calculating the CAI  (Sharp and Li 1987). This index evaluates the match between the CUPrefs of a particular gene and those in a reference set, in our case the human average CUPrefs. CAI values were calculated for each gene in the human PV data set. Because human PVs infect epithelial cells, CAI values were also calculated for the subset of human genes expressed in the epithelium. Figure  1  shows the cumulative frequency of CAI for human epithelial genes and for each gene in the human PVs. For all human PV genes, frequency distributions are shifted to lower CAI values compared with the reference human epithelial genes. WMW tests showed that for each of the seven human PV genes, the median CAI value is significantly lower than the median CAI value for the human epithelial genes (P < 0.
Discussion We have sought to understand the differential contribution of the different evolutionary forces shaping human PV CUPrefs. We first assessed adaptation to the host's CUPrefs, and showed that all genes in human PVs display poor adaptation to human CUPrefs. Our null, most parsimonious, hypothesis was that CUPrefs in human PVs should be close to CUPrefs in humans, because: 1) PVs do not encode for any element involved in translation and rely completely on their host's cell machinery to translate their genes and 2) the relationship of these viruses with their amniote hosts lineage is ancient  (Garcia-Vallve et al. 2005; Gottschling et al. 2011; Bravo and Felez-Sanchez 2015). Deviation from host's CUPrefs may lead to inefficient translation, in terms of decreased amount of translated protein, decreased quality of the synthesized protein, and/or decreased amount of properly folded protein  (Bravo and Mu ¨ller 2005; Drummond and Wilke 2008).
7 ). As some authors assume that GC3_4 composition reflects to some extent mutational pressure, this correlation would suggest that mutational pressures have a role patterning CUPrefs of human PVs genes, as it has been proposed for other DNA viruses  (Shackelton et al. 2006 ). However, PVs do not encode for any element of the genome replication machinery and rely instead in cellular polymerases for replication  (Park et al. 1994). Mutational biases associated to viral DNA replication should thus a priori be similar to those associated with cellular DNA replication, but it does not seem to be the case. Several mutation-based explanations between viral and cellular replication may account for the observed compositional differences. First, nucleotide composition biases in the human genome reflect mutational biases during replication in the germinal line, while nucleotide composition biases in PVs reflect mutational biases during replication in somatic cells  (Martincorena et al.
2007 ). The activity of schlafen 11 protein is to selectively inhibit translation from mRNAs enriched in A/Tending codons  (Li et al. 2012) , and many viruses infecting mammals are enriched precisely in A/T-ending codons  (Jenkins and Holmes 2003; Shackelton et al. 2006 ). The result is that, as a response against a viral infection, the cellular machinery shuts down specifically the translation of transcripts that are potentially of viral origin, using CUPrefs as a guide for pinpointing viral transcripts. In summary, we have presented here a thorough analysis of CUPrefs in human PV genes, connecting codon preferences with virus infection clinical presentation and with gene expression patterns. We have shown that, for viruses with a well-characterized infection cycle, genes expressed simultaneously tend to show similar CUPrefs.
Acknowledgments This work was supported by the disappeared  Spanish Ministry for Science and Innovation  (grant  CGL2010-16713  to I. G. B. ), and by grants by the IDIBELL (PhD fellowship to M. F. S. ), by the  Dexeus Foundation for Women's Health  (to I. G. B. ) and by the  Adolf Messer Stiftung  (personal grant to J. H. T. ).
Thus, we proposed in this paper a new concept: the Effective Indoor Thermal Time Constant (EITTC). By taking into consideration of both indoor heating/cooling system's performance and the building room's thermal property, the EITTC can be used directly to describe the indoor thermal response under existing indoor heating/cooling excitation and different outdoor conditions. The proposed indoor thermal modeling solution is presented in Fig. 1. Accordingly, this work is carried out in four steps: firstly, we presented the concept of EITTC by establishing a mathematical model of a typical low energy efficient room. Secondly, a WSN based real-time thermal data acquisition system and an ANN integrated Graphic User Interface (GUI) software are built, followed by experiments on a confined prototype and a typical office building of 40 years old.
III. WSN BASED HARDWARE AND ANN SOFTWARE DESIGN To make this work more applicable, we developed a set of industrial level hardware and software solutions including a WSN based thermal acquisition system, an ANN integrated Graphic User Interface (GUI) software and an infrared heating source (air-conditioner) remote control circuits. of the building room are henceforth defined as the outputs. To fit this MIMO system, a threelayered Back-Propagation Neural Network (BPNN) is chosen as the ANN model structure. The BPNN proposed by Rumelhart et al  [18]  is one of the most commonly used neural networks for its simplicity and efficiency. Hecht-Nielsen demonstrated that a three-layered BPNN is capable of approximating any continuous mapping  [19]. Previous research has also confirmed its performance in engineering applications  [20].
This formula has been used in several engineering problems for modeling and prediction with good results  [22]. One contribution we introduced in this work is "Step-Time" which defines a time interval to sequence the sensor data to form the training data matrix (see Fig. 8 ). Since the frequency of WSN acquisition is high, a single session of acquisitions contains a huge amount of sensor raw data in the software database. In order to train ANN model more efficiently, instead of taking all the sensor data from database, the training data matrix for the ANN model is selected sequentially from the raw sensor data according to the Step-Time. IV.
Six thermal sensors are placed horizontally at the height of 1. 10m 2. The experiments are mainly carried out in this room (See Fig. 10 ). The ANN models are automatically trained by sensor data and stored in the database. Figure  10. Room E106 in Université de Toulon, Var, France 2 According to air-conditioning industry standard, the room temperature is evaluated at the height of 1. 10m where the most human activities take place. V.
The ATLAS Metadata Interface (AMI) is now a mature application. Over the years, the number of users and the number of provided functions has dramatically increased. It is necessary to adapt the hardware infrastructure in a seamless way so that the quality of service remains high. We describe the AMI evolution since its beginning being served by a single MySQL backend database server to the current state having a cluster of virtual machines at French Tier1, an Oracle database at Lyon with complementary replication to the Oracle DB at CERN and AMI back-up server.
Introduction ATLAS  [1]  is one of the two general-purpose detectors at the Large Hadron Collider (LHC). It investigates a wide range of physics, from the search for the Higgs boson to extra dimensions and to particles that could make up dark matter. The ATLAS Metadata Interface (AMI) is a framework used by ATLAS for two major applications. Firstly, it is used for the dataset search tool, acting as a mediator between the Production System and the acquisition of real data. Secondly, the framework is used by Tag Collector, the tool for software release management. "Any fool can write code that a computer can understand" writes Martin Fowler in his book on refactoring  [2]. It is certain that anyone who has been involved with computer programs over a long period of time has seen applications thrown away and replaced by complete rewrites.
The prototype of AMI The first prototype of the AMI framework was developed in 2001. AMI has in two ancestors. The first one was a bookkeeping application for the ATLAS Liquid Argon sub-detector test beam acquisition. It was written in Java with a graphical interface. Data were uploaded asynchronously to a MySQL database. A web interface written in PHP was provided. The second ancestor was the first version of Tag Collector. This was a completely web-based application also written in PHP. It was quickly realised that a large number of database applications needed the same functions, and therefore a good design would enable the two functions. At this time the AMI developers were asked to provide bookkeeping for the first ATLAS data challenges. This was one of the catalysts for the establishment of our design principles.
Definition of the Architecture The basic architecture of AMI was established in the period 2002-2003. This phase of the development of AMI was extremely important. The importance of designing an application strong enough and flexible enough to withstand the inevitable evolutions in technology and requirements was recognized. We laid down some design principles. AMI should be independent of platform, operating system and database technology. It became clear that the software should be defined by 3 tiers. The core packages, or lowest tier, manage the remote connection to the database, and the transmission of SQL commands. Connections are indirect, the code uses logical connections parameters, and the real physical parameters are kept in a central database, which can be mirrored. This allows a flexible mechanism for geographic distribution of databases.
Initial Technology Choices It was decided to adopt Java for both the server and client code. Web interfaces were produced in HTML generated by the Java server code. Java is platform independent, and widely used both for database applications and web applications. The Java DataBase Connectivity (JDBC) interface is well adapted for use with multi-relational database engines. This choice has proved to be rational. The first deployment was on a single server at the LPSC, Grenoble. The database was a local MySQL installation. The evolution of the database infrastructure is described in section 6. The core of the AMI server is a command engine over a high level database engine. All commands sent to the server either through the web interface or through the command line client produce output in XML.
User management One of the features needed for Tag Collector is the management of user rights. A system with a high granularity was set up. Users are given a set of roles. Each role is associated with a set of commands which holders of the role can execute. Each role can be restricted to a set of AMI catalogues, and further qualification can be defined in a role validator classwhich could for instance restrict command action to particular records in a database table. User rights in AMI are not connected with user rights defined at the database level. In 2007, access to dataset metadata in ATLAS was confined to members of the collaboration therefore the management of users had to be extended beyond a simple username and password pair, to support the GRID Virtual Organization Membership Service (VOMS) mechanism  [6].
Any member of the ATLAS VO can read information in AMI. Writing operations require a particular AMI role, or a VOMS role mapped to an AMI role. It is not possible for AMI to use the CERN single sign-on mechanism because the master site is not at CERN. However in 2014 a module to manage some Tag Collector rights on software packages was linked to CERN group mailing lists which define the rights on the ATLAS SVN repository.
Software for Database Operations A database application with a large number of users must manage the database connections efficiently. A "home-made" connection pool was put into place in 2004. Since then, each AMI command is responsible for taking connections in the pool, and returning them at the end of the execution. Since AMI supports more than one database, a single command may involve update or insertion operations on more than one database. It was therefore necessary to extend the connection pool to manage transactions. All connections used by a command are held in a vector, and operations are committed (or not) when the connections are released. The future version of AMI will replace the original connection pool by the Tomcat JDBC Connection Pool  [7]  designed for highly concurrent environments and multi-core/cpu systems.