An automated machine learning approach for classifying infrastructure cost data

Data on infrastructure project costs are often unstructured and lack consistency. To enable costs to be compared within and between organizations, large amounts of data must be classified to a common standard, typically a manual process. This is time-consuming, error-prone, inconsistent, and subjective, as it is based on human judgment. This paper describes a novel approach for automating the process by harnessing natural language processing identifying the relevant keywords in the text descriptions and implementing machine learning classifiers to emulate the expert's knowledge. The task was to identify “extra over” cost items, conversion factors, and to recognize the correct work breakdown structure (WBS) category. The results show that 94% of the “extra over” cases were correctly classified, and 90% of cases that needed conversion, correctly predicting an associated conversion factor with 87% accuracy. Finally, the WBS categories were identified with 72% accuracy. The approach has the potential to provide a step change in the speed and accuracy of structuring and classifying infrastructure cost data for benchmarking

Experimental evaluation of a R134a/CO2 cascade refrigeration plant

We present the experimental evaluation of a R134a/CO2 cascade refrigeration plant designed for low evaporation temperature in commercial refrigeration applications. The test bench incorporates two single-stage vapour compression cycles driven by semi hermetic compressors coupled thermally through two brazed plate cascade heat exchangers working in parallel and controlled by electronic expansion valves. The experimental evaluation (45 steady-states) covers evaporating temperatures from 40 to 30 C and condensing from 30 to 50 C. In each steady-state, we conducted a sweep of the condensing temperature of the low temperature cycle with speed variation of the high temperature compressor. Here, the energy performance of the plant is analysed, focussing on the compressors' performance, temperature difference in the cascade heat exchanger, cooling capacity, COP and compressors discharge temperatures.The authors gratefully acknowledge Jaume I University of Spain, who financed the present study through the research project P1.B2013-10.Sanz Kock, C.; Llopis, R.; Sánchez, D.; Cabello, R.; Torrella Alcaraz, E. (2014). Experimental evaluation of a R134a/CO2 cascade refrigeration plant. Applied Thermal Engineering. 73(1):41-50. https://doi.org/10.1016/j.applthermaleng.2014.07.041S415073

Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations

Retinitis pigmentosa (RP) is a group of progressive inherited retinal dystrophies that cause visual impairment as a result of photoreceptor cell death. RP is heterogeneous, both clinically and genetically making difficult to establish precise genotype–phenotype correlations. In a Spanish family with autosomal recessive RP (arRP), homozygosity mapping and whole-exome sequencing led to the identification of a homozygous mutation (c.358_359delGT; p.Ala122Leufs*2) in the ZNF408 gene. A screening performed in 217 additional unrelated families revealed another homozygous mutation (c.1621C>T; p.Arg541Cys) in an isolated RP case. ZNF408 encodes a transcription factor that harbors 10 predicted C2H2-type fingers thought to be implicated in DNA binding. To elucidate the ZNF408 role in the retina and the pathogenesis of these mutations we have performed different functional studies. By immunohistochemical analysis in healthy human retina, we identified that ZNF408 is expressed in both cone and rod photoreceptors, in a specific type of amacrine and ganglion cells, and in retinal blood vessels. ZNF408 revealed a cytoplasmic localization and a nuclear distribution in areas corresponding with the euchromatin fraction. Immunolocalization studies showed a partial mislocalization of the p.Arg541Cys mutant protein retaining part of the WT protein in the cytoplasm. Our study demonstrates that ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing arRP with vitreous condensations supporting the evidence that this protein plays additional functions into the human retina.This work is supported by CIBERER (06/07/0036), FIS (PI013/00226), Ministry of Economy and Competitiveness-FEDER (BFU2012-36845), RETICS (RD12/0034/0010), Fundación ONCE, Fundaluce and grants BIO2011-27069 from the Spanish Ministry of Economy and Competitiveness, and PROMETEOII/2014/025 from the Conselleria de Educacio of the Valencia Community. PC is supported by Fundación Conchita Rábago (FCR), MC by Miguel Servet ISCIII (CP/03256) and dS by CAPES Foundation, Ministry of Education of Brazil

Experimental evaluation of an internal heat exchanger in a CO2 subcritical refrigeration cycle with gas-cooler

We present the experimental evaluation of an internal heat exchanger or suction-line/liquid-line heat exchanger in a CO2 subcritical refrigeration plant with gas-cooler. The plant, driven by a 1.5 kW CO2 semi hermetic compressor, uses brazed plate heat exchangers as condenser, evaporator and internal heat exchanger, an air finned tube gas-cooler and an electronic expansion valves. The evaluation (77 steadystates) covers evaporating temperatures from 40 to 25 C and condensing temperatures from 15 to 0 C, always at the nominal speed of the compressor. Here, the effect of the internal heat exchanger on the main energy parameters is analysed, i.e., cooling capacity, COP and heat rejection at gas-cooler and condenser. Also, the effect of the internal heat exchanger in a cascade cycle is analysed theoretically. It has been concluded that the internal heat exchanger does not improve the performance of the subcritical cycle, but it could improve the energy performance if it is used inside a cascade refrigeration system.The authors gratefully acknowledge Jaume I University of Spain, who financed the present study through the research project P1.B2013-10.Llopis Doménech, R.; Sanz Kock, C.; Cabello, R.; Sanchez, D.; Torrella Alcaraz, E. (2015). Experimental evaluation of an internal heat exchanger in a CO2 subcritical refrigeration cycle with gas-cooler. Applied Thermal Engineering. 80:31-41. https://doi.org/10.1016/j.applthermaleng.2015.01.040S31418

Agriculture in NW Iberia during the Bronze Age: a review of archaeobotanical data

The wide and diverse array of palaeoenvironmental studies that were carried out in Northwestern Iberia indicate that the Bronze Age corresponds to a phase of great landscape changes. Strong deforestation and erosion episodes are key-features and they are usually assumed to be anthropogenic. The archaeological and archaeobotanical records demonstrate that these trends are coincident with modi!cations on settlement pattern and agricultural systems. This work consists on a thorough revision of carpological data from 19 Bronze Age sites in order to understand agricultural practices in the region in this time period. Results reveal the increasing relevance of Panicum miliaceum and decreasing presence of naked barley which contrast with the previous periods. Carpological remains are not available in Early Bronze Age sites.Middle Bronze Age crops include naked and hulled forms of barley (Hordeum spp.) and wheat (Triticum spp.). Only one site provided occasional grains of Panicum miliaceum. Non-cereal crops are rare and comprise Linum, Papaver, Pisum sativum and Vicia faba. Still, there are few Middle Bronze Age sites with crop macroremains. Late Bronze Age sites with carpological remains of crops are more abundant but no newcrop is added. This is the phase when Panicummiliaceum became a conspicuous crop in regional agricultural strategies. Overall, a small diversity of pulses is recorded throughout the Bronze Age, contrasting with other Iberian regions. Acorns (Quercus) are the onlywild fruits consistently present in the archaeological sites and they probably had some relevance within the regional subsistence. It was possible to detect changes on settlement and agricultural levels and suggest how these are related to environmental and social changes. It is argued that agricultural productivity increased and pits were the main storage facilities used by Bronze Age communities. Although these structures are abundant in several sites, caution is neededwhile interpreting themand their !lls. Only in one site – Freixo – remains of cropswere found in primary deposition in a storage pit. Increasing agricultural productivity, including functionally diverse winter and spring crops seems to have been connected to settlement diversi!cation. This trend may have led to a more complementary and profuse use of local resources, enhancing the anthropogenic changes in the landscape mentioned above. This was a further step in the territorialisation process thatwould eventually lead to the complex scenario recorded in the Iron Age.info:eu-repo/semantics/publishedVersio

Mutation Screening of Multiple Genes in Spanish Patients with Autosomal Recessive Retinitis Pigmentosa by Targeted Resequencing

Retinitis Pigmentosa (RP) is a heterogeneous group of inherited retinal dystrophies characterised ultimately by the loss of photoreceptor cells. RP is the leading cause of visual loss in individuals younger than 60 years, with a prevalence of about 1 in 4000. The molecular genetic diagnosis of autosomal recessive RP (arRP) is challenging due to the large genetic and clinical heterogeneity. Traditional methods for sequencing arRP genes are often laborious and not easily available and a screening technique that enables the rapid detection of the genetic cause would be very helpful in the clinical practice. The goal of this study was to develop and apply microarray-based resequencing technology capable of detecting both known and novel mutations on a single high-throughput platform. Hence, the coding regions and exon/intron boundaries of 16 arRP genes were resequenced using microarrays in 102 Spanish patients with clinical diagnosis of arRP. All the detected variations were confirmed by direct sequencing and potential pathogenicity was assessed by functional predictions and frequency in controls. For validation purposes 4 positive controls for variants consisting of previously identified changes were hybridized on the array. As a result of the screening, we detected 44 variants, of which 15 are very likely pathogenic detected in 14 arRP families (14%). Finally, the design of this array can easily be transformed in an equivalent diagnostic system based on targeted enrichment followed by next generation sequencing

Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes

Gene expression signatures of toxicity and clinical response benefit both safety assessment and clinical practice; however, difficulties in connecting signature genes with the predicted end points have limited their application. The Microarray Quality Control Consortium II (MAQCII) project generated 262 signatures for ten clinical and three toxicological end points from six gene expression data sets, an unprecedented collection of diverse signatures that has permitted a wide-ranging analysis on the nature of such predictive models. A comprehensive analysis of the genes of these signatures and their nonredundant unions using ontology enrichment, biological network building and interactome connectivity analyses demonstrated the link between gene signatures and the biological basis of their predictive power. Different signatures for a given end point were more similar at the level of biological properties and transcriptional control than at the gene level. Signatures tended to be enriched in function and pathway in an end point and model-specific manner, and showed a topological bias for incoming interactions. Importantly, the level of biological similarity between different signatures for a given end point correlated positively with the accuracy of the signature predictions. These findings will aid the understanding, and application of predictive genomic signatures, and support their broader application in predictive medicine

Frequent CXCR4 tropism of HIV-1 subtype A and CRF02_AG during late-stage disease - indication of an evolving epidemic in West Africa

<p>Abstract</p> <p>Background</p> <p>HIV-1 is one of the fastest evolving pathogens, and is distinguished by geographic and genetic variants that have been classified into different subtypes and circulating recombinant forms (CRFs). Early in infection the primary coreceptor is CCR5, but during disease course CXCR4-using HIV-1 populations may emerge. This has been correlated with accelerated disease progression in HIV-1 subtype B. Basic knowledge of HIV-1 coreceptor tropism is important due to the recent introduction of coreceptor antagonists in antiretroviral therapy, and subtype-specific differences regarding how frequently HIV-1 CXCR4-using populations appear in late-stage disease need to be further investigated. To study how frequently CXCR4-using populations appear in late-stage disease among HIV-1 subtype A and CRF02_AG, we evaluated the accuracy of a recombinant virus phenotypic assay for these subtypes, and used it to determine the HIV-1 coreceptor tropism of plasma samples collected during late-stage disease in Guinea-Bissau. We also performed a genotypic analysis and investigated subtype-specific differences in the appearance of CXCR4 tropism late in disease.</p> <p>Results</p> <p>We found that the recombinant virus phenotypic assay accurately predicted HIV-1 coreceptor tropism of subtype A and CRF02_AG. Over the study period (1997-2007), we found an increasing and generally high frequency of CXCR4 tropism (86%) in CRF02_AG. By sequence analysis of the V3 region of our samples we developed a novel genotypic rule for predicting CXCR4 tropism in CRF02_AG, based on the combined criteria of the total number of charged amino acids and net charge. This rule had higher sensitivity than previously described genotypic rules and may be useful for development of future genotypic tools for this CRF. Finally, we conducted a literature analysis, combining data of 498 individuals in late-stage disease, and found high amounts of CXCR4 tropism for all major HIV-1 subtypes (60-77%), except for subtype C (15%).</p> <p>Conclusions</p> <p>The increase in CXCR4 tropism over time suggests an evolving epidemic of CRF02_AG. The results of the literature analysis demonstrate the need for further studies investigating subtype-specific emergence for CXCR4-tropism; this may be particularly important due to the introduction of CCR5-antagonists in HIV treatment regimens.</p

Molecular evolution of cyclin proteins in animals and fungi

<p>Abstract</p> <p>Background</p> <p>The passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which differ considerably in primary structure from one eukaryotic organism to another. Despite these lines of evidence, the relationship between the evolution of cyclins and their function is an open issue. Here we present the results of our study on the molecular evolution of A-, B-, D-, E-type cyclin proteins in animals and fungi.</p> <p>Results</p> <p>We constructed phylogenetic trees for these proteins, their ancestral sequences and analyzed patterns of amino acid replacements. The analysis of infrequently fixed atypical amino acid replacements in cyclins evidenced that accelerated evolution proceeded predominantly during paralog duplication or after it in animals and fungi and that it was related to aromorphic changes in animals. It was shown also that evolutionary flexibility of cyclin function may be provided by consequential reorganization of regions on protein surface remote from CDK binding sites in animal and fungal cyclins and by functional differentiation of paralogous cyclins formed in animal evolution.</p> <p>Conclusions</p> <p>The results suggested that changes in the number and/or nature of cyclin-binding proteins may underlie the evolutionary role of the alterations in the molecular structure of cyclins and their involvement in diverse molecular-genetic events.</p

Identification and Pathway Analysis of microRNAs with No Previous Involvement in Breast Cancer

microRNA expression signatures can differentiate normal and breast cancer tissues and can define specific clinico-pathological phenotypes in breast tumors. In order to further evaluate the microRNA expression profile in breast cancer, we analyzed the expression of 667 microRNAs in 29 tumors and 21 adjacent normal tissues using TaqMan Low-density arrays. 130 miRNAs showed significant differential expression (adjusted P value = 0.05, Fold Change = 2) in breast tumors compared to the normal adjacent tissue. Importantly, the role of 43 of these microRNAs has not been previously reported in breast cancer, including several evolutionary conserved microRNA*, showing similar expression rates to that of their corresponding leading strand. The expression of 14 microRNAs was replicated in an independent set of 55 tumors. Bioinformatic analysis of mRNA targets of the altered miRNAs, identified oncogenes like ERBB2, YY1, several MAP kinases, and known tumor-suppressors like FOXA1 and SMAD4. Pathway analysis identified that some biological process which are important in breast carcinogenesis are affected by the altered microRNA expression, including signaling through MAP kinases and TP53 pathways, as well as biological processes like cell death and communication, focal adhesion and ERBB2-ERBB3 signaling. Our data identified the altered expression of several microRNAs whose aberrant expression might have an important impact on cancer-related cellular pathways and whose role in breast cancer has not been previously described