Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water

Bacteroides spp. have been proposed as indicators of fecal contamination in microbial source tracking (MST) methodologies. The aim of this study was to develop new qPCR assays that target host-specific Bacteroidal 16S ribosomal RNA genes, to determine the source of fecal contamination in water. Denaturing gradient gel electrophoresis (DGGE) was used to select for host-specific bands of Bacteroides associated with a fecal pollution source and later to design four qPCR host-specific assays. A set of common primers for Bacteroides spp., four different Bacteroides spp. host-associated hydrolysis probes (human, cattle, pig, and poultry), and one hydrolysis probe for the Bacteroides genus were designed. This set of qPCR assays together with other previously developed Bacteroidetes MST targets were used to analyze water samples with fecal contamination from the four sources studied. The host-specific Bacteroides qPCRs designed for human (HMprobeBac), pig (PGprobeBac), and poultry (PLprobeBac) were highly specific for its sources (1.0, 0.97, and 1.0, respectively) although its sensitivity was lower (0.45, 0.50, and 0.73, respectively). The cattle-specific qPCR was totally unspecific and was discarded for future experiments. When compared to previously designed assays, the human and pig qPCRs showed better accuracies (0.86 and 0.84) than their counterparts HF183 and Pig-2-Bac (0.38 and 0.65). Thus, the newly designed human, pig, and poultry qPCR assays outperform other methods developed until date and may be useful for source tracking purpose

How Far Are Current Advisory Speeds from being Optimal? An Analysis Based on Safety Performance

Posting advisory speed signs at sharp horizontal curves to provide the driving public with a safe speed is a practice well established in the United States. The operational effectiveness of these signs has long been questioned in the current literature. The authors of this paper recently developed a function to model the expected safety effect of these signs. The function stems from a statistical analysis on crash data from 2-lane rural highways in the state of Oregon. In general, that research effort found that advisory speed signs tend to enhance safety. However, the authors also determined that advisory speed signs may not be displaying the value with the greatest potential safety benefit. Since the derived function proved meaningful from the engineering and human factors perspectives, these authors then extend the use of this function to compute and recommend the theoretically “optimal” advisory speed. A new posting procedure resulted from this effort. The authors compared the expected performance of advisory speeds from the proposed procedure to the speeds derived from current posting guidelines. A comparable performance suggests that current guidelines are close to the hypothetically “optimal” advisory speed. In general, both the current and new computational methods performed better than speeds determined by the ball bank indicator method. This paper also presents a field validation analysis of the engine function of the new posting method. The results confirmed the meaningfulness of the function, and therefore, of the potential benefit for determining safety-based advisory speeds with the method proposed in this paper.This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Transportation Research Board of the National Academies (TRB) and can be found at: http://www.trb.org/Main/Blurbs/154702.aspx.Keywords: Advisory speed, Optimal advisory speed, Side Friction Demand, ASCF, Safet

The EASR Corpora of European Portuguese, French, Hungarian and Polish elderly speech

Currently available speech recognisers do not usually work well with elderly speech. This is because several characteristics of speech (e.g. fundamental frequency, jitter, shimmer and harmonic noise ratio) change with age and because the acoustic models used by speech recognisers are typically trained with speech collected from younger adults only. To develop speech-driven applications capable of successfully recognising elderly speech, this type of speech data is needed for training acoustic models from scratch or for adapting acoustic models trained with younger adults’ speech. However, the availability of suitable elderly speech corpora is still very limited. This paper describes an ongoing project to design, collect, transcribe and annotate large elderly speech corpora for four European languages: Portuguese, French, Hungarian and Polish. The Portuguese, French and Polish corpora contain read speech only, whereas the Hungarian corpus also contains spontaneous command and control type of speech. Depending on the language in question, the corpora contain 76 to 205 hours of speech collected from 328 to 986 speakers aged 60 and over. The final corpora will come with manually verified orthographic transcriptions, as well as annotations for filled pauses, noises and damaged words.info:eu-repo/semantics/publishedVersio

The EASR corpora of European Portuguese, French, Hungarian and Polish elderly speech

Currently available speech recognisers do not usually work well with elderly speech. This is because several characteristics of speech (e.g. fundamental frequency, jitter, shimmer and harmonic noise ratio) change with age and because the acoustic models used by speech recognisers are typically trained with speech collected from younger adults only. To develop speech-driven applications capable of successfully recognising elderly speech, this type of speech data is needed for training acoustic models from scratch or for adapting acoustic models trained with younger adults’ speech. However, the availability of suitable elderly speech corpora is still very limited. This paper describes an ongoing project to design, collect, transcribe and annotate large elderly speech corpora for four European languages: Portuguese, French, Hungarian and Polish. The Portuguese, French and Polish corpora contain read speech only, whereas the Hungarian corpus also contains spontaneous command and control type of speech. Depending on the language in question, the corpora contain 76 to 205 hours of speech collected from 328 to 986 speakers aged 60 and over. The final corpora will come with manually verified orthographic transcriptions, as well as annotations for filled pauses, noises and damaged words.info:eu-repo/semantics/acceptedVersio

Negativity of the Wigner function as an indicator of nonclassicality

A measure of nonclassicality of quantum states based on the volume of the negative part of the Wigner function is proposed. We analyze this quantity for Fock states, squeezed displaced Fock states and cat-like states defined as coherent superposition of two Gaussian wave packets.Comment: 10 pages, 7 figure

Laboratório móvel para monitoramento, avaliação e gerência de atributos de sistemas de produção agrícola.

bitstream/CNPMS/18890/1/Doc_49.pd

A multidimensional systems biology analysis of cellular senescence in aging and disease.

BACKGROUND: Cellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of aging and has been linked to aging-related diseases. Many genes play a role in cellular senescence, yet a comprehensive understanding of its pathways is still lacking. RESULTS: We develop CellAge (http://genomics.senescence.info/cells), a manually curated database of 279 human genes driving cellular senescence, and perform various integrative analyses. Genes inducing cellular senescence tend to be overexpressed with age in human tissues and are significantly overrepresented in anti-longevity and tumor-suppressor genes, while genes inhibiting cellular senescence overlap with pro-longevity and oncogenes. Furthermore, cellular senescence genes are strongly conserved in mammals but not in invertebrates. We also build cellular senescence protein-protein interaction and co-expression networks. Clusters in the networks are enriched for cell cycle and immunological processes. Network topological parameters also reveal novel potential cellular senescence regulators. Using siRNAs, we observe that all 26 candidates tested induce at least one marker of senescence with 13 genes (C9orf40, CDC25A, CDCA4, CKAP2, GTF3C4, HAUS4, IMMT, MCM7, MTHFD2, MYBL2, NEK2, NIPA2, and TCEB3) decreasing cell number, activating p16/p21, and undergoing morphological changes that resemble cellular senescence. CONCLUSIONS: Overall, our work provides a benchmark resource for researchers to study cellular senescence, and our systems biology analyses reveal new insights and gene regulators of cellular senescence

Innate immune responses and antioxidant/oxidant imbalance are major determinants of human Chagas disease.

We investigated the pathological and diagnostic role of selected markers of inflammation, oxidant/antioxidant status, and cellular injury in human Chagas disease. METHODS: Seropositive/chagasic subjects characterized as clinically-symptomatic or clinically-asymptomatic (n = 116), seronegative/cardiac subjects (n = 102), and seronegative/healthy subjects (n = 45) were analyzed for peripheral blood biomarkers. RESULTS: Seropositive/chagasic subjects exhibited an increase in sera or plasma levels of myeloperoxidase (MPO, 2.8-fold), advanced oxidation protein products (AOPP, 56%), nitrite (5.7-fold), lipid peroxides (LPO, 12-17-fold) and malondialdehyde (MDA, 4-6-fold); and a decline in superoxide dismutase (SOD, 52%) and glutathione (GSH, 75%) contents. Correlation analysis identified a significant (p0.95). The MPO (r = 0.664) and LPO (r = 0.841) levels were also correlated with clinical disease state in chagasic subjects (p<0.001). Seronegative/cardiac subjects exhibited up to 77% decline in SOD, 3-5-fold increase in LPO and glutamate pyruvate transaminase (GPT) levels, and statistically insignificant change in MPO, AOPP, MDA, GPX, GSH, and creatine kinase (CK) levels. CONCLUSIONS: The interlinked effects of innate immune responses and antioxidant/oxidant imbalance are major determinants of human Chagas disease. The MPO, LPO and nitrite are excellent biomarkers for diagnosing seropositive/chagasic subjects, and MPO and LPO levels have potential utility in identifying clinical severity of Chagas diseaseFil: Dhiman, Monisha. University Of Texas Medical Branch. Department Of Microbiology & Immunology And Pathology; United State of America;Fil: Coronado, Yun A.. University Of Texas Medical Branch. Department Of Microbiology & Immunology And Pathology; United State of America;Fil: Vallejo, Cecilia K.. University Of Texas Medical Branch. Department Of Microbiology & Immunology And Pathology; United State of America;Fil: Petersen, John R.. University of Texas Medical Branch. Department of Pathology; United States of America;Fil: Ejilemele, Adetoum. University of Texas Medical Branch. Department of Pathology; United States of America;Fil: Nuñez, Sonia. Hospital Público de Gestión Descentralizada San Bernardo (HPGDSA); Argentina;Fil: Zago, María Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Salta. Instituto de Patologia Experimental; Argentina;Fil: Spratt, Heidi. Departments of Biochemistry and Molecular Biology and Preventive Medicine and Community Health. University of Texas Medical Branch; United States of America;Fil: Garg, Nisha Jain. University of Texas Medical Branch. Department of Pathology; United States of America

The Rewiring of Ubiquitination Targets in a Pathogenic Yeast Promotes Metabolic Flexibility, Host Colonization and Virulence

Funding: This work was funded by the European Research Council [http://erc.europa.eu/], AJPB (STRIFE Advanced Grant; C-2009-AdG-249793). The work was also supported by: the Wellcome Trust [www.wellcome.ac.uk], AJPB (080088, 097377); the UK Biotechnology and Biological Research Council [www.bbsrc.ac.uk], AJPB (BB/F00513X/1, BB/K017365/1); the CNPq-Brazil [http://cnpq.br], GMA (Science without Borders fellowship 202976/2014-9); and the National Centre for the Replacement, Refinement and Reduction of Animals in Research [www.nc3rs.org.uk], DMM (NC/K000306/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Acknowledgments We thank Dr. Elizabeth Johnson (Mycology Reference Laboratory, Bristol) for providing strains, and the Aberdeen Proteomics facility for the biotyping of S. cerevisiae clinical isolates, and to Euroscarf for providing S. cerevisiae strains and plasmids. We are grateful to our Microscopy Facility in the Institute of Medical Sciences for their expert help with the electron microscopy, and to our friends in the Aberdeen Fungal Group for insightful discussions.Peer reviewedPublisher PD