Death by acid rain: VAP or EXIT?

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Thorburn, Kentigern; Darbyshire, Andrew

2009-01-01

Ventilator-associated pneumonia (VAP) is a new (nosocomial) lower respiratory tract infection diagnosed in mechanically ventilated patients 48 or more hours after intubation. There is no gold standard for establishing the diagnosis and its pathogenesis is iatrogenic and multifactorial. Gastro-oesophageal reflux is common in mechanically ventilated children, but its role in VAP remains speculative. VAP is associated with increased mortality and morbidity, prolonged duration of ventilation and ...

Spinal Cord Stimulation (SCS) with Anatomically Guided (3D) Neural Targeting Shows Superior Chronic Axial Low Back Pain Relief Compared to Traditional SCS-LUMINA Study.

Science.gov (United States)

Veizi, Elias; Hayek, Salim M; North, James; Brent Chafin, T; Yearwood, Thomas L; Raso, Louis; Frey, Robert; Cairns, Kevin; Berg, Anthony; Brendel, John; Haider, Nameer; McCarty, Matthew; Vucetic, Henry; Sherman, Alden; Chen, Lilly; Mekel-Bobrov, Nitzan

2017-08-01

The aim of this study was to determine whether spinal cord stimulation (SCS) using 3D neural targeting provided sustained overall and low back pain relief in a broad routine clinical practice population. This was a multicenter, open-label observational study with an observational arm and retrospective analysis of a matched cohort. After IPG implantation, programming was done using a patient-specific, model-based algorithm to adjust for lead position (3D neural targeting) or previous generation software (traditional). Demographics, medical histories, SCS parameters, pain locations, pain intensities, disabilities, and safety data were collected for all patients. A total of 213 patients using 3D neural targeting were included, with a trial-to-implant ratio of 86%. Patients used seven different lead configurations, with 62% receiving 24 to 32 contacts, and a broad range of stimulation parameters utilizing a mean of 14.3 (±6.1) contacts. At 24 months postimplant, pain intensity decreased significantly from baseline (ΔNRS = 4.2, N = 169, P  pain subgroup (ΔNRS = 5.3, N = 91, P  low back pain also decreased significantly from baseline to 24 months (ΔNRS = 4.1, N = 70, P  pain responder rates of 51% (traditional SCS) and 74% (neural targeting SCS) and axial low back pain responder rates of 41% and 71% in the traditional SCS and neural targeting SCS cohorts, respectively. Lastly, complications occurred in a total of 33 of the 213 patients, with a 1.6% lead replacement rate and a 1.6% explant rate. Our results suggest that 3D neural targeting SCS and its associated hardware flexibility provide effective treatment for both chronic leg and chronic axial low back pain that is significantly superior to traditional SCS. © 2017 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

A Toxin-Antitoxin System VapBC15 from Synechocystis sp. PCC 6803 Shows Distinct Regulatory Features

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Qian Fei

2018-03-01

Full Text Available Type II toxin–antitoxin (TA systems play important roles in bacterial stress survival by regulating cell growth or death. They are highly abundant in cyanobacteria yet remain poorly characterized. Here, we report the identification and regulation of a putative type II TA system from Synechocystis PCC6803, VapBC15. The VapBC15 system is encoded by the chromosomal operon vapBC15. Exogenous expression of VapC15 dramatically arrested cell growth of Escherichia coli and reduced the numbers of colony-forming units (CFU. The VapC15 toxicity could be which was counteracted neutralized by simultaneous or delayed production of VapB15. Biochemical analysis demonstrated the formation of VapB15-VapC15 complexes by the physical interaction between VapB15 and VapC15. Notably, the VapB15 antitoxin up-regulated the transcription of the vapBC15 operon by directly binding to the promoter region, and the VapC15 toxin abolished the up-regulatory effect by destabilizing the binding. Moreover, VapB15 can be degraded by the proteases Lons and ClpXP2s from Synechocystis PCC6803, thus activating the latent toxicity of VapBC15. These findings suggest that VapBC15 represents a genuine TA system that utilizes a distinct mechanism to regulate toxin activity.

Human Papillomavirus 16 Infection Induces VAP-Dependent Endosomal Tubulation.

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Siddiqa, Abida; Massimi, Paola; Pim, David; Broniarczyk, Justyna; Banks, Lawrence

2018-03-15

Human papillomavirus (HPV) infection involves complex interactions with the endocytic transport machinery, which ultimately facilitates the entry of the incoming viral genomes into the trans -Golgi network (TGN) and their subsequent nuclear entry during mitosis. The endosomal pathway is a highly dynamic intracellular transport system, which consists of vesicular compartments and tubular extensions, although it is currently unclear whether incoming viruses specifically alter the endocytic machinery. In this study, using MICAL-L1 as a marker for tubulating endosomes, we show that incoming HPV-16 virions induce a profound alteration in global levels of endocytic tubulation. In addition, we also show a critical requirement for the endoplasmic reticulum (ER)-anchored protein VAP in this process. VAP plays an essential role in actin nucleation and endosome-to-Golgi transport. Indeed, the loss of VAP results in a dramatic decrease in the level of endosomal tubulation induced by incoming HPV-16 virions. This is also accompanied by a marked reduction in virus infectivity. In VAP knockdown cells, we see that the defect in virus trafficking occurs after capsid disassembly but prior to localization at the trans -Golgi network, with the incoming virion-transduced DNA accumulating in Vps29/TGN46-positive hybrid vesicles. Taken together, these studies demonstrate that infection with HPV-16 virions induces marked alterations of endocytic transport pathways, some of which are VAP dependent and required for the endosome-to-Golgi transport of the incoming viral L2/DNA complex. IMPORTANCE Human papillomavirus infectious entry involves multiple interactions with the endocytic transport machinery. In this study, we show that incoming HPV-16 virions induce a dramatic increase in endocytic tubulation. This tubulation requires ER-associated VAP, which plays a critical role in ensuring the delivery of cargoes from the endocytic compartments to the trans -Golgi network. Indeed, the loss of

Use of ventilator associated pneumonia bundle and statistical process control chart to decrease VAP rate in Syria.

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Alsadat, Reem; Al-Bardan, Hussam; Mazloum, Mona N; Shamah, Asem A; Eltayeb, Mohamed F E; Marie, Ali; Dakkak, Abdulrahman; Naes, Ola; Esber, Faten; Betelmal, Ibrahim; Kherallah, Mazen

2012-10-01

Implementation of ventilator associated pneumonia (VAP) bundle as a performance improvement project in the critical care units for all mechanically ventilated patients aiming to decrease the VAP rates. VAP bundle was implemented in 4 teaching hospitals after educational sessions and compliance rates along with VAP rates were monitored using statistical process control charts. VAP bundle compliance rates were steadily increasing from 33 to 80% in hospital 1, from 33 to 86% in hospital 2 and from 83 to 100% in hospital 3 during the study period. The VAP bundle was not applied in hospital 4 therefore no data was available. A target level of 95% was reached only in hospital 3. This correlated with a decrease in VAP rates from 30 to 6.4 per 1000 ventilator days in hospital 1, from 12 to 4.9 per 1000 ventilator days in hospital 3, whereas VAP rate failed to decrease in hospital 2 (despite better compliance) and it remained high around 33 per 1000 ventilator days in hospital 4 where VAP bundle was not implemented. VAP bundle has performed differently in different hospitals in our study. Prevention of VAP requires a multidimensional strategy that includes strict infection control interventions, VAP bundle implementation, process and outcome surveillance and education.

Is the gram stain useful in the microbiologic diagnosis of VAP? A meta-analysis.

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O'Horo, John C; Thompson, Deb; Safdar, Nasia

2012-08-01

In a meta-analysis examining respiratory specimen Gram stain for diagnosis of ventilator-associated pneumonia, absence of bacteria on Gram stain had a high negative predictive value, but a positive Gram stain correlated poorly with organisms recovered in culture. Rapid and accurate diagnosis of ventilator-associated pneumonia (VAP) is a major challenge and no generally accepted gold standard exists for VAP diagnosis. We conducted a meta-analysis to examine the role of respiratory specimen Gram stain to diagnose VAP, and the correlation with final culture results. In 21 studies, pooled sensitivity of Gram stain for VAP was 0.79 (95% confidence interval [CI], .77-0.81; P Gram stain for a VAP prevalence of 20%-30% was 91%, suggesting that VAP is unlikely with a negative Gram stain but the positive predictive value of Gram stain was only 40%. Pooled kappa was 0.42 for gram-positive organisms and 0.34 for gram-negative organisms, suggesting fair concordance between organisms on Gram stain and recovery by culture. Therefore, a positive Gram stain should not be used to narrow anti-infective therapy until culture results become available.

Antibiotic susceptibility patterns of different bacteria isolated from patients with ventilator associated pneumonia (vap).

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Alqurashi, Abdulrahman M

2005-09-01

Ventilator associated pneumonia (VAP) is a frequent complication of mechanical ventilation (MV) and it is a leading cause of death in MV patients. The development of VAP has been demonstrated as being due to aspiration of oropharyngeal secretion, ventilator tubing condensate, or gastric contents that are colonized with pathogenic microorganisms. The aim of the present study is to isolate and identify bacteria that cause VAP and to study antibiotic susceptibility. This study was carried out on 95 patients who fulfilled the diagnostic criteria for VAP. Quantitative cultures of endotracheal aspirates (EA) using a cut-off point of 10(6) cfu/ml was done. The microbiological results revealed that gram negative bacilli were the most common bacterial agents responsible for VAP and accounted for 78.8% of all the causative agents. The most common isolated organisms were Klebsiella pnemouniae (30.9 %) followed by Pseudomonas aeruginosa (22.5%), Staphylococcus aureus (21.2%), Eschericia coli (12.8 %), Proteus spp. (9.8%), and Citrobacter spp. (2.8%). Blood cultures were positive in 25.9% of patients with Klebsiella pnemouniae in about 33.3%. From this study, it can be concluded that VAP is an important nosocomial infection. EA is a simple procedure to obtain respiratory samples and perform sensitivity testing in patients with VAP. Also, the commonest cause of VAP is gram negative bacilli.

Molecular characterization of Rhodococcus equi isolates from horses in Poland: pVapA characteristics and plasmid new variant, 85-kb type V.

Science.gov (United States)

Witkowski, Lucjan; Rzewuska, Magdalena; Takai, Shinji; Chrobak-Chmiel, Dorota; Kizerwetter-Świda, Magdalena; Feret, Małgorzata; Gawryś, Marta; Witkowski, Maciej; Kita, Jerzy

2017-01-26

Rhodococcus equi is one of the most significant bacterial pathogens affecting foals up to 6 months of age worldwide. Rhodococcosis is present in Poland however information about molecular characterization of R. equi isolates is scarce. This study describes molecular characterization of Rhodococcus equi infection on 13 horse breeding farms in Poland between 2001 and 2012. Samples were collected by tracheobronchial aspiration from pneumonic foals or during necropsy. The R. equi isolates were genotyped by plasmid profiling and pulsed-field gel electrophoresis. Totally, 58 R. equi isolates were investigated. One isolate lost its plasmid. Among the 57 VapA-positive isolates, 48 contained 85-kb type I plasmid (82.8%), 8 contained 87-kb type I plasmid (13.8%). One isolate (1.7%) had a unique restriction cleavage pattern and the 2nd fragment of EcoRI digests of this plasmid DNA was about 2600 bases smaller than that of the 85 kb type I. This new plasmid variant was designated as the "85-kb type V". Among the 58 isolates typeable with VspI-PFGE, ten PFGE clusters were detected. The majority of foals were infected mostly with isolates of low genetic diversity. Most of clinical isolates of R. equi from foals in Poland contain pVapA 85-kb type I and 87-kb type I similarly to the other European countries and the United States. However, the new variant of pVapA 85-kb type V was identified. The chromosomal variability was detected among some of the investigated isolates and the presence of farm-specific isolates might be possible.

Nosocomial pneumonia in 27 ICUs in Europe: perspectives from the EU-VAP/CAP study.

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Koulenti, D; Tsigou, E; Rello, J

2017-11-01

We report on intensive care nosocomial pneumonia (NP) in Europe through a review of EU-VAP/CAP manuscripts: a prospective observational study, enrolling patients from 27 ICUs in nine European countries. From 2,436 eligible ICU patients, 827 cases presented NP, with 18.3 episodes of VAP per 1000 ventilator-days. Most common findings were worsening oxygenation, purulent respiratory secretions and temperature increase. At least three criteria from Clinical Pulmonary Infection score (CPIS) were present in 77.9 % of episodes, but only 0.2 % met six CPIS criteria. Diagnosis was confirmed mainly noninvasively (74.8 %), with half qualitative and quantitative cultures. The dominant isolate was S. aureus in Spain, France, Belgium and Ireland, P. aeruginosa in Italy and Portugal, Acinetobacter in Greece and Turkey, but Escherichia coli in Germany. NP resulted in 6 % higher mortality, longer ICU stay and duration of mechanical ventilation (12 and 10 days). COPD and age ≥45 years were not associated with higher VAP incidence but did correlate with increased mortality. Trauma had higher VAP incidence but lower mortality. Bacteremia (led by MRSA and Acinetobacter baumannii) was documented in 14.6 %, being associated with extra ICU stay and mortality. Vasopressors and ICUs with above 25 % prevalence of Potential Resistant Organisms (PRM) were independently associated with PRM, being documented in 50.7 % of patients with early-onset VAP without known risk factors. Most patients initially received combination therapy. Delay in appropriate antimicrobial choice significantly increased mortality, and LOS in survivors was six days longer (p < 0.05). In conclusion, NP management in Europe presents local differences and major shifts when compared to reports from North America, outcomes of randomized trials and general guidelines.

[The comparison of different bronchial aspirate culturing methods in patients with ventilator-associated pneumonia (VAP)].

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Kowalczyk, Wojciech; Rybicki, Zbigniew; Tomaszewski, Dariusz; Truszczyński, Andrzej; Guzek, Aneta

2011-01-01

Although broncho-alveolar lavage (BAL) culture and protected specimen brush (PSB) are regarded as the most effective methods in the diagnosis of VAP, a simple endotracheal aspiration (EA) is frequently performed during routine care, because of its simplicity and low cost. We compared the effectiveness of EA with BAL and PSB in VAP patients. Sixty-one adult VAP patients, ventilated for longer than 48 h, were cultured with all three methods. Positive cultures were obtained from 63.9% of patients, with Acinetobacter baumannii being the most common pathogen. There was a high positive correlation between simple aspirates and BAL (k 0.817, CI 0.664-0.840, p aspirates and PSB (k 0.667, CI 0.483-0.871, p aspirate culturing, compared to BAL and PSB, it can be used successfully in most cases.

p53 regulates the repair of DNA double-strand breaks by both homologous and non-homologous recombination

International Nuclear Information System (INIS)

Willers, H.; Powell, S.N.; Dahm-Daphi, J.

2003-01-01

Full text: p53 is known to suppress spontaneous homologous recombination (HR), while its role in non-homologous recombination (NHR) remains to be clarified. Here, we sought to determine the influence of p53 on the repair of chromosomal double-strand breaks (DSBs) by HR or NHR using specially designed recombination substrates that integrate into the genome. Isogenic mouse fibroblast pairs with or without expression of exogenous p53 protein were utilized. A reporter plasmid carrying a mutated XGPRT gene was chromosomally integrated and DSBs were generated within the plasmid by the I-SceI endonuclease. Subsequent homology-mediated repair from an episomal donor resulted in XGPRT reconstitution and cellular resistance to a selection antibiotic. Analogously, the repair of chromosomal I-SceI breaks by NHR using another novel reporter plasmid restored XGPRT translation. For p53-null cells, the mean frequency of I-SceI break repair via HR was 5.5 x 10 -4 . The p53-Val135 mutant, which previously has been shown to suppress spontaneous HR by 14-fold employing the same cell system and reporter gene, only caused a 2- to 3-fold suppression of break-induced HR. In contrast, a dramatic effect of p53 on repair via NHR was found. Preliminary sequence analysis indicated that there was at least a 1000-fold reduction of illegitimate repair events resulting in loss of sequence at the break sites. The observed effects were mediated by p53 mutants defective in regulation of the cell-cycle and apoptosis. The main findings were: (1) p53 virtually blocked illegitimate rejoining of chromosomal ends. (2) The suppression of homologous DSB repair was less pronounced than the inhibition of spontaneous HR. We hypothesize that p53 allows to a certain extent error-free homology-dependent repair to proceed, while blocking error-prone NHR. The data support and extent a previous model, in which p53 maintains genomic stability by regulating recombination independently of its transactivation function

Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri

DEFF Research Database (Denmark)

Xu, Kehan; Dedic, Emil; Brodersen, Ditlev Egeskov

2016-01-01

The VapC toxin from the Shigella flexneri 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a bona fide Mg2+-dependent ribonuclease and has been shown to target initiator t...

Comparison study between bacteriological aetiology and outcome of VAT & VAP

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Nasr H. Kahlil

2017-01-01

Conclusion: From the study we concluded that VAT infection is as severe as VAP and it needs more attention to prevent its presence as, once present, it usually progress to VAP increasing mortality rate in ICU.

A mutation in human VAP-B--MSP domain, present in ALS patients, affects the interaction with other cellular proteins.

Science.gov (United States)

Mitne-Neto, M; Ramos, C R R; Pimenta, D C; Luz, J S; Nishimura, A L; Gonzales, F A; Oliveira, C C; Zatz, M

2007-09-01

Amyotrophic Lateral Sclerosis (ALS) is the most common adult-onset Motor Neuron Disease (MND), characterized by motor neurons death in the cortex, brainstem and spinal cord. Ten loci linked to Familial ALS have been mapped. ALS8 is caused by a substitution of a proline by a serine in the Vesicle-Associated Membrane Protein-Associated protein-B/C (VAP-B/C). VAP-B belongs to a highly conserved family of proteins implicated in Endoplasmic Reticulum-Golgi and intra-Golgi transport and microtubules stabilization. Previous studies demonstrated that the P56S mutation disrupts the subcellular localization of VAP-B and that this position would be essential for Unfolded Protein Response (UPR) induced by VAP-B. In the present work we expressed and purified recombinant wild-type and P56S mutant VAP-B-MSP domain for the analysis of its interactions with other cellular proteins. Our findings suggest that the P56S mutation may lead to a less stable interaction of this endoplasmic reticulum protein with at least two other proteins: tubulin and GAPDH. These two proteins have been previously related to other forms of neurodegenerative diseases and are potential key points to understand ALS8 pathogenesis and other forms of MND. Understanding the role of these protein interactions may help the treatment of this devastating disease in the future.

Tombusviruses upregulate phospholipid biosynthesis via interaction between p33 replication protein and yeast lipid sensor proteins during virus replication in yeast

International Nuclear Information System (INIS)

Barajas, Daniel; Xu, Kai; Sharma, Monika; Wu, Cheng-Yu; Nagy, Peter D.

2014-01-01

Positive-stranded RNA viruses induce new membranous structures and promote membrane proliferation in infected cells to facilitate viral replication. In this paper, the authors show that a plant-infecting tombusvirus upregulates transcription of phospholipid biosynthesis genes, such as INO1, OPI3 and CHO1, and increases phospholipid levels in yeast model host. This is accomplished by the viral p33 replication protein, which interacts with Opi1p FFAT domain protein and Scs2p VAP protein. Opi1p and Scs2p are phospholipid sensor proteins and they repress the expression of phospholipid genes. Accordingly, deletion of OPI1 transcription repressor in yeast has a stimulatory effect on TBSV RNA accumulation and enhanced tombusvirus replicase activity in an in vitro assay. Altogether, the presented data convincingly demonstrate that de novo lipid biosynthesis is required for optimal TBSV replication. Overall, this work reveals that a (+)RNA virus reprograms the phospholipid biosynthesis pathway in a unique way to facilitate its replication in yeast cells. - Highlights: • Tombusvirus p33 replication protein interacts with FFAT-domain host protein. • Tombusvirus replication leads to upregulation of phospholipids. • Tombusvirus replication depends on de novo lipid synthesis. • Deletion of FFAT-domain host protein enhances TBSV replication. • TBSV rewires host phospholipid synthesis

Critical analysis of the factors associated with enteral feeding in preventing VAP: a systematic review.

Science.gov (United States)

Chen, Yu-Chih

2009-04-01

Ventilator-associated pneumonia (VAP) is a common cause of morbidity in critically ill patients. Appropriate enteral feeding is the most important factor associated with the prevention of VAP. However, the standardization of enteral feeding methods needs clarification. The purpose of this systematic review was to synthesize the factors associated with enteral feeding in order to prevent VAP and to describe the characteristics of these factors. A comprehensive search was undertaken involving all major databases from their inception to September 2008 using medical subject heading terms associated with enteral feeding in relation to VAP. The overall reference list of identified studies was audited, and eligible studies included randomized controlled trials, controlled before-and-after (pre-post) studies and meta-analyses. To generate the characteristics of the factors associated with VAP, the reported components of these trials were pinpointed and categorized. A total of 14 papers were found that had investigated the factors linking enteral feeding and VAP. For these, 11 were randomized controlled trials, 1 was a meta-analysis and 2 were case-controlled analyses. Twelve of these 14 studies were conducted at a single institute and 2 were conducted at multiple institutes. The sample sizes varied from 10 to 2,528 subjects. Three major issues were identified based on the purpose of study interventions, and these were the effects of feeding method (continuous vs. intermittent), feeding site on aspiration (gastric vs. small bowel), and the timing of enteral feeding (early vs. late). The evidence suggests that a correct choice of enteral feeding method can effectively reduce complications due to aspiration. Furthermore, intermittent enteral feeding and with a small residual volume feed can reduce gastroesophageal reflux, and increased total intake volume and early feeding can reduce ICU mortality. Nonetheless, the effects of these choices on preventing VAP still need further

Critical Analysis of the Factors Associated with Enteral Feeding in Preventing VAP: A Systematic Review

Directory of Open Access Journals (Sweden)

Yu-Chih Chen

2009-04-01

Full Text Available Ventilator-associated pneumonia (VAP is a common cause of morbidity in critically ill patients. Appropriate enteral feeding is the most important factor associated with the prevention of VAP. However, the standardization of enteral feeding methods needs clarification. The purpose of this systematic review was to synthesize the factors associated with enteral feeding in order to prevent VAP and to describe the characteristics of these factors. A comprehensive search was undertaken involving all major databases from their inception to September 2008 using medical subject heading terms associated with enteral feeding in relation to VAP. The overall reference list of identified studies was audited, and eligible studies included randomized controlled trials, controlled before-and-after (pre–post studies and meta-analyses. To generate the characteristics of the factors associated with VAP, the reported components of these trials were pinpointed and categorized. A total of 14 papers were found that had investigated the factors linking enteral feeding and VAP. For these, 11 were randomized controlled trials, 1 was a meta-analysis and 2 were case-controlled analyses. Twelve of these 14 studies were conducted at a single institute and 2 were conducted at multiple institutes. The sample sizes varied from 10 to 2,528 subjects. Three major issues were identified based on the purpose of study interventions, and these were the effects of feeding method (continuous vs. intermittent, feeding site on aspiration (gastric vs. small bowel, and the timing of enteral feeding (early vs. late. The evidence suggests that a correct choice of enteral feeding method can effectively reduce complications due to aspiration. Furthermore, intermittent enteral feeding and with a small residual volume feed can reduce gastroesophageal reflux, and increased total intake volume and early feeding can reduce ICU mortality. Nonetheless, the effects of these choices on preventing VAP

Analysis of ventilator associated pneumonia (VAP studies in Egyptian University Hospitals

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Amal Fathy

2013-01-01

Conclusion: It is important to establish large-scale multi center national studies to explore incidence of VAP, all possible risk factors (whether preventable or non preventable, causative organisms, and mortality due to VAP and its economic aspect.

Environmental concerns of supply chain sustainability (SCS)

Science.gov (United States)

Mokhtar, Mohd Faiz; Omar, Badrul; Nor, Nik Hisyamudin Muhd; Pauzi, Nur Fazlinda Mohd; Hasan, Sulaiman; Mohamed, W. A. Wan

2017-04-01

Environment concern is one important aspect for supply chain sustainability (SCS). Nowadays, company's activities give a lot of impact on the environment. Through these activities, there are other SCS issue of environment were identified. In this paper, the proposed SCS issue of environmental concern will be determined from Corporate Sustainability Report (CSR). Using a total weightage of 0.333 (after dividing into three aspects of sustainability), each proposed issues will be classified according to the company activities in order to determined weightage for each issue. Those weightages then will be used in developing of score metric for SCS in design phase. Result shows that the carbon footprint is the major concern for SCS of environment while environmental management system is a lowest concern for SCS environment.

Comparative Genomics of Rhodococcus equi Virulence Plasmids Indicates Host-Driven Evolution of the vap Pathogenicity Island.

Science.gov (United States)

MacArthur, Iain; Anastasi, Elisa; Alvarez, Sonsiray; Scortti, Mariela; Vázquez-Boland, José A

2017-05-01

The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently characterized the R. equi pangenome (Anastasi E, et al. 2016. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol. 8:3140-3148.) and we report here the comparative analysis of the virulence plasmid genomes. Plasmids within each host-associated type were highly similar despite their diverse origins. Variation was accounted for by scattered single nucleotide polymorphisms and short nucleotide indels, while larger indels-mostly in the plasticity region near the vap pathogencity island (PAI)-defined plasmid genomic subtypes. Only one of the plasmids analyzed, of pVAPN type, was exceptionally divergent due to accumulation of indels in the housekeeping backbone. Each host-associated plasmid type carried a unique PAI differing in vap gene complement, suggesting animal host-specific evolution of the vap multigene family. Complete conservation of the vap PAI was observed within each host-associated plasmid type. Both diversity of host-associated plasmid types and clonality of specific chromosomal-plasmid genomic type combinations were observed within the same R. equi phylogenomic subclade. Our data indicate that the overall strong conservation of the R. equi host-associated virulence plasmids is the combined result of host-driven selection, lateral transfer between strains, and geographical spread due to international livestock exchanges. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The C. elegans VAPB homolog VPR-1 is a permissive signal for gonad development.

Science.gov (United States)

Cottee, Pauline A; Cole, Tim; Schultz, Jessica; Hoang, Hieu D; Vibbert, Jack; Han, Sung Min; Miller, Michael A

2017-06-15

VAMP/synaptobrevin-associated proteins (VAPs) contain an N-terminal major sperm protein domain (MSPd) that is associated with amyotrophic lateral sclerosis. VAPs have an intracellular housekeeping function, as well as an extracellular signaling function mediated by the secreted MSPd. Here we show that the C. elegans VAP homolog VPR-1 is essential for gonad development. vpr-1 null mutants are maternal effect sterile due to arrested gonadogenesis following embryo hatching. Somatic gonadal precursor cells and germ cells fail to proliferate fully and complete their respective differentiation programs. Maternal or zygotic vpr-1 expression is sufficient to induce gonadogenesis and fertility. Genetic mosaic and cell type-specific expression studies indicate that vpr-1 activity is important in the nervous system, germ line and intestine. VPR-1 acts in parallel to Notch signaling, a key regulator of germline stem cell proliferation and differentiation. Neuronal vpr-1 expression is sufficient for gonadogenesis induction during a limited time period shortly after hatching. These results support the model that the secreted VPR-1 MSPd acts at least in part on gonadal sheath cell precursors in L1 to early L2 stage hermaphrodites to permit gonadogenesis. © 2017. Published by The Company of Biologists Ltd.

Mitochondrial pAL2-1 plasmid homologs are senescence factors in Podospora anserina independent of intrinsic senescence

NARCIS (Netherlands)

Diepeningen, van A.D.; Debets, A.J.M.; Slakhorst-Wandel, S.M.; Hoekstra, R.F.

2008-01-01

Since the first description of a linear mitochondrial plasmid in Podospora anserina, pAL2-1, and homologous plasmids have gone from being considered beneficial longevity plasmids, via neutral genetic elements, toward mutator plasmids causing senescence. The plasmid has an invertron structure, with

Mitochondrial pAL2-1 plasmid homologs are senescence factors in Podospora anserina independent of intrinsic senescence

NARCIS (Netherlands)

van Diepeningen, Anne D; Debets, Alfons J M; Slakhorst, S Marijke; Hoekstra, Rolf F

Since the first description of a linear mitochondrial plasmid in Podospora anserina, pAL2-1, and homologous plasmids have gone from being considered beneficial longevity plasmids, via neutral genetic elements, toward mutator plasmids causing senescence. The plasmid has an invertron structure, with

Vibrational frequency scaling factors for correlation consistent basis sets and the methods CC2 and MP2 and their spin-scaled SCS and SOS variants

Energy Technology Data Exchange (ETDEWEB)

Friese, Daniel H., E-mail: daniel.h.friese@uit.no [Centre for Theoretical and Computational Chemistry CTCC, Department of Chemistry, University of Tromsø, N-9037 Tromsø (Norway); Törk, Lisa; Hättig, Christof, E-mail: christof.haettig@rub.de [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44801 Bochum (Germany)

2014-11-21

We present scaling factors for vibrational frequencies calculated within the harmonic approximation and the correlated wave-function methods coupled cluster singles and doubles model (CC2) and Møller-Plesset perturbation theory (MP2) with and without a spin-component scaling (SCS or spin-opposite scaling (SOS)). Frequency scaling factors and the remaining deviations from the reference data are evaluated for several non-augmented basis sets of the cc-pVXZ family of generally contracted correlation-consistent basis sets as well as for the segmented contracted TZVPP basis. We find that the SCS and SOS variants of CC2 and MP2 lead to a slightly better accuracy for the scaled vibrational frequencies. The determined frequency scaling factors can also be used for vibrational frequencies calculated for excited states through response theory with CC2 and the algebraic diagrammatic construction through second order and their spin-component scaled variants.

Role of oral care to prevent VAP in mechanically ventilated Intensive Care Unit patients.

Science.gov (United States)

Gupta, A; Gupta, A; Singh, T K; Saxsena, A

2016-01-01

Ventilator associated pneumonia (VAP) is the most common nosocomial infection in Intensive Care Unit. One major factor causing VAP is the aspiration of oral colonization because of poor oral care practices. We feel the role of simple measure like oral care is neglected, despite the ample evidence of it being instrumental in preventing VAP.

Role of oral care to prevent VAP in mechanically ventilated Intensive Care Unit patients

OpenAIRE

A Gupta; A Gupta; T K Singh; A Saxsena

2016-01-01

Ventilator associated pneumonia (VAP) is the most common nosocomial infection in Intensive Care Unit. One major factor causing VAP is the aspiration of oral colonization because of poor oral care practices. We feel the role of simple measure like oral care is neglected, despite the ample evidence of it being instrumental in preventing VAP.

Role of oral care to prevent VAP in mechanically ventilated Intensive Care Unit patients

Directory of Open Access Journals (Sweden)

A Gupta

2016-01-01

Full Text Available Ventilator associated pneumonia (VAP is the most common nosocomial infection in Intensive Care Unit. One major factor causing VAP is the aspiration of oral colonization because of poor oral care practices. We feel the role of simple measure like oral care is neglected, despite the ample evidence of it being instrumental in preventing VAP.

VapC toxins drive cellular dormancy under uranium stress for the extreme thermoacidophile Metallosphaera prunae.

Science.gov (United States)

Mukherjee, Arpan; Wheaton, Garrett H; Counts, James A; Ijeomah, Brenda; Desai, Jigar; Kelly, Robert M

2017-07-01

When abruptly exposed to toxic levels of hexavalent uranium, the extremely thermoacidophilic archaeon Metallosphaera prunae, originally isolated from an abandoned uranium mine, ceased to grow, and concomitantly exhibited heightened levels of cytosolic ribonuclease activity that corresponded to substantial degradation of cellular RNA. The M. prunae transcriptome during 'uranium-shock' implicated VapC toxins as possible causative agents of the observed RNA degradation. Identifiable VapC toxins and PIN-domain proteins encoded in the M. prunae genome were produced and characterized, three of which (VapC4, VapC7, VapC8) substantially degraded M. prunae rRNA in vitro. RNA cleavage specificity for these VapCs mapped to motifs within M. prunae rRNA. Furthermore, based on frequency of cleavage sequences, putative target mRNAs for these VapCs were identified; these were closely associated with translation, transcription, and replication. It is interesting to note that Metallosphaera sedula, a member of the same genus and which has a nearly identical genome sequence but not isolated from a uranium-rich biotope, showed no evidence of dormancy when exposed to this metal. M. prunae utilizes VapC toxins for post-transcriptional regulation under uranium stress to enter a cellular dormant state, thereby providing an adaptive response to what would otherwise be a deleterious environmental perturbation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Homology modelling of Drosophila cytochrome P450 enzymes associated with insecticide resistance.

Science.gov (United States)

Jones, Robert T; Bakker, Saskia E; Stone, Deborah; Shuttleworth, Sally N; Boundy, Sam; McCart, Caroline; Daborn, Phillip J; ffrench-Constant, Richard H; van den Elsen, Jean M H

2010-10-01

Overexpression of the cytochrome P450 gene Cyp6g1 confers resistance against DDT and a broad range of other insecticides in Drosophila melanogaster Meig. In the absence of crystal structures of CYP6G1 or complexes with its substrates, structural studies rely on homology modelling and ligand docking to understand P450-substrate interactions. Homology models are presented for CYP6G1, a P450 associated with resistance to DDT and neonicotinoids, and two other enzymes associated with insecticide resistance in D. melanogaster, CYP12D1 and CYP6A2. The models are based on a template of the X-ray structure of the phylogenetically related human CYP3A4, which is known for its broad substrate specificity. The model of CYP6G1 has a much smaller active site cavity than the template. The cavity is also 'V'-shaped and is lined with hydrophobic residues, showing high shape and chemical complementarity with the molecular characteristics of DDT. Comparison of the DDT-CYP6G1 complex and a non-resistant CYP6A2 homology model implies that tight-fit recognition of this insecticide is important in CYP6G1. The active site can accommodate differently shaped substrates ranging from imidacloprid to malathion but not the pyrethroids permethrin and cyfluthrin. The CYP6G1, CYP12D1 and CYP6A2 homology models can provide a structural insight into insecticide resistance in flies overexpressing P450 enzymes with broad substrate specificities.

Processing ARM VAP data on an AWS cluster

Science.gov (United States)

Martin, T.; Macduff, M.; Shippert, T.

2017-12-01

The Atmospheric Radiation Measurement (ARM) Data Management Facility (DMF) manages over 18,000 processes and 1.3 TB of data each day. This includes many Value Added Products (VAPs) that make use of multiple instruments to produce the derived products that are scientifically relevant. A thermodynamic and cloud profile VAP is being developed to provide input to the ARM Large-eddy simulation (LES) ARM Symbiotic Simulation and Observation (LASSO) project (https://www.arm.gov/capabilities/vaps/lasso-122) . This algorithm is CPU intensive and the processing requirements exceeded the available DMF computing capacity. Amazon Web Service (AWS) along with CfnCluster was investigated to see how it would perform. This cluster environment is cost effective and scales dynamically based on demand. We were able to take advantage of autoscaling which allowed the cluster to grow and shrink based on the size of the processing queue. We also were able to take advantage of the Amazon Web Services spot market to further reduce the cost. Our test was very successful and found that cloud resources can be used to efficiently and effectively process time series data. This poster will present the resources and methodology used to successfully run the algorithm.

Appointing silver and bronze standards for noncovalent interactions: A comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches

International Nuclear Information System (INIS)

Burns, Lori A.; Marshall, Michael S.; Sherrill, C. David

2014-01-01

A systematic examination of noncovalent interactions as modeled by wavefunction theory is presented in comparison to gold-standard quality benchmarks available for 345 interaction energies of 49 bimolecular complexes. Quantum chemical techniques examined include spin-component-scaling (SCS) variations on second-order perturbation theory (MP2) [SCS, SCS(N), SCS(MI)] and coupled cluster singles and doubles (CCSD) [SCS, SCS(MI)]; also, method combinations designed to improve dispersion contacts [DW-MP2, MP2C, MP2.5, DW-CCSD(T)-F12]; where available, explicitly correlated (F12) counterparts are also considered. Dunning basis sets augmented by diffuse functions are employed for all accessible ζ-levels; truncations of the diffuse space are also considered. After examination of both accuracy and performance for 394 model chemistries, SCS(MI)-MP2/cc-pVQZ can be recommended for general use, having good accuracy at low cost and no ill-effects such as imbalance between hydrogen-bonding and dispersion-dominated systems or non-parallelity across dissociation curves. Moreover, when benchmarking accuracy is desirable but gold-standard computations are unaffordable, this work recommends silver-standard [DW-CCSD(T**)-F12/aug-cc-pVDZ] and bronze-standard [MP2C-F12/aug-cc-pVDZ] model chemistries, which support accuracies of 0.05 and 0.16 kcal/mol and efficiencies of 97.3 and 5.5 h for adenine·thymine, respectively. Choice comparisons of wavefunction results with the best symmetry-adapted perturbation theory [T. M. Parker, L. A. Burns, R. M. Parrish, A. G. Ryno, and C. D. Sherrill, J. Chem. Phys. 140, 094106 (2014)] and density functional theory [L. A. Burns, Á. Vázquez-Mayagoitia, B. G. Sumpter, and C. D. Sherrill, J. Chem. Phys. 134, 084107 (2011)] methods previously studied for these databases are provided for readers' guidance

ANTIBIOTIC SUSCEPTIBILITY PATTERNS OF DIFFERENT BACTERIA ISOLATED FROM PATIENTS WITH VENTILATOR ASSOCIATED PNEUMONIA (VAP)

OpenAIRE

Alqurashi, Abdulrahman M.

2005-01-01

Objective: Ventilator associated pneumonia (VAP) is a frequent complication of mechanical ventilation (MV) and it is a leading cause of death in MV patients. The development of VAP has been demonstrated as being due to aspiration of oropharyngeal secretion, ventilator tubing condensate, or gastric contents that are colonized with pathogenic microorganisms. The aim of the present study is to isolate and identify bacteria that cause VAP and to study antibiotic susceptibility. Material and Metho...

Critical Analysis of the Factors Associated with Enteral Feeding in Preventing VAP: A Systematic Review

OpenAIRE

Yu-Chih Chen

2009-01-01

Ventilator-associated pneumonia (VAP) is a common cause of morbidity in critically ill patients. Appropriate enteral feeding is the most important factor associated with the prevention of VAP. However, the standardization of enteral feeding methods needs clarification. The purpose of this systematic review was to synthesize the factors associated with enteral feeding in order to prevent VAP and to describe the characteristics of these factors. A comprehensive search was undertaken involving a...

Ventilator-Associated Pneumonia (VAP in a Patient with Guillain-Barre Syndrome

Directory of Open Access Journals (Sweden)

Anti Dharmayanti

2017-04-01

Full Text Available A 46-year-old man was admitted to ICU with a diagnosis at the time of admission of Guillain Barre Syndrome (GBS and sepsis due to suspected Ventilator-Associated Pneumoniae (VAP. Specimens for the following laboratory workup were inquired, i.e. complete blood count, culture and resistance workup using specimens obtained from the tip of suction pipe, urinalysis and urine culture, blood culture and resistance, procalcitonin and lactate levels. Neutrophilia was found along with increased procalcitonin and lactate levels, which supported the sepsis diagnosis. Moreover, the result of culture from suction pipe demonstrated colonies of Pseudomonas luteola MDRO, which might be originated from the oropharyngeal colonization of the patients due to poor oral hygiene and ineffective oral hygiene nursing; therefore, the colonies of the microorganism were swabbed away when obtaining the specimens. Ineffective oral hygiene nursing may have a potency to cause VAP and recurrent VAP.

Antibodies against homologous microbial caseinolytic proteases P characterise primary biliary cirrhosis.

Science.gov (United States)

Bogdanos, Dimitrios-Petrou; Baum, Harold; Sharma, Umesh C; Grasso, Alessandro; Ma, Yun; Burroughs, Andrew K; Vergani, Diego

2002-01-01

Antibodies to caseinolytic protease P(177-194) (ClpP(177-194)) of the proteolytic subunit of the Clp complex of Escherichia coli (E. coli) are uniquely present in primary biliary cirrhosis (PBC). Molecular mimicry between the regulatory subunit ClpX and the principal T-cell epitope of pyruvate dehydrogenase complex (PDC-E2) in PBC, has been proposed to account for this. Since ClpP is highly conserved among bacteria we investigated whether the micro-organisms triggering these antibodies may be other than E. coli. E. coli ClpP(177-194) is homologous with ClpP peptides of Yersinia enterocolitica (YEREN) and Haemophilus influenzae (HAEIN). Enzyme linked immunosorbent assay (ELISA) reactivity to these peptides was tested in 45 patients with PBC, 44 pathological and 32 healthy controls. Reactivity to at least one of the ClpP peptides was observed in 21 (47%) PBC patients, 5.8% pathological and 3.1% healthy controls (PECOLI ClpP(177-194), alone or in association with YEREN and/or HAEIN peptides, compared to three (14.2%) reactive with YEREN, two (9.5%) with YEREN/HAEIN and one (4.7%) with HAEIN peptide. Simultaneous reactivity to homologous sequences was due to cross-reactivity as confirmed by competition ELISAs. The PBC-specificity of anti-microbial ClpP reactivity is confirmed: the questions as to primary trigger(s) and relevance to PBC pathogenesis remain open.

Guidelines for the prevention of ventilator-associated pneumonia and their implementation. The Spanish "Zero-VAP" bundle.

Science.gov (United States)

Álvarez Lerma, F; Sánchez García, M; Lorente, L; Gordo, F; Añón, J M; Álvarez, J; Palomar, M; García, R; Arias, S; Vázquez-Calatayud, M; Jam, R

2014-05-01

"Zero-VAP" is a proposal for the implementation of a simultaneous multimodal intervention in Spanish intensive care units (ICU) consisting of a bundle of ventilator-associated pneumonia (VAP) prevention measures. An initiative of the Spanish Societies of Intensive Care Medicine and of Intensive Care Nurses, the project is supported by the Spanish Ministry of Health, and participation is voluntary. In addition to guidelines for VAP prevention, the "Zero-VAP" Project incorporates an integral patient safety program and continuous online validation of the application of the bundle. For the latter, VAP episodes and participation indices are entered into the web-based Spanish ICU Infection Surveillance Program "ENVIN-HELICS" database, which provides continuous information about local, regional and national VAP incidence rates. Implementation of the guidelines aims at the reduction of VAP to less than 9 episodes per 1000 days of mechanical ventilation. A total of 35 preventive measures were initially selected. A task force of experts used the Grading of Recommendations, Assessment, Development and Evaluation Working Group methodology to generate a list of 7 basic "mandatory" recommendations (education and training in airway management, strict hand hygiene for airway management, cuff pressure control, oral hygiene with chlorhexidine, semi-recumbent positioning, promoting measures that safely avoid or reduce time on ventilator, and discouraging scheduled changes of ventilator circuits, humidifiers and endotracheal tubes) and 3 additional "highly recommended" measures (selective decontamination of the digestive tract, aspiration of subglottic secretions, and a short course of iv antibiotic). We present the Spanish VAP prevention guidelines and describe the methodology used for the selection and implementation of the recommendations and the organizational structure of the project. Compared to conventional guideline documents, the associated safety assurance program, the

The function of probiotics on the treatment of ventilator-associated pneumonia (VAP): facts and gaps.

Science.gov (United States)

Karacaer, Feride; Hamed, Imen; Özogul, Fatih; Glew, Robert H; Özcengiz, Dilek

2017-09-01

Probiotics have been used for centuries in making fermented dairy products. The health benefits related to probiotics consumption are well recognized and they are generally regarded as safe (GRAS). Their therapeutic effects are due to the production of a variety of antimicrobial compounds, such as short-chain fatty acids, organic acids (such as lactic, acetic, formic, propionic and butyric acids), ethanol, hydrogen peroxide and bacteriocins. Ventilator-associated pneumonia (VAP) is a nosocomial infection associated with high mortality in intensive care units. VAP can result from endotracheal intubation and mechanical ventilation. These interventions increase the risk of infection as patients lose the natural barrier between the oropharynx and the trachea, which in turn facilitates the entry of pathogens through the aspiration of oropharyngeal secretions containing bacteria into the lung. In order to prevent this, probiotics have been used extensively against VAP. This review is an update containing information extracted from recent studies on the use of probiotics to treat VAP. In addition, probiotic safety, the therapeutic properties of probiotics, the probiotic strains used and the action of the probiotics mechanism are reviewed. Furthermore, the therapeutic effects of probiotic treatment procedures for VAP are compared to those of antibiotics. Finally, the influences of bacteriocin on the growth of human pathogens, and the side-effects and limitations of using probiotics for the treatment of VAP are addressed.

ARM Climate Research Facility Spectral Surface Albedo Value-Added Product (VAP) Report

Energy Technology Data Exchange (ETDEWEB)

McFarlane, S; Gaustad, K; Long, C; Mlawer, E

2011-07-15

This document describes the input requirements, output data products, and methodology for the Spectral Surface Albedo (SURFSPECALB) value-added product (VAP). The SURFSPECALB VAP produces a best-estimate near-continuous high spectral resolution albedo data product using measurements from multifilter radiometers (MFRs). The VAP first identifies best estimates for the MFR downwelling and upwelling shortwave irradiance values, and then calculates narrowband spectral albedo from these best-estimate irradiance values. The methodology for finding the best-estimate values is based on a simple process of screening suspect data and backfilling screened and missing data with estimated values when possible. The resulting best-estimate MFR narrowband spectral albedos are used to determine a daily surface type (snow, 100% vegetation, partial vegetation, or 0% vegetation). For non-snow surfaces, a piecewise continuous function is used to estimate a high spectral resolution albedo at 1 min temporal and 10 cm-1 spectral resolution.

High intensity low temperature (HILT) performance of space concentrator GaInP/GaInAs/Ge MJ SCs

Energy Technology Data Exchange (ETDEWEB)

Shvarts, Maxim Z., E-mail: shvarts@scell.ioffe.ru; Kalyuzhnyy, Nikolay A.; Mintairov, Sergey A.; Soluyanov, Andrei A.; Timoshina, Nailya Kh. [Ioffe Physical-Technical Institute, 26 Polytekhnicheskaya str., St.-Petersburg, 194021 (Russian Federation); Gudovskikh, Alexander S. [Saint-Petersburg Academic University - Nanotechnology Research and Education Centre RAS, St. Petersburg, 194021 (Russian Federation); Luque, Antonio [Ioffe Physical-Technical Institute, 26 Polytekhnicheskaya str., St.-Petersburg, 194021, Russia and Instituto de Energia Solar, Universidad Politecnica de Madrid, Madrid (Spain)

2014-09-26

In the work, the results of an investigation of GaInP/GaInAs/Ge MJ SCs intended for converting concentrated solar radiation, when operating at low temperatures (down to −190 °C) are presented. A kink of the cell I-V characteristic has been observed in the region close to V{sub oc} starting from −20°C at operation under concentrated sunlight. The causes for its occurrence have been analyzed and the reasons for formation of a built-in potential barrier for majority charge carriers at the n-GaInP/n-Ge isotype hetero-interface are discussed. The effect of charge carrier transport in n-GaInP/n-pGe heterostructures on MJ SC output characteristics at low temperatures has been studied including EL technique.

Pyrid-2-yl and 2-CyanoPhenyl fused heterocyclic compounds as human P2X3 inhibitors: a combined approach based on homology modelling, docking and QSAR analysis.

Science.gov (United States)

Janardhan, Sridhara; Seth, Subhendu; Viswanadhan, Vellarkad N

2014-02-01

P2X receptors are hetero-oligomeric proteins that function as membrane ion channels and are gated by extracellular ATP. The hP2X[Formula: see text] subunit is a constituent of the channels on a subset of sensory neurons involved in pain signaling, where ATP released by damaged and inflamed tissue can initiate action potentials. Hence, the inhibition of ATP-activated P2X3 receptor is an exciting approach for the treatment of inflammatory and neuropathic pain. Recently, the crystal structures of zebrafish P2X4 (zP2X4) were obtained in closed, apo state (PDB ID: 3I5D) and ATP-bound, open state (PDB ID: 4DW1). These structures were used to develop a homology model of human P2X3 (hP2X3 in order to identify through docking studies, the binding modes of known P2X3 inhibitors and their key active site interactions, along with a pharmacophore-based 3D-QSAR model for a series of 136 Pyrid-2-yl and 2-CyanoPhenyl fused heterocyclic compounds. These 3D-QSAR models have been developed with different combinations of training and test set divisions obtained by random separation, Jarvis-Patrick clustering, K-means clustering and sphere exclusion methods. The best predictive 3D-QSAR model resulted in training set R2 of 0.75, internal test set Q2 of 0.74, Pearson-R value of 0.87 and root mean square error of 0.37. The information generated by the pharmacophore model and docking analyses using the homology model provides valuable clues to design novel potent hP2X3 inhibitors.

Activities of wildtype and mutant p53 in suppression of homologous recombination as measured by a retroviral vector system

International Nuclear Information System (INIS)

Lu Xiongbin; Lozano, Guillermina; Donehower, Lawrence A.

2003-01-01

DNA repair of double strand breaks, interstrand DNA cross-links, and other types of DNA damage utilizes the processes of homologous recombination and non-homologous end joining to repair the damage. Aberrant homologous recombination is likely to be responsible for a significant fraction of chromosomal deletions, duplications, and translocations that are observed in cancer cells. To facilitate measurement of homologous recombination frequencies in normal cells, mutant cells, and cancer cells, we have developed a high titer retroviral vector containing tandem repeats of mutant versions of a GFP-Zeocin resistance fusion gene and an intact neomycin resistance marker. Recombination between the tandem repeats regenerates a functional GFP-Zeo R marker that can be easily scored. This retroviral vector was used to assess homologous recombination frequencies in human cancer cells and rodent fibroblasts with differing dosages of wild type or mutant p53. Absence of wild type p53 stimulated spontaneous and ionizing radiation-induced homologous recombination, confirming previous studies. Moreover, p53 +/- mouse fibroblasts show elevated levels of homologous recombination compared to their p53 +/+ counterparts following retroviral vector infection, indicating that p53 is haploinsufficient for suppression of homologous recombination. Transfection of vector-containing p53 null Saos-2 cells with various human cancer-associated p53 mutants revealed that these altered p53 proteins retain some recombination suppression function despite being totally inactive for transcriptional transactivation. The retroviral vector utilized in these studies may be useful in performing recombination assays on a wide array of cell types, including those not readily transfected by normal vectors

Model of OSBP-Mediated Cholesterol Supply to Aichi Virus RNA Replication Sites Involving Protein-Protein Interactions among Viral Proteins, ACBD3, OSBP, VAP-A/B, and SAC1.

Science.gov (United States)

Ishikawa-Sasaki, Kumiko; Nagashima, Shigeo; Taniguchi, Koki; Sasaki, Jun

2018-04-15

Positive-strand RNA viruses, including picornaviruses, utilize cellular machinery for genome replication. Previously, we reported that each of the 2B, 2BC, 2C, 3A, and 3AB proteins of Aichi virus (AiV), a picornavirus, forms a complex with the Golgi apparatus protein ACBD3 and phosphatidylinositol 4-kinase IIIβ (PI4KB) at viral RNA replication sites (replication organelles [ROs]), enhancing PI4KB-dependent phosphatidylinositol 4-phosphate (PI4P) production. Here, we demonstrate AiV hijacking of the cellular cholesterol transport system involving oxysterol-binding protein (OSBP), a PI4P-binding cholesterol transfer protein. AiV RNA replication was inhibited by silencing cellular proteins known to be components of this pathway, OSBP, the ER membrane proteins VAPA and VAPB (VAP-A/B), the PI4P-phosphatase SAC1, and PI-transfer protein β. OSBP, VAP-A/B, and SAC1 were present at RNA replication sites. We also found various previously unknown interactions among the AiV proteins (2B, 2BC, 2C, 3A, and 3AB), ACBD3, OSBP, VAP-A/B, and SAC1, and the interactions were suggested to be involved in recruiting the component proteins to AiV ROs. Importantly, the OSBP-2B interaction enabled PI4P-independent recruitment of OSBP to AiV ROs, indicating preferential recruitment of OSBP among PI4P-binding proteins. Protein-protein interaction-based OSBP recruitment has not been reported for other picornaviruses. Cholesterol was accumulated at AiV ROs, and inhibition of OSBP-mediated cholesterol transfer impaired cholesterol accumulation and AiV RNA replication. Electron microscopy showed that AiV-induced vesicle-like structures were close to ER membranes. Altogether, we conclude that AiV directly recruits the cholesterol transport machinery through protein-protein interactions, resulting in formation of membrane contact sites between the ER and AiV ROs and cholesterol supply to the ROs. IMPORTANCE Positive-strand RNA viruses utilize host pathways to modulate the lipid composition of

Sphingosine kinase-1, S1P transporter spinster homolog 2 and S1P2 mRNA expressions are increased in liver with advanced fibrosis in human.

Science.gov (United States)

Sato, Masaya; Ikeda, Hitoshi; Uranbileg, Baasanjav; Kurano, Makoto; Saigusa, Daisuke; Aoki, Junken; Maki, Harufumi; Kudo, Hiroki; Hasegawa, Kiyoshi; Kokudo, Norihiro; Yatomi, Yutaka

2016-08-26

The role of sphingosine 1-phosphate (S1P) in liver fibrosis or inflammation was not fully examined in human. Controversy exists which S1P receptors, S1P1 and S1P3 vs S1P2, would be importantly involved in its mechanism. To clarify these matters, 80 patients who received liver resection for hepatocellular carcinoma and 9 patients for metastatic liver tumor were enrolled. S1P metabolism was analyzed in background, non-tumorous liver tissue. mRNA levels of sphingosine kinase 1 (SK1) but not SK2 were increased in livers with fibrosis stages 3-4 compared to those with 0-2 and to normal liver. However, S1P was not increased in advanced fibrotic liver, where mRNA levels of S1P transporter spinster homolog 2 (SPNS2) but not S1P-degrading enzymes were enhanced. Furthermore, mRNA levels of S1P2 but not S1P1 or S1P3 were increased in advanced fibrotic liver. These increased mRNA levels of SK1, SPNS2 and S1P2 in fibrotic liver were correlated with α-smooth muscle actin mRNA levels in liver, and with serum ALT levels. In conclusion, S1P may be actively generated, transported to outside the cells, and bind to its specific receptor in human liver to play a role in fibrosis or inflammation. Altered S1P metabolism in fibrotic liver may be their therapeutic target.

VapD in Xylella fastidiosa Is a Thermostable Protein with Ribonuclease Activity.

Science.gov (United States)

Mendes, Juliano S; Santiago, André da S; Toledo, Marcelo A S; Rosselli-Murai, Luciana K; Favaro, Marianna T P; Santos, Clelton A; Horta, Maria Augusta C; Crucello, Aline; Beloti, Lilian L; Romero, Fabian; Tasic, Ljubica; de Souza, Alessandra A; de Souza, Anete P

2015-01-01

Xylella fastidiosa strain 9a5c is a gram-negative phytopathogen that is the causal agent of citrus variegated chlorosis (CVC), a disease that is responsible for economic losses in Brazilian agriculture. The most well-known mechanism of pathogenicity for this bacterial pathogen is xylem vessel occlusion, which results from bacterial movement and the formation of biofilms. The molecular mechanisms underlying the virulence caused by biofilm formation are unknown. Here, we provide evidence showing that virulence-associated protein D in X. fastidiosa (Xf-VapD) is a thermostable protein with ribonuclease activity. Moreover, protein expression analyses in two X. fastidiosa strains, including virulent (Xf9a5c) and nonpathogenic (XfJ1a12) strains, showed that Xf-VapD was expressed during all phases of development in both strains and that increased expression was observed in Xf9a5c during biofilm growth. This study is an important step toward characterizing and improving our understanding of the biological significance of Xf-VapD and its potential functions in the CVC pathosystem.

VapD in Xylella fastidiosa Is a Thermostable Protein with Ribonuclease Activity.

Directory of Open Access Journals (Sweden)

Juliano S Mendes

Full Text Available Xylella fastidiosa strain 9a5c is a gram-negative phytopathogen that is the causal agent of citrus variegated chlorosis (CVC, a disease that is responsible for economic losses in Brazilian agriculture. The most well-known mechanism of pathogenicity for this bacterial pathogen is xylem vessel occlusion, which results from bacterial movement and the formation of biofilms. The molecular mechanisms underlying the virulence caused by biofilm formation are unknown. Here, we provide evidence showing that virulence-associated protein D in X. fastidiosa (Xf-VapD is a thermostable protein with ribonuclease activity. Moreover, protein expression analyses in two X. fastidiosa strains, including virulent (Xf9a5c and nonpathogenic (XfJ1a12 strains, showed that Xf-VapD was expressed during all phases of development in both strains and that increased expression was observed in Xf9a5c during biofilm growth. This study is an important step toward characterizing and improving our understanding of the biological significance of Xf-VapD and its potential functions in the CVC pathosystem.

The cohesion protein SOLO associates with SMC1 and is required for synapsis, recombination, homolog bias and cohesion and pairing of centromeres in Drosophila Meiosis.

Science.gov (United States)

Yan, Rihui; McKee, Bruce D

2013-01-01

Cohesion between sister chromatids is mediated by cohesin and is essential for proper meiotic segregation of both sister chromatids and homologs. solo encodes a Drosophila meiosis-specific cohesion protein with no apparent sequence homology to cohesins that is required in male meiosis for centromere cohesion, proper orientation of sister centromeres and centromere enrichment of the cohesin subunit SMC1. In this study, we show that solo is involved in multiple aspects of meiosis in female Drosophila. Null mutations in solo caused the following phenotypes: 1) high frequencies of homolog and sister chromatid nondisjunction (NDJ) and sharply reduced frequencies of homolog exchange; 2) reduced transmission of a ring-X chromosome, an indicator of elevated frequencies of sister chromatid exchange (SCE); 3) premature loss of centromere pairing and cohesion during prophase I, as indicated by elevated foci counts of the centromere protein CID; 4) instability of the lateral elements (LE)s and central regions of synaptonemal complexes (SCs), as indicated by fragmented and spotty staining of the chromosome core/LE component SMC1 and the transverse filament protein C(3)G, respectively, at all stages of pachytene. SOLO and SMC1 are both enriched on centromeres throughout prophase I, co-align along the lateral elements of SCs and reciprocally co-immunoprecipitate from ovarian protein extracts. Our studies demonstrate that SOLO is closely associated with meiotic cohesin and required both for enrichment of cohesin on centromeres and stable assembly of cohesin into chromosome cores. These events underlie and are required for stable cohesion of centromeres, synapsis of homologous chromosomes, and a recombination mechanism that suppresses SCE to preferentially generate homolog crossovers (homolog bias). We propose that SOLO is a subunit of a specialized meiotic cohesin complex that mediates both centromeric and axial arm cohesion and promotes homolog bias as a component of chromosome

Homologous recombination in mammalian cells: effect of p53 and Bcl-2 proteins, replication inhibition and ionizing radiations

International Nuclear Information System (INIS)

Saintigny, Yannick

1999-01-01

The control of cell cycle, associated with the mechanisms of replication, DNA repair/recombination allows the cells to maintain their genetic integrity. The p53 protein ensures the control of G1/S transition. Its inactivation would allow to initial replication on damaged matrix and lead to the block of replication forks followed by DNA strand breaks, good substrates for recombination. This work shows that the expression of mutant p53 protein stimulates both spontaneous and radio-induced homologous recombination, independently of the control of cell cycle. Moreover, the use of a set of replication inhibitors show that inhibition of the replication elongation stimulates recombination more strongly than the initiation inhibition. Replication arrest by these inhibitors also significantly increases the number of DNA strand breaks. These results highlighted a point of action of p53 protein on the ultimate stages of the homologous recombination mechanism. Lastly, the expression of Bcl-2 protein inhibits apoptosis and increases survival, but specifically inhibits conservative recombination, after radiation as well as in absence of apoptotic stress. The extinction of this mechanism of DNA repair is associated with an increase of mutagenesis. Taken together, these results allow ta consider the maintenance of the genetic stability as a cellular network involving different pathways. A multiple stages model for tumoral progression can be deduced. (author) [fr

Recruitment of RecA homologs Dmc1p and Rad51p to the double-strand break repair site initiated by meiosis-specific endonuclease VDE (PI-SceI).

Science.gov (United States)

Fukuda, Tomoyuki; Ohya, Yoshikazu

2006-02-01

During meiosis, VDE (PI-SceI), a homing endonuclease in Saccharomyces cerevisiae, introduces a double-strand break (DSB) at its recognition sequence and induces homologous recombinational repair, called homing. Meiosis-specific RecA homolog Dmc1p, as well as mitotic RecA homolog Rad51p, acts in the process of meiotic recombination, being required for strand invasion and exchange. In this study, recruitment of Dmc1p and Rad51p to the VDE-induced DSB repair site is investigated by chromatin immunoprecipitation assay. It is revealed that Dmc1p and Rad51p are loaded to the repair site in an independent manner. Association of Rad51p requires other DSB repair proteins of Rad52p, Rad55p, and Rad57p, while loading of Dmc1p is facilitated by the different protein, Sae3p. Absence of Tid1p, which can bind both RecA homologs, appears specifically to cause an abnormal distribution of Dmc1p. Lack of Hop2, Mnd1p, and Sae1p does not impair recruitment of both RecA homologs. These findings reveal the discrete functions of each strand invasion protein in VDE-initiated homing, confirm the similarity between VDE-initiated homing and Spo11p-initiated meiotic recombination, and demonstrate the availability of VDE-initiated homing for the study of meiotic recombination.

Analysis of non-typeable Haemophilous influenzae VapC1 mutations reveals structural features required for toxicity and flexibility in the active site.

Directory of Open Access Journals (Sweden)

Brooke Hamilton

Full Text Available Bacteria have evolved mechanisms that allow them to survive in the face of a variety of stresses including nutrient deprivation, antibiotic challenge and engulfment by predator cells. A switch to dormancy represents one strategy that reduces energy utilization and can render cells resistant to compounds that kill growing bacteria. These persister cells pose a problem during treatment of infections with antibiotics, and dormancy mechanisms may contribute to latent infections. Many bacteria encode toxin-antitoxin (TA gene pairs that play an important role in dormancy and the formation of persisters. VapBC gene pairs comprise the largest of the Type II TA systems in bacteria and they produce a VapC ribonuclease toxin whose activity is inhibited by the VapB antitoxin. Despite the importance of VapBC TA pairs in dormancy and persister formation, little information exists on the structural features of VapC proteins required for their toxic function in vivo. Studies reported here identified 17 single mutations that disrupt the function of VapC1 from non-typeable H. influenzae in vivo. 3-D modeling suggests that side chains affected by many of these mutations sit near the active site of the toxin protein. Phylogenetic comparisons and secondary mutagenesis indicate that VapC1 toxicity requires an alternative active site motif found in many proteobacteria. Expression of the antitoxin VapB1 counteracts the activity of VapC1 mutants partially defective for toxicity, indicating that the antitoxin binds these mutant proteins in vivo. These findings identify critical chemical features required for the biological function of VapC toxins and PIN-domain proteins.

Localization of Cortical Oscillations Induced by SCS Using Coherence

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P. Sovka

2007-12-01

Full Text Available This paper suggests a method based on coherence analysis and scalp mapping of coherence suitable for more accurate localization of cortical oscillations induced by electric stimulation of the dorsal spinal cord (SCS, which were previously detected using spectral analysis. While power spectral density shows the increase of power during SCS only at small number of electrodes, coherence extends this area and sharpens its boundary simultaneously. Parameters of the method were experimentally optimized to maximize its reliability. SCS is applied to suppress chronic, intractable pain by patients, whom pharmacotherapy does not relieve. In our study, the pain developed in lower back and lower extremity as the result of unsuccessful vertebral discotomy, which is called failed-back surgery syndrome (FBSS. Our method replicated the results of previous analysis using PSD and extended them with more accurate localization of the area influenced by SCS.

Studies on 16α-Hydroxylation of Steroid Molecules and Regioselective Binding Mode in Homology-Modeled Cytochrome P450-2C11

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Hamed I. Ali

2011-01-01

Full Text Available We investigated the 16α-hydroxylation of steroid molecules and regioselective binding mode in homology-modeled cytochrome P450-2C11 to correlate the biological study with the computational molecular modeling. It revealed that there was a positive relationship between the observed inhibitory potencies and the binding free energies. Docking of steroid molecules into this homology-modeled CYP2C11 indicated that 16α-hydroxylation is favored with steroidal molecules possessing the following components, (1 a bent A-B ring configuration (5β-reduced, (2 C-3 α-hydroxyl group, (3 C-17β-acetyl group, and (4 methyl group at both the C-18 and C-19. These respective steroid components requirements were defined as the inhibitory contribution factor. Overall studies of the male rat CYP2C11 metabolism revealed that the above-mentioned steroid components requirements were essential to induce an effective inhibition of [3H]progesterone 16α-hydroxylation. As far as docking of homology-modeled CYP2C11 against investigated steroids is concerned, they are docked at the active site superimposed with flurbiprofen. It was also found that the distance between heme iron and C16α-H was between 4 to 6 Å and that the related angle was in the range of 180±45∘.

Knowledge of Pediatric Critical Care Nurses Regarding Evidence Based Guidelines for Prevention of Ventilator Associated Pneumonia (VAP)

Science.gov (United States)

Ahmed, Gehan EL Nabawy; Abosamra, Omyma Mostafa

2015-01-01

Ventilator associated pneumonia (VAP) is a costly, preventable, and often fatal consequence of medical therapy that increases hospital and intensive care stays in mechanically ventilated patients. The prevention of VAP is primarily the responsibility of the bedside nurse whose knowledge, beliefs, and practices influence the health outcome of ICU…

Topography Estimation of the Core Mantle Boundary with ScS Reverberations and Diffraction Waves

Science.gov (United States)

Hein, B. E.; Nakata, N.

2017-12-01

In this study, we use the propagation of global seismic waves to study the Core Mantle Boundary (CMB). We focus on the use of S-wave reflections at the CMB (ScS reverberations) and outer-core diffracted waves. It is difficult imaging the CMB with the ScS wave because the complexity of the structure in the near surface ( 50 km); the complex structure degrades the signal-to-noise ratio of of the ScS. To avoid estimating the structure in the crust, we rely on the concept of seismic interferometry to extract wave propagation through mantle, but not through the crust. Our approach is compute the deconvolution between the ScS (and its reverberation) and direct S waves generated by intermediate to deep earthquakes (>50 km depth). Through this deconvolution, we have the ability to filter out the direct S wave and retrieve the wave field propagating from only the hypocenter to the outer core, but not between the hypocenter to the receiver. After the deconvolution, we can isolate the CMB reflected waves from the complicated wave phenomena because of the near-surface structure. Utilizing intermediate and deep earthquakes is key since we can suppress the near-surface effect from the surface to the hypocenter of the earthquakes. The variation of such waves (e.g., travel-time perturbation and/or wavefield decorrelation) at different receivers and earthquakes provides the information of the topography of the CMB. In order to get a more detailed image of the topography of the CMB we use diffracted seismic waves such as Pdiff , Sdiff, and P'P'. By using two intermediate to deep earthquakes on a great circle path with a station we can extract the wave propagation between the two earthquakes to simplify the waveform, similar to how it is preformed using the ScS wave. We generate more illumination of the CMB by using diffracted waves rather than only using ScS reverberations. The accurate topography of CMB obtained by these deconvolution analyses may provide new insight of the

Biomarkers kinetics in the assessment of ventilator-associated pneumonia response to antibiotics - results from the BioVAP study

NARCIS (Netherlands)

Póvoa, Pedro; Martin-Loeches, Ignacio; Ramirez, Paula; Bos, Lieuwe D.; Esperatti, Mariano; Silvestre, Joana; Gili, Gisela; Goma, Gemma; Berlanga, Eugenio; Espasa, Mateu; Gonçalves, Elsa; Torres, Antoni; Artigas, Antonio

2017-01-01

Purpose: Our aim was to evaluate the role of biomarker kinetics in the assessment of ventilator-associated pneumonia (VAP) response to antibiotics. Materials and methods: We performed a prospective, multicenter, observational study to evaluate in 37 microbiologically documented VAP, the kinetics of

Beyond the SCS curve number: A new stochastic spatial runoff approach

Science.gov (United States)

Bartlett, M. S., Jr.; Parolari, A.; McDonnell, J.; Porporato, A. M.

2015-12-01

The Soil Conservation Service curve number (SCS-CN) method is the standard approach in practice for predicting a storm event runoff response. It is popular because its low parametric complexity and ease of use. However, the SCS-CN method does not describe the spatial variability of runoff and is restricted to certain geographic regions and land use types. Here we present a general theory for extending the SCS-CN method. Our new theory accommodates different event based models derived from alternative rainfall-runoff mechanisms or distributions of watershed variables, which are the basis of different semi-distributed models such as VIC, PDM, and TOPMODEL. We introduce a parsimonious but flexible description where runoff is initiated by a pure threshold, i.e., saturation excess, that is complemented by fill and spill runoff behavior from areas of partial saturation. To facilitate event based runoff prediction, we derive simple equations for the fraction of the runoff source areas, the probability density function (PDF) describing runoff variability, and the corresponding average runoff value (a runoff curve analogous to the SCS-CN). The benefit of the theory is that it unites the SCS-CN method, VIC, PDM, and TOPMODEL as the same model type but with different assumptions for the spatial distribution of variables and the runoff mechanism. The new multiple runoff mechanism description for the SCS-CN enables runoff prediction in geographic regions and site runoff types previously misrepresented by the traditional SCS-CN method. In addition, we show that the VIC, PDM, and TOPMODEL runoff curves may be more suitable than the SCS-CN for different conditions. Lastly, we explore predictions of sediment and nutrient transport by applying the PDF describing runoff variability within our new framework.

Social Conduct Scale (SCS: a psychometric investigation

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Caroline Tozzi Reppold

2016-01-01

Full Text Available Abstract The social conduct of an individual comprises all the interpersonal behaviors that he or she exhibits in the social contexts he or she is exposed to. The Social Conduct Scale (SCS is a self-report instrument developed to provide researchers and clinicians with information on prosocial, antisocial and oppositional-defiant tendencies of Portuguese-speaking children and adolescents. In the present study, we conducted an analysis of the criterion validity of the SCS by comparing the scores obtained from a large population-based sample (N= 1,172 against an offender (N= 129, a scholar (N= 31, and a clinic-referred (N= 24 sample of adolescents with marked previous conduct problems. As expected, antisocial youths had significantly higher means on antisocial behaviors and lower means on prosocial tendencies when compared to the population-based sample. Overall, findings supported the hypothesized criterion validity of the SCS. The instrument might play a role as a helpful resource for researchers, clinicians and practitioners interested in assessing the social conduct of Brazilian children and adolescents.

Isolation and identification of the human homolog of a new p53-binding protein, Mdmx

NARCIS (Netherlands)

Shvarts, A.; Bazuine, M.; Dekker, P.; Ramos, Y. F.; Steegenga, W. T.; Merckx, G.; van Ham, R. C.; van der Houven van Oordt, W.; van der Eb, A. J.; Jochemsen, A. G.

1997-01-01

We recently reported the identification of a mouse cDNA encoding a new p53-associating protein that we called Mdmx because of its structural similarity to Mdm2, a well-known p53-binding protein. Here we report the isolation of a cDNA encoding the human homolog of Mdmx. The ORF of the cDNA encodes a

Interference of Homologous Sequences on the SNP Study of CYP2A13 Gene

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Qinghua ZHOU

2010-02-01

Full Text Available Background and objective It has been proven that cytochrome P450 enzyme 2A13 (CYP2A13 played an important role in the association between single nucleotide polymorphisms (SNP and human diseases. Cytochrome P450 enzymes are a group of isoenzymes, whose sequence homology may interfere with the study for SNP. The aim of this study is to explore the interference on the SNP study of CYP2A13 caused by homologous sequences. Methods Taqman probe was applied to detect distribution of rs8192789 sites in 573 subjects, and BLAST method was used to analyze the amplified sequences. Partial sequences of CYP2A13 were emplified by PCR from 60 cases. The emplified sequences were TA cloned and sequenced. Results For rs8192789 loci in 573 cases, only 3 cases were TT, while the rest were CT heterozygotes, which was caused by homologous sequences. There are a large number of overlapping peaks in identical sequences of 60 cases, and the SNP of 101 amino acid site reported in the SNP database is not found. The cloned sequences are 247 bp, 235 bp fragments. Conclusion The homologous sequences may interfere the study for SNP of CYP2A13, and some SNP may not exist.

Two zebrafish G2A homologs activate multiple intracellular signaling pathways in acidic environment

Energy Technology Data Exchange (ETDEWEB)

Ichijo, Yuta; Mochimaru, Yuta [Laboratory of Cell Signaling Regulation, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571 (Japan); Azuma, Morio [Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, 3190-Gofuku, Toyama 930-8555 (Japan); Satou, Kazuhiro; Negishi, Jun [Laboratory of Cell Signaling Regulation, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571 (Japan); Nakakura, Takashi [Department of Anatomy, Graduate School of Medicine, Teikyo University, 2-11-1 Itabashi-Ku, Tokyo 173-8605 (Japan); Oshima, Natsuki [Laboratory of Cell Signaling Regulation, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571 (Japan); Mogi, Chihiro; Sato, Koichi [Laboratory of Signal Transduction, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512 (Japan); Matsuda, Kouhei [Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, 3190-Gofuku, Toyama 930-8555 (Japan); Okajima, Fumikazu [Laboratory of Signal Transduction, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512 (Japan); Tomura, Hideaki, E-mail: tomurah@meiji.ac.jp [Laboratory of Cell Signaling Regulation, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571 (Japan)

2016-01-01

Human G2A is activated by various stimuli such as lysophosphatidylcholine (LPC), 9-hydroxyoctadecadienoic acid (9-HODE), and protons. The receptor is coupled to multiple intracellular signaling pathways, including the G{sub s}-protein/cAMP/CRE, G{sub 12/13}-protein/Rho/SRE, and G{sub q}-protein/phospholipase C/NFAT pathways. In the present study, we examined whether zebrafish G2A homologs (zG2A-a and zG2A-b) could respond to these stimuli and activate multiple intracellular signaling pathways. We also examined whether histidine residue and basic amino acid residue in the N-terminus of the homologs also play roles similar to those played by human G2A residues if the homologs sense protons. We found that the zG2A-a showed the high CRE, SRE, and NFAT activities, however, zG2A-b showed only the high SRE activity under a pH of 8.0. Extracellular acidification from pH 7.4 to 6.3 ameliorated these activities in zG2A-a-expressing cells. On the other hand, acidification ameliorated the SRE activity but not the CRE and NFAT activities in zG2A-b-expressing cells. LPC or 9-HODE did not modify any activity of either homolog. The substitution of histidine residue at the 174{sup th} position from the N-terminus of zG2A-a to asparagine residue attenuated proton-induced CRE and NFAT activities but not SRE activity. The substitution of arginine residue at the 32nd position from the N-terminus of zG2A-a to the alanine residue also attenuated its high and the proton-induced CRE and NFAT activities. On the contrary, the substitution did not attenuate SRE activity. The substitution of the arginine residue at the 10th position from the N-terminus of zG2A-b to the alanine residue also did not attenuate its high or the proton-induced SRE activity. These results indicate that zebrafish G2A homologs were activated by protons but not by LPC and 9-HODE, and the activation mechanisms of the homologs were similar to those of human G2A. - Highlights: • Zebrafish two G2A homologs are proton

VAP/VAT: video analytics platform and test bed for testing and deploying video analytics

Science.gov (United States)

Gorodnichy, Dmitry O.; Dubrofsky, Elan

2010-04-01

Deploying Video Analytics in operational environments is extremely challenging. This paper presents a methodological approach developed by the Video Surveillance and Biometrics Section (VSB) of the Science and Engineering Directorate (S&E) of the Canada Border Services Agency (CBSA) to resolve these problems. A three-phase approach to enable VA deployment within an operational agency is presented and the Video Analytics Platform and Testbed (VAP/VAT) developed by the VSB section is introduced. In addition to allowing the integration of third party and in-house built VA codes into an existing video surveillance infrastructure, VAP/VAT also allows the agency to conduct an unbiased performance evaluation of the cameras and VA software available on the market. VAP/VAT consists of two components: EventCapture, which serves to Automatically detect a "Visual Event", and EventBrowser, which serves to Display & Peruse of "Visual Details" captured at the "Visual Event". To deal with Open architecture as well as with Closed architecture cameras, two video-feed capture mechanisms have been developed within the EventCapture component: IPCamCapture and ScreenCapture.

SCS-CN based time-distributed sediment yield model

Science.gov (United States)

Tyagi, J. V.; Mishra, S. K.; Singh, Ranvir; Singh, V. P.

2008-05-01

SummaryA sediment yield model is developed to estimate the temporal rates of sediment yield from rainfall events on natural watersheds. The model utilizes the SCS-CN based infiltration model for computation of rainfall-excess rate, and the SCS-CN-inspired proportionality concept for computation of sediment-excess. For computation of sedimentographs, the sediment-excess is routed to the watershed outlet using a single linear reservoir technique. Analytical development of the model shows the ratio of the potential maximum erosion (A) to the potential maximum retention (S) of the SCS-CN method is constant for a watershed. The model is calibrated and validated on a number of events using the data of seven watersheds from India and the USA. Representative values of the A/S ratio computed for the watersheds from calibration are used for the validation of the model. The encouraging results of the proposed simple four parameter model exhibit its potential in field application.

Impact of VAP bundle adherence among ventilated critically ill patients and its effectiveness in adult ICU

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Saad Rabie Samra

2017-01-01

Conclusion: The application of VAP bundle is a feasible reality that produces improvement in microbiological measures and nosocomal infection rates resulting in lowering mortality, shortened lengths of hospitalization and decreased medical care costs. However, education and periodic training remain a fundamental process of improving health services. VAPs were reduced by improving bundle compliance and ensuring the same standard of care to all ICU patients. Direct, on-site observation was a more accurate method of monitoring.

Regional Calibration of SCS-CN L-THIA Model: Application for Ungauged Basins

OpenAIRE

Jeon, Ji-Hong; Lim, Kyoung; Engel, Bernard

2014-01-01

Estimating surface runoff for ungauged watershed is an important issue. The Soil Conservation Service Curve Number (SCS-CN) method developed from long-term experimental data is widely used to estimate surface runoff from gaged or ungauged watersheds. Many modelers have used the documented SCS-CN parameters without calibration, sometimes resulting in significant errors in estimating surface runoff. Several methods for regionalization of SCS-CN parameters were evaluated. The regionalization met...

Field calibration and modification of scs design equation for predicting length of border under local conditions

International Nuclear Information System (INIS)

Choudhary, M.R.; Mustafa, U.S.

2009-01-01

Field tests were conducted to calibrate the existing SCS design equation in determining field border length using field data of different field lengths during 2nd and 3rd irrigations under local conditions. A single ring infiltrometer was used to estimate the water movement into and through the irrigated soil profile and in estimating the coefficients of Kostiakov infiltration function. Measurements of the unit discharge and time of advance were carried out during different irrigations on wheat irrigated fields having clay loam soil. The collected field data were used to calibrate the existing SCS design equation developed by USDA for testing its validity under local field conditions. SCS equation was modified further to improve its applicability. Results from the study revealed that the Kostiakov model over predicted the coefficients, which in turn overestimated the water advance length for boarder in the selected field using existing SCS design equation. However, the calibrated SCS design equation after parametric modification produced more satisfactory results encouraging the scientists to make its use at larger scale. (author)

A numerical analysis on thermal stratification phenomenon in the SCS piping

International Nuclear Information System (INIS)

Kim, Kwang Chu; Park, Man Heung; Youm, Hag Ki; Lee, Sun Ki; Kim, Tae Ryong

2003-01-01

A numerical study is performed to estimate on an unsteady thermal stratification phenomenon in the Shutdown Cooling System(SCS) piping branched off the Reactor Coolant System(RCS) piping of Nuclear Power Plant. In the results, turbulent penetration reaches to the 1 st isolation valve. At 500sec, the maximum temperature difference between top and bottom inner wall in piping is observed at the starting point of horizontal piping passing elbow. The temperature of coolant in the rear side of the 1 st isolation valve disk is very slowly increased and the inflection point in temperature difference curve for time is observed at 2700sec. At the beginning of turbulent penetration from RCS piping, the fast inflow generates the higher temperature for the inner wall than the outer wall in the SCS piping. In the case the hot-leg injection piping and the drain piping are connected to the SCS piping, the effect of thermal stratification in the SCS piping is decreased due to an increase of heat loss compared with no connection case. The hot-leg injection piping affected by turbulent penetration from the SCS piping has a severe temperature difference that exceeds criterion temperature stated in reference. But the drain piping located in the rear compared with the hot-leg injection piping shows a tiny temperature difference. In a viewpoint of designer, for the purpose of decreasing the thermal stratification effect, it is necessary to increase the length of vertical piping in the SCS piping, and to move the position of the hot-leg injection piping backward

Application of GIS-based SCS-CN method in West Bank catchments, Palestine

OpenAIRE

Sameer Shadeed; Mohammad Almasri

2010-01-01

Among the most basic challenges of hydrology are the prediction and quantification of catchment surface runoff. The runoff curve number (CN) is a key factor in determining runoff in the SCS (Soil Conservation Service) based hydrologic modeling method. The traditional SCS-CN method for calculating the composite curve number is very tedious and consumes a major portion of the hydrologic modeling time. Therefore, geographic information systems (GIS) are now being used in combination with the SCS...

Storage potential of ‘SCS426 Venice’ apples under different storage technologies

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Mariuccia Schlichting de Martin

2018-04-01

Full Text Available Abstract This study aimed to evaluate the storage potential of SCS426 Venice apples under different storage technologies. Fruits were harvested in an experimental orchard located in Fraiburgo, SC and stored for up to eight and ten months in 2013 and 2014, respectively. Apples were treated or not with methylcyclopropene (1-MCP and stored under air atmosphere (AA, 0.5±0.5 °C/RH 85±5% or controlled atmosphere (CA; 1.5 kPa of O2 and 1.5 kPa of CO2 at 0.7±0.5 °C/RH of 93±3%. Fruits were evaluated every two months of storage, after one and seven days of shelf life (23 ± 0.3 °C/RH 93±3%. The storage period of ‘SCS426 Venice’ apples under AA without 1-MCP application should not extend beyond six months. Under this storage condition, fruits had higher incidence of decay, ethylene production and respiratory rates, higher skin degreening, lower flesh firmness, titratable acidity and soluble solids content than fruits stored under CA or AA with 1-MCP. ‘SCS426 Venice’ apples develop flesh browning and superficial scald after long-term storage. ‘SCS426 Venice’ apples under AA treated with 1-MCP or under CA (regardless of 1-MCP application can be stored for more than eight months, keeping flesh firmness above 14 lb and low incidence of physiological disorders even after ten months of storage.

In vitro fertilization and sperm cryopreservation in the black-footed cat (Felis nigripes) and sand cat (Felis margarita).

Science.gov (United States)

Herrick, J R; Campbell, M; Levens, G; Moore, T; Benson, K; D'Agostino, J; West, G; Okeson, D M; Coke, R; Portacio, S C; Leiske, K; Kreider, C; Polumbo, P J; Swanson, W F

2010-03-01

Studies of in vitro fertilization (IVF) and sperm cryopreservation have been conducted in several small cat species, but virtually no data exist for black-footed cats (Felis nigripes) (BFCs) or sand cats (Felis margarita) (SCs). The objectives of this study were 1) to compare in vitro motility and acrosome status of fresh and cryopreserved (frozen in pellets on dry ice or in straws in liquid nitrogen vapor) BFC and SC spermatozoa cultured in feline-optimized culture medium (FOCM) or Ham F-10, 2) to assess ovarian responsiveness in BFCs and SCs following exogenous gonadotropin treatment and laparoscopic oocyte recovery, and 3) to evaluate the fertility of fresh and frozen-thawed spermatozoa from both species using homologous and heterologous (domestic cat oocytes) IVF in the two culture media. Motility and acrosomal integrity of fresh and frozen-thawed spermatozoa from BFCs and SCs were similar (P > 0.05) in both media during 6 h of culture. Although effects were more pronounced in SCs, cryopreservation in straws was superior (P 80% of recovered oocytes were of optimal (grade 1) quality. The BFC and SC spermatozoa fertilized 60.0%-79.4% of homologous and 37.7%-42.7% of heterologous oocytes in both culture media, with increased (P < 0.05) cleavage of homologous (SC) and heterologous (BFC and SC) oocytes in FOCM. These results provide the first information to date on the gamete biology of two imperiled cat species and further our capacity to apply reproductive technologies for their conservation.

Application of GIS-based SCS-CN method in West Bank catchments, Palestine

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Sameer Shadeed

2010-03-01

Full Text Available Among the most basic challenges of hydrology are the prediction and quantification of catchment surface runoff. The runoff curve number (CN is a key factor in determining runoff in the SCS (Soil Conservation Service based hydrologic modeling method. The traditional SCS-CN method for calculating the composite curve number is very tedious and consumes a major portion of the hydrologic modeling time. Therefore, geographic information systems (GIS are now being used in combination with the SCS-CN method. This paper assesses the modeling of flow in West Bank catchments using the GIS-based SCS-CN method. The West Bank, Palestine, is characterized as an arid to semi-arid region with annual rainfall depths ranging between 100 mm in the vicinity of the Jordan River to 700 mm in the mountains extending across the central parts of the region. The estimated composite curve number for the entire West Bank is about 50 assuming dry conditions. This paper clearly demonstrates that the integration of GIS with the SCS-CN method provides a powerful tool for estimating runoff volumes in West Bank catchments, representing arid to semi-arid catchments of Palestine.

Energetic, exergetic and economic analysis of an innovative Solar CombiSystem (SCS) producing thermal and electric energies: Application in residential and tertiary households

International Nuclear Information System (INIS)

Hazami, Majdi; Mehdaoui, Farah; Naili, Nabiha; Noro, Marco; Lazzarin, Renato; Guizani, AmenAllah

2017-01-01

Highlights: • The present work studies the potential of using innovative SCS in Tunisia. • In cold months the SCS provide about 50–75% of the total exergy provides. • The SCS produces between 70–150% of electric energy needs. • The SCS payback period (Pb) based on electric water heater was 10.2 years. • The SCS payback period (Pb) based on gas/gas town was about and 8.7 years. - Abstract: The endeavor of this paper is to study of the potential offered by the expenditure of an innovative Solar CombiSystem, SCS, used for the space heating load, the domestic hot water supply and the electric energy production. The investigation achieved in this work was based on an experimental and a simulation studies. A TRNSYS simulation program was achieved in order to evaluate the SCS monthly/annual thermal and electric performances. It was found that the proposed SCS covered between 20 and 45% of the SH energy needs by considering only solar energy. The result shows also that the SCS provided from 40 to 70% of the total DHW needs. It was also found that the SCS electric production ranged between 32 and 225 MJ/m 2 with a gain factor varying between 49 and 125%. An economic appraisal was also achieved to appraise the SCS feasibility. The results of the economic analysis show that the annual energy saved (ARE) and the payback period (Pb) based on electric water heater were respectively equal to 7618.3 kW h/year and 10.2 years. It was found that ARE and Pb based on gas/gas town were about 5825 m 3 and 8.7 years, respectively. The results of the economic analysis shows that the adoption of the SCS saves about 48% of electric energy and about 46% of gas/gas town kept back by the conventional system.

Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis

KAUST Repository

Zhang, Yanxia; van Dijk, Aalt D J; Scaffidi, Adrian; Flematti, Gavin R.; Hofmann, Manuel; Charnikhova, Tatsiana; Verstappen, Francel; Hepworth, Jo; van der Krol, Sander; Leyser, Ottoline; Smith, Steven M.; Zwanenburg, Binne; Al-Babili, Salim; Ruyter-Spira, Carolien; Bouwmeester, Harro J.

2014-01-01

Strigolactones (SLs) are a class of phytohormones and rhizosphere signaling compounds with high structural diversity. Three enzymes, carotenoid isomerase DWARF27 and carotenoid cleavage dioxygenases CCD7 and CCD8, were previously shown to convert all-trans-β-carotene to carlactone (CL), the SL precursor. However, how CL is metabolized to SLs has remained elusive. Here, by reconstituting the SL biosynthetic pathway in Nicotiana benthamiana, we show that a rice homolog of Arabidopsis More Axillary Growth 1 (MAX1), encodes a cytochrome P450 CYP711 subfamily member that acts as a CL oxidase to stereoselectively convert CL into ent-2'-epi-5-deoxystrigol (B-C lactone ring formation), the presumed precursor of rice SLs. A protein encoded by a second rice MAX1 homolog then catalyzes the conversion of ent-2'-epi-5-deoxystrigol to orobanchol. We therefore report that two members of CYP711 enzymes can catalyze two distinct steps in SL biosynthesis, identifying the first enzymes involved in B-C ring closure and a subsequent structural diversification step of SLs.

Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis

KAUST Repository

Zhang, Yanxia

2014-10-26

Strigolactones (SLs) are a class of phytohormones and rhizosphere signaling compounds with high structural diversity. Three enzymes, carotenoid isomerase DWARF27 and carotenoid cleavage dioxygenases CCD7 and CCD8, were previously shown to convert all-trans-β-carotene to carlactone (CL), the SL precursor. However, how CL is metabolized to SLs has remained elusive. Here, by reconstituting the SL biosynthetic pathway in Nicotiana benthamiana, we show that a rice homolog of Arabidopsis More Axillary Growth 1 (MAX1), encodes a cytochrome P450 CYP711 subfamily member that acts as a CL oxidase to stereoselectively convert CL into ent-2\\'-epi-5-deoxystrigol (B-C lactone ring formation), the presumed precursor of rice SLs. A protein encoded by a second rice MAX1 homolog then catalyzes the conversion of ent-2\\'-epi-5-deoxystrigol to orobanchol. We therefore report that two members of CYP711 enzymes can catalyze two distinct steps in SL biosynthesis, identifying the first enzymes involved in B-C ring closure and a subsequent structural diversification step of SLs.

SLUDGE PARTICLE SEPAPATION EFFICIENCIES DURING SETTLER TANK RETRIEVAL INTO SCS-CON-230

Energy Technology Data Exchange (ETDEWEB)

DEARING JI; EPSTEIN M; PLYS MG

2009-07-16

The purpose of this document is to release, into the Hanford Document Control System, FA1/0991, Sludge Particle Separation Efficiencies for the Rectangular SCS-CON-230 Container, by M. Epstein and M. G. Plys, Fauske & Associates, LLC, June 2009. The Sludge Treatment Project (STP) will retrieve sludge from the 105-K West Integrated Water Treatment System (IWTS) Settler Tanks and transfer it to container SCS-CON-230 using the Settler Tank Retrieval System (STRS). The sludge will enter the container through two distributors. The container will have a filtration system that is designed to minimize the overflow of sludge fines from the container to the basin. FAI/09-91 was performed to quantify the effect of the STRS on sludge distribution inside of and overflow out of SCS-CON-230. Selected results of the analysis and a system description are discussed. The principal result of the analysis is that the STRS filtration system reduces the overflow of sludge from SCS-CON-230 to the basin by roughly a factor of 10. Some turbidity can be expected in the center bay where the container is located. The exact amount of overflow and subsequent turbidity is dependent on the density of the sludge (which will vary with location in the Settler Tanks) and the thermal gradient between the SCS-CON-230 and the basin. Attachment A presents the full analytical results. These results are applicable specifically to SCS-CON-230 and the STRS filtration system's expected operating duty cycles.

Observed travel times for Multiply-reflected ScS waves from a deep-focus earthquake

Directory of Open Access Journals (Sweden)

A. F. ESPISOSA

1966-06-01

Full Text Available Tlie deep-focus Argentinean earthquake of December 8
1962, generated multiply reflected ScS phases which were recorded very
clearly at stations of the IGY and the TJSC&GS standardized worldwide
networks and at Canadian stations. The data gathered from this earthquake
for the multiply-reflected ScS and sScS were used to construct the
travel times and to extend them to shorter epicentral distances. These
new data brought to light an error in published travel times for the 2(ScS
phase.

Regional Calibration of SCS-CN L-THIA Model: Application for Ungauged Basins

Directory of Open Access Journals (Sweden)

Ji-Hong Jeon

2014-05-01

Full Text Available Estimating surface runoff for ungauged watershed is an important issue. The Soil Conservation Service Curve Number (SCS-CN method developed from long-term experimental data is widely used to estimate surface runoff from gaged or ungauged watersheds. Many modelers have used the documented SCS-CN parameters without calibration, sometimes resulting in significant errors in estimating surface runoff. Several methods for regionalization of SCS-CN parameters were evaluated. The regionalization methods include: (1 average; (2 land use area weighted average; (3 hydrologic soil group area weighted average; (4 area combined land use and hydrologic soil group weighted average; (5 spatial nearest neighbor; (6 inverse distance weighted average; and (7 global calibration method, and model performance for each method was evaluated with application to 14 watersheds located in Indiana. Eight watersheds were used for calibration and six watersheds for validation. For the validation results, the spatial nearest neighbor method provided the highest average Nash-Sutcliffe (NS value at 0.58 for six watersheds but it included the lowest NS value and variance of NS values of this method was the highest. The global calibration method provided the second highest average NS value at 0.56 with low variation of NS values. Although the spatial nearest neighbor method provided the highest average NS value, this method was not statistically different than other methods. However, the global calibration method was significantly different than other methods except the spatial nearest neighbor method. Therefore, we conclude that the global calibration method is appropriate to regionalize SCS-CN parameters for ungauged watersheds.

Mechanical Researches on Young's Modulus of SCS Nanostructures

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Qinhua Jin

2009-01-01

Full Text Available Nanostructures of SingleCrystalSilicon (SCS with superior electrical, mechanical, thermal, and optical properties are emerging in the development of novel nanodevices. Mechanical properties especially Young's modulus are essential in developing and utilizing such nanodevices. In this paper, experimental researches including bending tests, resonance tests, and tensile tests on Young' s modulus of nanoscaled SCS are reviewed, and their results are compared. It was found that the values of E measured by different testing methods cannot match to each other. As the differences cannot be explained as experimental errors, it should be understood by taking surface effect into account. With a simplified model, we qualitatively explained the difference in E value measured by tensile test and by resonance test for Si nanobeams.

Zebrafish homologs of genes within 16p11.2, a genomic region associated with brain disorders, are active during brain development, and include two deletion dosage sensor genes

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Alicia Blaker-Lee

2012-11-01

Deletion or duplication of one copy of the human 16p11.2 interval is tightly associated with impaired brain function, including autism spectrum disorders (ASDs, intellectual disability disorder (IDD and other phenotypes, indicating the importance of gene dosage in this copy number variant region (CNV. The core of this CNV includes 25 genes; however, the number of genes that contribute to these phenotypes is not known. Furthermore, genes whose functional levels change with deletion or duplication (termed ‘dosage sensors’, which can associate the CNV with pathologies, have not been identified in this region. Using the zebrafish as a tool, a set of 16p11.2 homologs was identified, primarily on chromosomes 3 and 12. Use of 11 phenotypic assays, spanning the first 5 days of development, demonstrated that this set of genes is highly active, such that 21 out of the 22 homologs tested showed loss-of-function phenotypes. Most genes in this region were required for nervous system development – impacting brain morphology, eye development, axonal density or organization, and motor response. In general, human genes were able to substitute for the fish homolog, demonstrating orthology and suggesting conserved molecular pathways. In a screen for 16p11.2 genes whose function is sensitive to hemizygosity, the aldolase a (aldoaa and kinesin family member 22 (kif22 genes were identified as giving clear phenotypes when RNA levels were reduced by ∼50%, suggesting that these genes are deletion dosage sensors. This study leads to two major findings. The first is that the 16p11.2 region comprises a highly active set of genes, which could present a large genetic target and might explain why multiple brain function, and other, phenotypes are associated with this interval. The second major finding is that there are (at least two genes with deletion dosage sensor properties among the 16p11.2 set, and these could link this CNV to brain disorders such as ASD and IDD.

Pola Kuman Penyebab Ventilator Associated Pneumonia(VAP dan Sensitivitas Terhadap Antibiotik di RSAB Harapan Kita

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Retno Widyaningsih

2016-11-01

Kesimpulan. Basil gram negatif aerob (79,5% merupakan mikroorganisme penyebab yang paling dominan. Ceftazidime, diikuti terhadap amikacin serta netilmicin masih mempunyai sensitivitas yang tinggi sehingga dapat dipakai sebagai terapi awal VAP.

Inhibitory Effect of Berberine on Zeste Homolog 2 (Ezh2 ...

African Journals Online (AJOL)

homolog 2 (Ezh2) expressions in KYSE450 human esophageal cancer cells. Methods: ... of the AXL receptor kinase. The results of ... effects of estrogen receptor antagonists on ..... protein EZH2 is involved in progression of prostate cancer.

Catchment area-based evaluation of the AMC-dependent SCS-CN-based rainfall-runoff models

Science.gov (United States)

Mishra, S. K.; Jain, M. K.; Pandey, R. P.; Singh, V. P.

2005-09-01

Using a large set of rainfall-runoff data from 234 watersheds in the USA, a catchment area-based evaluation of the modified version of the Mishra and Singh (2002a) model was performed. The model is based on the Soil Conservation Service Curve Number (SCS-CN) methodology and incorporates the antecedent moisture in computation of direct surface runoff. Comparison with the existing SCS-CN method showed that the modified version performed better than did the existing one on the data of all seven area-based groups of watersheds ranging from 0.01 to 310.3 km2.

Evolution of pH buffers and water homeostasis in eukaryotes: homology between humans and Acanthamoeba proteins.

Science.gov (United States)

Baig, Abdul M; Zohaib, R; Tariq, S; Ahmad, H R

2018-02-01

This study intended to trace the evolution of acid-base buffers and water homeostasis in eukaryotes. Acanthamoeba castellanii  was selected as a model unicellular eukaryote for this purpose. Homologies of proteins involved in pH and water regulatory mechanisms at cellular levels were compared between humans and A. castellanii. Amino acid sequence homology, structural homology, 3D modeling and docking prediction were done to show the extent of similarities between carbonic anhydrase 1 (CA1), aquaporin (AQP), band-3 protein and H + pump. Experimental assays were done with acetazolamide (AZM), brinzolamide and mannitol to observe their effects on the trophozoites of  A. castellanii.  The human CA1, AQP, band-3 protein and H + -transport proteins revealed similar proteins in Acanthamoeba. Docking showed the binding of AZM on amoebal AQP-like proteins.  Acanthamoeba showed transient shape changes and encystation at differential doses of brinzolamide, mannitol and AZM.  Conclusion: Water and pH regulating adapter proteins in Acanthamoeba and humans show significant homology, these mechanisms evolved early in the primitive unicellular eukaryotes and have remained conserved in multicellular eukaryotes.

The Mr 30,000-33,000 major protein components of the lateral elements of synaptonemal complexes of the rat

NARCIS (Netherlands)

Lammers, H.

1999-01-01

<p>Synaptonemal complexes (SCs) are intranuclear structures which are formed during meiotic prophase between homologous chromosomes. The SC consists of two protein-rich axes, either of which is found at the basis of one of the homologous chromosomes. These axes, called lateral elements (LEs),

Crystal Structure of the VapBC Toxin–Antitoxin Complex from Shigella flexneri Reveals a Hetero-Octameric DNA-Binding Assembly

DEFF Research Database (Denmark)

Dienemann, Christian; Bøggild, Andreas; Winther, Kristoffer S.

2011-01-01

the crystal structure of the intact Shigella flexneri VapBC TA complex, determined to 2.7 Å resolution. Both in solution and in the crystal structure, four molecules of each protein combine to form a large and globular hetero-octameric assembly with SpoVT/AbrB-type DNA-binding domains at each end and a total...

Rainfall-runoff modeling of the Chapel Branch Creek Watershed using GIS-based rational and SCS-CN methods

Science.gov (United States)

Elizabeth N. Mihalik; Norm S. Levine; Devendra M. Amatya

2008-01-01

Chapel Branch Creek (CBC), located within the Town of Santee adjacent to Lake Marion in Orangeburg County, SC, is listed on the SC 2004 303(d) list of impaired waterbodies due to elevated levels of nitrogen (N), phosphorus (P), chlorophyll-a, and pH. In this study, using a GIS-based approach, two runoff modeling methods, the Rational and SCS-CN methods, have been...

Application and comparison of the SCS-CN-based rainfall-runoff model in meso-scale watershed and field scale

Science.gov (United States)

Luo, L.; Wang, Z.

2010-12-01

Soil Conservation Service Curve Number (SCS-CN) based hydrologic model, has widely been used for agricultural watersheds in recent years. However, there will be relative error when applying it due to differentiation of geographical and climatological conditions. This paper introduces a more adaptable and propagable model based on the modified SCS-CN method, which specializes into two different scale cases of research regions. Combining the typical conditions of the Zhanghe irrigation district in southern part of China, such as hydrometeorologic conditions and surface conditions, SCS-CN based models were established. The Xinbu-Qiao River basin (area =1207 km2) and the Tuanlin runoff test area (area =2.87 km2)were taken as the study areas of basin scale and field scale in Zhanghe irrigation district. Applications were extended from ordinary meso-scale watershed to field scale in Zhanghe paddy field-dominated irrigated . Based on actual measurement data of land use, soil classification, hydrology and meteorology, quantitative evaluation and modifications for two coefficients, i.e. preceding loss and runoff curve, were proposed with corresponding models, table of CN values for different landuse and AMC(antecedent moisture condition) grading standard fitting for research cases were proposed. The simulation precision was increased by putting forward a 12h unit hydrograph of the field area, and 12h unit hydrograph were simplified. Comparison between different scales show that it’s more effectively to use SCS-CN model on field scale after parameters calibrated in basin scale These results can help discovering the rainfall-runoff rule in the district. Differences of established SCS-CN model's parameters between the two study regions are also considered. Varied forms of landuse and impacts of human activities were the important factors which can impact the rainfall-runoff relations in Zhanghe irrigation district.

RFID - based Staff Control System (SCS) in Kazakhstan

Science.gov (United States)

Saparkhojayev, N.

2015-06-01

RFID - based Staff Control System (SCS) will allow complete hands-free access control, monitoring the whereabouts of employee and record the attendance of the employee as well. Moreover, with a help of this system, it is possible to have a nice report at the end of the month and based on the total number of worked hours, the salary will be allocated to each personnel. The access tag can be read up to 10 centimeters from the RFID reader. The proposed system is based on UHF RFID readers, supported with antennas at gate and transaction sections, and employee identification cards containing RFID-transponders which are able to electronically store information that can be read / written even without the physical contact with the help of radio medium. This system is an innovative system, which describes the benefits of applying RFID- technology in the Education System process of Republic of Kazakhstan. This paper presents the experiments conducted to set up RFID based SCS.

RFID - based Staff Control System (SCS) in Kazakhstan

International Nuclear Information System (INIS)

Saparkhojayev, N

2015-01-01

RFID - based Staff Control System (SCS) will allow complete hands-free access control, monitoring the whereabouts of employee and record the attendance of the employee as well. Moreover, with a help of this system, it is possible to have a nice report at the end of the month and based on the total number of worked hours, the salary will be allocated to each personnel. The access tag can be read up to 10 centimeters from the RFID reader. The proposed system is based on UHF RFID readers, supported with antennas at gate and transaction sections, and employee identification cards containing RFID-transponders which are able to electronically store information that can be read / written even without the physical contact with the help of radio medium. This system is an innovative system, which describes the benefits of applying RFID- technology in the Education System process of Republic of Kazakhstan. This paper presents the experiments conducted to set up RFID based SCS. (paper)

p68 Sam is a substrate of the insulin receptor and associates with the SH2 domains of p85 PI3K.

Science.gov (United States)

Sánchez-Margalet, V; Najib, S

1999-07-23

The 68 kDa Src substrate associated during mitosis is an RNA binding protein with Src homology 2 and 3 domain binding sites. A role for Src associated in mitosis 68 as an adaptor protein in signaling transduction has been proposed in different systems such as T-cell receptors. In the present work, we have sought to assess the possible role of Src associated in mitosis 68 in insulin receptor signaling. We performed in vivo studies in HTC-IR cells and in vitro studies using recombinant Src associated in mitosis 68, purified insulin receptor and fusion proteins containing either the N-terminal or the C-terminal Src homology 2 domain of p85 phosphatidylinositol-3-kinase. We have found that Src associated in mitosis 68 is a substrate of the insulin receptor both in vivo and in vitro. Moreover, tyrosine-phosphorylated Src associated in mitosis 68 was found to associate with p85 phosphatidylinositol-3-kinase in response to insulin, as assessed by co-immunoprecipitation studies. Therefore, Src associated in mitosis 68 may be part of the signaling complexes of insulin receptor along with p85. In vitro studies demonstrate that Src associated in mitosis 68 associates with the Src homology 2 domains of p85 after tyrosine phosphorylation by the activated insulin receptor. Moreover, tyr-phosphorylated Src associated in mitosis 68 binds with a higher affinity to the N-terminal Src homology 2 domain of p85 compared to the C-terminal Src homology 2 domain of p85, suggesting a preferential association of Src associated in mitosis 68 with the N-terminal Src homology 2 domain of p85. This association may be important for the link of the signaling with RNA metabolism.

The SCS double hydrometer test in dispersive soil identification

CSIR Research Space (South Africa)

Maharaj, A

2013-09-01

Full Text Available The standard testing procedures for the Soil Conservation Service (SCS) Double Hydrometer test, the Pinhole Test, Crumb test and chemical analyses for the identification of potentially dispersive soils have recently been studied and problems...

Evaluation of Motor Neuron-Like Cell Differentiation of hEnSCs on Biodegradable PLGA Nanofiber Scaffolds.

Science.gov (United States)

Ebrahimi-Barough, Somayeh; Norouzi Javidan, Abbas; Saberi, Hoshangh; Joghataei, Mohammad Tghi; Rahbarghazi, Reza; Mirzaei, Esmaeil; Faghihi, Faezeh; Shirian, Sadegh; Ai, Armin; Ai, Jafar

2015-12-01

Human endometrium is a high-dynamic tissue that contains human endometrial stem cells (hEnSCs) which can be differentiated into a number of cell lineages. The differentiation of hEnSCs into many cell lineages such as osteoblast, adipocyte, and neural cells has been investigated previously. However, the differentiation of these stem cells into motor neuron-like cells has not been investigated yet. Different biochemical and topographical cues can affect the differentiation of stem cells into a specific cell. The aim of this study was to investigate the capability of hEnSCs to be differentiated into motor neuron-like cells under biochemical and topographical cues. The biocompatible and biodegradable poly(lactic-co-glycolic acid) (PLGA) electrospun nanofibrous scaffold was used as a topographical cue. Human EnSCs were cultured on the PLGA scaffold and tissue culture polystyrene (TCP), then differentiation of hEnSCs into motor neuron-like cells under induction media including retinoic acid (RA) and sonic hedgehog (Shh) were evaluated for 15 days. The proliferation rate of cells was assayed by using MTT assay. The morphology of cells was studied by scanning electron microscopy imaging, and the expression of motor neuron-specific markers by real-time PCR and immunocytochemistry. Results showed that survival and differentiation of hEnSCs into motor neuron-like cells on the PLGA scaffold were better than those on the TCP group. Taken together, the results suggest that differentiated hEnSCs on PLGA can provide a suitable, three-dimensional situation for neuronal survival and outgrowth for regeneration of the central nervous system, and these cells may be a potential candidate in cellular therapy for motor neuron diseases.

A Comprehensive Strategy for Accurate Mutation Detection of the Highly Homologous PMS2.

Science.gov (United States)

Li, Jianli; Dai, Hongzheng; Feng, Yanming; Tang, Jia; Chen, Stella; Tian, Xia; Gorman, Elizabeth; Schmitt, Eric S; Hansen, Terah A A; Wang, Jing; Plon, Sharon E; Zhang, Victor Wei; Wong, Lee-Jun C

2015-09-01

Germline mutations in the DNA mismatch repair gene PMS2 underlie the cancer susceptibility syndrome, Lynch syndrome. However, accurate molecular testing of PMS2 is complicated by a large number of highly homologous sequences. To establish a comprehensive approach for mutation detection of PMS2, we have designed a strategy combining targeted capture next-generation sequencing (NGS), multiplex ligation-dependent probe amplification, and long-range PCR followed by NGS to simultaneously detect point mutations and copy number changes of PMS2. Exonic deletions (E2 to E9, E5 to E9, E8, E10, E14, and E1 to E15), duplications (E11 to E12), and a nonsense mutation, p.S22*, were identified. Traditional multiplex ligation-dependent probe amplification and Sanger sequencing approaches cannot differentiate the origin of the exonic deletions in the 3' region when PMS2 and PMS2CL share identical sequences as a result of gene conversion. Our approach allows unambiguous identification of mutations in the active gene with a straightforward long-range-PCR/NGS method. Breakpoint analysis of multiple samples revealed that recurrent exon 14 deletions are mediated by homologous Alu sequences. Our comprehensive approach provides a reliable tool for accurate molecular analysis of genes containing multiple copies of highly homologous sequences and should improve PMS2 molecular analysis for patients with Lynch syndrome. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

All-ceramic or metal-ceramic tooth-supported fixed dental prostheses (FDPs)? A systematic review of the survival and complication rates. Part I: Single crowns (SCs).

Science.gov (United States)

Sailer, Irena; Makarov, Nikolay Alexandrovich; Thoma, Daniel Stefan; Zwahlen, Marcel; Pjetursson, Bjarni Elvar

2015-06-01

To assess the 5-year survival of metal-ceramic and all-ceramic tooth-supported single crowns (SCs) and to describe the incidence of biological, technical and esthetic complications. Medline (PubMed), Embase, Cochrane Central Register of Controlled Trials (CENTRAL) searches (2006-2013) were performed for clinical studies focusing on tooth-supported fixed dental prostheses (FDPs) with a mean follow-up of at least 3 years. This was complimented by an additional hand search and the inclusion of 34 studies from a previous systematic review [1,2]. Survival and complication rates were analyzed using robust Poisson's regression models to obtain summary estimates of 5-year proportions. Sixty-seven studies reporting on 4663 metal-ceramic and 9434 all-ceramic SCs fulfilled the inclusion criteria. Seventeen studies reported on metal-ceramic crowns, and 54 studies reported on all-ceramic crowns. Meta-analysis of the included studies indicated an estimated survival rate of metal-ceramic SCs of 94.7% (95% CI: 94.1-96.9%) after 5 years. This was similar to the estimated 5-year survival rate of leucit or lithium-disilicate reinforced glass ceramic SCs (96.6%; 95% CI: 94.9-96.7%), of glass infiltrated alumina SCs (94.6%; 95% CI: 92.7-96%) and densely sintered alumina and zirconia SCs (96%; 95% CI: 93.8-97.5%; 92.1%; 95% CI: 82.8-95.6%). In contrast, the 5-year survival rates of feldspathic/silica-based ceramic crowns were lower (pceramic and zirconia crowns exhibited significantly lower survival rates in the posterior region (pceramic fractures than metal-ceramic SCs (pceramic SCs than for metal-ceramic SCs. Survival rates of most types of all-ceramic SCs were similar to those reported for metal-ceramic SCs, both in anterior and posterior regions. Weaker feldspathic/silica-based ceramics should be limited to applications in the anterior region. Zirconia-based SCs should not be considered as primary option due to their high incidence of technical problems. Copyright © 2015 Academy

Direct Current Sputter Epitaxy of Heavily Doped p+ Layer for Monocrystalline Si Solar Cells

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Wenchang Yeh

2017-01-01

Full Text Available Sputter epitaxy of p+ layer for fabrication of Si solar cells (SCs was demonstrated. Hall carrier concentration of p+ layer was 2.6 × 1020 cm−3 owing to cosputtering of B with Si at low temperature, which had enabled heavy and shallow p+ dope layer. p+nn+ SCs were fabricated and influence of p+ and n+ layers was investigated. Internal quantum efficiency (IQE of p+nn+ SCs was 95% at visible light and was larger than 60% at ultraviolet (UV light when the p+ layer was thinner than 30 nm. At near infrared (NIR, extra increment on IQE was achieved by rear n+ back surface field (BSF layer with a thickness thinner than 100 nm.

A recurrent deletion syndrome at chromosome bands 2p11.2-2p12 flanked by segmental duplications at the breakpoints and including REEP1.

Science.gov (United States)

Stevens, Servi J C; Blom, Eveline W; Siegelaer, Ingrid T J; Smeets, Eric E J G L

2015-04-01

We identified an identical and recurrent 9.4-Mbp deletion at chromosome bands 2p11.2-2p12, which occurred de novo in two unrelated patients. It is flanked at the distal and proximal breakpoints by two homologous segmental duplications consisting of low copy repeat (LCR) blocks in direct orientation, which have >99% sequence identity. Despite the fact that the deletion was almost 10 Mbp in size, the patients showed a relatively mild clinical phenotype, that is, mild-to-moderate intellectual disability, a happy disposition, speech delay and delayed motor development. Their phenotype matches with that of previously described patients. The 2p11.2-2p12 deletion includes the REEP1 gene that is associated with spastic paraplegia and phenotypic features related to this are apparent in most 2p11.2-2p12 deletion patients, but not in all. Other hemizygous genes that may contribute to the clinical phenotype include LRRTM1 and CTNNA2. We propose a recurrent but rare 2p11.2-2p12 deletion syndrome based on (1) the identical, non-random localisation of the de novo deletion breakpoints in two unrelated patients and a patient from literature, (2) the patients' phenotypic similarity and their phenotypic overlap with other 2p deletions and (3) the presence of highly identical LCR blocks flanking both breakpoints, consistent with a non-allelic homologous recombination (NAHR)-mediated rearrangement.

Evaluation of SCS-CN method using a fully distributed physically based coupled surface-subsurface flow model

Science.gov (United States)

Shokri, Ali

2017-04-01

The hydrological cycle contains a wide range of linked surface and subsurface flow processes. In spite of natural connections between surface water and groundwater, historically, these processes have been studied separately. The current trend in hydrological distributed physically based model development is to combine distributed surface water models with distributed subsurface flow models. This combination results in a better estimation of the temporal and spatial variability of the interaction between surface and subsurface flow. On the other hand, simple lumped models such as the Soil Conservation Service Curve Number (SCS-CN) are still quite common because of their simplicity. In spite of the popularity of the SCS-CN method, there have always been concerns about the ambiguity of the SCS-CN method in explaining physical mechanism of rainfall-runoff processes. The aim of this study is to minimize these ambiguity by establishing a method to find an equivalence of the SCS-CN solution to the DrainFlow model, which is a fully distributed physically based coupled surface-subsurface flow model. In this paper, two hypothetical v-catchment tests are designed and the direct runoff from a storm event are calculated by both SCS-CN and DrainFlow models. To find a comparable solution to runoff prediction through the SCS-CN and DrainFlow, the variance between runoff predictions by the two models are minimized by changing Curve Number (CN) and initial abstraction (Ia) values. Results of this study have led to a set of lumped model parameters (CN and Ia) for each catchment that is comparable to a set of physically based parameters including hydraulic conductivity, Manning roughness coefficient, ground surface slope, and specific storage. Considering the lack of physical interpretation in CN and Ia is often argued as a weakness of SCS-CN method, the novel method in this paper gives a physical explanation to CN and Ia.

Is type 2 diabetes mellitus in mechanically ventilated adult trauma patients potentially related to the occurrence of ventilator-associated pneumonia?

Directory of Open Access Journals (Sweden)

Hadi Darvishi Khezri

2016-01-01

Full Text Available Background: Ventilator-associated pneumonia (VAP is a type of lung infection that typically affects critically ill patients undergoing mechanical ventilation (MV in the intensive care unit (ICU. Patients with type 2 diabetes mellitus (T2DM are considered to be more susceptible to several types of infections including community-acquired pneumonia. However, it is not clear whether T2DM is a risk factor for the development of VAP. The purpose of this study was to determine the risk of VAP for diabetic and nondiabetic mechanically ventilated trauma patients. Materials and Methods: This study is a secondary analysis of a prospective observational study of the history of T2DM in the ICU over a period of 1 year at Imam Khomeini Hospital in Iran. A total of 186 critically ill trauma patients who required at least 48 h of MV were monitored for the occurrence of VAP by their clinical pulmonary infection score (CPIS until ICU discharge, VAP diagnosis, or death. Results: Forty-one of the 186 patients developed VAP. The median time from hospitalization to VAP was 29.09 days (95% CI: 26.27-31.9. The overall incidence of VAP was 18.82 cases per 1,000 days of intubation (95% CI: 13.86-25.57. Risk of VAP in diabetic patients was greater than nondiabetic patients after adjustments for other potential factors [hazard ratio (HR: 10.12 [95% confidence interval (CI: 5.1-20.2; P < 0.0001]. Conclusion: The findings show that T2DM is associated with a significant increase in the occurrence of VAP in mechanically ventilated adult trauma patients.

Respective impact of implementation of prevention strategies, colonization with multiresistant bacteria and antimicrobial use on the risk of early- and late-onset VAP: An analysis of the OUTCOMEREA network.

Directory of Open Access Journals (Sweden)

Wafa Ibn Saied

Full Text Available The impact of prevention strategies and risk factors for early-onset (EOP versus late-onset (LOP ventilator-associated pneumonia (VAP are still debated.To evaluate, in a multicenter cohort, the risk factors for EOP and LOP, as the evolution of prevention strategies.7,784 patients with mechanical ventilation (MV for at least 48 hours were selected into the multicenter prospective OUTCOMEREA database (1997-2016. VAP occurring between the 3rd and 6th day of MV defined EOP, while those occurring after defined LOPs. We used a Fine and Gray subdistribution model to take the successful extubation into account as a competing event.Overall, 1,234 included patients developed VAP (EOP: 445 (36%; LOP: 789 (64%. Male gender was a risk factor for both EOP and LOP. Factors specifically associated with EOP were admission for respiratory distress, previous colonization with multidrug-resistant Pseudomonas aeruginosa, chest tube and enteral feeding within the first 2 days of MV. Antimicrobials administrated within the first 2 days of MV were all protective of EOP. ICU admission for COPD exacerbation or pneumonia were early risk factors for LOP, while imidazole and vancomycin use within the first 2 days of MV were protective factors. Late risk factors (between the 3rd and the 6th day of MV were the intra-hospital transport, PAO2-FIO2<200 mmHg, vasopressor use, and known colonization with methicillin-resistant Staphylococcus aureus. Among the antimicrobials administered between the 3rd and the 6th day, fluoroquinolones were the solely protective one.Contrarily to LOP, the risk of EOP decreased across the study time periods, concomitantly with an increase in the compliance with bundle of prevention measures.VAP risk factors are mostly different according to the pneumonia time of onset, which should lead to differentiated prevention strategies.

Validation of the Spanish versions of the long (26 items) and short (12 items) forms of the Self-Compassion Scale (SCS).

Science.gov (United States)

Garcia-Campayo, Javier; Navarro-Gil, Mayte; Andrés, Eva; Montero-Marin, Jesús; López-Artal, Lorena; Demarzo, Marcelo Marcos Piva

2014-01-10

Self-compassion is a key psychological construct for assessing clinical outcomes in mindfulness-based interventions. The aim of this study was to validate the Spanish versions of the long (26 item) and short (12 item) forms of the Self-Compassion Scale (SCS). The translated Spanish versions of both subscales were administered to two independent samples: Sample 1 was comprised of university students (n = 268) who were recruited to validate the long form, and Sample 2 was comprised of Aragon Health Service workers (n = 271) who were recruited to validate the short form. In addition to SCS, the Mindful Attention Awareness Scale (MAAS), the State-Trait Anxiety Inventory-Trait (STAI-T), the Beck Depression Inventory (BDI) and the Perceived Stress Questionnaire (PSQ) were administered. Construct validity, internal consistency, test-retest reliability and convergent validity were tested. The Confirmatory Factor Analysis (CFA) of the long and short forms of the SCS confirmed the original six-factor model in both scales, showing goodness of fit. Cronbach's α for the 26 item SCS was 0.87 (95% CI = 0.85-0.90) and ranged between 0.72 and 0.79 for the 6 subscales. Cronbach's α for the 12-item SCS was 0.85 (95% CI = 0.81-0.88) and ranged between 0.71 and 0.77 for the 6 subscales. The long (26-item) form of the SCS showed a test-retest coefficient of 0.92 (95% CI = 0.89-0.94). The Intraclass Correlation (ICC) for the 6 subscales ranged from 0.84 to 0.93. The short (12-item) form of the SCS showed a test-retest coefficient of 0.89 (95% CI: 0.87-0.93). The ICC for the 6 subscales ranged from 0.79 to 0.91. The long and short forms of the SCS exhibited a significant negative correlation with the BDI, the STAI and the PSQ, and a significant positive correlation with the MAAS. The correlation between the total score of the long and short SCS form was r = 0.92. The Spanish versions of the long (26-item) and short (12-item) forms of the SCS are valid and

Beyond the SCS-CN method: A theoretical framework for spatially lumped rainfall-runoff response

Science.gov (United States)

Bartlett, M. S.; Parolari, A. J.; McDonnell, J. J.; Porporato, A.

2016-06-01

Since its introduction in 1954, the Soil Conservation Service curve number (SCS-CN) method has become the standard tool, in practice, for estimating an event-based rainfall-runoff response. However, because of its empirical origins, the SCS-CN method is restricted to certain geographic regions and land use types. Moreover, it does not describe the spatial variability of runoff. To move beyond these limitations, we present a new theoretical framework for spatially lumped, event-based rainfall-runoff modeling. In this framework, we describe the spatially lumped runoff model as a point description of runoff that is upscaled to a watershed area based on probability distributions that are representative of watershed heterogeneities. The framework accommodates different runoff concepts and distributions of heterogeneities, and in doing so, it provides an implicit spatial description of runoff variability. Heterogeneity in storage capacity and soil moisture are the basis for upscaling a point runoff response and linking ecohydrological processes to runoff modeling. For the framework, we consider two different runoff responses for fractions of the watershed area: "prethreshold" and "threshold-excess" runoff. These occur before and after infiltration exceeds a storage capacity threshold. Our application of the framework results in a new model (called SCS-CNx) that extends the SCS-CN method with the prethreshold and threshold-excess runoff mechanisms and an implicit spatial description of runoff. We show proof of concept in four forested watersheds and further that the resulting model may better represent geographic regions and site types that previously have been beyond the scope of the traditional SCS-CN method.

Tyrosine Phosphorylation of the Lyn Src Homology 2 (SH2) Domain Modulates Its Binding Affinity and Specificity*

Science.gov (United States)

Jin, Lily L.; Wybenga-Groot, Leanne E.; Tong, Jiefei; Taylor, Paul; Minden, Mark D.; Trudel, Suzanne; McGlade, C. Jane; Moran, Michael F.

2015-01-01

Src homology 2 (SH2) domains are modular protein structures that bind phosphotyrosine (pY)-containing polypeptides and regulate cellular functions through protein-protein interactions. Proteomics analysis showed that the SH2 domains of Src family kinases are themselves tyrosine phosphorylated in blood system cancers, including acute myeloid leukemia, chronic lymphocytic leukemia, and multiple myeloma. Using the Src family kinase Lyn SH2 domain as a model, we found that phosphorylation at the conserved SH2 domain residue Y194 impacts the affinity and specificity of SH2 domain binding to pY-containing peptides and proteins. Analysis of the Lyn SH2 domain crystal structure supports a model wherein phosphorylation of Y194 on the EF loop modulates the binding pocket that engages amino acid side chains at the pY+2/+3 position. These data indicate another level of regulation wherein SH2-mediated protein-protein interactions are modulated by SH2 kinases and phosphatases. PMID:25587033

Comparison of the early response of human embryonic stem cells and human induced pluripotent stem cells to ionizing radiation.

Science.gov (United States)

Suchorska, Wiktoria Maria; Augustyniak, Ewelina; Łukjanow, Magdalena

2017-04-01

Despite the well-demonstrated efficacy of stem cell (SC) therapy, this approach has a number of key drawbacks. One important concern is the response of pluripotent SCs to treatment with ionizing radiation (IR), given that SCs used in regenerative medicine will eventually be exposed to IR for diagnostic or treatment‑associated purposes. Therefore, the aim of the present study was to examine and compare early IR‑induced responses of pluripotent SCs to assess their radioresistance and radiosensitivity. In the present study, 3 cell lines; human embryonic SCs (hESCs), human induced pluripotent SCs (hiPSCs) and primary human dermal fibroblasts (PHDFs); were exposed to IR at doses ranging from 0 to 15 gray (Gy). Double strand breaks (DSBs), and the gene expression of the following DNA repair genes were analyzed: P53; RAD51; BRCA2; PRKDC; and XRCC4. hiPSCs demonstrated greater radioresistance, as fewer DSBs were identified, compared with hESCs. Both pluripotent SC lines exhibited distinct gene expression profiles in the most common DNA repair genes that are involved in homologous recombination, non‑homologous end‑joining and enhanced DNA damage response following IR exposure. Although hESCs and hiPSCs are equivalent in terms of capacity for pluripotency and differentiation into 3 germ layers, the results of the present study indicate that these 2 types of SCs differ in gene expression following exposure to IR. Consequently, further research is required to determine whether hiPSCs and hESCs are equally safe for application in clinical practice. The present study contributes to a greater understanding of DNA damage response (DDR) mechanisms activated in pluripotent SCs and may aid in the future development of safe SC‑based clinical protocols.

Validity and extension of the SCS-CN method for computing infiltration and rainfall-excess rates

Science.gov (United States)

Mishra, Surendra Kumar; Singh, Vijay P.

2004-12-01

A criterion is developed for determining the validity of the Soil Conservation Service curve number (SCS-CN) method. According to this criterion, the existing SCS-CN method is found to be applicable when the potential maximum retention, S, is less than or equal to twice the total rainfall amount. The criterion is tested using published data of two watersheds. Separating the steady infiltration from capillary infiltration, the method is extended for predicting infiltration and rainfall-excess rates. The extended SCS-CN method is tested using 55 sets of laboratory infiltration data on soils varying from Plainfield sand to Yolo light clay, and the computed and observed infiltration and rainfall-excess rates are found to be in good agreement.

Purification, crystallization, small-angle X-ray scattering and preliminary X-ray diffraction analysis of the SH2 domain of the Csk-homologous kinase

International Nuclear Information System (INIS)

Gunn, Natalie J.; Gorman, Michael A.; Dobson, Renwick C. J.; Parker, Michael W.; Mulhern, Terrence D.

2011-01-01

The Src-homology 2 (SH2) domain of Csk-family protein tyrosine kinases acts as a conformational switch to regulate their catalytic activity, which in turn promotes the inhibition of their proto-oncogenic targets, the Src-family kinases. Here, the expression, purification, small-angle X-ray scattering and preliminary diffraction analysis of the SH2 domain of the Csk-homologous kinase is reported. The C-terminal Src kinase (Csk) and Csk-homologous kinase (CHK) are endogenous inhibitors of the proto-oncogenic Src family of protein tyrosine kinases (SFKs). Phosphotyrosyl peptide binding to their Src-homology 2 (SH2) domains activates Csk and CHK, enhancing their ability to suppress SFK signalling; however, the detailed mechanistic basis of this activation event is unclear. The CHK SH2 was expressed in Escherichia coli and the purified protein was characterized as monomeric by synchrotron small-angle X-ray scattering in-line with size-exclusion chromatography. The CHK SH2 crystallized in 0.2 M sodium bromide, 0.1 M bis-Tris propane pH 6.5 and 20% polyethylene glycol 3350 and the best crystals diffracted to ∼1.6 Å resolution. The crystals belonged to space group P2, with unit-cell parameters a = 25.8, b = 34.6, c = 63.2 Å, β = 99.4°

Serum Vascular Adhesion Protein-1 Predicts End-Stage Renal Disease in Patients with Type 2 Diabetes.

Directory of Open Access Journals (Sweden)

Hung-Yuan Li

Full Text Available Diabetes is the leading cause of end-stage renal disease (ESRD worldwide. Vascular adhesion protein-1 (VAP-1 participates in inflammation and catalyzes the deamination of primary amines into aldehydes, hydrogen peroxide, and ammonia, both of which are involved in the pathogenesis of diabetic complications. We have shown that serum VAP-1 is higher in patients with diabetes and in patients with chronic kidney disease (CKD, and can predict cardiovascular mortality in subjects with diabetes. In this study, we investigated if serum VAP-1 can predict ESRD in diabetic subjects.In this prospective cohort study, a total of 604 type 2 diabetic subjects were enrolled between 1996 to 2003 at National Taiwan University Hospital, Taiwan, and were followed for a median of 12.36 years. The development of ESRD was ascertained by linking our database with the nationally comprehensive Taiwan Society Nephrology registry. Serum VAP-1 concentrations at enrollment were measured by time-resolved immunofluorometric assay.Subjects with serum VAP-1 in the highest tertile had the highest incidence of ESRD (p<0.001. Every 1-SD increase in serum VAP-1 was associated with a hazard ratio of 1.55 (95%CI 1.12-2.14, p<0.01 for the risk of ESRD, adjusted for smoking, history of cardiovascular disease, body mass index, hypertension, HbA1c, duration of diabetes, total cholesterol, use of statins, ankle-brachial index, estimated GFR, and proteinuria. We developed a risk score comprising serum VAP-1, HbA1c, estimated GFR, and proteinuria, which could predict ESRD with good performance (area under the ROC curve = 0.9406, 95%CI 0.8871-0.9941, sensitivity = 77.3%, and specificity = 92.8%. We also developed an algorithm based on the stage of CKD and a risk score including serum VAP-1, which can stratify these subjects into 3 categories with an ESRD risk of 0.101%/year, 0.131%/year, and 2.427%/year, respectively.In conclusion, serum VAP-1 can predict ESRD and is a useful biomarker to

Comparison of HER2 gene amplification and KRAS alteration in eyelid sebaceous carcinomas with that in other eyelid tumors.

Science.gov (United States)

Kwon, Mi Jung; Shin, Hyung Sik; Nam, Eun Sook; Cho, Seong Jin; Lee, Min Joung; Lee, Samuel; Park, Hye-Rim

2015-05-01

Eyelid sebaceous carcinoma (SC) represents a highly aggressive malignancy. Despite the poor prognosis, genetic alterations as potential molecular targets are not available. KRAS mutation and HER2 gene amplification may be candidates related to their genetic alterations. We examined the HER2 and KRAS alteration status in eyelid SCs and compared it with that in other eyelid tumors. The controversial topics of the human papillomavirus (HPV) and p16 expression were also investigated. HER2 amplification was determined by silver in situ hybridization, while immunohistochemistry was performed to study protein expressions in 14 SCs and controls, including 23 other eyelid malignancies and 14 benign tumors. Peptide nucleic acid-mediated PCR clamping and direct sequencing were used to detect KRAS mutations. HER2 protein overexpression was observed in 85.7% (12/14) of the SCs, of which two-thirds showed HER2 gene amplification. HER2 protein overexpression and HER2 amplification were found more frequently in eyelid SCs than in other eyelid tumors. All SCs harbored wild type KRAS genes. No HPV infections were identified in the SCs. Nevertheless, p16 overexpression was found in 71.4% (10/14) of SCs, irrespective of the status of HPV infection. Furthermore, p16 overexpression in eyelid SCs was also significantly higher than that in other eyelid tumors. HER2 protein overexpression, HER2 gene amplifications, and wild type KRAS genes are common in eyelid SCs. HER2 gene amplification may represent potential therapeutic targets for the treatment of eyelid SCs. Copyright © 2014 Elsevier GmbH. All rights reserved.

Analysis of the Runoff for Watershed Using SCS-CN Method and Geographic Information Systems

OpenAIRE

P.Sundar Kumar; Dr.M.J.Ratna Kanth Babu,; Dr. T.V.Praveen; Venkata kumar.vagolu

2010-01-01

The Soil Conservation Service Curve Number (SCS-CN) method is widely used for predicting direct runoff volume for a given rainfall event. The applicability of the SCS-CN method and the runoff generation mechanism were thoroughly analyzed in a Mediterranean experimental watershed in Hyderabad. The region is characterized by a Mediterranean semi-arid climate. A detailed land cover and soil survey using remote sensing and GIS techniques, showed that the watershed is dominated by coarse soils wit...

Tyrosine phosphorylation of the Lyn Src homology 2 (SH2) domain modulates its binding affinity and specificity.

Science.gov (United States)

Jin, Lily L; Wybenga-Groot, Leanne E; Tong, Jiefei; Taylor, Paul; Minden, Mark D; Trudel, Suzanne; McGlade, C Jane; Moran, Michael F

2015-03-01

Src homology 2 (SH2) domains are modular protein structures that bind phosphotyrosine (pY)-containing polypeptides and regulate cellular functions through protein-protein interactions. Proteomics analysis showed that the SH2 domains of Src family kinases are themselves tyrosine phosphorylated in blood system cancers, including acute myeloid leukemia, chronic lymphocytic leukemia, and multiple myeloma. Using the Src family kinase Lyn SH2 domain as a model, we found that phosphorylation at the conserved SH2 domain residue Y(194) impacts the affinity and specificity of SH2 domain binding to pY-containing peptides and proteins. Analysis of the Lyn SH2 domain crystal structure supports a model wherein phosphorylation of Y(194) on the EF loop modulates the binding pocket that engages amino acid side chains at the pY+2/+3 position. These data indicate another level of regulation wherein SH2-mediated protein-protein interactions are modulated by SH2 kinases and phosphatases. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Mod two homology and cohomology

CERN Document Server

Hausmann, Jean-Claude

2014-01-01

Cohomology and homology modulo 2 helps the reader grasp more readily the basics of a major tool in algebraic topology. Compared to a more general approach to (co)homology this refreshing approach has many pedagogical advantages: It leads more quickly to the essentials of the subject, An absence of signs and orientation considerations simplifies the theory, Computations and advanced applications can be presented at an earlier stage, Simple geometrical interpretations of (co)chains. Mod 2 (co)homology was developed in the first quarter of the twentieth century as an alternative to integral homology, before both became particular cases of (co)homology with arbitrary coefficients. The first chapters of this book may serve as a basis for a graduate-level introductory course to (co)homology. Simplicial and singular mod 2 (co)homology are introduced, with their products and Steenrod squares, as well as equivariant cohomology. Classical applications include Brouwer's fixed point theorem, Poincaré duality, Borsuk-Ula...

The 1-dinar and ½-dinar banknotes from 1919: The first banknotes of the Kingdom of SCS

Directory of Open Access Journals (Sweden)

Pantelić Svetlana

2017-01-01

Full Text Available Since the National Bank of the Kingdom of SCS was not constituted until 26 February 1920, the Privileged National Bank of the Kingdom of Serbia released into circulation the banknotes of the Kingdom of SCS to replace its own 10- and 100-dinar banknotes payable in silver, according to the bylaw of the Ministry of Finance as of 17 November 1919. The 1-dinar banknote was released into circulation on 20 November and the 1/2-dinar banknote on 26 November 1919. The 1/2-dinar banknote was prepared in a private printing house in Zagreb, and the 1-dinar banknote in the Banque de France printing house in Paris. The withdrawal of the 1- and 1/2-dinar banknotes from circulation was never officially announced, but they were most probably withdrawn at the same time as the dinar-crown banknotes worth 1 dinar (4 crowns and 1/2 dinars (2 crowns.

Homological stabilizer codes

Energy Technology Data Exchange (ETDEWEB)

Anderson, Jonas T., E-mail: jonastyleranderson@gmail.com

2013-03-15

In this paper we define homological stabilizer codes on qubits which encompass codes such as Kitaev's toric code and the topological color codes. These codes are defined solely by the graphs they reside on. This feature allows us to use properties of topological graph theory to determine the graphs which are suitable as homological stabilizer codes. We then show that all toric codes are equivalent to homological stabilizer codes on 4-valent graphs. We show that the topological color codes and toric codes correspond to two distinct classes of graphs. We define the notion of label set equivalencies and show that under a small set of constraints the only homological stabilizer codes without local logical operators are equivalent to Kitaev's toric code or to the topological color codes. - Highlights: Black-Right-Pointing-Pointer We show that Kitaev's toric codes are equivalent to homological stabilizer codes on 4-valent graphs. Black-Right-Pointing-Pointer We show that toric codes and color codes correspond to homological stabilizer codes on distinct graphs. Black-Right-Pointing-Pointer We find and classify all 2D homological stabilizer codes. Black-Right-Pointing-Pointer We find optimal codes among the homological stabilizer codes.

Spinster homolog 2 (spns2 deficiency causes early onset progressive hearing loss.

Directory of Open Access Journals (Sweden)

Jing Chen

2014-10-01

Full Text Available Spinster homolog 2 (Spns2 acts as a Sphingosine-1-phosphate (S1P transporter in zebrafish and mice, regulating heart development and lymphocyte trafficking respectively. S1P is a biologically active lysophospholipid with multiple roles in signalling. The mechanism of action of Spns2 is still elusive in mammals. Here, we report that Spns2-deficient mice rapidly lost auditory sensitivity and endocochlear potential (EP from 2 to 3 weeks old. We found progressive degeneration of sensory hair cells in the organ of Corti, but the earliest defect was a decline in the EP, suggesting that dysfunction of the lateral wall was the primary lesion. In the lateral wall of adult mutants, we observed structural changes of marginal cell boundaries and of strial capillaries, and reduced expression of several key proteins involved in the generation of the EP (Kcnj10, Kcnq1, Gjb2 and Gjb6, but these changes were likely to be secondary. Permeability of the boundaries of the stria vascularis and of the strial capillaries appeared normal. We also found focal retinal degeneration and anomalies of retinal capillaries together with anterior eye defects in Spns2 mutant mice. Targeted inactivation of Spns2 in red blood cells, platelets, or lymphatic or vascular endothelial cells did not affect hearing, but targeted ablation of Spns2 in the cochlea using a Sox10-Cre allele produced a similar auditory phenotype to the original mutation, suggesting that local Spns2 expression is critical for hearing in mammals. These findings indicate that Spns2 is required for normal maintenance of the EP and hence for normal auditory function, and support a role for S1P signalling in hearing.

A new probability density function for spatial distribution of soil water storage capacity leads to SCS curve number method

OpenAIRE

Wang, Dingbao

2018-01-01

Following the Budyko framework, soil wetting ratio (the ratio between soil wetting and precipitation) as a function of soil storage index (the ratio between soil wetting capacity and precipitation) is derived from the SCS-CN method and the VIC type of model. For the SCS-CN method, soil wetting ratio approaches one when soil storage index approaches infinity, due to the limitation of the SCS-CN method in which the initial soil moisture condition is not explicitly represented. However, for the ...

A sediment graph model based on SCS-CN method

Science.gov (United States)

Singh, P. K.; Bhunya, P. K.; Mishra, S. K.; Chaube, U. C.

2008-01-01

SummaryThis paper proposes new conceptual sediment graph models based on coupling of popular and extensively used methods, viz., Nash model based instantaneous unit sediment graph (IUSG), soil conservation service curve number (SCS-CN) method, and Power law. These models vary in their complexity and this paper tests their performance using data of the Nagwan watershed (area = 92.46 km 2) (India). The sensitivity of total sediment yield and peak sediment flow rate computations to model parameterisation is analysed. The exponent of the Power law, β, is more sensitive than other model parameters. The models are found to have substantial potential for computing sediment graphs (temporal sediment flow rate distribution) as well as total sediment yield.

General calibration methodology for a combined Horton-SCS infiltration scheme in flash flood modeling

Science.gov (United States)

Gabellani, S.; Silvestro, F.; Rudari, R.; Boni, G.

2008-12-01

Flood forecasting undergoes a constant evolution, becoming more and more demanding about the models used for hydrologic simulations. The advantages of developing distributed or semi-distributed models have currently been made clear. Now the importance of using continuous distributed modeling emerges. A proper schematization of the infiltration process is vital to these types of models. Many popular infiltration schemes, reliable and easy to implement, are too simplistic for the development of continuous hydrologic models. On the other hand, the unavailability of detailed and descriptive information on soil properties often limits the implementation of complete infiltration schemes. In this work, a combination between the Soil Conservation Service Curve Number method (SCS-CN) and a method derived from Horton equation is proposed in order to overcome the inherent limits of the two schemes. The SCS-CN method is easily applicable on large areas, but has structural limitations. The Horton-like methods present parameters that, though measurable to a point, are difficult to achieve a reliable estimate at catchment scale. The objective of this work is to overcome these limits by proposing a calibration procedure which maintains the large applicability of the SCS-CN method as well as the continuous description of the infiltration process given by the Horton's equation suitably modified. The estimation of the parameters of the modified Horton method is carried out using a formal analogy with the SCS-CN method under specific conditions. Some applications, at catchment scale within a distributed model, are presented.

Analysis of the expression level and methylation of tumor protein p53, phosphatase and tensin homolog and mutS homolog 2 in N-methyl-N-nitrosourea-induced thymic lymphoma in C57BL/6 mice.

Science.gov (United States)

Huo, Xueyun; Li, Zhenkun; Zhang, Shuangyue; Li, Changlong; Guo, Meng; Lu, Jing; Lv, Jianyi; Du, Xiaoyan; Chen, Zhenwen

2017-10-01

Tumorigenesis is often caused by somatic mutation or epigenetic changes in genes that regulate aspects of cell death, proliferation and survival. Although the functions of multiple tumor suppressor genes have been well studied in isolation, how these genes cooperate during the progression of a single tumor remains unclear in numerous cases. The present study used N-methyl-N-nitrosourea (MNU), one of the most potent mutagenic nitrosourea compounds, to induce thymic lymphoma in C57BL/6J mice. Subsequently, the protein expression levels of phosphatase and tensin homolog (PTEN), transformation protein 53 and mutS homolog 2 (MSH2) were evaluated concomitantly in the thymus, liver, kidney and spleen of MNU-treated mice by western blotting. To determine whether changes in expression level were due to aberrant epigenetic regulation, the present study further examined the methylation status of each gene by MassARRAY analysis. During the tumorigenesis process of an MNU-induced single thymic lymphoma, the expression level of PTEN was revealed to be reduced in thymic lymphoma samples but not in normal or non-tumor thymus tissue samples. Furthermore, a marked reduction of P53 expression levels were demonstrated in thymic lymphomas and spleens with a metastatic tumor. Conversely, MSH2 upregulation was identified only in liver, kidney, and spleen samples that were infiltrated by thymic lymphoma cells. Furthermore, the present study revealed that a number of 5'-C-phosphate-G-3' sites located in the promoter of aberrantly expressed genes had significantly altered methylation statuses. These results improve the understanding of the course of mutagen-induced cancer, and highlight that epigenetic regulation may serve an important function in cancer.

[Effect of continuous aspiration of subglottic secretions on the prevention of ventilator-associated pneumonia in mechanically ventilated patients: a prospective, randomized, controlled clinical trial].

Science.gov (United States)

Yang, Cong-shan; Qiu, Hai-bo; Zhu, Yan-ping; Huang, Ying-zi; Xu, Xiao-ting; Gao, Liang

2008-08-01

To evaluate the effect of continuous aspiration of subglottic secretions (CASS) on the prevention of ventilator-associated pneumonia (VAP) in mechanically ventilated patients. Patients ventilated mechanically at the ICU from October, 2004 to April, 2006 were randomly divided into 2 groups: one group received CASS and the other did not (NASS group). CASS was performed immediately after admission for patients in the CASS group. The diagnosis of VAP was made based on clinical presentations, and the evaluation of VAP was done using simplified version of the clinical pulmonary infection score (CPIS). The general status of the patients, days of ventilated treatment, the volume of daily aspirated subglottic secretions, the morbidity and timing of VAP, days of stay in ICU and mortality within 28 days of hospitalization were recorded. One hundred and one patients were included in the study. There were 48 patients in the CASS group who were treated with mechanical ventilation more than 48 hours, and 43 patients in the NASS group. There was no significant difference in the general status of the patients and days of ventilation between 2 groups with the averaged score of APACHE II being 20.8 +/- 6.1. The average of CPIS was of 5.6 +/- 1.0 when VAP was diagnosed. The mean volume of aspirated subglottic secretions within the first 24 hours in the CASS group (n = 48) was (27.2 +/- 21.2) ml. The morbidity of VAP in the CASS and the NASS groups was 25.0% and 46.5% respectively (P = 0.032), and the length of time before the onset of VAP in these 2 groups was (7.3 +/- 4.2) days and (5.1 +/- 3.0) days respectively (P = 0.100). There was a significant increase in the percentage of gram-positive cocci from the lower respiratory tracts in the NASS group compared with that in the CASS group (P = 0.004). In the CASS group, the volume of the first daily aspirated subglottic secretions in patients with VAP was significantly less than that in patients without VAP (P = 0.006). The morbidity of

Model-based stimulation optimization for chronic pain suppression using percutaneous and surgical leads in spinal cord stimulation (SCS)

NARCIS (Netherlands)

Sankarasubramanian, V.

2013-01-01

The primary indication of SCS is chronic pain, in particular neuropathic pain. It is a highly debilitating condition, and in particular, is estimated to affect about one-fifth of the population in Europe (18% in the Netherlands). SCS, which uses electrical stimulation, is a valuable treatment for

Recovery of deficient homologous recombination in Brca2-depleted mouse cells by wild-type Rad51 expression.

Science.gov (United States)

Lee, Shauna A; Roques, Céline; Magwood, Alissa C; Masson, Jean-Yves; Baker, Mark D

2009-02-01

The BRCA2 tumor suppressor is important in maintaining genomic stability. BRCA2 is proposed to control the availability, cellular localization and DNA binding activity of the central homologous recombination protein, RAD51, with loss of BRCA2 resulting in defective homologous recombination. Nevertheless, the roles of BRCA2 in regulating RAD51 and how other proteins implicated in RAD51 regulation, such as RAD52 and RAD54 function relative to BRCA2 is not known. In this study, we tested whether defective homologous recombination in Brca2-depleted mouse hybridoma cells could be rectified by expression of mouse Rad51 or the Rad51-interacting mouse proteins, Rad52 and Rad54. In the Brca2-depleted cells, defective homologous recombination can be restored by over-expression of wild-type mouse Rad51, but not mouse Rad52 or Rad54. Correction of the homologous recombination defect requires Rad51 ATPase activity. A sizeable fraction ( approximately 50%) of over-expressed wild-type Rad51 is nuclear localized. The restoration of homologous recombination in the presence of a low (i.e., non-functional) level of Brca2 by wild-type Rad51 over-expression is unexpected. We suggest that Rad51 may access the nuclear compartment in a Brca2-independent manner and when Rad51 is over-expressed, the normal requirement for Brca2 control over Rad51 function in homologous recombination is dispensable. Our studies support loss of Rad51 function as a critical underlying factor in the homologous recombination defect in the Brca2-depleted cells.

General calibration methodology for a combined Horton-SCS infiltration scheme in flash flood modeling

Directory of Open Access Journals (Sweden)

S. Gabellani

2008-12-01

Full Text Available Flood forecasting undergoes a constant evolution, becoming more and more demanding about the models used for hydrologic simulations. The advantages of developing distributed or semi-distributed models have currently been made clear. Now the importance of using continuous distributed modeling emerges. A proper schematization of the infiltration process is vital to these types of models. Many popular infiltration schemes, reliable and easy to implement, are too simplistic for the development of continuous hydrologic models. On the other hand, the unavailability of detailed and descriptive information on soil properties often limits the implementation of complete infiltration schemes. In this work, a combination between the Soil Conservation Service Curve Number method (SCS-CN and a method derived from Horton equation is proposed in order to overcome the inherent limits of the two schemes. The SCS-CN method is easily applicable on large areas, but has structural limitations. The Horton-like methods present parameters that, though measurable to a point, are difficult to achieve a reliable estimate at catchment scale. The objective of this work is to overcome these limits by proposing a calibration procedure which maintains the large applicability of the SCS-CN method as well as the continuous description of the infiltration process given by the Horton's equation suitably modified. The estimation of the parameters of the modified Horton method is carried out using a formal analogy with the SCS-CN method under specific conditions. Some applications, at catchment scale within a distributed model, are presented.

DNA-PK, ATM and ATR collaboratively regulate p53-RPA interaction to facilitate homologous recombination DNA repair.

Science.gov (United States)

Serrano, M A; Li, Z; Dangeti, M; Musich, P R; Patrick, S; Roginskaya, M; Cartwright, B; Zou, Y

2013-05-09

Homologous recombination (HR) and nonhomologous end joining (NHEJ) are two distinct DNA double-stranded break (DSB) repair pathways. Here, we report that DNA-dependent protein kinase (DNA-PK), the core component of NHEJ, partnering with DNA-damage checkpoint kinases ataxia telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR), regulates HR repair of DSBs. The regulation was accomplished through modulation of the p53 and replication protein A (RPA) interaction. We show that upon DNA damage, p53 and RPA were freed from a p53-RPA complex by simultaneous phosphorylations of RPA at the N-terminus of RPA32 subunit by DNA-PK and of p53 at Ser37 and Ser46 in a Chk1/Chk2-independent manner by ATR and ATM, respectively. Neither the phosphorylation of RPA nor of p53 alone could dissociate p53 and RPA. Furthermore, disruption of the release significantly compromised HR repair of DSBs. Our results reveal a mechanism for the crosstalk between HR repair and NHEJ through the co-regulation of p53-RPA interaction by DNA-PK, ATM and ATR.

pH-Dependent Binding of Chloride to a Marine Alkaline Phosphatase Affects the Catalysis, Active Site Stability, and Dimer Equilibrium.

Science.gov (United States)

Hjörleifsson, Jens G; Ásgeirsson, Bjarni

2017-09-26

The effect of ionic strength on enzyme activity and stability varies considerably between enzymes. Ionic strength is known to affect the catalytic activity of some alkaline phosphatases (APs), such as Escherichia coli AP, but how ions affect APs is debated. Here, we studied the effect of various ions on a cold-adapted AP from Vibrio splendidus (VAP). Previously, we have found that the active form of VAP is extremely unstable at low ionic strengths. Here we show that NaCl increased the activity and stability of VAP and that the effect was pH-dependent in the range of pH 7-10. The activity profile as a function of pH formed two maxima, indicating a possible conformational change. Bringing the pH from the neutral to the alkaline range was accompanied by a large increase in both the K i for inorganic phosphate (product inhibition) and the K M for p-nitrophenyl phosphate. The activity transitions observed as the pH was varied correlated with structural changes as monitored by tryptophan fluorescence. Thermal and urea-induced inactivation was shown to be accompanied by neither dissociation of the active site metal ions nor dimer dissociation. This would suggest that the inactivation involved subtle changes in active site conformation. Furthermore, the VAP dimer equilibrium was studied for the first time and shown to highly favor dimerization, which was dependent on pH and NaCl concentration. Taken together, the data support a model in which anions bind to some specific acceptor in the active site of VAP, resulting in great stabilization and catalytic rate enhancement, presumably through a different mechanism.

Unusually high critical current of P-doped BaFe{sub 2}As{sub 2} single crystalline thin film

Energy Technology Data Exchange (ETDEWEB)

Kurth, Fritz; Engelmann, Jan; Schultz, Ludwig [IMW, IFW Dresden, Dresden (Germany); TU Dresden, Dresden (Germany); Tarantini, Chiara; Jaroszynski, Jan [ASC, NHMFL, Florida (United States); Grinenko, Vadim; Reich, Elke; Huehne, Ruben [IMW, IFW Dresden, Dresden (Germany); Haenisch, Jens [IMW, IFW Dresden, Dresden (Germany); ITEP, KIT, Karlsruhe (Germany); Mori, Yasohiro; Sakagami, Akihiro; Kawaguchi, Takahiko; Ikuta, Hiroshi [Department of Crystalline Materials Science, Nagoya University, Nagoya (Japan); Holzapfel, Bernhard [ITEP, KIT, Karlsruhe (Germany); Iida, Kazumasa [IMW, IFW Dresden, Dresden (Germany); Department of Crystalline Materials Science, Nagoya University, Nagoya (Japan)

2015-07-01

Microstructurally clean, isovalently P-doped BaFe{sub 2}As{sub 2} single crystalline thin films have been prepared by molecular beam epitaxy. These films show a superconducting transition temperature (T{sub c}) of over 30 K and high transport self-field critical current densities (J{sub c}) of over 6 MA/cm{sup 2} at 4.2 K, which are among the highest for Fe based superconductors. In-field J{sub c} exceeds 0.1 MA/cm{sup 2} at μ{sub 0}H = 35 T for H parallel ab and μ{sub 0}H = 18 T for H parallel c, respectively, in spite of moderate upper critical fields compared to other FeSCs with similar T{sub c}. This unusually high J{sub c} makes P-doped Ba-122 very favorable for high-field magnet applications.

Regulation of Rad51-Mediated Homologous Recombination by BRCA2, DSS1 and RAD52

DEFF Research Database (Denmark)

Rants, Louise Olthaver Juhl

Homologous recombination (HR) provides a mechanism to restore integrity and maintain stability of the genetic material. HR is a major pathway for repair of DNA double-strand breaks (DSB), recovery of broken replication forks and generation of meiotic crossovers. The defining step in HR is homolog......Homologous recombination (HR) provides a mechanism to restore integrity and maintain stability of the genetic material. HR is a major pathway for repair of DNA double-strand breaks (DSB), recovery of broken replication forks and generation of meiotic crossovers. The defining step in HR...... is homologous strand exchange directed by the RecA-related recombinase Rad51. BRCA2 participates in HR by mediating Rad51 homology-directed repair. Both BRCA2 and Rad51 are essential for HR, DNA repair, and the maintenance of genome stability. In the present study, we seek to understand the mechanism of BRCA2...... with RAD52-mediated repair at sites of CPT-induced DNA damage. The synthetic lethality approach using RAD52 small molecule inhibitors in brca-deficient cancers is a promising therapeutic strategy for cancer treatment....

Instability of seawater pH in the South China Sea during the mid-late Holocene: Evidence from boron isotopic composition of corals

Science.gov (United States)

Liu, Yajing; Liu, W.; Peng, Z.; Xiao, Y.; Wei, G.; Sun, W.; He, J.; Liu, Gaisheng; Chou, C.-L.

2009-01-01

We used positive thermal ionization mass spectrometry (PTIMS) to generate high precision ??11B records in Porites corals of the mid-late Holocene from the South China Sea (SCS). The ??11B values of the Holocene corals vary significantly, ranging from 22.2??? to 25.5???. The paleo-pH records of the SCS, reconstructed from the ??11B data, were not stable as previously thought but show a gradual increase from the Holocene thermal optimal and a sharp decrease to modern values. The latter is likely caused by the large amount of anthropogenic CO2 emissions since the Industrial Revolution but variations of atmospheric pCO2 cannot explain the pH change of the SCS before the Industrial Revolution. We suggest that variations of monsoon intensity during the mid-late Holocene may have driven the sea surface pH increase from the mid to late Holocene. Results of this study indicate that the impact of anthropogenic atmospheric CO2 emissions may have reversed the natural pH trend in the SCS since the mid-Holocene. Such ocean pH records in the current interglacial period can help us better understand the physical and biological controls on ocean pH and possibly predict the long-term impact of climate change on future ocean acidification. ?? 2008 Elsevier Ltd. All rights reserved.

Using a topographic index to distribute variable source area runoff predicted with the SCS curve-number equation

Science.gov (United States)

Lyon, Steve W.; Walter, M. Todd; Gérard-Marchant, Pierre; Steenhuis, Tammo S.

2004-10-01

Because the traditional Soil Conservation Service curve-number (SCS-CN) approach continues to be used ubiquitously in water quality models, new application methods are needed that are consistent with variable source area (VSA) hydrological processes in the landscape. We developed and tested a distributed approach for applying the traditional SCS-CN equation to watersheds where VSA hydrology is a dominant process. Predicting the location of source areas is important for watershed planning because restricting potentially polluting activities from runoff source areas is fundamental to controlling non-point-source pollution. The method presented here used the traditional SCS-CN approach to predict runoff volume and spatial extent of saturated areas and a topographic index, like that used in TOPMODEL, to distribute runoff source areas through watersheds. The resulting distributed CN-VSA method was applied to two subwatersheds of the Delaware basin in the Catskill Mountains region of New York State and one watershed in south-eastern Australia to produce runoff-probability maps. Observed saturated area locations in the watersheds agreed with the distributed CN-VSA method. Results showed good agreement with those obtained from the previously validated soil moisture routing (SMR) model. When compared with the traditional SCS-CN method, the distributed CN-VSA method predicted a similar total volume of runoff, but vastly different locations of runoff generation. Thus, the distributed CN-VSA approach provides a physically based method that is simple enough to be incorporated into water quality models, and other tools that currently use the traditional SCS-CN method, while still adhering to the principles of VSA hydrology.

Production of R,R-2,3-butanediol of ultra-high optical purity from Paenibacillus polymyxa ZJ-9 using homologous recombination.

Science.gov (United States)

Zhang, Li; Cao, Can; Jiang, Ruifan; Xu, Hong; Xue, Feng; Huang, Weiwei; Ni, Hao; Gao, Jian

2018-08-01

The present study describes the use of metabolic engineering to achieve the production of R,R-2,3-butanediol (R,R-2,3-BD) of ultra-high optical purity (>99.99%). To this end, the diacetyl reductase (DAR) gene (dud A) of Paenibacillus polymyxa ZJ-9 was knocked out via homologous recombination between the genome and the previously constructed targeting vector pRN5101-L'C in a process based on homologous single-crossover. PCR verification confirmed the successful isolation of the dud A gene disruption mutant P. polymyxa ZJ-9-△dud A. Moreover, fermentation results indicated that the optical purity of R,R-2,3-BD increased from about 98% to over 99.99%, with a titer of 21.62 g/L in Erlenmeyer flasks. The latter was further increased to 25.88 g/L by fed-batch fermentation in a 5-L bioreactor. Copyright © 2018 Elsevier Ltd. All rights reserved.

RUNOFF HYDROGRAPHS USING SNYDER AND SCS SYNTHETIC UNIT HYDROGRAPH METHODS: A CASE STUDY OF SELECTED RIVERS IN SOUTH WEST NIGERIA

Directory of Open Access Journals (Sweden)

Wahab Adebayo Salami

2017-01-01

Full Text Available This paper presents the development of runoff hydrographs for selected rivers in Ogun-Osun river catchment, south west, Nigeria using Snyder and Soil Conservation Service (SCS methods of synthetic unit hydrograph to determine the ordinates. The Soil Conservation Service (SCS curve Number method was used to estimate the excess rainfall from storm of different return periods. The peak runoff hydrographs were determined by convoluting the unit hydrographs ordinates with the excess rainfall and the value of peak flows obtained by both Snyder and SCS methods observed to vary from one river watershed to the other. The peak runoff hydrograph flows obtained based on the unit hydrograph ordinate determined with Snyder method for 20-yr, 50-yr, 100-yr, 200-yr and 500-yr, return period varied from 112.63m3/s and 13364.30m3/s, while those based on the SCS method varied from 304.43m3/s and 6466.84m3/s for the eight watersheds. However, the percentage difference shows that for values of peak flows obtained with Snyder and SCS methods varies from 13.14% to 63.30%. However, SCS method is recommended to estimate the ordinate required for the development of peak runoff hydrograph in the river watersheds because it utilized additional morphometric parameters such as watershed slope and the curve number (CN which is a function of the properties of the soil and vegetation cover of the watershed.

GIS Based Distributed Runoff Predictions in Variable Source Area Watersheds Employing the SCS-Curve Number

Science.gov (United States)

Steenhuis, T. S.; Mendoza, G.; Lyon, S. W.; Gerard Marchant, P.; Walter, M. T.; Schneiderman, E.

2003-04-01

Because the traditional Soil Conservation Service Curve Number (SCS-CN) approach continues to be ubiquitously used in GIS-BASED water quality models, new application methods are needed that are consistent with variable source area (VSA) hydrological processes in the landscape. We developed within an integrated GIS modeling environment a distributed approach for applying the traditional SCS-CN equation to watersheds where VSA hydrology is a dominant process. Spatial representation of hydrologic processes is important for watershed planning because restricting potentially polluting activities from runoff source areas is fundamental to controlling non-point source pollution. The methodology presented here uses the traditional SCS-CN method to predict runoff volume and spatial extent of saturated areas and uses a topographic index to distribute runoff source areas through watersheds. The resulting distributed CN-VSA method was incorporated in an existing GWLF water quality model and applied to sub-watersheds of the Delaware basin in the Catskill Mountains region of New York State. We found that the distributed CN-VSA approach provided a physically-based method that gives realistic results for watersheds with VSA hydrology.

Respective impact of implementation of prevention strategies, colonization with multiresistant bacteria and antimicrobial use on the risk of early- and late-onset VAP: An analysis of the OUTCOMEREA network

OpenAIRE

Ibn Saied, Wafa; Souweine, Bertrand; Garrouste-Orgeas, Maité; Ruckly, Stéphane; Darmon, Michael; Bailly, Sébastien; Cohen, Yves; Azoulay, Elie; Schwebel, Carole; Radjou, Aguila; Kallel, Hatem; Adrie, Christophe; Dumenil, Anne-Sylvie; Argaud, Laurent; Marcotte, Guillaume

2017-01-01

International audience; Rationale: The impact of prevention strategies and risk factors for early-onset (EOP) versus late-onset (LOP) ventilator -associated pneumonia (VAP) are still debated.Objectives: To evaluate, in a multicenter cohort, the risk factors for EOP and LOP, as the evolution of prevention strategies.Methods: 7,784 patients with mechanical ventilation (MV) for at least 48 hours were selected into the multicenter prospective OUTCOMEREA database (1997-2016). VAP occurring between...

Estimating Composite Curve Number Using an Improved SCS-CN Method with Remotely Sensed Variables in Guangzhou, China

OpenAIRE

Fan, Fenglei; Deng, Yingbin; Hu, Xuefei; Weng, Qihao

2013-01-01

The rainfall and runoff relationship becomes an intriguing issue as urbanization continues to evolve worldwide. In this paper, we developed a simulation model based on the soil conservation service curve number (SCS-CN) method to analyze the rainfall-runoff relationship in Guangzhou, a rapid growing metropolitan area in southern China. The SCS-CN method was initially developed by the Natural Resources Conservation Service (NRCS) of the United States Department of Agriculture (USDA), and is on...

Exploration of knowledge of, adherence to, attitude and barriers toward evidence-based guidelines (EBGs for prevention of ventilator-associated pneumonia (VAP in healthcare workers of pediatric cardiac intensive care units (PCICUs: A Quali-Quantitative survey

Directory of Open Access Journals (Sweden)

Leila Jahansefat

2016-09-01

Full Text Available Implementation of evidence-based guidelines (EBGs is an effective measure for prevention of ventilator-associated pneumonia (VAP. Appropriate knowledge, attitude and adherence of healthcare workers (HCWs to EBGs are necessary factors for implementation of EBGs. This study was conducted with objective of evaluation of knowledge, attitude, and adherence of HCWs to EBGs for prevention of VAP and exploration of the barriers of their implementation in clinical practice. Totally, a total number of 45 HCWs of two pediatric cardiac surgery ICU (PCICUs participated in this quali-quantitative survey. Knowledge, attitude and adherence of participants was evaluated by a validated multiple-choice questionnaire and barriers of implementation of EBGs was extracted from participants’ answer to an open-ended question of our self-made questionnaire. Knowledge of HCWs was poor and significantly different between nurse assistants (RAs, nurses (RNs, and physicians (MDs (respectively, 1.25±0.95, 4.53±1.73, and 5.54±2.01, P=0.001. Likewise, attit ude of HCWs is not positive and significantly different between NAs, RNs, and MDs (respectively, 32.96±2.42, 34.00±2.44, 36.81±4.35, P=0.003. The adherence of HCWs is not good and different between RAs, RNs, and MDs (respectively, 11.50±1.00, 13.13±1.83, and 17.18±6.06, P= 0.17. The Barriers of implementation of EBGs was categorized into four category of individual, organizational, social, and educational factors. Unsatisfying status of knowledge, attitude, and adherence of HCWs is a challenging concern of health-care system, especially in PICUs. In addition to these well-known factors, poor implementation of EBGs is related to many other barriers which should recognized and taken into consideration for designation of infection controlling programs.

U.S.-Vietnamese Security Cooperation for Access to the SCS

Science.gov (United States)

2015-06-16

of the claimants to islands in the SCS, China has more Coast Guard/MLE vessels than Japan, Indonesia, Malaysia , and the Philippines combined.7...45 In 2011, the U.S. looked at Vietnam, along with other Southeast Asian countries, for its Naval Medical ...human rights; culture, tourism , and sports; as well as continued annual defense dialogue meetings.47 Both Vietnam and the U.S. are concerned about

Characterization of fatty acid binding by the P2 myelin protein

International Nuclear Information System (INIS)

Gudaitis, P.G.; Weise, M.J.

1987-01-01

In recent years, significant sequence homology has been found between the P2 protein of peripheral myelin and intracellular retinoid- and fatty acid-binding proteins. They have found that salt extracts of bovine intradural nerve roots contain the P2 basic protein in association with free fatty acid. Preliminary results from quantitative analyses showed a ratio of 0.4-1.1 fatty acid (mainly oleate and palmitate) per P2 molecule. P2/ligand interactions were partially characterized using ( 3 H)-oleate in gel permeation assays and binding studies using lipidex to separated bound and free fatty acid. Methyloleate was found to displace ( 3 H)-oleate from P2, indicating that ligand binding interactions are predominantly hydrophobic in nature. On the other hand, myristic acid and retinol did not inhibit the binding of oleate to the protein, results consistent with a decided affinity for long chain fatty acids but not for the retinoids. The binding between P2 and oleic acid showed an apparent Kd in the micromolar range, a value comparable to those found for other fatty acid-binding proteins. From these results they conclude that P2 shares not only structural homology with certain fatty acid binding proteins but also an ability to bind long chain fatty acids. Although the significance of these similarities is not yet clear, they may, by analogy, expect P2 to have a role in PNS lipid metabolism

Speeding up spin-component-scaled third-order pertubation theory with the chain of spheres approximation: the COSX-SCS-MP3 method

Science.gov (United States)

Izsák, Róbert; Neese, Frank

2013-07-01

The 'chain of spheres' approximation, developed earlier for the efficient evaluation of the self-consistent field exchange term, is introduced here into the evaluation of the external exchange term of higher order correlation methods. Its performance is studied in the specific case of the spin-component-scaled third-order Møller--Plesset perturbation (SCS-MP3) theory. The results indicate that the approximation performs excellently in terms of both computer time and achievable accuracy. Significant speedups over a conventional method are obtained for larger systems and basis sets. Owing to this development, SCS-MP3 calculations on molecules of the size of penicillin (42 atoms) with a polarised triple-zeta basis set can be performed in ∼3 hours using 16 cores of an Intel Xeon E7-8837 processor with a 2.67 GHz clock speed, which represents a speedup by a factor of 8-9 compared to the previously most efficient algorithm. Thus, the increased accuracy offered by SCS-MP3 can now be explored for at least medium-sized molecules.

Purification, crystallization, small-angle X-ray scattering and preliminary X-ray diffraction analysis of the SH2 domain of the Csk-homologous kinase.

Science.gov (United States)

Gunn, Natalie J; Gorman, Michael A; Dobson, Renwick C J; Parker, Michael W; Mulhern, Terrence D

2011-03-01

The C-terminal Src kinase (Csk) and Csk-homologous kinase (CHK) are endogenous inhibitors of the proto-oncogenic Src family of protein tyrosine kinases (SFKs). Phosphotyrosyl peptide binding to their Src-homology 2 (SH2) domains activates Csk and CHK, enhancing their ability to suppress SFK signalling; however, the detailed mechanistic basis of this activation event is unclear. The CHK SH2 was expressed in Escherichia coli and the purified protein was characterized as monomeric by synchrotron small-angle X-ray scattering in-line with size-exclusion chromatography. The CHK SH2 crystallized in 0.2 M sodium bromide, 0.1 M bis-Tris propane pH 6.5 and 20% polyethylene glycol 3350 and the best crystals diffracted to ∼1.6 Å resolution. The crystals belonged to space group P2, with unit-cell parameters a=25.8, b=34.6, c=63.2 Å, β=99.4°.

Illustrating and homology modeling the proteins of the Zika virus [version 2; referees: 2 approved

Directory of Open Access Journals (Sweden)

Sean Ekins

2016-09-01

Full Text Available The Zika virus (ZIKV is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.

Low-Threshold Lasing from 2D Homologous Organic-Inorganic Hybrid Ruddlesden-Popper Perovskite Single Crystals.

Science.gov (United States)

Raghavan, Chinnambedu Murugesan; Chen, Tzu-Pei; Li, Shao-Sian; Chen, Wei-Liang; Lo, Chao-Yuan; Liao, Yu-Ming; Haider, Golam; Lin, Cheng-Chieh; Chen, Chia-Chun; Sankar, Raman; Chang, Yu-Ming; Chou, Fang-Cheng; Chen, Chun-Wei

2018-05-09

Organic-inorganic hybrid two-dimensional (2D) perovskites have recently attracted great attention in optical and optoelectronic applications due to their inherent natural quantum-well structure. We report the growth of high-quality millimeter-sized single crystals belonging to homologous two-dimensional (2D) hybrid organic-inorganic Ruddelsden-Popper perovskites (RPPs) of (BA) 2 (MA) n-1 Pb n I 3 n+1 ( n = 1, 2, and 3) by a slow evaporation at a constant-temperature (SECT) solution-growth strategy. The as-grown 2D hybrid perovskite single crystals exhibit excellent crystallinity, phase purity, and spectral uniformity. Low-threshold lasing behaviors with different emission wavelengths at room temperature have been observed from the homologous 2D hybrid RPP single crystals. Our result demonstrates that solution-growth homologous organic-inorganic hybrid 2D perovskite single crystals open up a new window as a promising candidate for optical gain media.

Determination of Critical Micellar Concentration of Homologous 2-Alkoxyphenylcarbamoyloxyethyl-Morpholinium Chlorides

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Lenka Stopková

2018-05-01

Full Text Available The critical micellar concentrations of selected alkyloxy homologues of local anesthetic 4-(2-{[(2-alkoxyphenylcarbamoyl]oxy}ethylmorpholin-4-ium chloride with nc = 2, 4, 5, 6, 7, 8, and 9 carbons in alkyloxy tail were determined by absorption spectroscopy in the UV–vis spectral region with the use of a pyrene probe. Within the homologous series of the studied amphiphilic compounds, the ln(cmc was observed to be dependent linearly on the number of carbon atoms nc in the hydrophobic tail: ln(cmc = 0.705–0.966 nc. The Gibbs free energy, necessary for the transfer of the methylene group of the alkoxy chain from the water phase into the inner part of the micelle at the temperature of 25 °C and pH ≈ 4.5–5.0, was found to be −2.39 kJ/mol. The experimentally determined cmc values showed good correlations with the predicted values of the bulkiness of the alkoxy tail expressed as the molar volume of substituent R, as well as with the surface tension of the compounds.

Use of VAP3D software in the construction of pathological anthropomorphic phantoms for dosimetric evaluations; Uso do software VAP3D na construcao de fantomas antropomorficos patologicos para avaliacoes dosimetricas

Energy Technology Data Exchange (ETDEWEB)

Lima, Lindeval Fernandes de [Universidade Federal de Pernambuco (DEM/UFPE), Recife, PE (Brazil). Dept. de Engenharia Mecanica; Vieira, Jose Wilson [Instituto Federal de Educacao, Ciencia e Tecnologia de Pernambuco, Recife, PE (Brazil); Lima, Fernando R.A., E-mail: falima@cnen.gov.b [Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil)

2011-10-26

This paper performs a new type of dosimetric evaluation, where it was used a phantom of pathological voxels (representative phantom of sick person). The software VAP3D (Visualization and Analysis of Phantoms 3D) were used for, from a healthy phantom (phantom representative of healthy person), to introduce three dimensional regions to simulate tumors. It was used the Monte Carlo ESGnrc code to simulate the X ray photon transport, his interaction with matter and evaluation of absorbed dose in organs and tissues from thorax region of the healthy phantom and his pathological version. This is a computer model of typical exposure for programming the treatments in radiodiagnostic

Improving runoff risk estimates: Formulating runoff as a bivariate process using the SCS curve number method

Science.gov (United States)

Shaw, Stephen B.; Walter, M. Todd

2009-03-01

The Soil Conservation Service curve number (SCS-CN) method is widely used to predict storm runoff for hydraulic design purposes, such as sizing culverts and detention basins. As traditionally used, the probability of calculated runoff is equated to the probability of the causative rainfall event, an assumption that fails to account for the influence of variations in soil moisture on runoff generation. We propose a modification to the SCS-CN method that explicitly incorporates rainfall return periods and the frequency of different soil moisture states to quantify storm runoff risks. Soil moisture status is assumed to be correlated to stream base flow. Fundamentally, this approach treats runoff as the outcome of a bivariate process instead of dictating a 1:1 relationship between causative rainfall and resulting runoff volumes. Using data from the Fall Creek watershed in western New York and the headwaters of the French Broad River in the mountains of North Carolina, we show that our modified SCS-CN method improves frequency discharge predictions in medium-sized watersheds in the eastern United States in comparison to the traditional application of the method.

Steam generator secondary pH during a steam generator tube rupture

International Nuclear Information System (INIS)

Adams, J.P.; Peterson, E.S.

1991-12-01

The Nuclear Regulatory Commission requires utilizes to determine the response of a pressurized water reactor to a steam generator tube rupture (SGTR) as part of the safety analysis for the plant. The SGTR analysis includes assumptions regarding the partitioning of iodine between liquid and vapor in steam generator secondary. Experimental studies have determined that the partitioning of iodine in water is very sensitive to the pH. Based on this experimental evidence, the NRC requested the INEL to perform an analytical assessment of secondary coolant system (SCS) pH during an SGTR. Design basis thermal and hydraulic calculations were used together with industry standard chemistry guidelines to determine the SCS chemical concentrations during an SGTR. These were used as input to the Facility for Analysis of Chemical Thermodynamics computer system to calculate the equilibrium pH in the SCS at various discrete time during an SGTR. The results of this analysis indicate that the SCS pH decreases from the initial value of 8.8 to approximately 6.5 by the end of the transient, independent of PWR design

Anti-Tribbles homolog 2 (TRIB2) autoantibodies in narcolepsy are associated with recent onset of cataplexy

DEFF Research Database (Denmark)

Kawashima, Minae; Lin, Ling; Tanaka, Susumu

2010-01-01

Recent studies have found increased autoantibodies against Tribbles homolog 2 (anti-TRIB2) and anti-streptolysin O (ASO) in narcolepsy. In this study, we replicated this finding with a primary focus on recent onset cases....

Specific distribution of the Saccharomyces cerevisiae linker histone homolog HHO1p in the chromatin

OpenAIRE

Freidkin, Ilya; Katcoff, Don J.

2001-01-01

In virtually all eukaryotic organisms, linker DNA between nucleosomes is associated with a histone termed linker histone or histone H1. In Saccharomyces cerevisiae, HHO1 encodes a putative linker histone with very significant homology to histone H1. The encoded protein is expressed in the nucleus, but has not been shown to affect global chromatin structure, nor has its deletion shown any detectable phenotype. In vitro chromatin assembly experiments with recombinant HHO1p have shown that it is...

Ventilator-associated pneumonia in ARDS patients: the impact of prone positioning. A secondary analysis of the PROSEVA trial.

Science.gov (United States)

Ayzac, L; Girard, R; Baboi, L; Beuret, P; Rabilloud, M; Richard, J C; Guérin, C

2016-05-01

The goal of this study was to assess the impact of prone positioning on the incidence of ventilator-associated pneumonia (VAP) and the role of VAP in mortality in a recent multicenter trial performed on patients with severe ARDS. An ancillary study of a prospective multicenter randomized controlled trial on early prone positioning in patients with severe ARDS. In suspected cases of VAP the diagnosis was based on positive quantitative cultures of bronchoalveolar lavage fluid or tracheal aspirate at the 10(4) and 10(7) CFU/ml thresholds, respectively. The VAP cases were then subject to central, independent adjudication. The cumulative probabilities of VAP were estimated in each position group using the Aalen-Johansen estimator and compared using Gray's test. A univariate and a multivariate Cox model was performed to assess the impact of VAP, used as a time-dependent covariate for mortality hazard during the ICU stay. In the supine and prone position groups, the incidence rate for VAP was 1.18 (0.86-1.60) and 1.54 (1.15-2.02) per 100 days of invasive mechanical ventilation (p = 0.10), respectively. The cumulative probability of VAP at 90 days was estimated at 46.5 % (27-66) in the prone group and at 33.5 % (23-44) in the supine group. The difference between the two cumulative probability curves was not statistically significant (p = 0.11). In the univariate Cox model, VAP was associated with an increase in the mortality rate during the ICU stay [HR 1.65 (1.05-2.61), p = 0.03]. HR increased to 2.2 (1.39-3.52) (p position group, age, SOFA score, McCabe score, and immunodeficiency. In severe ARDS patients prone positioning did not reduce the incidence of VAP and VAP was associated with higher mortality.

A PHF8 homolog in C. elegans promotes DNA repair via homologous recombination.

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Changrim Lee

Full Text Available PHF8 is a JmjC domain-containing histone demethylase, defects in which are associated with X-linked mental retardation. In this study, we examined the roles of two PHF8 homologs, JMJD-1.1 and JMJD-1.2, in the model organism C. elegans in response to DNA damage. A deletion mutation in either of the genes led to hypersensitivity to interstrand DNA crosslinks (ICLs, while only mutation of jmjd-1.1 resulted in hypersensitivity to double-strand DNA breaks (DSBs. In response to ICLs, JMJD-1.1 did not affect the focus formation of FCD-2, a homolog of FANCD2, a key protein in the Fanconi anemia pathway. However, the dynamic behavior of RPA-1 and RAD-51 was affected by the mutation: the accumulations of both proteins at ICLs appeared normal, but their subsequent disappearance was retarded, suggesting that later steps of homologous recombination were defective. Similar changes in the dynamic behavior of RPA-1 and RAD-51 were seen in response to DSBs, supporting a role of JMJD-1.1 in homologous recombination. Such a role was also supported by our finding that the hypersensitivity of jmjd-1.1 worms to ICLs was rescued by knockdown of lig-4, a homolog of Ligase 4 active in nonhomologous end-joining. The hypersensitivity of jmjd-1.1 worms to ICLs was increased by rad-54 knockdown, suggesting that JMJD-1.1 acts in parallel with RAD-54 in modulating chromatin structure. Indeed, the level of histone H3 Lys9 tri-methylation, a marker of heterochromatin, was higher in jmjd-1.1 cells than in wild-type cells. We conclude that the histone demethylase JMJD-1.1 influences homologous recombination either by relaxing heterochromatin structure or by indirectly regulating the expression of multiple genes affecting DNA repair.

Conjugative plasmid pAW63 brings new insights into the genesis of the Bacillus anthracis virulence plasmid pXO2 and of the Bacillus thuringiensis plasmid pBT9727

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Mahillon Jacques

2005-07-01

Full Text Available Abstract Background Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis belong to the genetically close-knit Bacillus cereus sensu lato group, a family of rod-shaped Gram-positive bacteria. pAW63 is the first conjugative plasmid from the B. cereus group to be completely sequenced. Results The 71,777 bp nucleotide sequence of pAW63 reveals a modular structure, including a 42 kb tra region encoding homologs of the Type IV secretion systems components VirB11, VirB4 and VirD4, as well as homologs of Gram-positive conjugation genes from Enterococcus, Lactococcus, Listeria, Streptococcus and Staphylococcus species. It also firmly establishes the existence of a common backbone between pAW63, pXO2 from Bacillus anthracis and pBT9727 from the pathogenic Bacillus thuringiensis serovar konkukian strain 97-27. The alignment of these three plasmids highlights the presence of well conserved segments, in contrast to distinct regions of high sequence plasticity. The study of their specific differences has provided a three-point reference framework that can be exploited to formulate solid hypotheses concerning the functionalities and the molecular evolution of these three closely related plasmids. This has provided insight into the chronology of their divergence, and led to the discovery of two Type II introns on pAW63, matching copies of the mobile element IS231L in different loci of pXO2 and pBT9727, and the identification on pXO2 of a 37 kb pathogenicity island (PAI containing the anthrax capsule genes. Conclusion The complete sequence determination of pAW63 has led to a functional map of the plasmid yielding insights into its conjugative apparatus, which includes T4SS-like components, as well as its resemblance to other large plasmids of Gram-positive bacteria. Of particular interest is the extensive homology shared between pAW63 and pXO2, the second virulence plasmid of B. anthracis, as well as pBT9727 from the pathogenic strain B. thuringiensis

Exotic open-flavor bcq¯q¯, bcs¯s¯ and qcq¯b¯, scs¯b¯ tetraquark states

Science.gov (United States)

Chen, Wei; Steele, T. G.; Zhu, Shi-Lin

2014-03-01

We study the exotic bcq¯q¯, bcs¯s¯ and qcq¯b¯, scs¯b¯ systems by constructing the corresponding tetraquark currents with JP=0+ and 1+. After investigating the two-point correlation functions and the spectral densities, we perform QCD sum rule analysis and extract the masses of these open-flavor tetraquark states. Our results indicate that the masses of both the scalar and axial vector tetraquark states are about 7.1-7.2 GeV for the bcq¯q¯ system and 7.2-7.3 GeV for the bcs¯s¯ system. For the qcq¯b¯ tetraquark states with JP=0+ and 1+, their masses are extracted to be around 7.1 GeV. The masses for the scalar and axial vector scs¯b¯ states are 7.1 and 6.9-7.1 GeV, respectively. The tetraquark states qcq¯b¯ and scs¯b¯ lie below the thresholds of D(*)B(*) and Ds(*)Bs(*) respectively, but they can decay into Bc plus a light meson. However, the tetraquark states bcq¯q¯ and bcs¯s¯ lie below the D(*)B¯(*) and Ds(*)B¯s(*) thresholds, suggesting dominantly weak decay mechanisms.

Providing the physical basis of SCS curve number method and its proportionality relationship from Richards' equation

Science.gov (United States)

Hooshyar, M.; Wang, D.

2016-12-01

The empirical proportionality relationship, which indicates that the ratio of cumulative surface runoff and infiltration to their corresponding potentials are equal, is the basis of the extensively used Soil Conservation Service Curve Number (SCS-CN) method. The objective of this paper is to provide the physical basis of the SCS-CN method and its proportionality hypothesis from the infiltration excess runoff generation perspective. To achieve this purpose, an analytical solution of Richards' equation is derived for ponded infiltration in shallow water table environment under the following boundary conditions: 1) the soil is saturated at the land surface; and 2) there is a no-flux boundary which moves downward. The solution is established based on the assumptions of negligible gravitational effect, constant soil water diffusivity, and hydrostatic soil moisture profile between the no-flux boundary and water table. Based on the derived analytical solution, the proportionality hypothesis is a reasonable approximation for rainfall partitioning at the early stage of ponded infiltration in areas with a shallow water table for coarse textured soils.

Pre-hospital intubation factors and pneumonia in trauma patients.

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Evans, Heather L; Warner, Keir; Bulger, Eileen M; Sharar, Sam R; Maier, Ronald V; Cuschieri, Joseph

2011-10-01

We reported similar rates of ventilator-associated pneumonia (VAP) previously in trauma patients intubated either in a pre-hospital (PH) venue or the emergency department. A subset of PH intubations with continuous quality assessment was re-examined to identify the intubation factors associated with VAP. The subgroup was derived from an existing data set of consecutive adult trauma patients intubated prior to Level I trauma center admission July 2007-July 2008. Intubation details recorded included bag-valve mask ventilation (BVM) and the presence of material in the airway. The diagnosis of VAP was made preferentially by quantitative bronchoalveolar lavage (BAL) cultures (≥ 10⁴ colony-forming units indicating infection). Baseline data, injury characteristics, and circumstances of intubation of patients with and without VAP were compared by univariable analysis. Detailed data were available for 197 patients; 32 (16.2%) developed VAP, on average 6.0±0.7 days after admission. Baseline characteristics were similar in the groups, but diabetes mellitus was more common in the VAP group (4 [12.5%] vs. 5 [3.0%]; p=0.02). There was a higher rate of blunt injury in the VAP patients (28 [87.5%] vs. 106 [64.2%]; p=0.01) and higher injury severity scores (33.1±2.8 vs. 23.0±1.0; p=0.0002) and chest Abbreviated Injury Scores (2.6±0.3 vs. 1.5±0.1; p=0.002). Lower Glasgow Coma Scale scores (7.9±0.9 vs. 9.9±0.4; p=0.04) and greater use of BVM (18 [56.3%] vs. 56 [34.0%]; p=0.02) were observed in patients who developed VAP. Among aspirations, 10 (31.3%) of patients with emesis developed VAP compared with only 4 (12.5%) with blood in the airway (p=0.003). Aspiration, along with depressed consciousness and greater injury severity, may predispose trauma patients to VAP. Prospective studies should focus on the quality and timing of aspiration relative to intubation to determine if novel interventions can prevent aspiration or decrease the risk of VAP after aspiration.

Deciphering of ADP-induced, phosphotyrosine-dependent signaling networks in human platelets by Src-homology 2 region (SH2)-profiling.

Science.gov (United States)

Schweigel, Hardy; Geiger, Jörg; Beck, Florian; Buhs, Sophia; Gerull, Helwe; Walter, Ulrich; Sickmann, Albert; Nollau, Peter

2013-03-01

Tyrosine phosphorylation plays a central role in signal transduction controlling many important biological processes. In platelets, the activity of several signaling proteins is controlled by tyrosine phosphorylation ensuring proper platelet activation and aggregation essential for regulation of the delicate balance between bleeding and hemostasis. Here, we applied Src-homology 2 region (SH2)-profiling for deciphering of the phosphotyrosine state of human platelets activated by adenosine diphosphate (ADP). Applying a panel of 31 SH2-domains, rapid and complex regulation of the phosphotyrosine state of platelets was observed after ADP stimulation. Specific inhibition of platelet P2Y receptors by synthetic drugs revealed a major role for the P2Y1 receptor in tyrosine phosphorylation. Concomitant activation of protein kinase A (PKA) abolished ADP-induced tyrosine phosphorylation in a time and concentration-dependent manner. Given the fact that PKA activity is negatively regulated by the P2Y12 receptor, our data provide evidence for a novel link of synergistic control of the state of tyrosine phosphorylation by both P2Y receptors. By SH2 domain pull down and MS/MS analysis, we identified distinct tyrosine phosphorylation sites in cell adhesion molecules, intracellular adapter proteins and phosphatases suggesting a major, functional role of tyrosine phosphorylation of theses candidate proteins in ADP-dependent signaling in human platelets. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Homotopic Chain Maps Have Equal s-Homology and d-Homology

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M. Z. Kazemi-Baneh

2016-01-01

Full Text Available The homotopy of chain maps on preabelian categories is investigated and the equality of standard homologies and d-homologies of homotopic chain maps is established. As a special case, if X and Y are the same homotopy type, then their nth d-homology R-modules are isomorphic, and if X is a contractible space, then its nth d-homology R-modules for n≠0 are trivial.

3' Phosphatase activity toward phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2] by voltage-sensing phosphatase (VSP).

Science.gov (United States)

Kurokawa, Tatsuki; Takasuga, Shunsuke; Sakata, Souhei; Yamaguchi, Shinji; Horie, Shigeo; Homma, Koichi J; Sasaki, Takehiko; Okamura, Yasushi

2012-06-19

Voltage-sensing phosphatases (VSPs) consist of a voltage-sensor domain and a cytoplasmic region with remarkable sequence similarity to phosphatase and tensin homolog deleted on chromosome 10 (PTEN), a tumor suppressor phosphatase. VSPs dephosphorylate the 5' position of the inositol ring of both phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P(3)] and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P(2)] upon voltage depolarization. However, it is unclear whether VSPs also have 3' phosphatase activity. To gain insights into this question, we performed in vitro assays of phosphatase activities of Ciona intestinalis VSP (Ci-VSP) and transmembrane phosphatase with tensin homology (TPTE) and PTEN homologous inositol lipid phosphatase (TPIP; one human ortholog of VSP) with radiolabeled PI(3,4,5)P(3). TLC assay showed that the 3' phosphate of PI(3,4,5)P(3) was not dephosphorylated, whereas that of phosphatidylinositol 3,4-bisphosphate [PI(3,4)P(2)] was removed by VSPs. Monitoring of PI(3,4)P(2) levels with the pleckstrin homology (PH) domain from tandem PH domain-containing protein (TAPP1) fused with GFP (PH(TAPP1)-GFP) by confocal microscopy in amphibian oocytes showed an increase of fluorescence intensity during depolarization to 0 mV, consistent with 5' phosphatase activity of VSP toward PI(3,4,5)P(3). However, depolarization to 60 mV showed a transient increase of GFP fluorescence followed by a decrease, indicating that, after PI(3,4,5)P(3) is dephosphorylated at the 5' position, PI(3,4)P(2) is then dephosphorylated at the 3' position. These results suggest that substrate specificity of the VSP changes with membrane potential.

Ventilator-associated pneumonia in patients assisted by veno-arterial extracorporeal membrane oxygenation support: Epidemiology and risk factors of treatment failure.

Science.gov (United States)

Bouglé, Adrien; Bombled, Camille; Margetis, Dimitri; Lebreton, Guillaume; Vidal, Charles; Coroir, Marine; Hajage, David; Amour, Julien

2018-01-01

Ventilator-associated pneumonia (VAP) is frequent in Intensive Care Unit (ICU) patients. In the specific case of patients treated with Veno-Arterial Extracorporeal Membrane Oxygenation Support (VA-ECMO), VAP treatment failures (VAP-TF) have been incompletely investigated. To investigate the risk factors of treatment failure (VAP-TF) in a large cohort of ICU patients treated with VA-ECMO, we conducted a retrospective study in a Surgical ICU about patients assisted with VA-ECMO between January 1, 2013, and December 31, 2014. Diagnosis of VAP was confirmed by a positive quantitative culture of a respiratory sample. VAP-TF was defined as composite of death attributable to pneumonia and relapse within 28 days of the first episode. In total, 152 patients underwent ECMO support for > 48h. During the VA-ECMO support, 85 (55.9%) patients developed a VAP, for a rate of 60.6 per 1000 ECMO days. The main pathogens identified were Pseudomonas aeruginosa and Enterobacteriaceae. VAP-TF occurred in 37.2% of patients and was associated with an increased 28-day mortality (Hazard Ratio 3.05 [1.66; 5.63], P<0.001), and VA-ECMO assistance duration (HR 1.47 [1.05-2.05], P = 0.025). Risk factors for VAP-TF were renal replacement therapy (HR 13.05 [1.73; 98.56], P = 0.013) and documentation of Pseudomonas aeruginosa (HR 2.36 [1.04; 5.35], P = 0.04). VAP in patients treated with VA-ECMO is associated with an increased morbidity and mortality. RRT and infection by Pseudomonas aeruginosa appear as strong risks factors of treatment failure. Further studies seem necessary to precise the best antibiotic management in these patients.

Backup Expression of the PhaP2 Phasin Compensates for phaP1 Deletion in Herbaspirillum seropedicae, Maintaining Fitness and PHB Accumulation.

Science.gov (United States)

Alves, Luis P S; Teixeira, Cícero S; Tirapelle, Evandro F; Donatti, Lucélia; Tadra-Sfeir, Michelle Z; Steffens, Maria B R; de Souza, Emanuel M; de Oliveira Pedrosa, Fabio; Chubatsu, Leda S; Müller-Santos, Marcelo

2016-01-01

Phasins are important proteins controlling poly-3-hydroxybutyrate (PHB) granules formation, their number into the cell and stability. The genome sequencing of the endophytic and diazotrophic bacterium Herbaspirillum seropedicae SmR1 revealed two homologous phasin genes. To verify the role of the phasins on PHB accumulation in the parental strain H. seropedicae SmR1, isogenic strains defective in the expression of phaP1, phaP2 or both genes were obtained by gene deletion and characterized in this work. Despite of the high sequence similarity between PhaP1 and PhaP2, PhaP1 is the major phasin in H. seropedicae, since its deletion reduced PHB accumulation by ≈50% in comparison to the parental and ΔphaP2. Upon deletion of phaP1, the expression of phaP2 was sixfold enhanced in the ΔphaP1 strain. The responsive backup expression of phaP2 partially rescued the ΔphaP1 mutant, maintaining about 50% of the parental PHB level. The double mutant ΔphaP1.2 did not accumulate PHB in any growth stage and showed a severe reduction of growth when glucose was the carbon source, a clear demonstration of negative impact in the fitness. The co-occurrence of phaP1 and phaP2 homologous in bacteria relatives of H. seropedicae, including other endophytes, indicates that the mechanism of phasin compensation by phaP2 expression may be operating in other organisms, showing that PHB metabolism is a key factor to adaptation and efficiency of endophytic bacteria.

Estimating Composite Curve Number Using an Improved SCS-CN Method with Remotely Sensed Variables in Guangzhou, China

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Qihao Weng

2013-03-01

Full Text Available The rainfall and runoff relationship becomes an intriguing issue as urbanization continues to evolve worldwide. In this paper, we developed a simulation model based on the soil conservation service curve number (SCS-CN method to analyze the rainfall-runoff relationship in Guangzhou, a rapid growing metropolitan area in southern China. The SCS-CN method was initially developed by the Natural Resources Conservation Service (NRCS of the United States Department of Agriculture (USDA, and is one of the most enduring methods for estimating direct runoff volume in ungauged catchments. In this model, the curve number (CN is a key variable which is usually obtained by the look-up table of TR-55. Due to the limitations of TR-55 in characterizing complex urban environments and in classifying land use/cover types, the SCS-CN model cannot provide more detailed runoff information. Thus, this paper develops a method to calculate CN by using remote sensing variables, including vegetation, impervious surface, and soil (V-I-S. The specific objectives of this paper are: (1 To extract the V-I-S fraction images using Linear Spectral Mixture Analysis; (2 To obtain composite CN by incorporating vegetation types, soil types, and V-I-S fraction images; and (3 To simulate direct runoff under the scenarios with precipitation of 57mm (occurred once every five years by average and 81mm (occurred once every ten years. Our experiment shows that the proposed method is easy to use and can derive composite CN effectively.

Srs2 and Mus81-Mms4 Prevent Accumulation of Toxic Inter-Homolog Recombination Intermediates.

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Kenji Keyamura

2016-07-01

Full Text Available Homologous recombination is an evolutionally conserved mechanism that promotes genome stability through the faithful repair of double-strand breaks and single-strand gaps in DNA, and the recovery of stalled or collapsed replication forks. Saccharomyces cerevisiae ATP-dependent DNA helicase Srs2 (a member of the highly conserved UvrD family of helicases has multiple roles in regulating homologous recombination. A mutation (srs2K41A resulting in a helicase-dead mutant of Srs2 was found to be lethal in diploid, but not in haploid, cells. In diploid cells, Srs2K41A caused the accumulation of inter-homolog joint molecule intermediates, increased the levels of spontaneous Rad52 foci, and induced gross chromosomal rearrangements. Srs2K41A lethality and accumulation of joint molecules were suppressed by inactivating Rad51 or deleting the Rad51-interaction domain of Srs2, whereas phosphorylation and sumoylation of Srs2 and its interaction with sumoylated proliferating cell nuclear antigen (PCNA were not required for lethality. The structure-specific complex of crossover junction endonucleases Mus81 and Mms4 was also required for viability of diploid, but not haploid, SRS2 deletion mutants (srs2Δ, and diploid srs2Δ mus81Δ mutants accumulated joint molecule intermediates. Our data suggest that Srs2 and Mus81-Mms4 have critical roles in preventing the formation of (or in resolving toxic inter-homolog joint molecules, which could otherwise interfere with chromosome segregation and lead to genetic instability.

Deregulated expression of E2F family members induces S-phase entry and overcomes p16INK4A-mediated growth suppression

DEFF Research Database (Denmark)

Lukas, J; Petersen, B O; Holm, K

1996-01-01

The E2F family of transcription factors regulate genes, whose products are essential for progression through the mammalian cell cycle. The transcriptional activity of the E2Fs is inhibited through the specific binding of the retinoblastoma protein, pRB, and the pRB homologs p107 and p130 to their......The E2F family of transcription factors regulate genes, whose products are essential for progression through the mammalian cell cycle. The transcriptional activity of the E2Fs is inhibited through the specific binding of the retinoblastoma protein, pRB, and the pRB homologs p107 and p130...

Trial of using antibodies as carriers of alkylating agents. Pt. 2. Evaluation of ability to form /sup 32/P-cyclophosphamide + immune antibody complexes with homologous antigen

Energy Technology Data Exchange (ETDEWEB)

Trzeciak, J; Felus, E; Nolewajka, E; Szaflarski, J; Dudziak, Z [Slaska Akademia Medyczna, Katowice (Poland)

1976-01-01

/sup 32/P-cyclophosphamide was found to combine with ..gamma..-globulin fractions of immune sera. Immune sera incubated with /sup 32/P-cyclophosphamide retained ability to react specifically with homologou antigen in vitro in the system: MN antigens of human erythrocytes + rabbit anti-MN antibody, and probably reacted selectively with target antigens in vivo in the system: antigens of guinea pig kidney tissue + rabbit antibodies against these antigens. Hemagglutination, passive hemagglutination and precipitation in agar gel tests were used in the experiments. Ability to combine of the immune antibody + /sup 32/P-cyclophosphamide complex with homologous antigens was evaluated by measurements of radioactivity of studied materials (erythrocyte agglutinates and organ homogenates). The results indicate feasibility of using immune antibodies as carriers of cytostatic agents.

Reply to comment by Fred L. Ogden et al. on "Beyond the SCS-CN method: A theoretical framework for spatially lumped rainfall-runoff response"

Science.gov (United States)

Bartlett, M. S.; Parolari, A. J.; McDonnell, J. J.; Porporato, A.

2017-07-01

Though Ogden et al. list several shortcomings of the original SCS-CN method, fit for purpose is a key consideration in hydrological modelling, as shown by the adoption of SCS-CN method in many design standards. The theoretical framework of Bartlett et al. [2016a] reveals a family of semidistributed models, of which the SCS-CN method is just one member. Other members include event-based versions of the Variable Infiltration Capacity (VIC) model and TOPMODEL. This general model allows us to move beyond the limitations of the original SCS-CN method under different rainfall-runoff mechanisms and distributions for soil and rainfall variability. Future research should link this general model approach to different hydrogeographic settings, in line with the call for action proposed by Ogden et al.

Xylanase production from Thermomyces lanuginosus VAPS-24 using low cost agro-industrial residues via hybrid optimization tools and its potential use for saccharification.

Science.gov (United States)

Kumar, Vishal; Chhabra, Deepak; Shukla, Pratyoosh

2017-11-01

The xylanase production from Thermomyces lanuginosus VAPS-24 has been optimized using OFAT (One factor at a time) approach using agro-industrial substrates. Further, central composite design (CCD) has been employed to optimize various process parameters such as temperature (45-55°C), carbon source concentration (1.5-2.5%), fermentation time (72-120h) and production medium pH (6-8). Maximum xylanase yield after RSM optimization was approximately double (119.91±2.53UmL -1 ) than un-optimized conditions (61.09±0.91UmL -1 ). Several hybrid statistical tools such as Genetic Algorithm-Response Surface Methodology (GA-RSM), Artificial Neural Network (ANN), Genetic Algorithm-Artificial Neural Network (GA-ANN) were employed to obtain more optimized process parameters to maximize the xylanase production and observed an increase of 10.50% xylanase production (132.51±3.27UmL -1 ) as compared to RSM response (119.91±2.53UmL -1 ). The various pretreated and untreated agricultural residues were subjected to saccharification by using crude xylanase in which the pretreated rice straw yielded maximum fermentable sugars 126.89mgg -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

Tumour suppressor protein p53 regulates the stress activated bilirubin oxidase cytochrome P450 2A6

Energy Technology Data Exchange (ETDEWEB)

Hu, Hao, E-mail: hao.hu1@uqconnect.edu.au [The University of Queensland, National Research Centre for Environmental Toxicology (Entox), 4072 Brisbane, Queensland (Australia); Yu, Ting, E-mail: t.yu2@uq.edu.au [The University of Queensland, National Research Centre for Environmental Toxicology (Entox), 4072 Brisbane, Queensland (Australia); Arpiainen, Satu, E-mail: Satu.Juhila@orion.fi [Institute of Biomedicine, Department of Pharmacology and Toxicology and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu (Finland); Lang, Matti A., E-mail: m.lang@uq.edu.au [The University of Queensland, National Research Centre for Environmental Toxicology (Entox), 4072 Brisbane, Queensland (Australia); Hakkola, Jukka, E-mail: Jukka.hakkola@oulu.fi [Institute of Biomedicine, Department of Pharmacology and Toxicology and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu (Finland); Abu-Bakar, A' edah, E-mail: a.abubakar@uq.edu.au [The University of Queensland, National Research Centre for Environmental Toxicology (Entox), 4072 Brisbane, Queensland (Australia)

2015-11-15

Human cytochrome P450 (CYP) 2A6 enzyme has been proposed to play a role in cellular defence against chemical-induced oxidative stress. The encoding gene is regulated by various stress activated transcription factors. This paper demonstrates that p53 is a novel transcriptional regulator of the gene. Sequence analysis of the CYP2A6 promoter revealed six putative p53 binding sites in a 3 kb proximate promoter region. The site closest to transcription start site (TSS) is highly homologous with the p53 consensus sequence. Transfection with various stepwise deletions of CYP2A6-5′-Luc constructs – down to − 160 bp from the TSS – showed p53 responsiveness in p53 overexpressed C3A cells. However, a further deletion from − 160 to − 74 bp, including the putative p53 binding site, totally abolished the p53 responsiveness. Electrophoretic mobility shift assay with a probe containing the putative binding site showed specific binding of p53. A point mutation at the binding site abolished both the binding and responsiveness of the recombinant gene to p53. Up-regulation of the endogenous p53 with benzo[α]pyrene – a well-known p53 activator – increased the expression of the p53 responsive positive control and the CYP2A6-5′-Luc construct containing the intact p53 binding site but not the mutated CYP2A6-5′-Luc construct. Finally, inducibility of the native CYP2A6 gene by benzo[α]pyrene was demonstrated by dose-dependent increases in CYP2A6 mRNA and protein levels along with increased p53 levels in the nucleus. Collectively, the results indicate that p53 protein is a regulator of the CYP2A6 gene in C3A cells and further support the putative cytoprotective role of CYP2A6. - Highlights: • CYP2A6 is an immediate target gene of p53. • Six putative p53REs located on 3 kb proximate CYP2A6 promoter region. • The region − 160 bp from TSS is highly homologous with the p53 consensus sequence. • P53 specifically bind to the p53RE on the − 160 bp region. • HNF4�

Sequence homolog-based molecular engineering for shifting the enzymatic pH optimum

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Fuqiang Ma

2016-09-01

Full Text Available Cell-free synthetic biology system organizes multiple enzymes (parts from different sources to implement unnatural catalytic functions. Highly adaption between the catalytic parts is crucial for building up efficient artificial biosynthetic systems. Protein engineering is a powerful technology to tailor various enzymatic properties including catalytic efficiency, substrate specificity, temperature adaptation and even achieve new catalytic functions. However, altering enzymatic pH optimum still remains a challenging task. In this study, we proposed a novel sequence homolog-based protein engineering strategy for shifting the enzymatic pH optimum based on statistical analyses of sequence-function relationship data of enzyme family. By two statistical procedures, artificial neural networks (ANNs and least absolute shrinkage and selection operator (Lasso, five amino acids in GH11 xylanase family were identified to be related to the evolution of enzymatic pH optimum. Site-directed mutagenesis of a thermophilic xylanase from Caldicellulosiruptor bescii revealed that four out of five mutations could alter the enzymatic pH optima toward acidic condition without compromising the catalytic activity and thermostability. Combination of the positive mutants resulted in the best mutant M31 that decreased its pH optimum for 1.5 units and showed increased catalytic activity at pH < 5.0 compared to the wild-type enzyme. Structure analysis revealed that all the mutations are distant from the active center, which may be difficult to be identified by conventional rational design strategy. Interestingly, the four mutation sites are clustered at a certain region of the enzyme, suggesting a potential “hot zone” for regulating the pH optima of xylanases. This study provides an efficient method of modulating enzymatic pH optima based on statistical sequence analyses, which can facilitate the design and optimization of suitable catalytic parts for the construction

Gastropulmonary Route of Infection and the Prevalence of Microaspiration in the Elderly Patients with Ventilator-Associated Pneumonia Verified by Molecular Microbiology-GM-PFGE.

Science.gov (United States)

Liu, Qing-hua; Zhang, Jing; Lin, Dian-jie; Mou, Xiao-yan; He, Li-xian; Qu, Jie-ming; Li, Hua-yin; Hu, Bi-jie; Zhu, Ying-min; Zhu, Du-ming; Gao, Xiao-dong

2015-04-01

Gastropulmonary route of infection was considered to be an important mechanism of ventilator-associated pneumonia (VAP). However there is little evidence to support this assumption. Moreover, the prevalence of microaspiration in elderly ventilated patients was not well understood. To confirm gastropulmonary infection route and investigate the prevalence of microaspiration in elderly ventilated patients using genome macrorestriction-pulsed field gel electrophoresis (GM-PFGE). Patients over 60 years old, expected to receive mechanical ventilation longer than 48 h, were prospectively enrolled from October 2009 to January 2012. Clinical data were collected and recorded until they died, developed pneumonia, or were extubated. Samples from gastric fluid, subglottic secretion and lower respiratory tract (LRT) were collected during the follow-up for microbiological examination. To evaluate the homogeneity, GM-PFGE was performed on strains responsible for VAP that had the same biochemical phenotype as those isolated from gastric juice and subglottic secretions sequentially. Among 44 VAP patients, 76 strains were isolated from LRT and considered responsible for VAP. Twenty-two isolates had the same biochemical phenotype with the corresponding gastric isolates. The homology was further confirmed using GM-PFGE in 12 episodes of VAP. Nearly 30% of VAPs were caused by microaspiration based on the analysis of bacterial phenotype or GM-PFGE. In addition, 58.3% patients with gastric colonization developed VAP, especially late-onset VAP (LOP). Gastropulmonary infection route exists in VAP especially LOP in elderly ventilated patients. It is one of the important mechanisms in the development of VAP.

Backup expression of the PhaP2 phasin compensates for phaP1 deletion in Herbaspirillum seropedicae, maintaining fitness and PHB accumulation

Directory of Open Access Journals (Sweden)

Luis Paulo Silveira Alves

2016-05-01

Full Text Available Phasins are important proteins controlling PHB granules formation, their number into the cell and stability. The genome sequencing of the endophytic and diazotrophic bacterium Herbaspirillum seropedicae SmR1 revealed two homologous phasin genes. To verify the role of the phasins on PHB accumulation in the parental strain H. seropedicae SmR1, isogenic strains defective in the expression of phaP1, phaP2 or both genes were obtained by gene deletion and characterized in this work. Despite of the high sequence similarity between PhaP1 and PhaP2, PhaP1 is the major phasin in H. seropedicae, since its deletion reduced PHB accumulation by ≈ 50 % in comparison to the parental and ΔphaP2. Upon deletion of phaP1, the expression of phaP2 was 6-fold enhanced in the ΔphaP1 strain. The responsive backup expression of phaP2 partially rescued the ΔphaP1 mutant, maintaining about 50% of the parental PHB level. The double mutant ΔphaP1.2 did not accumulate PHB in any growth stage and showed a severe reduction of growth when glucose was the carbon source, a clear demonstration of negative impact in the fitness. The co-occurrence of phaP1 and phaP2 homologous in bacteria relatives of H. seropedicae, including other endophytes, indicates that the mechanism of phasin compensation by phaP2 expression may be operating in other organisms, showing that PHB metabolism is a key factor to adaptation and efficiency of endophytic bacteria.

The analysis of SCS return momentum effects on the RCS water level during mid-loop operations

Energy Technology Data Exchange (ETDEWEB)

swang Seo, J.; Young Yang, J.; Tack Hwang, S. [Seoul National Univ. (Korea, Republic of)

1995-09-01

An accurate prediction of Reactor Coolant System (RCS) water levels is of importance in the determination of allowable operating range to ensure the safety during the mid-loop operations. However, complex hydraulic phenomena induced by Shutdown Cooling System (SCS) return momentum cause different water levels from those in the loop where the water level indicators are located. This was apparantly observed at the pre-core cold hydro test of the Younggwang Nuclear Unit 3 (YGN 3) in Korea. In this study, in order to analytically understand the effect of the SCS return momentum on the RCS water level and its general trend, a model using one-dimensional momentum equation, hydraulic jump, Bernoulli equation, flow resistance coefficient, and total water volume conservation has been developed to predict the RCS water levels at various RCS locations during the mid-loop conditions and the simulation results were compared with the test data. The analysis shows that the hydraulic jump in the operating cold legs in conjunction with the momentum loss throughout the RCS is the main cause creating the water level differences at various RCS locations. The prediction results provide good explanations for the test data and show the significant effect of the SCS return momentum on the RCS water levels.

The analysis of SCS return momentum effects on the RCS water level during mid-loop operations

International Nuclear Information System (INIS)

swang Seo, J.; Young Yang, J.; Tack Hwang, S.

1995-01-01

An accurate prediction of Reactor Coolant System (RCS) water levels is of importance in the determination of allowable operating range to ensure the safety during the mid-loop operations. However, complex hydraulic phenomena induced by Shutdown Cooling System (SCS) return momentum cause different water levels from those in the loop where the water level indicators are located. This was apparantly observed at the pre-core cold hydro test of the Younggwang Nuclear Unit 3 (YGN 3) in Korea. In this study, in order to analytically understand the effect of the SCS return momentum on the RCS water level and its general trend, a model using one-dimensional momentum equation, hydraulic jump, Bernoulli equation, flow resistance coefficient, and total water volume conservation has been developed to predict the RCS water levels at various RCS locations during the mid-loop conditions and the simulation results were compared with the test data. The analysis shows that the hydraulic jump in the operating cold legs in conjunction with the momentum loss throughout the RCS is the main cause creating the water level differences at various RCS locations. The prediction results provide good explanations for the test data and show the significant effect of the SCS return momentum on the RCS water levels

Mammalian Sir2 homolog SIRT3 regulates global mitochondrial lysine acetylation

DEFF Research Database (Denmark)

Lombard, David B; Alt, Frederick W; Cheng, Hwei-Ling

2007-01-01

Homologs of the Saccharomyces cerevisiae Sir2 protein, sirtuins, promote longevity in many organisms. Studies of the sirtuin SIRT3 have so far been limited to cell culture systems. Here, we investigate the localization and function of SIRT3 in vivo. We show that endogenous mouse SIRT3 is a solubl...

Striking similarity in the gene expression levels of individual Myc module members among ESCs, EpiSCs, and partial iPSCs.

Directory of Open Access Journals (Sweden)

Masataka Hirasaki

Full Text Available Predominant transcriptional subnetworks called Core, Myc, and PRC modules have been shown to participate in preservation of the pluripotency and self-renewality of embryonic stem cells (ESCs. Epiblast stem cells (EpiSCs are another cell type that possesses pluripotency and self-renewality. However, the roles of these modules in EpiSCs have not been systematically examined to date. Here, we compared the average expression levels of Core, Myc, and PRC module genes between ESCs and EpiSCs. EpiSCs showed substantially higher and lower expression levels of PRC and Core module genes, respectively, compared with those in ESCs, while Myc module members showed almost equivalent levels of average gene expression. Subsequent analyses revealed that the similarity in gene expression levels of the Myc module between these two cell types was not just overall, but striking similarities were evident even when comparing the expression of individual genes. We also observed equivalent levels of similarity in the expression of individual Myc module genes between induced pluripotent stem cells (iPSCs and partial iPSCs that are an unwanted byproduct generated during iPSC induction. Moreover, our data demonstrate that partial iPSCs depend on a high level of c-Myc expression for their self-renewal properties.

Self-Compassion Scale (SCS): Psychometric Properties of The French Translation and Its Relations with Psychological Well-Being, Affect and Depression.

Science.gov (United States)

Kotsou, Ilios; Leys, Christophe

2016-01-01

Over the past few years, the topic of self-compassion has attracted increasing attention from both scientific and clinical fields. The Self-Compassion Scale (SCS) was created to specifically capture this way of being kind and understanding towards oneself in moments of turmoil. In this article, we present a French adaptation of the SCS. We first explore the psychometric properties of this adaptation and then investigate its relation to psychological well-being. As in the original version of the SCS, the French adaptation has a strong 6-factor structure but a weaker hierarchical second order structure. However the bi-factor model yields a good omega index suggesting the relevance of a single score accounting for self-compassion. Moreover, there was a relation between the SCS and classical outcomes such as a positive relation with psychological well-being and negative relation with depressive symptoms. We then hypothesized that self-compassion would have a moderating role on the relation between affect and depression. This hypothesis was confirmed: expressing negative affect is correlated with depressive symptoms; however, being kind with oneself lowers depressive symptoms even when expressing negative affect. In conclusion, this research presents a valid self-compassion measure for French-speaking researchers and clinicians and outlines the need for further research on the concept of self-compassion.

[Comparision of risk factors and pathogens in patients with early- and late-onset ventilator-associated pneumonia in intensive care unit].

Science.gov (United States)

Liang, Y J; Li, Z L; Wang, L; Liu, B Y; Ding, R Y; Ma, X C

2017-10-01

Objective: To compare risk factors and bacterial etiology in patients with early-onset versus late-onset ventilator-associated pneumonia (VAP) in intensive care unit (ICU). Methods: This prospective cohort study enrolled mechanically ventilated patients hospitalized for more than 48 hours in the first affiliated hospital, China Medical University from Jan 2012 to Jun 2016. Subjects were classified by ventilator status: early-onset VAP (VAP) or late-onset VAP (≥ 5 d ventilation, L-VAP). Potential risk factors and pathogen were evaluated. Results: A total of 4 179 patients in adult ICU were screened, 3 989 (95.5%) of whom were mechanically ventilated, 962 patients with mechanical ventilation time ≥ 48 h. VAP developed in 142 patients. E-VAP and L-VAP had different potential risk factors based on statistical analysis.Independent risk factors for E-VAP included male ( OR =1.825, 95% CI 1.006-3.310), chronic obstructive pulmonary disease (COPD; OR =3.746, 95% CI 1.795-7.818), emergency intubation ( OR =1.932, 95% CI 1.139-3.276), aspiration ( OR =3.324, 95% CI 1.359-8.130). Whereas independent risk factors for L-VAP were coma ( OR =2.335, 95% CI 1.300-4.194), renal dysfunction ( OR =0.524, 95% CI 0.290-0.947), emergency intubation ( OR =2.184, 95% CI 1.334-3.574). Mortality in E-VAP and L-VAP group were both higher than the non-VAP group[30.2%(19/63)vs 19.8%(162/820), P =0.044; 29.1%(23/79) vs 19.8%(162/820), P =0.046]. The pathogens isolated from early-onset versus late-onset VAP were not significantly different between groups, which the most common ones were acinetobacter baumannii, pseudomonas aeruginosa and klebsiella pneumoniae. Conclusion: E-VAP and L-VAP have different risk factors, however related pathogens are similar. Different specific preventive strategies are suggested based on different onset of VAP.

Aging of mice is associated with p16(Ink4a)- and β-galactosidase-positive macrophage accumulation that can be induced in young mice by senescent cells.

Science.gov (United States)

Hall, Brandon M; Balan, Vitaly; Gleiberman, Anatoli S; Strom, Evguenia; Krasnov, Peter; Virtuoso, Lauren P; Rydkina, Elena; Vujcic, Slavoljub; Balan, Karina; Gitlin, Ilya; Leonova, Katerina; Polinsky, Alexander; Chernova, Olga B; Gudkov, Andrei V

2016-07-01

Senescent cells (SCs) have been considered a source of age-related chronic sterile systemic inflammation and a target for anti-aging therapies. To understand mechanisms controlling the amount of SCs, we analyzed the phenomenon of rapid clearance of human senescent fibroblasts implanted into SCID mice, which can be overcome when SCs were embedded into alginate beads preventing them from immunocyte attack. To identify putative SC killers, we analyzed the content of cell populations in lavage and capsules formed around the SC-containing beads. One of the major cell types attracted by secretory factors of SCs was a subpopulation of macrophages characterized by p16(Ink4a) gene expression and β-galactosidase activity at pH6.0 (β-gal(pH6)), thus resembling SCs. Consistently, mice with p16(Ink4a) promoter-driven luciferase, developed bright luminescence of their peritoneal cavity within two weeks following implantation of SCs embedded in alginate beads. p16(Ink4a)/β-gal(pH6)-expressing cells had surface biomarkers of macrophages F4/80 and were sensitive to liposomal clodronate used for the selective killing of cells capable of phagocytosis. At the same time, clodronate failed to kill bona fide SCs generated in vitro by genotoxic stress. Old mice with elevated proportion of p16(Ink4a)/β-gal(pH6)-positive cells in their tissues demonstrated reduction of both following systemic clodronate treatment, indicating that a significant proportion of cells previously considered to be SCs are actually a subclass of macrophages. These observations point at a significant role of p16(Ink4a)/β-gal(pH6)-positive macrophages in aging, which previously was attributed solely to SCs. They require re-interpretation of the mechanisms underlying rejuvenating effects following eradication of p16(Ink4a)/β-gal(pH6)-positive cells and reconsideration of potential cellular target for anti-aging treatment.

Successful prevention of ventilator-associated pneumonia in an intensive care setting.

Science.gov (United States)

Marra, Alexandre R; Cal, Ruy Guilherme Rodrigues; Silva, Cláudia Vallone; Caserta, Raquel Afonso; Paes, Angela Tavares; Moura, Denis Faria; dos Santos, Oscar Fernando Pavão; Edmond, Michael B; Durão, Marcelino Souza

2009-10-01

Ventilator-associated pneumonia (VAP) is one of the most common health care-associated infections (HAIs) in critical care settings. Our objective was to examine the effect of a series of interventions, implemented in 3 different periods to reduce the incidence of VAP in an intensive care unit (ICU). A quasiexperimental study was conducted in a medical-surgical ICU. Multiple interventions to optimize VAP prevention were performed during different phases. From March 2001 to December 2002 (phase 1: P1), some Centers for Disease Control and Prevention (CDC) evidence-based practices were implemented. From January 2003 to December 2006 (P2), we intervened in these processes at the same time that performance monitoring was occurring at the bedside, and, from January 2007 to September 2008 (P3), we continued P2 interventions and implemented the Institute for Healthcare Improvement's ventilator bundle plus oral decontamination with chlorhexidine and continuous aspiration of subglottic secretions. The incidence density of VAP in the ICU per 1000 patient-days was 16.4 in phase 1, 15.0 in phase 2, and 10.4 in phase 3, P=.05. Getting to zero VAP was possible only in P3 when compliance with all interventions exceeded 95%. These results suggest that reducing VAP rates to zero is a complex process that involves multiple performance measures and interventions.

The ubiquitin-homology protein, DAP-1, associates with tumor necrosis factor receptor (p60) death domain and induces apoptosis.

Science.gov (United States)

Liou, M L; Liou, H C

1999-04-09

The tumor necrosis factor receptor, p60 (TNF-R1), transduces death signals via the association of its cytoplasmic domain with several intracellular proteins. By screening a mammalian cDNA library using the yeast two-hybrid cloning technique, we isolated a ubiquitin-homology protein, DAP-1, which specifically interacts with the cytoplasmic death domain of TNF-R1. Sequence analysis reveals that DAP-1 shares striking sequence homology with the yeast SMT3 protein that is essential for the maintenance of chromosome integrity during mitosis (Meluh, P. B., and Koshland, D. (1995) Mol. Biol. Cell 6, 793-807). DAP-1 is nearly identical to PIC1, a protein that interacts with the PML tumor suppressor implicated in acute promyelocytic leukemia (Boddy, M. N., Howe, K., Etkin, L. D., Solomon, E., and Freemont, P. S. (1996) Oncogene 13, 971-982), and the sentrin protein, which associates with the Fas death receptor (Okura, T., Gong, L., Kamitani, T., Wada, T., Okura, I., Wei, C. F., Chang, H. M., and Yeh, E. T. (1996) J. Immunol. 157, 4277-4281). The in vivo interaction between DAP-1 and TNF-R1 was further confirmed in mammalian cells. In transient transfection assays, overexpression of DAP-1 suppresses NF-kappaB/Rel activity in 293T cells, a human kidney embryonic carcinoma cell line. Overexpression of either DAP-1 or sentrin causes apoptosis of TNF-sensitive L929 fibroblast cell line, as well as TNF-resistant osteosarcoma cell line, U2OS. Furthermore, the dominant negative Fas-associated death domain protein (FADD) protein blocks the cell death induced by either DAP-1 or FADD. Collectively, these observations highly suggest a role for DAP-1 in mediating TNF-induced cell death signaling pathways, presumably through the recruitment of FADD death effector.

[Preparation of monoclonal antibody against 4-amylphenol and homology modeling of its Fv fragment].

Science.gov (United States)

Cheng, Lei; Wu, Haizhen; Fei, Jing; Zhang, Lujia; Ye, Jiang; Zhang, Huizhan

2017-03-01

Objective To prepare and characterize a monoclonal antibody (mAb) against 4-amylphenol (4-AP), clone its cDNA sequence and make homology modeling for its Fv fragment. Methods A high-affinity anti-4-AP mAb was generated from a hybridoma cell line F10 using electrofusion between splenocytes from APA-BSA-immunized mouse and Sp2/0 myeloma cells. Then we extracted the mRNA of F10 cells and cloned the cDNA of mAb. The homology modeling and molecular docking of its Fv fragment was conducted with biological software. Results Under the optimum conditions, the ic-ELISA equation was y=A 2 +(A 1 -A 2 )/(1+(x/x 0 ) p ) (A 1 =1.28; A 2 =-0.066; x 0 =12560.75; p=0.74) with a correlation coefficient (R 2 ) of 0.997. The lowest detectable limit was 0.65 μg/mL. The heavy and light chains of mAb respectively belonged to IgG1 and Kappa. The homology modeling and molecular docking studies revealed that the binding of 4-Ap and mAb was attributed to the hydrogen bond and hydrophobic interactions. Conclusion The study successfully established a stable 4-AP mAb-secreting hybridoma cell line. The study on spatial structure of Fv fragment using homology modeling provided a reference for the development and design of single chain variable fragments.

Use of VAP3D software for production and manipulation of synthetic radiographies of anthropomorphic models

Energy Technology Data Exchange (ETDEWEB)

Lima, Lindeval Fernandes de, E-mail: lindeval@dmat.ufrr.b [Universidade Federal de Roraima (DMAT/UFRR), Boa Vista, RR (Brazil). Dept. de Matematica; Centro Regional de Ciencias Nucleares (CRCN-NE/CNEN-PE), Recife, PE (Brazil); Vieira, Jose W. [Instituto Federal de Educacao, Ciencia e Tecnologia de Pernambuco (IFPE), Recife, PE (Brazil); Universidade de Pernambuco (EPP/UPE), Recife, PE (Brazil). Escola Politecnica de Pernambuco; Lima, Fernando R.A., E-mail: falima@cnen.gov.b [Centro Regional de Ciencias Nucleares (CRCN-NE/CNEN-PE), Recife, PE (Brazil); Leal Neto, Viriato [Universidade Federal de Pernambuco (DEN/UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear

2011-07-01

The Grupo de Dosimetria Numerica has developed exposure computational models (ECM) involving a Monte Carlo code and voxel phantoms to simulate various situations of internal and external exposure to ionizing radiation. Most analyses of the produced results are presented in tables and graphics formats. An alternative to this traditional way of analyzing results is to save voxels of Regions of Interest (ROI) of the phantom irradiated with information like the location of the voxel and the energy deposited in it during the simulation. Such information can be saved to a text file and later turned into 3D objects. In this paper the VAP3D software has been used to read text files produced in simulations using the ECM of DEN (Nuclear Energy Dept. - UFPE), converting them into binary files of the type RAW, and visualize them. In order to reflect the radiosensitivity of the organs and tissues suggested by ICRP-60, for conversion of text file to binary, of the energy deposited values are multiplied by the weighting factor of the tissue to which the voxel belongs. The result of the multiplication is normalized to the interval [0, 255]. The files transformed are referred herein as synthetic radiographies. In VAP3D software, it is possible to generate stacks from theses radiographies in transverse, sagittal and coronal directions. In order to illustrate the production of synthetic radiographies, some images are presented in this paper, and dosimetric results are obtained from a variety of ROIs of the phantoms of DEN for radiological exams. (author)

Actinomycin D synergistically enhances the cytotoxicity of CDDP on KB cells by activating P53 via decreasing P53-MDM2 complex.

Science.gov (United States)

Wang, Lin; Pang, Xiao-Cong; Yu, Zi-Ru; Yang, Sheng-Qian; Liu, Ai-Lin; Wang, Jin-Hua; Du, Guan-Hua

2017-06-01

The aim of this study is to investigate the synergism of low dose of actinomycin D (LDActD) to the cytotoxicity of cisplatin (CDDP) on KB cells. The role of P53 reactivation by LDActD in the synergism and its mechanism were further studied. Cell viability was determined by MTT assay. Apoptosis was determined by AnnexinV-FITC/PI staining. Mitochondrial membrane potential (MMP) was detected by JC-1 staining. Expression of proteins was detected by Western blotting (WB) and/or immunofluorescence (IF). Molecular docking of actinomycin D (ACTD) to Mouse double minute 2 homolog (MDM2) and Mouse double minute 2 homolog X (MDMX). MDMX was analyzed by Discovery Studio. The content of P53-MDM2 complex was detected by ELISA assay. The cytotoxicity of CDDP was increased by the combination of LDActD in kinds of cancer cells. Molecular docking showed strong interaction between ACTD and MDM2/MDMX. Meanwhile, LDActD significantly decreased P53-MDM2 complex. Significant increase of the apoptotic activity by the combination therapy in KB cells is P53 upregulated modulator of apoptosis (PUMA) dependent. In addition to the decrease in MMP, LDActD increased P53 regulated protein and decreased BCL-XL in KB cells. LDActD efficiently enhanced the cytotoxicity of CDDP in cancer cells and induced P53-PUMA-dependent and mitochondria-mediated apoptosis in KB cells. The reactivation of P53 was probably achieved by disturbing the interaction of P53 and MDM2/MDMX.

A cut-off in ocular chemesthesis from vapors of homologous alkylbenzenes and 2-ketones as revealed by concentration-detection functions

International Nuclear Information System (INIS)

Cometto-Muniz, J. Enrique; Abraham, Michael H.

2008-01-01

Studies of homologous series of environmental vapors have shown that their chemesthetic (i.e., sensory irritation) potency increases with carbon chain length (that is, their detection thresholds decrease) until they reach a homolog that fails to be detected, even at vapor saturation. All ensuing homologs cannot be detected either. In this investigation, we measured concentration-detection (i.e., psychometric) functions for ocular chemesthesis from homologous alkylbenzenes (pentyl, hexyl, and heptyl benzene) and 2-ketones (undecanone, dodecanone, and tridecanone). Using a three-alternative forced-choice procedure against air blanks, we tested a total of 18 to 24 subjects, about half of them females, average age 31 years, ranging from 18 to 56 years. Stimuli were generated and presented by a computer-controlled, vapor delivery device whose output was quantified by gas chromatography. Exposure time was 6 s and delivery flow 2.5 L/min. Within the context of present and previous findings, the outcome indicated that the functions for heptylbenzene and 2-tridecanone reached a plateau where further increases in concentration did not enhance detection. We conclude that: a) a cut-off point in ocular chemesthetic detection is reached along homologous alkylbenzenes and 2-ketones at the level of heptylbenzene and 2-tridecanone, respectively, and b) the observed effect rests on the homologs exceeding a critical molecular size (or dimension) rather than on them failing to achieve a high enough vapor concentration

Colored Kauffman homology and super-A-polynomials

International Nuclear Information System (INIS)

Nawata, Satoshi; Ramadevi, P.; Zodinmawia

2014-01-01

We study the structural properties of colored Kauffman homologies of knots. Quadruple-gradings play an essential role in revealing the differential structure of colored Kauffman homology. Using the differential structure, the Kauffman homologies carrying the symmetric tensor products of the vector representation for the trefoil and the figure-eight are determined. In addition, making use of relations from representation theory, we also obtain the HOMFLY homologies colored by rectangular Young tableaux with two rows for these knots. Furthermore, the notion of super-A-polynomials is extended in order to encompass two-parameter deformations of PSL(2,ℂ) character varieties

The impact of hospital-wide use of a tapered-cuff endotracheal tube on the incidence of ventilator-associated pneumonia.

Science.gov (United States)

Bowton, David L; Hite, R Duncan; Martin, R Shayn; Sherertz, Robert

2013-10-01

Aspiration of colonized oropharyngeal secretions is a major factor in the pathogenesis of ventilator-associated pneumonia (VAP). A tapered-cuff endotracheal tube (ETT) has been demonstrated to reduce aspiration around the cuff. Whether these properties are efficacious in reducing VAP is not known. This 2-period, investigator-initiated observational study was designed to assess the efficacy of a tapered-cuff ETT to reduce the VAP rate. All intubated, mechanically ventilated patients over the age of 18 were included. During the baseline period a standard, barrel-shaped-cuff ETT (Mallinckrodt Hi-Lo) was used. All ETTs throughout the hospital were then replaced with a tapered-cuff ETT (TaperGuard). The primary outcome variable was the incidence of VAP per 1,000 ventilator days. We included 2,849 subjects, encompassing 15,250 ventilator days. The mean ± SD monthly VAP rate was 3.29 ± 1.79/1,000 ventilator days in the standard-cuff group and 2.77 ± 2.00/1,000 ventilator days in the tapered-cuff group (P = .65). While adherence to the VAP prevention bundle was high throughout the study, bundle adherence was significantly higher during the standard-cuff period (96.5 ± 2.7%) than in the tapered-cuff period (90.3 ± 3.5%, P = .01). In the setting of a VAP rate very near the average of ICUs in the United States, and where there was high adherence to a VAP prevention bundle, the use of a tapered-cuff ETT was not associated with a reduction in the VAP rate.

Timing of intubation and ventilator-associated pneumonia following injury.

Science.gov (United States)

Evans, Heather L; Zonies, David H; Warner, Keir J; Bulger, Eileen M; Sharar, Sam R; Maier, Ronald V; Cuschieri, Joseph

2010-11-01

In an emergency medical system with established rapid-sequence intubation protocols, prehospital (PH) intubation of patients with trauma is not associated with a higher rate of ventilator-associated pneumonia (VAP) than emergency department (ED) intubation. Retrospective observational cohort. Level I trauma center. Adult patients with trauma intubated in a PH or an ED setting from July 1, 2007, through July 31, 2008. Diagnosis of VAP by means of bronchoscopic alveolar lavage or clinical assessment when bronchoscopic alveolar lavage was impossible. Secondary outcomes included time to VAP, length of hospitalization, and in-hospital mortality. Of 572 patients, 412 (72.0%) underwent PH intubation. The ED group was older than the PH group (mean ages, 46.4 vs 39.1 years; P VAP (30 [18.8%] vs 71 [17.2%]; P = .66) or mean time to diagnosis (8.1 [1.2] vs 7.8 [1.0] days; P = .89). Logistic regression analysis identified history of drug abuse, lowest recorded ED systolic blood pressure, and injury severity score as 3 independent factors predictive of VAP. Prehospital intubation of patients with trauma is not associated with higher risk of VAP. Further investigation of intubation factors and the incidence and timing of aspiration is required to identify potentially modifiable factors to prevent VAP.

Properties and local environment of p-type and photoluminescent rare earths implanted into ZnO single crystals

CERN Document Server

Rita, EMC; Wahl, U; Soares, JC

This thesis presents an experimental study of the local environment of p-type and Rare- Earth dopants implanted in ZnO single-crystals (SCs). Various nuclear and bulk property techniques were combined in the following evaluations: Implantation damage annealing was evaluated in ZnO SCs implanted with Fe, Sr and Ca. P-type dopants Cu and Ag implanted ZnO SCs were studied revealing that the solubility of Cu in substituting Zn is considerably higher than that of Ag. These results are discussed within the scope of the ZnO p-type doping problematic with these elements. Experimental proofs of the As “anti-site” behavior in ZnO were for the first time attained, i.e., the majority of As atoms are substitutional at the Zn site (SZn), possibly surrounded by two Zn vacancies (VZn). This reinforces the theoretical prediction that As acts as an acceptor in ZnO via the AsZn-2VZn complex formation. The co-doping of ZnO SC with In (donor) and As (acceptor) was addressed. The most striking result is the possible In-As “p...

Evolution of Src Homology 2 (SH2) Domain to Recognize Sulfotyrosine.

Science.gov (United States)

Ju, Tong; Niu, Wei; Guo, Jiantao

2016-09-16

Protein tyrosine O-sulfation is considered as the most common type of post-translational tyrosine modification in nature and plays important roles in extracellular biomolecular interactions. To facilitate the mapping, biological study, and medicinal application of this type of post-translational modification, we seek to evolve a small protein scaffold that recognizes sulfotyrosine with high affinity. We focused our efforts on the engineering of the Src Homology 2 (SH2) domain, which represents the largest class of known phosphotyrosine-recognition domain in nature and has a highly evolvable binding pocket. By using phage display, we successfully engineered the SH2 domain to recognize sulfotyrosine with high affinity. The best mutant, SH2-60.1, displayed more than 1700 fold higher sulfotyrosine-binding affinity than that of the wild-type SH2 domain. We also demonstrated that the evolved SH2 domain mutants could be used to detect sulfoprotein levels on the cell surface. These evolved SH2 domain mutants can be potentially applied to the study of protein tyrosine O-sulfation with proper experimental designs.

Ten-year survival and complication rates of lithium-disilicate (Empress 2) tooth-supported crowns, implant-supported crowns, and fixed dental prostheses.

Science.gov (United States)

Teichmann, Maren; Göckler, Fabian; Weber, Volker; Yildirim, Murat; Wolfart, Stefan; Edelhoff, Daniel

2017-01-01

To prospectively evaluate the clinical long-term outcome of tooth-supported crowns (SCs), implant-supported crowns (ISCs), and fixed dental prostheses (FDPs) made of a lithium-disilicate glass-ceramic framework material (IPS Empress 2). Between 1997 and 1999, a total of 184 restorations (106 SCs, 32 ISCs, 33 FDPs, and 13 diverse restorations) were placed in 73 patients. Kaplan-Meier estimation was applied for survival and chipping-free rates. Inter-group comparison of both rates was realized by a log rank test and a 2×2 contingency table. Also, SCs and FDPs were compared regarding adhesive vs. conventional cementation, and anterior vs. posterior positioning, for impact on survival. Due to 14 dropouts (34 restorations) and reasonable exclusion of 19 other restorations, the final dataset included: i) 87 SCs [37 patients, mean observation time 11.4 (±3.8)years]; ii) 17 ISCs [12 patients, mean observation time 13.3 (±2.3)years; and iii) 27 FDPs [19 patients, mean observation time 8.9 (±5.4)years]. The 10-year survival rate/chipping-free rate for SCs were 86.1%/83.4%, for ISCs 93.8%/94.1%, and for FDPs were 51.9%/90.8%. Both ISCs and SCs had a significantly higher survival than FDPs (ISCs vs. FDPs: both tests p=0.001; SCs vs. FDPs: p=0.001 and p=0.005). Differences in the chipping-free rates did not reach significance. Also, neither the cementation mode nor positioning of the restoration had an impact on survival. SCs had a slightly lower outcome than can generally be expected from single crowns. In contrast, ICSs had a favorable outcome and the FDPs predominantly failed. The practitioner's choice of dental materials is based (at best) on long-term experience. The present 10-year results are based on comprehensive data analyses and show the high potential of lithium-disilicate as a reliable material, especially for single-unit restoration. Copyright © 2016 Elsevier Ltd. All rights reserved.

Efficient Detection of Copy Number Mutations in PMS2 Exons with a Close Homolog.

Science.gov (United States)

Herman, Daniel S; Smith, Christina; Liu, Chang; Vaughn, Cecily P; Palaniappan, Selvi; Pritchard, Colin C; Shirts, Brian H

2018-07-01

Detection of 3' PMS2 copy-number mutations that cause Lynch syndrome is difficult because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequences using PMS2 targets, maps sequences randomly among regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ranges. The method was trained on 1352 samples, including 8 known positives, and tested on 719 samples, including 17 known positives. Clinical implementation of the first version of this method detected new mutations in the training (N = 7) and test (N = 2) sets that had not been identified by our initial clinical testing pipeline. The described final method showed complete sensitivity in both sample sets and false-positive rates of 5% (training) and 7% (test), dramatically decreasing the number of cases needing additional mutation evaluation. This approach leveraged the differences between gene and pseudogene to distinguish between PMS2 and PMS2CL copy-number mutations. These methods enable efficient and sensitive Lynch syndrome screening for 3' PMS2 copy-number mutations and may be applied similarly to other genomic regions with highly homologous pseudogenes. Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Enhancer of Zeste Homolog 2 Overexpression in Nasopharyngeal Carcinoma: An Independent Poor Prognosticator That Enhances Cell Growth

International Nuclear Information System (INIS)

Hwang, Chung-Feng; Huang, Hsuan-Ying; Chen, Chang-Han; Chien, Chih-Yen; Hsu, Yao-Chung; Li, Chien-Feng

2012-01-01

Purpose: As a key component of polycomb-repressive complex 2, enhancer of zeste homolog 2 (EZH2) represses target genes through histone methylation and is frequently overexpressed and associated with poor prognosis in common carcinomas. For the first time, we reported EZH2 expression and its biological and clinical significance in nasopharyngeal carcinoma (NPC). Methods and Materials: In NPC cell lines and specimens, endogenous expression of EZH2 mRNA and protein was determined by semiquantitative reverse transcription–polymerase chain reaction and immunoblotting, respectively. To analyze the effect on cell growth, stable silencing of EZH2 was established in EZH2-expressing TW02 NPC cells with RNA interference. EZH2 immunolabeling was assessable for 89 primary NPC biopsy samples and correlated with clinicopathological variables, disease-specific survival (DSS), and overall survival (OS). Results: Growth activity of TW02 cells was significantly suppressed (p < 0.001) with stable EZH2 silencing. Compared with normal nasopharyngeal tissue, expression levels of EZH2 transcript and protein were apparently upregulated in NPC specimens. As a continuous variable, higher EZH2 expression preferentially occurred in NPCs of T3 to T4 stages (p = 0.03) and significantly predicted inferior DSS (p = 0.0010) and OS (p = 0.004). The prognostic implications for DSS (p = 0.010) and OS (p = 0.006) still remained valid when using the median (≥60%) of EZH2 immunolabeling index to dichotomize the cohort. In the multivariate model, higher EZH2 expression was an independent adverse factor of both DSS (p = 0.012) and OS (p = 0.011), along with American Joint Committee on Cancer Stages III to IV (p = 0.024 for DSS, p = 0.017 for OS). Conclusion: At least partly through promoting cell growth, EZH2 implicates disease progression, confers tumor aggressiveness, and represents an independent adverse prognosticator in patients with NPC.

DockoMatic 2.0: high throughput inverse virtual screening and homology modeling.

Science.gov (United States)

Bullock, Casey; Cornia, Nic; Jacob, Reed; Remm, Andrew; Peavey, Thomas; Weekes, Ken; Mallory, Chris; Oxford, Julia T; McDougal, Owen M; Andersen, Timothy L

2013-08-26

DockoMatic is a free and open source application that unifies a suite of software programs within a user-friendly graphical user interface (GUI) to facilitate molecular docking experiments. Here we describe the release of DockoMatic 2.0; significant software advances include the ability to (1) conduct high throughput inverse virtual screening (IVS); (2) construct 3D homology models; and (3) customize the user interface. Users can now efficiently setup, start, and manage IVS experiments through the DockoMatic GUI by specifying receptor(s), ligand(s), grid parameter file(s), and docking engine (either AutoDock or AutoDock Vina). DockoMatic automatically generates the needed experiment input files and output directories and allows the user to manage and monitor job progress. Upon job completion, a summary of results is generated by Dockomatic to facilitate interpretation by the user. DockoMatic functionality has also been expanded to facilitate the construction of 3D protein homology models using the Timely Integrated Modeler (TIM) wizard. The wizard TIM provides an interface that accesses the basic local alignment search tool (BLAST) and MODELER programs and guides the user through the necessary steps to easily and efficiently create 3D homology models for biomacromolecular structures. The DockoMatic GUI can be customized by the user, and the software design makes it relatively easy to integrate additional docking engines, scoring functions, or third party programs. DockoMatic is a free comprehensive molecular docking software program for all levels of scientists in both research and education.

Mmu-miR-615-3p regulates lipoapoptosis by inhibiting C/EBP homologous protein.

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Yasuhiro Miyamoto

Full Text Available Lipoapoptosis occurring due to an excess of saturated free fatty acids such as palmitate is a key pathogenic event in the initiation of nonalcoholic fatty liver disease. Palmitate loading of cells activates the endoplasmic reticulum stress response, including induction of the proapoptotic transcription factor C/EBP homologous protein (CHOP. Furthermore, the loss of microRNAs is implicated in regulating apoptosis under conditions of endoplasmic reticulum (ER stress. The aim of this study was to identify specific microRNAs regulating CHOP expression during palmitate-induced ER stress. Five microRNAs were repressed under palmitate-induced endoplasmic reticulum stress conditions in hepatocyte cell lines (miR-92b-3p, miR-328-3p, miR-484, miR-574-5p, and miR-615-3p. We identified miR-615-3p as a candidate microRNA which was repressed by palmitate treatment and regulated CHOP protein expression, by RNA sequencing and in silico analyses, respectively. There is a single miR-615-3p binding site in the 3'untranslated region (UTR of the Chop transcript. We characterized this as a functional binding site using a reporter gene-based assay. Augmentation of miR-615-3p levels, using a precursor molecule, repressed CHOP expression; and under these conditions palmitate- or tunicamycin-induced cell death were significantly reduced. Our results suggest that palmitate-induced apoptosis requires maximal expression of CHOP which is achieved via the downregulation of its repressive microRNA, miR-615-3p. We speculate that enhancement of miR-615-3p levels may be of therapeutic benefit by inhibiting palmitate-induced hepatocyte lipoapoptosis.

Direct association between the Ret receptor tyrosine kinase and the Src homology 2-containing adapter protein Grb7.

Science.gov (United States)

Pandey, A; Liu, X; Dixon, J E; Di Fiore, P P; Dixit, V M

1996-05-03

Adapter proteins containing Src homology 2 (SH2) domains link transmembrane receptor protein-tyrosine kinases to downstream signal transducing molecules. A family of SH2 containing adapter proteins including Grb7 and Grb10 has been recently identified. We had previously shown that Grb10 associates with Ret via its SH2 domain in an activation-dependent manner (Pandey, A., Duan, H., Di Fiore, P.P., and Dixit, V.M. (1995) J. Biol, Chem. 270, 21461-21463). We now demonstrate that the related adapter molecule Grb7 also associates with Ret in vitro and in vivo, and that the binding of the SH2 domain of Grb7 to Ret is direct. This binding is dependent upon Ret autophosphorylation since Grb7 is incapable of binding a kinase-defective mutant of Ret. Thus two members of the Grb family, Grb7 and Grb10, likely relay signals emanating from Ret to other, as yet, unidentified targets within the cell.

Use of VAP3D software in the construction of pathological anthropomorphic phantoms for dosimetric evaluations

International Nuclear Information System (INIS)

Lima, Lindeval Fernandes de; Lima, Fernando R.A.

2011-01-01

This paper performs a new type of dosimetric evaluation, where it was used a phantom of pathological voxels (representative phantom of sick person). The software VAP3D (Visualization and Analysis of Phantoms 3D) were used for, from a healthy phantom (phantom representative of healthy person), to introduce three dimensional regions to simulate tumors. It was used the Monte Carlo ESGnrc code to simulate the X ray photon transport, his interaction with matter and evaluation of absorbed dose in organs and tissues from thorax region of the healthy phantom and his pathological version. This is a computer model of typical exposure for programming the treatments in radiodiagnostic

An analytical solution of Richards' equation providing the physical basis of SCS curve number method and its proportionality relationship

Science.gov (United States)

Hooshyar, Milad; Wang, Dingbao

2016-08-01

The empirical proportionality relationship, which indicates that the ratio of cumulative surface runoff and infiltration to their corresponding potentials are equal, is the basis of the extensively used Soil Conservation Service Curve Number (SCS-CN) method. The objective of this paper is to provide the physical basis of the SCS-CN method and its proportionality hypothesis from the infiltration excess runoff generation perspective. To achieve this purpose, an analytical solution of Richards' equation is derived for ponded infiltration in shallow water table environment under the following boundary conditions: (1) the soil is saturated at the land surface; and (2) there is a no-flux boundary which moves downward. The solution is established based on the assumptions of negligible gravitational effect, constant soil water diffusivity, and hydrostatic soil moisture profile between the no-flux boundary and water table. Based on the derived analytical solution, the proportionality hypothesis is a reasonable approximation for rainfall partitioning at the early stage of ponded infiltration in areas with a shallow water table for coarse textured soils.

Evidence for a Chk2-BRCA1-BRCA2 pathway in controlling homologous recombination

International Nuclear Information System (INIS)

Powell, S.N.

2003-01-01

The BRCA2 protein is thought to play a role as a supportive protein for the assembly of Rad51 filaments at the sites of DNA damage or stalled DNA replication, and thereby facilitates the process of homologous recombination (HR). We provide direct evidence that the interaction of BRCA2 and Rad51, via the BRC repeat motifs of BRCA2, is the key to its function in HR. Furthermore, the BRCA2's role to facilitate HR is dependent on a replicating DNA template, closely linking the process of HR to DNA replication. To date, no other role for BRCA2 has been elucidated in-vivo. BRCA1, by contrast, has a complex series of functions including a supportive role in HR, a possible role in non-homologous recombination (NHR), transcriptional co-activation and E3 ubiquitin ligase activity. The protein undergoes extensive post-translational modification, principally by phosphorylation, in both S-phase and in response to DNA damage. We show that ATM-dependent modifications of BRCA1 are important for S-phase and G2/M checkpoints, but have no direct impact on DNA repair. However, a chk2 dependent modification of BRCA1 at serine-988, appears critical for the promotion of Rad51-dependent HR and the inhibition of Mre11/Rad50/NBS1- dependent repair. Direct modification of chk2 kinase activity, by over-expression of a kinase-dead chk2, results in an identical phenotype as seen with the S988A mutation of BRCA1. Taken together, these results suggest that a chk2-BRCA1-BRCA2 dependent pathway promotes error-free HR, suppresses error-prone NHR and thereby maintains genomic stability

Pure homology of algebraic varieties

OpenAIRE

Weber, Andrzej

2003-01-01

We show that for a complete complex algebraic variety the pure component of homology coincides with the image of intersection homology. Therefore pure homology is topologically invariant. To obtain slightly more general results we introduce "image homology" for noncomplete varieties.

[Spinal cord stimulation (SCS) as a treatment for the spread phenomenon related to complex regional pain syndrome type- I (CRPS-I )].

Science.gov (United States)

Goto, Shinichi; Taira, Takaomi; Hori, Tomokatsu

2009-09-01

The authors describe an experience of spinal cord stimulation (SCS) in a 30-year-old woman who developed complex regional pain syndrome type-I (CRPS-I) with spread phenomenon. She had received lumbar SCS under a diagnosis of CRPS-I in her left leg for 8 years. She had refractory pain in her right arm for the recent two years. There was no new lesion explaining her refractory pain on physical or radiological examination. Thus, the pain in her right upper arm was considered as spread phenomenon of CRPS-I. Test stimulation with cervical epidural spinal electrode showed good results and the pulse generator was implanted. It is suggested that the symptom of CRPS-I involving spread phenomenon was possibly due to a cortical reorganization. But a certain effect of SCS may be contributing to the favorable results of test stimulation for the treatment of CRPS-I with spread phenomenon in this case.

Comparative study of 2 oral care protocols in intensive care units.

Science.gov (United States)

Ory, Jérôme; Raybaud, Evelyne; Chabanne, Russell; Cosserant, Bernard; Faure, Jean Sébastien; Guérin, Renaud; Calvet, Laure; Pereira, Bruno; Mourgues, Charline; Guelon, Dominique; Traore, Ousmane

2017-03-01

The quality of oral care is important in limiting the emergence of ventilator-associated pneumonia (VAP) in intubated patients. Our main objective was to measure the quality improvement in oral care following the implementation of a new oral care protocol. We also monitored VAP rates. This was a cohort study of patients in 5 adult ICUs covering different specialties. During period 1, caregivers used a foam stick for oral care and during period 2 a stick and tooth brushing with aspiration. Oral chlorhexidine was used during both periods. The caregivers rated improvement in oral health on the basis of 4 criteria (tongue, mucous membranes, gingivae, and teeth). Caregiver satisfaction was also assessed. The incidence of VAP was monitored. A total of 2,030 intubated patients admitted to intensive care units benefited from oral care. The patient populations during the 2 periods were similar with regard to demographic data and VAP potential risk factors. Oral health was significantly better from the third day of oral care in period 2 onward (period 1, 6.4 ± 2.1; period 2, 5.6 ± 1.8; P = .043). Caregivers found the period 2 protocol easier to implement and more effective. VAP rates decreased significantly between the 2 periods (period 1, 12.8%; period 2, 8.5%; P = .002). Our study showed that the implementation of a simple strategy improved the quality of oral care of patients in intensive care units, and decreased VAP rates. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

CO2 driven endotracheal tube cuff control in critically ill patients: A randomized controlled study.

Science.gov (United States)

De Pascale, Gennaro; Pennisi, Mariano Alberto; Vallecoccia, Maria Sole; Bello, Giuseppe; Maviglia, Riccardo; Montini, Luca; Di Gravio, Valentina; Cutuli, Salvatore Lucio; Conti, Giorgio; Antonelli, Massimo

2017-01-01

To determine the safety and clinical efficacy of an innovative integrated airway system (AnapnoGuard™ 100 system) that continuously monitors and controls the cuff pressure (Pcuff), while facilitating the aspiration of subglottic secretions (SS). This was a prospective, single centre, open-label, randomized, controlled feasibility and safety trial. The primary endpoint of the study was the rate of device related adverse events (AE) and serious AE (SAE) as a result of using AnapnoGuard (AG) 100 during mechanical ventilation. Secondary endpoints were: (1) mechanical complications rate (2) ICU staff satisfaction; (3) VAP occurrence; (4) length of mechanical ventilation; (5) length of Intensive Care Unit stay and mortality; (6) volume of evacuated subglottic secretions. Sixty patients were randomized to be intubated with the AG endotracheal-tube (ETT) and connected to the AG 100 system allowing Pcuff adjustment and SS aspiration; or with an ETT combined with SS drainage and Pcuff controlled manually. No difference in adverse events rate was identified between the groups. The use of AG system was associated with a significantly higher incidence of Pcuff determinations in the safety range (97.3% vs. 71%; paspirated SS secretions: (192.0[64-413] ml vs. 150[50-200], p = 0.19 (total)); (57.8[20-88.7] ml vs. 50[18.7-62] ml, p = 0.11 (daily)). No inter-group difference was detected using AG system vs. controls in terms of post-extubation throat pain level (0 [0-2] vs. 0 [0-3]; p = 0.7), hoarseness (42.9% vs. 75%; p = 0.55) and tracheal mucosa oedema (16.7% vs. 10%; p = 0.65). Patients enrolled in the AG group had a trend to reduced VAP risk of ventilator-associated pneumonia(VAP) (14.8% vs. 40%; p = 0.06), which were more frequently monomicrobial (25% vs. 70%; p = 0.03). No statistically significant difference was observed in duration of mechanical ventilation, ICU stay, and mortality. The use AG 100 system and AG tube in critically ill intubated patients is safe and

Inhibition of tumor metastasis by a growth factor receptor bound protein 2 Src homology 2 domain-binding antagonist.

Science.gov (United States)

Giubellino, Alessio; Gao, Yang; Lee, Sunmin; Lee, Min-Jung; Vasselli, James R; Medepalli, Sampath; Trepel, Jane B; Burke, Terrence R; Bottaro, Donald P

2007-07-01

Metastasis, the primary cause of death in most forms of cancer, is a multistep process whereby cells from the primary tumor spread systemically and colonize distant new sites. Blocking critical steps in this process could potentially inhibit tumor metastasis and dramatically improve cancer survival rates; however, our understanding of metastasis at the molecular level is still rudimentary. Growth factor receptor binding protein 2 (Grb2) is a widely expressed adapter protein with roles in epithelial cell growth and morphogenesis, as well as angiogenesis, making it a logical target for anticancer drug development. We have previously shown that a potent antagonist of Grb2 Src homology-2 domain-binding, C90, blocks growth factor-driven cell motility in vitro and angiogenesis in vivo. We now report that C90 inhibits metastasis in vivo in two aggressive tumor models, without affecting primary tumor growth rate. These results support the potential efficacy of this compound in reducing the metastatic spread of primary solid tumors and establish a critical role for Grb2 Src homology-2 domain-mediated interactions in this process.

Superspace description of the homologous series Ga2O3(ZnO)m.

Science.gov (United States)

Michiue, Yuichi; Kimizuka, Noboru

2010-04-01

A unified description for the structures of the homologous series Ga(2)O(3)(ZnO)(m), gallium zinc oxide, is presented using the superspace formalism. The structures were treated as a compositely modulated structure consisting of two subsystems. One is constructed with metal ions and the other with O ions. The ideal model is given, in which the displacive modulations of ions are well described by the zigzag function with large amplitudes. Alternative settings are also proposed which are analogous to the so-called modular structures. The validity of the model has been confirmed by refinements for phases with m = 6 and m = 9 in the homologous series. A few complex phenomena in real structures are taken into account by modifying the ideal model.

Lectures on functor homology

CERN Document Server

Touzé, Antoine

2015-01-01

This book features a series of lectures that explores three different fields in which functor homology (short for homological algebra in functor categories) has recently played a significant role. For each of these applications, the functor viewpoint provides both essential insights and new methods for tackling difficult mathematical problems. In the lectures by Aurélien Djament, polynomial functors appear as coefficients in the homology of infinite families of classical groups, e.g. general linear groups or symplectic groups, and their stabilization. Djament’s theorem states that this stable homology can be computed using only the homology with trivial coefficients and the manageable functor homology. The series includes an intriguing development of Scorichenko’s unpublished results. The lectures by Wilberd van der Kallen lead to the solution of the general cohomological finite generation problem, extending Hilbert’s fourteenth problem and its solution to the context of cohomology. The focus here is o...

Accurate pKa calculation of the conjugate acids of alkanolamines, alkaloids and nucleotide bases by quantum chemical methods.

Science.gov (United States)

Gangarapu, Satesh; Marcelis, Antonius T M; Zuilhof, Han

2013-04-02

The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Homologous series of induced early mutants in indican rice. Pt.1. The production of homologous series of early mutants

International Nuclear Information System (INIS)

Chen Xiulan; Yang Hefeng; He Zhentian; Han Yuepeng; Liu Xueyu

1999-01-01

The percentage of homologous series of early mutants induced from the same Indican rice variety were almost the same (1.37%∼1.64%) in 1983∼1993, but the ones from the different eco-typical varieties were different. The early variety was 0.73%, the mid variety was 1.51%, and the late variety was 1.97%. The percentage of homologous series of early mutants from the varieties with the same pedigree and relationship were similar, but the one from the cog nation were lower than those from distant varieties. There are basic laws and characters in the homologous series of early mutants: 1. The inhibited phenotype is the basic of the homologous series of early mutants; 2. The production of the homologous series of early mutants is closely related with the growing period of the parent; 3. The parallel mutation of the stem and leaves are simultaneously happened with the variation of early or late maturing; 4. The occurrence of the homologous series of early mutants is in a state of imbalance. According to the law of parallel variability, the production of homologous series of early mutants can be predicted as long as the parents' classification of plant, pedigree and ecological type are identified. Therefore, the early breeding can be guided by the law of homologous series of early mutants

Structure of (Ga2O3)2(ZnO)13 and a unified description of the homologous series (Ga2O3)2(ZnO)(2n + 1).

Science.gov (United States)

Michiue, Yuichi; Kimizuka, Noboru; Kanke, Yasushi; Mori, Takao

2012-06-01

The structure of (Ga(2)O(3))(2)(ZnO)(13) has been determined by a single-crystal X-ray diffraction technique. In the monoclinic structure of the space group C2/m with cell parameters a = 19.66 (4), b = 3.2487 (5), c = 27.31 (2) Å, and β = 105.9 (1)°, a unit cell is constructed by combining the halves of the unit cell of Ga(2)O(3)(ZnO)(6) and Ga(2)O(3)(ZnO)(7) in the homologous series Ga(2)O(3)(ZnO)(m). The homologous series (Ga(2)O(3))(2)(ZnO)(2n + 1) is derived and a unified description for structures in the series is presented using the (3+1)-dimensional superspace formalism. The phases are treated as compositely modulated structures consisting of two subsystems. One is constructed by metal ions and another is by O ions. In the (3 + 1)-dimensional model, displacive modulations of ions are described by the asymmetric zigzag function with large amplitudes, which was replaced by a combination of the sawtooth function in refinements. Similarities and differences between the two homologous series (Ga(2)O(3))(2)(ZnO)(2n + 1) and Ga(2)O(3)(ZnO)(m) are clarified in (3 + 1)-dimensional superspace. The validity of the (3 + 1)-dimensional model is confirmed by the refinements of (Ga(2)O(3))(2)(ZnO)(13), while a few complex phenomena in the real structure are taken into account by modifying the model.

Binding Mode Prediction of 5-Hydroxytryptamine 2C Receptor Ligands by Homology Modeling and Molecular Docking Analysis

Energy Technology Data Exchange (ETDEWEB)

Ahmed, Asif; Nagarajan, Shanthi; Doddareddy, Munikumar Reddy; Cho, Yong Seo; Pae, Ae Nim [Korea Institute of Science and Technology, Seoul (Korea, Republic of)

2011-06-15

Serotonin or 5-hydroxytryptamine subtype 2C (5-HT{sub 2C}) receptor belongs to class A amine subfamily of Gprotein- coupled receptor (GPCR) super family and its ligands has therapeutic promise as anti-depressant and -obesity agents. So far, bovine rhodopsin from class A opsin subfamily was the mostly used X-ray crystal template to model this receptor. Here, we explained homology model using beta 2 adrenergic receptor (β2AR), the model was energetically minimized and validated by flexible ligand docking with known agonists and antagonists. In the active site Asp134, Ser138 of transmembrane 3 (TM3), Arg195 of extracellular loop 2 (ECL2) and Tyr358 of TM7 were found as important residues to interact with agonists. In addition to these, V208 of ECL2 and N351 of TM7 was found to interact with antagonists. Several conserved residues including Trp324, Phe327 and Phe328 were also found to contribute hydrophobic interaction. The predicted ligand binding mode is in good agreement with published mutagenesis and homology model data. This new template derived homology model can be useful for further virtual screening based lead identification.

Investigation of the direct runoff generation mechanism for the analysis of the SCS-CN method applicability to a partial area experimental watershed

OpenAIRE

Soulis, K. X.; Valiantzas, J. D.; Dercas, N.; Londra, P. A.

2009-01-01

The Soil Conservation Service Curve Number (SCS-CN) method is widely used for predicting direct runoff volume for a given rainfall event. The applicability of the SCS-CN method and the direct runoff generation mechanism were thoroughly analysed in a Mediterranean experimental watershed in Greece. The region is characterized by a Mediterranean semi-arid climate. A detailed land cover and soil survey using remote sensing and GIS techniques, showed that the watershed is dominated by coarse soils...

Micromechanics of fiber pull-out and crack bridging in SCS-6 SiC- CVD SiC composite system at high-temperature

International Nuclear Information System (INIS)

El-Azab, A.; Ghoniem, N.M.

1993-01-01

A micro mechanical model is developed to study fiber pull-out and crack bridging in fiber reinforced SiC-SiC composites with time dependent thermal creep. By analyzing the creep data for monolithic CVD SiC (matrix) and the SCS-6 SiC fibers in the temperature range 900-1250 degrees C, it is found that the matrix creep rates can be ignored in comparison to those of fibers. Two important relationships are obtained: (1) a time dependent relation between the pull-out stress and the relative sliding distance between the fiber and matrix for the purpose of analyzing pull-out experiments, and (2) the relation between the bridging stress and the crack opening displacement to be used in studying the mechanics and stability of matrix crack bridged by fibers at high temperatures. The present analysis can also be applied to Nicalon-reinforced CVD SiC matrix system since the Nicalon fibers exhibit creep characteristics similar to those of the SCS-6 fibers

Hyperoxia-induced p47phox activation and ROS generation is mediated through S1P transporter Spns2, and S1P/S1P1&2 signaling axis in lung endothelium.

Science.gov (United States)

Harijith, Anantha; Pendyala, Srikanth; Ebenezer, David L; Ha, Alison W; Fu, Panfeng; Wang, Yue-Ting; Ma, Ke; Toth, Peter T; Berdyshev, Evgeny V; Kanteti, Prasad; Natarajan, Viswanathan

2016-08-01

Hyperoxia-induced lung injury adversely affects ICU patients and neonates on ventilator assisted breathing. The underlying culprit appears to be reactive oxygen species (ROS)-induced lung damage. The major contributor of hyperoxia-induced ROS is activation of the multiprotein enzyme complex NADPH oxidase. Sphingosine-1-phosphate (S1P) signaling is known to be involved in hyperoxia-mediated ROS generation; however, the mechanism(s) of S1P-induced NADPH oxidase activation is unclear. Here, we investigated various steps in the S1P signaling pathway mediating ROS production in response to hyperoxia in lung endothelium. Of the two closely related sphingosine kinases (SphKs)1 and 2, which synthesize S1P from sphingosine, only Sphk1(-/-) mice conferred protection against hyperoxia-induced lung injury. S1P is metabolized predominantly by S1P lyase and partial deletion of Sgpl1 (Sgpl1(+/-)) in mice accentuated lung injury. Hyperoxia stimulated S1P accumulation in human lung microvascular endothelial cells (HLMVECs), and downregulation of S1P transporter spinster homolog 2 (Spns2) or S1P receptors S1P1&2, but not S1P3, using specific siRNA attenuated hyperoxia-induced p47(phox) translocation to cell periphery and ROS generation in HLMVECs. These results suggest a role for Spns2 and S1P1&2 in hyperoxia-mediated ROS generation. In addition, p47(phox) (phox:phagocyte oxidase) activation and ROS generation was also reduced by PF543, a specific SphK1 inhibitor in HLMVECs. Our data indicate a novel role for Spns2 and S1P1&2 in the activation of p47(phox) and production of ROS involved in hyperoxia-mediated lung injury in neonatal and adult mice. Copyright © 2016 the American Physiological Society.

CENTRAL REGION COMPONENT1, a Novel Synaptonemal Complex Component, Is Essential for Meiotic Recombination Initiation in Rice[C][W

Science.gov (United States)

Miao, Chunbo; Tang, Ding; Zhang, Honggen; Wang, Mo; Li, Yafei; Tang, Shuzhu; Yu, Hengxiu; Gu, Minghong; Cheng, Zhukuan

2013-01-01

In meiosis, homologous recombination entails programmed DNA double-strand break (DSB) formation and synaptonemal complex (SC) assembly coupled with the DSB repair. Although SCs display extensive structural conservation among species, their components identified are poorly conserved at the sequence level. Here, we identified a novel SC component, designated CENTRAL REGION COMPONENT1 (CRC1), in rice (Oryza sativa). CRC1 colocalizes with ZEP1, the rice SC transverse filament protein, to the central region of SCs in a mutually dependent fashion. Consistent with this colocalization, CRC1 interacts with ZEP1 in yeast two-hybrid assays. CRC1 is orthologous to Saccharomyces cerevisiae pachytene checkpoint2 (Pch2) and Mus musculus THYROID RECEPTOR-INTERACTING PROTEIN13 (TRIP13) and may be a conserved SC component. Additionally, we provide evidence that CRC1 is essential for meiotic DSB formation. CRC1 interacts with HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 (PAIR1) in vitro, suggesting that these proteins act as a complex to promote DSB formation. PAIR2, the rice ortholog of budding yeast homolog pairing1, is required for homologous chromosome pairing. We found that CRC1 is also essential for the recruitment of PAIR2 onto meiotic chromosomes. The roles of CRC1 identified here have not been reported for Pch2 or TRIP13. PMID:23943860

Central region component1, a novel synaptonemal complex component, is essential for meiotic recombination initiation in rice.

Science.gov (United States)

Miao, Chunbo; Tang, Ding; Zhang, Honggen; Wang, Mo; Li, Yafei; Tang, Shuzhu; Yu, Hengxiu; Gu, Minghong; Cheng, Zhukuan

2013-08-01

In meiosis, homologous recombination entails programmed DNA double-strand break (DSB) formation and synaptonemal complex (SC) assembly coupled with the DSB repair. Although SCs display extensive structural conservation among species, their components identified are poorly conserved at the sequence level. Here, we identified a novel SC component, designated central region component1 (CRC1), in rice (Oryza sativa). CRC1 colocalizes with ZEP1, the rice SC transverse filament protein, to the central region of SCs in a mutually dependent fashion. Consistent with this colocalization, CRC1 interacts with ZEP1 in yeast two-hybrid assays. CRC1 is orthologous to Saccharomyces cerevisiae pachytene checkpoint2 (Pch2) and Mus musculus THYROID receptor-interacting protein13 (TRIP13) and may be a conserved SC component. Additionally, we provide evidence that CRC1 is essential for meiotic DSB formation. CRC1 interacts with homologous pairing aberration in rice meiosis1 (PAIR1) in vitro, suggesting that these proteins act as a complex to promote DSB formation. PAIR2, the rice ortholog of budding yeast homolog pairing1, is required for homologous chromosome pairing. We found that CRC1 is also essential for the recruitment of PAIR2 onto meiotic chromosomes. The roles of CRC1 identified here have not been reported for Pch2 or TRIP13.

In-situ conversion of rGO/Ni2P composite from GO/Ni-MOF precursor with enhanced electrochemical property

Science.gov (United States)

Lv, Zijian; Zhong, Qin; Bu, Yunfei

2018-05-01

Owing to the metalloid characteristic and superior electrical conductivity, the metal phosphides have received increasing interests in energy storage systems. Here, xrGO/Ni2P composites are successfully synthesized via an In-situ phosphorization process with GO/Ni-MOF as precursors. Compared to pure Ni2P, the xrGO/Ni2P composites appear enhanced electrochemical properties in terms of the specific capacitance and cycling performance as electrodes for supercapacitors. Especially, the 2rGO/Ni2P electrode shows a highest specific capacitance of 890 F g-1 at 1 A g-1 among the obtained composites. The enhancement can be attributed to the inherited structure from Ni-MOF and the well assembled of rGO and Ni2P through the In-situ conversion process. Moreover, when applied as positive electrode in a hybrid supercapacitor, an energy density of 35.9 W h kg-1 at a power density of 752 W kg-1 has been achieved. This work provides an In-situ conversion strategy for the synthesis of rGO/Ni2P composite which might be a promising electrode material for SCs.

Improved Algorithm of SCS-CN Model Parameters in Typical Inland River Basin in Central Asia

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Wang, Jin J.; Ding, Jian L.; Zhang, Zhe; Chen, Wen Q.

2017-02-01

Rainfall-runoff relationship is the most important factor for hydrological structures, social and economic development on the background of global warmer, especially in arid regions. The aim of this paper is find the suitable method to simulate the runoff in arid area. The Soil Conservation Service Curve Number (SCS-CN) is the most popular and widely applied model for direct runoff estimation. In this paper, we will focus on Wen-quan Basin in source regions of Boertala River. It is a typical valley of inland in Central Asia. First time to use the 16m resolution remote sensing image about high-definition earth observation satellite “Gaofen-1” to provide a high degree accuracy data for land use classification determine the curve number. Use surface temperature/vegetation index (TS/VI) construct 2D scatter plot combine with the soil moisture absorption balance principle calculate the moisture-holding capacity of soil. Using original and parameter algorithm improved SCS-CN model respectively to simulation the runoff. The simulation results show that the improved model is better than original model. Both of them in calibration and validation periods Nash-Sutcliffe efficiency were 0.79, 0.71 and 0.66,038. And relative error were3%, 12% and 17%, 27%. It shows that the simulation accuracy should be further improved and using remote sensing information technology to improve the basic geographic data for the hydrological model has the following advantages: 1) Remote sensing data having a planar characteristic, comprehensive and representative. 2) To get around the bottleneck about lack of data, provide reference to simulation the runoff in similar basin conditions and data-lacking regions.

Interaction and dynamics of homologous pairing protein 2 (HOP2) and DNA studied by MD simulation

Science.gov (United States)

Moktan, Hem; Pezza, Roberto; Zhou, Donghua

2015-03-01

The homologous pairing protein 2 (Hop2) plays an important role in meiosis and DNA repair. Together with protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. We recently determined the NMR structure of the N-terminal domain of Hop2 and proposed a model of Protein-DNA complex based on NMR chemical shift perturbations and mutagenesis studies (Moktan, J Biol Chem 2014 10.1074/jbc.M114.548180). However structure and dynamics of the complex have not been studied at the atomic level yet. Here, we used classical MD simulations to study the interactions between the N-terminal HOP2 and DNA. The simulated results indicate that helix3 (H3) interacts with DNA in major groove and wing1 (W1) interacts mostly in minor groove mainly via direct hydrogen bonds. Also it is found that binding leads to reduced fluctuations in both protein and DNA. Several water bridge interactions have been identified. The residue-wise contributions to the interaction energy were evaluated. Also the functional motion of the protein is analyzed using principal component analysis. The results confirmed the importance of H3 and W1 for the stability of the complex, which is consistent with our previous experimental studies.

Rotational Isomers, Intramolecular Hydrogen Bond, and IR Spectra of o-Vinylphenol Homologs

Science.gov (United States)

Glazunov, V. P.; Berdyshev, D. V.; Balaneva, N. N.; Radchenko, O. S.; Novikov, V. L.

2018-03-01

The ν(OH) stretching-mode bands in solution IR spectra of five o-vinylphenol (o-VPh) homologs in the slightly polar solvents CCl4 and n-hexane were studied. Several rotamers with free OH groups were found in solutions of o-VPh and its methyl-substituted derivatives in n-hexane. The proportion of rotamers in o-VPh homologs with intramolecular hydrogen bonds (IHBs) O-H...π varied from 22 to 97% in the gas and cyclohexane according to B3LYP/cc-pVTZ calculations. The theoretically estimated effective enthalpies -ΔH of their IHBs varied in the range 0.20-2.24 kcal/mol.

Design of a SOFC/GT/SCs hybrid power system to supply a rural isolated microgrid

International Nuclear Information System (INIS)

Camblong, Haritza; Baudoin, Sylvain; Vechiu, Ionel; Etxeberria, Aitor

2016-01-01

Highlights: • A novel SOFC/GT/SCs HPS is connected to a rural microgrid through a 3LNPC inverter. • An operating strategy that maintains the SOFC power at its rated value is defined. • A robust digital controller that damps current oscillations is designed. • The efficiency, power quality, lifetime, and robustness of the HPS are considered. • An experimental test on an original HPS emulator validates the proposed solutions. - Abstract: The aim of this research study has been to design a Hybrid Power System (HPS) which works with biogas and whose main components are a Solid Oxide Fuel Cell (SOFC), a Gas microTurbine (GT), and a module of SuperCapacities (SCs). The HPS is the only power source of a rural isolated microgrid. Its structure, operating strategy, and controller have been designed considering the following criteria: efficiency, power quality, SOFC lifetime and robustness in stability and performance. The HPS structure includes a unique power converter, a 3-Level Neutral Point Clamped (3LNPC) inverter that connects the HPS to the AC microgrid. Regarding the selected operating strategy, it consists in regulating the SOFC power output to its rated value. Thus, the SCs and the GT must respond to the power demand variations. On the other hand, a study of the HPS shows that its dynamic behavior is not linear. Therefore, a special attention is put on designing a robust HPS controller. The control model is identified and the robust digital controller is designed using the “Tracking and Regulation with Independent Objectives” method. Simulation and experimental results show how the proposed structure, operating strategy, and controller allow ensuring a good behavior of the HPS from the point of view of the abovementioned four criteria.

Continuous aspiration of subglottic secretions in the prevention of ventilator-associated pneumonia in the postoperative period of major heart surgery.

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Bouza, Emilio; Pérez, María Jesús; Muñoz, Patricia; Rincón, Cristina; Barrio, José María; Hortal, Javier

2008-11-01

Aspiration of endotracheal secretions is a major step in the prevention of ventilator-associated pneumonia (VAP). We compared conventional and continuous aspiration of subglottic secretions (CASS) procedures in ventilated patients after major heart surgery (MHS). Randomized comparison during a 2-year period. A total of 714 patients were randomized (24 patients were excluded from the study; 359 CASS patients; 331 control subjects). The results for CASS patients and control subjects (per protocol and intention-to-treat analysis) were as follows: VAP incidence, 3.6% vs 5.3% (p = 0.2) and 3.8% vs 5.1%, respectively; incidence density, 17.9 vs 27.6 episodes per 1,000 days of mechanical ventilation (MV) [p = 0.18] and 18.9 vs 28.7 episodes per 1,000 days of MV, respectively; hospital antibiotic use in daily defined doses (DDDs), 1,213 vs 1,932 (p 48 h, the comparisons of CASS patients and control subjects were as follows: VAP incidence, 26.7% vs 47.5% (p = 0.04), respectively; incidence density, 31.5 vs 51.6 episodes per 1,000 days of MV, respectively (p = 0.03); median length of ICU stay, 7 vs 16.5 days (p = 0.01), respectively; hospital antibiotic use, 1,206 vs 1,877 DDD (p VAP (relative risk [RR], 6.07; 95% confidence interval [CI], 2.20 to 16.60; p VAP in patients who are at risk. CASS use should be encouraged, at least in patients undergoing MHS.

Blockade of vascular adhesion protein-1 inhibits lymphocyte infiltration in rat liver allograft rejection.

Science.gov (United States)

Martelius, Timi; Salaspuro, Ville; Salmi, Marko; Krogerus, Leena; Höckerstedt, Krister; Jalkanen, Sirpa; Lautenschlager, Irmeli

2004-12-01

Vascular adhesion protein-1 (VAP-1) has been shown to mediate lymphocyte adhesion to endothelia at sites of inflammation, but its functional role in vivo has not been tested in any rodent model. Here we report the effects of VAP-1 blockade on rat liver allograft rejection. BN recipients of PVG liver allografts (known to develop acute rejection by day 7) were treated with 2 mg/kg anti-VAP-1 (a new anti-rat VAP-1 mAb 174-5) or isotype-matched irrelevant antibody (NS1) every other day (n = 6/group) and one group with anti-VAP-1 2 mg/kg daily (n = 7). On day 7, samples were collected for transplant aspiration cytology, histology, and immunohistochemistry. Lymphocyte infiltration to the graft was clearly affected by VAP-blockade. The total inflammation, mainly the number of active lymphoid cells, in transplant aspiration cytology was significantly decreased in animals treated with anti-VAP-1 (4.7 +/- 1.0 and 2.4 +/- 1.0 corrected increment units, respectively) compared to control (6.6 +/- 1.0) (P VAP-1 plays an important role in lymphocyte infiltration to sites of inflammation, and, in particular, liver allograft rejection.

Multiscale analysis of nonlinear systems using computational homology

Energy Technology Data Exchange (ETDEWEB)

Konstantin Mischaikow; Michael Schatz; William Kalies; Thomas Wanner

2010-05-24

This is a collaborative project between the principal investigators. However, as is to be expected, different PIs have greater focus on different aspects of the project. This report lists these major directions of research which were pursued during the funding period: (1) Computational Homology in Fluids - For the computational homology effort in thermal convection, the focus of the work during the first two years of the funding period included: (1) A clear demonstration that homology can sensitively detect the presence or absence of an important flow symmetry, (2) An investigation of homology as a probe for flow dynamics, and (3) The construction of a new convection apparatus for probing the effects of large-aspect-ratio. (2) Computational Homology in Cardiac Dynamics - We have initiated an effort to test the use of homology in characterizing data from both laboratory experiments and numerical simulations of arrhythmia in the heart. Recently, the use of high speed, high sensitivity digital imaging in conjunction with voltage sensitive fluorescent dyes has enabled researchers to visualize electrical activity on the surface of cardiac tissue, both in vitro and in vivo. (3) Magnetohydrodynamics - A new research direction is to use computational homology to analyze results of large scale simulations of 2D turbulence in the presence of magnetic fields. Such simulations are relevant to the dynamics of black hole accretion disks. The complex flow patterns from simulations exhibit strong qualitative changes as a function of magnetic field strength. Efforts to characterize the pattern changes using Fourier methods and wavelet analysis have been unsuccessful. (4) Granular Flow - two experts in the area of granular media are studying 2D model experiments of earthquake dynamics where the stress fields can be measured; these stress fields from complex patterns of 'force chains' that may be amenable to analysis using computational homology. (5) Microstructure

Multiscale analysis of nonlinear systems using computational homology

Energy Technology Data Exchange (ETDEWEB)

Konstantin Mischaikow, Rutgers University/Georgia Institute of Technology, Michael Schatz, Georgia Institute of Technology, William Kalies, Florida Atlantic University, Thomas Wanner,George Mason University

2010-05-19

This is a collaborative project between the principal investigators. However, as is to be expected, different PIs have greater focus on different aspects of the project. This report lists these major directions of research which were pursued during the funding period: (1) Computational Homology in Fluids - For the computational homology effort in thermal convection, the focus of the work during the first two years of the funding period included: (1) A clear demonstration that homology can sensitively detect the presence or absence of an important flow symmetry, (2) An investigation of homology as a probe for flow dynamics, and (3) The construction of a new convection apparatus for probing the effects of large-aspect-ratio. (2) Computational Homology in Cardiac Dynamics - We have initiated an effort to test the use of homology in characterizing data from both laboratory experiments and numerical simulations of arrhythmia in the heart. Recently, the use of high speed, high sensitivity digital imaging in conjunction with voltage sensitive fluorescent dyes has enabled researchers to visualize electrical activity on the surface of cardiac tissue, both in vitro and in vivo. (3) Magnetohydrodynamics - A new research direction is to use computational homology to analyze results of large scale simulations of 2D turbulence in the presence of magnetic fields. Such simulations are relevant to the dynamics of black hole accretion disks. The complex flow patterns from simulations exhibit strong qualitative changes as a function of magnetic field strength. Efforts to characterize the pattern changes using Fourier methods and wavelet analysis have been unsuccessful. (4) Granular Flow - two experts in the area of granular media are studying 2D model experiments of earthquake dynamics where the stress fields can be measured; these stress fields from complex patterns of 'force chains' that may be amenable to analysis using computational homology. (5) Microstructure

Solar cells based on InP/GaP/Si structure

Science.gov (United States)

Kvitsiani, O.; Laperashvil, D.; Laperashvili, T.; Mikelashvili, V.

2016-10-01

Solar cells (SCs) based on III-V semiconductors are reviewed. Presented work emphases on the Solar Cells containing Quantum Dots (QDs) for next-generation photovoltaics. In this work the method of fabrication of InP QDs on III-V semiconductors is investigated. The original method of electrochemical deposition of metals: indium (In), gallium (Ga) and of alloys (InGa) on the surface of gallium phosphide (GaP), and mechanism of formation of InP QDs on GaP surface is presented. The possibilities of application of InP/GaP/Si structure as SC are discussed, and the challenges arising is also considered.

Zea mI, the maize homolog of the allergen-encoding Lol pI gene of rye grass.

Science.gov (United States)

Broadwater, A H; Rubinstein, A L; Chay, C H; Klapper, D G; Bedinger, P A

1993-09-15

Sequence analysis of a pollen-specific cDNA from maize has identified a homolog (Zea mI) of the gene (Lol pI) encoding the major allergen of rye-grass pollen. The protein encoded by the partial cDNA sequence is 59.3% identical and 72.7% similar to the comparable region of the reported amino acid sequence of Lol pIA. Southern analysis indicates that this cDNA represents a member of a small multigene family in maize. Northern analysis shows expression only in pollen, not in vegetative or female floral tissues. The timing of expression is developmentally regulated, occurring at a low level prior to the first pollen mitosis and at a high level after this postmeiotic division. Western analysis detects a protein in maize pollen lysates using polyclonal antiserum and monoclonal antibodies directed against purified Lolium perenne allergen.

Framework for event-based semidistributed modeling that unifies the SCS-CN method, VIC, PDM, and TOPMODEL

Science.gov (United States)

Bartlett, M. S.; Parolari, A. J.; McDonnell, J. J.; Porporato, A.

2016-09-01

Hydrologists and engineers may choose from a range of semidistributed rainfall-runoff models such as VIC, PDM, and TOPMODEL, all of which predict runoff from a distribution of watershed properties. However, these models are not easily compared to event-based data and are missing ready-to-use analytical expressions that are analogous to the SCS-CN method. The SCS-CN method is an event-based model that describes the runoff response with a rainfall-runoff curve that is a function of the cumulative storm rainfall and antecedent wetness condition. Here we develop an event-based probabilistic storage framework and distill semidistributed models into analytical, event-based expressions for describing the rainfall-runoff response. The event-based versions called VICx, PDMx, and TOPMODELx also are extended with a spatial description of the runoff concept of "prethreshold" and "threshold-excess" runoff, which occur, respectively, before and after infiltration exceeds a storage capacity threshold. For total storm rainfall and antecedent wetness conditions, the resulting ready-to-use analytical expressions define the source areas (fraction of the watershed) that produce runoff by each mechanism. They also define the probability density function (PDF) representing the spatial variability of runoff depths that are cumulative values for the storm duration, and the average unit area runoff, which describes the so-called runoff curve. These new event-based semidistributed models and the traditional SCS-CN method are unified by the same general expression for the runoff curve. Since the general runoff curve may incorporate different model distributions, it may ease the way for relating such distributions to land use, climate, topography, ecology, geology, and other characteristics.

Comparative analysis of Homo sapiens and Mus musculus cyclin-dependent kinase (CDK) inhibitor genes p16 (MTS1) and p15 (MTS2).

Science.gov (United States)

Jiang, P; Stone, S; Wagner, R; Wang, S; Dayananth, P; Kozak, C A; Wold, B; Kamb, A

1995-12-01

Cyclin-dependent kinase inhibitors are a growing family of molecules that regulate important transitions in the cell cycle. At least one of these molecules, p16, has been implicated in human tumorigenesis while its close homolog, p15, is induced by cell contact and transforming growth factor-beta (TGF-beta). To investigate the evolutionary and functional features of p15 and p16, we have isolated mouse (Mus musculus) homologs of each gene. Comparative analysis of these sequences provides evidence that the genes have similar functions in mouse and human. In addition, the comparison suggests that a gene conversion event is part of the evolution of the human p15 and p16 genes.

Influence of mesh structure on 2D full shallow water equations and SCS Curve Number simulation of rainfall/runoff events

Science.gov (United States)

Caviedes-Voullième, Daniel; García-Navarro, Pilar; Murillo, Javier

2012-07-01

SummaryHydrological simulation of rain-runoff processes is often performed with lumped models which rely on calibration to generate storm hydrographs and study catchment response to rain. In this paper, a distributed, physically-based numerical model is used for runoff simulation in a mountain catchment. This approach offers two advantages. The first is that by using shallow-water equations for runoff flow, there is less freedom to calibrate routing parameters (as compared to, for example, synthetic hydrograph methods). The second, is that spatial distributions of water depth and velocity can be obtained. Furthermore, interactions among the various hydrological processes can be modeled in a physically-based approach which may depend on transient and spatially distributed factors. On the other hand, the undertaken numerical approach relies on accurate terrain representation and mesh selection, which also affects significantly the computational cost of the simulations. Hence, we investigate the response of a gauged catchment with this distributed approach. The methodology consists of analyzing the effects that the mesh has on the simulations by using a range of meshes. Next, friction is applied to the model and the response to variations and interaction with the mesh is studied. Finally, a first approach with the well-known SCS Curve Number method is studied to evaluate its behavior when coupled with a shallow-water model for runoff flow. The results show that mesh selection is of great importance, since it may affect the results in a magnitude as large as physical factors, such as friction. Furthermore, results proved to be less sensitive to roughness spatial distribution than to mesh properties. Finally, the results indicate that SCS-CN may not be suitable for simulating hydrological processes together with a shallow-water model.

CO2 driven endotracheal tube cuff control in critically ill patients: A randomized controlled study.

Directory of Open Access Journals (Sweden)

Gennaro De Pascale

Full Text Available To determine the safety and clinical efficacy of an innovative integrated airway system (AnapnoGuard™ 100 system that continuously monitors and controls the cuff pressure (Pcuff, while facilitating the aspiration of subglottic secretions (SS.This was a prospective, single centre, open-label, randomized, controlled feasibility and safety trial. The primary endpoint of the study was the rate of device related adverse events (AE and serious AE (SAE as a result of using AnapnoGuard (AG 100 during mechanical ventilation. Secondary endpoints were: (1 mechanical complications rate (2 ICU staff satisfaction; (3 VAP occurrence; (4 length of mechanical ventilation; (5 length of Intensive Care Unit stay and mortality; (6 volume of evacuated subglottic secretions. Sixty patients were randomized to be intubated with the AG endotracheal-tube (ETT and connected to the AG 100 system allowing Pcuff adjustment and SS aspiration; or with an ETT combined with SS drainage and Pcuff controlled manually.No difference in adverse events rate was identified between the groups. The use of AG system was associated with a significantly higher incidence of Pcuff determinations in the safety range (97.3% vs. 71%; p<0.01 and a trend to a greater volume of aspirated SS secretions: (192.0[64-413] ml vs. 150[50-200], p = 0.19 (total; (57.8[20-88.7] ml vs. 50[18.7-62] ml, p = 0.11 (daily. No inter-group difference was detected using AG system vs. controls in terms of post-extubation throat pain level (0 [0-2] vs. 0 [0-3]; p = 0.7, hoarseness (42.9% vs. 75%; p = 0.55 and tracheal mucosa oedema (16.7% vs. 10%; p = 0.65. Patients enrolled in the AG group had a trend to reduced VAP risk of ventilator-associated pneumonia(VAP (14.8% vs. 40%; p = 0.06, which were more frequently monomicrobial (25% vs. 70%; p = 0.03. No statistically significant difference was observed in duration of mechanical ventilation, ICU stay, and mortality.The use AG 100 system and AG tube in critically ill

HAL-2 promotes homologous pairing during Caenorhabditis elegans meiosis by antagonizing inhibitory effects of synaptonemal complex precursors.

Science.gov (United States)

Zhang, Weibin; Miley, Natasha; Zastrow, Michael S; MacQueen, Amy J; Sato, Aya; Nabeshima, Kentaro; Martinez-Perez, Enrique; Mlynarczyk-Evans, Susanna; Carlton, Peter M; Villeneuve, Anne M

2012-01-01

During meiosis, chromosomes align with their homologous pairing partners and stabilize this alignment through assembly of the synaptonemal complex (SC). Since the SC assembles cooperatively yet is indifferent to homology, pairing and SC assembly must be tightly coordinated. We identify HAL-2 as a key mediator in this coordination, showing that HAL-2 promotes pairing largely by preventing detrimental effects of SC precursors (SYP proteins). hal-2 mutants fail to establish pairing and lack multiple markers of chromosome movement mediated by pairing centers (PCs), chromosome sites that link chromosomes to cytoplasmic microtubules through nuclear envelope-spanning complexes. Moreover, SYP proteins load inappropriately along individual unpaired chromosomes in hal-2 mutants, and markers of PC-dependent movement and function are restored in hal-2; syp double mutants. These and other data indicate that SYP proteins can impede pairing and that HAL-2 promotes pairing predominantly but not exclusively by counteracting this inhibition, thereby enabling activation and regulation of PC function. HAL-2 concentrates in the germ cell nucleoplasm and colocalizes with SYP proteins in nuclear aggregates when SC assembly is prevented. We propose that HAL-2 functions to shepherd SYP proteins prior to licensing of SC assembly, preventing untimely interactions between SC precursors and chromosomes and allowing sufficient accumulation of precursors for rapid cooperative assembly upon homology verification.

Efficacy of intermittent sub-glottic suctioning in prevention of ventilator-associated pneumonia- A preliminary study of 100 patients

Directory of Open Access Journals (Sweden)

M N Vijai

2016-01-01

Full Text Available Background and Aims: Oropharyngeal colonisation followed by aspiration of contaminated secretions is the major cause for ventilator-associated pneumonia (VAP. Pooled secretions present in the sub-glottic area above inflated endotracheal tube cuff may be aspirated into the lower airways. It was hypothesised that intermittent suctioning of sub-glottic secretions would prevent VAP. Methods: Group I (n = 50 patients were intubated with HiLo Evac™ endotracheal (ET tube with facility for sub-glottic suctioning, and Group II (n = 50 patients were intubated with HiLo Contour™ ET tube without such facility. In the Group I, sub-glottic suctioning was performed every 2 h. Incidence of VAP, mean ventilator days, Intensive Care Unit (ICU stay and mortality were compared. Qualitative variables were reported as percentages and were compared by Chi-square test or unpaired two-tailed, Fisher′s exact test, as appropriate, to analyse the significance of difference between the two groups. Results: The two groups were similar with respect to demographic characteristics. VAP was seen in 6% of patients in Group I and 22% of patients in Group II (P = 0.021. Both early- and late-onset VAPs were significantly reduced in Group I. Both ventilator days (8.0 vs. 6.45; P = 0.001 and ICU stay (8.33 vs. 6.33; P = 0.001 on the day of onset of VAP were significantly more in the Group I. Total ventilator days were significantly less (6.52 vs. 8.32; P = 0.006 with lower incidence of mortality (36% vs. 48%; P = 0.224 in the Group I. Conclusion: Intermittent sub-glottic suctioning reduces the incidence of VAP including late-onset VAP.

Efficacy of intermittent sub-glottic suctioning in prevention of ventilator-associated pneumonia- A preliminary study of 100 patients.

Science.gov (United States)

Vijai, M N; Ravi, Parli R; Setlur, Rangaraj; Vardhan, Harsh

2016-05-01

Oropharyngeal colonisation followed by aspiration of contaminated secretions is the major cause for ventilator-associated pneumonia (VAP). Pooled secretions present in the sub-glottic area above inflated endotracheal tube cuff may be aspirated into the lower airways. It was hypothesised that intermittent suctioning of sub-glottic secretions would prevent VAP. Group I (n = 50) patients were intubated with HiLo Evac™ endotracheal (ET) tube with facility for sub-glottic suctioning, and Group II (n = 50) patients were intubated with HiLo Contour™ ET tube without such facility. In the Group I, sub-glottic suctioning was performed every 2 h. Incidence of VAP, mean ventilator days, Intensive Care Unit (ICU) stay and mortality were compared. Qualitative variables were reported as percentages and were compared by Chi-square test or unpaired two-tailed, Fisher's exact test, as appropriate, to analyse the significance of difference between the two groups. The two groups were similar with respect to demographic characteristics. VAP was seen in 6% of patients in Group I and 22% of patients in Group II (P = 0.021). Both early- and late-onset VAPs were significantly reduced in Group I. Both ventilator days (8.0 vs. 6.45; P = 0.001) and ICU stay (8.33 vs. 6.33; P = 0.001) on the day of onset of VAP were significantly more in the Group I. Total ventilator days were significantly less (6.52 vs. 8.32; P = 0.006) with lower incidence of mortality (36% vs. 48%; P = 0.224) in the Group I. Intermittent sub-glottic suctioning reduces the incidence of VAP including late-onset VAP.

Effect of high temperature annealing on the microstructure of SCS-6 SiC fibers

Science.gov (United States)

Ning, X. J.; Pirouz, P.; Bhatt, R. T.

1992-01-01

The effect of annealing the SCS-6 SiC fiber for one hour at 2000 C in an argon atmosphere is reported. The SiC grains in the fiber coarsen appreciably and the intergranular carbon films segregate to the grain junctions. It would appear that grain growth in the outer part of the fiber is primarily responsible for the loss in fiber strength and improvement in fiber creep resistance.

Supine position and nonmodifiable risk factors for ventilator-associated pneumonia in trauma patients.

Science.gov (United States)

Michetti, Christopher P; Prentice, Heather A; Rodriguez, Jennifer; Newcomb, Anna

2017-02-01

We studied trauma-specific conditions precluding semiupright positioning and other nonmodifiable risk factors for their influence on ventilator-associated pneumonia (VAP). We performed a retrospective study at a Level I trauma center from 2008 to 2012 on ICU patients aged ≥15, who were intubated for more than 2 days. Using backward logistic regression, a composite of 4 factors (open abdomen, acute spinal cord injury, spine fracture, spine surgery) that preclude semiupright positioning (supine composite) and other variables were analyzed. In total, 77 of 374 (21%) patients had VAP. Abbreviated Injury Score head/neck greater than 2 (odds ratio [OR] 2.79, P = .006), esophageal obturator airway (OR 4.25, P = .015), red cell/plasma transfusion in the first 2 intensive care unit days (OR 2.59, P = .003), and 11 or more ventilator days (OR 17.38, P VAP risk factors, whereas supine composite, scene vs emergency department airway intervention, brain injury, and coma were not. Factors that may temporarily preclude semiupright positioning in intubated trauma patients were not associated with a higher risk for VAP. Copyright © 2016 Elsevier Inc. All rights reserved.

Assessment of a training programme for the prevention of ventilator-associated pneumonia.

Science.gov (United States)

Jam Gatell, M Rosa; Santé Roig, Montserrat; Hernández Vian, Óscar; Carrillo Santín, Esther; Turégano Duaso, Concepción; Fernández Moreno, Inmaculada; Vallés Daunis, Jordi

2012-01-01

Ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in intensive care units (ICUs). Most published studies have analysed nurses' theoretical knowledge about a specific procedure; however, the transfer of this knowledge to the practice has received little attention. To assess the impact of training session on nurses' knowledge regarding VAP, compliance with VAP preventive measures, VAP incidence and determining whether nursing workload affects compliance. A prospective, quasiexperimental, pre- and post-study of the nursing team in a 16-bed medical/surgical ICU. Pre-intervention phase: a questionnaire to assess nurses' knowledge of VAP prevention measures, direct observation and review of clinical records to assess compliance. Intervention phase: eight training sessions for nurses. The post-intervention phase mirrored the pre-intervention phase. Nurses answered more questions correctly on the post-intervention questionnaire than on the pre-intervention (17·87 ± 2·69 versus 15·91 ± 2·68, p = 0·002). Compliance with the following measures was better during the post-intervention period (p = 0·001): use of the smallest possible nasogastric tube, controlled aspiration of subglottic secretions and endotracheal tube cuff pressure, use of oral chlorhexidine and recording the endotracheal tube fixation number. VAP incidence remained unchanged throughout the study. However, a trend towards lower incidence of late (>4 days after intubation) VAP was observed (4·6 versus 3·1 episodes/1000 ventilation days, p = 0·37). The programme improved both knowledge of and compliance with VAP preventive measures, although improved knowledge did not always result in improved compliance. © 2012 The Authors. Nursing in Critical Care © 2012 British Association of Critical Care Nurses.

Assessment of a training programme for the prevention of ventilator-associated pneumonia

Science.gov (United States)

Jam Gatell, M Rosa; Santé Roig, Montserrat; Hernández Vian, Óscar; Carrillo Santín, Esther; Turégano Duaso, Concepción; Fernández Moreno, Inmaculada; Vallés Daunis, Jordi

2012-01-01

Background Ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in intensive care units (ICUs). Most published studies have analysed nurses' theoretical knowledge about a specific procedure; however, the transfer of this knowledge to the practice has received little attention. Aim To assess the impact of training session on nurses' knowledge regarding VAP, compliance with VAP preventive measures, VAP incidence and determining whether nursing workload affects compliance. Method A prospective, quasiexperimental, pre- and post-study of the nursing team in a 16-bed medical/surgical ICU. Pre-intervention phase: a questionnaire to assess nurses' knowledge of VAP prevention measures, direct observation and review of clinical records to assess compliance. Intervention phase: eight training sessions for nurses. The post-intervention phase mirrored the pre-intervention phase. Findings Nurses answered more questions correctly on the post-intervention questionnaire than on the pre-intervention (17·87 ± 2·69 versus 15·91 ± 2·68, p = 0·002). Compliance with the following measures was better during the post-intervention period (p = 0·001): use of the smallest possible nasogastric tube, controlled aspiration of subglottic secretions and endotracheal tube cuff pressure, use of oral chlorhexidine and recording the endotracheal tube fixation number. VAP incidence remained unchanged throughout the study. However, a trend towards lower incidence of late (>4 days after intubation) VAP was observed (4·6 versus 3·1 episodes/1000 ventilation days, p = 0·37). Conclusion The programme improved both knowledge of and compliance with VAP preventive measures, although improved knowledge did not always result in improved compliance. PMID:23061618

Diagnostic Performance of Soluble Triggering Receptor Expressed on Myeloid Cells-1 in Ventilator-Associated Pneumonia of Patients with Ischemic Stroke

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Yuetian Yu

2017-01-01

Full Text Available Objective. To investigate the effect of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1 in serum, bronchoalveolar lavage fluid (BALF, endotracheal aspiration (ETA, and exhaled breath condensate (EBC samples as early biomarkers for the diagnosis of ventilator-associated pneumonia (VAP in patients with ischemic stroke. Methods. One hundred and thirty-two patients with clinically suspected VAP were enrolled in this study. Bronchoscopy was performed on the day of clinically suspected VAP. sTREM-1 levels in serum, BALF, ETA, and EBC were measured. VAP was diagnosed by quantitative cultures of BALF (≥104 cfu/mL. Results. VAP was confirmed in 76 (57.58% cases. Patients with VAP showed significantly higher sTREM-1 in BALF [32.35 (IQR, 30.08–41.72 versus 18.92 (11.89–31.72] pg/mL and in EBC [1.57 (IQR, 1.02–2.61 versus 0.41 (0.19–1.61] pg/mL than patients without VAP. The area under the curve was 0.813 (p<0.001. The optimum cut-off value for sTREM-1 in BALF was 23.61 pg/mL, yielding sensitivity and specificity of 85.5% and 73.1%. sTREM-1 in BALF had excellent correlation with that in EBC (R2 = 0.78, p<0.05. Conclusions. sTREM-1 in EBC and BALF had good diagnostic performance in differentiating patients with and without VAP.

Loss of Ubr2, an E3 ubiquitin ligase, leads to chromosome fragility and impaired homologous recombinational repair

International Nuclear Information System (INIS)

Ouyang, Yan; Kwon, Yong Tae; An, Jee Young; Eller, Danny; Tsai, S.-C.; Diaz-Perez, Silvia; Troke, Joshua J.; Teitell, Michael A.; Marahrens, York

2006-01-01

The N-end rule pathway of protein degradation targets proteins with destabilizing N-terminal residues. Ubr2 is one of the E3 ubiquitin ligases of the mouse N-end rule pathway. We have previously shown that Ubr2 -/- male mice are infertile, owing to the arrest of spermatocytes between the leptotene/zygotene and pachytene of meiosis I, the failure of chromosome pairing, and subsequent apoptosis. Here, we report that mouse fibroblast cells derived from Ubr2 -/- embryos display genome instability. The frequency of chromosomal bridges and micronuclei were much higher in Ubr2 -/- fibroblasts than in +/+ controls. Metaphase chromosome spreads from Ubr2 -/- cells revealed a high incidence of spontaneous chromosomal gaps, indicating chromosomal fragility. These fragile sites were generally replicated late in S phase. Ubr2 -/- cells were hypersensitive to mitomycin C, a DNA cross-linking agent, but displayed normal sensitivity to gamma-irradiation. A reporter assay showed that Ubr2 -/- cells are significantly impaired in the homologous recombination repair of a double strand break. In contrast, Ubr2 -/- cells appeared normal in an assay for non-homologous end joining. Our results therefore unveil the role of the ubiquitin ligase Ubr2 in maintaining genome integrity and in homologous recombination repair

Loss of Ubr2, an E3 ubiquitin ligase, leads to chromosome fragility and impaired homologous recombinational repair

Energy Technology Data Exchange (ETDEWEB)

Ouyang, Yan [Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Kwon, Yong Tae [Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 (United States); An, Jee Young [Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 (United States); Eller, Danny [Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Tsai, S.-C. [Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Diaz-Perez, Silvia [Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Troke, Joshua J. [Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Teitell, Michael A. [Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States); Marahrens, York [Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 (United States)]. E-mail: ymarahrens@mednet.ucla.edu

2006-04-11

The N-end rule pathway of protein degradation targets proteins with destabilizing N-terminal residues. Ubr2 is one of the E3 ubiquitin ligases of the mouse N-end rule pathway. We have previously shown that Ubr2{sup -/-} male mice are infertile, owing to the arrest of spermatocytes between the leptotene/zygotene and pachytene of meiosis I, the failure of chromosome pairing, and subsequent apoptosis. Here, we report that mouse fibroblast cells derived from Ubr2{sup -/-} embryos display genome instability. The frequency of chromosomal bridges and micronuclei were much higher in Ubr2{sup -/-} fibroblasts than in +/+ controls. Metaphase chromosome spreads from Ubr2{sup -/-} cells revealed a high incidence of spontaneous chromosomal gaps, indicating chromosomal fragility. These fragile sites were generally replicated late in S phase. Ubr2{sup -/-} cells were hypersensitive to mitomycin C, a DNA cross-linking agent, but displayed normal sensitivity to gamma-irradiation. A reporter assay showed that Ubr2{sup -/-} cells are significantly impaired in the homologous recombination repair of a double strand break. In contrast, Ubr2{sup -/-} cells appeared normal in an assay for non-homologous end joining. Our results therefore unveil the role of the ubiquitin ligase Ubr2 in maintaining genome integrity and in homologous recombination repair.

HIV-1 and herpes simplex virus type-2 genital shedding among co-infected women using self-collected swabs in Chiang Rai, Thailand.

Science.gov (United States)

Forhan, S E; Dunne, E F; Sternberg, M R; Whitehead, S J; Leelawiwat, W; Thepamnuay, S; Chen, C; Evans-Strickfaden, Tt; McNicholl, J M; Markowitz, L E

2012-08-01

We analysed 528 genital self-collected swabs (SCS) from 67 HIV-1 and herpes simplex virus type-2 (HSV-2) co-infected women collected during the placebo month of a randomized crossover clinical trial of suppressive acyclovir in Chiang Rai, Thailand. In this first longitudinal study of HIV-1 and HSV-2 co-infected women using genital SCS specimens, we found frequent mucosal HIV-1 shedding. Overall, 372 (70%) swabs had detectable HIV-1 RNA with median HIV-1 viral load of 2.61 log(10) copies/swab. We found no statistically significant association between detectable HIV-1 RNA and HSV-2 DNA in the same SCS specimen (adjusted odds ratio [aOR] 1.40; 95% confidence intervals [CI], 0.78-2.60, P = 0.25). Only baseline HIV-1 plasma viral load was independently associated with genital HIV-1 RNA shedding (aOR, 7.6; 95% CI, 3.3-17.2, P genital sampling, and inclusion of genital sites other than the cervix.

A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package

Science.gov (United States)

Motomura, Kenta; Nakamura, Morikazu; Otaki, Joji M.

2013-01-01

Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs) or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions) and dissimilarities (e.g., behaviors of low-rank samples) between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs. PMID:24688703

A FREQUENCY-BASED LINGUISTIC APPROACH TO PROTEIN DECODING AND DESIGN: SIMPLE CONCEPTS, DIVERSE APPLICATIONS, AND THE SCS PACKAGE

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Kenta Motomura

2013-02-01

Full Text Available Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions and dissimilarities (e.g., behaviors of low-rank samples between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs.

The ZW sex microchromosomes of an Australian dragon lizard share no homology with those of other reptiles or birds.

Science.gov (United States)

Ezaz, Tariq; Moritz, Benjamin; Waters, Paul; Marshall Graves, Jennifer A; Georges, Arthur; Sarre, Stephen D

2009-01-01

Reptiles show a diverse array of sex chromosomal systems but, remarkably, the Z sex chromosomes of chicken are homologous to the ZW sex chromosomes of a species of gecko, Gekko hokouensis, suggesting an ancient but common origin. This is in contrast to the ZW sex chromosomes of snakes and a species of soft-shelled turtle, Pelodiscus sinensis, which are nonhomologous to those of chicken or each other and appear to have been independently derived. In this paper, we determine what homology, if any, the sex chromosomes of the Australian dragon lizard Pogona vitticeps shares with those of snake and chicken by mapping the dragon homologs of five snake Z chromosome genes (WAC, KLF6, TAX1BP1, RAB5A, and CTNNB1) and five chicken Z chromosome genes (ATP5A1, GHR, DMRT1, CHD1, and APTX) to chromosomes in the dragon. The dragon homologs of snake and chicken sex chromosome genes map to chromosomes 6 and chromosome 2, respectively, in the dragon and that DMRT1, the bird sex-determining gene, is not located on the sex chromosomes of P. vitticeps. Indeed, our data show that the dragon homolog to the chicken Z chromosome is likely to be wholly contained within chromosome 2 in P. vitticeps, which suggests that the sex-determining factor in P. vitticeps is not the sex-determining gene of chicken. Homology between chicken Z chromosome and G. hokouensis ZW chromosome pairs has been interpreted as retention of ancient ZW sex chromosomes in which case the nonhomologous sex chromosomes of snake and dragons would be independently derived. Our data add another case of independently derived sex chromosomes in a squamate reptile, which makes retention of ancient sex chromosome homology in the squamates less plausible. Alternatively, the conservation between the bird Z chromosome and the G. hokouensis ZW chromosomes pairs is coincidental, may be an example of convergent evolution, its status as the Z chromosome having been independently derived in birds and G. hokouensis.

Frequent downregulation of BTB and CNC homology 2 expression in Epstein-Barr virus-positive diffuse large B-cell lymphoma.

Science.gov (United States)

Noujima-Harada, Mai; Takata, Katsuyoshi; Miyata-Takata, Tomoko; Sakurai, Hiroaki; Igarashi, Kazuhiko; Ito, Etsuro; Nagakita, Keina; Taniguchi, Kohei; Ohnishi, Nobuhiko; Omote, Shizuma; Tabata, Tetsuya; Sato, Yasuharu; Yoshino, Tadashi

2017-05-01

Diffuse large B-cell lymphoma (DLBCL) is the most common B-cell lymphoma subtype, and the Epstein-Barr virus (EBV)-positive subtype of DLBCL is known to show a more aggressive clinical behavior than the EBV-negative one. BTB and CNC homology 2 (BACH2) has been highlighted as a tumor suppressor in hematopoietic malignancies; however, the role of BACH2 in EBV-positive DLBCL is unclear. In the present study, BACH2 expression and its significance were studied in 23 EBV-positive and 43 EBV-negative patient samples. Immunohistochemistry revealed BACH2 downregulation in EBV-positive cases (P < 0.0001), although biallelic deletion of BACH2 was not detected by FISH. Next, we analyzed the contribution of BACH2 negativity to aggressiveness in EBV-positive B-cell lymphomas using FL-18 (EBV-negative) and FL-18-EB cells (FL-18 sister cell line, EBV-positive). In BACH2-transfected FL-18-EB cells, downregulation of phosphorylated transforming growth factor-β-activated kinase 1 (pTAK1) and suppression in p65 nuclear fractions were observed by Western blot analysis contrary to non-transfected FL-18-EB cells. In patient samples, pTAK1 expression and significant nuclear p65, p50, and p52 localization were detected immunohistochemically in BACH2-negative DLBCL (P < 0.0001, P = 0.006, and P = 0.001, respectively), suggesting that BACH2 downregulation contributes to constitutive activation of the nuclear factor-κB pathway through TAK1 phosphorylation in BACH2-negative DLBCL (most EBV-positive cases). Although further molecular and pathological studies are warranted to clarify the detailed mechanisms, downregulation of BACH2 may contribute to constitutive activation of the nuclear factor-κB pathway through TAK1 activation. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

Analysis of the runoff generation mechanism for the investigation of the SCS-CN method applicability to a partial area experimental watershed

Science.gov (United States)

Soulis, K. X.; Valiantzas, J. D.; Dercas, N.; Londra, P. A.

2009-01-01

The Soil Conservation Service Curve Number (SCS-CN) method is widely used for predicting direct runoff volume for a given rainfall event. The applicability of the SCS-CN method and the runoff generation mechanism were thoroughly analysed in a Mediterranean experimental watershed in Greece. The region is characterized by a Mediterranean semi-arid climate. A detailed land cover and soil survey using remote sensing and GIS techniques, showed that the watershed is dominated by coarse soils with high hydraulic conductivities, whereas a smaller part is covered with medium textured soils and impervious surfaces. The analysis indicated that the SCS-CN method fails to predict runoff for the storm events studied, and that there is a strong correlation between the CN values obtained from measured runoff and the rainfall depth. The hypothesis that this correlation could be attributed to the existence of an impermeable part in a very permeable watershed was examined in depth, by developing a numerical simulation water flow model for predicting surface runoff generated from each of the three soil types of the watershed. Numerical runs were performed using the HYDRUS-1D code. The results support the validity of this hypothesis for most of the events examined where the linear runoff formula provides better results than the SCS-CN method. The runoff coefficient of this formula can be taken equal to the percentage of the impervious area. However, the linear formula should be applied with caution in case of extreme events with very high rainfall intensities. In this case, the medium textured soils may significantly contribute to the total runoff and the linear formula may significantly underestimate the runoff produced.

Phosphosite mapping of P-type plasma membrane H+-ATPase in homologous and heterologous environments

DEFF Research Database (Denmark)

Rudashevskaya, Elena; Ye, Juanying; Jensen, Ole Nørregaard

2012-01-01

Phosphorylation is an important posttranslational modification of proteins in living cells and primarily serves regulatory purposes. Several methods were employed for isolating phosphopeptides from proteolytically digested plasma membranes of Arabidopsis thaliana. After a mass spectrometric...... of the phosphosites identified in AHA2 were identical in the plant and fungal systems even though none of the target sequences in AHA2 show homology to proteins of the fungal host. These findings suggest an unexpected accessibility of the terminal regulatory domain of plasma membrane H(+)-ATPase to protein kinase...... analysis of the resulting peptides we could identify 10 different phosphorylation sites in plasma membrane H(+)-ATPases AHA1, AHA2, AHA3, and AHA4/11, five of which have not been reported before, bringing the total number of phosphosites up to 11, which is substantially higher than reported so far for any...

Chemical shift homology in proteins

International Nuclear Information System (INIS)

Potts, Barbara C.M.; Chazin, Walter J.

1998-01-01

The degree of chemical shift similarity for homologous proteins has been determined from a chemical shift database of over 50 proteins representing a variety of families and folds, and spanning a wide range of sequence homologies. After sequence alignment, the similarity of the secondary chemical shifts of C α protons was examined as a function of amino acid sequence identity for 37 pairs of structurally homologous proteins. A correlation between sequence identity and secondary chemical shift rmsd was observed. Important insights are provided by examining the sequence identity of homologous proteins versus percentage of secondary chemical shifts that fall within 0.1 and 0.3 ppm thresholds. These results begin to establish practical guidelines for the extent of chemical shift similarity to expect among structurally homologous proteins

Novel Method to Improve Radiologist Agreement in Interpretation of Serial Chest Radiographs in the ICU

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Denise A Castro

2015-01-01

Full Text Available Objectives: To determine whether a novel method and device, called a variable attenuation plate (VAP, which equalizes chest radiographic appearance and allows for synchronization of manual image windowing with comparison studies, would improve consistency in interpretation. Materials and Methods: Research ethics board approved the prospective cohort pilot study, which included 50 patients in the intensive care unit (ICU undergoing two serial chest radiographs with a VAP placed on each one of them. The VAP allowed for equalization of density and contrast between the patients′ serial chest radiographs. Three radiologists interpreted all the studies with and without the use of VAP. Kappa and percent agreement was used to calculate agreement between radiologists′ interpretations with and without the plate. Results: Radiologist agreement was substantially higher with the VAP method, as compared to that with the non-VAP method. Kappa values between Radiologists A and B, A and C, and B and C were 46%, 55%, and 51%, respectively, which improved to 73%, 81%, and 66%, respectively, with the use of VAP. Discrepant report impressions (i.e., one radiologist′s impression of unchanged versus one or both of the other radiologists stating improved or worsened in their impression ranged from 24 to 28.6% without the use of VAP and from 10 to 16% with the use of VAP (χ2 = 7.454, P < 0.01. Opposing views (i.e., one radiologist′s impression of improved and one of the others stating disease progression or vice versa were reported in 7 (12% cases in the non-VAP group and 4 (7% cases in the VAP group (χ2 = 0.85, P = 0.54. Conclusion: Numerous factors play a role in image acquisition and image quality, which can contribute to poor consistency and reliability of portable chest radiographic interpretations. Radiologists′ agreement of image interpretation can be improved by use of a novel method consisting of a VAP and associated software and has the potential

Computing Homology Group Generators of Images Using Irregular Graph Pyramids

OpenAIRE

Peltier , Samuel; Ion , Adrian; Haxhimusa , Yll; Kropatsch , Walter; Damiand , Guillaume

2007-01-01

International audience; We introduce a method for computing homology groups and their generators of a 2D image, using a hierarchical structure i.e. irregular graph pyramid. Starting from an image, a hierarchy of the image is built, by two operations that preserve homology of each region. Instead of computing homology generators in the base where the number of entities (cells) is large, we first reduce the number of cells by a graph pyramid. Then homology generators are computed efficiently on...

Identification of putative substrates for cynomolgus monkey cytochrome P450 2C8 by substrate depletion assays with 22 human P450 substrates and inhibitors.

Science.gov (United States)

Hosaka, Shinya; Murayama, Norie; Satsukawa, Masahiro; Uehara, Shotaro; Shimizu, Makiko; Iwasaki, Kazuhide; Iwano, Shunsuke; Uno, Yasuhiro; Yamazaki, Hiroshi

2016-07-01

Cynomolgus monkeys are widely used in drug developmental stages as non-human primate models. Previous studies used 89 compounds to investigate species differences associated with cytochrome P450 (P450 or CYP) function that reported monkey specific CYP2C76 cleared 19 chemicals, and homologous CYP2C9 and CYP2C19 metabolized 17 and 30 human CYP2C9 and/or CYP2C19 substrates/inhibitors, respectively. In the present study, 22 compounds selected from viewpoints of global drug interaction guidances and guidelines were further evaluated to seek potential substrates for monkey CYP2C8, which is highly homologous to human CYP2C8 (92%). Amodiaquine, montelukast, quercetin and rosiglitazone, known as substrates or competitive inhibitors of human CYP2C8, were metabolically depleted by recombinant monkey CYP2C8 at relatively high rates. Taken together with our reported findings of the slow eliminations of amodiaquine and montelukast by monkey CYP2C9, CYP2C19 and CYP2C76, the present results suggest that these at least four chemicals may be good marker substrates for monkey CYP2C8. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Ammonium ion transport by the AMT/Rh homolog TaAMT1;1 is stimulated by acidic pH

DEFF Research Database (Denmark)

Søgaard, Rikke; Alsterfjord, Magnus; Macaulay, Nanna

2009-01-01

It is unclear how ammonia is transported by proteins from the Amt/Mep/Rh superfamily. We investigated this for the ammonium transporter TaAMT1;1 from wheat expressed in Xenopus oocytes by two-electrode voltage clamp and radio-labeled uptakes. Inward currents were activated by NH (4......) (+) or methylammonium ions (MeA(+)). Importantly, currents increased fivefold when the external pH was decreased from 7.4 to 5.5; this type of pH dependence is unique and is a strong indication of NH (4) (+) or MeA(+) transport. This was confirmed by the close correlation between the uptake of radio-labeled Me......A(+) and MeA(+)-induced currents. Homology models of members of the Amt/Mep/Rh superfamily exhibited major divergences in their cytoplasmic regions. A point mutation in this region of TaAMT1;1 abolished the pH sensitivity and decreased the apparent affinities for NH (4) (+) and MeA(+). We suggest a model...

Increase in the Accuracy of Calculating Length of Horizontal Cable SCS in Civil Engineering

Science.gov (United States)

Semenov, A.

2017-11-01

A modification of the method for calculating the horizontal cable consumption of SCS established at civil engineering facilities is proposed. The proposed procedure preserves the prototype simplicity and provides a 5 percent accuracy increase. The values of the achieved accuracy are justified, their compliance with the practice of real projects is proved. The method is brought to the level of the engineering algorithm and formalized in the form of 12/70 rule.

Impact of pathogen-directed antimicrobial therapy for ventilator-associated pneumonia in trauma patients on charges and recurrence.

Science.gov (United States)

Sharpe, John P; Magnotti, Louis J; Weinberg, Jordan A; Swanson, Joseph M; Wood, G Christopher; Fabian, Timothy C; Croce, Martin A

2015-04-01

Ventilator-associated pneumonia (VAP) represents one of the driving forces behind antibiotic use in the ICU. In a previous study, we established a defined algorithm for treatment of hospital-acquired VAP dictated by the causative pathogen. The purpose of the current study was to evaluate the impact of this algorithm for hospital-acquired VAP on recurrence and charges in trauma patients. Patients with VAP secondary to MRSA, Acinetobacter baumannii, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, or Enterobacteriaceae during 5 years subsequent to the previous study were evaluated. All VAP were diagnosed using quantitative cultures of the bronchoalveolar lavage effluent. Duration of antimicrobial therapy was dictated by the causative pathogen. If microbiologic resolution, defined as 10(5) colony-forming units/mL on subsequent bronchoalveolar lavage performed within 2 weeks after completion of appropriate therapy. Five hundred and twenty-nine VAP episodes were identified in 381 patients. Overall recurrence was unchanged compared with the previous study (1.5% vs 2%; p = 0.3). There was a decrease in the number of bronchoalveolar lavages performed per patient compared with the previous study (1.6 vs 2.3; p = 0.24) and a reduction of 4.8 antibiotic days per VAP episode compared with the previous study. Both changes resulted in a cumulative reduction of $3,535.04 per patient, for a savings of $1.35 million during the study period. Hospital-acquired VAP can be managed effectively by a defined course of therapy dictated by the causative pathogen. Adherence to an established algorithm simplified the management of VAP and contributed to a cumulative reduction in patient charges without impacting recurrence. Copyright © 2015 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Comparison of Performance between Genetic Algorithm and SCE-UA for Calibration of SCS-CN Surface Runoff Simulation

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Ji-Hong Jeon

2014-11-01

Full Text Available Global optimization methods linked with simulation models are widely used for automated calibration and serve as useful tools for searching for cost-effective alternatives for environmental management. A genetic algorithm (GA and shuffled complex evolution (SCE-UA algorithm were linked with the Long-Term Hydrologic Impact Assessment (L-THIA model, which employs the curve number (SCS-CN method. The performance of the two optimization methods was compared by automatically calibrating L-THIA for monthly runoff from 10 watersheds in Indiana. The selected watershed areas ranged from 32.7 to 5844.1 km2. The SCS-CN values and total five-day rainfall for adjustment were optimized, and the objective function used was the Nash-Sutcliffe value (NS value. The GA method rapidly reached the optimal space until the 10th generating population (generation, and after the 10th generation solutions increased dispersion around the optimal space, called a cross hair pattern, because of mutation rate increase. The number of looping executions influenced the performance of model calibration for the SCE-UA and GA method. The GA method performed better for the case of fewer loop executions than the SCE-UA method. For most watersheds, calibration performance using GA was better than for SCE-UA until the 50th generation when the number of model loop executions was around 5150 (one generation has 100 individuals. However, after the 50th generation of the GA method, the SCE-UA method performed better for calibrating monthly runoff compared to the GA method. Optimized SCS-CN values for primary land use types were nearly the same for the two methods, but those for minor land use types and total five-day rainfall for AMC adjustment were somewhat different because those parameters did not significantly influence calculation of the objective function. The GA method is recommended for cases when model simulation takes a long time and the model user does not have sufficient time

Structure-based design of an osteoclast-selective, nonpeptide Src homology 2 inhibitor with in vivo antiresorptive activity

Science.gov (United States)

Shakespeare, William; Yang, Michael; Bohacek, Regine; Cerasoli, Franklin; Stebbins, Karin; Sundaramoorthi, Raji; Azimioara, Mihai; Vu, Chi; Pradeepan, Selvi; Metcalf, Chester; Haraldson, Chad; Merry, Taylor; Dalgarno, David; Narula, Surinder; Hatada, Marcos; Lu, Xiaode; van Schravendijk, Marie Rose; Adams, Susan; Violette, Shelia; Smith, Jeremy; Guan, Wei; Bartlett, Catherine; Herson, Jay; Iuliucci, John; Weigele, Manfred; Sawyer, Tomi

2000-01-01

Targeted disruption of the pp60src (Src) gene has implicated this tyrosine kinase in osteoclast-mediated bone resorption and as a therapeutic target for the treatment of osteoporosis and other bone-related diseases. Herein we describe the discovery of a nonpeptide inhibitor (AP22408) of Src that demonstrates in vivo antiresorptive activity. Based on a cocrystal structure of the noncatalytic Src homology 2 (SH2) domain of Src complexed with citrate [in the phosphotyrosine (pTyr) binding pocket], we designed 3′,4′-diphosphonophenylalanine (Dpp) as a pTyr mimic. In addition to its design to bind Src SH2, the Dpp moiety exhibits bone-targeting properties that confer osteoclast selectivity, hence minimizing possible undesired effects on other cells that have Src-dependent activities. The chemical structure AP22408 also illustrates a bicyclic template to replace the post-pTyr sequence of cognate Src SH2 phosphopeptides such as Ac-pTyr-Glu-Glu-Ile (1). An x-ray structure of AP22408 complexed with Lck (S164C) SH2 confirmed molecular interactions of both the Dpp and bicyclic template of AP22408 as predicted from molecular modeling. Relative to the cognate phosphopeptide, AP22408 exhibits significantly increased Src SH2 binding affinity (IC50 = 0.30 μM for AP22408 and 5.5 μM for 1). Furthermore, AP22408 inhibits rabbit osteoclast-mediated resorption of dentine in a cellular assay, exhibits bone-targeting properties based on a hydroxyapatite adsorption assay, and demonstrates in vivo antiresorptive activity in a parathyroid hormone-induced rat model. PMID:10944210

Structural Characterization of Monomeric/Dimeric State of p59fyn SH2 Domain.

Science.gov (United States)

Huculeci, Radu; Kieken, Fabien; Garcia-Pino, Abel; Buts, Lieven; van Nuland, Nico; Lenaerts, Tom

2017-01-01

Src homology 2 (SH2) domains are key modulators in various signaling pathways allowing the recognition of phosphotyrosine sites of different proteins. Despite the fact that SH2 domains acquire their biological functions in a monomeric state, a multitude of reports have shown their tendency to dimerize. Here, we provide a technical description on how to isolate and characterize by gel filtration, circular dichroism (CD), and nuclear magnetic resonance (NMR) each conformational state of p59 fyn SH2 domain.

Mistletoe lectin is not the only cytotoxic component in fermented preparations of Viscum album from white fir (Abies pectinata

Directory of Open Access Journals (Sweden)

Ramos Mac

2007-05-01

Full Text Available Abstract Background Preparations of mistletoe (Viscum album are the form of cancer treatment that is most frequently used in the complementary medicine. Previous work has shown that these preparations are able to exert cytotoxic effects on carcinoma cells, the extent of which might be influenced by the host tree species and by the content of mistletoe lectin. Methods Using colorimetric assays, we have now compared the cytotoxic effects of Viscum album preparations (VAPs obtained from mistletoe growing on oak (Quercus robur and Q. petraea, VAP-Qu, apple tree (Malus domestica,, VAP-M, pine (Pinus sylvestris, VAP-P or white fir (Abies pectinata, VAP-A, on the in vitro growth of breast and bladder carcinoma cell lines. While MFM-223, KPL-1, MCF-7 and HCC-1937 were the breast carcinoma cell lines chosen, the panel of tested bladder carcinoma cells comprised the T-24, TCC-SUP, UM-UC-3 and J-82 cell lines. Results Each of the VAPs inhibited cell growth, but the extent of this inhibition differed with the preparation and with the cell line. The concentrations of VAP-Qu, VAP-M and VAP-A which led to a 50 % reduction of cell growth (IC50 varied between 0.6 and 0.03 mg/ml. Higher concentrations of VAP-P were required to obtain a comparable effect. Purified mistletoe lectin I (MLI led to an inhibition of breast carcinoma cell growth at concentrations lower than those of VAPs, but the sensitivity towards purified MLI did not parallel that towards VAPs. Bladder carcinoma cells were in most cases more sensitive to VAPs treatment than breast carcinoma cells. The total mistletoe lectin content was very high in VAP-Qu (54 ng/mg extract, intermediate in VAP-M (25 ng/mg extract, and very low in VAP-P (1.3 ng/mg extract and in VAP-A (1 ng/mg extract. As to be expected from the low content of mistletoe lectin, VAP-P led to relatively weak cytotoxic effects. Most remarkably, however, the lectin-poor VAP-A revealed a cytotoxic effect comparable to, or even stronger

Investigation of room-temperature wafer bonded GaInP/GaAs/InGaAsP triple-junction solar cells

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Yang, Wen-xian; Dai, Pan; Ji, Lian; Tan, Ming; Wu, Yuan-yuan [Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences (CAS), Suzhou 215123 (China); Uchida, Shiro [Department of Mechanical Science and Engineering Faculty of Engineering, Chiba Institute of Technology, 2-17-1, Tsudanuma, Narashino, Chiba 275-0016 (Japan); Lu, Shu-long, E-mail: sllu2008@sinano.ac.cn [Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences (CAS), Suzhou 215123 (China); Yang, Hui [Key Lab of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences (CAS), Suzhou 215123 (China)

2016-12-15

Highlights: • High quality InGaAsP material with a bandgap of 1.0 eV was grown by MBE. • Room-temperature wafer-bonded GaInP/GaAs/InGaAsP SCs were fabricated. • An efficiency of 30.3% of wafer-bonded triple-junction SCs was obtained. - Abstract: We report on the fabrication of III–V compound semiconductor multi-junction solar cells using the room-temperature wafer bonding technique. GaInP/GaAs dual-junction solar cells on GaAs substrate and InGaAsP single junction solar cell on InP substrate were separately grown by all-solid state molecular beam epitaxy (MBE). The two cells were then bonded to a triple-junction solar cell at room-temperature. A conversion efficiency of 30.3% of GaInP/GaAs/InGaAsP wafer-bonded solar cell was obtained at 1-sun condition under the AM1.5G solar simulator. The result suggests that the room-temperature wafer bonding technique and MBE technique have a great potential to improve the performance of multi-junction solar cell.

VAP3D: a software for dosimetric analysis and visualization of phantons

International Nuclear Information System (INIS)

Lima, Lindeval Fernandes de; Lima, Fernando Roberto de Andrade

2011-01-01

The anthropomorphic models used in computational dosimetry of the ionizing radiation, usually called voxel phantom, are produced from image stacks CT (Computed Tomography) or MRI (Magnetic Resonance Imaging) obtained from patient or volunteer scanning. These phantoms are the geometry to be radiated in the computing arrangements of exposure, using a Monte Carlo code, allowing the estimation of the energy deposited in each voxel of the virtual body. From these data collected in the simulation, it is possible to evaluate the average absorbed dose in various organs and tissues radiosensitive cataloged by the International Commission on Radiological Protection (ICRP). Therefore, a computational model of the exhibition is constituted primarily by the Monte Carlo code to simulate the transport, deposition and interaction of radiation and the phantom being irradiated. The construction of voxel phantoms requires computer skills like a transformation format of images, compression of 2D images for 3D image construction, quantization, resampling and image segmentation, among others. Hardly the computational dosimetry researcher finds all these skills into a single software and often this results in a decrease in the pace of their research or the use, sometimes inadequate, the alternative tools. This paper presents the VAP3D (Visualization and Analysis of Phantoms), a software developed with Qt/VTK with C++, in order to operationalize some of the tasks mentioned above. The current version has been based on DIP software (Digital Imaging Processing), containing the File menu, Conversions and tools, where the user interacts with the software. (author)

Crystallization and preliminary X-ray crystallographic characterization of a cyclic nucleotide-binding homology domain from the mouse EAG potassium channel

International Nuclear Information System (INIS)

Marques-Carvalho, Maria João; Morais-Cabral, João Henrique

2012-01-01

The crystallization conditions and preliminary crystal characterization of the cytoplasmic cyclic nucleotide-binding homology domain from the mouse EAG potassium channel are reported. The members of the family of voltage-gated KCNH potassium channels play important roles in cardiac and neuronal repolarization, tumour proliferation and hormone secretion. These channels have a C-terminal cytoplasmic domain which is homologous to cyclic nucleotide-binding domains (CNB-homology domains), but it has been demonstrated that channel function is not affected by cyclic nucleotides and that the domain does not bind nucleotides in vitro. Here, the crystallization and preliminary crystallographic analysis of a CNB-homology domain from a member of the KCNH family, the mouse EAG channel, is reported. X-ray diffraction data were collected to 2.2 Å resolution and the crystal belonged to the hexagonal space group P3 1 21

A prospective randomized trial comparing homologous and autologous fibrin sealants for the control of alveolar air leak.

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Kılıç, Burcu; Erşen, Ezel; Demirkaya, Ahmet; Kara, H Volkan; Alizade, Nurlan; İşcan, Mehlika; Kaynak, Kamil; Turna, Akif

2017-09-01

Postoperative air leak is a common complication seen after pulmonary resection. It is a significant reason of morbidity and also leads to greater hospital cost owing to prolonged length of stay. The purpose of this study is to compare homologous sealant with autologous one to prevent air leak following pulmonary resection. A total of 57 patients aged between 20 and 79 (mean age: 54.36) who underwent pulmonary resection other than pneumonectomy (lobar or sublobar resections) were analyzed. There were 47 males (83%) and 10 females (17%). Patients who intraoperatively had air leaks were randomized to receive homologous (Tisseel; n=28) or autologous (Vivostat; n=29) fibrin sealant. Differences among groups in terms of air leak, prolonged air leak, hospital stay, amount of air leak were analyzed. Indications for surgery were primary lung cancer in 42 patients (71.9%), secondary malignancy in 5 patients (8.8%), and benign disease in 10 patients (17.5%). Lobectomy was performed in 40 patients (70.2%), whereas 17 patients (29.8%) had wedge resection. Thirteen (46.4%) patients developed complications in patients receiving homologous sealant while 11 (38.0%) patients had complication in autologous sealant group (P=0.711). Median duration of air leak was 3 days in two groups. Time to intercostal drain removal was 3.39 and 3.38 days in homologous and autologous sealant group respectively (P=0.978). Mean hospital stay was 5.5 days in patients receiving homologous sealant whereas it was 5.0 days in patients who had autologous agent (P=0.140). There were no significant differences between groups in terms of measured maximum air leak (P=0.823) and mean air leak (P=0.186). There was no significant difference in the incidence of complications between two groups (P=0.711). Autologous and heterologous fibrin sealants are safe and acts similarly in terms of air leak and hospital stay in patients who had resectional surgery.

Characterization of TRZ1, a yeast homolog of the human candidate prostate cancer susceptibility gene ELAC2 encoding tRNase Z

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Chen Yuan

2005-05-01

Full Text Available Abstract Background In humans, mutation of ELAC2 is associated with an increased risk of prostate cancer. ELAC2 has been shown to have tRNase Z activity and is associated with the γ-tubulin complex. Results In this work, we show that the yeast homolog of ELAC2, encoded by TRZ1 (tRNase Z 1, is involved genetically in RNA processing. The temperature sensitivity of a trz1 mutant can be rescued by multiple copies of REX2, which encodes a protein with RNA 3' processing activity, suggesting a role of Trz1p in RNA processing in vivo. Trz1p has two putative nucleotide triphosphate-binding motifs (P-loop and a conserved histidine motif. The histidine motif and the putative nucleotide binding motif at the C-domain are important for Trz1p function because mutant proteins bearing changes to the critical residues in these motifs are unable to rescue deletion of TRZ1. The growth defect exhibited by trz1 yeast is not complemented by the heterologous ELAC2, suggesting that Trz1p may have additional functions in yeast. Conclusion Our results provide genetic evidence that prostate cancer susceptibility gene ELAC2 may be involved in RNA processing, especially rRNA processing and mitochondrial function.

Edaphic factors controlling summer (rainy season) greenhouse gas emissions (CO_2 and CH_4) from semiarid mangrove soils (NE-Brazil)

International Nuclear Information System (INIS)

Nóbrega, Gabriel N.; Ferreira, Tiago O.; Siqueira Neto, M.; Queiroz, Hermano M.; Artur, Adriana G.; Mendonça, Eduardo De S.; Silva, Ebenezer De O.

2016-01-01

The soil attributes controlling the CO_2, and CH_4 emissions were assessed in semiarid mangrove soils (NE-Brazil) under different anthropogenic activities. Soil samples were collected from different mangroves under different anthropogenic impacts, e.g., shrimp farming (Jaguaribe River); urban wastes (Cocó River) and a control site (Timonha River). The sites were characterized according to the sand content; physicochemical parameters (Eh and pH); total organic C; soil C stock (SCS) and equivalent SCS (SCS_E_Q_V); total P and N; dissolved organic C (DOC); and the degree of pyritization (DOP). The CO_2 and CH_4 fluxes from the soils were assessed using static closed chambers. Higher DOC and SCS and the lowest DOP promote greater CO_2 emission. The CH_4 flux was only observed at Jaguaribe which presented higher DOP, compared to that found in mangroves from humid tropical climates. Semiarid mangrove soils cannot be characterized as important greenhouse gas sources, compared to humid tropical mangroves. - Highlights: • GHG emission was associated with different soil characteristics. • Highest CO_2 emissions were found in mangroves with larger dissolved C and lower DOP. • Less CH_4 flux was due to low DOP in semiarid mangrove soils.

A novel porcine model of ventilator-associated pneumonia caused by oropharyngeal challenge with Pseudomonas aeruginosa.

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Li Bassi, Gianluigi; Rigol, Montserrat; Marti, Joan-Daniel; Saucedo, Lina; Ranzani, Otavio T; Roca, Ignasi; Cabanas, Maria; Muñoz, Laura; Giunta, Valeria; Luque, Nestor; Rinaudo, Mariano; Esperatti, Mariano; Fernandez-Barat, Laia; Ferrer, Miquel; Vila, Jordi; Ramirez, Jose; Torres, Antoni

2014-05-01

Animal models of ventilator-associated pneumonia (VAP) in primates, sheep, and pigs differ in the underlying pulmonary injury, etiology, bacterial inoculation methods, and time to onset. The most common ovine and porcine models do not reproduce the primary pathogenic mechanism of the disease, through the aspiration of oropharyngeal pathogens, or the most prevalent human etiology. Herein the authors characterize a novel porcine model of VAP due to aspiration of oropharyngeal secretions colonized by Pseudomonas aeruginosa. Ten healthy pigs were intubated, positioned in anti-Trendelenburg, and mechanically ventilated for 72 h. Three animals did not receive bacterial challenge, whereas in seven animals, a P. aeruginosa suspension was instilled into the oropharynx. Tracheal aspirates were cultured and respiratory mechanics were recorded. On autopsy, lobar samples were obtained to corroborate VAP through microbiological and histological studies. In animals not challenged, diverse bacterial colonization of the airways was found and monolobar VAP rarely developed. In animals with P. aeruginosa challenge, colonization of tracheal secretion increased up to 6.39 ± 0.34 log colony-forming unit (cfu)/ml (P VAP was confirmed in six of seven pigs, in 78% of the cases developed in the dependent lung segments (right medium and lower lobes, P = 0.032). The static respiratory system elastance worsened to 41.5 ± 5.8 cm H2O/l (P = 0.001). The authors devised a VAP model caused by aspiration of oropharyngeal P. aeruginosa, a frequent causative pathogen of human VAP. The model also overcomes the practical and legislative limitations associated with the use of primates. The authors' model could be employed to study pathophysiologic mechanisms, as well as novel diagnostic/preventive strategies.

Pneumonia prevention in intubated patients given sucralfate versus proton-pump inhibitors and/or histamine II receptor blockers.

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Grindlinger, Gene A; Cairo, Sarah B; Duperre, Carole B

2016-12-01

Ventilator-associated pneumonia (VAP) is a common cause of infectious morbidity and mortality in the intensive care unit (ICU). The type of stress-ulcer prophylaxis (SUP) given to ventilated patients may, in part, be responsible. We observed an increase in VAP as ventilator bundle compliance increased and a decrease in VAP when bundle compliance decreased. We reasoned that SUP which raises gastric pH such as proton-pump inhibitors (PPIs) and histamine II (H2) receptor antagonists as opposed to SUP which does not raise pH such as sucralfate (S) may be responsible and also may alter the causative bacteria. This is a single-center retrospective cohort analysis of all intubated, adult surgical patients admitted to the surgical ICU between January and June during the 3-y period 2012-2014. Demographics, APACHE II, Injury Severity Score, VAP occurrence, culprit bacteria, ventilator days, and ICU days were recorded based on the type of SUP given. There were 45 instances of VAP in the 504 study patients, 33 in the PPI/H2 group, and 12 in the S group (P < 0.01). VAP per 1000 ventilator days were 10.2 for PPI/H2 and 3.7 for S (P < 0.01). Culprit bacteria were mostly Pseudomonas, gram-negative bacilli, and methicillin-resistant Staphylococcus aureus in PPI/H2 patients (n = 29) compared with oropharyngeal flora in S patients (n = 6; P < 0.001). There was a substantial difference in VAP occurrence and in the culprit bacteria between S and PPI/H2 treated patients due perhaps to gastric alkalization. Copyright © 2016 Elsevier Inc. All rights reserved.

Andrographolide induces vascular smooth muscle cell apoptosis through a SHP-1-PP2A-p38MAPK-p53 cascade.

Science.gov (United States)

Chen, Yu-Ying; Hsieh, Cheng-Ying; Jayakumar, Thanasekaran; Lin, Kuan-Hung; Chou, Duen-Suey; Lu, Wan-Jung; Hsu, Ming-Jen; Sheu, Joen-Rong

2014-07-10

The abnormal growth of vascular smooth muscle cells (VSMCs) is considered a critical pathogenic process in inflammatory vascular diseases. We have previously demonstrated that protein phosphatase 2 A (PP2A)-mediated NF-κB dephosphorylation contributes to the anti-inflammatory properties of andrographolide, a novel NF-κB inhibitor. In this study, we investigated whether andrographolide causes apoptosis, and characterized its apoptotic mechanisms in rat VSMCs. Andrographolide activated the p38 mitogen-activated protein kinase (p38MAPK), leading to p53 phosphorylation. Phosphorylated p53 subsequently transactivated the expression of Bax, a pro-apoptotic protein. Transfection with pp2a small interfering RNA (siRNA) suppressed andrographolide-induced p38MAPK activation, p53 phosphorylation, and caspase 3 activation. Andrographolide also activated the Src homology 1 domain-containing protein tyrosine phosphatase (SHP-1), and induced PP2A dephosphorylation, both of which were inhibited by the SHP-1 inhibitor sodium stibogluconate (SSG) or shp-1 siRNA. SSG or shp-1 siRNA prevented andrographolide-induced apoptosis. These results suggest that andrographolide activates the PP2A-p38MAPK-p53-Bax cascade, causing mitochondrial dysfunction and VSMC death through an SHP-1-dependent mechanism.

Conditional Loss of Pten in Myogenic Progenitors Leads to Postnatal Skeletal Muscle Hypertrophy but Age-Dependent Exhaustion of Satellite Cells.

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Yue, Feng; Bi, Pengpeng; Wang, Chao; Li, Jie; Liu, Xiaoqi; Kuang, Shihuan

2016-11-22

Skeletal muscle stem cells (satellite cells [SCs]) are normally maintained in a quiescent (G 0 ) state. Muscle injury not only activates SCs locally, but also alerts SCs in distant uninjured muscles via circulating factors. The resulting G Alert SCs are adapted to regenerative cues and regenerate injured muscles more efficiently, but whether they provide any long-term benefits to SCs is unknown. Here, we report that embryonic myogenic progenitors lacking the phosphatase and tensin homolog (Pten) exhibit enhanced proliferation and differentiation, resulting in muscle hypertrophy but fewer SCs in adult muscles. Interestingly, Pten null SCs are predominantly in the G Alert state, even in the absence of an injury. The G Alert SCs are deficient in self-renewal and subjected to accelerated depletion during regeneration and aging and fail to repair muscle injury in old mice. Our findings demonstrate a key requirement of Pten in G 0 entry of SCs and provide functional evidence that prolonged G Alert leads to stem cell depletion and regenerative failure. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Resolving the Gordian Knot: Srs2 Strips Intermediates Formed during Homologous Recombination.

Science.gov (United States)

Ghodke, Harshad; Lewis, Jacob S; van Oijen, Antoine M

2018-03-01

Cells use a suite of specialized enzymes to repair chromosomal double-strand breaks (DSBs). Two recent studies describe how single-molecule fluorescence imaging techniques are used in the direct visualization of some of the key molecular steps involved. De Tullio et al. and Kaniecki et al. watch individual Srs2 helicase molecules disrupt repair intermediates formed by RPA, Rad51, and Rad52 on DNA during homologous recombination. Copyright © 2017 Elsevier Ltd. All rights reserved.

Promotion of BRCA2-Dependent Homologous Recombination by DSS1 via RPA Targeting and DNA Mimicry.

Science.gov (United States)

Zhao, Weixing; Vaithiyalingam, Sivaraja; San Filippo, Joseph; Maranon, David G; Jimenez-Sainz, Judit; Fontenay, Gerald V; Kwon, Youngho; Leung, Stanley G; Lu, Lucy; Jensen, Ryan B; Chazin, Walter J; Wiese, Claudia; Sung, Patrick

2015-07-16

The tumor suppressor BRCA2 is thought to facilitate the handoff of ssDNA from replication protein A (RPA) to the RAD51 recombinase during DNA break and replication fork repair by homologous recombination. However, we find that RPA-RAD51 exchange requires the BRCA2 partner DSS1. Biochemical, structural, and in vivo analyses reveal that DSS1 allows the BRCA2-DSS1 complex to physically and functionally interact with RPA. Mechanistically, DSS1 acts as a DNA mimic to attenuate the affinity of RPA for ssDNA. A mutation in the solvent-exposed acidic domain of DSS1 compromises the efficacy of RPA-RAD51 exchange. Thus, by targeting RPA and mimicking DNA, DSS1 functions with BRCA2 in a two-component homologous recombination mediator complex in genome maintenance and tumor suppression. Our findings may provide a paradigm for understanding the roles of DSS1 in other biological processes. Copyright © 2015 Elsevier Inc. All rights reserved.

Investigation of the direct runoff generation mechanism for the analysis of the SCS-CN method applicability to a partial area experimental watershed

Science.gov (United States)

Soulis, K. X.; Valiantzas, J. D.; Dercas, N.; Londra, P. A.

2009-05-01

The Soil Conservation Service Curve Number (SCS-CN) method is widely used for predicting direct runoff volume for a given rainfall event. The applicability of the SCS-CN method and the direct runoff generation mechanism were thoroughly analysed in a Mediterranean experimental watershed in Greece. The region is characterized by a Mediterranean semi-arid climate. A detailed land cover and soil survey using remote sensing and GIS techniques, showed that the watershed is dominated by coarse soils with high hydraulic conductivities, whereas a smaller part is covered with medium textured soils and impervious surfaces. The analysis indicated that the SCS-CN method fails to predict runoff for the storm events studied, and that there is a strong correlation between the CN values obtained from measured runoff and the rainfall depth. The hypothesis that this correlation could be attributed to the existence of an impermeable part in a very permeable watershed was examined in depth, by developing a numerical simulation water flow model for predicting surface runoff generated from each of the three soil types of the watershed. Numerical runs were performed using the HYDRUS-1D code. The results support the validity of this hypothesis for most of the events examined where the linear runoff formula provides better results than the SCS-CN method. The runoff coefficient of this formula can be taken equal to the percentage of the impervious area. However, the linear formula should be applied with caution in case of extreme events with very high rainfall intensities. In this case, the medium textured soils may significantly contribute to the total runoff and the linear formula may significantly underestimate the runoff produced.

Investigation of the direct runoff generation mechanism for the analysis of the SCS-CN method applicability to a partial area experimental watershed

Directory of Open Access Journals (Sweden)

K. X. Soulis

2009-05-01

Full Text Available The Soil Conservation Service Curve Number (SCS-CN method is widely used for predicting direct runoff volume for a given rainfall event. The applicability of the SCS-CN method and the direct runoff generation mechanism were thoroughly analysed in a Mediterranean experimental watershed in Greece. The region is characterized by a Mediterranean semi-arid climate. A detailed land cover and soil survey using remote sensing and GIS techniques, showed that the watershed is dominated by coarse soils with high hydraulic conductivities, whereas a smaller part is covered with medium textured soils and impervious surfaces. The analysis indicated that the SCS-CN method fails to predict runoff for the storm events studied, and that there is a strong correlation between the CN values obtained from measured runoff and the rainfall depth. The hypothesis that this correlation could be attributed to the existence of an impermeable part in a very permeable watershed was examined in depth, by developing a numerical simulation water flow model for predicting surface runoff generated from each of the three soil types of the watershed. Numerical runs were performed using the HYDRUS-1D code. The results support the validity of this hypothesis for most of the events examined where the linear runoff formula provides better results than the SCS-CN method. The runoff coefficient of this formula can be taken equal to the percentage of the impervious area. However, the linear formula should be applied with caution in case of extreme events with very high rainfall intensities. In this case, the medium textured soils may significantly contribute to the total runoff and the linear formula may significantly underestimate the runoff produced.

Edaphic factors controlling summer (rainy season) greenhouse gas emissions (CO2 and CH4) from semiarid mangrove soils (NE-Brazil).

Science.gov (United States)

Nóbrega, Gabriel N; Ferreira, Tiago O; Siqueira Neto, M; Queiroz, Hermano M; Artur, Adriana G; Mendonça, Eduardo De S; Silva, Ebenezer De O; Otero, Xosé L

2016-01-15

The soil attributes controlling the CO2, and CH4 emissions were assessed in semiarid mangrove soils (NE-Brazil) under different anthropogenic activities. Soil samples were collected from different mangroves under different anthropogenic impacts, e.g., shrimp farming (Jaguaribe River); urban wastes (Cocó River) and a control site (Timonha River). The sites were characterized according to the sand content; physicochemical parameters (Eh and pH); total organic C; soil C stock (SCS) and equivalent SCS (SCSEQV); total P and N; dissolved organic C (DOC); and the degree of pyritization (DOP). The CO2 and CH4 fluxes from the soils were assessed using static closed chambers. Higher DOC and SCS and the lowest DOP promote greater CO2 emission. The CH4 flux was only observed at Jaguaribe which presented higher DOP, compared to that found in mangroves from humid tropical climates. Semiarid mangrove soils cannot be characterized as important greenhouse gas sources, compared to humid tropical mangroves.

A simplified prevention bundle with dual hand hygiene audit reduces early-onset ventilator-associated pneumonia in cardiovascular surgery units: An interrupted time-series analysis.

Directory of Open Access Journals (Sweden)

Kang-Cheng Su

Full Text Available To investigate the effect of a simplified prevention bundle with alcohol-based, dual hand hygiene (HH audit on the incidence of early-onset ventilation-associated pneumonia (VAP.This 3-year, quasi-experimental study with interrupted time-series analysis was conducted in two cardiovascular surgery intensive care units in a medical center. Unaware external HH audit (eHH performed by non-unit-based observers was a routine task before and after bundle implementation. Based on the realistic ICU settings, we implemented a 3-component bundle, which included: a compulsory education program, a knowing internal HH audit (iHH performed by unit-based observers, and a standardized oral care (OC protocol with 0.1% chlorhexidine gluconate. The study periods comprised 4 phases: 12-month pre-implementation phase 1 (eHH+/education-/iHH-/OC-, 3-month run-in phase 2 (eHH+/education+/iHH+/OC+, 15-month implementation phase 3 (eHH+/education+/iHH+/OC+, and 6-month post-implementation phase 4 (eHH+/education-/iHH+/OC-.A total of 2553 ventilator-days were observed. VAP incidences (events/1000 ventilator days in phase 1-4 were 39.1, 40.5, 15.9, and 20.4, respectively. VAP was significantly reduced by 59% in phase 3 (vs. phase 1, incidence rate ratio [IRR] 0.41, P = 0.002, but rebounded in phase 4. Moreover, VAP incidence was inversely correlated to compliance of OC (r2 = 0.531, P = 0.001 and eHH (r2 = 0.878, P < 0.001, but not applied for iHH, despite iHH compliance was higher than eHH compliance during phase 2 to 4. Compared to eHH, iHH provided more efficient and faster improvements for standard HH practice. The minimal compliances required for significant VAP reduction were 85% and 75% for OC and eHH (both P < 0.05, IRR 0.28 and 0.42, respectively.This simplified prevention bundle effectively reduces early-onset VAP incidence. An unaware HH compliance correlates with VAP incidence. A knowing HH audit provides better improvement in HH practice. Accordingly, we suggest

Diagnostic Performance of Soluble Triggering Receptor Expressed on Myeloid Cells-1 in Ventilator-Associated Pneumonia of Patients with Ischemic Stroke.

Science.gov (United States)

Yu, Yuetian; Zhu, Cheng; Liu, Chunyan; Gao, Yuan; Yin, Rong; Cao, Jianguo

2017-01-01

Objective . To investigate the effect of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) in serum, bronchoalveolar lavage fluid (BALF), endotracheal aspiration (ETA), and exhaled breath condensate (EBC) samples as early biomarkers for the diagnosis of ventilator-associated pneumonia (VAP) in patients with ischemic stroke. Methods . One hundred and thirty-two patients with clinically suspected VAP were enrolled in this study. Bronchoscopy was performed on the day of clinically suspected VAP. sTREM-1 levels in serum, BALF, ETA, and EBC were measured. VAP was diagnosed by quantitative cultures of BALF (≥10 4  cfu/mL). Results . VAP was confirmed in 76 (57.58%) cases. Patients with VAP showed significantly higher sTREM-1 in BALF [32.35 (IQR, 30.08-41.72) versus 18.92 (11.89-31.72)] pg/mL and in EBC [1.57 (IQR, 1.02-2.61) versus 0.41 (0.19-1.61)] pg/mL than patients without VAP. The area under the curve was 0.813 ( p VAP.

Targeting of OSBP-related protein 3 (ORP3) to endoplasmic reticulum and plasma membrane is controlled by multiple determinants

International Nuclear Information System (INIS)

Lehto, Markku; Hynynen, Riikka; Karjalainen, Katja; Kuismanen, Esa; Hyvaerinen, Kati; Olkkonen, Vesa M.

2005-01-01

The intracellular targeting determinants of oxysterol binding protein (OSBP)-related protein 3 (ORP3) were studied using a series of truncated and point mutated constructs. The pleckstrin homology (PH) domain of ORP3 binds the phosphoinositide-3-kinase (PI3K) products, PI(3,4)P 2 and PI(3,4,5)P 3 . A functional PH domain and flanking sequences are crucial for the plasma membrane (PM) targeting of ORP3. The endoplasmic reticulum (ER) targeting of ORP3 is regulated the by a FFAT motif (EFFDAxE), which mediates interaction with VAMP-associated protein (VAP)-A. The targeting function of the FFAT motif dominates over that of the PH domain. In addition, the exon 10/11 region modulates interaction of ORP3 with the ER and the nuclear membrane. Analysis of a chimeric ORP3:OSBP protein suggests that ligand binding by the C-terminal domain of OSBP induces allosteric changes that activate the N-terminal targeting modules of ORP3. Notably, over-expression of ORP3 together with VAP-A induces stacked ER membrane structures also known as organized smooth ER (OSER). Moreover, lipid starvation promotes formation of dilated peripheral ER (DPER) structures dependent on the ORP3 protein. Based on the present data, we introduce a model for the inter-relationships of the functional domains of ORP3 in the membrane targeting of the protein

Edaphic factors controlling summer (rainy season) greenhouse gas emissions (CO{sub 2} and CH{sub 4}) from semiarid mangrove soils (NE-Brazil)

Energy Technology Data Exchange (ETDEWEB)

Nóbrega, Gabriel N. [Departamento de Ciência do Solo, Escola Superior de Agricultura Luiz de Queiroz, ESALQ/USP, Av.Pádua Dias 11, Piracicaba, São Paulo 13.418-260 (Brazil); Ferreira, Tiago O., E-mail: toferreira@usp.br [Departamento de Ciência do Solo, Escola Superior de Agricultura Luiz de Queiroz, ESALQ/USP, Av.Pádua Dias 11, Piracicaba, São Paulo 13.418-260 (Brazil); Siqueira Neto, M. [Laboratório de Biogeoquímica Ambiental, Centro de Energia Nuclear na Agricultura, CENA/USP, Av. Centenário 303, Piracicaba, São Paulo 13.400-970 (Brazil); Queiroz, Hermano M.; Artur, Adriana G. [Departamento de Ciências do Solo, Universidade Federal do Ceará, UFC, Av. Mister Hull 2977, Campus do Pici, Fortaleza, Ceará 60.440-554 (Brazil); Mendonça, Eduardo De S. [Departamento de Produção Vegetal, Universidade Federal do Espírito Santo, UFES, Alto Universitário s/n, Alegre, Espírito Santo 29.500-000 (Brazil); Silva, Ebenezer De O. [Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisa de Agroindústria Tropical, Pós Colheita, Dra. Sara Mesquita Street, 2270, Planalto Pici, Fortaleza, Ceará 60.511-110 (Brazil); and others

2016-01-15

The soil attributes controlling the CO{sub 2}, and CH{sub 4} emissions were assessed in semiarid mangrove soils (NE-Brazil) under different anthropogenic activities. Soil samples were collected from different mangroves under different anthropogenic impacts, e.g., shrimp farming (Jaguaribe River); urban wastes (Cocó River) and a control site (Timonha River). The sites were characterized according to the sand content; physicochemical parameters (Eh and pH); total organic C; soil C stock (SCS) and equivalent SCS (SCS{sub EQV}); total P and N; dissolved organic C (DOC); and the degree of pyritization (DOP). The CO{sub 2} and CH{sub 4} fluxes from the soils were assessed using static closed chambers. Higher DOC and SCS and the lowest DOP promote greater CO{sub 2} emission. The CH{sub 4} flux was only observed at Jaguaribe which presented higher DOP, compared to that found in mangroves from humid tropical climates. Semiarid mangrove soils cannot be characterized as important greenhouse gas sources, compared to humid tropical mangroves. - Highlights: • GHG emission was associated with different soil characteristics. • Highest CO{sub 2} emissions were found in mangroves with larger dissolved C and lower DOP. • Less CH{sub 4} flux was due to low DOP in semiarid mangrove soils.

Ventilator-associated pneumonia: Its incidence, the risk factor and drug resistance pattern in a tertiary care hospital

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Sourabh Mitra

2015-01-01

Full Text Available Background: Ventilator-associated pneumonia (VAP is an infection of the lung that develops 48 h or longer after mechanical ventilation. Objectives: The present study was aimed to find out the bacteriological profile of VAP along with the resistance pattern of bacteriological isolates. Materials and Methods: A prospective observational study was conducted from January 2013 to May 2014 among 791 patients admitted in critical care units of our tertiary care hospital. After selection by applying inclusion and exclusion criteria endotracheal aspirates were collected from ventilated patients. Samples were subjected to further processing by Gram-staining, culture, biochemical testing and antibiogram. Results : Out of 791 patients admitted in intensive care unit in this tertiary care hospital with VAP 540 (68.2% patients were culture positive. Pseudomonas aeruginosa was most commonly isolated pathogen of both early onset and late onset VAP. In early VAP Acinetobacter baumannii showed 62.5% metallo-beta-lactamase (MBL positivity. P. aeruginosa showed 27.5% MBL positivity, whereas in late onset VAP, 71.4% A. baumannii isolates and 75.8% P. aeruginosa isolates showed MBL positivity, respectively. Conclusion : Simple prevention of aspiration, sterilization of equipments, hand washing of personnel can reduce VAP in hospital care setting.

High-dose Sulbactam Treatment for Ventilator-Associated Pneumonia Caused by Carbapenem-Resistant

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In Beom Jeong

2016-11-01

Full Text Available Background Several antibiotics can be used to treat ventilator-associated pneumonia caused by carbapenem-resistant A. baumannii (CRAB-VAP including high-dose sulbactam. However, the effectiveness of high-dose sulbactam therapy is not well known. We report our experience with high-dose sulbactam for treatment of CRAB-VAP. Methods Medical records of patients with CRAB-VAP who were given high-dose sulbactam between May 2013 and June 2015 were reviewed. Results Fifty-eight patients with CRAB-VAP were treated with high-dose sulbactam. The mean age was 72.0 ± 15.2 years, and the acute physiology and chronic health evaluation II (APACHE II score was 15.1 ± 5.10 at the time of CRAB-VAP diagnosis. Early clinical improvement was observed in 65.5% of patients, and 30-day mortality was 29.3%. Early clinical failure (odds ratio [OR]: 8.720, confidence interval [CI]: 1.346-56.484; p = 0.023 and APACHE II score ≥ 14 at CRAB-VAP diagnosis (OR: 10.934, CI: 1.047-114.148; p = 0.046 were associated with 30-day mortality. Conclusions High-dose sulbactam therapy may be effective for the treatment of CRAB-VAP. However, early clinical failure was observed in 35% of patients and was associated with poor outcome.

Construction of a novel kind of expression plasmid by homologous recombination in Saccharomyces cerevisiae

Institute of Scientific and Technical Information of China (English)

CHEN; Xiangling

2005-01-01

[1]Brunelli, J. P., Pall, M. L., A series of yeast vectors for expression of cDNAs and other DNA sequences, Yeast, 1993, 9: 1299―1308.[2]Sikorski, R. S., Hieter, P., A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae, Genetics, 1989, 122: 19―27.[3]Bonneaud, N., Ozier-Kalogerogoulos, O., Li, G. et al., A family of low and high copy replicative, integrative and single-stranded S. cerevisiae /E. coli shuttle vector, Yeast, 1991, 7: 609―615.[4]Huo, K. K., Yu, L. L., Chen, X. J., Li, Y. Y., A stable vector for high-level expression and secretion of human interferon alpha A in yeast, Science in China, Ser. B, 1993, 36(5): 557―567.[5]Zhou, Z. X., Yuan, H. Y., He, W. et al., Expression of the modified HBsAg gene SA-28 directed by a constitutive promoter, Journal of Fudan university (Natural Science), 2000, 39(3): 264―268.[6]Paques, F., Haber, J. E., Multiple pathways of recombination induces by double-strand breaks in Saccharomyces cerevisiae, Microbiology and Molecular Biology Reviews, 1999, 63(2): 349―404.[7]Martin, K., Damage-induced recombination in the yeast Saccharomyces cerevisiae, Mutation Research, 2000, 451: 91―105.[8]Alira, S., Tomoko, O., Homologous recombination and the roles of double-strand breaks, TIBS, 1995, 20: 387―391.[9]Patrick, S., Kelly, M. T., Stephen, V. K., Recombination factor of Saccharomyces cerevisiae, Mutation Research, 2000, 451: 257―275.[10]Manivasakam, P., Weber, S. C., McElver, J., Schiestl, R. H., Micro-homology mediated PCR targeting in Saccharomyces cerevisiae, Nucleic Acids Res., 1995, 23(14): 2799―2800.[11]Baudin, A., Lacroute, F., Cullin, C., A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae, Nucleic Acids Res., 1993, 21(14): 3329―3330.[12]Hua, S. B., Qiu, M., Chan, E., Zhu, L., Luo, Y., Minimum length of sequence homology required for in vivo cloning by homolo-gous recombination in yeast, Plasmid, 1997, 38(2

Reactions of R(2)P-P(SiMe(3))Li with [(R'(3)P)(2)PtCl(2)]. A general and efficient entry to phosphanylphosphinidene complexes of platinum. Syntheses and structures of [(eta(2)-P=(i)Pr(2))Pt(p-Tol(3)P)(2)], [(eta(2)-P=(t)Bu(2))Pt(p-Tol(3)P)(2)], [{eta(2)-P=(N(i)Pr(2))(2)}Pt(p-Tol(3)P)(2)] and [{(Et(2)PhP)(2)Pt}(2)P(2)].

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Domańska-Babul, Wioleta; Chojnacki, Jaroslaw; Matern, Eberhard; Pikies, Jerzy

2009-01-07

The reactions of lithium derivatives of diphosphanes R(2)P-P(SiMe(3))Li (R = (t)Bu, (i)Pr, Et(2)N and (i)Pr(2)N) with [(R'(3)P)(2)PtCl(2)] (R'(3)P = Et(3)P, Et(2)PhP, EtPh(2)P and p-Tol(3)P) proceed in a facile manner to afford side-on bonded phosphanylphosphinidene complexes of platinum [(eta(2)-P=R(2))Pt(PR'(3))(2)]. The related reactions of Ph(2)P-P(SiMe(3))Li with [(R'(3)P)(2)PtCl(2)] did not yield [(eta(2)-P=PPh(2))Pt(PR'(3))(2)] and resulted mainly in the formation of [{(R'(3)P)(2)Pt}(2)P(2)], Ph(2)P-PLi-PPh(2), (Me(3)Si)(2)PLi and (Me(3)Si)(3)P. Crystallographic data are reported for the compounds [(eta(2)-P=R(2))Pt(p-Tol(3)P)(2)] (R = (t)Bu, (i)Pr, ((i)Pr(2)N)(2)P) and for [{(Et(2)PhP)(2)Pt}(2)P(2)].

An Amphiphysin-Like Domain in Fus2p Is Required for Rvs161p Interaction and Cortical Localization

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Richard A. Stein

2016-02-01

Full Text Available Cell–cell fusion fulfils essential roles in fertilization, development and tissue repair. In the budding yeast, Saccharomyces cerevisiae, fusion between two haploid cells of opposite mating type generates the diploid zygote. Fus2p is a pheromone-induced protein that regulates cell wall removal during mating. Fus2p shuttles from the nucleus to localize at the shmoo tip, bound to Rvs161p, an amphiphysin. However, Rvs161p independently binds a second amphiphysin, Rvs167p, playing an essential role in endocytosis. To understand the basis of the Fus2p–Rvs161p interaction, we analyzed Fus2p structural domains. A previously described N-terminal domain (NTD is necessary and sufficient to regulate nuclear/cytoplasmic trafficking of Fus2p. The Dbl homology domain (DBH binds GTP-bound Cdc42p; binding is required for cell fusion, but not localization. We identified an approximately 200 amino acid region of Fus2p that is both necessary and sufficient for Rvs161p binding. The Rvs161p binding domain (RBD contains three predicted alpha-helices; structural modeling suggests that the RBD adopts an amphiphysin-like structure. The RBD contains a 13-amino-acid region, conserved with Rvs161p and other amphiphysins, which is essential for binding. Mutations in the RBD, predicted to affect membrane binding, abolish cell fusion without affecting Rvs161p binding. We propose that Fus2p/Rvs161p form a novel heterodimeric amphiphysin required for cell fusion. Rvs161p binding is required but not sufficient for Fus2p localization. Mutations in the C-terminal domain (CTD of Fus2p block localization, but not Rvs161p binding, causing a significant defect in cell fusion. We conclude that the Fus2p CTD mediates an additional, Rvs161p-independent interaction at the shmoo tip.

The amino terminal end determines the stability and assembling capacity of eukaryotic ribosomal stalk proteins P1 and P2.

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Camargo, Hendricka; Nusspaumer, Gretel; Abia, David; Briceño, Verónica; Remacha, Miguel; Ballesta, Juan P G

2011-05-01

The eukaryotic ribosomal proteins P1 and P2 bind to protein P0 through their N-terminal domain to form the essential ribosomal stalk. A mutational analysis points to amino acids at positions 2 and 3 as determinants for the drastic difference of Saccharomyces cerevisiae P1 and P2 half-life, and suggest different degradation mechanisms for each protein type. Moreover, the capacity to form P1/P2 heterodimers is drastically affected by mutations in the P2β four initial amino acids, while these mutations have no effect on P1β. Binding of P2β and, to a lesser extent, P1β to the ribosome is also seriously affected showing the high relevance of the amino acids in the first turn of the NTD α-helix 1 for the stalk assembly. The negative effect of some mutations on ribosome binding can be reversed by the presence of the second P1/P2 couple in the ribosome, indicating a stabilizing structural influence between the two heterodimers. Unexpectedly, some mutations totally abolish heterodimer formation but allow significant ribosome binding and, therefore, a previous P1 and P2 association seems not to be an absolute requirement for stalk assembly. Homology modeling of the protein complexes suggests that the mutated residues can affect the overall protein conformation. © The Author(s) 2011. Published by Oxford University Press.

Effect of enhanced ultraviolet germicidal irradiation in the heating ventilation and air conditioning system on ventilator-associated pneumonia in a neonatal intensive care unit.

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Ryan, R M; Wilding, G E; Wynn, R J; Welliver, R C; Holm, B A; Leach, C L

2011-09-01

The objective of this study was to test the hypothesis that enhanced ultraviolet germicidal irradiation (eUVGI) installed in our neonatal intensive care unit (NICU) heating ventilation and air conditioning system (HVAC) would decrease HVAC and NICU environment microbes, tracheal colonization and ventilator-associated pneumonia (VAP). The study was designed as a prospective interventional pre- and post-single-center study. University-affiliated Regional Perinatal Center NICU. Intubated patients in the NICU were evaluated for colonization, and a high-risk sub-population of infants <30 weeks gestation ventilated for ≥ 14 days was studied for VAP. eUVGI was installed in the NICU's remote HVACs. The HVACs, NICU environment and intubated patients' tracheas were cultured pre- and post-eUVGI for 12 months. The high-risk patients were studied for VAP (positive bacterial tracheal culture, increased ventilator support, worsening chest radiograph and ≥ 7 days of antibiotics). Pseudomonas, Klebsiella, Serratia, Acinetobacter, Staphylococcus aureus and Coagulase-negative Staphylococcus species were cultured from all sites. eUVGI significantly decreased HVAC organisms (baseline 500,000 CFU cm(-2); P=0.015) and NICU environmental microbes (P<0.0001). Tracheal microbial loads decreased 45% (P=0.004), and fewer patients became colonized. VAP in the high-risk cohort fell from 74% (n=31) to 39% (n=18), P=0.04. VAP episodes per patient decreased (Control: 1.2 to eUVGI: 0.4; P=0.004), and antibiotic usage was 62% less (P=0.013). eUVGI decreased HVAC microbial colonization and was associated with reduced NICU environment and tracheal microbial colonization. Significant reductions in VAP and antibiotic use were also associated with eUVGI in this single-center study. Large randomized multicenter trials are needed.

Animal Ca2+ release-activated Ca2+ (CRAC channels appear to be homologous to and derived from the ubiquitous cation diffusion facilitators

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Tamang Dorjee G

2010-06-01

Full Text Available Abstract Background Antigen stimulation of immune cells triggers Ca2+ entry through Ca2+ release-activated Ca2+ (CRAC channels, promoting an immune response to pathogens. Defects in a CRAC (Orai channel in humans gives rise to the hereditary Severe Combined Immune Deficiency (SCID syndrome. We here report results that define the evolutionary relationship of the CRAC channel proteins of animals, and the ubiquitous Cation Diffusion Facilitator (CDF carrier proteins. Findings CDF antiporters derived from a primordial 2 transmembrane spanner (TMS hairpin structure by intragenic triplication to yield 6 TMS proteins. Four programs (IC/GAP, GGSEARCH, HMMER and SAM were evaluated for identifying sequence similarity and establishing homology using statistical means. Overall, the order of sensitivity (similarity detection was IC/GAP = GGSEARCH > HMMER > SAM, but the use of all four programs was superior to the use of any two or three of them. Members of the CDF family appeared to be homologous to members of the 4 TMS Orai channel proteins. Conclusions CRAC channels derived from CDF carriers by loss of the first two TMSs of the latter. Based on statistical analyses with multiple programs, TMSs 3-6 in CDF carriers are homologous to TMSs 1-4 in CRAC channels, and the former was the precursor of the latter. This is an unusual example of how a functionally and structurally more complex protein may have predated a simpler one.

Evaluation of the New Centers for Disease Control and Prevention Ventilator-Associated Event Module and Criteria in Critically Ill Children in Greece.

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Iosifidis, Elias; Chochliourou, Elpis; Violaki, Asimenia; Chorafa, Elisavet; Psachna, Stavroula; Roumpou, Afroditi; Sdougka, Maria; Roilides, Emmanuel

2016-10-01

OBJECTIVE To evaluate the new adult Centers for Disease Control and Prevention (CDC) ventilator-associated event (VAE) module in critically ill children and compare with the traditionally used CDC definition for ventilator-associated pneumonia (VAP). DESIGN Retrospective observational study of mechanically ventilated children in a pediatric intensive care unit in Greece January 1-December 31, 2011. METHODS Assessment of new adult CDC VAE module including 3 definition tiers: ventilator-associated condition (VAC), infection-related VAC, and possible/probable ventilator-associated pneumonia (VAE-VAP); comparison with traditional CDC criteria for clinically defined pneumonia in mechanically ventilated children (PNEU-VAP). We recorded Pediatric Risk of Mortality score at admission (PRISM III), number of ventilator-days, and outcome. RESULTS Among 119 patients with mechanical ventilation (median [range] number of ventilator-days, 7 [1-183]), 19 patients experienced VAC. Criteria for VAE-VAP were fulfilled in 12 of 19 patients with VAC (63%). Children with either VAC or VAE-VAP were on ventilation more days than patients without these conditions (16.5 vs 5 d, P=.0006 and 18 vs 5 d, PVAC (31.6%), than the patients without new VAE-VAP (14%, P=.007) or VAC (15%, P=.1), respectively. No significant association was found between PNEU-VAP and death. Incidences of PNEU-VAP and VAE-VAP were similar, but the agreement was poor. CONCLUSIONS VAE-VAP and PNEU-VAP found similar prevalence in critically ill children but with poor agreement. However, excess of death was significantly associated only with VAE-VAP. Infect Control Hosp Epidemiol 2016:1-5.

Geometric homology revisited

OpenAIRE

Ruffino, Fabio Ferrari

2013-01-01

Given a cohomology theory, there is a well-known abstract way to define the dual homology theory using the theory of spectra. In [4] the author provides a more geometric construction of the homology theory, using a generalization of the bordism groups. Such a generalization involves in its definition the vector bundle modification, which is a particular case of the Gysin map. In this paper we provide a more natural variant of that construction, which replaces the vector bundle modification wi...

Multidrug resistance transporters Snq2p and Pdr5p mediate caffeine efflux in Saccharomyces cerevisiae.

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Tsujimoto, Yoshiyuki; Shimizu, Yoshihiro; Otake, Kazuya; Nakamura, Tatsuya; Okada, Ryutaro; Miyazaki, Toshitaka; Watanabe, Kunihiko

2015-01-01

SNQ2 was identified as a caffeine-resistance gene by screening a genomic library of Saccharomyces cerevisiae in a multicopy vector YEp24. SNQ2 encodes an ATP-binding cassette transporter and is highly homologous to PDR5. Multicopy of PDR5 also conferred resistance to caffeine, while its resistance was smaller than that of SNQ2. Residual caffeine contents were analyzed after transiently exposing cells to caffeine. The ratios of caffeine contents were 21.3 ± 8.8% (YEp24-SNQ2) and 81.9 ± 8.7% (YEp24-PDR5) relative to control (YEp24, 100%). In addition, multicopies of SNQ2 or PDR5 conferred resistance to rhodamine 6G (R6G), which was widely used as a substrate for transport assay. R6G was exported by both transporters, and their efflux activities were inhibited by caffeine with half-maximal inhibitory concentrations of 5.3 ± 1.9 (YEp24-SNQ2) and 17.2 ± 9.6 mM (YEp24-PDR5). These results demonstrate that Snq2p is a more functional transporter of caffeine than Pdr5p in yeast cells.

Costs and risk factors for ventilator-associated pneumonia in a Turkish University Hospital's Intensive Care Unit: A case-control study

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Serin Simay

2004-04-01

Full Text Available Abstract Background Ventilator-associated pneumonia (VAP which is an important part of all nosocomial infections in intensive care unit (ICU is a serious illness with substantial morbidity and mortality, and increases costs of hospital care. We aimed to evaluate costs and risk factors for VAP in adult ICU. Methods This is a-three year retrospective case-control study. The data were collected between 01 January 2000 and 31 December 2002. During the study period, 132 patients were diagnosed as nosocomial pneumonia of 731 adult medical-surgical ICU patients. Of these only 37 VAP patients were assessed, and multiple nosocomially infected patients were excluded from the study. Sixty non-infected ICU patients were chosen as control patients. Results Median length of stay in ICU in patients with VAP and without were 8.0 (IQR: 6.5 and 2.5 (IQR: 2.0 days respectively (P Conclusion Respiratory failure, coma, depressed consciousness, enteral feeding and length of stay are independent risk factors for developing VAP. The cost of VAP is approximately five-fold higher than non-infected patients.

Human Fanconi anemia monoubiquitination pathway promotes homologous DNA repair.

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Nakanishi, Koji; Yang, Yun-Gui; Pierce, Andrew J; Taniguchi, Toshiyasu; Digweed, Martin; D'Andrea, Alan D; Wang, Zhao-Qi; Jasin, Maria

2005-01-25

Fanconi anemia (FA) is a recessive disorder characterized by congenital abnormalities, progressive bone-marrow failure, and cancer susceptibility. Cells from FA patients are hypersensitive to agents that produce DNA crosslinks and, after treatment with these agents, have pronounced chromosome breakage and other cytogenetic abnormalities. Eight FANC genes have been cloned, and the encoded proteins interact in a common cellular pathway. DNA-damaging agents activate the monoubiquitination of FANCD2, resulting in its targeting to nuclear foci that also contain BRCA1 and BRCA2/FANCD1, proteins involved in homology-directed DNA repair. Given the interaction of the FANC proteins with BRCA1 and BRCA2, we tested whether cells from FA patients (groups A, G, and D2) and mouse Fanca-/- cells with a targeted mutation are impaired for this repair pathway. We find that both the upstream (FANCA and FANCG) and downstream (FANCD2) FA pathway components promote homology-directed repair of chromosomal double-strand breaks (DSBs). The FANCD2 monoubiquitination site is critical for normal levels of repair, whereas the ATM phosphorylation site is not. The defect in these cells, however, is mild, differentiating them from BRCA1 and BRCA2 mutant cells. Surprisingly, we provide evidence that these proteins, like BRCA1 but unlike BRCA2, promote a second DSB repair pathway involving homology, i.e., single-strand annealing. These results suggest an early role for the FANC proteins in homologous DSB repair pathway choice.

p44 and p34 subunits of the BTF2/TFIIH transcription factor have homologies with SSL1, a yeast protein involved in DNA repair.

NARCIS (Netherlands)

S. Humbert; H. van Vuuren; Y. Lutz; J.H.J. Hoeijmakers (Jan); J-M. Egly (Jean-Marc); V. Moncollin

1994-01-01

textabstractThe human BTF2 (TFIIH) transcription factor is a multisubunit protein involved in transcription initiation by RNA polymerase II (B) as well as in DNA repair. In addition to the previously characterized p62 and p89/ERCC3 subunits, we have cloned two other subunits of BTF2, p44 and p34.

Homologous Recombination—Experimental Systems, Analysis and Significance

Science.gov (United States)

Kuzminov, Andrei

2014-01-01

Homologous recombination is the most complex of all recombination events that shape genomes and produce material for evolution. Homologous recombination events are exchanges between DNA molecules in the lengthy regions of shared identity, catalyzed by a group of dedicated enzymes. There is a variety of experimental systems in E. coli and Salmonella to detect homologous recombination events of several different kinds. Genetic analysis of homologous recombination reveals three separate phases of this process: pre-synapsis (the early phase), synapsis (homologous strand exchange) and post-synapsis (the late phase). In E. coli, there are at least two independent pathway of the early phase and at least two independent pathways of the late phase. All this complexity is incongruent with the originally ascribed role of homologous recombination as accelerator of genome evolution: there is simply not enough duplication and repetition in enterobacterial genomes for homologous recombination to have a detectable evolutionary role, and therefore not enough selection to maintain such a complexity. At the same time, the mechanisms of homologous recombination are uniquely suited for repair of complex DNA lesions called chromosomal lesions. In fact, the two major classes of chromosomal lesions are recognized and processed by the two individual pathways at the early phase of homologous recombination. It follows, therefore, that homologous recombination events are occasional reflections of the continual recombinational repair, made possible in cases of natural or artificial genome redundancy. PMID:26442506

Increased expression of enhancer of Zeste Homolog 2 (EZH2) differentiates squamous cell carcinoma from normal skin and actinic keratosis.

Science.gov (United States)

Xie, Qiang; Wang, Hongbei; Heilman, Edward R; Walsh, Michael G; Haseeb, M A; Gupta, Raavi

2014-01-01

Enhancer of Zeste Homolog 2 (EZH2) is a polycomb group protein that has been shown to be involved in the progression of multiple human cancers including melanoma. The expression of EZH2 in normal skin and in pre-malignant and malignant cutaneous squamous cell carcinoma (SCC) has not been studied. We examined the expression of EZH2 in normal skin, actinic keratosis (AK), SCC in situ, well-differentiated (SCC-WD), moderately-differentiated (SCC-MD) and poorly-differentiated SCC (SCC-PD) to ascertain whether EZH2 expression differentiates these conditions. Immunohistochemical staining for EZH2 was performed on formalin-fixed paraffin-embedded biopsies and a tissue microarray containing normal skin, AK, SCC in situ, and SCC of different grades. In comparison to the normal skin, EZH2 expression in actinic keratosis was increased (p=0.03). Similarly, EZH2 expression in all of the neoplastic conditions studied (SCC in situ, SCC-WD, SCC-MD and SCC-PD) was greatly increased in comparison to both the normal skin and actinic keratosis (p≤0.001). EZH2 expression increases incrementally from normal skin to AK and further to SCC, suggesting a role for EZH2 in the progression and differentiation of SCC. EZH2 expression may be used as a diagnostic marker for differentiating SCC from AK or normal skin.

Characterization of Group V Dubnium Homologs on DGA Extraction Chromatography Resin from Nitric and Hydrofluoric Acid Matrices

Energy Technology Data Exchange (ETDEWEB)

Despotopulos, J D; Sudowe, R

2012-02-21

Studies of the chemical properties of superheavy elements (SHE) pose interesting challenges due to their short half-lives and low production rates. Chemical systems must have extremely fast kinetics, fast enough kinetics to be able to examine the chemical properties of interest before the SHE decays to another nuclide. To achieve chemistry on such time scales, the chemical system must also be easily automated. Most importantly however, a chemical system must be developed which provides suitable separation and kinetics before an on-line study of a SHE can be performed. Relativistic effects make studying the chemical properties of SHEs interesting due to the impact these effects could have on the SHEs chemical properties. Relativistic effects arise when the velocity of the s orbital electrons approach the speed of light. As this velocity increases, the Bohr radius of the inner electron orbitals decreases and there is an increase in the particles mass. This contraction results in a destabilization of the energy of the outer d and f electron orbitals (5f and 6d in the case of SHE), which can cause these to expand due to their increased shielding from the nuclear charge. Another relativistic effect is the spin-orbit splitting for p, d, and f orbitals into j = 1 {+-} 1/2 states. This can lead most interestingly to a possible increased stability of element 114, which due to large spin-orbit splitting of the 7p orbital and the relativistically stabilized 7p{sub 1/2} and 7s orbital gives rise to a closed shell ground state of 7s{sup 2}7p{sub 1/2}{sup 2}. The homologs of element 105, dubnium (Db), Ta and Nb and the pseudo-homolog Pa, are well known to hydrolyze and form both neutral and non-neutral monoatomic and polyatomic species that may cause issues with extraction from a given chemical system. Early ion-exchange and solvent-extraction studies show mixed results for the behavior of Db. Some studies show Db behaving most similar to Ta, while others show it behaving

[Multicenter survey on ventilator-associated pneumonia prevention in intensive care].

Science.gov (United States)

Fischer, M-O; Garreau, N; Jarno, P; Villers, D; Dufour Trivini, M; Gérard, J-L; Fellahi, J-L; Hanouz, J-L; Parienti, J-J

2013-12-01

Ventilator-associated pneumonia (VAP) is the most common hospital-acquired infection in intensive care unit (ICU). The aim of the study was to evaluate the follow-up of the guidelines for VAP prevention. Retrospective, observational and multicenter study. During one year, all patients with mechanical ventilation over 48 hours were included in the CCLIN-Ouest Network. The demographic characteristics of the patients, the use of specific protocol for VAP prevention and the density of incidence of VAP were recorded. The use of a protocol for preventing VAP (absence, incomplete, complete and care bundle (i.e. complete prevention of VAP with weaning mechanical protocol and sedation protocol)) was collected. 26 ICU with 5742 patients were included. Ten ICU (38%; 2595 patients) had no protocol for VAP prevention, eight ICU (31%; 1821 patients) had an incomplete protocol, five ICU (19%; 561 patients) had a complete protocol and three ICU (12%; 765 patients) had a care bundle. The density of incidence of VAP was 14.8‰ (Interquartile range [IQR]: 10.2-0.1) for no protocol group, 15.6‰ [IQR: 12.6-6.2] for incomplete protocol group, 11.0‰ [IQR: 9.1-14.0] for complete protocol group and 12.9‰ [5-7,7-9,9-12] for care bundle group (P=0.742). The compliance to prevention of VAP was poor. Proposals for improving practice are discussed. Copyright © 2013. Published by Elsevier SAS.

Milrinone and thyroid hormone stimulate myocardial membrane Ca2+-ATPase activity and share structural homologies.

Science.gov (United States)

Mylotte, K M; Cody, V; Davis, P J; Davis, F B; Blas, S D; Schoenl, M

1985-01-01

We have recently shown that thyroid hormone in physiological concentrations stimulates sarcolemma-enriched rabbit-myocardial-membrane Ca2+-ATPase in vitro. In this study, milrinone [2-methyl-5-cyano-(3,4'-bipyridin)-6(1H)-one], a cardiac inotropic agent, was thyromimetic in the same system. At clinically achievable concentrations (50-500 nM), milrinone significantly stimulated membrane Ca2+-ATPase in vitro. This action was antagonized by W-7 [N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide], an agent that also blocks thyroid hormone action on the Ca2+-ATPase, at concentrations as low as 5 microM. Progressive additions of milrinone to membranes incubated with a fixed concentration of thyroxine (0.10 nM) or triiodothyronine resulted in a progressive obliteration of the thyroid hormone effect on Ca2+-ATPase. Amrinone [5-amino-(3,4'-bipyridin)-6(1H)-one], the parent bipyridine of milrinone, had no effect on myocardial Ca2+-ATPase activity. X-ray crystallographic analysis of milrinone and amrinone revealed structural homologies between the phenolic ring of thyroxine and the substituted ring of milrinone, whereas amrinone did not share these homologies. The mechanism(s) of the inotropic actions of thyroxine and of milrinone is not clearly understood, but these observations implicate Ca2+-ATPase, a calcium pump-associated enzyme, as one mediator of the effects on the heart of these two compounds. PMID:2933747

Productive Homologous and Non-homologous Recombination of Hepatitis C Virus in Cell Culture

Science.gov (United States)

Li, Yi-Ping; Mikkelsen, Lotte S.; Gottwein, Judith M.; Bukh, Jens

2013-01-01

Genetic recombination is an important mechanism for increasing diversity of RNA viruses, and constitutes a viral escape mechanism to host immune responses and to treatment with antiviral compounds. Although rare, epidemiologically important hepatitis C virus (HCV) recombinants have been reported. In addition, recombination is an important regulatory mechanism of cytopathogenicity for the related pestiviruses. Here we describe recombination of HCV RNA in cell culture leading to production of infectious virus. Initially, hepatoma cells were co-transfected with a replicating JFH1ΔE1E2 genome (genotype 2a) lacking functional envelope genes and strain J6 (2a), which has functional envelope genes but does not replicate in culture. After an initial decrease in the number of HCV positive cells, infection spread after 13–36 days. Sequencing of recovered viruses revealed non-homologous recombinants with J6 sequence from the 5′ end to the NS2–NS3 region followed by JFH1 sequence from Core to the 3′ end. These recombinants carried duplicated sequence of up to 2400 nucleotides. HCV replication was not required for recombination, as recombinants were observed in most experiments even when two replication incompetent genomes were co-transfected. Reverse genetic studies verified the viability of representative recombinants. After serial passage, subsequent recombination events reducing or eliminating the duplicated region were observed for some but not all recombinants. Furthermore, we found that inter-genotypic recombination could occur, but at a lower frequency than intra-genotypic recombination. Productive recombination of attenuated HCV genomes depended on expression of all HCV proteins and tolerated duplicated sequence. In general, no strong site specificity was observed. Non-homologous recombination was observed in most cases, while few homologous events were identified. A better understanding of HCV recombination could help identification of natural recombinants

A genetic screen identifies Tor as an interactor of VAPB in a Drosophila model of amyotrophic lateral sclerosis

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Senthilkumar Deivasigamani

2014-10-01

Full Text Available Amyotrophic Lateral Sclerosis (ALS is a progressive neurodegenerative disorder characterized by selective death of motor neurons. In 5–10% of the familial cases, the disease is inherited because of mutations. One such mutation, P56S, was identified in human VAPB that behaves in a dominant negative manner, sequestering wild type protein into cytoplasmic inclusions. We have conducted a reverse genetic screen to identify interactors of Drosophila VAPB. We screened 2635 genes and identified 103 interactors, of which 45 were enhancers and 58 were suppressors of VAPB function. Interestingly, the screen identified known ALS loci – TBPH, alsin2 and SOD1. Also identified were genes involved in cellular energetics and homeostasis which were used to build a gene regulatory network of VAPB modifiers. One key modifier identified was Tor, whose knockdown reversed the large bouton phenotype associated with VAP(P58S expression in neurons. A similar reversal was seen by over-expressing Tuberous Sclerosis Complex (Tsc1,2 that negatively regulates TOR signaling as also by reduction of S6K activity. In comparison, the small bouton phenotype associated with VAP(wt expression was reversed with Tsc1 knock down as well as S6K-CA expression. Tor therefore interacts with both VAP(wt and VAP(P58S, but in a contrasting manner. Reversal of VAP(P58S bouton phenotypes in larvae fed with the TOR inhibitor Rapamycin suggests upregulation of TOR signaling in response to VAP(P58S expression. The VAPB network and further mechanistic understanding of interactions with key pathways, such as the TOR cassette, will pave the way for a better understanding of the mechanisms of onset and progression of motor neuron disease.

A genetic screen identifies Tor as an interactor of VAPB in a Drosophila model of amyotrophic lateral sclerosis.

Science.gov (United States)

Deivasigamani, Senthilkumar; Verma, Hemant Kumar; Ueda, Ryu; Ratnaparkhi, Anuradha; Ratnaparkhi, Girish S

2014-10-31

Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disorder characterized by selective death of motor neurons. In 5-10% of the familial cases, the disease is inherited because of mutations. One such mutation, P56S, was identified in human VAPB that behaves in a dominant negative manner, sequestering wild type protein into cytoplasmic inclusions. We have conducted a reverse genetic screen to identify interactors of Drosophila VAPB. We screened 2635 genes and identified 103 interactors, of which 45 were enhancers and 58 were suppressors of VAPB function. Interestingly, the screen identified known ALS loci - TBPH, alsin2 and SOD1. Also identified were genes involved in cellular energetics and homeostasis which were used to build a gene regulatory network of VAPB modifiers. One key modifier identified was Tor, whose knockdown reversed the large bouton phenotype associated with VAP(P58S) expression in neurons. A similar reversal was seen by over-expressing Tuberous Sclerosis Complex (Tsc1,2) that negatively regulates TOR signaling as also by reduction of S6K activity. In comparison, the small bouton phenotype associated with VAP(wt) expression was reversed with Tsc1 knock down as well as S6K-CA expression. Tor therefore interacts with both VAP(wt) and VAP(P58S), but in a contrasting manner. Reversal of VAP(P58S) bouton phenotypes in larvae fed with the TOR inhibitor Rapamycin suggests upregulation of TOR signaling in response to VAP(P58S) expression. The VAPB network and further mechanistic understanding of interactions with key pathways, such as the TOR cassette, will pave the way for a better understanding of the mechanisms of onset and progression of motor neuron disease. © 2014. Published by The Company of Biologists Ltd.

Lectures on homology with internal symmetries

International Nuclear Information System (INIS)

Solovyov, Yu.

1993-09-01

Homology with internal symmetries is a natural generalization of cyclic homology introduced, independently, by Connes and Tsygan, which has turned out to be a very useful tool in a number of problems of algebra, geometry topology, analysis and mathematical physics. It suffices to say cycling homology and cohomology are successfully applied in the index theory of elliptic operators on foliations, in the description of the homotopy type of pseudoisotopy spaces, in the theory of characteristic classes in algebraic K-theory. They are also applied in noncommutative differential geometry and in the cohomology of Lie algebras, the branches of mathematics which brought them to life in the first place. Essentially, we consider dihedral homology, which was successfully applied for the description of the homology type of groups of homeomorphisms and diffeomorphisms of simply connected manifolds. (author). 27 refs

Incidence, characteristic and outcomes of ventilator-associated pneumonia among type 2 diabetes patients: An observational population-based study in Spain.

Science.gov (United States)

Jiménez-Trujillo, Isabel; Jiménez-García, Rodrigo; de Miguel-Díez, Javier; de Miguel-Yanes, José M; Hernández-Barrera, Valentín; Méndez-Bailón, Manuel; Pérez-Farinós, Napoleón; Salinero-Fort, Miguel-Ángel; López-de-Andrés, Ana

2017-05-01

To describe incidence, characteristics and outcomes of ventilator-associated pneumonia (VAP) during hospitalization among patients with or without type 2 diabetes (T2DM). We used the Spanish national hospital discharge database to select all hospitalization with VAP in subjects aged 40years or more from 2010 to 2014. We analyzed incidence, patient comorbidities, procedures, pneumonia pathogens and in-hospital outcomes according to diabetes status (T2DM and no-diabetes). We used propensity score analysis to estimate the effect of T2DM on in-hospital mortality RESULTS: In 7952 admissions, the patient developed a VAP (13.6% with T2DM). Adjusted incidence rate of VAP was slightly, but significantly, higher in T2DM than in non-diabetic patients (36.46[95% CI 34.41-38.51] vs. 32.57[95% CI 31.40-33.74] cases per 100,000/inhabitants). T2DM people were older and had higher Charlson comorbidity index than non-diabetic people. T2DM patients had a lower mean number of failing organs than non-diabetic patients (1.20 SD 1.17 vs. 1.45 SD 1.44, ppatients and 37.91% for non-diabetic patients (ppatients. In-hospital mortality was higher among the older patients and those with more co-morbid conditions. T2DM does not predict higher mortality in VAP during hospitalization. Copyright © 2017 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

Localization and roles of Ski8p protein in Sordaria meiosis and delineation of three mechanistically distinct steps of meiotic homolog juxtaposition.

Science.gov (United States)

Tessé, Sophie; Storlazzi, Aurora; Kleckner, Nancy; Gargano, Silvana; Zickler, Denise

2003-10-28

Ski8p is implicated in degradation of non-poly(A) and double-stranded RNA, and in meiotic DNA recombination. We have identified the Sordaria macrospora SKI8 gene. Ski8p is cytoplasmically localized in all vegetative and sexual cycle cells, and is nuclear localized, specifically in early-mid-meiotic prophase, in temporal correlation with Spo11p, the meiotic double-strand break (DSB) transesterase. Localizations of Ski8p and Spo11p are mutually interdependent. ski8 mutants exhibit defects in vegetative growth, entry into the sexual program, and sporulation. Diverse meiotic defects, also seen in spo11 mutants, are diagnostic of DSB absence, and they are restored by exogenous DSBs. These results suggest that Ski8p promotes meiotic DSB formation by acting directly within meiotic prophase chromosomes. Mutant phenotypes also divide meiotic homolog juxtaposition into three successive, mechanistically distinct steps; recognition, presynaptic alignment, and synapsis, which are distinguished by their differential dependence on DSBs.

Development of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC)

Science.gov (United States)

Michelacci, Valeria; Orsini, Massimiliano; Knijn, Arnold; Delannoy, Sabine; Fach, Patrick; Caprioli, Alfredo; Morabito, Stefano

2016-01-01

Shiga-toxin producing Escherichia coli (STEC) strains possess a large accessory genome composed of virulence genes existing in multiple allelic variants, which sometimes segregate with specific STEC subpopulations. We analyzed the allelic variability of 91 virulence genes of STEC by Real Time PCR followed by melting curves analysis in 713 E. coli strains including 358 STEC. The 91 genes investigated were located on the locus of enterocyte effacement (LEE), OI-57, and OI-122 pathogenicity islands and displayed a total of 476 alleles in the study population. The combinations of the 91 alleles of each strain were termed allelic signatures and used to perform cluster analyses. We termed such an approach High Resolution Virulence Allelic Profiling (HReVAP) and used it to investigate the phylogeny of STEC of multiple serogroups. The dendrograms obtained identified groups of STEC segregating approximately with the serogroups and allowed the identification of subpopulations within the single groups. The study of the allelic signatures provided further evidence of the coevolution of the LEE and OI-122, reflecting the occurrence of their acquisition through a single event. The HReVAP analysis represents a sensitive tool for studying the evolution of LEE-positive STEC. PMID:26941726

Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress

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Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S.

2016-01-01

Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress.

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Therese Wilhelm

2016-05-01

Full Text Available Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es. Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3% rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing, and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and

Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress.

Science.gov (United States)

Wilhelm, Therese; Ragu, Sandrine; Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S

2016-05-01

Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

Compositional Homology and Creative Thinking

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Salvatore Tedesco

2015-05-01

Full Text Available The concept of homology is the most solid theoretical basis elaborated by the morphological thinking during its history. The enucleation of some general criteria for the interpretation of homology is today a fundamental tool for life sciences, and for restoring their own opening to the question of qualitative innovation that arose so powerfully in the original Darwinian project. The aim of this paper is to verify the possible uses of the concept of compositional homology in order to provide of an adequate understanding of the dynamics of creative thinking.

Rational Homological Stability for Automorphisms of Manifolds

DEFF Research Database (Denmark)

Grey, Matthias

In this thesis we prove rational homological stability for the classifying spaces of the homotopy automorphisms and block di↵eomorphisms of iterated connected sums of products of spheres of a certain connectivity.The results in particular apply to the manifolds       Npg,q  = (#g(Sp x Sq)) - int...... with coefficients in the homology of the universal covering, which is studied using rational homology theory. The result for the block di↵eomorphisms is deduced from the homological stability for the homotopy automorphisms upon using Surgery theory. Themain theorems of this thesis extend the homological stability...

Cloning and characterization of the ddc homolog encoding L-2,4-diaminobutyrate decarboxylase in Enterobacter aerogenes.

Science.gov (United States)

Yamamoto, S; Mutoh, N; Tsuzuki, D; Ikai, H; Nakao, H; Shinoda, S; Narimatsu, S; Miyoshi, S I

2000-05-01

L-2,4-diaminobutyrate decarboxylase (DABA DC) catalyzes the formation of 1,3-diaminopropane (DAP) from DABA. In the present study, the ddc gene encoding DABA DC from Enterobacter aerogenes ATCC 13048 was cloned and characterized. Determination of the nucleotide sequence revealed an open reading frame of 1470 bp encoding a 53659-Da protein of 490 amino acids, whose deduced NH2-terminal sequence was identical to that of purified DABA DC from E. aerogenes. The deduced amino acid sequence was highly similar to those of Acinetobacter baumannii and Haemophilus influenzae DABA DCs encoded by the ddc genes. The lysine-307 of the E. aerogenes DABA DC was identified as the pyridoxal 5'-phosphate binding residue by site-directed mutagenesis. Furthermore, PCR analysis revealed the distribution of E. aerogenes ddc homologs in some other species of Enterobacteriaceae. Such a relatively wide occurrence of the ddc homologs implies biological significance of DABA DC and its product DAP.

SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins.

Science.gov (United States)

Park, Mi-Jeong; Sheng, Ren; Silkov, Antonina; Jung, Da-Jung; Wang, Zhi-Gang; Xin, Yao; Kim, Hyunjin; Thiagarajan-Rosenkranz, Pallavi; Song, Seohyeon; Yoon, Youngdae; Nam, Wonhee; Kim, Ilshin; Kim, Eui; Lee, Dong-Gyu; Chen, Yong; Singaram, Indira; Wang, Li; Jang, Myoung Ho; Hwang, Cheol-Sang; Honig, Barry; Ryu, Sungho; Lorieau, Justin; Kim, You-Me; Cho, Wonhwa

2016-04-07

The Src-homology 2 (SH2) domain is a protein interaction domain that directs myriad phosphotyrosine (pY)-signaling pathways. Genome-wide screening of human SH2 domains reveals that ∼90% of SH2 domains bind plasma membrane lipids and many have high phosphoinositide specificity. They bind lipids using surface cationic patches separate from pY-binding pockets, thus binding lipids and the pY motif independently. The patches form grooves for specific lipid headgroup recognition or flat surfaces for non-specific membrane binding and both types of interaction are important for cellular function and regulation of SH2 domain-containing proteins. Cellular studies with ZAP70 showed that multiple lipids bind its C-terminal SH2 domain in a spatiotemporally specific manner and thereby exert exquisite spatiotemporal control over its protein binding and signaling activities in T cells. Collectively, this study reveals how lipids control SH2 domain-mediated cellular protein-protein interaction networks and suggest a new strategy for therapeutic modulation of pY-signaling pathways. Copyright © 2016 Elsevier Inc. All rights reserved.

Satellite-derived land covers for runoff estimation using SCS-CN method in Chen-You-Lan Watershed, Taiwan

Science.gov (United States)

Zhang, Wen-Yan; Lin, Chao-Yuan

2017-04-01

The Soil Conservation Service Curve Number (SCS-CN) method, which was originally developed by the USDA Natural Resources Conservation Service, is widely used to estimate direct runoff volume from rainfall. The runoff Curve Number (CN) parameter is based on the hydrologic soil group and land use factors. In Taiwan, the national land use maps were interpreted from aerial photos in 1995 and 2008. Rapid updating of post-disaster land use map is limited due to the high cost of production, so the classification of satellite images is the alternative method to obtain the land use map. In this study, Normalized Difference Vegetation Index (NDVI) in Chen-You-Lan Watershed was derived from dry and wet season of Landsat imageries during 2003 - 2008. Land covers were interpreted from mean value and standard deviation of NDVI and were categorized into 4 groups i.e. forest, grassland, agriculture and bare land. Then, the runoff volume of typhoon events during 2005 - 2009 were estimated using SCS-CN method and verified with the measured runoff data. The result showed that the model efficiency coefficient is 90.77%. Therefore, estimating runoff by using the land cover map classified from satellite images is practicable.

Accurate pKa Calculation of the Conjugate Acids of Alkanolamines, Alkaloids and Nucleotide Bases by Quantum Chemical Methods

NARCIS (Netherlands)

Gangarapu, S.; Marcelis, A.T.M.; Zuilhof, H.

2013-01-01

The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum

Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins*

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Inaba, Satomi; Numoto, Nobutaka; Ogawa, Shuhei; Morii, Hisayuki; Ikura, Teikichi; Abe, Ryo; Ito, Nobutoshi; Oda, Masayuki

2017-01-01

Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases. PMID:27927989

Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins.

Science.gov (United States)

Inaba, Satomi; Numoto, Nobutaka; Ogawa, Shuhei; Morii, Hisayuki; Ikura, Teikichi; Abe, Ryo; Ito, Nobutoshi; Oda, Masayuki

2017-01-20

Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

[Comparison of endotracheal aspiration and mini-BAL culture results in the diagnosis of ventilator-associated pneumonia].

Science.gov (United States)

Artuk, Cumhur; Gül, Hanefi Cem; Mert, Gürkan; Karakaş, Ahmet; Bedir, Orhan; Eyigün, Can Polat

2012-07-01

The objective of this study was to compare the results of cultures obtained by mini-bronchoalveolar lavage (BAL) and endotracheal aspiration (ETA) techniques, used for rapid and accurate determination of pathogens causing ventilator-associated pneumonia (VAP) in intensive care units. Of the 92 patients on mechanical ventilation followed at the emergency intensive care unit of our hospital between June 2010 and June 2011, 30 (32.2%) patients were diagnosed as VAP and they were included in this study. VAP diagnosis were based on the clinical and radiological findings. Clinical pulmonary infection score (CPIS) of > 6 was accepted as the clinical criteria of VAP. Initially ETA samples were collected from the patients followed by mini-BAL sampling 15 minutes later, together with urine and two blood cultures. Microbiological evaluation and identification were performed by conventional methods and Phoenix 100 (BD Diagnostic Systems, ABD) automated system. In quantitative culture analysis, > 10.000 cfu/ml for BAL and > 100.000 cfu/ml for ETA were accepted as the positive result. The mean ages of VAP-developed (n= 30; 18 were male) and nondeveloped (n= 62; 39 were male) patients were 68.23 ± 16.19 and 52.16 ± 10.41 years, respectively, and the mean durations of mechanical ventilation were 29.57 ± 15.78 and 12.11 ± 6.01 days, respectively. Multivariate logistic regression analysis showed that older age (pVAP development. There was also a statistically significant difference in CPIS values between patients who developed VAP and not (6.8 ± 1.15 and 2.71 ± 1.06, respectively; pVAP diagnosis was found to be useful in patients on mechanical ventilation. In our study, a total of 16 strains (six A.baumannii, three P.aeruginosa, one K.pneumoniae, six S.aureus) were isolated from ETA cultures, while 34 strains (16 A.baumannii, six P.aeruginosa, four K.pneumoniae, two E.coli, six S.aureus) were isolated from mini-BAL cultures of 30 VAP patients. The contamination rate for ETA

STUDY OF THE ISOLATES OF SUSPECTED VAP, PREVALENCE OF THE DIFFERENT ORGANISMS AND MIC PATTERNS IN A TERTIARY CARE HOSPITAL

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Swagnik Roy

2017-01-01

Full Text Available BACKGROUND The development of nosocomial infections mostly ventilator-associated pneumonia due to prolonged stay in the ICUs varies grossly in different outcomes including increased morbidity and mortality. The American Thoracic Society (ATS guidelines recommend that quantitative cultures can be performed on ETA or samples collected either bronchoscopically or nonbronchosopically. 1 More importantly, recent small trials have repeatedly shown that there is no advantage of bronchoscopic cultures over quantitative endotracheal aspirate. 2,3,4 Detection of causative organisms and their antibiotic MIC determination is absolutely necessary to initiate the specific antibiotic with appropriate dose thereby reducing the adverse effects of inadequate antibiotic treatment on the patient prognosis. MATERIALS AND METHODS The prospective study was carried out during the period from August 2012 to January 2015 in Department of Microbiology from the samples those were received as a routine culture from VAP suspected patients from the ICU. There were 373 samples from which 123 were culture positives. Inclusion criteria were all the patients 18 years and more age group who were intubated in mechanical ventilator and others were excluded in the study. Clinical Pulmonary Infection Score (CPIS was given to each patient included in the study on daily basis. CPIS of greater than six was used as diagnostic criteria for VAP. 5 Clinically diagnosed ventilator-associated pneumonia were observed and clinical parameters were recorded from their medical records and bedside charts. All patients with clinical and radiological signs suggestive of pneumonia on admission. Endotracheal aspirate was collected by using a 22-inch Romsons suction catheter. Chest vibration or percussion for 10 mins. was used. Only 1 ETA sample was collected from each patient and was immediately taken to the laboratory for processing. RESULTS Klebsiella pneumonia was isolated 39.02%, Pseudomonas

Matrix factorizations and homological mirror symmetry on the torus

International Nuclear Information System (INIS)

Knapp, Johanna; Omer, Harun

2007-01-01

We consider matrix factorizations and homological mirror symmetry on the torus T 2 using a Landau-Ginzburg description. We identify the basic matrix factorizations of the Landau-Ginzburg superpotential and compute the full spectrum taking into account the explicit dependence on bulk and boundary moduli. We verify homological mirror symmetry by comparing three-point functions in the A-model and the B-model

Implementation of a real-time compliance dashboard to help reduce SICU ventilator-associated pneumonia with the ventilator bundle.

Science.gov (United States)

Zaydfudim, Victor; Dossett, Lesly A; Starmer, John M; Arbogast, Patrick G; Feurer, Irene D; Ray, Wayne A; May, Addison K; Pinson, C Wright

2009-07-01

Ventilator-associated pneumonia (VAP) causes significant morbidity and mortality in critically ill surgical patients. Recent studies suggest that the success of preventive measures is dependent on compliance with ventilator bundle parameters. Implementation of an electronic dashboard will improve compliance with the bundle parameters and reduce rates of VAP in our surgical intensive care unit (SICU). Time series analysis of VAP rates between January 2005 and July 2008, with dashboard implementation in July 2007. Multidisciplinary SICU at a tertiary-care referral center with a stable case mix during the study period. Patients admitted to the SICU between January 2005 and July 2008. Infection control data were used to establish rates of VAP and total ventilator days. For the time series analysis, VAP rates were calculated as quarterly VAP events per 1000 ventilator days. Ventilator bundle compliance was analyzed after dashboard implementation. Differences between expected and observed VAP rates based on time series analysis were used to estimate the effect of intervention. Average compliance with the ventilator bundle improved from 39% in August 2007 to 89% in July 2008 (P dashboard (P = .01). Quarterly VAP rates were significantly reduced in the November 2007 through January 2008 and February through April 2008 periods (P dashboard improved compliance with ventilator bundle measures and is associated with reduced rates of VAP in our SICU.

Homological algebra in -abelian categories

Indian Academy of Sciences (India)

Deren Luo

2017-08-16

Aug 16, 2017 ... Homological algebra in n-abelian categories. 627. We recall the Comparison lemma, together with its dual, plays a central role in the sequel. Lemma 2.1 [13, Comparison lemma 2.1]. Let C be an additive category and X ∈ Ch. ≥0(C) a complex such that for all k ≥ 0the morphism dk+1. X is a weak cokernel ...

S1P transporter SPNS2 regulates proper postnatal retinal morphogenesis.

Science.gov (United States)

Fang, Chao; Bian, Ganlan; Ren, Pan; Xiang, Jie; Song, Jun; Yu, Caiyong; Zhang, Qian; Liu, Ling; Chen, Kun; Liu, Fangfang; Zhang, Kun; Wu, Chunfeng; Sun, Ruixia; Hu, Dan; Ju, Gong; Wang, Jian

2018-02-08

Spinster homolog 2 (SPNS2) is the membrane transporter of sphingosine-1-phosphate (S1P), and it participates in several physiologic processes by activating different S1P receptors (S1PRs). However, its functions in the nervous system remain largely unclear. We explored the important role of SPNS2 in the process of retinal morphogenesis using a spns2-deficient rat model. In the absence of the functional SPNS2 transporter, we observed progressively aggravating laminar disorganization of the epithelium at the postnatal stage of retinal development. Disrupted cell polarity, delayed cell-cycle exit of retinal progenitor cells, and insufficient migration of newborn neurons were proposed in this study as potential mechanisms accounting for this structural disorder. In addition, we analyzed the expression profiles of spns2 and s1prs, and proposed that SPNS2 regulated retinal morphogenesis by establishing the S1P level in the eye and activating S1PR3 signaling. These data indicate that SPNS2 is indispensable for normal retinal morphogenesis and provide new insights on the role of S1P in the developing retina using an established in vivo model.-Fang, C., Bian, G., Ren, P., Xiang, J., Song, J., Yu, C., Zhang, Q., Liu, L., Chen, K., Liu, F., Zhang, K., Wu, C., Sun, R., Hu, D., Ju, G., Wang, J. S1P transporter SPNS2 regulates proper postnatal retinal morphogenesis.

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

DEFF Research Database (Denmark)

Nielsen, Morten; Lundegaard, Claus; Lund, Ole

2010-01-01

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.......0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models.......3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is...

Combined HQSAR, topomer CoMFA, homology modeling and docking studies on triazole derivatives as SGLT2 inhibitors.

Science.gov (United States)

Yu, Shuling; Yuan, Jintao; Zhang, Yi; Gao, Shufang; Gan, Ying; Han, Meng; Chen, Yuewen; Zhou, Qiaoqiao; Shi, Jiahua

2017-06-01

Sodium-glucose cotransporter 2 (SGLT2) is a promising target for diabetes therapy. We aimed to develop computational approaches to identify structural features for more potential SGLT2 inhibitors. In this work, 46 triazole derivatives as SGLT2 inhibitors were studied using a combination of several approaches, including hologram quantitative structure-activity relationships (HQSAR), topomer comparative molecular field analysis (CoMFA), homology modeling, and molecular docking. HQSAR and topomer CoMFA were used to construct models. Molecular docking was conducted to investigate the interaction of triazole derivatives and homology modeling of SGLT2, as well as to validate the results of the HQSAR and topomer CoMFA models. The most effective HQSAR and topomer CoMFA models exhibited noncross-validated correlation coefficients of 0.928 and 0.891 for the training set, respectively. External predictions were made successfully on a test set and then compared with previously reported models. The graphical results of HQSAR and topomer CoMFA were proven to be consistent with the binding mode of the inhibitors and SGLT2 from molecular docking. The models and docking provided important insights into the design of potent inhibitors for SGLT2.

Homology in Electromagnetic Boundary Value Problems

Directory of Open Access Journals (Sweden)

Pellikka Matti

2010-01-01

Full Text Available We discuss how homology computation can be exploited in computational electromagnetism. We represent various cellular mesh reduction techniques, which enable the computation of generators of homology spaces in an acceptable time. Furthermore, we show how the generators can be used for setting up and analysis of an electromagnetic boundary value problem. The aim is to provide a rationale for homology computation in electromagnetic modeling software.

Homological stability for unordered configuration spaces

DEFF Research Database (Denmark)

Randal-Williams, Oscar

2013-01-01

This paper consists of two related parts. In the first part we give a self-contained proof of homological stability for the spaces C_n(M;X) of configurations of n unordered points in a connected open manifold M with labels in a path-connected space X, with the best possible integral stability range...... of the spaces C_n(M) can be considered stable when M is a closed manifold. In this case there are no stabilisation maps, but one may still ask if the dimensions of the homology groups over some field stabilise with n. We prove that this is true when M is odd-dimensional, or when the field is F_2 or Q...

Candida spp. airway colonization: A potential risk factor for Acinetobacter baumannii ventilator-associated pneumonia.

Science.gov (United States)

Tan, Xiaojiang; Zhu, Song; Yan, Dongxing; Chen, Weiping; Chen, Ruilan; Zou, Jian; Yan, Jingdong; Zhang, Xiangdong; Farmakiotis, Dimitrios; Mylonakis, Eleftherios

2016-08-01

This retrospective study was conducted to identify potential risk factors for Acinetobacter baumannii (A. baumannii) ventilator-associated pneumonia (VAP) and evaluate the association between Candida spp. airway colonization and A. baumannii VAP. Intensive care unit (ICU) patients who were on mechanical ventilation (MV) for ≥48 hours were divided into the following groups: patients with and without Candida spp. airway colonization; colonized patients receiving antifungal treatment or not; patients with A. baumannii VAP and those without VAP. Logistic regression analysis and propensity score matching were used to identify factors independently associated with A. baumannii VAP. Among 618 eligible patients, 264 (43%) had Candida spp. airway colonization and 114 (18%) developed A. baumannii VAP. Along with MV for ≥7 days (adjusted odds ratio [aOR] 8.9, 95% confidence intervals [95% CI] 4.9-15.8) and presence of a central venous catheter (aOR 3.2, 95% CI 1.1-9), Candida spp. airway colonization (aOR 2.6, 95% CI 1.6-4.3) was identified as an independent risk factor for A. baumannii VAP. Patients with Candida spp. airway colonization were more likely to develop A. baumannii VAP than non-colonized patients (23% vs 15%, P=.01 and 34% vs. 15%, PCandida spp. airway colonization (43%) and A. baumannii VAP (18%) were common in ICU patients who were on mechanical ventilation for at least 48 hours. Candida spp. airway colonization was an independent risk factor for subsequent A. baumannii VAP. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Homological stability of diffeomorphism groups

DEFF Research Database (Denmark)

Berglund, Alexander; Madsen, Ib Henning

2013-01-01

In this paper we prove a stability theorem for block diffeomorphisms of 2d -dimensional manifolds that are connected sums of S d ×S d . Combining this with a recent theorem of S. Galatius and O. Randal-Williams and Morlet’s lemma of disjunction, we determine the homology of the classifying space ...

PCR artifact in testing for homologous recombination in genomic editing in zebrafish.

Directory of Open Access Journals (Sweden)

Minho Won

Full Text Available We report a PCR-induced artifact in testing for homologous recombination in zebrafish. We attempted to replace the lnx2a gene with a donor cassette, mediated by a TALEN induced double stranded cut. The donor construct was flanked with homology arms of about 1 kb at the 5' and 3' ends. Injected embryos (G0 were raised and outcrossed to wild type fish. A fraction of the progeny appeared to have undergone the desired homologous recombination, as tested by PCR using primer pairs extending from genomic DNA outside the homology region to a site within the donor cassette. However, Southern blots revealed that no recombination had taken place. We conclude that recombination happened during PCR in vitro between the donor integrated elsewhere in the genome and the lnx2a locus. We conclude that PCR alone may be insufficient to verify homologous recombination in genome editing experiments in zebrafish.

In Vivo Interplay between p27Kip1, GATA3, ATOH1, and POU4F3 Converts Non-sensory Cells to Hair Cells in Adult Mice

Directory of Open Access Journals (Sweden)

Bradley J. Walters

2017-04-01

Full Text Available Summary: Hearing loss is widespread and persistent because mature mammalian auditory hair cells (HCs are nonregenerative. In mice, the ability to regenerate HCs from surrounding supporting cells (SCs declines abruptly after postnatal maturation. We find that combining p27Kip1 deletion with ectopic ATOH1 expression surmounts this age-related decline, leading to conversion of SCs to HCs in mature mouse cochleae and after noise damage. p27Kip1 deletion, independent of canonical effects on Rb-family proteins, upregulated GATA3, a co-factor for ATOH1 that is lost from SCs with age. Co-activation of GATA3 or POU4F3 and ATOH1 promoted conversion of SCs to HCs in adult mice. Activation of POU4F3 alone also converted mature SCs to HCs in vivo. These data illuminate a genetic pathway that initiates auditory HC regeneration and suggest p27Kip1, GATA3, and POU4F3 as additional therapeutic targets for ATOH1-mediated HC regeneration. : Auditory hair cells are nonregenerative, resulting in persistent hearing loss upon damage. Walters et al. find that manipulating two genes, p27Kip1 and Atoh1, induces the conversion of nonsensory cells to hair cells in adult mice. This effect is mediated by GATA3 and POU4F3, where POU4F3 alone was found to convert nonsensory cells. Keywords: regeneration, aging, differentiation, proliferation, development, cancer, sensory, cochlea, hearing

Runoff Potentiality of a Watershed through SCS and Functional Data Analysis Technique

Directory of Open Access Journals (Sweden)

M. I. Adham

2014-01-01

Full Text Available Runoff potentiality of a watershed was assessed based on identifying curve number (CN, soil conservation service (SCS, and functional data analysis (FDA techniques. Daily discrete rainfall data were collected from weather stations in the study area and analyzed through lowess method for smoothing curve. As runoff data represents a periodic pattern in each watershed, Fourier series was introduced to fit the smooth curve of eight watersheds. Seven terms of Fourier series were introduced for the watersheds 5 and 8, while 8 terms of Fourier series were used for the rest of the watersheds for the best fit of data. Bootstrapping smooth curve analysis reveals that watersheds 1, 2, 3, 6, 7, and 8 are with monthly mean runoffs of 29, 24, 22, 23, 26, and 27 mm, respectively, and these watersheds would likely contribute to surface runoff in the study area. The purpose of this study was to transform runoff data into a smooth curve for representing the surface runoff pattern and mean runoff of each watershed through statistical method. This study provides information of runoff potentiality of each watershed and also provides input data for hydrological modeling.

Runoff Potentiality of a Watershed through SCS and Functional Data Analysis Technique

Science.gov (United States)

Adham, M. I.; Shirazi, S. M.; Othman, F.; Rahman, S.; Yusop, Z.; Ismail, Z.

2014-01-01

Runoff potentiality of a watershed was assessed based on identifying curve number (CN), soil conservation service (SCS), and functional data analysis (FDA) techniques. Daily discrete rainfall data were collected from weather stations in the study area and analyzed through lowess method for smoothing curve. As runoff data represents a periodic pattern in each watershed, Fourier series was introduced to fit the smooth curve of eight watersheds. Seven terms of Fourier series were introduced for the watersheds 5 and 8, while 8 terms of Fourier series were used for the rest of the watersheds for the best fit of data. Bootstrapping smooth curve analysis reveals that watersheds 1, 2, 3, 6, 7, and 8 are with monthly mean runoffs of 29, 24, 22, 23, 26, and 27 mm, respectively, and these watersheds would likely contribute to surface runoff in the study area. The purpose of this study was to transform runoff data into a smooth curve for representing the surface runoff pattern and mean runoff of each watershed through statistical method. This study provides information of runoff potentiality of each watershed and also provides input data for hydrological modeling. PMID:25152911

Molecular modeling used to evaluate CYP2C9-dependent metabolism: homology modeling, molecular dynamics and docking simulations.

Science.gov (United States)

Mendieta-Wejebe, Jessica E; Correa-Basurto, José; García-Segovia, Erika M; Ceballos-Cancino, Gisela; Rosales-Hernández, Martha C

2011-07-01

Cytochrome P450 (CYP) 2C9 is the principal isoform of the CYP2C subfamily in the human liver and is involved in the oxidation of several endogenous and xenobiotic compounds, including many therapeutic drugs. The metabolism of drugs by CYP2C9 can yield either safe or toxic products, which may be related to the recognition and binding modes of the substrates to this isoform. These interactions can be studied using in silico methods such as quantum chemistry, molecular dynamics and docking simulations, which can also be useful for predicting the structure of metabolites. In these types of studies, the ligand and the protein must be tridimensional models; thus, the protein can be built by homology modeling or retrieved from the Protein Data Bank. Therefore, the current review emphasizes the importance of using in silico methods to predict the metabolism of CYP2C9 because these computational tools have allowed the description of the principal characteristics of the active site of this isoform at the molecular level and the chemical properties of its ligands.

SCS-CN parameter determination using rainfall-runoff data in heterogeneous watersheds. The two-CN system approach

OpenAIRE

K. X. Soulis; J. D. Valiantzas

2011-01-01

The Soil Conservation Service Curve Number (SCS-CN) approach is widely used as a simple method for predicting direct runoff volume for a given rainfall event. The CN values can be estimated by being selected from tables. However, it is more accurate to estimate the CN value from measured rainfall-runoff data (assumed available) in a watershed. Previous researchers indicated that the CN values calculated from measured rainfall-runoff data vary systematically with the rainfall depth. The...

Pea VEGETATIVE2 Is an FD Homolog That Is Essential for Flowering and Compound Inflorescence Development.

Science.gov (United States)

Sussmilch, Frances C; Berbel, Ana; Hecht, Valérie; Vander Schoor, Jacqueline K; Ferrándiz, Cristina; Madueño, Francisco; Weller, James L

2015-04-01

As knowledge of the gene networks regulating inflorescence development in Arabidopsis thaliana improves, the current challenge is to characterize this system in different groups of crop species with different inflorescence architecture. Pea (Pisum sativum) has served as a model for development of the compound raceme, characteristic of many legume species, and in this study, we characterize the pea VEGETATIVE2 (VEG2) locus, showing that it is critical for regulation of flowering and inflorescence development and identifying it as a homolog of the bZIP transcription factor FD. Through detailed phenotypic characterizations of veg2 mutants, expression analyses, and the use of protein-protein interaction assays, we find that VEG2 has important roles during each stage of development of the pea compound inflorescence. Our results suggest that VEG2 acts in conjunction with multiple FLOWERING LOCUS T (FT) proteins to regulate expression of downstream target genes, including TERMINAL FLOWER1, LEAFY, and MADS box homologs, and to facilitate cross-regulation within the FT gene family. These findings further extend our understanding of the mechanisms underlying compound inflorescence development in pea and may have wider implications for future manipulation of inflorescence architecture in related legume crop species. © 2015 American Society of Plant Biologists. All rights reserved.

Estimating enthalpy of vaporization from vapor pressure using Trouton's rule.

Science.gov (United States)

MacLeod, Matthew; Scheringer, Martin; Hungerbühler, Konrad

2007-04-15

The enthalpy of vaporization of liquids and subcooled liquids at 298 K (delta H(VAP)) is an important parameter in environmental fate assessments that consider spatial and temporal variability in environmental conditions. It has been shown that delta H(VAP)P for non-hydrogen-bonding substances can be estimated from vapor pressure at 298 K (P(L)) using an empirically derived linear relationship. Here, we demonstrate that the relationship between delta H(VAP)and PL is consistent with Trouton's rule and the ClausiusClapeyron equation under the assumption that delta H(VAP) is linearly dependent on temperature between 298 K and the boiling point temperature. Our interpretation based on Trouton's rule substantiates the empirical relationship between delta H(VAP) degree and P(L) degrees for non-hydrogen-bonding chemicals with subcooled liquid vapor pressures ranging over 15 orders of magnitude. We apply the relationship between delta H(VAP) degrees and P(L) degrees to evaluate data reported in literature reviews for several important classes of semivolatile environmental contaminants, including polycyclic aromatic hydrocarbons, chlorobenzenes, polychlorinated biphenyls and polychlorinated dibenzo-dioxins and -furans and illustrate the temperature dependence of results from a multimedia model presented as a partitioning map. The uncertainty associated with estimating delta H(VAP)degrees from P(L) degrees using this relationship is acceptable for most environmental fate modeling of non-hydrogen-bonding semivolatile organic chemicals.

Imipenem, meropenem, or doripenem to treat patients with Pseudomonas aeruginosa ventilator-associated pneumonia.

Science.gov (United States)

Luyt, Charles-Edouard; Aubry, Alexandra; Lu, Qin; Micaelo, Maïté; Bréchot, Nicolas; Brossier, Florence; Brisson, Hélène; Rouby, Jean-Jacques; Trouillet, Jean-Louis; Combes, Alain; Jarlier, Vincent; Chastre, Jean

2014-01-01

Only limited data exist on Pseudomonas aeruginosa ventilator-associated pneumonia (VAP) treated with imipenem, meropenem, or doripenem. Therefore, we conducted a prospective observational study in 169 patients who developed Pseudomonas aeruginosa VAP. Imipenem, meropenem, and doripenem MICs for Pseudomonas aeruginosa isolates were determined using Etests and compared according to the carbapenem received. Among the 169 isolates responsible for the first VAP episode, doripenem MICs were lower (Pimipenem and meropenem (MIC50s, 0.25, 2, and 0.38, respectively); 61%, 64%, and 70% were susceptible to imipenem, meropenem, and doripenem, respectively (P was not statistically significant). Factors independently associated with carbapenem resistance were previous carbapenem use (within 15 days) and mechanical ventilation duration before VAP onset. Fifty-six (33%) patients had at least one VAP recurrence, and 56 (33%) died. Factors independently associated with an unfavorable outcome (recurrence or death) were a high day 7 sequential organ failure assessment score and mechanical ventilation dependency on day 7. Physicians freely prescribed a carbapenem to 88 patients: imipenem for 32, meropenem for 24, and doripenem for 32. The remaining 81 patients were treated with various antibiotics. Imipenem-, meropenem-, and doripenem-treated patients had similar VAP recurrence rates (41%, 25%, and 22%, respectively; P=0.15) and mortality rates (47%, 25%, and 22%, respectively; P=0.07). Carbapenem resistance emerged similarly among patients treated with any carbapenem. No carbapenem was superior to another for preventing carbapenem resistance emergence.

Homology in vertebrates bone mineral structure

International Nuclear Information System (INIS)

Batdehmbehrehl, G.; Chultehm, D.; Sangaa, D.

1999-01-01

Using the neutron diffraction method a domination of low crystal syngonic (sp. gr. P63/m) phase Ca 5 [PO 4 ] 3 (OH, F, Cl) in bull and sheep bones as well as in the fossil dinosaur bone has been established and crystal phases in all the bones have identical structure (homology). The result becomes to be an important contribution to fundamental science such as biological evolution and to be useful in medical practice and solution of radiobiological problems connected with vertebrates and man. (author)

Event-related cortical processing in neuropathic pain under long-term spinal cord stimulation.

Science.gov (United States)

Weigel, Ralf; Capelle, H Holger; Flor, Herta; Krauss, Joachim K

2015-01-01

Several mechanisms were suggested in the past to explain the beneficial effect of spinal cord stimulation (SCS) in patients suffering from neuropathic pain. Little is known about potential supraspinal mechanisms. In this study cortical signaling of patients with neuropathic pain and successful long-term treatment with SCS was analyzed. Observational study. University hospital, neurosurgical department, outpatient clinic for movement disorders and pain, institute for cognitive and clinical neuroscience. Nine patients with neuropathic pain of a lower extremity with a lasting response to chronic SCS were included. Cortical activity was analyzed using event-related potentials of the electroencephalogram after non-painful and painful stimulation. Each patient was tested under the effect of long-term SCS and 24 hours after cessation of SCS. Cortical areas involved in the peaks of evoked potentials were localized using a source localization method based on a fixed dipole model. Detection threshold and intensity of non-painful stimulation did not differ significantly on both sides. Pain threshold was significantly lower on the neuropathic side under the effect of SCS (P = 0.03). Bilateral pain thresholds were significantly lower (P = 0.03 healthy side, P = 0.003 neuropathic side) in 5 patients with increased pain after cessation of SCS. Under the effect of SCS cortical negativities (N1, N2, N3) and positivities (P1) demonstrated bilaterally comparable amplitudes. After cessation of SCS, decreased threshold for peripheral stimulation resulted in lowered negativities on both sides. The positivity P1 was differentially regulated and was reduced more contralateral to the unaffected side. N2 was localized at the sensory representation of the leg within the homunculus. The main vector of P1 was localized within the cingular cortex (CC) and moved more anteriorly under the effect of SCS. The exact time span that SCS continues to have an effect is not known. However, due to patient

Cost assessment of a new oral care program in the intensive care unit to prevent ventilator-associated pneumonia.

Science.gov (United States)

Ory, Jérôme; Mourgues, Charline; Raybaud, Evelyne; Chabanne, Russell; Jourdy, Jean Christophe; Belard, Fabien; Guérin, Renaud; Cosserant, Bernard; Faure, Jean Sébastien; Calvet, Laure; Pereira, Bruno; Guelon, Dominique; Traore, Ousmane; Gerbaud, Laurent

2018-06-01

Ventilator-associated pneumonia (VAP) is the most frequent hospital-acquired infections in intensive care units (ICU). In the bundle of care to prevent the VAP, the oral care is very important strategies, to decrease the oropharyngeal bacterial colonization and presence of causative bacteria of VAP. In view of the paucity of medical economics studies, our objective was to determine the cost of implementing this oral care program for preventing VAP. In five ICUs, during period 1, caregivers used a foam stick for oral care and, during period 2, a stick and tooth brushing with aspiration. Budgetary effect of the new program from the hospital's point of view was analyzed for both periods. The costs avoided were calculated from the incidence density of VAP (cases per 1000 days of intubation). The cost study included device cost, benefit lost, and ICU cost (medication, employer and employee contributions, blood sample analysis…). A total of 2030 intubated patients admitted to the ICUs benefited from oral care. The cost of implementing the study protocol was estimated to be €11,500 per year. VAP rates decreased significantly between the two periods (p1 = 12.8% and p2 = 8.5%, p = 0.002). The VAP revenue was ranged from €28,000 to €45,000 and the average cost from €39,906 to €42,332. The total cost assessment calculated was thus around €1.9 million in favor of the new oral care program. Our study showed that the implementation of a simple strategy improved the quality of patient care is economically viable. NCT02400294.

Knowledge of Critical Care Provider on Prevention of Ventilator Associated Pneumonia

Directory of Open Access Journals (Sweden)

Passang Chiki Sherpa

2014-01-01

Full Text Available Background: Ventilator-associated pneumonia (VAP continues to be an important cause of morbidity and mortality in ventilated patient. Prevention of VAP in critically ill patient is significant concern for health care team in intensive care units (ICUs. Knowledge on prevention of VAP would have a significant impact on patient outcome. Aims and Objectives: To assess knowledge on prevention of VAP in critical care providers and to find the association between knowledge on prevention of VAP and educational qualification and years of experience in ICUs. Settings and Design: The study was conducted in 5 different ICUs of Kasturba Hospital, Manipal, and using descriptive study design. Material and Methods: The study involved a purposive sample of 138 critical care providers. Critical care providers who were willing to participate in the study were included. Tools on demographic proforma and self-administered structured knowledge questionnaire on prevention of VAP were developed and content validity was established. The reliability of the tools was established.The data was categorized and analyzed by using descriptive and inferential statistics. The SPSS 16.0 version was used for the analysis of the study. Result: Majority 89.1% of the participant were 20-29 years, 63% unmarried 51.4% had completed diploma course and majority 81.2% were from nursing discipline. The study revealed that only 55.80% of subjects were having adequate knowledge on prevention of VAP based on median score. There was no significant association between knowledge score and educational qualification (÷²=0, p=0.833, years of experience in ICU (÷²= 2.221, p=0.329.

Structure of the interleukin-2 tyrosine kinase Src homology 2 domain; comparison between X-ray and NMR-derived structures

International Nuclear Information System (INIS)

Joseph, Raji E.; Ginder, Nathaniel D.; Hoy, Julie A.; Nix, Jay C.; Fulton, D. Bruce; Honzatko, Richard B.; Andreotti, Amy H.

2012-01-01

The interleukin-2 tyrosine kinase Src homology 2 domain was crystallized and its structure was solved to 2.35 Å resolution. The structure reveals a domain-swapped dimer that is related to other dimeric SH2 domains solved previously. The cis–trans-prolyl isomerization that is evident from solution studies of Itk SH2 cannot be observed in the crystal structure. The crystal structure of the interleukin-2 tyrosine kinase Src homology domain (Itk SH2) is described and it is found that unlike in studies of this domain using NMR spectroscopy, cis–trans-prolyl isomerization is not readily detected in the crystal structure. Based on similarities between the Itk SH2 crystal form and the cis form of the Itk SH2 NMR structure, it is concluded that it is likely that the prolyl imide bond at least in part adopts the cis conformation in the crystal form. However, the lack of high-resolution data and the dynamic nature of the proline-containing loop mean that the precise imide-bond conformation cannot be determined and prolyl cis–trans isomerization in the crystal cannot be ruled out. Given the preponderance of structures that have been solved by X-ray crystallography in the Protein Data Bank, this result supports the notion that prolyl isomerization in folded proteins has been underestimated among known structures. Interestingly, while the precise status of the proline residue is ambiguous, Itk SH2 crystallizes as a domain-swapped dimer. The domain-swapped structure of Itk SH2 is similar to the domain-swapped SH2 domains of Grb2 and Nck, with domain swapping occurring at the β-meander region of all three SH2 domains. Thus, for Itk SH2 structural analysis by NMR spectroscopy and X-ray crystallography revealed very different structural features: proline isomerization versus domain-swapped dimerization, respectively

Kajian Model Estimasi Volume Limpasan Permukaan, Debit Puncak Aliran, dan Erosi Tanah dengan Model Soil Conservation Service (SCS, Rasional Dan Modified Universal Soil Loss Equation (MUSLE (Studi Kasus di DAS Keduang, Wonogiri

Directory of Open Access Journals (Sweden)

Ugro Hari Murtiono

2008-12-01

Full Text Available Hydrologic modelling has been developing and it is usefull for basic data in managing water resources. The aim of the reseach is to estimate volume runoff, maximum discharge, and soil erosion with SCS, Rational, and MUSLE models on Keduang Watershed. Explain the data analysis, and flow to get the data. SCS parameters model use are: runoff, rainfall, deferent between rainfall runoff. The deferent rainfall between runoff relationship kurva Runoff Coefisient (Curve Nunmber/CN. This Coefisient connected with Soil Hydrology Group (antecedent moisture content/AMC, landuse, and cultivation method. Rational parameters model use are: runoff coefisient, soil type, slope, land cover, rainfall intensity, and watershed areas. MUSLE parameters model use are: rainfall erosifity (RM, soil erodibility (K, slope length (L, slope (S, land cover (C, and soil conservation practice (P. The result shows that the conservation service models be applied Keduang Watershed, Wonogiri is over estimed abaut 29.54 %, Rational model is over estimed abaut 49.96 %, and MUSLE model is over estimed abaut 48.47 %.

New superhindered polydentate polyphosphine ligands P(CH2CH2P(t)Bu2)3, PhP(CH2CH2P(t)Bu2)2, P(CH2CH2CH2P(t)Bu2)3, and their ruthenium(II) chloride complexes.

Science.gov (United States)

Gilbert-Wilson, Ryan; Field, Leslie D; Bhadbhade, Mohan M

2012-03-05

The synthesis and characterization of the extremely hindered phosphine ligands, P(CH(2)CH(2)P(t)Bu(2))(3) (P(2)P(3)(tBu), 1), PhP(CH(2)CH(2)P(t)Bu(2))(2) (PhP(2)P(2)(tBu), 2), and P(CH(2)CH(2)CH(2)P(t)Bu(2))(3) (P(3)P(3)(tBu), 3) are reported, along with the synthesis and characterization of ruthenium chloro complexes RuCl(2)(P(2)P(3)(tBu)) (4), RuCl(2)(PhP(2)P(2)(tBu)) (5), and RuCl(2)(P(3)P(3)(tBu)) (6). The bulky P(2)P(3)(tBu) (1) and P(3)P(3)(tBu) (3) ligands are the most sterically encumbered PP(3)-type ligands so far synthesized, and in all cases, only three phosphorus donors are able to bind to the metal center. Complexes RuCl(2)(PhP(2)P(2)(tBu)) (5) and RuCl(2)(P(3)P(3)(tBu)) (6) were characterized by crystallography. Low temperature solution and solid state (31)P{(1)H} NMR were used to demonstrate that the structure of RuCl(2)(P(2)P(3)(tBu)) (4) is probably analogous to that of RuCl(2)(PhP(2)P(2)(tBu)) (5) which had been structurally characterized.

Bone morphogenetic protein 4 induces differentiation of colorectal cancer stem cells and increases their response to chemotherapy in mice.

Science.gov (United States)

Lombardo, Ylenia; Scopelliti, Alessandro; Cammareri, Patrizia; Todaro, Matilde; Iovino, Flora; Ricci-Vitiani, Lucia; Gulotta, Gaspare; Dieli, Francesco; de Maria, Ruggero; Stassi, Giorgio

2011-01-01

The limited clinical response observed in many patients with colorectal cancer may be related to the presence of chemoresistant colorectal cancer stem cells (CRC-SCs). Bone morphogenetic protein 4 (BMP4) promotes the differentiation of normal colonic stem cells. We investigated whether BMP4 might be used to induce differentiation of CRC-SCs and for therapeutic purposes. CRC-SCs were isolated from 25 tumor samples based on expression of CD133 or using a selection culture medium. BMP4 expression and activity on CRC-SCs were evaluated in vitro; progeny of the stem cells were evaluated by immunofluorescence, immunoblot, and flow cytometry analyses. The potential therapeutic effect of BMP4 was assessed in immunocompromised mice after injection of CRC-SCs that responded to chemotherapy (n = 4) or that did not (n = 2). CRC-SCs did not express BMP4 whereas differentiated cells did. Recombinant BMP4 promoted differentiation and apoptosis of CRC-SCs in 12 of 15 independent experiments; this effect did not depend on Small Mothers against decapentaplegic (Smad)4 expression level or microsatellite stability. BMP4 activated the canonical and noncanonical BMP signaling pathways, including phosphoInositide 3-kinase (PI3K) and PKB (protein kinase B)/AKT. Mutations in PI3K or loss of Phosphatase and Tensin homolog (PTEN) in Smad4-defective tumors made CRC-SCs unresponsive to BMP4. Administration of BMP4 to immunocompromised mice with tumors that arose from CRC-SCs increased the antitumor effects of 5-fluorouracil and oxaliplatin. BMP4 promotes terminal differentiation, apoptosis, and chemosensitization of CRC-SCs in tumors that do not have simultaneous mutations in Smad4 and constitutive activation of PI3K. BMP4 might be developed as a therapeutic agent against cancer stem cells in advanced colorectal tumors. Copyright © 2011 AGA Institute. Published by Elsevier Inc. All rights reserved.

The Drosophila HEM-2/NAP1 homolog KETTE controls axonal pathfinding and cytoskeletal organization.

Science.gov (United States)

Hummel, T; Leifker, K; Klämbt, C

2000-04-01

In Drosophila, the correct formation of the segmental commissures depends on neuron-glial interactions at the midline. The VUM midline neurons extend axons along which glial cells migrate in between anterior and posterior commissures. Here, we show that the gene kette is required for the normal projection of the VUM axons and subsequently disrupts glial migration. Axonal projection defects are also found for many other moto- and interneurons. In addition, kette affects the cell morphology of mesodermal and epidermal derivatives, which show an abnormal actin cytoskeleton. The KETTE protein is homologous to the transmembrane protein HEM-2/NAP1 evolutionary conserved from worms to vertebrates. In vitro analysis has shown a specific interaction of the vertebrate HEM-2/NAP1 with the SH2-SH3 adapter protein NCK and the small GTPase RAC1, which both have been implicated in regulating cytoskeleton organization and axonal growth. Hypomorphic kette mutations lead to axonal defects similar to mutations in the Drosophila NCK homolog dreadlocks. Furthermore, we show that kette and dock mutants genetically interact. NCK is thought to interact with the small G proteins RAC1 and CDC42, which play a role in axonal growth. In line with these observations, a kette phenocopy can be obtained following directed expression of mutant DCDC42 or DRAC1 in the CNS midline. In addition, the kette mutant phenotype can be partially rescued by expression of an activated DRAC1 transgene. Our data suggest an important role of the HEM-2 protein in cytoskeletal organization during axonal pathfinding.

Activation of phosphatidylinositol-3 kinase by nerve growth factor involves indirect coupling of the trk proto-oncogene with src homology 2 domains.

Science.gov (United States)

Ohmichi, M; Decker, S J; Saltiel, A R

1992-10-01

Growth factor receptor tyrosine kinases can form stable associations with intracellular proteins that contain src homology (SH) 2 domains, including the p85 regulatory subunit of phosphatidylinositol (PI)-3 kinase. The activation of this enzyme by growth factors is evaluated in PC12 pheochromocytoma cells and NIH 3T3 fibroblasts expressing the pp140c-trk nerve growth factor (NGF) receptor (3T3-c-trk). NGF causes the rapid stimulation of PI-3 kinase activity detected in anti-phosphotyrosine, but not in anti-trk, immunoprecipitates. This effect coincides with the tyrosine phosphorylation of two proteins, with molecular masses of of 100 kd and 110 kd, that coimmunoprecipitate with p85. Similar phosphorylation patterns are induced when an immobilized fusion protein containing the amino-terminal SH2 domain of p85 is used to precipitate tyrosine-phosphorylated proteins. Thus, although NGF produces the rapid activation of PI-3 kinase through a mechanism that involves tyrosine phosphorylation, there is no evidence for tyrosine phosphorylation of p85, or for its ligand-dependent association with the NGF receptor. Perhaps another phosphoprotein may link the NGF receptor to this enzyme.

2-N, 6-O-sulfated chitosan-assisted BMP-2 immobilization of PCL scaffolds for enhanced osteoinduction

Energy Technology Data Exchange (ETDEWEB)

Cao, Lingyan [Key Laboratory for Ultrafine Materials of Ministry of Education, East China University of Science and Technology, Shanghai 200237 (China); Engineering Research Center for Biomedical Materials of Ministry of Education, East China University of Science and Technology, Shanghai 200237 (China); CSIRO Manufacturing, Bayview Avenue, Clayton, Victoria 3168 (Australia); Department of Prosthodontics, College of Stomatology, Ninth People' s Hospital, School of Medicine, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai 200011 (China); Yu, Yuanman [Key Laboratory for Ultrafine Materials of Ministry of Education, East China University of Science and Technology, Shanghai 200237 (China); Engineering Research Center for Biomedical Materials of Ministry of Education, East China University of Science and Technology, Shanghai 200237 (China); Wang, Jing, E-mail: biomatwj@163.com [Key Laboratory for Ultrafine Materials of Ministry of Education, East China University of Science and Technology, Shanghai 200237 (China); Engineering Research Center for Biomedical Materials of Ministry of Education, East China University of Science and Technology, Shanghai 200237 (China); Werkmeister, Jerome A [CSIRO Manufacturing, Bayview Avenue, Clayton, Victoria 3168 (Australia); McLean, Keith M, E-mail: Keith.McLean@csiro.au [CSIRO Manufacturing, Bayview Avenue, Clayton, Victoria 3168 (Australia); Liu, Changsheng, E-mail: liucs@ecust.edu.cn [Key Laboratory for Ultrafine Materials of Ministry of Education, East China University of Science and Technology, Shanghai 200237 (China); Engineering Research Center for Biomedical Materials of Ministry of Education, East China University of Science and Technology, Shanghai 200237 (China)

2017-05-01

The aim of this study was to develop a 2-N, 6-O-sulfated chitosan (26SCS) modified electrospun fibrous PCL scaffold for bone morphogenetic protein-2 (BMP-2) delivery to improve osteoinduction. The PCL scaffold was modified by an aminolysis reaction using ethylenediamine (ED) and 26SCS was immobilized via electrostatic interactions (PCL-N-S). Scaffolds were characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and contact angle measurements. In vitro BMP-2 adsorption and release kinetics indicated that modified PCL-N-S scaffolds showed higher levels of binding of BMP-2 (about 30–100 times), moderative burst release (about one third), and prolonged releasing time compared to the unmodified PCL scaffold. The bioactivity of released BMP-2 determined by alkaline phosphatase (ALP) activity assay was maintained and improved 8– 12 times with increasing concentration of immobilized 26SCS on the scaffolds. In vitro studies demonstrated that bone marrow mesenchymal stem cells (BMSCs) attached more readily to the PCL-N-S scaffolds with increased spreading. In conclusion, 26SCS modified PCL scaffolds can be a potent system for the sustained and bioactive delivery of BMP-2. - Graphical abstract: Limited self-regenerating capacity of human body makes the reconstruction of critical size bone defect a significant challenge. Although bone morphogenetic protein-2 (BMP-2) is an important differentiation factor inducing bone regeneration, it's short half-life in vivo and potent side effect at high dosage still show lots of concerns in the clinical use. Herein, modification of electrospun PCL scaffolds was presented through immobilizing of sulfated chitosan (26SCS). The modified scaffolds effectively improve the binding capacity of BMP-2 and exhibited an enhanced bioactivity and sustained release in vitro. Thus, the use of 26SCS modified PCL scaffolds combined with BMP-2 could be a useful scaffold for tissue

Productive homologous and non-homologous recombination of hepatitis C virus in cell culture

DEFF Research Database (Denmark)

Scheel, Troels K H; Galli, Andrea; Li, Yi-Ping

2013-01-01

. In addition, recombination is an important regulatory mechanism of cytopathogenicity for the related pestiviruses. Here we describe recombination of HCV RNA in cell culture leading to production of infectious virus. Initially, hepatoma cells were co-transfected with a replicating JFH1ΔE1E2 genome (genotype 2a......) lacking functional envelope genes and strain J6 (2a), which has functional envelope genes but does not replicate in culture. After an initial decrease in the number of HCV positive cells, infection spread after 13-36 days. Sequencing of recovered viruses revealed non-homologous recombinants with J6...

Scaffold protein enigma homolog 1 overcomes the repression of myogenesis activation by inhibitor of DNA binding 2

Energy Technology Data Exchange (ETDEWEB)

Nakatani, Miyuki [Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, 464-8106 (Japan); Ito, Jumpei [Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, 464-8106 (Japan); Japan Society for the Promotion of Science, Tokyo, 102-0083 (Japan); Koyama, Riko [Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, 464-8106 (Japan); Iijima, Masumi; Yoshimoto, Nobuo [The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047 (Japan); Niimi, Tomoaki [Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, 464-8106 (Japan); Kuroda, Shun' ichi [Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, 464-8106 (Japan); The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047 (Japan); Maturana, Andrés D., E-mail: maturana@agr.nagoya-u.ac.jp [Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, 464-8106 (Japan)

2016-05-27

Enigma Homolog 1 (ENH1) is a scaffold protein for signaling proteins and transcription factors. Previously, we reported that ENH1 overexpression promotes the differentiation of C2C12 myoblasts. However, the molecular mechanism underlying the role of ENH1 in the C2C12 cells differentiation remains elusive. ENH1 was shown to inhibit the proliferation of neuroblastoma cells by sequestering Inhibitor of DNA binding protein 2 (Id2) in the cytosol. Id2 is a repressor of basic Helix-Loop-Helix transcription factors activity and prevents myogenesis. Here, we found that ENH1 overcome the Id2 repression of C2C12 cells myogenic differentiation and that ENH1 overexpression promotes mice satellite cells activation, the first step toward myogenic differentiation. In addition, we show that ENH1 interacted with Id2 in C2C12 cells and mice satellite cells. Collectively, our results suggest that ENH1 plays an important role in the activation of myogenesis through the repression of Id2 activity. -- Highlights: •Enigma Homolog 1 (ENH1) is a scaffold protein. •ENH1 binds to inhibitor of DNA binding 2 (Id2) in myoblasts. •ENH1 overexpression overcomes the Id2's repression of myogenesis. •The Id2-ENH1 complex play an important role in the activation of myogenesis.

Comparison of Performance between Genetic Algorithm and SCE-UA for Calibration of SCS-CN Surface Runoff Simulation

OpenAIRE

Jeon, Ji-Hong; Park, Chan-Gi; Engel, Bernard

2014-01-01

Global optimization methods linked with simulation models are widely used for automated calibration and serve as useful tools for searching for cost-effective alternatives for environmental management. A genetic algorithm (GA) and shuffled complex evolution (SCE-UA) algorithm were linked with the Long-Term Hydrologic Impact Assessment (L-THIA) model, which employs the curve number (SCS-CN) method. The performance of the two optimization methods was compared by automatically calibrating L-THI...

A Long-Gap Peripheral Nerve Injury Therapy Using Human Skeletal Muscle-Derived Stem Cells (Sk-SCs: An Achievement of Significant Morphological, Numerical and Functional Recovery.

Directory of Open Access Journals (Sweden)

Tetsuro Tamaki

Full Text Available Losses in vital functions of the somatic motor and sensory nervous system are induced by severe long-gap peripheral nerve transection injury. In such cases, autologous nerve grafts are the gold standard treatment, despite the unavoidable sacrifice of other healthy functions, whereas the prognosis is not always favorable. Here, we use human skeletal muscle-derived stem cells (Sk-SCs to reconstitute the function after long nerve-gap injury. Muscles samples were obtained from the amputated legs from 9 patients following unforeseen accidents. The Sk-SCs were isolated using conditioned collagenase solution, and sorted as CD34+/45- (Sk-34 and CD34-/45-/29+ (Sk-DN/29+ cells. Cells were separately cultured/expanded under optimal conditions for 2 weeks, then injected into the athymic nude mice sciatic nerve long-gap model (7-mm bridging an acellular conduit. After 8-12 weeks, active cell engraftment was observed only in the Sk-34 cell transplanted group, showing preferential differentiation into Schwann cells and perineurial/endoneurial cells, as well as formation of the myelin sheath and perineurium/endoneurium surrounding regenerated axons, resulted in 87% of numerical recovery. Differentiation into vascular cell lineage (pericyte and endothelial cells were also observed. A significant tetanic tension recovery (over 90% of downstream muscles following electrical stimulation of the sciatic nerve (at upper portion of the gap was also achieved. In contrast, Sk-DN/29+ cells were completely eliminated during the first 4 weeks, but relatively higher numerical (83% vs. 41% in axon and functional (80% vs. 60% in tetanus recovery than control were observed. Noteworthy, significant increase in the formation of vascular networks in the conduit during the early stage (first 2 weeks of recovery was observed in both groups with the expression of key factors (mRNA and protein levels, suggesting the paracrine effects to angiogenesis. These results suggested that the

A Long-Gap Peripheral Nerve Injury Therapy Using Human Skeletal Muscle-Derived Stem Cells (Sk-SCs): An Achievement of Significant Morphological, Numerical and Functional Recovery.

Science.gov (United States)

Tamaki, Tetsuro; Hirata, Maki; Nakajima, Nobuyuki; Saito, Kosuke; Hashimoto, Hiroyuki; Soeda, Shuichi; Uchiyama, Yoshiyasu; Watanabe, Masahiko

2016-01-01

Losses in vital functions of the somatic motor and sensory nervous system are induced by severe long-gap peripheral nerve transection injury. In such cases, autologous nerve grafts are the gold standard treatment, despite the unavoidable sacrifice of other healthy functions, whereas the prognosis is not always favorable. Here, we use human skeletal muscle-derived stem cells (Sk-SCs) to reconstitute the function after long nerve-gap injury. Muscles samples were obtained from the amputated legs from 9 patients following unforeseen accidents. The Sk-SCs were isolated using conditioned collagenase solution, and sorted as CD34+/45- (Sk-34) and CD34-/45-/29+ (Sk-DN/29+) cells. Cells were separately cultured/expanded under optimal conditions for 2 weeks, then injected into the athymic nude mice sciatic nerve long-gap model (7-mm) bridging an acellular conduit. After 8-12 weeks, active cell engraftment was observed only in the Sk-34 cell transplanted group, showing preferential differentiation into Schwann cells and perineurial/endoneurial cells, as well as formation of the myelin sheath and perineurium/endoneurium surrounding regenerated axons, resulted in 87% of numerical recovery. Differentiation into vascular cell lineage (pericyte and endothelial cells) were also observed. A significant tetanic tension recovery (over 90%) of downstream muscles following electrical stimulation of the sciatic nerve (at upper portion of the gap) was also achieved. In contrast, Sk-DN/29+ cells were completely eliminated during the first 4 weeks, but relatively higher numerical (83% vs. 41% in axon) and functional (80% vs. 60% in tetanus) recovery than control were observed. Noteworthy, significant increase in the formation of vascular networks in the conduit during the early stage (first 2 weeks) of recovery was observed in both groups with the expression of key factors (mRNA and protein levels), suggesting the paracrine effects to angiogenesis. These results suggested that the human Sk-SCs

Evaluation of soil loss estimation using the RUSLE model and SCS-CN method in hillslope mining areas

Directory of Open Access Journals (Sweden)

Narayan Kayet

2018-03-01

Full Text Available Mining operations result in the generation of barren land and spoil heaps which are subject to high erosion rate during the rainy season. The present study uses the Revised Universal Soil Loss Equation (RUSLE and SCS-CN (Soil Conservation Service - Curve Number process to estimate in Kiruburu and Meghahatuburu mining sites areas. The geospatial model of annual average soil loss rate was determined by integrating environmental variables parameters in a raster pixels-based GIS framework. GIS layers with, rainfall passivity and runoff erosivity (R, soil erodibility (K, slope length and steepness (LS, cover management(C and conservation practice (P factors were calculated to determine their effects on annual soil erosion in the study area. The coefficient of determination (r2 was 0.834, which indicates a strong correlation of soil loss with runoff and rainfall. Sub -watersheds 5,9,10 and 2 experienced high level of highly runoff. Average annual soil loss was calculated (30*30 m raster grid cell to determine the critical soil loss areas (Sub-watershed 9 and 5. Total soil erosion area was classified into five class, slight (10,025 ha, moderate (3125 ha, high (973 ha, very high (260 ha and severe (53 ha. The resulting map shows greatest soil erosion of >40 t h-1 y-1 (severe through connection to grassland, degraded and open forestry on the erect mining side-escutcheon. The Landsat pan sharpening image and DGPS survey field data were used in the verification of soil erosion results.

Application of the homology method for quantification of low-attenuation lung region in patients with and without COPD

Directory of Open Access Journals (Sweden)

Nishio M

2016-09-01

Full Text Available Mizuho Nishio,1 Kazuaki Nakane,2 Yutaka Tanaka3 1Clinical PET Center, Institute of Biomedical Research and Innovation, Hyogo, Japan; 2Department of Molecular Pathology, Osaka University Graduate School of Medicine and Health Science, Osaka, Japan; 3Department of Radiology, Chibune General Hospital, Osaka, Japan Background: Homology is a mathematical concept that can be used to quantify degree of contact. Recently, image processing with the homology method has been proposed. In this study, we used the homology method and computed tomography images to quantify emphysema.Methods: This study included 112 patients who had undergone computed tomography and pulmonary function test. Low-attenuation lung regions were evaluated by the homology method, and homology-based emphysema quantification (b0, b1, nb0, nb1, and R was performed. For comparison, the percentage of low-attenuation lung area (LAA% was also obtained. Relationships between emphysema quantification and pulmonary function test results were evaluated by Pearson’s correlation coefficients. In addition to the correlation, the patients were divided into the following three groups based on guidelines of the Global initiative for chronic Obstructive Lung Disease: Group A, nonsmokers; Group B, smokers without COPD, mild COPD, and moderate COPD; Group C, severe COPD and very severe COPD. The homology-based emphysema quantification and LAA% were compared among these groups.Results: For forced expiratory volume in 1 second/forced vital capacity, the correlation coefficients were as follows: LAA%, -0.603; b0, -0.460; b1, -0.500; nb0, -0.449; nb1, -0.524; and R, -0.574. For forced expiratory volume in 1 second, the coefficients were as follows: LAA%, -0.461; b0, -0.173; b1, -0.314; nb0, -0.191; nb1, -0.329; and R, -0.409. Between Groups A and B, difference in nb0 was significant (P-value = 0.00858, and those in the other types of quantification were not significant.Conclusion: Feasibility of the

Metabolites with Gram-negative bacteria quorum sensing inhibitory activity from the marine animal endogenic fungus Penicillium sp. SCS-KFD08.

Science.gov (United States)

Kong, Fan Dong; Zhou, Li Man; Ma, Qing Yun; Huang, Sheng Zhuo; Wang, Pei; Dai, Hao Fu; Zhao, You Xing

2017-01-01

Three new compounds named penicitor A, aculene E and penicitor B, as well as four known compounds, were isolated from the fermentation broth of Penicillium sp. SCS-KFD08 associated with a marine animal Sipunculus nudus from the Haikou bay of China. Their planar structures and absolute configurations were unambiguously elucidated by spectroscopic data, Mosher's method, CD spectrum analysis along with quantum ECD calculation. Among them, compounds 2-7 showed quorum sensing inhibitory activity against Chromobacterium violaceum CV026, and could significantly reduce violacein production in N-hexanoyl-l-homoserine lactone (C6-HSL) induced C. violaceum CV026 cultures at sub-inhibitory concentrations.

Homology with vesicle fusion mediator syntaxin-1a predicts determinants ofepimorphin/syntaxin-2 function in mammary epithelial morphogenesis

Energy Technology Data Exchange (ETDEWEB)

Chen, Connie S.; Nelson, Celeste M.; Khauv, Davitte; Bennett, Simone; Radisky, Evette S.; Hirai, Yohei; Bissell, Mina J.; Radisky, Derek C.

2009-06-03

We have shown that branching morphogenesis of mammary ductal structures requires the action of the morphogen epimorphin/syntaxin-2. Epimorphin, originally identified as an extracellular molecule, is identical to syntaxin-2, an intracellular molecule that is a member of the extensively investigated syntaxin family of proteins that mediate vesicle trafficking. We show here that although epimorphin/syntaxin-2 is highly homologous to syntaxin-1a, only epimorphin/syntaxin-2 can stimulate mammary branching morphogenesis. We construct a homology model of epimorphin/syntaxin-2 based on the published structure of syntaxin-1a, and we use this model to identify the structural motif responsible for the morphogenic activity. We identify four residues located within the cleft between helices B and C that differ between syntaxin-1a and epimorphin/syntaxin-2; through site-directed mutagenesis of these four amino acids, we confer the properties of epimorphin for cell adhesion, gene activation, and branching morphogenesis onto the inactive syntaxin-1a template. These results provide a dramatic demonstration of the use of structural information about one molecule to define a functional motif of a second molecule that is related at the sequence level but highly divergent functionally.

Rac1 controls Schwann cell myelination through cAMP and NF2/merlin

Science.gov (United States)

Guo, Li; Moon, Chandra; Niehaus, Karen; Zheng, Yi; Ratner, Nancy

2013-01-01

During peripheral nervous system development, Schwann cells (SCs) surrounding single large axons differentiate into myelinating SCs. Previous studies implicate RhoGTPases in SC myelination, but the mechanisms involved in RhoGTPase regulation of SC myelination are unknown. Here, we show that SC myelination is arrested in Rac1 conditional knockout (Rac1-CKO) mice. Rac1 knockout abrogated phosphorylation of the effector p21-activated kinase (PAK) and decreased NF2/merlin phosphorylation. Mutation of NF2/merlin rescued the myelin deficit in Rac1-CKO mice in vivo, and the shortened processes in cultured Rac1-CKO SCs in vitro. Mechanistically, cyclic adenosine monophosphate (cAMP) levels and E-cadherin expression were decreased in the absence of Rac1, and both were restored by mutation of NF2/merlin. Reduced cAMP is a cause of the myelin deficiency in Rac1-CKO mice, as elevation of cAMP by rolipram in Rac1-CKO mice in vivo allowed myelin formation. Thus NF2/merlin and cAMP function downstream of Rac1 signaling in SC myelination, and cAMP levels control Rac1-regulated SC myelination. PMID:23197717