Agreement and reliability of pelvic floor measurements during rest and on maximum Valsalva maneuver using three-dimensional translabial ultrasound and virtual reality imaging.

PubMed

Speksnijder, L; Oom, D M J; Koning, A H J; Biesmeijer, C S; Steegers, E A P; Steensma, A B

2016-08-01

Imaging of the levator ani hiatus provides valuable information for the diagnosis and follow-up of patients with pelvic organ prolapse (POP). This study compared measurements of levator ani hiatal volume during rest and on maximum Valsalva, obtained using conventional three-dimensional (3D) translabial ultrasound and virtual reality imaging. Our objectives were to establish their agreement and reliability, and their relationship with prolapse symptoms and POP quantification (POP-Q) stage. One hundred women with an intact levator ani were selected from our tertiary clinic database. Information on clinical symptoms were obtained using standardized questionnaires. Ultrasound datasets were analyzed using a rendered volume with a slice thickness of 1.5 cm, at the level of minimal hiatal dimensions, during rest and on maximum Valsalva. The levator area (in cm(2) ) was measured and multiplied by 1.5 to obtain the levator ani hiatal volume (in cm(3) ) on conventional 3D ultrasound. Levator ani hiatal volume (in cm(3) ) was measured semi-automatically by virtual reality imaging using a segmentation algorithm. Twenty patients were chosen randomly to analyze intra- and interobserver agreement. The mean difference between levator hiatal volume measurements on 3D ultrasound and by virtual reality was 1.52 cm(3) (95% CI, 1.00-2.04 cm(3) ) at rest and 1.16 cm(3) (95% CI, 0.56-1.76 cm(3) ) during maximum Valsalva (P < 0.001). Both intra- and interobserver intraclass correlation coefficients were ≥ 0.96 for conventional 3D ultrasound and > 0.99 for virtual reality. Patients with prolapse symptoms or POP-Q Stage ≥ 2 had significantly larger hiatal measurements than those without symptoms or POP-Q Stage < 2. Levator ani hiatal volume at rest and on maximum Valsalva is significantly smaller when using virtual reality compared with conventional 3D ultrasound; however, this difference does not seem clinically important. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd.

A Novel Technique to Measure In Vivo Uterine Suspensory Ligament Stiffness

PubMed Central

Smith, Tovia M.; Luo, Jiajia; Hsu, Yvonne; Ashton-Miller, James A.; Delancey, John O.L.

2013-01-01

Objective To describe a new computer-controlled research apparatus for measuring in vivo uterine ligament force-displacement behavior and stiffness and to present pilot data in women with and without prolapse. Study Design Seventeen women with varying uterine support underwent testing in the operating room (OR) after anesthetic induction. A tripod-mounted computer-controlled linear servoactuator was used to quantify force-displacement behavior of the cervix and supporting ligaments. The servoactuator applied a caudally-directed force to a tenaculum at 4 mm/s velocity until the traction force reached 17.8N (4 lbs.). Cervix location on POP-Q in clinic, in the OR at rest, and with minimal force (<1.1N), and maximum force (17.8N) was recorded. Ligament “stiffness” between minimum and maximum force was calculated. Results The mean (SD) subject age was 54.5 (12.7) years, parity 2.9 (1.1), BMI 29.0 (4.3) kg/m2, and POP-Q point C −3.1 (3.9) cm. POP-Q point C was most strongly correlated with cervix location at maximum force (r=+0.68, p=.003) and at rest (r=+0.62, p=.009). Associations between cervix location at minimum force (r=+0.46, p=.059) and ligament stiffness (r= −0.44,p=.079) were not statistically significant. Cervix location in the OR with minimal traction lay below the lowest point found on POP-Q for 13 women. Conclusions POP-Q point C was strongly correlated with cervix location at rest and at maximum traction force; however only 19% of the variation in POP-Q point C location was explained by ligament stiffness. The cervix location in the OR at minimal traction lay below POP-Q point C value in ¾ of women. PMID:23747493

Associations between blood persistent organic pollutants and 25-hydroxyvitamin D3 in pregnancy.

PubMed

Morales, Eva; Gascon, Mireia; Martinez, David; Casas, Maribel; Ballester, Ferran; Rodríguez-Bernal, Clara L; Ibarluzea, Jesus; Marina, Loreto Santa; Espada, Mercedes; Goñi, Fernando; Vizcaino, Esther; Grimalt, Joan O; Sunyer, Jordi

2013-07-01

Persistent organic pollutants (POPs) are suggested to contribute to lower vitamin D levels; however, studies in humans are scarce and have never focused on pregnancy, a susceptibility period for vitamin D deficiency. We investigated whether serum levels of POPs were associated with circulating 25-hydroxyvitamin D3 [25(OH)D3] concentration in pregnancy. Cross-sectional associations of serum concentrations of eight POPs with plasma 25(OH)D3 concentration were analyzed in 2031 pregnant women participating in the Spanish population-based cohort INfancia y Medio Ambiente (INMA) Project. Serum concentrations of POPs were measured by gas chromatography and plasma 25(OH)D3 concentration was measured by high-performance liquid chromatography in pregnancy (mean 13.3±1.5weeks of gestation). Multivariable regression models were performed to assess the relationship between blood concentrations of POPs and 25(OH)D3. An inverse linear relationship was found between serum concentration of PCB180 and circulating 25(OH)D3. Multivariate linear regression models showed higher PCB180 levels to be associated with lower 25(OH)D3 concentration: quartile Q4 vs. quartile Q1, coefficient=-1.59, 95% CI -3.27, 0.08, p trend=0.060. A non-monotonic inverse relationship was found between the sum of predominant PCB congeners (PCB 180, 153 and 138) and 25(OH)D3 concentration: coefficient (95% CI) for quartile Q2 vs. Q1 [-0.50 (-1.94, 0.94)], quartile Q3 vs. Q1 [-1.56 (-3.11, -0.02)] and quartile Q4 vs. Q1 [-1.21 (-2.80, 0.38)], p trend=0.081. No significant associations were found between circulating 25(OH)D3 and serum levels of p,p'-DDE, p,p'-DDT, HCB, and ß-HCH. Our results suggest that the background exposure to PCBs may result in lower 25(OH)D3 concentration in pregnant women. Copyright © 2013 Elsevier Ltd. All rights reserved.

Admixture mapping of pelvic organ prolapse in African Americans from the Women’s Health Initiative Hormone Therapy trial

PubMed Central

Hartmann, Katherine E.; Aldrich, Melinda C.; Ward, Renee M.; Wu, Jennifer M.; Park, Amy J.; Graff, Mariaelisa; Qi, Lihong; Nassir, Rami; Wallace, Robert B.; O'Sullivan, Mary J.; North, Kari E.; Velez Edwards, Digna R.; Edwards, Todd L.

2017-01-01

Evidence suggests European American (EA) women have two- to five-fold increased odds of having pelvic organ prolapse (POP) when compared with African American (AA) women. However, the role of genetic ancestry in relation to POP risk is not clear. Here we evaluate the association between genetic ancestry and POP in AA women from the Women’s Health Initiative Hormone Therapy trial. Women with grade 1 or higher classification, and grade 2 or higher classification for uterine prolapse, cystocele or rectocele at baseline or during follow-up were considered to have any POP (N = 805) and moderate/severe POP (N = 156), respectively. Women with at least two pelvic exams with no indication for POP served as controls (N = 344). We performed case-only, and case-control admixture-mapping analyses using multiple logistic regression while adjusting for age, BMI, parity and global ancestry. We evaluated the association between global ancestry and POP using multiple logistic regression. European ancestry at the individual level was not associated with POP risk. Case-only and case-control local ancestry analyses identified two ancestry-specific loci that may be associated with POP. One locus (Chromosome 15q26.2) achieved empirically-estimated statistical significance and was associated with decreased POP odds (considering grade ≥2 POP) with each unit increase in European ancestry (OR: 0.35; 95% CI: 0.30, 0.57; p-value = 1.48x10-5). This region includes RGMA, a potent regulator of the BMP family of genes. The second locus (Chromosome 1q42.1-q42.3) was associated with increased POP odds with each unit increase in European ancestry (Odds ratio [OR]: 1.69; 95% confidence interval [CI]: 1.28, 2.22; p-value = 1.93x10-4). Although this region did not reach statistical significance after considering multiple comparisons, it includes potentially relevant genes including TBCE, and ACTA1. Unique non-overlapping European and African ancestry-specific susceptibility loci may be associated with increased POP risk. PMID:28582460

[POP-Q indication points, Aa and Ba, involve in diagnosis and prognosis of occult stress urinary incontinence complicated with pelvic organ prolapse].

PubMed

Liu, Cheng; Wu, Wenying; Yang, Qing; Hu, Ming; Zhao, Yang; Hong, Li

2015-06-01

To investigate the correlation between pelvic organ prolapse quantitation (POP-Q) indication points and the incidence of occult stress urinary incontinence (OSUI) and its impact on prognosis. Retrospective study medical records of 93 patients with pelvic organ prolapse (POP) staged at III-IV, of which underwent pelvic reconstruction operations with Prolift system from Jan. 2007 to Sept. 2012. None of these patients had clinical manifestations of stress urinary incontinence (SUI) before surgery, and in which 44 patients were included in study group (POP complicated with OSUI) because they were identified with OSUI, another 49 patients as control group (simple POP). Follow-up and collecting datas including POP-Q, stress test, urodynamic recordings, incidence of de novo SUI, statistic analyzing by logistic regression and receiver operating characteristic curve (ROC). (1) The study group had a much higher incidence of 30% (13/44) on de novo SUI than that of control group (4%, 2/49; P < 0.01). (2) Vaginal delivery (OR = 5.327, 95% CI: 1.120-25.347), constipation (OR = 5.789, 95% CI: 1.492-22.459), preoperative OSUI (OR = 13.695, 95% CI: 2.980-62.944), anterior vaginal wall prolapse (OR = 6.115, 95% CI: 1.231-30.379) were identified as dependent risk factors for de novo SUI by logistic regression analysis. (3) For POP patients that complicated with OSUI, we chose a cutoff value of +1.5 cm for Aa point as the threshold to predicting incidence of de novo SUI according to ROC curve, area under the curve (AUC) was 0.889 (P < 0.05), the sensitivity reached 88.9% and specificity was 73.9%. According to ROC curve of Ba point, a cutoff value of +2.5 cm was chosen as the threshold to predicting incidence of de novo SUI post-operation, it had a sensitivity of 66.7% and specificity of 82.6%, AUC was 0.766 (P < 0.05). Pre-operative OSUI is a dependent risk factor of de novo SUI for advanced POP patients. Aa and Ba points are correlated with preoperative OSUI, and it is worthy to be considered as a risk predictor on forecasting the incidence of de novo SUI post pelvic reconstruction surgery.

Characterizing Pelvic Organ Prolapse in Adult Spina Bifida Patients.

PubMed

Liu, Joceline S; Vo, Amanda X; Doolittle, Johnathan; Hamoui, Nabeel; Lewicky-Gaupp, Christina; Kielb, Stephanie J

2016-11-01

To report the distribution of pelvic organ prolapse (POP) stages in adult spina bifida (SB) patients. The severity of POP in the SB population has not been previously reported. Retrospective review of SB patients ≥18 years with a documented POP quantification examination between 2006 and 2014 were included. Patient demographics, gestation, parity, POP quantification examinations and prolapse symptoms were obtained. Thirty-three SB patients were identified with a mean age of 33.2 years. Five patients (15.2%) had stage 0 prolapse, 12 (36.4%) had stage 1, 12 (36.4%) had stage 2, 3 (9.1%) had stage 3, and 1 (3.0%) had stage 4. Of the 16 patients with advanced POP (stage 2 prolapse or greater), only 6 patients (37.5%) reported symptoms related to POP. All 6 symptomatic patients endorsed sensation of a vaginal bulge. Two of the 6 patients also reported dyspareunia. Additionally, 1 patient with advanced POP presented with vaginal bulge, noted by a caregiver, and cervical bleeding, but was otherwise asymptomatic. Twenty-four patients (72.7%) were nulliparous, and 12 of the 24 nulliparous patients (50%) demonstrated prolapse. Despite young age and frequent nulliparity, patients with SB are more likely to have POP than the general population. Additionally, the majority of SB patients with prolapse are asymptomatic. Assessment of pelvic organ prolapse should be included in the evaluation of adult SB females due to the low rate of symptoms even in the setting of advanced stage prolapse and potential impact on both urinary and bowel function. Copyright © 2016 Elsevier Inc. All rights reserved.

The feasibility of transvaginal robotic surgery in the repair of pelvic organ prolapse.

PubMed

Yaghnam, Ibrahim; Thomas, Dominique; Rosenblatt, Peter; Chughtai, Bilal

2017-08-01

Pelvic organ prolapse (POP), the descent of one or more pelvic organs, occurs in an estimated 40 to 60% of parous women. Conventional transvaginal surgery for POP has been plagued with high failure rates. The purpose was to determine the safety and feasibility of robotic transvaginal POP surgery. The da Vinci Surgical Robot, SI was used in the POP surgical procedures. There were two cadavers (aged 18 and 78 years of age; BMI 17.2 and 19.2 respectively). POP-Q scores before intervention were stage 1 for both cadavers. The visualization of anatomical landmarks and the placement of sutures at these locations were successful. Robotic transvaginal POP is a feasible option for POP surgery. Further studies are warranted to determine the role of robotic transvaginal POP repair.

quantGenius: implementation of a decision support system for qPCR-based gene quantification.

PubMed

Baebler, Špela; Svalina, Miha; Petek, Marko; Stare, Katja; Rotter, Ana; Pompe-Novak, Maruša; Gruden, Kristina

2017-05-25

Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification. We have developed "quantGenius" ( http://quantgenius.nib.si ), an open-access web application for a reliable qPCR-based quantification of nucleic acids. The quantGenius workflow interactively guides the user through data import, quality control (QC) and calculation steps. The input is machine- and chemistry-independent. Quantification is performed using the standard curve approach, with normalization to one or several reference genes. The special feature of the application is the implementation of user-guided QC-based decision support system, based on qPCR standards, that takes into account pipetting errors, assay amplification efficiencies, limits of detection and quantification of the assays as well as the control of PCR inhibition in individual samples. The intermediate calculations and final results are exportable in a data matrix suitable for further statistical analysis or visualization. We additionally compare the most important features of quantGenius with similar advanced software tools and illustrate the importance of proper QC system in the analysis of qPCR data in two use cases. To our knowledge, quantGenius is the only qPCR data analysis tool that integrates QC-based decision support and will help scientists to obtain reliable results which are the basis for biologically meaningful data interpretation.

Levels of select PCB and PBDE congeners in human post-mortem brain reveal possible environmental involvement in 15q11-q13 duplication autism spectrum disorder

PubMed Central

Mitchell, Michelle M.; Woods, Rima; Chi, Lai-Har; Schmidt, Rebecca J.; Pessah, Isaac N.; Kostyniak, Paul J.; LaSalle, Janine M.

2013-01-01

Persistent organic pollutants (POPs), including polychlorinated biphenyls (PCBs) and polybrominated diphenylethers (PBDEs) that bioaccumulate in lipid-rich tissues are of concern as developmental neurotoxicants. Epigenetic mechanisms such as DNA methylation act at the interface of genetic and environmental factors implicated in autism-spectrum disorders. The relationship between POP levels and DNA methylation patterns in individuals with and without neurodevelopmental disorders has not been previously investigated. In this study, a total of 107 human frozen post-mortem brain samples were analyzed for 8 PCBs and 7 PBDEs by GC-micro electron capture detector and GC/MS using negative chemical ionization. Human brain samples were grouped as neurotypical controls (n=43), neurodevelopmental disorders with known genetic basis (n=32, including Down, Rett, Prader-Willi, Angelman, and 15q11-q13 duplication syndromes), and autism of unknown etiology (n=32). Unexpectedly, PCB 95 was significantly higher in the genetic neurodevelopmental group, but not idiopathic autism, as compared to neurotypical controls. Interestingly, samples with detectable PCB 95 levels were almost exclusively those with maternal 15q11-q13 duplication (Dup15q) or deletion in Prader-Willi syndrome. When sorted by birth year, Dup15q samples represented five out of six of genetic neurodevelopmental samples born after the 1976 PCB ban exhibiting detectable PCB 95 levels. Dup15q was the strongest predictor of PCB 95 exposure over age, gender, or year of birth. Dup15q brain showed lower levels of repetitive DNA methylation measured by LINE-1 pyrosequencing, but methylation levels were confounded by year of birth. These results demonstrate a novel paradigm by which specific POPs may predispose to genetic copy number variation of 15q11-q13. PMID:22930557

Perineal body stretch during labor does not predict perineal laceration, postpartum incontinence, or postpartum sexual function: a cohort study.

PubMed

Meriwether, Kate V; Rogers, Rebecca G; Dunivan, Gena C; Alldredge, Jill K; Qualls, Clifford; Migliaccio, Laura; Leeman, Lawrence

2016-08-01

The perineum stretches naturally during obstetrical labor, but it is unknown whether this stretch has a negative impact on pelvic floor outcomes after a vaginal birth (VB). We aimed to evaluate whether perineal stretch was associated with postpartum pelvic floor dysfunction, and we hypothesized that greater perineal stretch would correlate with worsened outcomes. This was a prospective cohort study of primiparous women who had a VB. Perineal body (PB) length was measured antepartum, during labor, and 6 months postpartum. We determined the maximum PB (PBmax) measurements during the second stage of labor and PB change (ΔPB) between time points. Women completed functional questionnaires and had a Pelvic Organ Prolapse Quantification (POP-Q) system exam 6 months postpartum. We analyzed the relationship of PB measurements to perineal lacerations and postpartum outcomes, including urinary, anal, and fecal incontinence, sexual activity and function, and POP-Q measurements. Four hundred and forty-eight women with VB and a mean age of 24 ± 5.0 years with rare (5 %) third- or fourth-degree lacerations were assessed. During the second stage of labor, 270/448 (60 %) had perineal measurements. Mean antepartum PB length was 3.7 ± 0.8 cm, with a maximum mean PB length (PBmax) during the second stage of 6.1 ± 1.5 cm, an increase of 65 %. The change in PB length (ΔPB) from antepartum to 6 months postpartum was a net decrease (-0.39 ± 1.02 cm). PB change and PBmax were not associated with perineal lacerations or outcomes postpartum (all p > 0.05). PB stretch during labor is unrelated to perineal laceration, postpartum incontinence, sexual activity, or sexual function.

Adduct ion-targeted qualitative and quantitative analysis of polyoxypregnanes by ultra-high pressure liquid chromatography coupled with triple quadrupole mass spectrometry.

PubMed

Wu, Xu; Zhu, Lin; Ma, Jiang; Ye, Yang; Lin, Ge

2017-10-25

Polyoxypregnane and its glycosides (POPs) are frequently present in plants of Asclepiadaceae family, and have a variety of biological activities. There is a great need to comprehensively profile these phytochemicals and to quantify them for monitoring their contents in the herbs and the biological samples. However, POPs undergo extensive adduct ion formation in ESI-MS, which has posed a challenge for qualitative and quantitative analysis of POPs. In the present study, we took the advantage of such extensive adduct ion formation to investigate the suitability of adduct ion-targeted analysis of POPs. For the qualitative analysis, we firstly demonstrated that the sodium and ammonium adduct ion-targeted product ion scans (PIS) provided adequate MS/MS fragmentations for structural characterization of POPs. Aided with precursor ion (PI) scans, which showed high selectivity and sensitivity and improved peak assignment confidence in conjunction with full scan (FS), the informative adduct ion-targeted PIS enabled rapid POPs profiling. For the quantification, we used formic acid rather than ammonium acetate as an additive in the mobile phase to avoid simultaneous formation of sodium and ammonium adduct ions, and greatly improved reproducibility of MS response of POPs. By monitoring the solely formed sodium adduct ions [M+Na] + , a method for simultaneous quantification of 25 POPs in the dynamic multiple reaction monitoring mode was then developed and validated. Finally, the aforementioned methods were applied to qualitative and quantitative analysis of POPs in the extract of a traditional Chinses medicinal herb, Marsdenia tenacissima (Roxb.) Wight et Arn., and in the plasma obtained from the rats treated with this herb. The results demonstrated that adduct ion formation could be optimized for the qualitative and quantitative analysis of POPs, and our developed PI/FS-PIS scanning and sole [M+Na] + ion monitoring significantly improved the analysis of POPs in both herbal and biological samples. This study also provides implications for the analysis of other compounds which undergo extensive adduct ion formation in ESI-MS. Copyright © 2017 Elsevier B.V. All rights reserved.

Alterations of cytochrome P450 and the occurrence of persistent organic pollutants in tilapia caged in the reservoirs of the Iguaçu River.

PubMed

Yamamoto, F Y; Diamante, G D; Santana, M S; Santos, D R; Bombardeli, R; Martins, C C; Oliveira Ribeiro, C A; Schlenk, D

2018-05-15

Environmental chemicals originating from human activities, such as persistent organic pollutants (POPs), may interfere with the endocrine system of aquatic organisms. The effect of these chemicals on biota and human populations is of high public concern but remains poorly understood, especially in aquatic environments of South America. The aim of this study was to investigate the bioavailability of POPs and the related effects in caged male tilapia (Oreochromis niloticus) in four cascading reservoirs of the Iguaçu River, Southern Brazil. POPs including organochlorine pesticides (OCPs), polychlorinated biphenyl (PCBs), and polybrominated diphenyl ethers (PBDEs) were determined in the reservoir water and tissue samples of tilapia after two months of exposure. The PCB levels in water (14.7 ng L -1 ) were 14 times higher than the limits permitted by the Brazilian legislation in the Salto Santiago (SS) reservoir. Similarly, concentrations of aldrin and its metabolites (6.05 ng L -1 ) detected in the water sample of the Salto Osório (SO) reservoir were also above the permitted limits. RT-qPCR analysis revealed different transcript levels of cytochrome P450 enzymes (CYP1A and CYP3A) in the liver among the four groups, with induced activity in tilapia from the SS reservoir. Quantification of the CYP3A mRNA expression and catalytic activity showed higher values for fish caged at the SS reservoir. The fish from this site also had a higher number of eosinophils observed in the testes. Although overt measurements of endocrine disruption were not observed in caged fish, alteration of CYP enzymes with co-occurrence of organochlorine contaminants in water may suggest bioavailability of contaminants from agricultural sources to biota. Additional studies with feral or caged animals for a longer duration may be necessary to evaluate the risks of the waterways to humans and wildlife. Copyright © 2018 Elsevier Ltd. All rights reserved.

Obesity and stress urinary incontinence in women: compromised continence mechanism or excess bladder pressure during cough?

PubMed

Swenson, Carolyn W; Kolenic, Giselle E; Trowbridge, Elisa R; Berger, Mitchell B; Lewicky-Gaupp, Christina; Margulies, Rebecca U; Morgan, Daniel M; Fenner, Dee E; DeLancey, John O

2017-09-01

We compared two hypotheses as to why obesity is associated with stress urinary incontinence (SUI): (1) obesity increases demand on the continence system (e.g. higher cough pressure) and (2) obesity compromises urethral function and urethrovaginal support. A secondary analysis was performed using data from a case-control study of SUI in women. Measurements of urethrovaginal support (POP-Q point Aa, urethral axis), urethral function (maximal urethral closure pressure, MUCP), and measures of continence system demand (intravesical pressures at rest and during maximal cough) were analyzed. Cases and controls were divided into three body mass index (BMI) groups: normal (18.5-24.9 kg/m 2 ); overweight (25.0-29.9 kg/m 2 ); and obese (≥30 kg/m 2 ). Logistic regression models where created to investigate variables related to SUI for each BMI group. Structural equation modeling was used to test the direct and indirect relationships among BMI, SUI, maximal cough pressure, MUCP, and POP-Q point Aa. The study included 108 continent controls and 103 women with SUI. MUCP was the factor most strongly associated with SUI in all BMI groups. Maximal cough pressure was significantly associated with SUI in obese women (OR 3.191, 95% CI 1.326, 7.683; p < 0.01), but not in normal weight or overweight women. Path model analysis showed a significant relationship between BMI and SUI through maximal cough pressure (indirect effect, p = 0.038), but not through MUCP (indirect effect, p = 0.243) or POP-Q point Aa (indirect effect, p = 0.410). Our results support the first hypothesis that obesity is associated with SUI because of increased intravesical pressure, which therefore increases demand on the continence mechanism.

Long-term outcomes of synthetic transobturator nonabsorbable anterior mesh versus anterior colporrhaphy in symptomatic, advanced pelvic organ prolapse surgery.

PubMed

Lo, Tsia-Shu; Pue, Leng Boi; Tan, Yiap Loong; Wu, Pei-Ying

2014-02-01

Anterior vaginal mesh (AVM) combined with sacrospinous ligament fixation (SSF) yields better long-term success rates over anterior colporrhaphy (AC) in advanced pelvic organ prolapse (POP) surgery, with a low rate of mesh-related complications. Medical records of 198 patients who underwent surgery for POP between January 2006 and March 2010 were reviewed retrospectively. Patients' assessment at baseline and third-year postoperative follow-up were analyzed. SSF plus AC or AVM was performed for apical and anterior compartment repair. Primary outcome was objective cure [Pelvic Organ Prolapse Quantification (POP-Q) stage ≤ 1)], and subjective cure defined as negative response to questions 2 and 3 on the POPDI-6. Secondary outcomes were complications, symptoms severity and quality of life as measured with validated questionnaires. Post-operative data were available for 186 patients, 72 in AC group and 114 in AVM group were analyzed. The mean age, parity and operating time in AVM group were significantly higher as compared to AC group. The overall objective and subjective cure rate in AVM group was significantly higher than AC group (90.3 % and 88.6 % versus 73.6 % and 70.8 %, with P value = 0.003 and 0.002 respectively). Mesh exposure rate was 3.5 %. Improvement in both POPDI-6 and PISQ-12 in AVM group was statistically significant compared to AC group. Transobturator synthetic nonabsorbable AVM combined with SSF yielded a favorable and sustainable result over 5 years as compared to traditional AC, both in anatomical and subjective success rate. Mesh related morbidities were low and acceptable.

A pelvic floor muscle training program in postmenopausal women: A randomized controlled trial.

PubMed

Alves, Fabíola K; Riccetto, Cássio; Adami, Délcia B V; Marques, Joseane; Pereira, Larissa C; Palma, Paulo; Botelho, Simone

2015-06-01

The purpose of this study was to investigate if a specific pelvic floor muscle training (PFMT) program effectively increases pelvic floor muscle (PFM) contractility and decreases anterior pelvic organ prolapse (POP) as well as urogynecological symptoms, in postmenopausal women. The mean outcome measure of this study was the pelvic floor surface electromyography (sEMG) activity. A clinical, randomized, blinded-assessor and controlled study was conducted with 46 postmenopausal women. Thirty women completed this study (mean age of 65.93 years), divided into two groups: Treatment Group - TG (n=18) and Control Group - CG (n=12). The evaluation was carried out using digital palpation, sEMG, pelvic organ prolapse quantification (POP-Q) as well as validated questionnaires by the International Consultation on Incontinence Questionnaires to investigate urogynecological symptoms. The treatment protocol consisted of 12 group sessions, twice a week, with 30 min of duration each. These data were then submitted to statistical analyses by the Statistical Analysis System for Windows software, with a significance level of 5%. The pelvic floor muscle contractility increased after PFMT, evaluated by sEMG (p=0.003) and digital palpation (p=0.001), accompanied by a decrease in urinary symptoms (p<0.001 for ICIQ-OAB scores e 0.036 for ICIQ UI-SF) as well as anterior pelvic organ prolapse (p=0.03). This preliminary study suggests that the applied PFMT program could be an effective way to increase PFM contractility, as well as to decrease both anterior pelvic organ prolapse and urinary symptoms, in postmenopausal women. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Elastin density: Link between histological and biomechanical properties of vaginal tissue in women with pelvic organ prolapse?

PubMed

de Landsheere, Laurent; Brieu, Mathias; Blacher, Silvia; Munaut, Carine; Nusgens, Betty; Rubod, Chrystèle; Noel, Agnès; Foidart, Jean-Michel; Nisolle, Michelle; Cosson, Michel

2016-04-01

The aim of the study was to correlate histological and biomechanical characteristics of the vaginal wall in women with pelvic organ prolapse (POP). Tissue samples were collected from the anterior [point Ba; POP Questionnaire (POP-Q)] and/or posterior (point Bp; POP-Q) vaginal wall of 15 women who underwent vaginal surgery for POP. Both histological and biomechanical assessments were performed from the same tissue samples in 14 of 15 patients. For histological assessment, the density of collagen and elastin fibers was determined by combining high-resolution virtual imaging and computer-assisted digital image analysis. For biomechanical testing, uniaxial tension tests were performed to evaluate vaginal tissue stiffness at low (C0) and high (C1) deformation rates. Biomechanical testing highlights the hyperelastic behavior of the vaginal wall. At low strains (C0), vaginal tissue appeared stiffer when elastin density was low. We found a statistically significant inverse relationship between C0 and the elastin/collagen ratio (p = 0.048) in the lamina propria. However, at large strain levels (C1), no clear relationship was observed between elastin density or elastin/collagen ratio and stiffness, likely reflecting the large dispersion of the mechanical behavior of the tissue samples. Histological and biomechanical properties of the vaginal wall vary from patient to patient. This study suggests that elastin density deserves consideration as a relevant factor of vaginal stiffness in women with POP.

Good Models Gone Bad: Quantifying and Predicting Parameter-Induced Climate Model Simulation Failures

NASA Astrophysics Data System (ADS)

Lucas, D. D.; Klein, R.; Tannahill, J.; Brandon, S.; Covey, C. C.; Domyancic, D.; Ivanova, D. P.

2012-12-01

Simulations using IPCC-class climate models are subject to fail or crash for a variety of reasons. Statistical analysis of the failures can yield useful insights to better understand and improve the models. During the course of uncertainty quantification (UQ) ensemble simulations to assess the effects of ocean model parameter uncertainties on climate simulations, we experienced a series of simulation failures of the Parallel Ocean Program (POP2). About 8.5% of our POP2 runs failed for numerical reasons at certain combinations of parameter values. We apply support vector machine (SVM) classification from the fields of pattern recognition and machine learning to quantify and predict the probability of failure as a function of the values of 18 POP2 parameters. The SVM classifiers readily predict POP2 failures in an independent validation ensemble, and are subsequently used to determine the causes of the failures via a global sensitivity analysis. Four parameters related to ocean mixing and viscosity are identified as the major sources of POP2 failures. Our method can be used to improve the robustness of complex scientific models to parameter perturbations and to better steer UQ ensembles. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and was funded by the Uncertainty Quantification Strategic Initiative Laboratory Directed Research and Development Project at LLNL under project tracking code 10-SI-013 (UCRL LLNL-ABS-569112).

Assessment of the psychometric properties of the Short-Form Prolapse/Urinary Incontinence Sexual Questionnaire (PISQ-12) following surgical placement of Prolift+M: a transvaginal partially absorbable mesh system for the treatment of pelvic organ prolapse.

PubMed

Roy, Sanjoy; Mohandas, Anita; Coyne, Karin; Gelhorn, Heather; Gauld, Judi; Sikirica, Vanja; Milani, Alfredo L

2012-04-01

Impairment of sexual function is a significant problem among women suffering from pelvic organ prolapse (POP). Because anatomical measures of POP do not always correspond with patients' subjective reports of their condition, patient-reported outcome measures may provide additional valuable information regarding the experiences of women who have undergone surgery. The Pelvic Organ Prolapse/Urinary Incontinence Sexual Questionnaire (PISQ-12) is a validated, widely used condition-specific questionnaire focused on sexual function among patients with POP or urinary incontinence. This study aims to report sexual function outcomes as measured by PISQ-12 and to evaluate the psychometric characteristics of the questionnaire following surgical mesh implant for the treatment of POP. The PISQ-12 was used to measure sexual function, while a set of other measures, namely, Pelvic Organ Prolapse Quantification, Patient Global Impression of Change, Pelvic Floor Distress Inventory, Pelvic Floor Impact Questionnaire, and Surgical Satisfaction Questionnaire, was used for validation. Data for the study were collected from a prospective multicenter, single-arm study of surgical POP repair via the transvaginal placement of a partially absorbable mesh system. For baseline, month 3, and month 12 following POP surgery, several psychometric properties of the PISQ-12 were evaluated, including internal consistency (Cronbach's alpha), concurrent validity, discriminant validity, and responsiveness. As measured by the PISQ-12 questionnaire, statistically significant improvements were observed in the composite summary score as well as all three subscale scores at 1 year. The PISQ-12 generally demonstrated good psychometric properties including internal consistency reliability, validity, and responsiveness. The PISQ-12 items had good distributional properties at baseline, with substantial ceiling effects at follow-up visits reflecting improvements experienced by the patients. The PISQ-12 is a valid measure of sexual function in studies involving patients with POP. © 2012 International Society for Sexual Medicine.

Dynamic 3T Pelvic Floor Magnetic Resonance Imaging in Women Progressing from the Nulligravida to Primiparous State

PubMed Central

Lockhart, Mark E.; Bates, G. Wright; Morgan, Desiree E.; Beasley, Timothy M.; Richter, Holly E.

2017-01-01

Introduction and Hypothesis To prospectively characterize dynamic pelvic 3Tesla magnetic resonance imaging (dp3T MRI) findings in nulligravida women and characterize changes 6 months after delivery in the same woman. Methods In this prospective study, nulligravida women seeking assisted reproductive technology for pregnancy were recruited. After physical examination by Pelvic Organ Prolapse Quantification (POP-Q), Brinks assessment and measures including the Pelvic Floor Distress Inventory-20 and Pelvic Floor Impact Questionnaire-7, pre-pregnancy dp3T MRI at rest, with strain, and evacuation were performed. Assessments were repeated ≥6 months postpartum. Analysis included Welch and paired t-tests for continuous variables, Fisher’s Exact Test for differences in categorical outcomes, and paired t-tests for postpartum symptoms. Results Nineteen subjects (mean±SD age, 31±5 years) completed baseline clinical and dp3T MRI studies, 15 delivered and 10 (30.5±3 years) completed pre-pregnancy and post-delivery clinical and dp3T MRI assessments. There were no significant changes in scores of validated questionnaires (all p>0.05) or on POP-Q measures post-delivery. Two (20%) subjects without pre-pregnancy levator tears had tears on MRI post-delivery. MRI measures of pelvic organ descent were increased post-delivery. Seventeen pelvic soft tissue parameters increased by greater than 10% post-delivery including 5/70 (7.1%), 17/110 (15.5%), and 50/110 (45.5%) values exceeding thresholds at rest, strain, and evacuation, respectively. Conclusions Dynamic pelvic 3T Magnetic Resonance Imaging detected levator tears and increased pelvic organ descent, which can be directly attributed to pregnancy and delivery. PMID:28871385

Failure analysis of parameter-induced simulation crashes in climate models

NASA Astrophysics Data System (ADS)

Lucas, D. D.; Klein, R.; Tannahill, J.; Ivanova, D.; Brandon, S.; Domyancic, D.; Zhang, Y.

2013-01-01

Simulations using IPCC-class climate models are subject to fail or crash for a variety of reasons. Quantitative analysis of the failures can yield useful insights to better understand and improve the models. During the course of uncertainty quantification (UQ) ensemble simulations to assess the effects of ocean model parameter uncertainties on climate simulations, we experienced a series of simulation crashes within the Parallel Ocean Program (POP2) component of the Community Climate System Model (CCSM4). About 8.5% of our CCSM4 simulations failed for numerical reasons at combinations of POP2 parameter values. We apply support vector machine (SVM) classification from machine learning to quantify and predict the probability of failure as a function of the values of 18 POP2 parameters. A committee of SVM classifiers readily predicts model failures in an independent validation ensemble, as assessed by the area under the receiver operating characteristic (ROC) curve metric (AUC > 0.96). The causes of the simulation failures are determined through a global sensitivity analysis. Combinations of 8 parameters related to ocean mixing and viscosity from three different POP2 parameterizations are the major sources of the failures. This information can be used to improve POP2 and CCSM4 by incorporating correlations across the relevant parameters. Our method can also be used to quantify, predict, and understand simulation crashes in other complex geoscientific models.

Failure analysis of parameter-induced simulation crashes in climate models

NASA Astrophysics Data System (ADS)

Lucas, D. D.; Klein, R.; Tannahill, J.; Ivanova, D.; Brandon, S.; Domyancic, D.; Zhang, Y.

2013-08-01

Simulations using IPCC (Intergovernmental Panel on Climate Change)-class climate models are subject to fail or crash for a variety of reasons. Quantitative analysis of the failures can yield useful insights to better understand and improve the models. During the course of uncertainty quantification (UQ) ensemble simulations to assess the effects of ocean model parameter uncertainties on climate simulations, we experienced a series of simulation crashes within the Parallel Ocean Program (POP2) component of the Community Climate System Model (CCSM4). About 8.5% of our CCSM4 simulations failed for numerical reasons at combinations of POP2 parameter values. We applied support vector machine (SVM) classification from machine learning to quantify and predict the probability of failure as a function of the values of 18 POP2 parameters. A committee of SVM classifiers readily predicted model failures in an independent validation ensemble, as assessed by the area under the receiver operating characteristic (ROC) curve metric (AUC > 0.96). The causes of the simulation failures were determined through a global sensitivity analysis. Combinations of 8 parameters related to ocean mixing and viscosity from three different POP2 parameterizations were the major sources of the failures. This information can be used to improve POP2 and CCSM4 by incorporating correlations across the relevant parameters. Our method can also be used to quantify, predict, and understand simulation crashes in other complex geoscientific models.

The S.A.C.S. (Satisfaction-Anatomy-Continence-Safety) score for evaluating pelvic organ prolapse surgery: a proposal for an outcome-based scoring system.

PubMed

Mearini, Luigi; Zucchi, Alessandro; Nunzi, Elisabetta; Di Biase, Manuel; Bini, Vittorio; Costantini, Elisabetta

2015-07-01

To date, there is no overall consensus on the definition of cure after surgery for pelvic organ prolapse (POP). The aim of the study was to design and test the scoring system S.A.C.S. (Satisfaction-Anatomy-Continence-Safety) to assess and compare the outcomes of POP repair. A total of 233 women underwent open sacrocolpopexy. The S.A.C.S. outcome scoring system was scheduled at 24 months of follow-up, and each component was detected according to: Satisfaction by mean of Patient Global Improvement Inventory scale, Anatomy by mean of POP Quantification system and bulge symptom, Continence by mean of pad use, and Safety by mean of the Clavien-Dindo classification of surgical complications. Each component produced a binary nominal categorical variable (1 or 0), with a total score of 4 representing cure. As a comparative tool, patients answered a simple yes/no question: "If you had to undergo surgery all over again, would you still do it?". The degree of concordance was estimated using Cohen's Kappa test. According to the S.A.C.S. scoring system, only 160 patients (68.6 %) reached the maximum score of cure. Sensitivity of the S.A.C.S. score was 74.1 %, specificity was 90 %, total diagnostic capacity was 75.5 %. The S.A.C.S. score internal consistency was good; the k-coefficient was higher for the satisfaction component of the score (k = 0.560). This study proposes an original, simple post-operative scoring system integrating satisfaction, anatomy, continence, and safety reports for patients undergoing surgery for POP, providing a complete, although perfectible, method to accurately report outcomes in all clinical scenarios.

Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: applications and considerations.

PubMed

Kim, Jaai; Lim, Juntaek; Lee, Changsoo

2013-12-01

Quantitative real-time PCR (qPCR) has been widely used in recent environmental microbial ecology studies as a tool for detecting and quantifying microorganisms of interest, which aids in better understandings of the complexity of wastewater microbial communities. Although qPCR can be used to provide more specific and accurate quantification than other molecular techniques, it does have limitations that must be considered when applying it in practice. This article reviews the principle of qPCR quantification and its applications to microbial ecology studies in various wastewater treatment environments. Here we also address several limitations of qPCR-based approaches that can affect the validity of quantification data: template nucleic acid quality, nucleic acid extraction efficiency, specificity of group-specific primers and probes, amplification of nonviable DNA, gene copy number variation, and limited number of sequences in the database. Even with such limitations, qPCR is reportedly among the best methods for quantitatively investigating environmental microbial communities. The application of qPCR is and will continue to be increasingly common in studies of wastewater treatment systems. To obtain reliable analyses, however, the limitations that have often been overlooked must be carefully considered when interpreting the results. Copyright © 2013 Elsevier Inc. All rights reserved.

Iliococcygeus fixation for the treatment of apical vaginal prolapse: efficacy and safety at 5 years of follow-up.

PubMed

Serati, Maurizio; Braga, Andrea; Bogani, Giorgio; Leone Roberti Maggiore, Umberto; Sorice, Paola; Ghezzi, Fabio; Salvatore, Stefano

2015-07-01

Sacrocolpopexy is considered the gold standard treatment for vaginal vault prolapse. However, the vaginal approach is very common, with 80-90 % of procedures being performed via this route. The aim of this study was to evaluate the safety and efficacy of iliococcygeus (ICG) fixation in the treatment of vaginal vault prolapse, with a minimum follow-up of 5 years. We prospectively enrolled women with symptomatic vaginal vault prolapse (Pelvic Organ Prolapse Quantification [POP-Q] stage ≥2) who were treated with ICG fixation. Subjective success was defined in the case of Patient Global Impression of Improvement ≤ 2 and an absence of bulging symptoms. Objective success was defined as stage of prolapse < 2 in all compartments. Overall success rate was defined as women without prolapse symptoms, PGI-I ≤ 2, stage of prolapse < 2, and no need for other surgery. All women filled in the Prolapse Quality of Life (P-QOL) questionnaire both at the preoperative visit and at every follow-up visit. Multiple logistic regression was performed to identify factors involved in the risk of recurrent POP. After a median (range) follow-up of 68.8 (60-92) months the subjective, objective, and overall cure rates were 88.6 % (39 out of 44), 84.1 % (37 out of 44), and 84.1 % (37 out of 44) respectively. Only preoperative stage IV vault descensus independently predicted POP recurrence after iliococcygeus fixation (OR: 8.78 [95 % CI: 1.31-9.42]; p < 0.001). Iliococcygeus fixation is a safe and effective surgical technique for the treatment of vaginal vault prolapse with long-lasting effectiveness.

Synthetic Graft Augmentation in Vaginal Prolapse Surgery: Long-Term Objective and Subjective Outcomes.

PubMed

Meyer, Isuzu; McGwin, Gerald; Swain, Thomas A; Alvarez, Mitchell D; Ellington, David R; Richter, Holly E

2016-01-01

To report long-term objectives and subjective outcomes in women who underwent prolapse surgery with a synthetic graft augmentation. Retrospective analysis (Canadian Task Force classification II-3). University hospital in the southeastern United States. Women with symptomatic pelvic organ prolapse who underwent transvaginal graft augmentation using the Prolift mesh system between July 2006 and December 2008 for a minimum 5-year follow-up. Subjects completed the Pelvic Floor Distress Inventory (PFDI-20), the Pelvic Floor Impact Questionnaire (PFIQ-7), the Pelvic Organ Prolapse/Urinary Incontinence Sexual Function Questionnaire (PISQ), and the Patient Satisfaction Questionnaire. Subjects also underwent postoperative physical examination with Pelvic Organ Prolapse Quantification (POP-Q) and vaginal pain/stricture assessment. Long-term postoperative findings were compared with preoperative baseline data. Of 208 eligible subjects, 70 completed the questionnaires only, and 48 of these 70 provided both postoperative examination and questionnaire data. The mean duration of follow-up was 7.0 ± 0.7 years (range, 5.8-8.1 years). POP-Q measurements of Ba (point B anterior), Bp (B posterior), C (cervix), GH (genital hiatus), PB (perineal body), and overall pelvic organ prolapse stage were significantly improved (all p < .001 except for PB, p = .006). PFIQ-7 (total, Urinary Impact Questionnaire, and Pelvic Organ Prolapse Impact Questionnaire) and PFDI-20 (total, Urinary Distress Inventory, and Pelvic Organ Prolapse Distress Inventory) scores significantly improved (all p < .001). No differences were noted in the colorectal-anal subscales (Colorectal-Anal Impact Questionnaire and Colorectal-Anal Distress Inventory) and PISQ scores at >5-year follow-up (all p > .05). Satisfaction rates were 15.7% for not at all, 35.7% for somewhat, and 48.6% for completely satisfied. Complications included graft exposure (n = 3; 6%) and dyspareunia (n = 25; 36%). Women undergoing transvaginal prolapse surgery using a synthetic graft continue to have positive objective and subjective outcomes, leading to significantly improved quality of life at a minimum 5-year follow-up. Copyright © 2016 AAGL. Published by Elsevier Inc. All rights reserved.

Experiences and expectations of women with urogenital prolapse: a quantitative and qualitative exploration.

PubMed

Srikrishna, S; Robinson, D; Cardozo, L; Cartwright, R

2008-10-01

To explore the expectations and goals of women undergoing surgery for urogenital prolapse using both a quantitative quality of life approach exploring symptom bother and a qualitative interview-based approach exploring patient goals and expectations. Prospective observational study. Tertiary referral centre for urogynaecology. Forty-three women with symptomatic pelvic organ prolapse were recruited from the waiting list for pelvic floor reconstructive surgery. All women were assessed with a structured clinical interview on an individual basis. The data obtained were transcribed verbatim and then analysed thematically based on the grounded theory. Individual codes and subcodes were identified to develop a coding framework. The prolapse quality-of-life (pQoL) questionnaire was used to determine the impact of pelvic organ prolapse on the woman's daily life. We arbitrarily classified 'bother' as minimal, mild, moderate and marked if scores ranged from 0 to 25, 25-50, 50-75 and 75-100, respectively. The degree of prolapse was objectively quantified using the pelvic organ prolapse quantification (POP-Q) system. Quantitative data were analysed using SPSS. Ethical approval was obtained from the Kings College Hospital Ethics Committee. Quantitative data from POP-Q, subjective data from pQoL, qualitative data based on the structured clinical interview. Forty-three women were recruited over the first 1 year of the study. Their mean age was 56 years (range 36-78) and mean parity was 2 (range 0-6). The mean ordinal stage of the prolapse was 2 (range stages 1-4). Quantitative analysis of the pQoL data suggested that the main domains affected were prolapse impact on life (mean score 74.71) and personal relationships (mean score 46.66). Qualitative analysis based on the clinical interview suggested that these women were most affected by the actual physical symptoms of prolapse (bulge, pain and bowel problems) as well by the impact prolapse has on their sexual function. While disease-specific QoL questionnaires allow broad comparisons to be made assessing patient bother, they may lack the sensitivity to assess individual symptoms. A qualitative approach may individualize patient care and ultimately improve patient satisfaction and overall outcome when treating women complaining of urogenital prolapse.

Reliability and validity of the Tigrigna version of the Pelvic Floor Distress Inventory-Short Form 20 (PFDI-20) and Pelvic Floor Impact Questionnaire-7 (PFIQ-7).

PubMed

Goba, Gelila K; Legesse, Awol Yeman; Zelelow, Yibrah Berhe; Gebreselassie, Mussie Alemayehu; Rogers, Rebecca G; Kenton, Kimberly S; Mueller, Margaret G

2018-03-13

This study adapted the Pelvic Floor Distress Inventory-Short Form 20 (PFDI-20) and the Pelvic Floor Impact Questionnaire-7 (PFIQ-7) into the Tigrigna language of northern Ethiopia and validated the their reliability and validity through patient interviews. Expert translation, cognitive interviewing, and patient interviews using translated questionnaires were conducted. A subset of women was reinterviewed 1 week later. Intraclass correlation coefficients (ICC), Bland-Altman analysis, and Cronbach's alpha values were assessed. Total and subscale scores were compared between women with and without pelvic floor disorders (PFDs) using the Mann-Whitney U test. Spearman's correlation coefficients were used to compare severity of pelvic organ prolapse (POP) stage according to the POP Quantification (POP-Q) system and PFDI-20 and PFIQ-7 and subscale scores. Ten women participated in cognitive interviewing and 118 age 49 ± 10 years, mean ± standard deviation (SD) with and without PFDs were interviewed using the translated questionnaires, both of which presented adequate face validity and test-retest reliability [intraclass correlation coefficient (ICC) 0.765-0.969, p < 0.001]. Construct validity was significant between clinical symptoms and full forms (p <0.001) and their subscales (p <0.001), except for the Pelvic Organ Prolapse Impact Questionnaire (POPIQ). Differences between first and second scores on total PFDI-20 and PFIQ-7 and subscales largely fell within 0 ± 1.96 SD. Cronbach's alpha values were 0.891-0.930 for PFDI-20 and 0.909-0.956 for PFIQ-7 (p < 0.001). Analysis of known groups showed differences PFDI-20 and PFIQ-7 scores between women with and without PFDs (p <0.001 for full forms and subscales, except for anal incontinence (AI) and the Urinary Impact Questionnaire (UIQ)/POPIQ. The translated Tigrigna versions of the PFDI-20 and PFIQ-7 questionnaires are reliable, valid, and feasible tools to evaluate symptoms and quality of life (QoL) of Tigrigna-speaking Ethiopian women with PFDs.

Quantification Bias Caused by Plasmid DNA Conformation in Quantitative Real-Time PCR Assay

PubMed Central

Lin, Chih-Hui; Chen, Yu-Chieh; Pan, Tzu-Ming

2011-01-01

Quantitative real-time PCR (qPCR) is the gold standard for the quantification of specific nucleic acid sequences. However, a serious concern has been revealed in a recent report: supercoiled plasmid standards cause significant over-estimation in qPCR quantification. In this study, we investigated the effect of plasmid DNA conformation on the quantification of DNA and the efficiency of qPCR. Our results suggest that plasmid DNA conformation has significant impact on the accuracy of absolute quantification by qPCR. DNA standard curves shifted significantly among plasmid standards with different DNA conformations. Moreover, the choice of DNA measurement method and plasmid DNA conformation may also contribute to the measurement error of DNA standard curves. Due to the multiple effects of plasmid DNA conformation on the accuracy of qPCR, efforts should be made to assure the highest consistency of plasmid standards for qPCR. Thus, we suggest that the conformation, preparation, quantification, purification, handling, and storage of standard plasmid DNA should be described and defined in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) to assure the reproducibility and accuracy of qPCR absolute quantification. PMID:22194997

Evaluation of limited blood sampling population input approaches for kinetic quantification of [18F]fluorothymidine PET data.

PubMed

Contractor, Kaiyumars B; Kenny, Laura M; Coombes, Charles R; Turkheimer, Federico E; Aboagye, Eric O; Rosso, Lula

2012-03-24

Quantification of kinetic parameters of positron emission tomography (PET) imaging agents normally requires collecting arterial blood samples which is inconvenient for patients and difficult to implement in routine clinical practice. The aim of this study was to investigate whether a population-based input function (POP-IF) reliant on only a few individual discrete samples allows accurate estimates of tumour proliferation using [18F]fluorothymidine (FLT). Thirty-six historical FLT-PET data with concurrent arterial sampling were available for this study. A population average of baseline scans blood data was constructed using leave-one-out cross-validation for each scan and used in conjunction with individual blood samples. Three limited sampling protocols were investigated including, respectively, only seven (POP-IF7), five (POP-IF5) and three (POP-IF3) discrete samples of the historical dataset. Additionally, using the three-point protocol, we derived a POP-IF3M, the only input function which was not corrected for the fraction of radiolabelled metabolites present in blood. The kinetic parameter for net FLT retention at steady state, Ki, was derived using the modified Patlak plot and compared with the original full arterial set for validation. Small percentage differences in the area under the curve between all the POP-IFs and full arterial sampling IF was found over 60 min (4.2%-5.7%), while there were, as expected, larger differences in the peak position and peak height.A high correlation between Ki values calculated using the original arterial input function and all the population-derived IFs was observed (R2 = 0.85-0.98). The population-based input showed good intra-subject reproducibility of Ki values (R2 = 0.81-0.94) and good correlation (R2 = 0.60-0.85) with Ki-67. Input functions generated using these simplified protocols over scan duration of 60 min estimate net PET-FLT retention with reasonable accuracy.

Rapid quantification of plant-powdery mildew interactions by qPCR and conidiospore counts.

PubMed

Weßling, Ralf; Panstruga, Ralph

2012-08-31

The powdery mildew disease represents a valuable patho-system to study the interaction between plant hosts and obligate biotrophic fungal pathogens. Numerous discoveries have been made on the basis of the quantitative evaluation of plant-powdery mildew interactions, especially in the context of hyper-susceptible and/or resistant plant mutants. However, the presently available methods to score the pathogenic success of powdery mildew fungi are laborious and thus not well suited for medium- to high-throughput analysis. Here we present two new protocols that allow the rapid quantitative assessment of powdery mildew disease development. One procedure depends on quantitative polymerase chain reaction (qPCR)-based evaluation of fungal biomass, while the other relies on the quantification of fungal conidiospores. We validated both techniques using the powdery mildew pathogen Golovinomyces orontii on a set of hyper-susceptible and resistant Arabidopsis thaliana mutants and found that both cover a wide dynamic range of one to two (qPCR) and four to five (quantification of conidia) orders of magnitude, respectively. The two approaches yield reproducible results and are easy to perform without specialized equipment. The qPCR and spore count assays rapidly and reproducibly quantify powdery mildew pathogenesis. Our methods are performed at later stages of infection and discern mutant phenotypes accurately. The assays therefore complement currently used procedures of powdery mildew quantification and can overcome some of their limitations. In addition, they can easily be adapted to other plant-powdery mildew patho-systems.

Quantification of tidal parameters from Solar System data

NASA Astrophysics Data System (ADS)

Lainey, Valéry

2016-11-01

Tidal dissipation is the main driver of orbital evolution of natural satellites and a key point to understand the exoplanetary system configurations. Despite its importance, its quantification from observations still remains difficult for most objects of our own Solar System. In this work, we overview the method that has been used to determine, directly from observations, the tidal parameters, with emphasis on the Love number k_2 and the tidal quality factor Q. Up-to-date values of these tidal parameters are summarized. Last, an assessment on the possible determination of the tidal ratio k_2/Q of Uranus and Neptune is done. This may be particularly relevant for coming astrometric campaigns and future space missions focused on these systems.

Porcine dermis compared with polypropylene mesh for laparoscopic sacrocolpopexy: a randomized controlled trial.

PubMed

Culligan, Patrick J; Salamon, Charbel; Priestley, Jennifer L; Shariati, Amir

2013-01-01

To compare the surgical outcomes 12 months after laparoscopic sacrocolpopexy performed with porcine dermis and the current gold standard of polypropylene mesh. Patients scheduled for laparoscopic sacrocolpopexy were eligible for this randomized controlled trial. Both our clinical research nurse and the patients were blinded as to which material was used. Our primary end point was objective anatomic cure defined as no pelvic organ prolapse quantification (POP-Q) points Stage 2 or greater at any postoperative interval. Our sample size calculation called for 57 patients in each group to achieve 90% power to detect a 23% difference in objective anatomic cure at 12 months (α=0.05). Our secondary end point was clinical cure. Any patient with a POP-Q point greater than zero, or Point C less than or equal to -5, or any complaints of prolapse symptoms whatsoever on Pelvic Floor Distress Inventory-20 or Pelvic Floor Impact Questionnaire, Short Form 7, or reoperation for prolapse were considered "clinical failures"; the rest were "clinical cures." Statistical comparisons were performed using the χ or independent samples t test as appropriate. As expected, there were no preoperative differences between the porcine (n=57) and mesh (n=58) groups. The 12-month objective anatomic cure rates for the porcine and mesh groups were 80.7% and 86.2%, respectively (P=.24), and the "clinical cure" rates for the porcine and mesh groups were 84.2% and 89.7%, respectively (P=.96). Pelvic Floor Distress Inventory-20 and Pelvic Floor Impact Questionnaire, Short Form 7 score improvements were significant for both groups with no differences found between groups. There were no major operative complications. There were similar outcomes in subjective or objective results 12 months after laparoscopic sacrocolpopexy performed with either porcine dermis or polypropylene mesh. ClinicalTrials.gov, www.clinicaltrials.gov, NCT00564083. I.

Forceps delivery is associated with increased risk of pelvic organ prolapse and muscle trauma: a cross-sectional study 16-24 years after first delivery.

PubMed

Volløyhaug, I; Mørkved, S; Salvesen, Ø; Salvesen, K Å

2015-10-01

To study possible associations between mode of delivery and pelvic organ prolapse (POP) and pelvic floor muscle trauma 16-24 years after first delivery and, in particular, to identify differences between forceps and vacuum delivery. This was a cross-sectional study including 608 women who delivered their first child in 1990-1997 and were examined with POP quantification (POP-Q) and pelvic floor ultrasound in 2013-2014. Outcome measures were POP ≥ Stage 2 or previous prolapse surgery, levator avulsion and levator hiatal area on Valsalva. Univariable and multivariable logistic regression analyses and ANCOVA were applied to identify outcome variables associated with mode of delivery. Comparing forceps to vacuum delivery, the adjusted odds ratios (aOR) were 1.72 (95% CI, 1.06-2.79; P = 0.03) for POP ≥ Stage 2 or previous prolapse surgery and 4.16 (95% CI, 2.28-7.59; P < 0.01) for levator avulsion. Hiatal area on Valsalva was larger, with adjusted mean difference (aMD) of 4.75 cm(2) (95% CI, 2.46-7.03; P < 0.01). Comparing forceps with normal vaginal delivery, the adjusted odds ratio (aOR) was 1.74 (95% CI, 1.12-2.68; P = 0.01) for POP ≥ Stage 2 or surgery and 4.35 (95% CI, 2.56-7.40; P < 0.01) for levator avulsion; hiatal area on Valsalva was larger, with an aMD of 3.84 cm(2) (95% CI, 1.78-5.90; P < 0.01). Comparing Cesarean delivery with normal vaginal delivery, aOR was 0.06 (95% CI, 0.02-0.14; P < 0.01) for POP ≥ Stage 2 or surgery and crude OR was 0.00 (95% CI, 0.00-0.30; P < 0.01) for levator avulsion; hiatal area on Valsalva was smaller, with an aMD of -8.35 cm(2) (95% CI, -10.87 to -5.84; P < 0.01). No differences were found between vacuum and normal vaginal delivery. We found that mode of delivery was associated with POP and pelvic floor muscle trauma in women from a general population, 16-24 years after their first delivery. Forceps was associated with significantly more POP, levator avulsion and larger hiatal areas than were vacuum and normal vaginal deliveries. There were no statistically significant differences between vacuum and normal vaginal deliveries. Cesarean delivery was associated with significantly less POP and pelvic floor muscle trauma than were normal or operative vaginal delivery. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd.

Source, Managemnt and Quantification of Unintentional POPs (PCDDD/Fs) in Nepal

NASA Astrophysics Data System (ADS)

Charitra Sah, Ram

2010-05-01

The aim to prepare and present this paper is to highlight the source, management and quantification of the unintentional POPs in an unindustrialized least developing landlocked small country Nepal. The methodology adopted for this is the review of the relevant research documents and national initiative towards addressing this issues complemented with sharing of the first hand experience from the implementation of the POPs management activities undertaken by our organization. Nepal is a small country of size 147181 sq.km but having large sources of POPs including unintentional POPs (PCDD/Fs) mainly because of weak enforcement of the existing environment related laws, standards and international commitment including POPs Convention. Country became homes to about 75 tons of Obsolete Pesticide since last 30 years including about 44 percent (33 tons out of 75) are of known POPs. These obsolete pesticides including identified POPs have been poorly stored in some about 25 locations throughout the country. The major warehouse accommodating about 50 tons at Amlekhgunj has been located just in front of a high school where about 1000 children are being studying and found to have some health related problem due to the gasses emission from the warehouse as well as school playground field contaminated with these POPs pesticides. The playground soil contamination has been found from routine examination of the soil samples. In addition to pesticides including POPs were used in the agriculture and public health field in the past, there are several other practices as well as anthropogenic activities producing PCDD/Fs. The annual inventory of countrywide emission of unintentional POPs was estimated to be 312.55 g TEQ for Nepal (MOE 2004). This is very high for a country like Nepal least developing in terms of industrial and economy. This estimation was based on the UNEP Toolkit which has included the broad categories of waste such as waste incineration, ferrous and non ferrous metal production, power generation and cooking using biomass, production of mineral products, transportation, uncontrolled combustion processes production of chemicals and consumer goods, disposal and land filling and miscellaneous. However, it does not account all the sources of the unintentional POPs emission. There are increasing amount of PCDD/Fs emission from other unidentified and/or under estimate sources. An another estimates just for medical waste incineration amount to be 57.37 g TEQ / year based on the current rate of medical waste generation, incineration proportion and considering small box-type batch incinerator with no afterburner as it is mostly adopted in all individual health care institutions. Toward management of POPs, earlier government is not found to be serious as there is still provision of waste incineration in its waste management guidelines including medical waste and has also given Environment Impact Assessment (EIA) clearance to some of the project with waste incineration components. It is important to make the highlight here that the waste incinerator no matter of its art of standards is the indentified major source of unintentional POPs such as PCDD/Fs the known human carcinogen. However, in the recent years, there was increasing concerned of the government as it has come up with the National Implementation Plan (NIP) for Stockholm Convention on Persistent Organic Pollutants with clear identification, prioritization as well as developed program of action linked with monitoring and reporting mechanism. Some of the recent development projects with FAO and GTZ towards realization of the few prioritized plan of action about the sound management of obsolete pesticides including POPs can be considered as remarkable positive progress towards overall development in this field which upon successful implementation will help to improve the country situation. Key words: unintentional POPs, source, management

Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification.

PubMed

Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Paik, Young-Ki

2017-12-01

Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modification options can increase processing time, false-positive errors in large and complicated MS data sets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity. Unfortunately, this technique has less proteome coverage, resulting in limitations in the detection of novel and whole peptide sequences in biological samples. To solve these problems, we previously developed the "Combo-Spec Search" method, which uses manually multiple references and simulated spectral library searching to analyze whole proteomes in a biological sample. In this study, we have developed a new analytical interface tool called "Epsilon-Q" to enhance the functions of both the Combo-Spec Search method and label-free protein quantification. Epsilon-Q performs automatically multiple spectral library searching, class-specific false-discovery rate control, and result integration. It has a user-friendly graphical interface and demonstrates good performance in identifying and quantifying proteins by supporting standard MS data formats and spectrum-to-spectrum matching powered by SpectraST. Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec search method, called the Epsilon-Q system, it shows a synergistic function by outperforming other sequence DB search engines for identifying and quantifying low-abundance proteins in biological samples. The Epsilon-Q system can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification.

A Java program for LRE-based real-time qPCR that enables large-scale absolute quantification.

PubMed

Rutledge, Robert G

2011-03-02

Linear regression of efficiency (LRE) introduced a new paradigm for real-time qPCR that enables large-scale absolute quantification by eliminating the need for standard curves. Developed through the application of sigmoidal mathematics to SYBR Green I-based assays, target quantity is derived directly from fluorescence readings within the central region of an amplification profile. However, a major challenge of implementing LRE quantification is the labor intensive nature of the analysis. Utilizing the extensive resources that are available for developing Java-based software, the LRE Analyzer was written using the NetBeans IDE, and is built on top of the modular architecture and windowing system provided by the NetBeans Platform. This fully featured desktop application determines the number of target molecules within a sample with little or no intervention by the user, in addition to providing extensive database capabilities. MS Excel is used to import data, allowing LRE quantification to be conducted with any real-time PCR instrument that provides access to the raw fluorescence readings. An extensive help set also provides an in-depth introduction to LRE, in addition to guidelines on how to implement LRE quantification. The LRE Analyzer provides the automated analysis and data storage capabilities required by large-scale qPCR projects wanting to exploit the many advantages of absolute quantification. Foremost is the universal perspective afforded by absolute quantification, which among other attributes, provides the ability to directly compare quantitative data produced by different assays and/or instruments. Furthermore, absolute quantification has important implications for gene expression profiling in that it provides the foundation for comparing transcript quantities produced by any gene with any other gene, within and between samples.

A Java Program for LRE-Based Real-Time qPCR that Enables Large-Scale Absolute Quantification

PubMed Central

Rutledge, Robert G.

2011-01-01

Background Linear regression of efficiency (LRE) introduced a new paradigm for real-time qPCR that enables large-scale absolute quantification by eliminating the need for standard curves. Developed through the application of sigmoidal mathematics to SYBR Green I-based assays, target quantity is derived directly from fluorescence readings within the central region of an amplification profile. However, a major challenge of implementing LRE quantification is the labor intensive nature of the analysis. Findings Utilizing the extensive resources that are available for developing Java-based software, the LRE Analyzer was written using the NetBeans IDE, and is built on top of the modular architecture and windowing system provided by the NetBeans Platform. This fully featured desktop application determines the number of target molecules within a sample with little or no intervention by the user, in addition to providing extensive database capabilities. MS Excel is used to import data, allowing LRE quantification to be conducted with any real-time PCR instrument that provides access to the raw fluorescence readings. An extensive help set also provides an in-depth introduction to LRE, in addition to guidelines on how to implement LRE quantification. Conclusions The LRE Analyzer provides the automated analysis and data storage capabilities required by large-scale qPCR projects wanting to exploit the many advantages of absolute quantification. Foremost is the universal perspective afforded by absolute quantification, which among other attributes, provides the ability to directly compare quantitative data produced by different assays and/or instruments. Furthermore, absolute quantification has important implications for gene expression profiling in that it provides the foundation for comparing transcript quantities produced by any gene with any other gene, within and between samples. PMID:21407812

Application of Focused Ultrasound-Assisted Extraction for the Quantification of Persistent Organic Pollutions in Liver Tissue of Giant Toad (Rhinella marina).

PubMed

Flores-Ramírez, R; Espinosa-Reyes, G; Cilia-López, V G; González-Mille, D J; Rodríguez-Aguilar, M; Díaz de León-Martínez, L; Díaz-Barriga, F

2017-02-01

A simple and rapid focused ultrasound extraction method was developed for the determination of Persistent Organic Pollutants (POPs) in liver tissue obtained of giant toad (Rhinella marina) using a gas chromatography coupled to a mass detector with electron impact ionization. The performed method for POPs, was validated in fortified matrix, showing linearity from the LOQ up to 100 ng/mL; LODs and LOQs for each compound were between 1.7 and 4.8 and 3.5-7.5 ng/mL, respectively. Recovery rates were among 79%-116% for POPs determined. Finally, the method was applied in liver samples of giant toads found in a malarial area in Mexico. The sensitivity of the proposed method was good enough to ensure reliable determination of target analytes at concentration levels commonly found in this kind of samples.

Elvis to Eminem: quantifying the price of fame through early mortality of European and North American rock and pop stars.

PubMed

Bellis, Mark A; Hennell, Tom; Lushey, Clare; Hughes, Karen; Tocque, Karen; Ashton, John R

2007-10-01

Rock and pop stars are frequently characterised as indulging in high-risk behaviours, with high-profile deaths amongst such musicians creating an impression of premature mortality. However, studies to date have not quantified differences between mortality experienced by such stars and general populations. This study measures survival rates of famous musicians (n = 1064) from their point of fame and compares them to matched general populations in North America and Europe. We describe and utilise a novel actuarial survival methodology which allows quantification of excess post-fame mortality in pop stars. Individuals from North America and Europe performing on any album in the All-Time Top 1000 albums from the music genres rock, punk, rap, R&B, electronica and new age. From 3 to 25 years post fame, both North American and European pop stars experience significantly higher mortality (more than 1.7 times) than demographically matched populations in the USA and UK, respectively. After 25 years of fame, relative mortality in European (but not North American) pop stars begins to return to population levels. Five-year post-fame survival rates suggest differential mortality between stars and general populations was greater in those reaching fame before 1980. Pop stars can suffer high levels of stress in environments where alcohol and drugs are widely available, leading to health-damaging risk behaviour. However, their behaviour can also influence would-be stars and devoted fans. Collaborations between health and music industries should focus on improving both pop star health and their image as role models to wider populations.

Multiplex Droplet Digital PCR Protocols for Quantification of GM Maize Events.

PubMed

Dobnik, David; Spilsberg, Bjørn; Bogožalec Košir, Alexandra; Štebih, Dejan; Morisset, Dany; Holst-Jensen, Arne; Žel, Jana

2018-01-01

The standard-curve based simplex quantitative polymerase chain reaction (qPCR) has been the gold standard for DNA target quantification for more than a decade. The large and growing number of individual analyses needed to test for genetically modified organisms (GMOs) is reducing the cost-effectiveness of qPCR. Droplet digital PCR (ddPCR) enables absolute quantification without standard curves, avoids the amplification efficiency bias observed with qPCR, allows more accurate estimations at low target copy numbers and, in combination with multiplexing, significantly improves cost efficiency. Here we describe two protocols for multiplex quantification of GM maize events: (1) nondiscriminating, with multiplex quantification of targets as a group (12 GM maize lines) and (2) discriminating, with multiplex quantification of individual targets (events). The first enables the quantification of twelve European Union authorized GM maize events as a group with only two assays, but does not permit determination of the individual events present. The second protocol enables the quantification of four individual targets (three GM events and one endogene) in a single reaction. Both protocols can be modified for quantification of any other DNA target.

Quantitative Analysis of Food and Feed Samples with Droplet Digital PCR

PubMed Central

Morisset, Dany; Štebih, Dejan; Milavec, Mojca; Gruden, Kristina; Žel, Jana

2013-01-01

In this study, the applicability of droplet digital PCR (ddPCR) for routine analysis in food and feed samples was demonstrated with the quantification of genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of GMOs in products. However, its use is limited for detecting and quantifying very small numbers of DNA targets, as in some complex food and feed matrices. Using ddPCR duplex assay, we have measured the absolute numbers of MON810 transgene and hmg maize reference gene copies in DNA samples. Key performance parameters of the assay were determined. The ddPCR system is shown to offer precise absolute and relative quantification of targets, without the need for calibration curves. The sensitivity (five target DNA copies) of the ddPCR assay compares well with those of individual qPCR assays and of the chamber digital PCR (cdPCR) approach. It offers a dynamic range over four orders of magnitude, greater than that of cdPCR. Moreover, when compared to qPCR, the ddPCR assay showed better repeatability at low target concentrations and a greater tolerance to inhibitors. Finally, ddPCR throughput and cost are advantageous relative to those of qPCR for routine GMO quantification. It is thus concluded that ddPCR technology can be applied for routine quantification of GMOs, or any other domain where quantitative analysis of food and feed samples is needed. PMID:23658750

Functional characterization of the 19q12 amplicon in grade III breast cancers

PubMed Central

2012-01-01

Introduction The 19q12 locus is amplified in a subgroup of oestrogen receptor (ER)-negative grade III breast cancers. This amplicon comprises nine genes, including cyclin E1 (CCNE1), which has been proposed as its 'driver'. The aim of this study was to identify the genes within the 19q12 amplicon whose expression is required for the survival of cancer cells harbouring their amplification. Methods We investigated the presence of 19q12 amplification in a series of 313 frozen primary breast cancers and 56 breast cancer cell lines using microarray comparative genomic hybridisation (aCGH). The nine genes mapping to the smallest region of amplification on 19q12 were silenced using RNA interference in phenotypically matched breast cancer cell lines with (MDA-MB-157 and HCC1569) and without (Hs578T, MCF7, MDA-MB-231, ZR75.1, JIMT1 and BT474) amplification of this locus. Genes whose silencing was selectively lethal in amplified cells were taken forward for further validation. The effects of cyclin-dependent kinase 2 (CDK2) silencing and chemical inhibition were tested in cancer cells with and without CCNE1 amplification. Results 19q12 amplification was identified in 7.8% of ER-negative grade III breast cancer. Of the nine genes mapping to this amplicon, UQCRFS1, POP4, PLEKHF1, C19ORF12, CCNE1 and C19ORF2 were significantly over-expressed when amplified in primary breast cancers and/or breast cancer cell lines. Silencing of POP4, PLEKHF1, CCNE1 and TSZH3 selectively reduced cell viability in cancer cells harbouring their amplification. Cancer cells with CCNE1 amplification were shown to be dependent on CDK2 expression and kinase activity for their survival. Conclusions The 19q12 amplicon may harbour more than a single 'driver', given that expression of POP4, PLEKHF1, CCNE1 and TSZH3 is required for the survival of cancer cells displaying their amplification. The observation that cancer cells harbouring CCNE1 gene amplification are sensitive to CDK2 inhibitors provides a rationale for the testing of these chemical inhibitors in a subgroup of patients with ER-negative grade III breast cancers. PMID:22433433

Performance Evaluation of the Real-Q Cytomegalovirus (CMV) Quantification Kit Using Two Real-Time PCR Systems for Quantifying CMV DNA in Whole Blood.

PubMed

Park, Jong Eun; Kim, Ji Youn; Yun, Sun Ae; Lee, Myoung Keun; Huh, Hee Jae; Kim, Jong Won; Ki, Chang Seok

2016-11-01

Standardized cytomegalovirus (CMV) DNA quantification is important for managing CMV disease. We evaluated the performance of the Real-Q CMV Quantification Kit (Real-Q assay; BioSewoom, Korea) using whole blood (WB), with nucleic acid extraction using MagNA Pure 96 (Roche Diagnostics, Germany). Real-time PCR was performed on two platforms: the 7500 Fast real-time PCR (7500 Fast; Applied Biosystems, USA) and CFX96 real-time PCR detection (CFX96; Bio-Rad, USA) systems. The WHO international standard, diluted with CMV-negative WB, was used to validate the analytical performance. We used 90 WB clinical samples for comparison with the artus CMV RG PCR kit (artus assay; Qiagen, Germany). Limits of detections (LODs) in 7500 Fast and CFX96 were 367 and 479 IU/mL, respectively. The assay was linear from the LOD to 10⁶ IU/mL (R² ≥0.9886). The conversion factors from copies to IU in 7500 Fast and CFX96 were 0.95 and 1.06, respectively. Compared with the artus assay, for values <1,000 copies/mL, 100% of the samples had a variation <0.7 log₁₀ copies/mL; >1,000 copies/mL, 73.3% and 80.6% of samples in 7500 Fast and CFX96, respectively, had <0.5 log₁₀ copies/mL. The Real-Q assay is useful for quantifying CMV in WB with the two real-time PCR platforms.

Does the prevalence of levator ani muscle avulsion differ when assessed using tomographic ultrasound imaging at rest vs on maximum pelvic floor muscle contraction?

PubMed

van Delft, K; Thakar, R; Sultan, A H; Kluivers, K B

2015-07-01

It has been suggested that transperineal ultrasound images obtained during maximum pelvic floor muscle contraction improve the diagnosis of levator ani muscle (LAM) avulsion by comparison with those obtained at rest. The objective of this study was to establish, using transperineal tomographic ultrasound imaging (TUI), the correlation between LAM avulsion diagnosed at rest and that on contraction. Primiparous women were examined 3 months postpartum by Pelvic Organ Prolapse Quantification (POP-Q) assessment and for LAM avulsion clinically by digital palpation and by transperineal TUI performed at rest and on pelvic floor muscle contraction. LAM avulsion was diagnosed on TUI when the three central slices were abnormal. A comparison was made between LAM avulsion diagnosed at rest and on maximum contraction. Two independent blinded investigators performed the analyses and a third investigator resolved discrepancies. One hundred and ninety primiparae were analyzed providing 380 results for comparison, as right and left LAM were analyzed independently. LAM avulsion was found in 36 (9.5%) images obtained at rest and in 35 (9.2%) on contraction, revealing moderate correlation between the two (ICC, 0.58 (95% CI, 0.51-0.64)). Twenty-two cases of LAM avulsion were identified both at rest and on contraction. One woman had LAM avulsion on palpation, which was seen on TUI as LAM avulsion on contraction, but not at rest. More cases of anterior and posterior compartment prolapse were found in women with LAM avulsion diagnosed on contraction only compared to LAM avulsion observed at rest only (POP-Q assessment point Ba, -1.8 vs -2.5 (P = 0.075) and point Bp, -2.5 vs -2.8 (P = 0.072)). Findings on transperineal TUI performed in women at rest and on contraction correlate reasonably well. However, given the trend towards an association with signs of pelvic floor dysfunction, diagnosis of LAM avulsion on contraction seems to be more reliable. Consistency in technique and interpretation should be maintained. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.

Postpartum pelvic floor muscle training and pelvic organ prolapse--a randomized trial of primiparous women.

PubMed

Bø, Kari; Hilde, Gunvor; Stær-Jensen, Jette; Siafarikas, Franziska; Tennfjord, Merete Kolberg; Engh, Marie Ellstrøm

2015-01-01

Pelvic organ prolapse (POP) is a common and distressing condition. The aim of the present study was to evaluate the effect of pelvic floor muscle training (PFMT) on prevention and treatment of symptoms and signs of POP in primiparous postpartum women. This was a parallel group assessor blind randomized controlled trial. One hundred seventy-five primiparous postpartum women, mean age 29.8 years (standard deviation 4.1), stratified on major levator ani defects or no defect diagnosed by 3-/4-dimensional ultrasound, participated in a 4-month PFMT starting at 6-8 weeks' postpartum or control. All participants had thorough individual instruction and assessment of ability to perform correct pelvic floor muscle contractions. The PFMT group followed a supervised, weekly group training program and performed 3 sets of 8-12 daily maximal contractions at home. Main outcome was POP stage II or greater assessed by POP quantification and bladder neck position assessed by 3-/4- dimensional transperineal ultrasonography. Secondary outcome was symptoms of vaginal bulge using International Consultation on Incontinence Vaginal Symptoms questionnaire. Ninety-six percent of the intervention group adhered to ≥80% of both group and home training sessions. At postintervention, there was no significant risk difference in POP (rational ratio, 1.62; 95% confidence interval, 0.55-4.75), bladder neck position or symptoms of vaginal bulging. No effect was found of postpartum PFMT on POP in primiparous women. More randomized controlled trials are needed before strong conclusions can be drawn on the effect of PFMT on POP in the particular population. Copyright © 2015 Elsevier Inc. All rights reserved.

Elvis to Eminem: quantifying the price of fame through early mortality of European and North American rock and pop stars

PubMed Central

Bellis, Mark A; Hennell, Tom; Lushey, Clare; Hughes, Karen; Tocque, Karen; Ashton, John R

2007-01-01

Background Rock and pop stars are frequently characterised as indulging in high‐risk behaviours, with high‐profile deaths amongst such musicians creating an impression of premature mortality. However, studies to date have not quantified differences between mortality experienced by such stars and general populations. Objective This study measures survival rates of famous musicians (n = 1064) from their point of fame and compares them to matched general populations in North America and Europe. Design We describe and utilise a novel actuarial survival methodology which allows quantification of excess post‐fame mortality in pop stars. Participants Individuals from North America and Europe performing on any album in the All‐Time Top 1000 albums from the music genres rock, punk, rap, R&B, electronica and new age. Results From 3 to 25 years post fame, both North American and European pop stars experience significantly higher mortality (more than 1.7 times) than demographically matched populations in the USA and UK, respectively. After 25 years of fame, relative mortality in European (but not North American) pop stars begins to return to population levels. Five‐year post‐fame survival rates suggest differential mortality between stars and general populations was greater in those reaching fame before 1980. Conclusion Pop stars can suffer high levels of stress in environments where alcohol and drugs are widely available, leading to health‐damaging risk behaviour. However, their behaviour can also influence would‐be stars and devoted fans. Collaborations between health and music industries should focus on improving both pop star health and their image as role models to wider populations. PMID:17873227

Optimization of PCR for quantification of simian immunodeficiency virus (SIV) genomic RNA in plasma of rhesus macaques (Macaca mulatta) using armored RNA

PubMed Central

Monjure, C. J.; Tatum, C. D.; Panganiban, A. T.; Arainga, M.; Traina-Dorge, V.; Marx, P. A.; Didier, E. S.

2014-01-01

Introduction Quantification of plasma viral load (PVL) is used to monitor disease progression in SIV-infected macaques. This study was aimed at optimizing of performance characteristics of the quantitative PCR (qPCR) PVL assay. Methods The PVL quantification procedure was optimized by inclusion of an exogenous control Hepatitis C Virus armored RNA (aRNA), a plasma concentration step, extended digestion with proteinase K, and a second RNA elution step. Efficiency of viral RNA (vRNA) extraction was compared using several commercial vRNA extraction kits. Various parameters of qPCR targeting the gag region of SIVmac239, SIVsmE660 and the LTR region of SIVagmSAB were also optimized. Results Modifications of the SIV PVL qPCR procedure increased vRNA recovery, reduced inhibition and improved analytical sensitivity. The PVL values determined by this SIV PVL qPCR correlated with quantification results of SIV-RNA in the same samples using the “industry standard” method of branched-DNA (bDNA) signal amplification. Conclusions Quantification of SIV genomic RNA in plasma of rhesus macaques using this optimized SIV PVL qPCR is equivalent to the bDNA signal amplification method, less costly and more versatile. Use of heterologous aRNA as an internal control is useful for optimizing performance characteristics of PVL qPCRs. PMID:24266615

Optimization of PCR for quantification of simian immunodeficiency virus genomic RNA in plasma of rhesus macaques (Macaca mulatta) using armored RNA.

PubMed

Monjure, C J; Tatum, C D; Panganiban, A T; Arainga, M; Traina-Dorge, V; Marx, P A; Didier, E S

2014-02-01

Quantification of plasma viral load (PVL) is used to monitor disease progression in SIV-infected macaques. This study was aimed at optimizing of performance characteristics of the quantitative PCR (qPCR) PVL assay. The PVL quantification procedure was optimized by inclusion of an exogenous control hepatitis C virus armored RNA (aRNA), a plasma concentration step, extended digestion with proteinase K, and a second RNA elution step. Efficiency of viral RNA (vRNA) extraction was compared using several commercial vRNA extraction kits. Various parameters of qPCR targeting the gag region of SIVmac239, SIVsmE660, and the LTR region of SIVagmSAB were also optimized. Modifications of the SIV PVL qPCR procedure increased vRNA recovery, reduced inhibition and improved analytical sensitivity. The PVL values determined by this SIV PVL qPCR correlated with quantification results of SIV RNA in the same samples using the 'industry standard' method of branched-DNA (bDNA) signal amplification. Quantification of SIV genomic RNA in plasma of rhesus macaques using this optimized SIV PVL qPCR is equivalent to the bDNA signal amplification method, less costly and more versatile. Use of heterologous aRNA as an internal control is useful for optimizing performance characteristics of PVL qPCRs. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Modeling qRT-PCR dynamics with application to cancer biomarker quantification.

PubMed

Chervoneva, Inna; Freydin, Boris; Hyslop, Terry; Waldman, Scott A

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used for molecular diagnostics and evaluating prognosis in cancer. The utility of mRNA expression biomarkers relies heavily on the accuracy and precision of quantification, which is still challenging for low abundance transcripts. The critical step for quantification is accurate estimation of efficiency needed for computing a relative qRT-PCR expression. We propose a new approach to estimating qRT-PCR efficiency based on modeling dynamics of polymerase chain reaction amplification. In contrast, only models for fluorescence intensity as a function of polymerase chain reaction cycle have been used so far for quantification. The dynamics of qRT-PCR efficiency is modeled using an ordinary differential equation model, and the fitted ordinary differential equation model is used to obtain effective polymerase chain reaction efficiency estimates needed for efficiency-adjusted quantification. The proposed new qRT-PCR efficiency estimates were used to quantify GUCY2C (Guanylate Cyclase 2C) mRNA expression in the blood of colorectal cancer patients. Time to recurrence and GUCY2C expression ratios were analyzed in a joint model for survival and longitudinal outcomes. The joint model with GUCY2C quantified using the proposed polymerase chain reaction efficiency estimates provided clinically meaningful results for association between time to recurrence and longitudinal trends in GUCY2C expression.

Development of a quantitative loop-mediated isothermal amplification assay for the field detection of Erysiphe necator.

PubMed

Thiessen, Lindsey D; Neill, Tara M; Mahaffee, Walter F

2018-01-01

Plant pathogen detection systems have been useful tools to monitor inoculum presence and initiate management schedules. More recently, a loop-mediated isothermal amplification (LAMP) assay was successfully designed for field use in the grape powdery mildew pathosystem; however, false negatives or false positives were prevalent in grower-conducted assays due to the difficulty in perceiving the magnesium pyrophosphate precipitate at low DNA concentrations. A quantitative LAMP (qLAMP) assay using a fluorescence resonance energy transfer-based probe was assessed by grape growers in the Willamette Valley of Oregon. Custom impaction spore samplers were placed at a research vineyard and six commercial vineyard locations, and were tested bi-weekly by the lab and by growers. Grower-conducted qLAMP assays used a beta-version of the Smart-DART handheld LAMP reaction devices (Diagenetix, Inc., Honolulu, HI, USA), connected to Android 4.4 enabled, Bluetooth-capable Nexus 7 tablets for output. Quantification by a quantitative PCR assay was assumed correct to compare the lab and grower qLAMP assay quantification. Growers were able to conduct and interpret qLAMP results; however, the Erysiphe necator inoculum quantification was unreliable using the beta-Smart-DART devices. The qLAMP assay developed was sensitive to one spore in early testing of the assay, but decreased to >20 spores by the end of the trial. The qLAMP assay is not likely a suitable management tool for grape powdery mildew due to losses in sensitivity and decreasing costs and portability for other, more reliable molecular tools.

Overcoming Heparin-Associated RT-qPCR Inhibition and Normalization Issues for microRNA Quantification in Patients with Acute Myocardial Infarction.

PubMed

Coelho-Lima, Jose; Mohammed, Ashfaq; Cormack, Suzanne; Jones, Samuel; Das, Rajiv; Egred, Mohaned; Panahi, Pedram; Ali, Simi; Spyridopoulos, Ioakim

2018-06-11

 Cardiac-enriched micro ribonucleic acids (miRNAs) are released into the circulation following ST-elevation myocardial infarction (STEMI). Lack of standardized approaches for reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) data normalization and presence of RT-qPCR inhibitors (e.g. heparin) in patient blood samples have prevented reproducible miRNA quantification in this cohort and subsequent translation of these biomarkers to clinical practice.  Using a RT-qPCR miRNA screening platform, we identified and validated an endogenous circulating miRNA as a normalization control. In addition, we assessed the effects of in vivo and in vitro anticoagulant drugs administration (heparin and bivalirudin) on three RT-qPCR normalization strategies (global miRNA mean, exogenous spike-in control [cel-miR-39] and endogenous miRNA control). Finally, we evaluated the effect of heparin and its in vitro inhibition with heparinase on the quantification of cardiac-enriched miRNAs in STEMI patients.  miR-425-5p was validated as an endogenous miRNA control. Heparin administration in vitro and in vivo inhibited all RT-qPCR normalization strategies. In contrast, bivalirudin had no effects on cel-miR-39 or miR-425-5p quantification. In vitro RNA sample treatment with 0.3 U of heparinase overcame heparin-induced over-estimation of cardiac-enriched miRNA levels and improved their correlation with high-sensitivity troponin T.  miRNA quantification in STEMI patients receiving heparin is jeopardized by its effect on all RT-qPCR normalization approaches. Use of samples from bivalirudin-treated patients or in vitro treatment of heparin-contaminated samples with heparinase are suitable alternatives for miRNA quantification in this cohort. Finally, we reinforce the evidence that cardiac-enriched miRNAs early after myocardial reperfusion reflect the severity of cardiac injury. Schattauer GmbH Stuttgart.

Pelvic floor dysfunction--does menopause duration matter?

PubMed

Trutnovsky, Gerda; Guzman-Rojas, Rodrigo; Martin, Andrew; Dietz, Hans P

2013-10-01

To explore the effect of menopause and hormone replacement therapy on pelvic organ prolapse and pelvic floor muscle function. The records of patients who attended a tertiary urogynaecological center were reviewed retrospectively. A standardised interview included menopausal age, i.e. years since last period or onset of menopausal symptoms, current or previous hormone use. The clinical examination included prolapse assessment (POP-Q) and palpation of the levator ani muscle. 4D transperineal ultrasound, supine and after voiding, was performed in all patients. Volume data sets were analysed for pelvic organ descent and measures of contractility and distensibility of the pelvic floor at a later date, blinded to all clinical data. Of 311 women seen during the inclusion period, 65% were postmenopausal. Current systemic or local hormone use was reported by 7% and 6%, respectively. 163 women (52%) reported prolapse symptoms with a mean bother of 5.7/10. Significant pelvic organ prolapse was found on clinical examination (POP-Q stage≥2) in 77%, and diagnosed on ultrasound in 61%. On multivariate analysis, controlling for calendaric age, parity and levator avulsion, there was no evidence for menopausal age as an independent predictor of any symptom and sign of pelvic organ prolapse and pelvic floor muscle function. Local oestrogen use and past or present hormone replacement therapy had no detectable effect on any pelvic floor parameter. Hormone deficiency following menopause is unlikely to play a major role in pelvic organ support and levator ani function. Hence, both do not appear to be substantially influenced by local or systemic hormone replacement therapy. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Comparison of viable plate count, turbidity measurement and real-time PCR for quantification of Porphyromonas gingivalis.

PubMed

Clais, S; Boulet, G; Van Kerckhoven, M; Lanckacker, E; Delputte, P; Maes, L; Cos, P

2015-01-01

The viable plate count (VPC) is considered as the reference method for bacterial enumeration in periodontal microbiology but shows some important limitations for anaerobic bacteria. As anaerobes such as Porphyromonas gingivalis are difficult to culture, VPC becomes time-consuming and less sensitive. Hence, efficient normalization of experimental data to bacterial cell count requires alternative rapid and reliable quantification methods. This study compared the performance of VPC with that of turbidity measurement and real-time PCR (qPCR) in an experimental context using highly concentrated bacterial suspensions. Our TaqMan-based qPCR assay for P. gingivalis 16S rRNA proved to be sensitive and specific. Turbidity measurements offer a fast method to assess P. gingivalis growth, but suffer from high variability and a limited dynamic range. VPC was very time-consuming and less repeatable than qPCR. Our study concludes that qPCR provides the most rapid and precise approach for P. gingivalis quantification. Although our data were gathered in a specific research context, we believe that our conclusions on the inferior performance of VPC and turbidity measurements in comparison to qPCR can be extended to other research and clinical settings and even to other difficult-to-culture micro-organisms. Various clinical and research settings require fast and reliable quantification of bacterial suspensions. The viable plate count method (VPC) is generally seen as 'the gold standard' for bacterial enumeration. However, VPC-based quantification of anaerobes such as Porphyromonas gingivalis is time-consuming due to their stringent growth requirements and shows poor repeatability. Comparison of VPC, turbidity measurement and TaqMan-based qPCR demonstrated that qPCR possesses important advantages regarding speed, accuracy and repeatability. © 2014 The Society for Applied Microbiology.

Vaginal hysterectomy with apical fixation and anterior vaginal wall repair for prolapse: surgical technique and medium-term results.

PubMed

Marschke, Juliane; Pax, Carlo Michael; Beilecke, Kathrin; Schwab, Frank; Tunn, Ralf

2018-03-24

Stabilization of the vaginal apex (level 1) is an important component of operations to correct pelvic organ prolapse (POP). We report functional and anatomical results and patient-reported outcomes of our technique of vaginal vault fixation at the time of vaginal hysterectomy. One hundred and nine patients-mean 69 years, range 50.4-83.8; body mass index (BMI) 26.3, range 17.7-39.5-with symptomatic stage 2-3 uterine prolapse combined with stage 3-4 cystocele underwent vaginal hysterectomy with anterior vaginal wall repair; the apex was formed with high closure of the peritoneum and incorporation of the uterosacral and round ligaments. Only absorbable sutures were used. Follow-up included clinical examination with Pelvic Organ Prolapse Quantification system (POP-Q) scoring, introital ultrasonography, quality of life (QoL) Likert scale, and the German Pelvic Floor Questionnaire. Seventy patients (64%) were available for a follow-up after a mean of 2.8 years (range, 1.6-4.2). At follow-up, point C was stage 0 in 55 (78.6%) women and stage 1 in 15 (21.4%). The anterior vaginal wall was stage 0 or 1 in 35 (50%), stage 2 (no cystocele beyond the hymen) in 34 (49%), and stage 3 in 1 (1.4%). Vaginal length (VL) was 9 cm. Four women (4%) were reoperated for prolapse: two for recurrent anterior compartment prolapse and two for de novo rectocele. Postvoid residuals >150 ml were seen in 21(30%) patients preoperatively and resolved postoperatively in 20. Urgency occurred in nine (13%), stress urinary incontinence (SUI) in ten (14%), and nocturia in 19 (27%). No patient had discomfort at the vaginal vault and 62 patients (87%) reported improved QoL, which did not correlate with anatomical results. Cystocele ≥ 2° at follow-up was associated with BMI >25 (p = 0.03). Our surgical technique without permanent material offers good apical support and functional and subjective results. Anatomical improvement was achieved in all cases of cystocele repair. Recurrent cystoceles are often asymptomatic.

A retrospective comparison of two vaginal mesh kits in the management of anterior and apical vaginal prolapse: long-term results for apical fixation and quality of life.

PubMed

Lamblin, Gery; Gouttenoire, Chloé; Panel, Laure; Moret, Stéphanie; Chene, Gautier; Courtieu, Christophe

2016-12-01

To compare apical correction in stage ≥3 cystocele between two mesh kits. This was a retrospective, nonrandomized study that compared two groups matched on anterior/apical POP-Q stage: 84 received Elevate Ant™ single-incision mesh (Elevate Ant group) and 42 Perigee™ transvaginal mesh (Perigee group). Follow-up at 1 and 2 years comprised objective (POP-Q) and subjective (PFDI-20, PFIQ-7, PISQ-12) assessments. The primary endpoint was objective success: 2-year apical POP-Q stage ≤1. Secondary endpoints were anterior POP-Q stage, subjective results and complications. Groups were comparable in terms of age (66.6 and 64.7 years, respectively; p = 0.19), BMI (both 25.4 kg/m 2 ; p = 0.93), and history of hysterectomy (7.2 % and 14.3 %; p = 0.21) or prolapse surgery (12 % and 14.3 %; p = 0.72). Operative time was shorter in the Elevate Ant group (54.1 vs. 62.5 min; p = 0.048), and the 2-year objective apical success rate was higher (92.9 % vs. 66.7 %; p < 0.0001), with better point C correction (-5 vs. -3.8; p = 0.006). Function improved in both groups, with significantly better PFIQ-7 (p = 0.03) and PFDI-20 (p = 0.02) scores in the Elevate Ant group at 2 years. Vaginal exposure was not seen in the Elevate Ant group but occurred in two patients in the Perigee group (p = 0.33). Factors associated with success were age >65 years (OR 7.16, 95 % CI 1.83 - 27.97) and treatment with Elevate Ant mesh (OR 10.16, 95 % CI 2.78 - 37.14). Postoperative stress urinary incontinence rate was greater with the Elevate Ant group (29.8 % and 16.7 %; p = 0.11). The use of the Elevate Ant mesh was associated with significantly better apical correction at 2 years. Function improved in both groups, but with a significantly better PFDI-20 score in the Elevate Ant group at 1 and 2 years. The postoperative stress urinary incontinence rate, however, tended to be greater in the Elevate Ant group. The results need confirming with longer follow-up of these cohorts and in randomized studies.

Data for free--can an electronic medical record provide outcome data for incontinence/prolapse repair procedures?

PubMed

Steidl, Matthew; Zimmern, Philippe

2013-01-01

We determined whether a custom computer program can improve the extraction and accuracy of key outcome measures from progress notes in an electronic medical record compared to a traditional data recording system for incontinence and prolapse repair procedures. Following institutional review board approval, progress notes were exported from the Epic electronic medical record system for outcome measure extraction by a custom computer program. The extracted data (D1) were compared against a manually maintained outcome measures database (D2). This work took place in 2 phases. During the first phase, volatile data such as questionnaires and standardized physical examination findings using the POP-Q (pelvic organ prolapse quantification) system were extracted from existing progress notes. The second phase used a progress note template incorporating key outcome measures to evaluate improvement in data accuracy and extraction rates. Phase 1 compared 6,625 individual outcome measures from 316 patients in D2 to 3,534 outcome measures extracted from progress notes in D1, resulting in an extraction rate of 53.3%. A subset of 3,763 outcome measures from D1 was created by excluding data that did not exist in the extraction, yielding an accuracy rate of 93.9%. With the use of the template in phase 2, the extraction rate improved to 91.9% (273 of 297) and the accuracy rate improved to 100% (273 of 273). In the field of incontinence and prolapse, the disciplined use of an electronic medical record template containing a preestablished set of key outcome measures can provide the ideal interface between required documentation and clinical research. Copyright © 2013 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Determination of Sphingosine-1-Phosphate in Human Plasma Using Liquid Chromatography Coupled with Q-Tof Mass Spectrometry

PubMed Central

Egom, Emmanuel E.; Fitzgerald, Ross; Canning, Rebecca; Pharithi, Rebabonye B.; Murphy, Colin; Maher, Vincent

2017-01-01

Evidence suggests that high-density lipoprotein (HDL) components distinct from cholesterol, such as sphingosine-1-phosphate (S1P), may account for the anti-atherothrombotic effects attributed to this lipoprotein. The current method for the determination of plasma levels of S1P as well as levels associated with HDL particles is still cumbersome an assay method to be worldwide practical. Recently, a simplified protocol based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) for the sensitive and specific quantification of plasma levels of S1P with good accuracy has been reported. This work utilized a triple quadrupole (QqQ)-based LC-MS/MS system. Here we adapt that method for the determination of plasma levels of S1P using a quadrupole time of flight (Q-Tof) based LC-MS system. Calibration curves were linear in the range of 0.05 to 2 µM. The lower limit of quantification (LOQ) was 0.05 µM. The concentration of S1P in human plasma was determined to be 1 ± 0.09 µM (n = 6). The average accuracy over the stated range of the method was found to be 100 ± 5.9% with precision at the LOQ better than 10% when predicting the calibration standards. The concentration of plasma S1P in the prepared samples was stable for 24 h at room temperature. We have demonstrated the quantification of plasma S1P using Q-Tof based LC-MS with very good sensitivity, accuracy, and precision that can used for future studies in this field. PMID:28820460

Analytical Validation of Quantitative Real-Time PCR Methods for Quantification of Trypanosoma cruzi DNA in Blood Samples from Chagas Disease Patients

PubMed Central

Ramírez, Juan Carlos; Cura, Carolina Inés; Moreira, Otacilio da Cruz; Lages-Silva, Eliane; Juiz, Natalia; Velázquez, Elsa; Ramírez, Juan David; Alberti, Anahí; Pavia, Paula; Flores-Chávez, María Delmans; Muñoz-Calderón, Arturo; Pérez-Morales, Deyanira; Santalla, José; Guedes, Paulo Marcos da Matta; Peneau, Julie; Marcet, Paula; Padilla, Carlos; Cruz-Robles, David; Valencia, Edward; Crisante, Gladys Elena; Greif, Gonzalo; Zulantay, Inés; Costales, Jaime Alfredo; Alvarez-Martínez, Miriam; Martínez, Norma Edith; Villarroel, Rodrigo; Villarroel, Sandro; Sánchez, Zunilda; Bisio, Margarita; Parrado, Rudy; Galvão, Lúcia Maria da Cunha; da Câmara, Antonia Cláudia Jácome; Espinoza, Bertha; de Noya, Belkisyole Alarcón; Puerta, Concepción; Riarte, Adelina; Diosque, Patricio; Sosa-Estani, Sergio; Guhl, Felipe; Ribeiro, Isabela; Aznar, Christine; Britto, Constança; Yadón, Zaida Estela; Schijman, Alejandro G.

2015-01-01

An international study was performed by 26 experienced PCR laboratories from 14 countries to assess the performance of duplex quantitative real-time PCR (qPCR) strategies on the basis of TaqMan probes for detection and quantification of parasitic loads in peripheral blood samples from Chagas disease patients. Two methods were studied: Satellite DNA (SatDNA) qPCR and kinetoplastid DNA (kDNA) qPCR. Both methods included an internal amplification control. Reportable range, analytical sensitivity, limits of detection and quantification, and precision were estimated according to international guidelines. In addition, inclusivity and exclusivity were estimated with DNA from stocks representing the different Trypanosoma cruzi discrete typing units and Trypanosoma rangeli and Leishmania spp. Both methods were challenged against 156 blood samples provided by the participant laboratories, including samples from acute and chronic patients with varied clinical findings, infected by oral route or vectorial transmission. kDNA qPCR showed better analytical sensitivity than SatDNA qPCR with limits of detection of 0.23 and 0.70 parasite equivalents/mL, respectively. Analyses of clinical samples revealed a high concordance in terms of sensitivity and parasitic loads determined by both SatDNA and kDNA qPCRs. This effort is a major step toward international validation of qPCR methods for the quantification of T. cruzi DNA in human blood samples, aiming to provide an accurate surrogate biomarker for diagnosis and treatment monitoring for patients with Chagas disease. PMID:26320872

Pelvic floor dysfunction in the immediate puerperium, and 1 month and 3 months after vaginal or cesarean delivery.

PubMed

Colla, Cássia; L Paiva, Luciana; Ferla, Lia; B Trento, Maria J; M P de Vargas, Isadora; A Dos Santos, Bianca; Ferreira, Charles F; L Ramos, José G

2018-06-07

To identify and assess postpartum pelvic floor dysfunction (PFD) between vaginal delivery, elective cesarean delivery (ECD), and intrapartum cesarean delivery (ICD). The present prospective observational study included women aged at least 18 years with no history of pelvic surgery or lower urinary tract malformation, and who had not undergone pelvic floor muscle (PFM) training in the preceding 12 months, who underwent delivery at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil between August 1, 2016, and May 31, 2017. Participants were assessed at 48 hours (phase 1), 1 month (phase 2), and 3 months (phase 3) after delivery. Assessments included the International Consultation on Incontinence Questionnaire, Short Form (ICIQ-SF); the Jorge-Wexner anal incontinence scale; a self-rated visual analog scale for pelvic pain; the pelvic organ prolapse quantification (POP-Q) system; and a PFM perineometer. A total of 227 women were assessed in phase 1 (141 vaginal deliveries; 28 ICDs; and 58 ECDs), 79 in phase 2, and 41 in phase 3. The ICIQ-SF, Jorge-Wexner scale, visual analog scale, and perineometer measurements did not identify significant differences in relation to the type of delivery (P>0.05). The type of delivery was not associated with differences in the short-term development of postpartum PFD. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

U.S. EPA, Pesticide Product Label, DIURON MUP, 06/20/2007

EPA Pesticide Factsheets

2011-04-21

... tl:J.~''' L'B )'\\:iri'.-:.I.lnE~!o"i~·'·· I'~'n',;,:t.!,~. uec 'i,;joc~lclru.Ao:., I co!. :;.y,.,..J':"Q ..... j L~:' tl'-~ pop,i:c~ J'o':.,istc?((: ~1!..c-+ ... l..h~~~".p.~-I'I2. I ...

Quantification of sterol lipids in plants by quadrupole time-of-flight mass spectrometry

PubMed Central

Wewer, Vera; Dombrink, Isabel; vom Dorp, Katharina; Dörmann, Peter

2011-01-01

Glycerolipids, sphingolipids, and sterol lipids constitute the major lipid classes in plants. Sterol lipids are composed of free and conjugated sterols, i.e., sterol esters, sterol glycosides, and acylated sterol glycosides. Sterol lipids play crucial roles during adaption to abiotic stresses and plant-pathogen interactions. Presently, no comprehensive method for sterol lipid quantification in plants is available. We used nanospray ionization quadrupole-time-of-flight mass spectrometry (Q-TOF MS) to resolve and identify the molecular species of all four sterol lipid classes from Arabidopsis thaliana. Free sterols were derivatized with chlorobetainyl chloride. Sterol esters, sterol glycosides, and acylated sterol glycosides were ionized as ammonium adducts. Quantification of molecular species was achieved in the positive mode after fragmentation in the presence of internal standards. The amounts of sterol lipids quantified by Q-TOF MS/MS were validated by comparison with results obtained with TLC/GC. Quantification of sterol lipids from leaves and roots of phosphate-deprived A. thaliana plants revealed changes in the amounts and molecular species composition. The Q-TOF method is far more sensitive than GC or HPLC. Therefore, Q-TOF MS/MS provides a comprehensive strategy for sterol lipid quantification that can be adapted to other tandem mass spectrometers. PMID:21382968

Transport of persistent organic pollutants by microplastics in estuarine conditions

NASA Astrophysics Data System (ADS)

Bakir, Adil; Rowland, Steven J.; Thompson, Richard C.

2014-03-01

Microplastics represent an increasing source of anthropogenic contamination in aquatic environments, where they may also act as scavengers and transporters of persistent organic pollutants. As estuaries are amongst the most productive aquatic systems, it is important to understand sorption behaviour and transport of persistent organic pollutants (POPs) by microplastics along estuarine gradients. The effects of salinity sorption equilibrium kinetics on the distribution coefficients (Kd) of phenanthrene (Phe) and 4,4‧-DDT, onto polyvinyl chloride (PVC) and onto polyethylene (PE) were therefore investigated. A salinity gradient representing freshwater, estuarine and marine conditions, with salinities corresponding to 0 (MilliQ water, 690 μS/cm), 8.8, 17.5, 26.3 and 35 was used. Salinity had no significant effect on the time required to reach equilibrium onto PVC or PE and neither did it affect desorption rates of contaminants from plastics. Although salinity had no effect on sorption capacity of Phe onto plastics, a slight decrease in sorption capacity was observed for DDT with salinity. Salinity had little effect on sorption behaviour and POP/plastic combination was shown to be a more important factor. Transport of Phe and DDT from riverine to brackish and marine waters by plastic is therefore likely to be much more dependent on the aqueous POP concentration than on salinity. The physical characteristics of the polymer and local environmental conditions (e.g. plastic density, particle residence time in estuaries) will affect the physical transport of contaminated plastics. A transport model of POPs by microplastics under estuarine conditions is proposed. Transport of Phe and DDT by PVC and PE from fresh and brackish water toward fully marine conditions was the most likely net direction for contaminant transport and followed the order: Phe-PE >> DDT-PVC = DDT-PE >> Phe-PVC.

Static Mechanical Loading Influences the Expression of Extracellular Matrix and Cell Adhesion Proteins in Vaginal Cells Derived From Premenopausal Women With Severe Pelvic Organ Prolapse.

PubMed

Kufaishi, Hala; Alarab, May; Drutz, Harold; Lye, Stephen; Shynlova, Oksana

2016-08-01

Primary human vaginal cells derived from women with severe pelvic organ prolapse (POP-HVCs) demonstrate altered cellular characteristics as compared to cells derived from asymptomatic women (control-HVCs). Using computer-controllable Flexcell stretch unit, we examined whether POP-HVCs react differently to mechanical loading as compared to control-HVCs by the expression of extracellular matrix (ECM) components, cell-ECM adhesion proteins, and ECM degrading and maturating enzymes. Vaginal tissue biopsies from premenopausal patients with Pelvic Organ Prolapse Quantification System stage ≥3 (n = 8) and asymptomatic controls (n = 7) were collected during vaginal hysterectomy or repair. Human vaginal cells were isolated by enzymatic digestion, seeded on collagen (COLI)-coated plates, and stretched (24 hours, 25% elongation). Total RNA was extracted, and 84 genes were screened using Human ECM and Adhesion Molecules polymerase chain reaction array; selected genes were verified by quantitative reverse transcription-polymerase chain reaction. Stretch-conditioned media (SCM) were collected and analyzed by protein array, immunoblotting, and zymography. In mechanically stretched control-HVCs, transcript levels of integrins (ITGA1, ITGA4, ITGAV, and ITGB1) and matrix metalloproteinases (MMPs) 2, 8, and 13 were downregulated (P < .05); in POP-HVCs, MMP1, MMP3, and MMP10, ADAMTS8 and 13, tissue inhibitor of metalloproteinases (TIMPs) 1 to 3, ITGA2, ITGA4, ITGA6, ITGB1, contactin (CNTN1), catenins (A1 and B1), and laminins (A3 and C1) were significantly upregulated, whereas COLs (1, 4, 5, 6, 11, and 12) and LOXL1 were downregulated. Human vaginal cells massively secrete MMPs and TIMPs proteins; MMP1, MMP8, MMP9 protein expression and MMP2 gelatinase activity were increased, whereas TIMP2 decreased in SCM from POP-HVCs compared to control-HVCs. Primary human vaginal cells derived from women with severe pelvic organ prolapse and control-HVCs react differentially to in vitro mechanical stretch. Risk factors that induce stretch may alter ECM composition and cell-ECM interaction in pelvic floor tissue leading to the abatement of pelvic organ support and subsequent POP development. © The Author(s) 2016.

qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Christopher B., E-mail: Christopher.jackson@insel.ch; Gallati, Sabina, E-mail: sabina.gallati@insel.ch; Schaller, Andre, E-mail: andre.schaller@insel.ch

2012-07-06

Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serialmore » qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two genomes is demonstrated and which evaluates systematically the impact of DNA degradation on quantification of mtDNA copy number.« less

The Physics of Popping Corn.

ERIC Educational Resources Information Center

Hunt, Robert G.

1991-01-01

Presents a framework for teachers to use the thermodynamic system of popping corn to generate student interest. Examines the popping mechanism and the role of steam in, the heat required during, and the energy efficiency of the popping process. (MDH)

Detection and Quantification of Viable and Nonviable Trypanosoma cruzi Parasites by a Propidium Monoazide Real-Time Polymerase Chain Reaction Assay

PubMed Central

Cancino-Faure, Beatriz; Fisa, Roser; Alcover, M. Magdalena; Jimenez-Marco, Teresa; Riera, Cristina

2016-01-01

Molecular techniques based on real-time polymerase chain reaction (qPCR) allow the detection and quantification of DNA but are unable to distinguish between signals from dead or live cells. Because of the lack of simple techniques to differentiate between viable and nonviable cells, the aim of this study was to optimize and evaluate a straightforward test based on propidium monoazide (PMA) dye action combined with a qPCR assay (PMA-qPCR) for the selective quantification of viable/nonviable epimastigotes of Trypanosoma cruzi. PMA has the ability to penetrate the plasma membrane of dead cells and covalently cross-link to the DNA during exposure to bright visible light, thereby inhibiting PCR amplification. Different concentrations of PMA (50–200 μM) and epimastigotes of the Maracay strain of T. cruzi (1 × 105–10 parasites/mL) were assayed; viable and nonviable parasites were tested and quantified by qPCR with a TaqMan probe specific for T. cruzi. In the PMA-qPCR assay optimized at 100 μM PMA, a significant qPCR signal reduction was observed in the nonviable versus viable epimastigotes treated with PMA, with a mean signal reduction of 2.5 logarithm units and a percentage of signal reduction > 98%, in all concentrations of parasites assayed. This signal reduction was also observed when PMA-qPCR was applied to a mixture of live/dead parasites, which allowed the detection of live cells, except when the concentration of live parasites was low (10 parasites/mL). The PMA-qPCR developed allows differentiation between viable and nonviable epimastigotes of T. cruzi and could thus be a potential method of parasite viability assessment and quantification. PMID:27139452

PopF1 and PopF2, Two Proteins Secreted by the Type III Protein Secretion System of Ralstonia solanacearum, Are Translocators Belonging to the HrpF/NopX Family†

PubMed Central

Meyer, Damien; Cunnac, Sébastien; Guéneron, Mareva; Declercq, Céline; Van Gijsegem, Frédérique; Lauber, Emmanuelle; Boucher, Christian; Arlat, Matthieu

2006-01-01

Ralstonia solanacearum GMI1000 is a gram-negative plant pathogen which contains an hrp gene cluster which codes for a type III protein secretion system (TTSS). We identified two novel Hrp-secreted proteins, called PopF1 and PopF2, which display similarity to one another and to putative TTSS translocators, HrpF and NopX, from Xanthomonas spp. and rhizobia, respectively. They also show similarities with TTSS translocators of the YopB family from animal-pathogenic bacteria. Both popF1 and popF2 belong to the HrpB regulon and are required for the interaction with plants, but PopF1 seems to play a more important role in virulence and hypersensitive response (HR) elicitation than PopF2 under our experimental conditions. PopF1 and PopF2 are not necessary for the secretion of effector proteins, but they are required for the translocation of AvrA avirulence protein into tobacco cells. We conclude that PopF1 and PopF2 are type III translocators belonging to the HrpF/NopX family. The hrpF gene of Xanthomonas campestris pv. campestris partially restored HR-inducing ability to popF1 popF2 mutants of R. solanacearum, suggesting that translocators of R. solanacearum and Xanthomonas are functionally conserved. Finally, R. solanacearum strain UW551, which does not belong to the same phylotype as GMI1000, also possesses two putative translocator proteins. However, although one of these proteins is clearly related to PopF1 and PopF2, the other seems to be different and related to NopX proteins, thus showing that translocators might be variable in R. solanacearum. PMID:16788199

Management Engineering Team Application of Officer Grade Requirements Method.

DTIC Science & Technology

1980-12-01

td l sti h ’tI i I111 I m~ tA fo~i l~vlAld ltllt% 11",1 01i All ipil ll ppi lt d I hC AlAd dIA fact* I 1 IVIICA the 11 Ill* 1 cI 1Al 1. 10110I...tiaftSuperviso OAFSC Date Lt 02 Pop4gI75-o.P.Q-j2Q&A=Ma4-54, l53 AF OFFICER POSITION DESCRIPTION 30 Instructions to Incumbent To: Designated Officer 1. As

Legionella detection by culture and qPCR: Comparing apples and oranges.

PubMed

Whiley, Harriet; Taylor, Michael

2016-01-01

Legionella spp. are the causative agent of Legionnaire's disease and an opportunistic pathogen of significant public health concern. Identification and quantification from environmental sources is crucial for identifying outbreak origins and providing sufficient information for risk assessment and disease prevention. Currently there are a range of methods for Legionella spp. quantification from environmental sources, but the two most widely used and accepted are culture and real-time polymerase chain reaction (qPCR). This paper provides a review of these two methods and outlines their advantages and limitations. Studies from the last 10 years which have concurrently used culture and qPCR to quantify Legionella spp. from environmental sources have been compiled. 26/28 studies detected Legionella at a higher rate using qPCR compared to culture, whilst only one study detected equivalent levels of Legionella spp. using both qPCR and culture. Aggregating the environmental samples from all 28 studies, 2856/3967 (72%) tested positive for the presence of Legionella spp. using qPCR and 1331/3967 (34%) using culture. The lack of correlation between methods highlights the need to develop an acceptable standardized method for quantification that is sufficient for risk assessment and management of this human pathogen.

Digital Droplet PCR: CNV Analysis and Other Applications.

PubMed

Mazaika, Erica; Homsy, Jason

2014-07-14

Digital droplet PCR (ddPCR) is an assay that combines state-of-the-art microfluidics technology with TaqMan-based PCR to achieve precise target DNA quantification at high levels of sensitivity and specificity. Because quantification is achieved without the need for standard assays in an easy to interpret, unambiguous digital readout, ddPCR is far simpler, faster, and less error prone than real-time qPCR. The basic protocol can be modified with minor adjustments to suit a wide range of applications, such as CNV analysis, rare variant detection, SNP genotyping, and transcript quantification. This unit describes the ddPCR workflow in detail for the Bio-Rad QX100 system, but the theory and data interpretation are generalizable to any ddPCR system. Copyright © 2014 John Wiley & Sons, Inc.

Validated reverse transcription droplet digital PCR serves as a higher order method for absolute quantification of Potato virus Y strains.

PubMed

Mehle, Nataša; Dobnik, David; Ravnikar, Maja; Pompe Novak, Maruša

2018-05-03

RNA viruses have a great potential for high genetic variability and rapid evolution that is generated by mutation and recombination under selection pressure. This is also the case of Potato virus Y (PVY), which comprises a high diversity of different recombinant and non-recombinant strains. Consequently, it is hard to develop reverse transcription real-time quantitative PCR (RT-qPCR) with the same amplification efficiencies for all PVY strains which would enable their equilibrate quantification; this is specially needed in mixed infections and other studies of pathogenesis. To achieve this, we initially transferred the PVY universal RT-qPCR assay to a reverse transcription droplet digital PCR (RT-ddPCR) format. RT-ddPCR is an absolute quantification method, where a calibration curve is not needed, and it is less prone to inhibitors. The RT-ddPCR developed and validated in this study achieved a dynamic range of quantification over five orders of magnitude, and in terms of its sensitivity, it was comparable to, or even better than, RT-qPCR. RT-ddPCR showed lower measurement variability. We have shown that RT-ddPCR can be used as a reference tool for the evaluation of different RT-qPCR assays. In addition, it can be used for quantification of RNA based on in-house reference materials that can then be used as calibrators in diagnostic laboratories.

Sexual function in women following transvaginal mesh procedures for the treatment of pelvic organ prolapse.

PubMed

Liang, Ching-Chung; Lo, Tsia-Shu; Tseng, Ling-Hong; Lin, Yi-Hao; Lin, Yu-Jr; Chang, Shuenn-Dhy

2012-10-01

Synthetic mesh kits recently adopted in pelvic reconstructive surgeries have achieved great surgical efficacy, but the effects of transvaginal synthetic mesh procedures on women's sexual function are still controversial. This study was conducted to demonstrate sexual function in women before and after surgery with transvaginal mesh (TVM) repair for pelvic organ prolapse (POP). A total of 93 sexually active women scheduled for correcting POP with synthetic mesh kits were recruited. In addition to urogynecological history, pelvic examination by the Pelvic Organ Prolapse Quantification system, and urodynamic testing, consenting participants were asked to complete the Pelvic Organ Prolapse/Urinary Incontinence Sexual Questionnaire (PISQ-12) to evaluate sexual function before and after surgery. At the 3-month urodynamic studies, among the 25 patients with coexistent urodynamic stress incontinence (USI) who had undergone a concomitant transobturator suburethral tape procedure (TOT), 1 (4 %) had persistent USI; 8 of 68 (11.8 %) patients with a negative pessary test developed postoperative USI. Six-month prolapse recurrence rates following TVM alone and TVM with concomitant TOT were 9 and 12 %, respectively. The total PISQ-12 score after surgery showed worse results in the TVM alone group but not in the TVM with concomitant TOT group. The individual scores of PISQ-12 after surgery demonstrated prolapse-related items improved in both TVM groups; sexual function worsened in dyspareunia and behavior domains. Our data revealed that transvaginal synthetic mesh procedures for the treatment of POP generated favorable clinical outcomes, but situations might worsen in dyspareunia and behavior domains, thereby invoking a negative emotional reaction during intercourse after surgery.

Development of a rapid method to quantify Salmonella Typhimurium using a combination of MPN with qPCR and a shortened time incubation.

PubMed

Kim, Sun Ae; Park, Si Hong; Lee, Sang In; Ricke, Steven C

2017-08-01

A novel method was developed for the specific quantification of S. Typhimurium using a most-probable-number (MPN) combined with qPCR and a shortened incubation time (MPN-qPCR-SIT). For S. Typhimurium enumeration, dilutions of samples were transferred into three wells on a microtiter plate and the plate was incubated for 4 h. The S. Typhimurium presence in the wells was identified using a qPCR and populations were determined based on an MPN calculation. The R 2 between the MPN-qPCR-SIT and conventional MPN exhibited a high level of correlation (0.9335-0.9752), suggesting that the MPN-qPCR-SIT offers a reliable alternative method for S. Typhimurium quantification. Although plating and qPCR were limited in their ability to detect low levels of S. Typhimurium (e.g. 0.18 log MPN/ml), these levels could be successfully detected with the MPN-qPCR-SIT. Chicken breast samples inoculated with S. Typhimurium were incubated at 0, 4, and 24 h and incubated samples were subjected to microbiome analysis. Levels of Salmonella and Enterobacteriaceae increased significantly with incubation time. The obvious benefits of the MPN-qPCR-SIT are: 1) a further confirmation step is not required, 2) the detection limit is as low as conventional MPN, but 3) is more rapid, requiring approximately 7 h to simultaneously complete quantification. Copyright © 2017 Elsevier Ltd. All rights reserved.

Prevalence of Hydronephrosis in Women With Advanced Pelvic Organ Prolapse.

PubMed

Dancz, Christina E; Walker, Daphne; Thomas, Diane; Özel, Begüm

2015-08-01

To describe the prevalence of hydronephrosis in advanced pelvic organ prolapse (POP) and to describe clinical and urodynamic parameters associated with hydronephrosis. Prospective, observational cohort study examining the prevalence of hydronephrosis in advanced POP. Women with a POP-Q examination of at least +1 for points C, Aa, or Ba were enrolled and screened for hydronephrosis. Basic demographics, clinical, and urodynamic findings among women with and without hydronephrosis were compared. The University of Southern California IRB approved this protocol. A total of 180 participants were enrolled. Fifty-five women had some hydronephrosis, for a prevalence of 30.6% (24.3%-37.6%). Mean age was 57.9 (±9.0) years and mean body mass index was 29.2 kg/m(2) (± 4.6). Of the participants, 80.6% were postmenopausal. The presence of diabetes mellitus was significantly associated with hydronephrosis (8% without vs 21.8% with, P = .009), as was the degree of anterior and apical (median Aa, Ba, C, and D higher with hydronephrosis than without, P <.01) but not posterior POP (median Ap and Bp, P = .13, and .2, respectively). On multichannel urodynamics, participants with hydronephrosis had higher mean post void residuals (64.8 vs 38.5 mL, P = .007), lower mean first leak (199.6 vs 280.8 mL, P = .006), and higher mean maximum cystometric capacity (525.2 vs 476.7 mL, P = .02) compared with participants without hydronephrosis. The prevalence of hydronephrosis in women with advanced POP is 30.6%. Clinical factors associated with hydronephrosis include degree of anterior or apical POP and diabetes mellitus. Urodynamic factors associated with hydronephrosis include elevated postvoid residuals, larger cystometric capacity, and lower volume at first leak. Copyright © 2015 Elsevier Inc. All rights reserved.

Review and Recommendations for the Interagency Ship Structure Committee’s Fiscal 1980 Research Program

DTIC Science & Technology

1979-03-01

fracture-toughness tests and material performance in ships. Fracture criteria remains a field that resists satisfactory quantification, yet it is a...identical conditions of temperature, loading rate, and test material . Specimen configurations (e.g. bend and tensile), specimen dimensions, load train...compliance, and material characteristics should be systematically varied. In each test the specimen should be unloaded immediately after pop- in and the

Specific metabolic activity of ripening bacteria quantified by real-time reverse transcription PCR throughout Emmental cheese manufacture.

PubMed

Falentin, Hélène; Postollec, Florence; Parayre, Sandrine; Henaff, Nadine; Le Bivic, Pierre; Richoux, Romain; Thierry, Anne; Sohier, Danièle

2010-11-15

Bacterial communities of fermented foods are usually investigated by culture-dependent methods. Real-time quantitative PCR (qPCR) and reverse transcription (RT)-qPCR offer new possibilities to quantify the populations present and their metabolic activity. The aim of this work was to develop qPCR and RT-qPCR methods to assess the metabolic activity and the stress level of the two species used as ripening cultures in Emmental cheese manufacture, Propionibacterium freudenreichii and Lactobacillus paracasei. Three small scale (1/100) microbiologically controlled Emmental cheeses batches were manufactured and inoculated with Lactobacillus helveticus, Streptococcus thermophilus, P. freudenreichii and L. paracasei. At 12 steps of cheese manufacture and ripening, the populations of P. freudenreichii and L. paracasei were quantified by numerations on agar media and by qPCR. 16S, tuf and groL transcript levels were quantified by RT-qPCR. Sampling was carried out in triplicate. qPCR and RT-qPCR assessments were specific, efficient and linear. The quantification limit was 10(3) copies of cells or cDNA/g of cheese. Cell quantifications obtained by qPCR gave similar results than plate count for P. freudenreichii growth and 0.5 to 1 log lower in the stationary phase. Bacterial counts and qPCR quantifications showed that L. paracasei began to grow during the pressing step while P. freudenreichii began to grow from the beginning of ripening (in the cold room). Tuf cDNA quantification results suggested that metabolic activity of L. paracasei reached a maximum during the first part of the ripening (in cold room) and decreased progressively during ripening (in the warm room). Metabolic activity of P. freudenreichii was maximum at the end of cold ripening room and was stable during the first two weeks in warm room. After lactate exhaustion (after two weeks of warm room), the number of tuf cDNA decreased reflecting reduced metabolic activity. For L. paracasei, groL cDNA were stable during ripening. For P. freudenreichii, groL1 gene was highly-expressed during acidification, while groL2 gene highly expression was only observed at the end of the ripening stage after lactate (carbon substrate of P. freudenreichii) exhaustion. The potential use of 16S and tuf genes for the normalization of cDNA quantification throughout an Emmental cheese manufacture is discussed. For the first time, specific gene expression was performed by RT-qPCR yielding metabolic activity and stress response evaluation for L. paracasei and P. freudenreichii in cheese. Copyright © 2010 Elsevier B.V. All rights reserved.

NQO1 and CYP450 reductase decrease the systemic exposure of rifampicin-quinone and mediate its redox cycle in rats.

PubMed

Shi, Fuguo; Li, Xiaobing; Pan, Hong; Ding, Li

2017-01-05

Rifampicin (RIF) is used in regimens for infections caused by Mycobacteria accompanied by serious adverse reactions. Rifampicin-quinone (RIF-Q) is a major autoxidation product of RIF. It is not clear whether RIF-Q plays a role in RIF induced adverse reactions. Investigation of the systemic exposure of RIF-Q is helpful to better understand the role of RIF-Q in RIF induced adverse reactions. In this study, a simple and reproducible high performance liquid chromatography-mass spectrometry (LC-MS) method involving a procedure to prevent the RIF from oxidation for simultaneous quantification of RIF and RIF-Q in rat plasma has been developed and validated, and applied to elucidate the systemic exposure of RIF-Q in rats. The pharmacokinetics data showed that the systemic exposure of RIF-Q was very low (0.67% of RIF, AUC 0-24 ) in rats after oral administration of RIF. However, RIF-Q may undergo the redox cycle in vivo by the evidence that the majority of RIF-Q was reduced to RIF after an oral dose of RIF-Q. Pretreatment with the NAD(P)H: quinone oxidoreductase 1 (NQO1) specific inhibitor dicoumarol and/or cytochrome P450 reductase (CPR) inhibitor diphenyleneiodonium suppressed the redox cycle and significantly increased the systemic exposure of RIF-Q. The inhibitors also attenuated the redox cycle induced reactive oxygen species formation and cytotoxicity in RIF-Q-treated HepG2 cells. These results indicate that NQO1 and CPR play an important role in redox cycle of RIF-Q and may thus contribute to RIF-induced adverse reactions. Copyright © 2016 Elsevier B.V. All rights reserved.

Q&A: The space crusader

NASA Astrophysics Data System (ADS)

Cowen, Ron

2014-05-01

US astronomer Neil deGrasse Tyson, director of New York's Hayden Planetarium, currently hosts the television series Cosmos -- an update of Carl Sagan's 1980 show -- broadcast in 181 countries and 45 languages. As it winds down, Tyson talks about the rich mix of science and pop culture, the 'neurosynaptic snapshot' of public responses to his tweets, and his momentous meeting with Sagan.

A Systems Biology Approach Reveals Converging Molecular Mechanisms that Link Different POPs to Common Metabolic Diseases.

PubMed

Ruiz, Patricia; Perlina, Ally; Mumtaz, Moiz; Fowler, Bruce A

2016-07-01

A number of epidemiological studies have identified statistical associations between persistent organic pollutants (POPs) and metabolic diseases, but testable hypotheses regarding underlying molecular mechanisms to explain these linkages have not been published. We assessed the underlying mechanisms of POPs that have been associated with metabolic diseases; three well-known POPs [2,3,7,8-tetrachlorodibenzodioxin (TCDD), 2,2´,4,4´,5,5´-hexachlorobiphenyl (PCB 153), and 4,4´-dichlorodiphenyldichloroethylene (p,p´-DDE)] were studied. We used advanced database search tools to delineate testable hypotheses and to guide laboratory-based research studies into underlying mechanisms by which this POP mixture could produce or exacerbate metabolic diseases. For our searches, we used proprietary systems biology software (MetaCore™/MetaDrug™) to conduct advanced search queries for the underlying interactions database, followed by directional network construction to identify common mechanisms for these POPs within two or fewer interaction steps downstream of their primary targets. These common downstream pathways belong to various cytokine and chemokine families with experimentally well-documented causal associations with type 2 diabetes. Our systems biology approach allowed identification of converging pathways leading to activation of common downstream targets. To our knowledge, this is the first study to propose an integrated global set of step-by-step molecular mechanisms for a combination of three common POPs using a systems biology approach, which may link POP exposure to diseases. Experimental evaluation of the proposed pathways may lead to development of predictive biomarkers of the effects of POPs, which could translate into disease prevention and effective clinical treatment strategies. Ruiz P, Perlina A, Mumtaz M, Fowler BA. 2016. A systems biology approach reveals converging molecular mechanisms that link different POPs to common metabolic diseases. Environ Health Perspect 124:1034-1041; http://dx.doi.org/10.1289/ehp.1510308.

Sampling and Pooling Methods for Capturing Herd Level Antibiotic Resistance in Swine Feces using qPCR and CFU Approaches

PubMed Central

Mellerup, Anders; Ståhl, Marie

2015-01-01

The aim of this article was to define the sampling level and method combination that captures antibiotic resistance at pig herd level utilizing qPCR antibiotic resistance gene quantification and culture-based quantification of antibiotic resistant coliform indicator bacteria. Fourteen qPCR assays for commonly detected antibiotic resistance genes were developed, and used to quantify antibiotic resistance genes in total DNA from swine fecal samples that were obtained using different sampling and pooling methods. In parallel, the number of antibiotic resistant coliform indicator bacteria was determined in the same swine fecal samples. The results showed that the qPCR assays were capable of detecting differences in antibiotic resistance levels in individual animals that the coliform bacteria colony forming units (CFU) could not. Also, the qPCR assays more accurately quantified antibiotic resistance genes when comparing individual sampling and pooling methods. qPCR on pooled samples was found to be a good representative for the general resistance level in a pig herd compared to the coliform CFU counts. It had significantly reduced relative standard deviations compared to coliform CFU counts in the same samples, and therefore differences in antibiotic resistance levels between samples were more readily detected. To our knowledge, this is the first study to describe sampling and pooling methods for qPCR quantification of antibiotic resistance genes in total DNA extracted from swine feces. PMID:26114765

Quantitative detection of antibiotic resistance genes using magnetic/luminescent core-shell nanoparticles

NASA Astrophysics Data System (ADS)

Son, Ahjeong; Hristova, Krassimira R.; Dosev, Dosi; Kennedy, Ian M.

2008-02-01

Nanoscale magnetic/luminescent core-shell particles were used for DNA quantification in a hybridization-in-solution format. We demonstrated a simple, high-throughput, and non-PCR based DNA assay for quantifying antibiotic resistance gene tetQ. Fe 3O 4/Eu:Gd IIO 3 nanoparticles (NPs) synthesized by spray pyrolysis were biofunctionalized by passive adsorption of NeutrAvidin. Following immobilization of biotinylated probe DNA on the particles' surfaces, target dsDNA and signaling probe DNA labeled with Cy3 were hybridized with NPs-probe DNA. Hybridized DNA complexes were separated from solution by a magnet, while non-hybridized DNA remained in solution. A linear quantification (R2 = 0.99) of a target tetQ gene was achieved based on the normalized fluorescence (Cy3/NPs) of DNANP hybrids. A real-time qPCR assay was used for evaluation of the NPs assay sensitivity and range of quantification. The quantity of antibiotic resistance tetQ genes in activated sludge microcosms, with and without addition of tetracycline or triclosan has been determined, indicating the potential of the optimized assay for monitoring the level of antibiotic resistance in environmental samples. In addition, the tetQ gene copy numbers in microcosms determined by NPhybridization were well correlated with the numbers measured by real-time qPCR assay (R2 = 0.92).

Effect of simple and radical hysterectomy on quality of life - analysis of all aspects of pelvic floor dysfunction.

PubMed

Selcuk, Selcuk; Cam, Cetin; Asoglu, Mehmet Resit; Kucukbas, Mehmet; Arinkan, Arzu; Cikman, Muzaffer Seyhan; Karateke, Ates

2016-03-01

The impact of simple and radical hysterectomy on all aspects of pelvic floor dysfunctions was evaluated in current study. This retrospective cohort study included 142 patients; 58 women (40.8%) who have undergone simple, 41 (28.8%) radical hysterectomy, and 43 (30.2%) women without any surgical intervention to serve as the control group. The validated versions of the Urogenital Distress Inventory (UDI-6), Incontinence Impact Questionnaire (IIQ-7), Pelvic Floor and Incontinence Sexual Impact Questionnaire (PISQ-12), Wexner Incontinence Scale score and pelvic organ prolapse quantification (POP-Q) system were used in detailed evaluation of pelvic floor dysfunction. One-way ANOVA and Pearson's chi square tests were performed in statistical analysis. It was found that there were significant differences in irritative and obstructive scores of UDI-6 between Type III hysterectomy group and Type I hysterectomy group. In addition, patients of Type I hysterectomy had significant higher irritative and obstructive scores than the control group. Type III hysterectomy had the most significant deteriorating effect on sexual life, based on scores of PISQ-12 compared to both Type I hysterectomy group and control group. Hysterectomy results in detrimental effects on the quality of life (QoL) regarding all aspects of pelvic floor functions especially in women of radical hysterectomy. Urinary dysfunctional symptoms like urgency, obstruction and especially sexual problems are more bothersome and difficult to overcome. The impact of hysterectomy on QoL should be investigated as a whole and may be more profound than previously thought. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Overestimation of the Legionella spp. load in environmental samples by quantitative real-time PCR: pretreatment with propidium monoazide as a tool for the assessment of an association between Legionella concentration and sanitary risk.

PubMed

Ditommaso, Savina; Ricciardi, Elisa; Giacomuzzi, Monica; Arauco Rivera, Susan R; Ceccarelli, Adriano; Zotti, Carla M

2014-12-01

Quantitative polymerase chain reaction (qPCR) offers rapid, sensitive, and specific detection of Legionella in environmental water samples. In this study, qPCR and qPCR combined with propidium monoazide (PMA-qPCR) were both applied to hot-water system samples and compared to traditional culture techniques. In addition, we evaluated the ability of PMA-qPCR to monitor the efficacy of different disinfection strategies. Comparison between the quantification obtained by culture and by qPCR or PMA-qPCR on environmental water samples confirms that the concentration of Legionella estimated by GU/L is generally higher than that estimated in CFU/L. Our results on 57 hot-water-system samples collected from 3 different sites show that: i) qPCR results were on average 178-fold higher than the culture results (Δ log10=2.25), ii) PMA-qPCR results were on average 27-fold higher than the culture results (Δ log10=1.43), iii) propidium monoazide-induced signal reduction in qPCR were nearly 10-fold (Δ log10=0.95), and that iv) different degrees of correlations between the 3 methods might be explained by different matrix properties, but also by different disinfection methods affecting cultivability of Legionella. In our study, we calculated the logarithmic differences between the results obtained by PMA-qPCR and those obtained by culture, and we suggested an algorithm for the interpretation of PMA-qPCR results for the routine monitoring of healthcare water systems using a commercial qPCR system (iQ-check real-time PCR kit; Bio-Rad, Marnes-la-Coquette, France). Copyright © 2014 Elsevier Inc. All rights reserved.

[Performance evaluation of Abbott RealTime HBV Quantification Kit for HBV viral load by real-time PCR].

PubMed

Kim, Myeong Hee; Cha, Choong Hwan; An, Dongheui; Choi, Sung Eun; Oh, Heung Bum

2008-04-01

Hepatitis B virus (HBV) DNA quantification is necessary for starting and monitoring of antiviral therapy in patients with chronic hepatitis B. This study was intended to assess the clinical performance of Abbott RealTime HBV Quantification kit (Abbott Laboratories, USA). The performance was evaluated in terms of precision, linearity, detection sensitivity, cross-reactivity, and carry-over. A correlation with the Real-Q HBV Quantification kit (BioSewoom Inc., Korea) was also examined using serum samples from 64 patients diagnosed with chronic hepatitis B and underwent lamivudine therapy in Asan Medical Center. We verified the trueness of the system by comparing the outputs with the assigned values of the BBI panel (BBI Diagnostics, USA). Within-run and between-run coefficients of variation (CV) were 3.56-4.71% and 3.03-4.98%, respectively. Linearity was manifested ranging from 53 to 10(9)copies/mL and the detection sensitivity was verified to be 51 copies/mL. None of hepatitis C virus showed cross-reactivity. No cross-contamination occurred when negative and positive samples were alternatively placed in a row. It showed a good correlation with the Real-Q HBV (r(2)=0.9609) and the test results for the BBI panel were also well agreed to the assigned values (r(2)=0.9933). The performance of Abbott RealTime HBV Quantification kit was excellent; thus, it should be widely used in starting and monitoring of antiviral therapy in Korean patients with chronic hepatitis B.

Structural Investigation of Phosphorus in CaO-SiO2-P2O5 Ternary Glass

NASA Astrophysics Data System (ADS)

Wang, Zhanjun; Cai, Shengjia; Zhang, Mei; Guo, Min; Zhang, Zuotai

2017-04-01

The system of CaO-SiO2-P2O5 ternary glass is not only among the major constituents of steelmaking slags in iron and steel industry, but also play a significant role in other industrial process, such as chemical engineering and glass industry. In the present study, the structure of CaO-SiO2-P2O5 ternary glass with varying P2O5 content from 0 to 15 wt pct at a fixed CaO/SiO2 = 1.4 was investigated using molecular dynamics (MD) simulation combined with X-ray photoelectron spectroscopy and Raman spectra techniques. The results indicated that P5+ ions have a higher affinity to Ca2+ ions which are then stripped away from the silicate network with the addition of P2O5, resulting in the formation of Ca-O-P and Si-O-Si linkages. In addition, almost all P5+ ions displayed as {{Q}}_{{P}}0 ( {{Q}}_{{P}}n , n is the number of bridging oxygen in one [PO4]-tetrahedra units) and a small fraction of P5+ ions behave as {{Q}}_{{P}}1 (P-O-P) and P-O-Si. The enhanced degree of polymerization can be detected from the increase of {{X}}_{{Si}}3 and X_{{P}}1 /X_{{P}}0 (mole fraction of {{Q}}_{{Si}}i or {{Q}}_{{P}}i ). Furthermore, the ratio of Raman scattering coefficients for Q_{{Si}}i /Q_{{Si}}1 and Q_{{P}}i /Q_{{P}}1 were determined by combining MD simulated result with Raman spectra, which were considered to be suitable to the present study.

Rapid and Easy Protocol for Quantification of Next-Generation Sequencing Libraries.

PubMed

Hawkins, Steve F C; Guest, Paul C

2018-01-01

The emergence of next-generation sequencing (NGS) over the last 10 years has increased the efficiency of DNA sequencing in terms of speed, ease, and price. However, the exact quantification of a NGS library is crucial in order to obtain good data on sequencing platforms developed by the current market leader Illumina. Different approaches for DNA quantification are available currently and the most commonly used are based on analysis of the physical properties of the DNA through spectrophotometric or fluorometric methods. Although these methods are technically simple, they do not allow exact quantification as can be achieved using a real-time quantitative PCR (qPCR) approach. A qPCR protocol for DNA quantification with applications in NGS library preparation studies is presented here. This can be applied in various fields of study such as medical disorders resulting from nutritional programming disturbances.

Consistency in trophic magnification factors of cyclic methyl siloxanes in pelagic freshwater food webs leading to brown trout.

PubMed

Borgå, Katrine; Fjeld, Eirik; Kierkegaard, Amelie; McLachlan, Michael S

2013-12-17

Cyclic volatile methyl siloxanes (cVMS) concentrations were analyzed in the pelagic food web of two Norwegian lakes (Mjøsa, Randsfjorden), and in brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) collected in a reference lake (Femunden), in 2012. Lakes receiving discharge from wastewater treatment plants (Mjøsa and Randsfjorden) had cVMS concentrations in trout that were up to 2 orders of magnitude higher than those in Femunden, where most samples were close to the limit of quantification (LOQ). Food web biomagnification of cVMS in Mjøsa and Randsfjorden was quantified by estimation of trophic magnification factors (TMFs). TMF for legacy persistent organic pollutants (POPs) were analyzed for comparison. Both decamethylcyclopentasiloxane (D5) and dodecamethylcyclohexasiloxane (D6) biomagnified with TMFs of 2.9 (2.1-4.0) and 2.3 (1.8-3.0), respectively. Octamethylcyclotetrasiloxane (D4) was below the LOQ in the majority of samples and had substantially lower biomagnification than for D5 and D6. The cVMS TMFs did not differ between the lakes, whereas the legacy POP TMFs were higher in Mjøsa than inRandsfjorden. Whitefish had lower cVMS bioaccumulation compared to legacy POPs, and affected the TMF significance for cVMS, but not for POPs. TMFs of D5 and legacy contaminants in Lake Mjøsa were consistent with those previously measured in Mjøsa.

Pelvic floor muscle training versus watchful waiting or pessary treatment for pelvic organ prolapse (POPPS): design and participant baseline characteristics of two parallel pragmatic randomized controlled trials in primary care.

PubMed

Wiegersma, Marian; Panman, Chantal M C R; Kollen, Boudewijn J; Vermeulen, Karin M; Schram, Aaltje J; Messelink, Embert J; Berger, Marjolein Y; Lisman-Van Leeuwen, Yvonne; Dekker, Janny H

2014-02-01

Pelvic floor muscle training (PFMT) and pessaries are commonly used in the conservative treatment of pelvic organ prolapse (POP). Because there is a lack of evidence regarding the optimal choice between these two interventions, we designed the "Pelvic Organ prolapse in primary care: effects of Pelvic floor muscle training and Pessary treatment Study" (POPPS). POPPS consists of two parallel open label randomized controlled trials performed in primary care, in women aged ≥55 years, recruited through a postal questionnaire. In POPPS trial 1, women with mild POP receive either PFMT or watchful waiting. In POPPS trial 2, women with advanced POP receive either PFMT or pessary treatment. Patient recruitment started in 2009 and was finished in December 2012. Primary outcome of both POPPS trials is improvement in POP-related symptoms. Secondary outcomes are quality of life, sexual function, POP-Q stage, pelvic floor muscle function, post-void residual volume, patients' perception of improvement, and costs. All outcomes are measured 3, 12, and 24 months after the start of treatment. Cost-effectiveness will be calculated based on societal costs, using the PFDI-20 and the EQ-5D as outcomes. In this paper the POPPS design, the encountered challenges and our solutions, and participant baseline characteristics are presented. For both trials the target numbers of patients in each treatment group are achieved, giving this study sufficient power to lead to promising results. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Space Station Freedom avionics technology

NASA Technical Reports Server (NTRS)

Edwards, A.

1990-01-01

The Space Station Freedom Program (SSFP) encompasses the design, development, test, evaluation, verification, launch, assembly, and operation and utilization of a set of spacecraft in low earth orbit (LEO) and their supporting facilities. The spacecraft set includes: the Space Station Manned Base (SSMB), a European Space Agency (ESA) provided Man-Tended Free Flyer (MTFF) at an inclination of 28.5 degrees and nominal attitude of 410 km, a USA provided Polar Orbiting Platform (POP), and an ESA provided POP in sun-synchronous, near polar orbits at a nominal altitude of 822 km. The SSMB will be assembled using the National Space Transportation System (NSTS). The POPs and the MTFF will be launched by Expendable Launch Vehicles (ELVs): a Titan 4 for the US POP and an Ariane for the ESA POP and MTFF. The US POP will for the most part use derivatives of systems flown on unmanned LEO spacecraft. The SSMB portion of the overall program is presented.

qFlow Cytometry-Based Receptoromic Screening: A High-Throughput Quantification Approach Informing Biomarker Selection and Nanosensor Development.

PubMed

Chen, Si; Weddell, Jared; Gupta, Pavan; Conard, Grace; Parkin, James; Imoukhuede, Princess I

2017-01-01

Nanosensor-based detection of biomarkers can improve medical diagnosis; however, a critical factor in nanosensor development is deciding which biomarker to target, as most diseases present several biomarkers. Biomarker-targeting decisions can be informed via an understanding of biomarker expression. Currently, immunohistochemistry (IHC) is the accepted standard for profiling biomarker expression. While IHC provides a relative mapping of biomarker expression, it does not provide cell-by-cell readouts of biomarker expression or absolute biomarker quantification. Flow cytometry overcomes both these IHC challenges by offering biomarker expression on a cell-by-cell basis, and when combined with calibration standards, providing quantitation of biomarker concentrations: this is known as qFlow cytometry. Here, we outline the key components for applying qFlow cytometry to detect biomarkers within the angiogenic vascular endothelial growth factor receptor family. The key aspects of the qFlow cytometry methodology include: antibody specificity testing, immunofluorescent cell labeling, saturation analysis, fluorescent microsphere calibration, and quantitative analysis of both ensemble and cell-by-cell data. Together, these methods enable high-throughput quantification of biomarker expression.

The impact of targeting repetitive BamHI-W sequences on the sensitivity and precision of EBV DNA quantification.

PubMed

Sanosyan, Armen; Fayd'herbe de Maudave, Alexis; Bollore, Karine; Zimmermann, Valérie; Foulongne, Vincent; Van de Perre, Philippe; Tuaillon, Edouard

2017-01-01

Viral load monitoring and early Epstein-Barr virus (EBV) DNA detection are essential in routine laboratory testing, especially in preemptive management of Post-transplant Lymphoproliferative Disorder. Targeting the repetitive BamHI-W sequence was shown to increase the sensitivity of EBV DNA quantification, but the variability of BamHI-W reiterations was suggested to be a source of quantification bias. We aimed to assess the extent of variability associated with BamHI-W PCR and its impact on the sensitivity of EBV DNA quantification using the 1st WHO international standard, EBV strains and clinical samples. Repetitive BamHI-W- and LMP2 single- sequences were amplified by in-house qPCRs and BXLF-1 sequence by a commercial assay (EBV R-gene™, BioMerieux). Linearity and limits of detection of in-house methods were assessed. The impact of repeated versus single target sequences on EBV DNA quantification precision was tested on B95.8 and Raji cell lines, possessing 11 and 7 copies of the BamHI-W sequence, respectively, and on clinical samples. BamHI-W qPCR demonstrated a lower limit of detection compared to LMP2 qPCR (2.33 log10 versus 3.08 log10 IU/mL; P = 0.0002). BamHI-W qPCR underestimated the EBV DNA load on Raji strain which contained fewer BamHI-W copies than the WHO standard derived from the B95.8 EBV strain (mean bias: - 0.21 log10; 95% CI, -0.54 to 0.12). Comparison of BamHI-W qPCR versus LMP2 and BXLF-1 qPCR showed an acceptable variability between EBV DNA levels in clinical samples with the mean bias being within 0.5 log10 IU/mL EBV DNA, whereas a better quantitative concordance was observed between LMP2 and BXLF-1 assays. Targeting BamHI-W resulted to a higher sensitivity compared to LMP2 but the variable reiterations of BamHI-W segment are associated with higher quantification variability. BamHI-W can be considered for clinical and therapeutic monitoring to detect an early EBV DNA and a dynamic change in viral load.

The impact of targeting repetitive BamHI-W sequences on the sensitivity and precision of EBV DNA quantification

PubMed Central

Fayd’herbe de Maudave, Alexis; Bollore, Karine; Zimmermann, Valérie; Foulongne, Vincent; Van de Perre, Philippe; Tuaillon, Edouard

2017-01-01

Background Viral load monitoring and early Epstein-Barr virus (EBV) DNA detection are essential in routine laboratory testing, especially in preemptive management of Post-transplant Lymphoproliferative Disorder. Targeting the repetitive BamHI-W sequence was shown to increase the sensitivity of EBV DNA quantification, but the variability of BamHI-W reiterations was suggested to be a source of quantification bias. We aimed to assess the extent of variability associated with BamHI-W PCR and its impact on the sensitivity of EBV DNA quantification using the 1st WHO international standard, EBV strains and clinical samples. Methods Repetitive BamHI-W- and LMP2 single- sequences were amplified by in-house qPCRs and BXLF-1 sequence by a commercial assay (EBV R-gene™, BioMerieux). Linearity and limits of detection of in-house methods were assessed. The impact of repeated versus single target sequences on EBV DNA quantification precision was tested on B95.8 and Raji cell lines, possessing 11 and 7 copies of the BamHI-W sequence, respectively, and on clinical samples. Results BamHI-W qPCR demonstrated a lower limit of detection compared to LMP2 qPCR (2.33 log10 versus 3.08 log10 IU/mL; P = 0.0002). BamHI-W qPCR underestimated the EBV DNA load on Raji strain which contained fewer BamHI-W copies than the WHO standard derived from the B95.8 EBV strain (mean bias: - 0.21 log10; 95% CI, -0.54 to 0.12). Comparison of BamHI-W qPCR versus LMP2 and BXLF-1 qPCR showed an acceptable variability between EBV DNA levels in clinical samples with the mean bias being within 0.5 log10 IU/mL EBV DNA, whereas a better quantitative concordance was observed between LMP2 and BXLF-1 assays. Conclusions Targeting BamHI-W resulted to a higher sensitivity compared to LMP2 but the variable reiterations of BamHI-W segment are associated with higher quantification variability. BamHI-W can be considered for clinical and therapeutic monitoring to detect an early EBV DNA and a dynamic change in viral load. PMID:28850597

VARIATION OF THE EXPRESSION OF ENDOGENOUS "HOUSEKEEPING" GENES IN B[A]P TREATED MOUSE LUNGS MEASURED BY qRT-PCR

EPA Science Inventory

Quantitative RT-PCR is frequently used to analyze gene expression in different experimental systems. In this assay, housekeeping genes are frequently used to normalize for the variability between samples (relative quantification). We have examined the utility of using qRT-PCR and...

Quantitative detection method for Roundup Ready soybean in food using duplex real-time PCR MGB chemistry.

PubMed

Samson, Maria Cristina; Gullì, Mariolina; Marmiroli, Nelson

2010-07-01

Methodologies that enable the detection of genetically modified organisms (GMOs) (authorized and non-authorized) in food and feed strongly influence the potential for adequate updating and implementation of legislation together with labeling requirements. Quantitative polymerase chain reaction (qPCR) systems were designed to boost the sensitivity and specificity on the identification of GMOs in highly degraded DNA samples; however, such testing will become economically difficult to cope with due to increasing numbers of approved genetically modified (GM) lines. Multiplexing approaches are therefore in development to provide cost-efficient solution. Construct-specific primers and probe were developed for quantitative analysis of Roundup Ready soybean (RRS) event glyphosate-tolerant soybean (GTS) 40-3-2. The lectin gene (Le1) was used as a reference gene, and its specificity was verified. RRS- and Le1-specific quantitative real-time PCR (qRTPCR) were optimized in a duplex platform that has been validated with respect to limit of detection (LOD) and limit of quantification (LOQ), as well as accuracy. The analysis of model processed food samples showed that the degradation of DNA has no adverse or little effects on the performance of quantification assay. In this study, a duplex qRTPCR using TaqMan minor groove binder-non-fluorescent quencher (MGB-NFQ) chemistry was developed for specific detection and quantification of RRS event GTS 40-3-2 that can be used for practical monitoring in processed food products.

Species identification and quantification in meat and meat products using droplet digital PCR (ddPCR).

PubMed

Floren, C; Wiedemann, I; Brenig, B; Schütz, E; Beck, J

2015-04-15

Species fraud and product mislabelling in processed food, albeit not being a direct health issue, often results in consumer distrust. Therefore methods for quantification of undeclared species are needed. Targeting mitochondrial DNA, e.g. CYTB gene, for species quantification is unsuitable, due to a fivefold inter-tissue variation in mtDNA content per cell resulting in either an under- (-70%) or overestimation (+160%) of species DNA contents. Here, we describe a reliable two-step droplet digital PCR (ddPCR) assay targeting the nuclear F2 gene for precise quantification of cattle, horse, and pig in processed meat products. The ddPCR assay is advantageous over qPCR showing a limit of quantification (LOQ) and detection (LOD) in different meat products of 0.01% and 0.001%, respectively. The specificity was verified in 14 different species. Hence, determining F2 in food by ddPCR can be recommended for quality assurance and control in production systems. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

HBsAg quantification to predict natural history and treatment outcome in chronic hepatitis B patients.

PubMed

Martinot-Peignoux, Michelle; Asselah, Tarik; Marcellin, Patrick

2013-08-01

There is a growing interest in serum HBsAg quantification (qHbsAg). HBsAg titers are negatively correlated with liver fibrosis in HBeAg(+) patients. In HBeAg(-) HBsAg level <1000 IU/ml and HBV-DNA titer <2000 IU/ml accurately identify inactive carriers. During PEG-IFN treatment qHBsAg identifies patients with no benefit from therapy at week 12, allowing stopping or switched- "week 12 stopping rule". During nucleos(t)ide analogues the role of qHBsAg need to be clarified. In clinical practice qHBsAg is a simple and reproducible tool that may be used in association with HBV-DNA to classify patients during the natural history of HBV and to monitor therapy. Copyright © 2013 Elsevier Inc. All rights reserved.

Brominated Flame Retardants and Other Persistent Organohalogenated Compounds in Relation to Timing of Puberty in a Longitudinal Study of Girls.

PubMed

Windham, Gayle C; Pinney, Susan M; Voss, Robert W; Sjödin, Andreas; Biro, Frank M; Greenspan, Louise C; Stewart, Susan; Hiatt, Robert A; Kushi, Lawrence H

2015-10-01

Exposure to hormonally active chemicals could plausibly affect pubertal timing, so we are investigating this in the Breast Cancer and the Environment Research Program. Our goal was to examine persistent organic pollutants (POPs) in relation to pubertal onset. Ethnically diverse cohorts of 6- to 8-year-old girls (n = 645) provided serum for measure of polybrominated diphenyl ethers (PBDEs), polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), and lipids. Tanner stages [breast (B) and pubic hair (PH)], and body mass index (BMI) were measured at up to seven annual clinic visits. Using accelerated failure time models, we calculated time ratios (TRs) for age at Tanner stages 2 or higher (2+) and POPs quartiles (Q1-4), adjusting for confounders (race/ethnicity, site, caregiver education, and income). We also calculated prevalence ratios (PRs) of Tanner stages 2+ at time of blood sampling. Cross-sectionally, the prevalence of B2+ and PH2+ was inversely related to chemical serum concentrations; but after adjustment for confounders, only the associations with B2+, not PH2+, were statistically significant. Longitudinally, the age at pubertal transition was consistently older with greater chemical concentrations; for example: adjusted TR for B2+ and Q4 for ΣPBDE = 1.05; 95% CI: 1.02, 1.08, for ΣPCB = 1.05; 95% CI: 1.01, 1.08, and for ΣOCP = 1.10; 95% CI: 1.06, 1.14, indicating median ages of about 6 and 11 months older than least exposed, and with similar effect estimates for PH2+. Adjusting for BMI attenuated associations for PCBs and OCPs but not for PBDEs. This first longitudinal study of puberty in girls with serum POPs measurements (to our knowledge) reveals a delay in onset with higher concentrations.

Establishment of a real-time PCR method for quantification of geosmin-producing Streptomyces spp. in recirculating aquaculture systems.

PubMed

Auffret, Marc; Pilote, Alexandre; Proulx, Emilie; Proulx, Daniel; Vandenberg, Grant; Villemur, Richard

2011-12-15

Geosmin and 2-methylisoborneol (MIB) have been associated with off-flavour problems in fish and seafood products, generating a strong negative impact for aquaculture industries. Although most of the producers of geosmin and MIB have been identified as Streptomyces species or cyanobacteria, Streptomyces spp. are thought to be responsible for the synthesis of these compounds in indoor recirculating aquaculture systems (RAS). The detection of genes involved in the synthesis of geosmin and MIB can be a relevant indicator of the beginning of off-flavour events in RAS. Here, we report a real-time polymerase chain reaction (qPCR) protocol targeting geoA sequences that encode a germacradienol synthase involved in geosmin synthesis. New geoA-related sequences were retrieved from eleven geosmin-producing Actinomycete strains, among them two Streptomyces strains isolated from two RAS. Combined with geoA-related sequences available in gene databases, we designed primers and standards suitable for qPCR assays targeting mainly Streptomyces geoA. Using our qPCR protocol, we succeeded in measuring the level of geoA copies in sand filter and biofilters in two RAS. This study is the first to apply qPCR assays to detect and quantify the geosmin synthesis gene (geoA) in RAS. Quantification of geoA in RAS could permit the monitoring of the level of geosmin producers prior to the occurrence of geosmin production. This information will be most valuable for fish producers to manage further development of off-flavour events. Copyright © 2011 Elsevier Ltd. All rights reserved.

A novel qPCR protocol for the specific detection and quantification of the fuel-deteriorating fungus Hormoconis resinae.

PubMed

Martin-Sanchez, Pedro M; Gorbushina, Anna A; Kunte, Hans-Jörg; Toepel, Jörg

2016-07-01

A wide variety of fungi and bacteria are known to contaminate fuels and fuel systems. These microbial contaminants have been linked to fuel system fouling and corrosion. The fungus Hormoconis resinae, a common jet fuel contaminant, is used in this study as a model for developing innovative risk assessment methods. A novel qPCR protocol to detect and quantify H. resinae in, and together with, total fungal contamination of fuel systems is reported. Two primer sets, targeting the markers RPB2 and ITS, were selected for their remarkable specificity and sensitivity. These primers were successfully applied on fungal cultures and diesel samples demonstrating the validity and reliability of the established qPCR protocol. This novel tool allows clarification of the current role of H. resinae in fuel contamination cases, as well as providing a technique to detect fungal outbreaks in fuel systems. This tool can be expanded to other well-known fuel-deteriorating microorganisms.

POP levels in beans from Mediterranean and tropical areas.

PubMed

Di Bella, Giuseppa; Haddaoui, Imen; Lo Turco, Vincenzo; Potortì, Angela Giorgia; Fede, Maria Rita; Dugo, Giacomo

2017-06-01

Despite the importance of beans as food, few studies are conducted to control their contamination by persistent organic pollutants (POPs), compounds of great importance because of their toxicity and tendency to accumulate in food chains. In order to evaluate the human exposure to POPs by the consumption of beans a monitoring programme was conducted on polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) residues in samples coming from Italy, Mexico, India, Japan, Ghana and Ivory Coast. All beans were extracted with an accelerated solvents extractor in triplicate; the clean-up step was done with a Florisil column; identification and quantification was carried out using a TSQ Quantum XLS Ultra GC-MS/MS in selected reaction monitoring mode. Results revealed concentrations of ∑PAHs ranged from 7.31 µg kg -1 to 686 µg kg -1 , ∑PCBs between 1.85 µg kg -1 and 43.1 µg kg -1 and ∑OCPs ranged from 1.37 µg kg -1 to 71.8 µg kg -1 . Our results showed that beans coming from Ivory Coast are the most exposed to the risk of contamination by all the pollutants investigated. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Quantitative volumetric Raman imaging of three dimensional cell cultures

NASA Astrophysics Data System (ADS)

Kallepitis, Charalambos; Bergholt, Mads S.; Mazo, Manuel M.; Leonardo, Vincent; Skaalure, Stacey C.; Maynard, Stephanie A.; Stevens, Molly M.

2017-03-01

The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment. We demonstrate visualization and quantification of fine details in cell shape, cytoplasm, nucleus, lipid bodies and cytoskeletal structures in 3D with unprecedented biomolecular specificity for vibrational microspectroscopy.

Quantification of hookworm ova from wastewater matrices using quantitative PCR.

PubMed

Gyawali, Pradip; Ahmed, Warish; Sidhu, Jatinder P; Jagals, Paul; Toze, Simon

2017-07-01

A quantitative PCR (qPCR) assay was used to quantify Ancylostoma caninum ova in wastewater and sludge samples. We estimated the average gene copy numbers for a single ovum using a mixed population of ova. The average gene copy numbers derived from the mixed population were used to estimate numbers of hookworm ova in A. caninum seeded and unseeded wastewater and sludge samples. The newly developed qPCR assay estimated an average of 3.7×10 3 gene copies per ovum, which was then validated by seeding known numbers of hookworm ova into treated wastewater. The qPCR estimated an average of (1.1±0.1), (8.6±2.9) and (67.3±10.4) ova for treated wastewater that was seeded with (1±0), (10±2) and (100±21) ova, respectively. The further application of the qPCR assay for the quantification of A. caninum ova was determined by seeding a known numbers of ova into the wastewater matrices. The qPCR results indicated that 50%, 90% and 67% of treated wastewater (1L), raw wastewater (1L) and sludge (~4g) samples had variable numbers of A. caninum gene copies. After conversion of the qPCR estimated gene copy numbers to ova for treated wastewater, raw wastewater, and sludge samples, had an average of 0.02, 1.24 and 67 ova, respectively. The result of this study indicated that qPCR can be used for the quantification of hookworm ova from wastewater and sludge samples; however, caution is advised in interpreting qPCR generated data for health risk assessment. Copyright © 2017. Published by Elsevier B.V.

Acoustic signal emission monitoring as a novel method to predict steam pops during radiofrequency ablation: preliminary observations.

PubMed

Chik, William W B; Kosobrodov, Roman; Bhaskaran, Abhishek; Barry, Michael Anthony Tony; Nguyen, Doan Trang; Pouliopoulos, Jim; Byth, Karen; Sivagangabalan, Gopal; Thomas, Stuart P; Ross, David L; McEwan, Alistair; Kovoor, Pramesh; Thiagalingam, Aravinda

2015-04-01

Steam pop is an explosive rupture of cardiac tissue caused by tissue overheating above 100 °C, resulting in steam formation, predisposing to serious complications associated with radiofrequency (RF) ablations. However, there are currently no reliable techniques to predict the occurrence of steam pops. We propose the utility of acoustic signals emitted during RF ablation as a novel method to predict steam pop formation and potentially prevent serious complications. Radiofrequency generator parameters (power, impedance, and temperature) were temporally recorded during ablations performed in an in vitro bovine myocardial model. The acoustic system consisted of HTI-96-min hydrophone, microphone preamplifier, and sound card connected to a laptop computer. The hydrophone has the frequency range of 2 Hz to 30 kHz and nominal sensitivity in the range -240 to -165 dB. The sound was sampled at 96 kHz with 24-bit resolution. Output signal from the hydrophone was fed into the camera audio input to synchronize the video stream. An automated system was developed for the detection and analysis of acoustic events. Nine steam pops were observed. Three distinct sounds were identified as warning signals, each indicating rapid steam formation and its release from tissue. These sounds had a broad frequency range up to 6 kHz with several spectral peaks around 2-3 kHz. Subjectively, these warning signals were perceived as separate loud clicks, a quick succession of clicks, or continuous squeaking noise. Characteristic acoustic signals were identified preceding 80% of pops occurrence. Six cardiologists were able to identify 65% of acoustic signals accurately preceding the pop. An automated system identified the characteristic warning signals in 85% of cases. The mean time from the first acoustic signal to pop occurrence was 46 ± 20 seconds. The automated system had 72.7% sensitivity and 88.9% specificity for predicting pops. Easily identifiable characteristic acoustic emissions predictably occur before imminent steam popping during RF ablations. Such acoustic emissions can be carefully monitored during an ablation and may be useful to prevent serious complications during RF delivery. © 2014 Wiley Periodicals, Inc.

Prefunctionalized Porous Organic Polymers: Effective Supports of Surface Palladium Nanoparticles for the Enhancement of Catalytic Performances in Dehalogenation.

PubMed

Zhong, Hong; Liu, Caiping; Zhou, Hanghui; Wang, Yangxin; Wang, Ruihu

2016-08-22

Three porous organic polymers (POPs) containing H, COOMe, and COO(-) groups at 2,6-bis(1,2,3-triazol-4-yl)pyridyl (BTP) units (i.e., POP-1, POP-2, and POP-3, respectively) were prepared for the immobilization of metal nanoparticles (NPs). The ultrafine palladium NPs are uniformly encapsulated in the interior pores of POP-1, whereas uniform- and dual-distributed palladium NPs are located on the external surface of POP-2 and POP-3, respectively. The presence of carboxylate groups not only endows POP-3 an outstanding dispersibility in H2 O/EtOH, but also enables the palladium NPs at the surface to show the highest catalytic activity, stability, and recyclability in dehalogenation reactions of chlorobenzene at 25 °C. The palladium NPs on the external surface are effectively stabilized by the functionalized POPs containing BTP units and carboxylate groups, which provides a new insight for highly efficient catalytic systems based on surface metal NPs of porous materials. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Baseline metal enrichment from Population III star formation in cosmological volume simulations

NASA Astrophysics Data System (ADS)

Jaacks, Jason; Thompson, Robert; Finkelstein, Steven L.; Bromm, Volker

2018-04-01

We utilize the hydrodynamic and N-body code GIZMO coupled with our newly developed sub-grid Population III (Pop III) Legacy model, designed specifically for cosmological volume simulations, to study the baseline metal enrichment from Pop III star formation at z > 7. In this idealized numerical experiment, we only consider Pop III star formation. We find that our model Pop III star formation rate density (SFRD), which peaks at ˜ 10- 3 M⊙ yr- 1 Mpc- 1 near z ˜ 10, agrees well with previous numerical studies and is consistent with the observed estimates for Pop II SFRDs. The mean Pop III metallicity rises smoothly from z = 25 to 7, but does not reach the critical metallicity value, Zcrit = 10-4 Z⊙, required for the Pop III to Pop II transition in star formation mode until z ≃ 7. This suggests that, while individual haloes can suppress in situ Pop III star formation, the external enrichment is insufficient to globally terminate Pop III star formation. The maximum enrichment from Pop III star formation in star-forming dark matter haloes is Z ˜ 10-2 Z⊙, whereas the minimum found in externally enriched haloes is Z ≳ 10-7 Z⊙. Finally, mock observations of our simulated IGM enriched with Pop III metals produce equivalent widths similar to observations of an extremely metal-poor damped Lyman alpha system at z = 7.04, which is thought to be enriched by Pop III star formation only.

76 FR 60842 - Announcement of Requirements and Registration for “popHealth Tools Development Challenge”

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-30

... selections based upon the following criteria: 1. Ability to integrate with popHealth system and build upon... DEPARTMENT OF HEALTH AND HUMAN SERVICES Announcement of Requirements and Registration for ``popHealth Tools Development Challenge'' AGENCY: Office of the National Coordinator for Health Information...

Quantification of EVI1 transcript levels in acute myeloid leukemia by RT-qPCR analysis: A study by the ALFA Group.

PubMed

Smol, Thomas; Nibourel, Olivier; Marceau-Renaut, Alice; Celli-Lebras, Karine; Berthon, Céline; Quesnel, Bruno; Boissel, Nicolas; Terré, Christine; Thomas, Xavier; Castaigne, Sylvie; Dombret, Hervé; Preudhomme, Claude; Renneville, Aline

2015-12-01

EVI1 overexpression confers poor prognosis in acute myeloid leukemia (AML). Quantification of EVI1 expression has been mainly assessed by real-time quantitative PCR (RT-qPCR) based on relative quantification of EVI1-1D splice variant. In this study, we developed a RT-qPCR assay to perform quantification of EVI1 expression covering the different splice variants. A sequence localized in EVI1 exons 14 and 15 was cloned into plasmids that were used to establish RT-qPCR standard curves. Threshold values to define EVI1 overexpression were determined using 17 bone marrow (BM) and 31 peripheral blood (PB) control samples and were set at 1% in BM and 0.5% in PB. Samples from 64 AML patients overexpressing EVI1 included in the ALFA-0701 or -0702 trials were collected at diagnosis and during follow-up (n=152). Median EVI1 expression at AML diagnosis was 23.3% in BM and 3.6% in PB. EVI1 expression levels significantly decreased between diagnostic and post-induction samples, with an average variation from 21.6% to 3.56% in BM and from 4.0% to 0.22% in PB, but did not exceed 1 log10 reduction. Our study demonstrates that the magnitude of reduction in EVI1 expression levels between AML diagnosis and follow-up is not sufficient to allow sensitive detection of minimal residual disease. Copyright © 2015 Elsevier Ltd. All rights reserved.

Plasma protein absolute quantification by nano-LC Q-TOF UDMSE for clinical biomarker verification

PubMed Central

ILIES, MARIA; IUGA, CRISTINA ADELA; LOGHIN, FELICIA; DHOPLE, VISHNU MUKUND; HAMMER, ELKE

2017-01-01

Background and aims Proteome-based biomarker studies are targeting proteins that could serve as diagnostic, prognosis, and prediction molecules. In the clinical routine, immunoassays are currently used for the absolute quantification of such biomarkers, with the major limitation that only one molecule can be targeted per assay. The aim of our study was to test a mass spectrometry based absolute quantification method for the verification of plasma protein sets which might serve as reliable biomarker panels for the clinical practice. Methods Six EDTA plasma samples were analyzed after tryptic digestion using a high throughput data independent acquisition nano-LC Q-TOF UDMSE proteomics approach. Synthetic Escherichia coli standard peptides were spiked in each sample for the absolute quantification. Data analysis was performed using ProgenesisQI v2.0 software (Waters Corporation). Results Our method ensured absolute quantification of 242 non redundant plasma proteins in a single run analysis. The dynamic range covered was 105. 86% were represented by classical plasma proteins. The overall median coefficient of variation was 0.36, while a set of 63 proteins was found to be highly stable. Absolute protein concentrations strongly correlated with values reviewed in the literature. Conclusions Nano-LC Q-TOF UDMSE proteomic analysis can be used for a simple and rapid determination of absolute amounts of plasma proteins. A large number of plasma proteins could be analyzed, while a wide dynamic range was covered with low coefficient of variation at protein level. The method proved to be a reliable tool for the quantification of protein panel for biomarker verification in the clinical practice. PMID:29151793

Validation of the traditional Chinese version of the prolapse quality of life questionnaire (P-QOL) in a Mandarin-speaking Taiwanese population.

PubMed

Chuang, Fei-Chi; Chu, Li-Ching; Kung, Fu-Tsai; Huang, Kuan-Hui

2016-10-01

To validate the traditional Chinese translated version of the prolapse quality of life questionnaire (P-QOL). The P-QOL questionnaire was translated into traditional Chinese characters and administered to women recruited from gynecologic outpatient clinics of Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan. After the test-retest reliability and internal consistency were established in a pilot study, all participants completed the P-QOL questionnaire and were examined in the lithotomy position using the Pelvic Organ Prolapse Quantification System (POP-Q). The construct validity was assessed by comparing symptom scores and quality-of-life domain scores between symptomatic and asymptomatic women. Of the 244 women recruited, 159 were symptomatic for pelvic organ prolapse, and 85 were asymptomatic. The test-retest reliability confirmed a significant positive monotonic correlation between the total scores of each domain (n = 30, Spearman's rho was from 0.411 to 0.888, p < 0.05 of all). All items achieved a Cronbach α > 0.80 showing good internal consistency. Among the 18 symptom questions, the scores differed significantly between symptomatic and asymptomatic women for 12/18 symptom questions. These 12 questions referred to the prolapse/vaginal symptoms. All the quality of life domains differed significantly (p < 0.05) between symptomatic and asymptomatic women except for the domain of sleep/energy (p = 0.108). The traditional Chinese language version of the P-QOL is a reliable instrument for the assessment of symptom severity and impact on quality of life in women with pelvic organ prolapse. Copyright © 2016. Published by Elsevier B.V.

Membrane and Chaperone Recognition by the Major Translocator Protein PopB of the Type III Secretion System of Pseudomonas aeruginosa*

PubMed Central

Discola, Karen F.; Förster, Andreas; Boulay, François; Simorre, Jean-Pierre; Attree, Ina; Dessen, Andréa; Job, Viviana

2014-01-01

The type III secretion system is a widespread apparatus used by pathogenic bacteria to inject effectors directly into the cytoplasm of eukaryotic cells. A key component of this highly conserved system is the translocon, a pore formed in the host membrane that is essential for toxins to bypass this last physical barrier. In Pseudomonas aeruginosa the translocon is composed of PopB and PopD, both of which before secretion are stabilized within the bacterial cytoplasm by a common chaperone, PcrH. In this work we characterize PopB, the major translocator, in both membrane-associated and PcrH-bound forms. By combining sucrose gradient centrifugation experiments, limited proteolysis, one-dimensional NMR, and β-lactamase reporter assays on eukaryotic cells, we show that PopB is stably inserted into bilayers with its flexible N-terminal domain and C-terminal tail exposed to the outside. In addition, we also report the crystal structure of the complex between PcrH and an N-terminal region of PopB (residues 51–59), which reveals that PopB lies within the concave face of PcrH, employing mostly backbone residues for contact. PcrH is thus the first chaperone whose structure has been solved in complex with both type III secretion systems translocators, revealing that both molecules employ the same surface for binding and excluding the possibility of formation of a ternary complex. The characterization of the major type III secretion system translocon component in both membrane-bound and chaperone-bound forms is a key step for the eventual development of antibacterials that block translocon assembly. PMID:24297169

Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology.

PubMed

Smith, Cindy J; Osborn, A Mark

2009-01-01

Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in 'real time' during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.

Adaptive Photothermal Emission Analysis Techniques for Robust Thermal Property Measurements of Thermal Barrier Coatings

NASA Astrophysics Data System (ADS)

Valdes, Raymond

The characterization of thermal barrier coating (TBC) systems is increasingly important because they enable gas turbine engines to operate at high temperatures and efficiency. Phase of photothermal emission analysis (PopTea) has been developed to analyze the thermal behavior of the ceramic top-coat of TBCs, as a nondestructive and noncontact method for measuring thermal diffusivity and thermal conductivity. Most TBC allocations are on actively-cooled high temperature turbine blades, which makes it difficult to precisely model heat transfer in the metallic subsystem. This reduces the ability of rote thermal modeling to reflect the actual physical conditions of the system and can lead to higher uncertainty in measured thermal properties. This dissertation investigates fundamental issues underpinning robust thermal property measurements that are adaptive to non-specific, complex, and evolving system characteristics using the PopTea method. A generic and adaptive subsystem PopTea thermal model was developed to account for complex geometry beyond a well-defined coating and substrate system. Without a priori knowledge of the subsystem characteristics, two different measurement techniques were implemented using the subsystem model. In the first technique, the properties of the subsystem were resolved as part of the PopTea parameter estimation algorithm; and, the second technique independently resolved the subsystem properties using a differential "bare" subsystem. The confidence in thermal properties measured using the generic subsystem model is similar to that from a standard PopTea measurement on a "well-defined" TBC system. Non-systematic bias-error on experimental observations in PopTea measurements due to generic thermal model discrepancies was also mitigated using a regression-based sensitivity analysis. The sensitivity analysis reported measurement uncertainty and was developed into a data reduction method to filter out these "erroneous" observations. It was found that the adverse impact of bias-error can be greatly reduced, leaving measurement observations with only random Gaussian noise in PopTea thermal property measurements. Quantifying the influence of the coating-substrate interface in PopTea measurements is important to resolving the thermal conductivity of the coating. However, the reduced significance of this interface in thicker coating systems can give rise to large uncertainties in thermal conductivity measurements. A first step towards improving PopTea measurements for such circumstances has been taken by implementing absolute temperature measurements using harmonically-sustained two-color pyrometry. Although promising, even small uncertainties in thermal emission observations were found to lead to significant noise in temperature measurements. However, PopTea analysis on bulk graphite samples were able to resolve its thermal conductivity to the expected literature values.

Effect of a Home-Based Virtual Reality Intervention for Children with Cerebral Palsy Using Super Pop VR Evaluation Metrics: A Feasibility Study.

PubMed

Chen, Yuping; Garcia-Vergara, Sergio; Howard, Ayanna M

2015-01-01

Objective. The purpose of this pilot study was to determine whether Super Pop VR, a low-cost virtual reality (VR) system, was a feasible system for documenting improvement in children with cerebral palsy (CP) and whether a home-based VR intervention was effective. Methods. Three children with CP participated in this study and received an 8-week VR intervention (30 minutes × 5 sessions/week) using the commercial EyeToy Play VR system. Reaching kinematics measured by Super Pop VR and two fine motor tools (Bruininks-Oseretsky Test of Motor Proficiency second edition, BOT-2, and Pediatric Motor Activity Log, PMAL) were tested before, mid, and after intervention. Results. All children successfully completed the evaluations using the Super Pop VR system at home where 85% of the reaches collected were used to compute reaching kinematics, which is compatible with literature using expensive motion analysis systems. Only the child with hemiplegic CP and more impaired arm function improved the reaching kinematics and functional use of the affected hand after intervention. Conclusion. Super Pop VR proved to be a feasible evaluation tool in children with CP.

Effect of a Home-Based Virtual Reality Intervention for Children with Cerebral Palsy Using Super Pop VR Evaluation Metrics: A Feasibility Study

PubMed Central

Chen, Yuping; Garcia-Vergara, Sergio; Howard, Ayanna M.

2015-01-01

Objective. The purpose of this pilot study was to determine whether Super Pop VR, a low-cost virtual reality (VR) system, was a feasible system for documenting improvement in children with cerebral palsy (CP) and whether a home-based VR intervention was effective. Methods. Three children with CP participated in this study and received an 8-week VR intervention (30 minutes × 5 sessions/week) using the commercial EyeToy Play VR system. Reaching kinematics measured by Super Pop VR and two fine motor tools (Bruininks-Oseretsky Test of Motor Proficiency second edition, BOT-2, and Pediatric Motor Activity Log, PMAL) were tested before, mid, and after intervention. Results. All children successfully completed the evaluations using the Super Pop VR system at home where 85% of the reaches collected were used to compute reaching kinematics, which is compatible with literature using expensive motion analysis systems. Only the child with hemiplegic CP and more impaired arm function improved the reaching kinematics and functional use of the affected hand after intervention. Conclusion. Super Pop VR proved to be a feasible evaluation tool in children with CP. PMID:26457202

qRT-PCR quantification of the biological control agent Trichoderma harzianum in peat and compost-based growing media.

PubMed

Beaulieu, Robert; López-Mondéjar, Rubén; Tittarelli, Fabio; Ros, Margarita; Pascual, José Antonio

2011-02-01

To ensure proper use of Trichoderma harzianum in agriculture, accurate data must be obtained in population monitoring. The effectiveness of qRT-PCR to quantify T. harzianum in different growing media was compared to the commonly used techniques of colony counting and qPCR. Results showed that plate counting and qPCR offered similar T. harzianum quantification patterns of an initial rapid increase in fungal population that decreased over time. However, data from qRT-PCR showed a population curve of active T. harzianum with a delayed onset of initial growth which then increased throughout the experiment. Results demonstrated that T. harzianum can successfully grow in these media and that qRT-PCR can offer a more distinct representation of active T. harzianum populations. Additionally, compost amended with T. harzianum exhibited a lower Fusarium oxysporum infection rate (67%) and lower percentage of fresh weight loss (11%) in comparison to amended peat (90% infection rate, 23% fresh weight loss). Copyright © 2010 Elsevier Ltd. All rights reserved.

Software-Enabled Distributed Network Governance: The PopMedNet Experience.

PubMed

Davies, Melanie; Erickson, Kyle; Wyner, Zachary; Malenfant, Jessica; Rosen, Rob; Brown, Jeffrey

2016-01-01

The expanded availability of electronic health information has led to increased interest in distributed health data research networks. The distributed research network model leaves data with and under the control of the data holder. Data holders, network coordinating centers, and researchers have distinct needs and challenges within this model. The concerns of network stakeholders are addressed in the design and governance models of the PopMedNet software platform. PopMedNet features include distributed querying, customizable workflows, and auditing and search capabilities. Its flexible role-based access control system enables the enforcement of varying governance policies. Four case studies describe how PopMedNet is used to enforce network governance models. Trust is an essential component of a distributed research network and must be built before data partners may be willing to participate further. The complexity of the PopMedNet system must be managed as networks grow and new data, analytic methods, and querying approaches are developed. The PopMedNet software platform supports a variety of network structures, governance models, and research activities through customizable features designed to meet the needs of network stakeholders.

A trial of patient-oriented problem-solving system for immunology teaching in China: a comparison with dialectic lectures

PubMed Central

2013-01-01

Background The most common teaching method used in China is lecturing, but recently, efforts have been widely undertaken to promote the transition from teacher-centered to student-centered education. The patient-oriented problem-solving (POPS) system is an innovative teaching-learning method that permits students to work in small groups to solve clinical problems, promotes self-learning, encourages clinical reasoning and develops long-lasting memory. To our best knowledge, however, POPS has never been applied in teaching immunology in China. The aim of this study was to develop POPS in teaching immunology and assess students’ and teachers’ perception to POPS. Methods 321 second-year medical students were divided into two groups: I and II. Group I, comprising 110 students, was taught by POPS, and 16 immunology teachers witnessed the whole teaching process. Group II including the remaining 211 students was taught through traditional lectures. The results of the pre- and post-test of both groups were compared. Group I students and teachers then completed a self-structured feedback questionnaire for analysis before a discussion meeting attended only by the teachers was held. Results Significant improvement in the mean difference between the pre- and post-test scores of those in Groups I and II was seen, demonstrating the effectiveness of POPS teaching. Most students responded that POPS facilitates self-learning, helps them to understand topics and creates interest, and 88.12% of students favored POPS over simple lectures. Moreover, while they responded that POPS facilitated student learning better than lectures, teachers pointed out that limited teaching resources would make it difficult for wide POPS application in China. Conclusions While POPS can break up the monotony of dialectic lectures and serve as a better teaching method, it may not be feasible for the current educational environment in China. The main reason for this is the relative shortage of teaching resources such as space, library facilities and well-trained teachers. PMID:23356717

A trial of patient-oriented problem-solving system for immunology teaching in China: a comparison with dialectic lectures.

PubMed

Zhang, Zhiren; Liu, Wei; Han, Junfeng; Guo, Sheng; Wu, Yuzhang

2013-01-28

The most common teaching method used in China is lecturing, but recently, efforts have been widely undertaken to promote the transition from teacher-centered to student-centered education. The patient-oriented problem-solving (POPS) system is an innovative teaching-learning method that permits students to work in small groups to solve clinical problems, promotes self-learning, encourages clinical reasoning and develops long-lasting memory. To our best knowledge, however, POPS has never been applied in teaching immunology in China. The aim of this study was to develop POPS in teaching immunology and assess students' and teachers' perception to POPS. 321 second-year medical students were divided into two groups: I and II. Group I, comprising 110 students, was taught by POPS, and 16 immunology teachers witnessed the whole teaching process. Group II including the remaining 211 students was taught through traditional lectures. The results of the pre- and post-test of both groups were compared. Group I students and teachers then completed a self-structured feedback questionnaire for analysis before a discussion meeting attended only by the teachers was held. Significant improvement in the mean difference between the pre- and post-test scores of those in Groups I and II was seen, demonstrating the effectiveness of POPS teaching. Most students responded that POPS facilitates self-learning, helps them to understand topics and creates interest, and 88.12% of students favored POPS over simple lectures. Moreover, while they responded that POPS facilitated student learning better than lectures, teachers pointed out that limited teaching resources would make it difficult for wide POPS application in China. While POPS can break up the monotony of dialectic lectures and serve as a better teaching method, it may not be feasible for the current educational environment in China. The main reason for this is the relative shortage of teaching resources such as space, library facilities and well-trained teachers.

Ultrahigh-performance liquid chromatography electrospray ionization Q-Orbitrap mass spectrometry for the analysis of 451 pesticide residues in fruits and vegetables: method development and validation.

PubMed

Wang, Jian; Chow, Willis; Chang, James; Wong, Jon W

2014-10-22

This paper presents an application of ultrahigh-performance liquid chromatography electrospray ionization quadrupole Orbitrap high-resolution mass spectrometry (UHPLC/ESI Q-Orbitrap MS) for the determination of 451 pesticide residues in fruits and vegetables. Pesticides were extracted from samples using the QuEChERS (quick, easy, cheap, effective, rugged, and safe) procedure. UHPLC/ESI Q-Orbitrap MS in full MS scan mode acquired full MS data for quantification, and UHPLC/ESI Q-Orbitrap Full MS/dd-MS(2) (i.e., data-dependent scan mode) obtained product ion spectra for identification. UHPLC/ESI Q-Orbitrap MS quantification was achieved using matrix-matched standard calibration curves along with the use of isotopically labeled standards or a chemical analogue as internal standards to achieve optimal method accuracy. The method performance characteristics include overall recovery, intermediate precision, and measurement uncertainty evaluated according to a nested experimental design. For the 10 matrices studied, 94.5% of the pesticides in fruits and 90.7% in vegetables had recoveries between 81 and 110%; 99.3% of the pesticides in fruits and 99.1% of the pesticides in vegetables had an intermediate precision of ≤20%; and 97.8% of the pesticides in fruits and 96.4% of the pesticides in vegetables showed measurement uncertainty of ≤50%. Overall, the UHPLC/ESI Q-Orbitrap MS demonstrated acceptable performance for the quantification of pesticide residues in fruits and vegetables. The UHPLC/ESI Q-Orbitrap Full MS/dd-MS(2) along with library matching showed great potential for identification and is being investigated further for routine practice.

Spatial association of prolyl oligopeptidase, inositol 1,4,5-triphosphate type 1 receptor, substance P and its neurokinin-1 receptor in the rat brain: an immunohistochemical colocalization study.

PubMed

Myöhänen, T T; Venäläinen, J I; Garcia-Horsman, J A; Männistö, P T

2008-06-02

Prolyl oligopeptidase (POP) is a serine endopeptidase which hydrolyzes proline-containing peptides shorter than 30 amino acids. It has been suggested that POP is associated with cognitive functions, possibly via the cleavage of neuropeptides such as substance P (SP). Recently, several studies have also linked POP to the inositol 1,4,5-triphosphate (IP(3)) signaling. However, the neuroanatomical interactions between these substances are not known. We used double-labeled immunofluorescence to determine the POP colocalization with SP, SP receptor (neurokinin-1 receptor, NK-1R) and IP(3) type 1 receptor (IP(3)R1) in the rat brain. Furthermore, since striatal and cortical GABAergic neurons are involved in SP neurotransmission, we studied the coexpression of POP, SP and GABA by triple-labeled immunofluorescence. POP was moderately present in IP(3)R1-containing cells in cortex; the colocalization was particularly high in the thalamus, hippocampal CA1 field and cerebellar Purkinje cells. Colocalization of POP with SP and NK1-receptor was infrequent throughout the brain, though some POP and SP coexpression was observed in cerebellar Purkinje cells. We also found that POP partially colocalized with SP-containing GABAergic neurons in striatum and cortex. Our findings support the view that POP is at least spatially associated with the IP(3)-signaling in the thalamus, hippocampus and cerebellar Purkinje cells. This might point to a role for POP in the regulation of long-term potentiation and/or depression. Moreover, the low degree of colocalization of POP, SP and its NK-1R suggests that a transport system is needed either for POP or SP to make hydrolysis possible and that POP may act both intra- and extracellularly.

Anthropometric Source Book. Volume 2: A Handbook of Anthropometric Data

DTIC Science & Technology

1978-07-01

a.mw* % A W " " -I4 0-4DB~M’a~P Z.=22014 MO ZW=O𔃾WW4L" 0 "OBCOO&WWOWWBAB z z 34 " 14 0-44 BBP o z:.~Bwz 1 Wz0 V1O󈧵 j =P.’)ON- 01-0 e e o 0 t...4 c: P) POP~f pol IV)~) ~ P)V) t) PFrW)WW))m x dCY4 0- -a I.- - 0 ~ ItTt t: 1 1 % t’Q.4 O’*t%if! N D Dc ! 4 1Dff~ ffa ul In .4 NV4 W v4 q4v4 v4 NUM

Nonlinear characterization of elasticity using quantitative optical coherence elastography.

PubMed

Qiu, Yi; Zaki, Farzana R; Chandra, Namas; Chester, Shawn A; Liu, Xuan

2016-11-01

Optical coherence elastography (OCE) has been used to perform mechanical characterization on biological tissue at the microscopic scale. In this work, we used quantitative optical coherence elastography (qOCE), a novel technology we recently developed, to study the nonlinear elastic behavior of biological tissue. The qOCE system had a fiber-optic probe to exert a compressive force to deform tissue under the tip of the probe. Using the space-division multiplexed optical coherence tomography (OCT) signal detected by a spectral domain OCT engine, we were able to simultaneously quantify the probe deformation that was proportional to the force applied, and to quantify the tissue deformation. In other words, our qOCE system allowed us to establish the relationship between mechanical stimulus and tissue response to characterize the stiffness of biological tissue. Most biological tissues have nonlinear elastic behavior, and the apparent stress-strain relationship characterized by our qOCE system was nonlinear an extended range of strain, for a tissue-mimicking phantom as well as biological tissues. Our experimental results suggested that the quantification of force in OCE was critical for accurate characterization of tissue mechanical properties and the qOCE technique was capable of differentiating biological tissues based on the elasticity of tissue that is generally nonlinear.

Geomorphic Evidences of Pleistocene Deformations in the Western Pyrenees (France)

NASA Astrophysics Data System (ADS)

Lacan, P.; Nivière, B.; Rousset, D.; Sénéchal, P.

2007-12-01

Due to its intraplate position, the on-going tectonic activity of the Western Pyrenees is only revealed by a moderate and diffuse seismicity. This seismicity presents a general E-W pattern and is distributed along the northern flank of the chain in the western part. We focus here on the Arudy area that suffered from one of the major Pyrenean instrumental earthquakes (M=5,1) in 1980. An early Cretaceous normal fault of the Iberian margin is probably the seismic source of this event. The late Cretaceous inversion of the margin, first in a left-lateral strike-slip mode and then in a more frontal convergence, resulted in a shallow pop-up geometry near Arudy. This pop-up attests of the presence in depth of a crustal discontinuity. The present-day geodynamic arrangement might reactivate this accident in a right lateral mode. This reactivation leads to a strain partitioning between the deep crustal discontinuity and the shallow pop-up that achieved respectively the lateral and frontal components of the displacement. Folding of Quaternary terrace remnants above the thrusts limiting the pop-up, attests of the Pleistocene activity of the structure. Growth of alluvial depocenters in the footwall of these thrusts revealed by near-surface geophysical surveys (electric tomography and ground penetrating radar) attest too of this activity. This deformation resulted in ca 1500 m long and 5-10 m high folds during the middle to late Pleistocene. Using a strain partitioning model, this quantification of the near-surface deformation allows to estimate the displacement achieved by the blind crustal discontinuity. So the seismic hazard due to this fault is better constrained. Project funded by Région Aquitaine and TTI Production.

Comment on "Acoustical observation of bubble oscillations induced by bubble popping"

NASA Astrophysics Data System (ADS)

Blanc, É.; Ollivier, F.; Antkowiak, A.; Wunenburger, R.

2015-03-01

We have reproduced the experiment of acoustic monitoring of spontaneous popping of single soap bubbles standing in air reported by Ding et al. [2aa Phys. Rev. E 75, 041601 (2007), 10.1103/PhysRevE.75.041601]. By using a single microphone and two different signal acquisition systems recording in parallel the signal at the microphone output, among them the system used by Ding et al., we have experimentally evidenced that the acoustic precursors of bubble popping events detected by Ding et al. actually result from an acausal artifact of the signal processing performed by their acquisition system which lies outside of its prescribed working frequency range. No acoustic precursor of popping could be evidenced with the microphone used in these experiments, whose sensitivity is 1 V Pa-1 and frequency range is 500 Hz-100 kHz.

Identification and quantification of virulence factors of enterotoxigenic Escherichia coli by high-resolution melting curve quantitative PCR.

PubMed

Wang, Weilan; Zijlstra, Ruurd T; Gänzle, Michael G

2017-05-15

Diagnosis of enterotoxigenic E. coli (ETEC) associated diarrhea is complicated by the diversity of E.coli virulence factors. This study developed a multiplex quantitative PCR assay based on high-resolution melting curves analysis (HRM-qPCR) to identify and quantify genes encoding five ETEC fimbriae related to diarrhea in swine, i.e. K99, F41, F18, F6 and K88. Five fimbriae expressed by ETEC were amplified in multiple HRM-qPCR reactions to allow simultaneous identification and quantification of five target genes. The assay was calibrated to allow quantification of the most abundant target gene, and validated by analysis of 30 samples obtained from piglets with diarrhea and healthy controls, and comparison to standard qPCR detection. The five amplicons with melting temperatures (Tm) ranging from 74.7 ± 0.06 to 80.5 ± 0.15 °C were well-separated by HRM-qPCR. The area of amplicons under the melting peak correlated linearly to the proportion of the template in the calibration mixture if the proportion exceeded 4.8% (K88) or <1% (all other amplicons). The suitability of the method was evaluated using 30 samples from weaned pigs aged 6-7 weeks; 14 of these animals suffered from diarrhea in consequence of poor sanitary conditions. Genes encoding fimbriae and enterotoxins were quantified by HRM-qPCR and/or qPCR. The multiplex HRM-qPCR allowed accurate analysis when the total gene copy number of targets was more than 1 × 10 5 / g wet feces and the HRM curves were able to simultaneously distinguish fimbriae genes in the fecal samples. The relative quantification of the most abundant F18 based on melting peak area was highly correlated (P < 0.001; r 2  = 0.956) with that of individual qPCR result but the correlation for less abundant fimbriae was much lower. The multiplex HRM assay identifies ETEC virulence factors specifically and efficiently. It correctly indicated the predominant fimbriae type and additionally provides information of presence/ absence of other fimbriae types and it could find broad applications for pathogen diagnosis.

Optimization and Verification of Droplet Digital PCR Even-Specific Methods for the Quantification of GM Maize DAS1507 and NK603.

PubMed

Grelewska-Nowotko, Katarzyna; Żurawska-Zajfert, Magdalena; Żmijewska, Ewelina; Sowa, Sławomir

2018-05-01

In recent years, digital polymerase chain reaction (dPCR), a new molecular biology technique, has been gaining in popularity. Among many other applications, this technique can also be used for the detection and quantification of genetically modified organisms (GMOs) in food and feed. It might replace the currently widely used real-time PCR method (qPCR), by overcoming problems related to the PCR inhibition and the requirement of certified reference materials to be used as a calibrant. In theory, validated qPCR methods can be easily transferred to the dPCR platform. However, optimization of the PCR conditions might be necessary. In this study, we report the transfer of two validated qPCR methods for quantification of maize DAS1507 and NK603 events to the droplet dPCR (ddPCR) platform. After some optimization, both methods have been verified according to the guidance of the European Network of GMO Laboratories (ENGL) on analytical method verification (ENGL working group on "Method Verification." (2011) Verification of Analytical Methods for GMO Testing When Implementing Interlaboratory Validated Methods). Digital PCR methods performed equally or better than the qPCR methods. Optimized ddPCR methods confirm their suitability for GMO determination in food and feed.

Quantitative Component Analysis of Solid Mixtures by Analyzing Time Domain 1H and 19F T1 Saturation Recovery Curves (qSRC).

PubMed

Stueber, Dirk; Jehle, Stefan

2017-07-01

Prevalent polymorphism and complicated phase behavior of active pharmaceutical ingredients (APIs) often result in remarkable differences in the respective biochemical and physical API properties. Consequently, API form characterization and quantification play a central role in the pharmaceutical industry from early drug development to manufacturing. Here we present a novel and proficient quantification protocol for solid mixtures (qSRC) based on the measurement and mathematical fitting of T 1 nuclear magnetic resonance (NMR) saturation recovery curves collected on a bench top time-domain NMR instrument. The saturation recovery curves of the relevant pure components are used as fingerprints. Employing a bench top NMR instrument possesses clear benefits. These instruments exhibit a small footprint, do not present any special requirements on lab space, and required sample handling is simple and fast. The qSRC analysis can easily be conducted in a conventional laboratory setting as well as in an industrial production environment, making it a versatile tool with the potential for widespread application. The accuracy and efficiency of the qSRC method is illustrated using 1 H and 19 F T 1 data of selected pharmaceutical model compounds, as well as utilizing 1 H T 1 data of an actual binary API anhydrous polymorph system of a Merck & Co., Inc. compound formerly developed as a hepatitis C virus drug. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Multiplex Real-Time qPCR Assay for Simultaneous and Sensitive Detection of Phytoplasmas in Sesame Plants and Insect Vectors

PubMed Central

Ikten, Cengiz; Ustun, Rustem; Catal, Mursel; Yol, Engin; Uzun, Bulent

2016-01-01

Phyllody, a destructive and economically important disease worldwide caused by phytoplasma infections, is characterized by the abnormal development of floral structures into stunted leafy parts and contributes to serious losses in crop plants, including sesame (Sesamum indicum L.). Accurate identification, differentiation, and quantification of phyllody-causing phytoplasmas are essential for effective management of this plant disease and for selection of resistant sesame varieties. In this study, a diagnostic multiplex qPCR assay was developed using TaqMan® chemistry based on detection of the 16S ribosomal RNA gene of phytoplasmas and the 18S ribosomal gene of sesame. Phytoplasma and sesame specific primers and probes labeled with different fluorescent dyes were used for simultaneous amplification of 16SrII and 16SrIX phytoplasmas in a single tube. The multiplex real-time qPCR assay allowed accurate detection, differentiation, and quantification of 16SrII and 16SrIX groups in 109 sesame plant and 92 insect vector samples tested. The assay was found to have a detection sensitivity of 1.8 x 102 and 1.6 x 102 DNA copies for absolute quantification of 16SrII and 16SrIX group phytoplasmas, respectively. Relative quantification was effective and reliable for determination of phyllody phytoplasma DNA amounts normalized to sesame DNA in infected plant tissues. The development of this qPCR assay provides a method for the rapid measurement of infection loads to identify resistance levels of sesame genotypes against phyllody phytoplasma disease. PMID:27195795

A stand-alone tree demography and landscape structure module for Earth system models: integration with global forest data

NASA Astrophysics Data System (ADS)

Haverd, V.; Smith, B.; Nieradzik, L. P.; Briggs, P. R.

2014-02-01

Poorly constrained rates of biomass turnover are a key limitation of Earth system models (ESM). In light of this, we recently proposed a new approach encoded in a model called Populations-Order-Physiology (POP), for the simulation of woody ecosystem stand dynamics, demography and disturbance-mediated heterogeneity. POP is suitable for continental to global applications and designed for coupling to the terrestrial ecosystem component of any ESM. POP bridges the gap between first generation Dynamic Vegetation Models (DVMs) with simple large-area parameterisations of woody biomass (typically used in current ESMs) and complex second generation DVMs, that explicitly simulate demographic processes and landscape heterogeneity of forests. The key simplification in the POP approach, compared with second-generation DVMs, is to compute physiological processes such as assimilation at grid-scale (with CABLE or a similar land surface model), but to partition the grid-scale biomass increment among age classes defined at sub grid-scale, each subject to its own dynamics. POP was successfully demonstrated along a savanna transect in northern Australia, replicating the effects of strong rainfall and fire disturbance gradients on observed stand productivity and structure. Here, we extend the application of POP to a range of forest types around the globe, employing paired observations of stem biomass and density from forest inventory data to calibrate model parameters governing stand demography and biomass evolution. The calibrated POP model is then coupled to the CABLE land surface model and the combined model (CABLE-POP) is evaluated against leaf-stem allometry observations from forest stands ranging in age from 3 to 200 yr. Results indicate that simulated biomass pools conform well with observed allometry. We conclude that POP represents a preferable alternative to large-area parameterisations of woody biomass turnover, typically used in current ESMs.

Quantification of concentrated Chinese medicine granules by quantitative polymerase chain reaction.

PubMed

Lo, Yat-Tung; Shaw, Pang-Chui

2017-10-25

Determination of the amount of constituent in a multi-herb product is important for quality control. In concentrated Chinese medicine granules (CCMG), no dregs are left after dissolution of the CCMG. This study is the first to examine the feasibility of using quantitative polymerase chain reaction (qPCR) to find the amount of CCMG in solution form. DNA was extracted from Hirudo and Zaocys CCMG mixed at different ratios and amplified in qPCR using species-specific primers. The threshold cycle (C T ) obtained was compared with the respective standard curves. Results showed that reproducible quantification results could be obtained (1) for 5-50mg CCMG using a modified DNA extraction protocol, (2) amongst DNA extracted from the same batch of CCMG and (3) amongst different batches of CCMG from the same company. This study demonstrated the constitute amount of CCMG in a mixture could be determined using qPCR. This work has extended the application of DNA techniques for the quantification of herbal products and this approach may be developed for quality assurance in the CCMG industry. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantification of Plasma miRNAs by Digital PCR for Cancer Diagnosis

PubMed Central

Ma, Jie; Li, Ning; Guarnera, Maria; Jiang, Feng

2013-01-01

Analysis of plasma microRNAs (miRNAs) by quantitative polymerase chain reaction (qPCR) provides a potential approach for cancer diagnosis. However, absolutely quantifying low abundant plasma miRNAs is challenging with qPCR. Digital PCR offers a unique means for assessment of nucleic acids presenting at low levels in plasma. This study aimed to evaluate the efficacy of digital PCR for quantification of plasma miRNAs and the potential utility of this technique for cancer diagnosis. We used digital PCR to quantify the copy number of plasma microRNA-21-5p (miR-21–5p) and microRNA-335–3p (miR-335–3p) in 36 lung cancer patients and 38 controls. Digital PCR showed a high degree of linearity and quantitative correlation with miRNAs in a dynamic range from 1 to 10,000 copies/μL of input, with high reproducibility. qPCR exhibited a dynamic range from 100 to 1×107 copies/μL of input. Digital PCR had a higher sensitivity to detect copy number of the miRNAs compared with qPCR. In plasma, digital PCR could detect copy number of both miR-21–5p and miR-335–3p, whereas qPCR was only able to assess miR-21–5p. Quantification of the plasma miRNAs by digital PCR provided 71.8% sensitivity and 80.6% specificity in distinguishing lung cancer patients from cancer-free subjects. PMID:24277982

Optimized methods for total nucleic acid extraction and quantification of the bat white-nose syndrome fungus, Pseudogymnoascus destructans, from swab and environmental samples.

PubMed

Verant, Michelle L; Bohuski, Elizabeth A; Lorch, Jeffery M; Blehert, David S

2016-03-01

The continued spread of white-nose syndrome and its impacts on hibernating bat populations across North America has prompted nationwide surveillance efforts and the need for high-throughput, noninvasive diagnostic tools. Quantitative real-time polymerase chain reaction (qPCR) analysis has been increasingly used for detection of the causative fungus, Pseudogymnoascus destructans, in both bat- and environment-associated samples and provides a tool for quantification of fungal DNA useful for research and monitoring purposes. However, precise quantification of nucleic acid from P. destructans is dependent on effective and standardized methods for extracting nucleic acid from various relevant sample types. We describe optimized methodologies for extracting fungal nucleic acids from sediment, guano, and swab-based samples using commercial kits together with a combination of chemical, enzymatic, and mechanical modifications. Additionally, we define modifications to a previously published intergenic spacer-based qPCR test for P. destructans to refine quantification capabilities of this assay. © 2016 The Author(s).

Optimized methods for total nucleic acid extraction and quantification of the bat white-nose syndrome fungus, Pseudogymnoascus destructans, from swab and environmental samples

USGS Publications Warehouse

Verant, Michelle; Bohuski, Elizabeth A.; Lorch, Jeffrey M.; Blehert, David

2016-01-01

The continued spread of white-nose syndrome and its impacts on hibernating bat populations across North America has prompted nationwide surveillance efforts and the need for high-throughput, noninvasive diagnostic tools. Quantitative real-time polymerase chain reaction (qPCR) analysis has been increasingly used for detection of the causative fungus, Pseudogymnoascus destructans, in both bat- and environment-associated samples and provides a tool for quantification of fungal DNA useful for research and monitoring purposes. However, precise quantification of nucleic acid fromP. destructans is dependent on effective and standardized methods for extracting nucleic acid from various relevant sample types. We describe optimized methodologies for extracting fungal nucleic acids from sediment, guano, and swab-based samples using commercial kits together with a combination of chemical, enzymatic, and mechanical modifications. Additionally, we define modifications to a previously published intergenic spacer–based qPCR test for P. destructans to refine quantification capabilities of this assay.

Geographical information systems as a tool for monitoring tobacco industry advertising.

PubMed

Vardavas, C I; Connolly, G N; Kafatos, A G

2009-06-01

Although the use of a geographical information systems (GIS) approach is usually applied to epidemiological disease outbreaks and environmental exposure mapping, it has significant potential as a tobacco control research tool in monitoring point-of-purchase (POP) tobacco advertising. An ecological study design approach was applied so as to primarily evaluate and interpret the spatial density and intensity of POP and tobacco industry advertisements within <300 m to high schools in Greece with the application of GIS methodology combining mapping, photographing and global positioning data. The GIS approach identified 133 POP and 44 billboards within 300 m of the school gates of Heraklion schools. On average 13 POP (range 4-21) and 4.4 billboards (range 1-9) were located per school, and all had at least 1 POP within 20 m of the school gate. On average (SD) 9 (6) tobacco advertisements per POP (range 0-25) were noted, and 80% of them were below child height. The GIS protocol identified that kiosks, that were excepted from the Greek ban on tobacco advertising, in comparison to other POP, were found not only to be closer and visible from the school gates (44.1% vs 10.8%, p<0.001) but were also found to have more external advertisements (8 (5) vs 5 (3), p<0.001). This study demonstrates the effectiveness of a GIS system in monitoring tobacco industry advertising on a large population-based scale and implies its use as a standardised method for monitoring tobacco industry strategies and tobacco control efforts.

A Two-component NADPH Oxidase (NOX)-like System in Bacteria Is Involved in the Electron Transfer Chain to the Methionine Sulfoxide Reductase MsrP*

PubMed Central

Juillan-Binard, Céline; Picciocchi, Antoine; Andrieu, Jean-Pierre; Petit-Hartlein, Isabelle; Caux-Thang, Christelle; Vivès, Corinne; Nivière, Vincent

2017-01-01

MsrPQ is a newly identified methionine sulfoxide reductase system found in bacteria, which appears to be specifically involved in the repair of periplasmic proteins oxidized by hypochlorous acid. It involves two proteins: a periplasmic one, MsrP, previously named YedY, carrying out the Msr activity, and MsrQ, an integral b-type heme membrane-spanning protein, which acts as the specific electron donor to MsrP. MsrQ, previously named YedZ, was mainly characterized by bioinformatics as a member of the FRD superfamily of heme-containing membrane proteins, which include the NADPH oxidase proteins (NOX/DUOX). Here we report a detailed biochemical characterization of the MsrQ protein from Escherichia coli. We optimized conditions for the overexpression and membrane solubilization of an MsrQ-GFP fusion and set up a purification scheme allowing the production of pure MsrQ. Combining UV-visible spectroscopy, heme quantification, and site-directed mutagenesis of histidine residues, we demonstrated that MsrQ is able to bind two b-type hemes through the histidine residues conserved between the MsrQ and NOX protein families. In addition, we identify the E. coli flavin reductase Fre, which is related to the dehydrogenase domain of eukaryotic NOX enzymes, as an efficient cytosolic electron donor to the MsrQ heme moieties. Cross-linking experiments as well as surface Plasmon resonance showed that Fre interacts with MsrQ to form a specific complex. Taken together, these data support the identification of the first prokaryotic two-component protein system related to the eukaryotic NOX family and involved in the reduction of periplasmic oxidized proteins. PMID:28028176

Evaluation of four commercial quantitative real-time PCR kits with inhibited and degraded samples.

PubMed

Holmes, Amy S; Houston, Rachel; Elwick, Kyleen; Gangitano, David; Hughes-Stamm, Sheree

2018-05-01

DNA quantification is a vital step in forensic DNA analysis to determine the optimal input amount for DNA typing. A quantitative real-time polymerase chain reaction (qPCR) assay that can predict DNA degradation or inhibitors present in the sample prior to DNA amplification could aid forensic laboratories in creating a more streamlined and efficient workflow. This study compares the results from four commercial qPCR kits: (1) Investigator® Quantiplex® Pro Kit, (2) Quantifiler® Trio DNA Quantification Kit, (3) PowerQuant® System, and (4) InnoQuant® HY with high molecular weight DNA, low template samples, degraded samples, and DNA spiked with various inhibitors.The results of this study indicate that all kits were comparable in accurately predicting quantities of high quality DNA down to the sub-picogram level. However, the InnoQuant(R) HY kit showed the highest precision across the DNA concentration range tested in this study. In addition, all kits performed similarly with low concentrations of forensically relevant PCR inhibitors. However, in general, the Investigator® Quantiplex® Pro Kit was the most tolerant kit to inhibitors and provided the most accurate quantification results with higher concentrations of inhibitors (except with salt). PowerQuant® and InnoQuant® HY were the most sensitive to inhibitors, but they did indicate significant levels of PCR inhibition. When quantifying degraded samples, each kit provided different degradation indices (DI), with Investigator® Quantiplex® Pro indicating the largest DI and Quantifiler® Trio indicating the smallest DI. When the qPCR kits were paired with their respective STR kit to genotype highly degraded samples, the Investigator® 24plex QS and GlobalFiler® kits generated more complete profiles when the small target concentrations were used for calculating input amount.

GMO quantification: valuable experience and insights for the future.

PubMed

Milavec, Mojca; Dobnik, David; Yang, Litao; Zhang, Dabing; Gruden, Kristina; Zel, Jana

2014-10-01

Cultivation and marketing of genetically modified organisms (GMOs) have been unevenly adopted worldwide. To facilitate international trade and to provide information to consumers, labelling requirements have been set up in many countries. Quantitative real-time polymerase chain reaction (qPCR) is currently the method of choice for detection, identification and quantification of GMOs. This has been critically assessed and the requirements for the method performance have been set. Nevertheless, there are challenges that should still be highlighted, such as measuring the quantity and quality of DNA, and determining the qPCR efficiency, possible sequence mismatches, characteristics of taxon-specific genes and appropriate units of measurement, as these remain potential sources of measurement uncertainty. To overcome these problems and to cope with the continuous increase in the number and variety of GMOs, new approaches are needed. Statistical strategies of quantification have already been proposed and expanded with the development of digital PCR. The first attempts have been made to use new generation sequencing also for quantitative purposes, although accurate quantification of the contents of GMOs using this technology is still a challenge for the future, and especially for mixed samples. New approaches are needed also for the quantification of stacks, and for potential quantification of organisms produced by new plant breeding techniques.

Quantification of rapid environmental redox processes with quick-scanning x-ray absorption spectroscopy (Q-XAS)

PubMed Central

Ginder-Vogel, Matthew; Landrot, Gautier; Fischel, Jason S.; Sparks, Donald L.

2009-01-01

Quantification of the initial rates of environmental reactions at the mineral/water interface is a fundamental prerequisite to determining reaction mechanisms and contaminant transport modeling and predicting environmental risk. Until recently, experimental techniques with adequate time resolution and elemental sensitivity to measure initial rates of the wide variety of environmental reactions were quite limited. Techniques such as electron paramagnetic resonance and Fourier transform infrared spectroscopies suffer from limited elemental specificity and poor sensitivity to inorganic elements, respectively. Ex situ analysis of batch and stirred-flow systems provides high elemental sensitivity; however, their time resolution is inadequate to characterize rapid environmental reactions. Here we apply quick-scanning x-ray absorption spectroscopy (Q-XAS), at sub-second time-scales, to measure the initial oxidation rate of As(III) to As(V) by hydrous manganese(IV) oxide. Using Q-XAS, As(III) and As(V) concentrations were determined every 0.98 s in batch reactions. The initial apparent As(III) depletion rate constants (t < 30 s) measured with Q-XAS are nearly twice as large as rate constants measured with traditional analytical techniques. Our results demonstrate the importance of developing analytical techniques capable of analyzing environmental reactions on the same time scale as they occur. Given the high sensitivity, elemental specificity, and time resolution of Q-XAS, it has many potential applications. They could include measuring not only redox reactions but also dissolution/precipitation reactions, such as the formation and/or reductive dissolution of Fe(III) (hydr)oxides, solid-phase transformations (i.e., formation of layered-double hydroxide minerals), or almost any other reaction occurring in aqueous media that can be measured using x-ray absorption spectroscopy. PMID:19805269

Quantification of quercetin glycosides in 6 onion cultivars and comparisons of hydrolysis-HPLC and spectrophotometric methods in measuring total quercetin concentrations.

PubMed

Yoo, Kil Sun; Lee, Eun Jin; Patil, Bhimanagouda S

2010-03-01

This study was performed to purify and quantify quercetin glycosides (QG) and aglycone (free) quercetin (Q) in 6 selected onion cultivars and to compare analytical approaches based on high-performance liquid chromatography (HPLC) and spectrophotometry for the quantification of total quercetin (TQ) concentrations. Individual mono- and di-glycoside Q compounds were purified using a semipreparative HPLC and identified by comparing spectral data and by confirming corresponding peaks of QG and Q after incomplete enzyme-hydrolysis. Purified QG were quantified as Q by enzyme-hydrolysis/HPLC. TQ concentrations obtained from 20 onion bulbs with enzyme-hydrolysis/HPLC, no-hydrolysis/HPLC, and a spectrophotometric method without prior hydrolysis were significantly correlated (r(2)= 0.99) and were about 15% higher, identical, or 10% less than those concentrations by a standard acid-hydrolysis/HPLC method, respectively. During enzyme-hydrolysis of onion extracts, progressive reduction of the QG and formation of the corresponding mono-glycosides and Q were monitored using an analytical HPLC. TQ ranged from 83 to 330 microg/g F.W. in 6 selected cultivars of long-day or short-day onions. Q3,4'G and Q4'G were the 2 major compounds and comprised approximately between 94% and 97% of TQ in onions.

Application of Magnetic Nanoparticles in Pretreatment Device for POPs Analysis in Water

NASA Astrophysics Data System (ADS)

Chu, Dongzhi; Kong, Xiangfeng; Wu, Bingwei; Fan, Pingping; Cao, Xuan; Zhang, Ting

2018-01-01

In order to reduce process time and labour force of POPs pretreatment, and solve the problem that extraction column was easily clogged, the paper proposed a new technology of extraction and enrichment which used magnetic nanoparticles. Automatic pretreatment system had automatic sampling unit, extraction enrichment unit and elution enrichment unit. The paper briefly introduced the preparation technology of magnetic nanoparticles, and detailly introduced the structure and control system of automatic pretreatment system. The result of magnetic nanoparticles mass recovery experiments showed that the system had POPs analysis preprocessing capability, and the recovery rate of magnetic nanoparticles were over 70%. In conclusion, the author proposed three points optimization recommendation.

New molecular settings to support in vivo anti-malarial assays.

PubMed

Bahamontes-Rosa, Noemí; Alejandre, Ane Rodriguez; Gomez, Vanesa; Viera, Sara; Gomez-Lorenzo, María G; Sanz-Alonso, Laura María; Mendoza-Losana, Alfonso

2016-03-08

Quantitative real-time PCR (qPCR) is now commonly used as a method to confirm diagnosis of malaria and to differentiate recrudescence from re-infection, especially in clinical trials and in reference laboratories where precise quantification is critical. Although anti-malarial drug discovery is based on in vivo murine efficacy models, use of molecular analysis has been limited. The aim of this study was to develop qPCR as a valid methodology to support pre-clinical anti-malarial models by using filter papers to maintain material for qPCR and to compare this with traditional methods. FTA technology (Whatman) is a rapid and safe method for extracting nucleic acids from blood. Peripheral blood samples from mice infected with Plasmodium berghei, P. yoelii, or P. falciparum were kept as frozen samples or as spots on FTA cards. The extracted genetic material from both types of samples was assessed for quantification by qPCR using sets of specific primers specifically designed for Plasmodium 18S rRNA, LDH, and CytB genes. The optimal conditions for nucleic acid extraction from FTA cards and qPCR amplification were set up, and were confirmed to be suitable for parasite quantification using DNA as template after storage at room temperature for as long as 26 months in the case of P. berghei samples and 52 months for P. falciparum and P. yoelii. The quality of DNA extracted from the FTA cards for gene sequencing and microsatellite amplification was also assessed. This is the first study to report the suitability of FTA cards and qPCR assay to quantify parasite load in samples from in vivo efficacy models to support the drug discovery process.

Novel primers and PCR protocols for the specific detection and quantification of Sphingobium suberifaciens in situ

USDA-ARS?s Scientific Manuscript database

The pathogen causing corky root on lettuce, Sphingobium suberifaciens, is recalcitrant to standard epidemiological methods. Primers were selected from 16S rDNA sequences useful for the specific detection and quantification of S. suberifaciens. Conventional (PCR) and quantitative (qPCR) PCR protocols...

Droplet digital PCR (ddPCR) vs quantitative real-time PCR (qPCR) approach for detection and quantification of Merkel cell polyomavirus (MCPyV) DNA in formalin fixed paraffin embedded (FFPE) cutaneous biopsies.

PubMed

Arvia, Rosaria; Sollai, Mauro; Pierucci, Federica; Urso, Carmelo; Massi, Daniela; Zakrzewska, Krystyna

2017-08-01

Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma and high viral load in the skin was proposed as a risk factor for the occurrence of this tumour. MCPyV DNA was detected, with lower frequency, in different skin cancers but since the viral load was usually low, the real prevalence of viral DNA could be underestimated. To evaluate the performance of two assays (qPCR and ddPCR) for MCPyV detection and quantification in formalin fixed paraffin embedded (FFPE) tissue samples. Both assays were designed to simultaneous detection and quantification of both MCPyV as well as house-keeping DNA in clinical samples. The performance of MCPyV quantification was investigated using serial dilutions of cloned target DNA. We also evaluated the applicability of both tests for the analysis of 76 FFPE cutaneous biopsies. The two approaches resulted equivalent with regard to the reproducibility and repeatability and showed a high degree of linearity in the dynamic range tested in the present study. Moreover, qPCR was able to quantify ≥10 5 copies per reaction, while the upper limit of ddPCR was 10 4 copies. There was not significant difference between viral load measured by the two methods The detection limit of both tests was 0,15 copies per reaction, however, the number of positive samples obtained by ddPCR was higher than that obtained by qPCR (45% and 37% respectively). The ddPCR represents a better method for detection of MCPyV in FFPE biopsies, mostly these containing low copies number of viral genome. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantification of terpene trilactones in Ginkgo biloba with a 1H NMR method.

PubMed

Liang, Tingfu; Miyakawa, Takuya; Yang, Jinwei; Ishikawa, Tsutomu; Tanokura, Masaru

2018-06-01

Ginkgo biloba L. has been used as a herbal medicine in the traditional treatment of insufficient blood flow, memory deficits, and cerebral insufficiency. The terpene trilactone components, the bioactive agents of Ginkgo biloba L., have also been reported to exhibit useful functionality such as anti-inflammatory and neuroprotective effects. Therefore, in the present research, we attempted to analyze quantitatively the terpene trilactone components in Ginkgo biloba leaf extract, with quantitative 1 H NMR (qNMR) and obtained almost identical results to data reported using HPLC. Application of the qNMR method for the analysis of the terpene trilactone contents in commercial Ginkgo extract products, such as soft gel capsules and tablets, produced the same levels noted in package labels. Thus, qNMR is an alternative method for quantification of the terpene trilactone components in commercial Ginkgo extract products.

LATE POP III STAR FORMATION DURING THE EPOCH OF REIONIZATION: RESULTS FROM THE RENAISSANCE SIMULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Hao; Norman, Michael L.; O’Shea, Brian W.

2016-06-01

We present results on the formation of Population III (Pop III) stars at redshift 7.6 from the Renaissance Simulations, a suite of extremely high-resolution and physics-rich radiation transport hydrodynamics cosmological adaptive-mesh refinement simulations of high-redshift galaxy formation performed on the Blue Waters supercomputer. In a survey volume of about 220 comoving Mpc{sup 3}, we found 14 Pop III galaxies with recent star formation. The surprisingly late formation of Pop III stars is possible due to two factors: (i) the metal enrichment process is local and slow, leaving plenty of pristine gas to exist in the vast volume; and (ii) strongmore » Lyman–Werner radiation from vigorous metal-enriched star formation in early galaxies suppresses Pop III formation in (“not so”) small primordial halos with mass less than ∼3 × 10{sup 7} M {sub ⊙}. We quantify the properties of these Pop III galaxies and their Pop III star formation environments. We look for analogs to the recently discovered luminous Ly α emitter CR7, which has been interpreted as a Pop III star cluster within or near a metal-enriched star-forming galaxy. We find and discuss a system similar to this in some respects, however, the Pop III star cluster is far less massive and luminous than CR7 is inferred to be.« less

Most unwanted.

PubMed Central

Fisher, B E

1999-01-01

Persistent organic pollutants (POPs) can travel thousands of miles, accumulate in the food chain, and persist in the environment, taking as long as centuries to degrade. POPs are known to play a role in birth defects, cancer, immune system dysfunction, and reproductive problems in wildlife. While the effects of POPs on human health are unclear, many researchers believe that long-term exposure contributes to increasing rates of birth defects, fertility problems, greater susceptibility to disease, diminished intelligence, and certain cancers. Twelve POPs have been identified by the United Nations Environment Programme as requiring urgent regulatory attention. They include the pesticides aldrin, chlordane, DDT, dieldrin, endrin, heptachlor, hexachlorobenzene, mirex, and toxaphene. Of the remaining three POPs, polychlorinated biphenyls are industrial products (used in electrical transformers), and dioxins and furans are unintentional by-products of industrial processes. PMID:9872725

Determining Fungi rRNA Copy Number by PCR

EPA Science Inventory

The goal of this project is to improve the quantification of indoor fungal pollutants via the specific application of quantitative PCR (qPCR). Improvement will be made in the controls used in current qPCR applications. This work focuses on the use of two separate controls within ...

Detection and quantification limits of the EPA Enterococcus qPCR method

EPA Science Inventory

The U.S. EPA will be recommending a quantitative polymerase chain reaction (qPCR) method targeting Enterococcus spp. as an option for monitoring recreational beach water quality in 2013 and has published preliminary proposed water quality criteria guidelines for the method. An im...

A review of optimization and quantification techniques for chemical exchange saturation transfer (CEST) MRI toward sensitive in vivo imaging

PubMed Central

Guo, Yingkun; Zheng, Hairong; Sun, Phillip Zhe

2015-01-01

Chemical exchange saturation transfer (CEST) MRI is a versatile imaging method that probes the chemical exchange between bulk water and exchangeable protons. CEST imaging indirectly detects dilute labile protons via bulk water signal changes following selective saturation of exchangeable protons, which offers substantial sensitivity enhancement and has sparked numerous biomedical applications. Over the past decade, CEST imaging techniques have rapidly evolved due to contributions from multiple domains, including the development of CEST mathematical models, innovative contrast agent designs, sensitive data acquisition schemes, efficient field inhomogeneity correction algorithms, and quantitative CEST (qCEST) analysis. The CEST system that underlies the apparent CEST-weighted effect, however, is complex. The experimentally measurable CEST effect depends not only on parameters such as CEST agent concentration, pH and temperature, but also on relaxation rate, magnetic field strength and more importantly, experimental parameters including repetition time, RF irradiation amplitude and scheme, and image readout. Thorough understanding of the underlying CEST system using qCEST analysis may augment the diagnostic capability of conventional imaging. In this review, we provide a concise explanation of CEST acquisition methods and processing algorithms, including their advantages and limitations, for optimization and quantification of CEST MRI experiments. PMID:25641791

A comparative study of digital RT-PCR and RT-qPCR for quantification of Hepatitis A virus and Norovirus in lettuce and water samples.

PubMed

Coudray-Meunier, Coralie; Fraisse, Audrey; Martin-Latil, Sandra; Guillier, Laurent; Delannoy, Sabine; Fach, Patrick; Perelle, Sylvie

2015-05-18

Sensitive and quantitative detection of foodborne enteric viruses is classically achieved by quantitative RT-PCR (RT-qPCR). Recently, digital PCR (dPCR) was described as a novel approach to genome quantification without need for a standard curve. The performance of microfluidic digital RT-PCR (RT-dPCR) was compared to RT-qPCR for detecting the main viruses responsible for foodborne outbreaks (human Noroviruses (NoV) and Hepatitis A virus (HAV)) in spiked lettuce and bottled water. Two process controls (Mengovirus and Murine Norovirus) were used and external amplification controls (EAC) were added to examine inhibition of RT-qPCR and RT-dPCR. For detecting viral RNA and cDNA, the sensitivity of the RT-dPCR assays was either comparable to that of RT-qPCR (RNA of HAV, NoV GI, Mengovirus) or slightly (around 1 log10) decreased (NoV GII and MNV-1 RNA and of HAV, NoV GI, NoV GII cDNA). The number of genomic copies determined by dPCR was always from 0.4 to 1.7 log10 lower than the expected numbers of copies calculated by using the standard qPCR curve. Viral recoveries calculated by RT-dPCR were found to be significantly higher than by RT-qPCR for NoV GI, HAV and Mengovirus in water, and for NoV GII and HAV in lettuce samples. The RT-dPCR assay proved to be more tolerant to inhibitory substances present in lettuce samples. This absolute quantitation approach may be useful to standardize quantification of enteric viruses in bottled water and lettuce samples and may be extended to quantifying other human pathogens in food samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Paperless Procurement: The Impact of Advanced Automation

DTIC Science & Technology

1992-09-01

System. POPS = Paperless Order Processing System; RADMIS = Research and Development Management Information System; SAACONS=Standard Army Automated... order processing system, which then updates the contractor’s production (or delivery) scheduling and contract accounting applications. In return, the...used by the DLA’s POPS. 3-5 into an EDI delivery order and pass it directly to the distributor’s or manufacturer’s order processing system. That

A stand-alone tree demography and landscape structure module for Earth system models: integration with inventory data from temperate and boreal forests

NASA Astrophysics Data System (ADS)

Haverd, V.; Smith, B.; Nieradzik, L. P.; Briggs, P. R.

2014-08-01

Poorly constrained rates of biomass turnover are a key limitation of Earth system models (ESMs). In light of this, we recently proposed a new approach encoded in a model called Populations-Order-Physiology (POP), for the simulation of woody ecosystem stand dynamics, demography and disturbance-mediated heterogeneity. POP is suitable for continental to global applications and designed for coupling to the terrestrial ecosystem component of any ESM. POP bridges the gap between first-generation dynamic vegetation models (DVMs) with simple large-area parameterisations of woody biomass (typically used in current ESMs) and complex second-generation DVMs that explicitly simulate demographic processes and landscape heterogeneity of forests. The key simplification in the POP approach, compared with second-generation DVMs, is to compute physiological processes such as assimilation at grid-scale (with CABLE (Community Atmosphere Biosphere Land Exchange) or a similar land surface model), but to partition the grid-scale biomass increment among age classes defined at sub-grid-scale, each subject to its own dynamics. POP was successfully demonstrated along a savanna transect in northern Australia, replicating the effects of strong rainfall and fire disturbance gradients on observed stand productivity and structure. Here, we extend the application of POP to wide-ranging temporal and boreal forests, employing paired observations of stem biomass and density from forest inventory data to calibrate model parameters governing stand demography and biomass evolution. The calibrated POP model is then coupled to the CABLE land surface model, and the combined model (CABLE-POP) is evaluated against leaf-stem allometry observations from forest stands ranging in age from 3 to 200 year. Results indicate that simulated biomass pools conform well with observed allometry. We conclude that POP represents an ecologically plausible and efficient alternative to large-area parameterisations of woody biomass turnover, typically used in current ESMs.

Development of a qPCR Method for the Identification and Quantification of Two Closely Related Tuna Species, Bigeye Tuna (Thunnus obesus) and Yellowfin Tuna (Thunnus albacares), in Canned Tuna.

PubMed

Bojolly, Daline; Doyen, Périne; Le Fur, Bruno; Christaki, Urania; Verrez-Bagnis, Véronique; Grard, Thierry

2017-02-01

Bigeye tuna (Thunnus obesus) and yellowfin tuna (Thunnus albacares) are among the most widely used tuna species for canning purposes. Not only substitution but also mixing of tuna species is prohibited by the European regulation for canned tuna products. However, as juveniles of bigeye and yellowfin tunas are very difficult to distinguish, unintentional substitutions may occur during the canning process. In this study, two mitochondrial markers from NADH dehydrogenase subunit 2 and cytochrome c oxidase subunit II genes were used to identify bigeye tuna and yellowfin tuna, respectively, utilizing TaqMan qPCR methodology. Two different qPCR-based methods were developed to quantify the percentage of flesh of each species used for can processing. The first one was based on absolute quantification using standard curves realized with these two markers; the second one was founded on relative quantification with the universal 12S rRNA gene as the endogenous gene. On the basis of our results, we conclude that our methodology could be applied to authenticate these two closely related tuna species when used in a binary mix in tuna cans.

Development of qPCR systems to quantify shoot infections by canker-causing pathogens in stone fruits and nut crops.

PubMed

Luo, Y; Gu, S; Felts, D; Puckett, R D; Morgan, D P; Michailides, T J

2017-02-01

To develop real-time PCR assays for quantification of shoot infection levels of canker disease of stone fruits and nut crops caused by six fungal pathogen groups. This study focused on six major canker-causing fungal pathogen groups: Phomopsis sp., Botryosphaeria dothidea, Lasiodiplodia sp., Cytospora sp., Neofusicoccum sp. and Diplodia sp., occurring in stone fruits and nut crops in California. DNA primers were designed to specifically target each of the six pathogen groups after the specificity tests using canker-causing and non-canker-causing pathogens and by using DNA sequences of other species from GenBank using blast. The quantitative real-time PCR (qPCR) systems were developed and used to quantify the infection levels of inoculated dried plum shoots. For Neofusicoccum sp. and Phomopsis sp., which were used in inoculation of walnut shoots, the values of the molecular severity ranged from 5·60 to 6·94 during the 16 days of latent infection period. The qPCR assays were more efficient, accurate and precise to quantify latent infections caused by canker-causing pathogens as compared to the traditional plating methods. This study demonstrated the potential of using the developed qPCR systems for epidemiological studies on canker diseases of woody plants. © 2016 The Society for Applied Microbiology.

Pop tests of storable biopropellant liquid apogee engine

NASA Astrophysics Data System (ADS)

Kuroda, Yukio; Tadano, Makoto; Sato, Masahiro; Kusaka, Kazuo; Kobayashi, Hideyuki; Iihara, Sigeyasu; Ban, Hiroyuki

1994-10-01

A pressure-fed, blowdown, hydrazine/NTO apogee propulsion system had been selected for the ETS-6. One of the problems encountered during the development of the engine was the occurrence of pops (popping) at the higher operating chamber pressures. Pops are irregular high amplitude pressure pulses. It is generally agreed that pops is a liquid spray/gas two-phase explosion triggered by a local explosion near the jet impingement region. The effects of operating parameters on pops observed in the development tests of the apogee engine for the ETS-6 were inconsistent with those reported earlier for single impingement injectors; pops with the apogee engine injectors was more likely to occur at higher chamber pressures, higher injection velocities, and higher propellant temperatures. Pops data were correlated fairly well in chamber pressures (bar-P(sub c)) vs. fuel Reynolds number (R(sub ef)) plane. However, the range of operating parameters for the above correlation were very narrow since they were obtained during injector screening tests for a particular application to the apogee engine. It was also felt that the above correlation was too simplistic to capture any effect of design parameters of multi-element injectors. In the present study, the demarcation between pops and the pops-free region was determined in broader operating ranges and design parameters. The range of bar-P(sub c) and R(sub ef) was extended by exchanging graphite nozzle throat inserts with different throat diameters. The injectors were carefully selected to obtain effects, if any, of (1) film cooling fraction, (2) secondary mixing, and (3) number of elements and/or fuel orifice diameters. It was found that there was a threshold fuel Reynolds number below which no pops were observed at any chamber pressures and that the pops region curve in the bar-P(sub c)-R(sub ef) plane had two branches: upper branches and lower branches.

The characterization and certification of a quantitative reference material for Legionella detection and quantification by qPCR.

PubMed

Baume, M; Garrelly, L; Facon, J P; Bouton, S; Fraisse, P O; Yardin, C; Reyrolle, M; Jarraud, S

2013-06-01

The characterization and certification of a Legionella DNA quantitative reference material as a primary measurement standard for Legionella qPCR. Twelve laboratories participated in a collaborative certification campaign. A candidate reference DNA material was analysed through PCR-based limiting dilution assays (LDAs). The validated data were used to statistically assign both a reference value and an associated uncertainty to the reference material. This LDA method allowed for the direct quantification of the amount of Legionella DNA per tube in genomic units (GU) and the determination of the associated uncertainties. This method could be used for the certification of all types of microbiological standards for qPCR. The use of this primary standard will improve the accuracy of Legionella qPCR measurements and the overall consistency of these measurements among different laboratories. The extensive use of this certified reference material (CRM) has been integrated in the French standard NF T90-471 (April 2010) and in the ISO Technical Specification 12 869 (Anon 2012 International Standardisation Organisation) for validating qPCR methods and ensuring the reliability of these methods. © 2013 The Society for Applied Microbiology.

A Rapid Protocol of Crude RNA/DNA Extraction for RT-qPCR Detection and Quantification of 'Candidatus Phytoplasma prunorum'

PubMed Central

Minguzzi, Stefano; Terlizzi, Federica; Lanzoni, Chiara; Poggi Pollini, Carlo; Ratti, Claudio

2016-01-01

Many efforts have been made to develop a rapid and sensitive method for phytoplasma and virus detection. Taking our cue from previous works, different rapid sample preparation methods have been tested and applied to Candidatus Phytoplasma prunorum (‘Ca. P. prunorum’) detection by RT-qPCR. A duplex RT-qPCR has been optimized using the crude sap as a template to simultaneously amplify a fragment of 16S rRNA of the pathogen and 18S rRNA of the host plant. The specific plant 18S rRNA internal control allows comparison and relative quantification of samples. A comparison between DNA and RNA contribution to qPCR detection is provided, showing higher contribution of the latter. The method presented here has been validated on more than a hundred samples of apricot, plum and peach trees. Since 2013, this method has been successfully applied to monitor ‘Ca. P. prunorum’ infections in field and nursery. A triplex RT-qPCR assay has also been optimized to simultaneously detect ‘Ca. P. prunorum’ and Plum pox virus (PPV) in Prunus. PMID:26742106

Maternal exposure to a mixture of persistent organic pollutants (POPs) affects testis histology, epididymal sperm count and induces sperm DNA fragmentation in mice.

PubMed

Khezri, Abdolrahman; Lindeman, Birgitte; Krogenæs, Anette K; Berntsen, Hanne F; Zimmer, Karin E; Ropstad, Erik

2017-08-15

Persistent organic pollutants (POPs) are widespread throughout the environment and some are suspected to induce reproductive toxicity. As animals and humans are exposed to complex mixtures of POPs, it is reasonable to assess how such mixtures could interact with the reproductive system. Our aim is to investigate how maternal exposure to a mixture of 29 different persistent organic pollutants, formulated to mimic the relative POP levels in the food basket of the Scandinavian population, could alter reproductive endpoints. Female mice were exposed via feed from weaning, during pregnancy and lactation in 3 exposure groups (control (C), low (L) and high (H)). Testicular morphometric endpoints, epididymal sperm concentration and sperm DNA integrity were assessed in adult male offspring. We found that the number of tubules, proportion of tubule compartments and epididymal sperm concentration significantly decreased in both POP exposed groups. Epididymal sperm from both POP exposed groups showed increased DNA fragmentation. It is concluded that maternal exposure to a defined POP mixture relevant to human exposure can affect testicular development, sperm production and sperm chromatin integrity. Copyright © 2017 Elsevier Inc. All rights reserved.

Novel HPLC-UV Method for Simultaneous Determination of Fat-soluble Vitamins and Coenzyme Q10 in Medicines and Supplements.

PubMed

Temova-Rakuša, Žane; Srečnik, Eva; Roškar, Robert

2017-09-01

A precise, accurate and rapid HPLC-UV method for simultaneous determination of fat-soluble vitamins (vitamin D3, E-acetate, K1, β-carotene, A-palmitate) and coenzyme Q10 was developed and validated according to ICH guidelines. Optimal chromatographic separation of the analytes in minimal analysis time (8 min) was achieved on a Luna C18 150 × 4.6 mm column using a mixture of acetonitrile, tetrahydrofuran and water (50:45:5, v/v/v). The described reversed phase HPLC method is the first published for quantification of these five fat-soluble vitamins and coenzyme Q10 within a single chromatographic run. The method was further applied for quantification of the analytes in selected liquid and solid dosage forms, registered as nutritional supplements and prescription medicines, which confirmed its suitability for routine analysis.

Evaluation of digital PCR for absolute RNA quantification.

PubMed

Sanders, Rebecca; Mason, Deborah J; Foy, Carole A; Huggett, Jim F

2013-01-01

Gene expression measurements detailing mRNA quantities are widely employed in molecular biology and are increasingly important in diagnostic fields. Reverse transcription (RT), necessary for generating complementary DNA, can be both inefficient and imprecise, but remains a quintessential RNA analysis tool using qPCR. This study developed a Transcriptomic Calibration Material and assessed the RT reaction using digital (d)PCR for RNA measurement. While many studies characterise dPCR capabilities for DNA quantification, less work has been performed investigating similar parameters using RT-dPCR for RNA analysis. RT-dPCR measurement using three, one-step RT-qPCR kits was evaluated using single and multiplex formats when measuring endogenous and synthetic RNAs. The best performing kit was compared to UV quantification and sensitivity and technical reproducibility investigated. Our results demonstrate assay and kit dependent RT-dPCR measurements differed significantly compared to UV quantification. Different values were reported by different kits for each target, despite evaluation of identical samples using the same instrument. RT-dPCR did not display the strong inter-assay agreement previously described when analysing DNA. This study demonstrates that, as with DNA measurement, RT-dPCR is capable of accurate quantification of low copy RNA targets, but the results are both kit and target dependent supporting the need for calibration controls.

Digital PCR as a tool to measure HIV persistence.

PubMed

Rutsaert, Sofie; Bosman, Kobus; Trypsteen, Wim; Nijhuis, Monique; Vandekerckhove, Linos

2018-01-30

Although antiretroviral therapy is able to suppress HIV replication in infected patients, the virus persists and rebounds when treatment is stopped. In order to find a cure that can eradicate the latent reservoir, one must be able to quantify the persisting virus. Traditionally, HIV persistence studies have used real-time PCR (qPCR) to measure the viral reservoir represented by HIV DNA and RNA. Most recently, digital PCR is gaining popularity as a novel approach to nucleic acid quantification as it allows for absolute target quantification. Various commercial digital PCR platforms are nowadays available that implement the principle of digital PCR, of which Bio-Rad's QX200 ddPCR is currently the most used platform in HIV research. Quantification of HIV by digital PCR is proving to be a valuable improvement over qPCR as it is argued to have a higher robustness to mismatches between the primers-probe set and heterogeneous HIV, and forfeits the need for a standard curve, both of which are known to complicate reliable quantification. However, currently available digital PCR platforms occasionally struggle with unexplained false-positive partitions, and reliable segregation between positive and negative droplets remains disputed. Future developments and advancements of the digital PCR technology are promising to aid in the accurate quantification and characterization of the persistent HIV reservoir.

Choice of reference measurements affects quantification of long diffusion time behaviour using stimulated echoes.

PubMed

Kleinnijenhuis, Michiel; Mollink, Jeroen; Lam, Wilfred W; Kinchesh, Paul; Khrapitchev, Alexandre A; Smart, Sean C; Jbabdi, Saad; Miller, Karla L

2018-02-01

To demonstrate how reference data affect the quantification of the apparent diffusion coefficient (ADC) in long diffusion time measurements with diffusion-weighted stimulated echo acquisition mode (DW-STEAM) measurements, and to present a modification to avoid contribution from crusher gradients in DW-STEAM. For DW-STEAM, reference measurements at long diffusion times have significant b 0 value, because b = 0 cannot be achieved in practice as a result of the need for signal spoiling. Two strategies for acquiring reference data over a range of diffusion times were considered: constant diffusion weighting (fixed-b 0 ) and constant gradient area (fixed-q 0 ). Fixed-b 0 and fixed-q 0 were compared using signal calculations for systems with one and two diffusion coefficients, and experimentally using data from postmortem human corpus callosum samples. Calculations of biexponential diffusion decay show that the ADC is underestimated for reference images with b > 0, which can induce an apparent time-dependence for fixed-q 0 . Restricted systems were also found to be affected. Experimentally, the exaggeration of the diffusion time-dependent effect under fixed-q 0 versus fixed-b 0 was in a range predicted theoretically, accounting for 62% (longitudinal) and 35% (radial) of the time dependence observed in white matter. Variation in the b-value of reference measurements in DW-STEAM can induce artificial diffusion time dependence in ADC, even in the absence of restriction. Magn Reson Med 79:952-959, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Thermo-optical Characterization of Photothermal Optical Phase Shift Detection in Extended-Nano Channels and UV Detection of Biomolecules.

PubMed

Shimizu, Hisashi; Miyawaki, Naoya; Asano, Yoshihiro; Mawatari, Kazuma; Kitamori, Takehiko

2017-06-06

The expansion of microfluidics research to nanofluidics requires absolutely sensitive and universal detection methods. Photothermal detection, which utilizes optical absorption and nonradiative relaxation, is promising for the sensitive detection of nonlabeled biomolecules in nanofluidic channels. We have previously developed a photothermal optical phase shift (POPS) detection method to detect nonfluorescent molecules sensitively, while a rapid decrease of the sensitivity in nanochannels and the introduction of an ultraviolet (UV) excitation system were issues to be addressed. In the present study, our primary aim is to characterize the POPS signal in terms of the thermo-optical properties and quantitatively evaluate the causes for the decrease in sensitivity. The UV excitation system is then introduced into the POPS detector to realize the sensitive detection of nonlabeled biomolecules. The UV-POPS detection system is designed and constructed from scratch based on a symmetric microscope. The results of simulations and experiments reveal that the sensitivity decreases due to a reduction of the detection volume, dissipation of the heat, and cancellation of the changes in the refractive indices. Finally, determination of the concentration of a nonlabeled protein (bovine serum albumin) is performed in a very thin 900 nm deep nanochannel. As a result, the limit of detection (LOD) is 2.3 μM (600 molecules in the 440 attoliter detection volume), which is as low as that previously obtained for our visible POPS detector. UV-POPS detection is thus expected be a powerful technique for the study of biomolecules, including DNAs and proteins confined in nanofluidic channels.

Sources and characteristics of organochlorine pesticides in the soil and sediment along the Kaidu-Peacock River, Northwest of China

NASA Astrophysics Data System (ADS)

Chen, Wei; Qi, Shihua; Peng, Fei; Qu, Chengkai; Zhang, Yuan; Xing, Xinli; Zhang, Jiaquan

2016-04-01

Organochlorine pesticides (OCPs) are a sub-group of persistent organic pollutants (POPs), which have raised the concerns from researchers all around the world for several decades. But very little research has been conducted on POPs in the arid zone of Northwest China. More than 100 soil and sediment samples were collected from Kaidu-Peacock River of Xinjiang, Northwest of China, to investigate the organochlorine pesticides (OCPs) in this region analysed by the gas chromatograph equipped with a mass selective detector (GC-MSD). Our pre-study in 2006 (Chen et al. 2011) in the same region, showed that OCPs except o,p'-DDT were detected in sediments from the Peacock River. Similar results were found in the whole river catchment in this investigation. DDTs, HCHs, chlordanes and endosulfans were the dominant OCPs residual in the soil and sediments. This study confirmed that POPs, such as OCPs in this region were contributed to by both local emissions and long-term atmospheric transport and may pose risks to human health and the ecosystem. Chen, W., Jing, M., Bu, J., Ellis Burnet, J., Qi, S., Song, Q., Ke, Y., Miao, J., Liu, M. & Yang, C. (2011) Organochlorine pesticides in the surface water and sediments from the Peacock River Drainage Basin in Xinjiang, China: a study of an arid zone in Central Asia. Environmental Monitoring and Assessment, 177, 1-21.

The influence of global climate change on the environmental fate of persistent organic pollutants: A review with emphasis on the Northern Hemisphere and the Arctic as a receptor

NASA Astrophysics Data System (ADS)

Ma, Jianmin; Hung, Hayley; Macdonald, Robie W.

2016-11-01

Following worldwide bans and restrictions on the use of many persistent organic pollutants (POPs) from the late 1970s, their regional and global distributions have become governed increasingly by phase partitioning between environmental reservoirs, such as air, water, soil, vegetation and ice, where POPs accumulated during the original applications. Presently, further transport occurs within the atmospheric and aquatic reservoirs. Increasing temperatures provide thermodynamic forcing to drive these chemicals out of reservoirs, like soil, vegetation, water and ice, and into the atmosphere where they can be transported rapidly by winds and then recycled among environmental media to reach locations where lower temperatures prevail (e.g., polar regions and high elevations). Global climate change, widely considered as global warming, is also manifested by changes in hydrological systems and in the cryosphere; with the latter now exhibiting widespread loss of ice cover on the Arctic Ocean and thawing of permafrost. All of these changes alter the cycling and fate of POPs. There is abundant evidence from observations and modeling showing that climate variation has an effect on POPs levels in biotic and abiotic environments. This article reviews recent progress in research on the effects of climate change on POPs with the intention of promoting awareness of the importance of interactions between climate and POPs in the geophysical and ecological systems.

Multi-laboratory comparison of quantitative PCR assays for detection and quantification of Fusarium virguliforme from soybean roots and soil

USDA-ARS?s Scientific Manuscript database

Accurate identification and quantification of Fusarium virguliforme, the cause of sudden death syndrome (SDS) in soybean, within root tissue and soil are important tasks. Several quantitative PCR (qPCR) assays have been developed but there are no reports comparing their use in sensitive and specific...

Quantification of viable bacterial starter cultures of Virgibacillus sp. and Tetragenococcus halophilus in fish sauce fermentation by real-time quantitative PCR.

PubMed

Udomsil, Natteewan; Chen, Shu; Rodtong, Sureelak; Yongsawatdigul, Jirawat

2016-08-01

Real-time quantitative polymerase chain reaction (qPCR) methods were developed for the quantification of Virgibacillus sp. SK37 and Tetragenococcus halophilus MS33, which were added as starter cultures in fish sauce fermentation. The PCR assays were coupled with propidium monoazide (PMA) treatment of samples to selectively quantify viable cells and integrated with exogenous recombinant Escherichia coli cells to control variabilities in analysis procedures. The qPCR methods showed species-specificity for both Virgibacillus halodenitrificans and T. halophilus as evaluated using 6 reference strains and 28 strains of bacteria isolated from fish sauce fermentation. The qPCR efficiencies were 101.1% for V. halodenitrificans and 90.2% for T. halophilus. The quantification limits of the assays were 10(3) CFU/mL and 10(2) CFU/mL in fish sauce samples with linear correlations over 4 Logs for V. halodenitrificans and T. halophilus, respectively. The matrix effect was not observed when evaluated using fish sauce samples fermented for 1-6 months. The developed PMA-qPCR methods were successfully applied to monitor changes of Virgibacillus sp. SK37 and T. halophilus MS33 in a mackerel fish sauce fermentation model where culture-dependent techniques failed to quantify the starter cultures. The results demonstrated the usability of the methods as practical tools for monitoring the starter cultures in fish sauce fermentation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Simultaneous Analysis of Iridoid Glycosides and Anthraquinones in Morinda officinalis Using UPLC-QqQ-MS/MS and UPLC-Q/TOF-MSE.

PubMed

Zhao, Xiangsheng; Wei, Jianhe; Yang, Meihua

2018-05-03

Morinda officinalis is an important herbal medicine and functional food, and its main constituents include anthraquinone and iridoid glycosides. Quantification of the main compounds is a necessary step to understand the quality and therapeutic properties of M. officinalis , but this has not yet been performed based on liquid chromatography/tandem mass spectrometry (LC-MS/MS). Analytes were extracted from M. officinalis by reflux method. Ultrahigh-performance liquid chromatography coupled with a triple quadrupole mass spectrometry (UPLC-QqQ-MS) using multiple reaction monitoring (MRM) mode was applied for quantification. Fragmentation pathways of deacetyl asperulosidic acid and rubiadin were investigated based on UPLC with quadrupole time-of-flight tandem mass spectrometry (Q/TOF-MS) in the MS E centroid mode. The method showed a good linearity over a wide concentration range (R² ≥ 0.9930). The limits of quantification of six compounds ranged from 2.6 to 27.57 ng/mL. The intra- and inter-day precisions of the investigated components exhibited an RSD within 4.5% with mean recovery rates of 95.32⁻99.86%. Contents of selected compounds in M. officinalis varied significantly depending on region. The fragmentation pathway of deacetyl asperulosidic and rubiadin was proposed. A selective and sensitive method was developed for determining six target compounds in M. officinalis by UPLC-MS/MS. Furthermore, the proposed method will be helpful for quality control and identification main compounds of M. officinalis .

Application of PCR and real-time PCR for monitoring cyanobacteria, Microcystis spp. and Cylindrospermopsis raciborskii in Macau freshwater reservoir

NASA Astrophysics Data System (ADS)

Zhang, Weiying; Lou, Inchio; Ung, Wai Kin; Kong, Yijun; Mok, Kai Meng

2014-06-01

Freshwater algal blooms have become a growing concern world-wide. They are caused by a high level of cyanobacteria, predominantly Microcystis spp. and Cylindrospermopsis raciborskii, which can produce microcystin and cylindrospermopsin, respectively. Longtime exposure to these cyanotoxins may affect public health, thus reliable detection, quantification, and enumeration of these harmful algae species has become a priority in water quality management. Traditional manual enumeration of algal bloom cells primarily involves microscopic identification which limited by inaccuracy and time-consumption.With the development of molecular techniques and an increasing number of microbial sequences available in the Genbank database, the use of molecular methods can be used for more rapid, reliable, and accurate detection and quantification. In this study, multiplex polymerase chain reaction (PCR) and real-time quantitative PCR (qPCR) techniques were developed and applied for monitoring cyanobacteria Microcystis spp. and C. raciborskii in the Macau Storage Reservoir (MSR). The results showed that the techniques were successful for identifying and quantifying the species in pure cultures and mixed cultures, and proved to be a potential application for water sampling in MSR. When the target species were above 1 million cells/L, similar cell numbers estimated by microscopic enumeration and qPCR were obtained. Further quantification in water samples indicated that the ratio of the estimated number of cell by microscopy and qPCR was 0.4-12.9 for cyanobacteria and 0.2-3.9 for C. raciborskii. However, Microcystis spp. was not observed by manual enumeration, while it was detected at low levels by qPCR, suggesting that qPCR is more sensitive and accurate. Thus the molecular approaches provide an additional reliable monitoring option to traditional microscopic enumeration for the ecosystems monitoring program.

Application of a Master Equation for Quantitative mRNA Analysis Using qRT-PCR

USDA-ARS?s Scientific Manuscript database

The qRT-PCR has been widely accepted as the assay of choice for mRNA quantification. Gene expression as measured by mRNA dynamics varies in response to different conditions and environmental stimuli. For conventional practice, housekeeping genes have been applied as internal reference for data nor...

Changes in glance behaviour when using a visual eco-driving system - A field study.

PubMed

Ahlstrom, Christer; Kircher, Katja

2017-01-01

While in-vehicle eco-driving support systems have the potential to reduce greenhouse gas emissions and save fuel, they may also distract drivers, especially if the system makes use of a visual interface. The objective of this study is to investigate the visual behaviour of drivers interacting with such a system, implemented on a five-inch screen mounted above the middle console. Ten drivers participated in a real-world, on-road driving study where they drove a route nine times (2 pre-baseline drives, 5 treatment drives, 2 post-baseline drives). The route was 96 km long and consisted of rural roads, urban roads and a dual-lane motorway. The results show that drivers look at the system for 5-8% of the time, depending on road type, with a glance duration of about 0.6 s, and with 0.05% long glances (>2s) per kilometre. These figures are comparable to what was found for glances to the speedometer in this study. Glance behaviour away from the windscreen is slightly increased in treatment as compared to pre- and post-baseline, mirror glances decreased in treatment and post-baseline compared to pre-baseline, and speedometer glances increased compared to pre-baseline. The eco-driving support system provided continuous information interspersed with additional advice pop-ups (announced by a beep) and feedback pop-ups (no auditory cue). About 20% of sound initiated advice pop-ups were disregarded, and the remaining cases were usually looked at within the first two seconds. About 40% of the feedback pop-ups were disregarded. The amount of glances to the system immediately before the onset of a pop-up was clearly higher for feedback than for advice. All in all, the eco-driving support system under investigation is not likely to have a strong negative impact on glance behaviour. However, there is room for improvements. We recommend that eco-driving information is integrated with the speedometer, that optional activation of sound alerts for intermittent information is made available, and that the pop-up duration should be extended to facilitate self-regulation of information intake. Copyright © 2016 Elsevier Ltd. All rights reserved.

IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT.

PubMed

Arntzen, Magnus Ø; Koehler, Christian J; Barsnes, Harald; Berven, Frode S; Treumann, Achim; Thiede, Bernd

2011-02-04

Isobaric peptide labeling plays an important role in relative quantitative comparisons of proteomes. Isobaric labeling techniques utilize MS/MS spectra for relative quantification, which can be either based on the relative intensities of reporter ions in the low mass region (iTRAQ and TMT) or on the relative intensities of quantification signatures throughout the spectrum due to isobaric peptide termini labeling (IPTL). Due to the increased quantitative information found in MS/MS fragment spectra generated by the recently developed IPTL approach, new software was required to extract the quantitative information. IsobariQ was specifically developed for this purpose; however, support for the reporter ion techniques iTRAQ and TMT is also included. In addition, to address recently emphasized issues about heterogeneity of variance in proteomics data sets, IsobariQ employs the statistical software package R and variance stabilizing normalization (VSN) algorithms available therein. Finally, the functionality of IsobariQ is validated with data sets of experiments using 6-plex TMT and IPTL. Notably, protein substrates resulting from cleavage by proteases can be identified as shown for caspase targets in apoptosis.

Development of Quantitative Real-Time PCR Assays for Detection and Quantification of Surrogate Biological Warfare Agents in Building Debris and Leachate▿

PubMed Central

Saikaly, Pascal E.; Barlaz, Morton A.; de los Reyes, Francis L.

2007-01-01

Evaluation of the fate and transport of biological warfare (BW) agents in landfills requires the development of specific and sensitive detection assays. The objective of the current study was to develop and validate SYBR green quantitative real-time PCR (Q-PCR) assays for the specific detection and quantification of surrogate BW agents in synthetic building debris (SBD) and leachate. Bacillus atrophaeus (vegetative cells and spores) and Serratia marcescens were used as surrogates for Bacillus anthracis (anthrax) and Yersinia pestis (plague), respectively. The targets for SYBR green Q-PCR assays were the 16S-23S rRNA intergenic transcribed spacer (ITS) region and recA gene for B. atrophaeus and the gyrB, wzm, and recA genes for S. marcescens. All assays showed high specificity when tested against 5 ng of closely related Bacillus and Serratia nontarget DNA from 21 organisms. Several spore lysis methods that include a combination of one or more of freeze-thaw cycles, chemical lysis, hot detergent treatment, bead beat homogenization, and sonication were evaluated. All methods tested showed similar threshold cycle values. The limit of detection of the developed Q-PCR assays was determined using DNA extracted from a pure bacterial culture and DNA extracted from sterile water, leachate, and SBD samples spiked with increasing quantities of surrogates. The limit of detection for B. atrophaeus genomic DNA using the ITS and B. atrophaeus recA Q-PCR assays was 7.5 fg per PCR. The limits of detection of S. marcescens genomic DNA using the gyrB, wzm, and S. marcescens recA Q-PCR assays were 7.5 fg, 75 fg, and 7.5 fg per PCR, respectively. Quantification of B. atrophaeus vegetative cells and spores was linear (R2 > 0.98) over a 7-log-unit dynamic range down to 101 B. atrophaeus cells or spores. Quantification of S. marcescens (R2 > 0.98) was linear over a 6-log-unit dynamic range down to 102 S. marcescens cells. The developed Q-PCR assays are highly specific and sensitive and can be used for monitoring the fate and transport of the BW surrogates B. atrophaeus and S. marcescens in building debris and leachate. PMID:17720820

The population health record: concepts, definition, design, and implementation.

PubMed

Friedman, Daniel J; Parrish, R Gibson

2010-01-01

In 1997, the American Medical Informatics Association proposed a US information strategy that included a population health record (PopHR). Despite subsequent progress on the conceptualization, development, and implementation of electronic health records and personal health records, minimal progress has occurred on the PopHR. Adapting International Organization for Standarization electronic health records standards, we define the PopHR as a repository of statistics, measures, and indicators regarding the state of and influences on the health of a defined population, in computer processable form, stored and transmitted securely, and accessible by multiple authorized users. The PopHR is based upon an explicit population health framework and a standardized logical information model. PopHR purpose and uses, content and content sources, functionalities, business objectives, information architecture, and system architecture are described. Barriers to implementation and enabling factors and a three-stage implementation strategy are delineated.

A quantitative strategy to detect changes in accessibility of protein regions to chemical modification on heterodimerization

PubMed Central

Dreger, Mathias; Leung, Bo Wah; Brownlee, George G; Deng, Tao

2009-01-01

We describe a method for studying quantitative changes in accessibility of surface lysine residues of the PB1 subunit of the influenza RNA polymerase as a result of association with the PA subunit to form a PB1-PA heterodimer. Our method combines two established methods: (i) the chemical modification of surface lysine residues of native proteins by N-hydroxysuccinimidobiotin (NHS-biotin) and (ii) the stable isotope labeling of amino acids in cell culture (SILAC) followed by tryptic digestion and mass spectrometry. By linking the chemical modification with the SILAC methodology for the first time, we obtain quantitative data on chemical modification allowing subtle changes in accessibility to be described. Five regions in the PB1 monomer showed altered reactivity to NHS-biotin when compared with the [PB1-PA] heterodimer. Mutational analysis of residues in two such regions—at K265 and K481 of PB1, which were about three- and twofold, respectively, less accessible to biotinylation in the PB1-PA heterodimer compared with the PB1 monomer, demonstrated that both K265 and K481 were crucial for polymerase function. This novel assay of quantitative profiling of biotinylation patterns (Q-POP assay) highlights likely conformational changes at important functional sites, as observed here for PB1, and may provide information on protein–protein interaction interfaces. The Q-POP assay should be a generally applicable approach and may detect novel functional sites suitable for targeting by drugs. PMID:19517532

Colonization and Intrusive Invasion of Potato Psyllid by 'Candidatus Liberibacter solanacearum'.

PubMed

Cicero, Joseph M; Fisher, Tonja W; Qureshi, Jawwad A; Stansly, Philip A; Brown, Judith K

2017-01-01

Previous studies have shown that the fastidious bacterial plant pathogen 'Candidatus Liberibacter solanacearum' (CLso) is transmitted circulatively and propagatively by the potato psyllid (PoP) Bactericera cockerelli. In this study, the temporal and spatial interrelationships between CLso PoP were investigated by scanning electron microscopy of the digestive system of PoP immature and adult instars and salivary glands of adults post CLso ingestion. CLso biofilms were not detectable on the outer midgut surface of the first and second instars; however, for third to fifth instars and teneral and mature adults, biofilms were observed in increasing numbers in each successive developmental stage. In adult PoP midguts, CLso cells were observed between the basal lamina and basal epithelial cell membranes; in basal laminar perforations, on the outer basal laminar surface, and in the ventricular lumen, epithelial cytosol, and filter chamber periventricular space. CLso were also abundantly visible in the salivary gland pericellular spaces and in the epidermal cell cytosol of the head. Collectively, these results point to an intrusive, systemic invasion of PoP by CLso that employs an endo/exocytosis-like mechanism, in the context of a propagative, circulative mode of transmission.

Effect of Population III Multiplicity on Dark Star Formation

NASA Technical Reports Server (NTRS)

Stacy, Athena; Pawlik, Andreas H.; Bromm, Volker; Loeb, Abraham

2012-01-01

We numerically study the mutual interaction between dark matter (DM) and Population III (Pop III) stellar systems in order to explore the possibility of Pop III dark stars within this physical scenario. We perform a cosmological simulation, initialized at z approx. 100, which follows the evolution of gas and DM. We analyze the formation of the first mini halo at z approx. 20 and the subsequent collapse of the gas to densities of 10(exp 12)/cu cm. We then use this simulation to initialize a set of smaller-scale 'cut-out' simulations in which we further refine the DM to have spatial resolution similar to that of the gas. We test multiple DM density profiles, and we employ the sink particle method to represent the accreting star-forming region. We find that, for a range of DM configurations, the motion of the Pop III star-disk system serves to separate the positions of the protostars with respect to the DM density peak, such that there is insufficient DM to influence the formation and evolution of the protostars for more than approx. 5000 years. In addition, the star-disk system causes gravitational scattering of the central DM to lower densities, further decreasing the influence of DM over time. Any DM-powered phase of Pop III stars will thus be very short-lived for the typical multiple system, and DM will not serve to significantly prolong the life of Pop III stars.

Determination of mycotoxins in different food commodities by ultra-high-pressure liquid chromatography coupled to triple quadrupole mass spectrometry.

PubMed

Beltrán, Eduardo; Ibáñez, María; Sancho, Juan Vicente; Hernández, Félix

2009-06-01

A rapid multianalyte-multiclass method with little sample manipulation has been developed for the simultaneous determination of eleven mycotoxins in different food commodities by using ultra-high-pressure liquid chromatography coupled to triple quadrupole mass spectrometry (UHPLC/MS/MS). Toxins were extracted from the samples with acetonitrile/water (80:20, v/v) 0.1% HCOOH and, after a two-fold dilution with water, directly injected into the system. Thanks to the fast high-resolution separation of UHPLC, the eleven mycotoxins were separated by gradient elution in only 4 min. The method has been validated in three food matrices (maize kernels, dry pasta (wheat), and eight-multicereal babyfood (wheat, maize, rice, oat, barley, rye, sorghum, millet)) at four different concentration levels. Satisfactory recoveries were obtained (70-110%) and precision (expressed as relative standard deviation) was typically below 15% with very few exceptions. Quantification of samples was carried out with matrix-matched standards calibration. The lowest concentration successfully validated in sample was as low as 0.5 microg/kg for aflatoxins and ochratoxin A in babyfood, and 20 microg/kg for the rest of the selected mycotoxins in all matrices tested. Deoxynivalenol could be only validated at 200 microg/kg, due the poor sensitivity for this mycotoxin analysis. With only two exceptions (HT-2 and deoxynivalenol), the limits of detection (LODs), estimated for a signal-to-noise ratio of 3 from the chromatograms of samples spiked at the lowest level validated, varied between 0.1 and 1 microg/kg in the three food matrices tested. The method was applied to the analysis of different kinds of samples. Positive findings were confirmed by acquiring two transitions (Q quantification, q confirmation) and evaluating the Q/q ratio. Copyright (c) 2009 John Wiley & Sons, Ltd.

Review Article: Persistent organic pollutants and landfills - a review of past experiences and future challenges.

PubMed

Weber, Roland; Watson, Alan; Forter, Martin; Oliaei, Fardin

2011-01-01

The landfilling and dumping of persistent organic pollutants (POPs) and other persistent hazardous compounds, such as polychlorinated biphenyls (PCBs), hexachlorocyclohaxane (HCH), polybrominated diphenylether (PBDEs) or perfluorooctane sulfonic acid (PFOS) can have significant adverse environmental consequences. This paper reviews past experiences with such disposal practices and highlights their unsustainability due to the risks of contamination of ecosystems, the food chain, together with ground and drinking water supplies. The use and associated disposal of POPs have been occurring for over 50 years. Concurrent with the phase-out of some of the most hazardous chemicals, the production of new POPs, such as brominated and fluorinated compounds has increased since the 1990s. These latter compounds are commonly used in a wide range of consumer goods, and as consumer products reach the end of their useful lives, ultimately enter waste recycling and disposal systems, in particular at municipal landfills. Because of their very slow, or lack of degradability, POPs will persist in landfills for many decades and possibly centuries. Over these extended time periods engineered landfill systems and their liners are likely to degrade, thus posing a contemporary and future risk of releasing large contaminant loads to the environment. This review highlights the necessity for alternative disposal methods for POP wastes, including destruction or complete removal from potential environmental release. In addition to such end of pipe solutions a policy change in the use pattern of persistent toxic chemicals is inevitable. In addition, inventories for the location and quantity of POPs in landfills, together with an assessment of their threat to ecosystems, drinking water and food resources are identified as key measures to facilitate appropriate management of risks. Finally the challenges of POP wastes in transition/developing countries, the risk of increased leaching of POPs from landfills due to climate change, and the possible negative impact of natural attenuation processes are considered.

Detecting, anticipating, and predicting critical transitions in spatially extended systems.

PubMed

Kwasniok, Frank

2018-03-01

A data-driven linear framework for detecting, anticipating, and predicting incipient bifurcations in spatially extended systems based on principal oscillation pattern (POP) analysis is discussed. The dynamics are assumed to be governed by a system of linear stochastic differential equations which is estimated from the data. The principal modes of the system together with corresponding decay or growth rates and oscillation frequencies are extracted as the eigenvectors and eigenvalues of the system matrix. The method can be applied to stationary datasets to identify the least stable modes and assess the proximity to instability; it can also be applied to nonstationary datasets using a sliding window approach to track the changing eigenvalues and eigenvectors of the system. As a further step, a genuinely nonstationary POP analysis is introduced. Here, the system matrix of the linear stochastic model is time-dependent, allowing for extrapolation and prediction of instabilities beyond the learning data window. The methods are demonstrated and explored using the one-dimensional Swift-Hohenberg equation as an example, focusing on the dynamics of stochastic fluctuations around the homogeneous stable state prior to the first bifurcation. The POP-based techniques are able to extract and track the least stable eigenvalues and eigenvectors of the system; the nonstationary POP analysis successfully predicts the timing of the first instability and the unstable mode well beyond the learning data window.

Detecting, anticipating, and predicting critical transitions in spatially extended systems

NASA Astrophysics Data System (ADS)

Kwasniok, Frank

2018-03-01

A data-driven linear framework for detecting, anticipating, and predicting incipient bifurcations in spatially extended systems based on principal oscillation pattern (POP) analysis is discussed. The dynamics are assumed to be governed by a system of linear stochastic differential equations which is estimated from the data. The principal modes of the system together with corresponding decay or growth rates and oscillation frequencies are extracted as the eigenvectors and eigenvalues of the system matrix. The method can be applied to stationary datasets to identify the least stable modes and assess the proximity to instability; it can also be applied to nonstationary datasets using a sliding window approach to track the changing eigenvalues and eigenvectors of the system. As a further step, a genuinely nonstationary POP analysis is introduced. Here, the system matrix of the linear stochastic model is time-dependent, allowing for extrapolation and prediction of instabilities beyond the learning data window. The methods are demonstrated and explored using the one-dimensional Swift-Hohenberg equation as an example, focusing on the dynamics of stochastic fluctuations around the homogeneous stable state prior to the first bifurcation. The POP-based techniques are able to extract and track the least stable eigenvalues and eigenvectors of the system; the nonstationary POP analysis successfully predicts the timing of the first instability and the unstable mode well beyond the learning data window.

Non-invasive quantitative pulmonary V/Q imaging using Fourier decomposition MRI at 1.5T.

PubMed

Kjørstad, Åsmund; Corteville, Dominique M R; Henzler, Thomas; Schmid-Bindert, Gerald; Zöllner, Frank G; Schad, Lothar R

2015-12-01

Techniques for quantitative pulmonary perfusion and ventilation using the Fourier Decomposition method were recently demonstrated. We combine these two techniques and show that ventilation-perfusion (V/Q) imaging is possible using only a single MR acquisition of less than thirty seconds. The Fourier Decomposition method is used in combination with two quantification techniques, which extract baselines from within the images themselves and thus allows quantification. For the perfusion, a region assumed to consist of 100% blood is utilized, while for the ventilation the zero-frequency component is used. V/Q-imaging is then done by dividing the quantified ventilation map with the quantified perfusion map. The techniques were used on ten healthy volunteers and fifteen patients diagnosed with lung cancer. A mean V/Q-ratio of 1.15 ± 0.22 was found for the healthy volunteers and a mean V/Q-ratio of 1.93 ± 0.83 for the non-afflicted lung in the patients. Mean V/Q-ratio in the afflicted (tumor-bearing) lung was found to be 1.61 ± 1.06. Functional defects were clearly visible in many of the patient images, but 5 of 15 patient images had to be excluded due to artifacts or low SNR, indicating a lack of robustness. Non-invasive, quantitative V/Q-imaging is possible using Fourier Decomposition MRI. The method requires only a single acquisition of less than 30 seconds, but robustness in patients remains an issue. Copyright © 2015. Published by Elsevier GmbH.

A survey of tools for the analysis of quantitative PCR (qPCR) data.

PubMed

Pabinger, Stephan; Rödiger, Stefan; Kriegner, Albert; Vierlinger, Klemens; Weinhäusel, Andreas

2014-09-01

Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

Pomegranate peel and peel extracts: chemistry and food features.

PubMed

Akhtar, Saeed; Ismail, Tariq; Fraternale, Daniele; Sestili, Piero

2015-05-01

The present review focuses on the nutritional, functional and anti-infective properties of pomegranate (Punica granatum L.) peel (PoP) and peel extract (PoPx) and on their applications as food additives, functional food ingredients or biologically active components in nutraceutical preparations. Due to their well-known ethnomedical relevance and chemical features, the biomolecules available in PoP and PoPx have been proposed, for instance, as substitutes of synthetic food additives, as nutraceuticals and chemopreventive agents. However, because of their astringency and anti-nutritional properties, PoP and PoPx are not yet considered as ingredients of choice in food systems. Indeed, considering the prospects related to both their health promoting activity and chemical features, the nutritional and nutraceutical potential of PoP and PoPx seems to be still underestimated. The present review meticulously covers the wide range of actual and possible applications (food preservatives, stabilizers, supplements, prebiotics and quality enhancers) of PoP and PoPx components in various food products. Given the overall properties of PoP and PoPx, further investigations in toxicological and sensory aspects of PoP and PoPx should be encouraged to fully exploit the health promoting and technical/economic potential of these waste materials as food supplements. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Mixture of Persistent Organic Pollutants and Perfluorooctanesulfonic Acid Induces Similar Behavioural Responses, but Different Gene Expression Profiles in Zebrafish Larvae

PubMed Central

Khezri, Abdolrahman; Fraser, Thomas W. K.; Nourizadeh-Lillabadi, Rasoul; Kamstra, Jorke H.; Berg, Vidar; Zimmer, Karin E.; Ropstad, Erik

2017-01-01

Persistent organic pollutants (POPs) are widespread in the environment and some may be neurotoxic. As we are exposed to complex mixtures of POPs, we aimed to investigate how a POP mixture based on Scandinavian human blood data affects behaviour and neurodevelopment during early life in zebrafish. Embryos/larvae were exposed to a series of sub-lethal doses and behaviour was examined at 96 h post fertilization (hpf). In order to determine the sensitivity window to the POP mixture, exposure models of 6 to 48 and 48 to 96 hpf were used. The expression of genes related to neurological development was also assessed. Results indicate that the POP mixture increases the swimming speed of larval zebrafish following exposure between 48 to 96 hpf. This behavioural effect was associated with the perfluorinated compounds, and more specifically with perfluorooctanesulfonic acid (PFOS). The expression of genes related to the stress response, GABAergic, dopaminergic, histaminergic, serotoninergic, cholinergic systems and neuronal maintenance, were altered. However, there was little overlap in those genes that were significantly altered by the POP mixture and PFOS. Our findings show that the POP mixture and PFOS can have a similar effect on behaviour, yet alter the expression of genes relevant to neurological development differently. PMID:28146072

Movement System Impairment-Guided Approach to the Physical Therapist Treatment of a Patient With Postpartum Pelvic Organ Prolapse and Mixed Urinary Incontinence: Case Report.

PubMed

Kurz, Jenny; Borello-France, Diane

2017-04-01

Women with postpartum pelvic organ prolapse (POP) and urinary incontinence are often treated by physical therapists specializing in women's health. Movement system impairments often coexist in this patient population. The purpose of this case report is to describe the physical therapist treatment of a woman with postpartum POP complicated by additional pelvic symptoms. A 31-year-old woman presented with postpartum POP, diastasis recti, urinary incontinence, and constipation. Movement system impairments were consistent with a physical therapist diagnosis of femoral adduction-medial rotation syndrome exacerbated by levator ani muscle weakness and incoordination and impaired intra-abdominal pressure regulation. Interventions, based on a movement system guided approach, included postural correction; pelvic-floor, abdominal, and hip muscle strengthening; functional training to correct identified movement faults; and patient education. Movement system impairment outcomes included: correction of femoral adduction-medial rotation and knee hyperextension during standing at rest, ambulation, and exercise; increased hip muscle strength; and effective regulation of intra-abdominal pressure (resolution of breath holding with the Valsalva maneuver) during all transitional movements and therapeutic exercise. The patient also demonstrated reductions in POP, urinary, and colorectal symptom severity that exceeded the minimal clinically important difference. Additionally, she demonstrated a reduction in diastasis rectus distance. A movement system impairment-guided approach led the physical therapist to consider impairments outside the pelvic floor that could have contributed to the patient's pelvic symptoms. Using this approach, the patient achieved resolution of musculoskeletal and movement impairments and reductions in POP, urinary and colorectal symptoms, and symptom-related distress. © 2016 American Physical Therapy Association

dPCR: A Technology Review

PubMed Central

Quan, Phenix-Lan; Sauzade, Martin

2018-01-01

Digital Polymerase Chain Reaction (dPCR) is a novel method for the absolute quantification of target nucleic acids. Quantification by dPCR hinges on the fact that the random distribution of molecules in many partitions follows a Poisson distribution. Each partition acts as an individual PCR microreactor and partitions containing amplified target sequences are detected by fluorescence. The proportion of PCR-positive partitions suffices to determine the concentration of the target sequence without a need for calibration. Advances in microfluidics enabled the current revolution of digital quantification by providing efficient partitioning methods. In this review, we compare the fundamental concepts behind the quantification of nucleic acids by dPCR and quantitative real-time PCR (qPCR). We detail the underlying statistics of dPCR and explain how it defines its precision and performance metrics. We review the different microfluidic digital PCR formats, present their underlying physical principles, and analyze the technological evolution of dPCR platforms. We present the novel multiplexing strategies enabled by dPCR and examine how isothermal amplification could be an alternative to PCR in digital assays. Finally, we determine whether the theoretical advantages of dPCR over qPCR hold true by perusing studies that directly compare assays implemented with both methods. PMID:29677144

Detection of Rare Drug Resistance Mutations by Digital PCR in a Human Influenza A Virus Model System and Clinical Samples

PubMed Central

Bushell, Claire A.; Grant, Paul R.; Cowen, Simon; Gutierrez-Aguirre, Ion; O'Sullivan, Denise M.; Žel, Jana; Milavec, Mojca; Foy, Carole A.; Nastouli, Eleni; Garson, Jeremy A.; Huggett, Jim F.

2015-01-01

Digital PCR (dPCR) is being increasingly used for the quantification of sequence variations, including single nucleotide polymorphisms (SNPs), due to its high accuracy and precision in comparison with techniques such as quantitative PCR (qPCR) and melt curve analysis. To develop and evaluate dPCR for SNP detection using DNA, RNA, and clinical samples, an influenza virus model of resistance to oseltamivir (Tamiflu) was used. First, this study was able to recognize and reduce off-target amplification in dPCR quantification, thereby enabling technical sensitivities down to 0.1% SNP abundance at a range of template concentrations, a 50-fold improvement on the qPCR assay used routinely in the clinic. Second, a method was developed for determining the false-positive rate (background) signal. Finally, comparison of dPCR with qPCR results on clinical samples demonstrated the potential impact dPCR could have on clinical research and patient management by earlier (trace) detection of rare drug-resistant sequence variants. Ultimately this could reduce the quantity of ineffective drugs taken and facilitate early switching to alternative medication when available. In the short term such methods could advance our understanding of microbial dynamics and therapeutic responses in a range of infectious diseases such as HIV, viral hepatitis, and tuberculosis. Furthermore, the findings presented here are directly relevant to other diagnostic areas, such as the detection of rare SNPs in malignancy, monitoring of graft rejection, and fetal screening. PMID:26659206

Detection of Rare Drug Resistance Mutations by Digital PCR in a Human Influenza A Virus Model System and Clinical Samples.

PubMed

Whale, Alexandra S; Bushell, Claire A; Grant, Paul R; Cowen, Simon; Gutierrez-Aguirre, Ion; O'Sullivan, Denise M; Žel, Jana; Milavec, Mojca; Foy, Carole A; Nastouli, Eleni; Garson, Jeremy A; Huggett, Jim F

2016-02-01

Digital PCR (dPCR) is being increasingly used for the quantification of sequence variations, including single nucleotide polymorphisms (SNPs), due to its high accuracy and precision in comparison with techniques such as quantitative PCR (qPCR) and melt curve analysis. To develop and evaluate dPCR for SNP detection using DNA, RNA, and clinical samples, an influenza virus model of resistance to oseltamivir (Tamiflu) was used. First, this study was able to recognize and reduce off-target amplification in dPCR quantification, thereby enabling technical sensitivities down to 0.1% SNP abundance at a range of template concentrations, a 50-fold improvement on the qPCR assay used routinely in the clinic. Second, a method was developed for determining the false-positive rate (background) signal. Finally, comparison of dPCR with qPCR results on clinical samples demonstrated the potential impact dPCR could have on clinical research and patient management by earlier (trace) detection of rare drug-resistant sequence variants. Ultimately this could reduce the quantity of ineffective drugs taken and facilitate early switching to alternative medication when available. In the short term such methods could advance our understanding of microbial dynamics and therapeutic responses in a range of infectious diseases such as HIV, viral hepatitis, and tuberculosis. Furthermore, the findings presented here are directly relevant to other diagnostic areas, such as the detection of rare SNPs in malignancy, monitoring of graft rejection, and fetal screening. Copyright © 2016 Whale et al.

Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9

PubMed Central

Kanitkar, Yogendra H.; Stedtfeld, Robert D.; Steffan, Robert J.; Hashsham, Syed A.

2016-01-01

Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA are commonly used to quantify Dehalococcoides spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (vcrA, bvcA, and tceA) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain Dehalococcoides species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only vcrA was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for vcrA and tceA genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used Dehalococcoides species-containing cultures. PMID:26746711

Detection and quantification of pestivirus in experimentally infected pregnant ewes and their progeny.

PubMed

Hurtado, Ana; Sanchez, Isbene; Bastida, Felix; Minguijón, Esmeralda; Juste, Ramón A; García-Pérez, Ana L

2009-11-05

Border disease virus (BDV) causes important reproductive losses, and eradication strategies focus on the identification and removal of persistently infected animals arising after in uterine infection. BDV infection dynamics were studied in 13 ewes experimentally infected with BDV-4 genotype at 3 phases of pregnancy [days 108 (group A), 76 (group B) and 55 (group C)] by quantification of viral RNA in blood collected on days -1 to parturition using quantitative real-time RT-PCR (qRT-PCR). Viral RNA loads were also measured in blood/foetal fluid and tissue samples from their offspring at lambing (3 foetuses, 7 stillborns, 15 lambs). qRT-PCR results were compared with those obtained by conventional RT-PCR and used to predict persistent infections. Viral RNA was detected in the ewes between days 2-15 p.i. The viraemia reached its highest peak between days 6-7 p.i. with a second peak at days 11-12 p.i. qRT-PCR was significantly faster to perform (less than 1 h) than conventional RT-PCR and detected BDV RNA in more ewes, being detection more continuous and prolonged in time. The virus was detected in peripheral blood in a higher percentage of lambs than in tissues, where differences in viral genome copies were more marked. Skin and cerebral cortex showed the highest viral RNA loads, and spleen and spinal cord the lowest. High viral RNA loads were observed in several animals in group B and all in group C, infected during middle and early foetal development, respectively, but also in one lamb from group A, infected during late foetal development. Serology and viral genome copy number estimates in blood and tissues were used to establish a quantitative cut-off threshold for transient viraemia. Viral RNA quantification showed potential for the discrimination between persistent infections and transient viraemia using single-time point blood sampling and raised questions regarding foetal immune system development and the occurrence of persistent infections.

Evaluation and selection of internal reference genes from two- and six-row U.S. malting barley varieties throughout micromalting for use in RT-qPCR

USDA-ARS?s Scientific Manuscript database

Reverse Transcription quantitative Polymerase Chain Reaction (qRT-PCR) is a popular method for measuring transcript abundance. The most commonly used method of interpretation is relative quantification and thus necessitates the use of normalization controls (i.e. reference genes) to standardize tran...

Influences of sample interference and interference controls on quantification of enterococci fecal indicator bacteria in surface water samples by the qPCR method

EPA Science Inventory

A quantitative polymerase chain reaction (qPCR) method for the detection of entercocci fecal indicator bacteria has been shown to be generally applicable for the analysis of temperate fresh (Great Lakes) and marine coastal waters and for providing risk-based determinations of wat...

Standardization of enterococci density estimates by EPA qPCR methods and comparison of beach action value exceedances in river waters with culture methods

EPA Science Inventory

The U.S.EPA has published recommendations for calibrator cell equivalent (CCE) densities of enterococci in recreational waters determined by a qPCR method in its 2012 Recreational Water Quality Criteria (RWQC). The CCE quantification unit stems from the calibration model used to ...

An outcome evaluation of a prison-based life-skills program: the power of people.

PubMed

Clark, Valerie A; Duwe, Grant

2015-04-01

The Power of People (PoP) is a personal leadership development course that was originally developed in a non-correctional setting and now serves as a prison-based life skills course. This study examined PoP's effect on four different types of recidivism: rearrest, reconviction, reincarceration, and technical violation revocation. The results of the analyses revealed that PoP does not have a significant effect on any of the four measures of recidivism. Following established principles of effective correctional treatment, we make several recommendations that could improve PoP's effectiveness on recidivism outcomes. Overall, this study provides guidance on how to make programs not originally designed for correctional systems into effective recidivism-reducing tools. © The Author(s) 2013.

The application of absolute quantitative (1)H NMR spectroscopy in drug discovery and development.

PubMed

Singh, Suruchi; Roy, Raja

2016-07-01

The identification of a drug candidate and its structural determination is the most important step in the process of the drug discovery and for this, nuclear magnetic resonance (NMR) is one of the most selective analytical techniques. The present review illustrates the various perspectives of absolute quantitative (1)H NMR spectroscopy in drug discovery and development. It deals with the fundamentals of quantitative NMR (qNMR), the physiochemical properties affecting qNMR, and the latest referencing techniques used for quantification. The precise application of qNMR during various stages of drug discovery and development, namely natural product research, drug quantitation in dosage forms, drug metabolism studies, impurity profiling and solubility measurements is elaborated. To achieve this, the authors explore the literature of NMR in drug discovery and development between 1963 and 2015. It also takes into account several other reviews on the subject. qNMR experiments are used for drug discovery and development processes as it is a non-destructive, versatile and robust technique with high intra and interpersonal variability. However, there are several limitations also. qNMR of complex biological samples is incorporated with peak overlap and a low limit of quantification and this can be overcome by using hyphenated chromatographic techniques in addition to NMR.

Development and Evaluation of a Parallel Reaction Monitoring Strategy for Large-Scale Targeted Metabolomics Quantification.

PubMed

Zhou, Juntuo; Liu, Huiying; Liu, Yang; Liu, Jia; Zhao, Xuyang; Yin, Yuxin

2016-04-19

Recent advances in mass spectrometers which have yielded higher resolution and faster scanning speeds have expanded their application in metabolomics of diverse diseases. Using a quadrupole-Orbitrap LC-MS system, we developed an efficient large-scale quantitative method targeting 237 metabolites involved in various metabolic pathways using scheduled, parallel reaction monitoring (PRM). We assessed the dynamic range, linearity, reproducibility, and system suitability of the PRM assay by measuring concentration curves, biological samples, and clinical serum samples. The quantification performances of PRM and MS1-based assays in Q-Exactive were compared, and the MRM assay in QTRAP 6500 was also compared. The PRM assay monitoring 237 polar metabolites showed greater reproducibility and quantitative accuracy than MS1-based quantification and also showed greater flexibility in postacquisition assay refinement than the MRM assay in QTRAP 6500. We present a workflow for convenient PRM data processing using Skyline software which is free of charge. In this study we have established a reliable PRM methodology on a quadrupole-Orbitrap platform for evaluation of large-scale targeted metabolomics, which provides a new choice for basic and clinical metabolomics study.

Approach trajectory planning system for maximum concealment

NASA Technical Reports Server (NTRS)

Warner, David N., Jr.

1986-01-01

A computer-simulation study was undertaken to investigate a maximum concealment guidance technique (pop-up maneuver), which military aircraft may use to capture a glide path from masked, low-altitude flight typical of terrain following/terrain avoidance flight enroute. The guidance system applied to this problem is the Fuel Conservative Guidance System. Previous studies using this system have concentrated on the saving of fuel in basically conventional land and ship-based operations. Because this system is based on energy-management concepts, it also has direct application to the pop-up approach which exploits aircraft performance. Although the algorithm was initially designed to reduce fuel consumption, the commanded deceleration is at its upper limit during the pop-up and, therefore, is a good approximation of a minimum-time solution. Using the model of a powered-lift aircraft, the results of the study demonstrated that guidance commands generated by the system are well within the capability of an automatic flight-control system. Results for several initial approach conditions are presented.

Brominated Flame Retardants and Other Persistent Organohalogenated Compounds in Relation to Timing of Puberty in a Longitudinal Study of Girls

PubMed Central

Pinney, Susan M.; Voss, Robert W.; Sjödin, Andreas; Biro, Frank M.; Greenspan, Louise C.; Stewart, Susan; Hiatt, Robert A.; Kushi, Lawrence H.

2015-01-01

Background Exposure to hormonally active chemicals could plausibly affect pubertal timing, so we are investigating this in the Breast Cancer and the Environment Research Program. Objectives Our goal was to examine persistent organic pollutants (POPs) in relation to pubertal onset. Methods Ethnically diverse cohorts of 6- to 8-year-old girls (n = 645) provided serum for measure of polybrominated diphenyl ethers (PBDEs), polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), and lipids. Tanner stages [breast (B) and pubic hair (PH)], and body mass index (BMI) were measured at up to seven annual clinic visits. Using accelerated failure time models, we calculated time ratios (TRs) for age at Tanner stages 2 or higher (2+) and POPs quartiles (Q1–4), adjusting for confounders (race/ethnicity, site, caregiver education, and income). We also calculated prevalence ratios (PRs) of Tanner stages 2+ at time of blood sampling. Results Cross-sectionally, the prevalence of B2+ and PH2+ was inversely related to chemical serum concentrations; but after adjustment for confounders, only the associations with B2+, not PH2+, were statistically significant. Longitudinally, the age at pubertal transition was consistently older with greater chemical concentrations; for example: adjusted TR for B2+ and Q4 for ΣPBDE = 1.05; 95% CI: 1.02, 1.08, for ΣPCB = 1.05; 95% CI: 1.01, 1.08, and for ΣOCP = 1.10; 95% CI: 1.06, 1.14, indicating median ages of about 6 and 11 months older than least exposed, and with similar effect estimates for PH2+. Adjusting for BMI attenuated associations for PCBs and OCPs but not for PBDEs. Conclusions This first longitudinal study of puberty in girls with serum POPs measurements (to our knowledge) reveals a delay in onset with higher concentrations. Citation Windham GC, Pinney SM, Voss RW, SjÖdin A, Biro FM, Greenspan LC, Stewart S, Hiatt RA, Kushi LH. 2015. Brominated flame retardants and other persistent organohalogenated compounds in relation to timing of puberty in a longitudinal study of girls. Environ Health Perspect 123:1046–1052; http://dx.doi.org/10.1289/ehp.1408778 PMID:25956003

Unified Program for the Specification of Hurricane Boundary Layer Winds Over Surfaces of Specified Roughness.

DTIC Science & Technology

1992-09-01

commercial products. rFnn APWn.,W REPORT DOCUMENTATION PAGE oJ_ NO_ o____ PUNK GOPo m=for ta.meuarnca €4 rwmton It "s to "Wuqe I a"oW a•. ama, Wmusma e tune...soa No.. W Q:- .i0 -0. 0d ~ C. m to 0 .9.0 . ~ n e a IV to a * e * a C . c Pop *e * * * . . ci .,e a e ON:O Cm. 40C -a.’ a . . w a. .W o . t. ftl mn

Inter-laboratory analysis of selected genetically modified plant reference materials with digital PCR.

PubMed

Dobnik, David; Demšar, Tina; Huber, Ingrid; Gerdes, Lars; Broeders, Sylvia; Roosens, Nancy; Debode, Frederic; Berben, Gilbert; Žel, Jana

2018-01-01

Digital PCR (dPCR), as a new technology in the field of genetically modified (GM) organism (GMO) testing, enables determination of absolute target copy numbers. The purpose of our study was to test the transferability of methods designed for quantitative PCR (qPCR) to dPCR and to carry out an inter-laboratory comparison of the performance of two different dPCR platforms when determining the absolute GM copy numbers and GM copy number ratio in reference materials certified for GM content in mass fraction. Overall results in terms of measured GM% were within acceptable variation limits for both tested dPCR systems. However, the determined absolute copy numbers for individual genes or events showed higher variability between laboratories in one third of the cases, most possibly due to variability in the technical work, droplet size variability, and analysis of the raw data. GMO quantification with dPCR and qPCR was comparable. As methods originally designed for qPCR performed well in dPCR systems, already validated qPCR assays can most generally be used for dPCR technology with the purpose of GMO detection. Graphical abstract The output of three different PCR-based platforms was assessed in an inter-laboratory comparison.

Student performance and their perception of a patient-oriented problem-solving approach with audiovisual aids in teaching pathology: a comparison with traditional lectures

PubMed Central

Singh, Arjun

2011-01-01

Purpose We use different methods to train our undergraduates. The patient-oriented problem-solving (POPS) system is an innovative teaching–learning method that imparts knowledge, enhances intrinsic motivation, promotes self learning, encourages clinical reasoning, and develops long-lasting memory. The aim of this study was to develop POPS in teaching pathology, assess its effectiveness, and assess students’ preference for POPS over didactic lectures. Method One hundred fifty second-year MBBS students were divided into two groups: A and B. Group A was taught by POPS while group B was taught by traditional lectures. Pre- and posttest numerical scores of both groups were evaluated and compared. Students then completed a self-structured feedback questionnaire for analysis. Results The mean (SD) difference in pre- and post-test scores of groups A and B was 15.98 (3.18) and 7.79 (2.52), respectively. The significance of the difference between scores of group A and group B teaching methods was 16.62 (P < 0.0001), as determined by the z-test. Improvement in post-test performance of group A was significantly greater than of group B, demonstrating the effectiveness of POPS. Students responded that POPS facilitates self-learning, helps in understanding topics, creates interest, and is a scientific approach to teaching. Feedback response on POPS was strong in 57.52% of students, moderate in 35.67%, and negative in only 6.81%, showing that 93.19% students favored POPS over simple lectures. Conclusion It is not feasible to enforce the PBL method of teaching throughout the entire curriculum; However, POPS can be incorporated along with audiovisual aids to break the monotony of dialectic lectures and as alternative to PBL. PMID:23745071

Student performance and their perception of a patient-oriented problem-solving approach with audiovisual aids in teaching pathology: a comparison with traditional lectures.

PubMed

Singh, Arjun

2011-01-01

We use different methods to train our undergraduates. The patient-oriented problem-solving (POPS) system is an innovative teaching-learning method that imparts knowledge, enhances intrinsic motivation, promotes self learning, encourages clinical reasoning, and develops long-lasting memory. The aim of this study was to develop POPS in teaching pathology, assess its effectiveness, and assess students' preference for POPS over didactic lectures. One hundred fifty second-year MBBS students were divided into two groups: A and B. Group A was taught by POPS while group B was taught by traditional lectures. Pre- and posttest numerical scores of both groups were evaluated and compared. Students then completed a self-structured feedback questionnaire for analysis. The mean (SD) difference in pre- and post-test scores of groups A and B was 15.98 (3.18) and 7.79 (2.52), respectively. The significance of the difference between scores of group A and group B teaching methods was 16.62 (P < 0.0001), as determined by the z-test. Improvement in post-test performance of group A was significantly greater than of group B, demonstrating the effectiveness of POPS. Students responded that POPS facilitates self-learning, helps in understanding topics, creates interest, and is a scientific approach to teaching. Feedback response on POPS was strong in 57.52% of students, moderate in 35.67%, and negative in only 6.81%, showing that 93.19% students favored POPS over simple lectures. It is not feasible to enforce the PBL method of teaching throughout the entire curriculum; However, POPS can be incorporated along with audiovisual aids to break the monotony of dialectic lectures and as alternative to PBL.

Neurotoxicity of Persistent Organic Pollutants: Possible Mode(s) of Action and Further Considerations

PubMed Central

Kodavanti, Prasada Rao S.

2005-01-01

Persistent organic pollutants (POPs) are long-lived toxic organic compounds and are of major concern for human and ecosystem health. Although the use of most POPs is banned in most countries, some organochlorine pesticides are still being used in several parts of the world. Although environmental levels of some POPs such as polychlorinated biphenyls (PCBs) have declined, newly emerging POPs such as polybrominated diphenyl ethers (PBDEs) have been increasing considerably. Exposure to POPs has been associated with a wide spectrum of effects including reproductive, developmental, immunologic, carcinogenic, and neurotoxic effects. It is of particular concern that neurotoxic effects of some POPs have been observed in humans at low environmental concentrations. This review focuses on PCBs as a representative chemical class of POPs and discusses the possible mode(s) of action for the neurotoxic effects with emphasis on comparing dose-response and structure-activity relationships (SAR) with other structurally related chemicals. There is sufficient epidemiological and experimental evidence showing that PCB exposure is associated with motor and cognitive deficits in humans and animal models. Although several potential mode(s) of actions were postulated for PCB-induced neurotoxic effects, changes in neurotransmitter systems, altered intracellular signalling processes, and thyroid hormone imbalance are predominant ones. These three potential mechanisms are discussed in detail in vitro and in vivo. In addition, SAR was conducted on other structurally similar chemicals to see if they have a common mode(s) of action. Relative potency factors for several of these POPs were calculated based on their effects on intracellular signalling processes. This is a comprehensive review comparing molecular effects at the cellular level to the neurotoxic effects seen in the whole animal for environmentally relevant POPs. PMID:18648619

Correlation pattern recognition: optimal parameters for quality standards control of chocolate marshmallow candy

NASA Astrophysics Data System (ADS)

Flores, Jorge L.; García-Torales, G.; Ponce Ávila, Cristina

2006-08-01

This paper describes an in situ image recognition system designed to inspect the quality standards of the chocolate pops during their production. The essence of the recognition system is the localization of the events (i.e., defects) in the input images that affect the quality standards of pops. To this end, processing modules, based on correlation filter, and segmentation of images are employed with the objective of measuring the quality standards. Therefore, we designed the correlation filter and defined a set of features from the correlation plane. The desired values for these parameters are obtained by exploiting information about objects to be rejected in order to find the optimal discrimination capability of the system. Regarding this set of features, the pop can be correctly classified. The efficacy of the system has been tested thoroughly under laboratory conditions using at least 50 images, containing 3 different types of possible defects.

Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA

PubMed Central

Jann, Johann-Christoph; Nowak, Daniel; Nolte, Florian; Fey, Stephanie; Nowak, Verena; Obländer, Julia; Pressler, Jovita; Palme, Iris; Xanthopoulos, Christina; Fabarius, Alice; Platzbecker, Uwe; Giagounidis, Aristoteles; Götze, Katharina; Letsch, Anne; Haase, Detlef; Schlenk, Richard; Bug, Gesine; Lübbert, Michael; Ganser, Arnold; Germing, Ulrich; Haferlach, Claudia; Hofmann, Wolf-Karsten; Mossner, Maximilian

2017-01-01

Background Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings. Methods For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers. Results Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77–0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring. Conclusions In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities. PMID:28600436

A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System

PubMed Central

Coudray-Meunier, Coralie; Fraisse, Audrey; Martin-Latil, Sandra; Delannoy, Sabine; Fach, Patrick; Perelle, Sylvie

2016-01-01

Human enteric viruses are recognized as the main causes of food- and waterborne diseases worldwide. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR). A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The performance of high-throughput PCR methods was investigated for detecting 19 human pathogenic viruses and two main process controls used in food virology. The conventional real-time PCR system was compared to the RT-dPCR and RT-qPCR array. Based on the number of genome copies calculated by spectrophotometry, sensitivity was found to be slightly better with RT-qPCR than with RT-dPCR for 14 viruses by a factor range of from 0.3 to 1.6 log10. Conversely, sensitivity was better with RT-dPCR than with RT-qPCR for seven viruses by a factor range of from 0.10 to 1.40 log10. Interestingly, the number of genome copies determined by RT-dPCR was always from 1 to 2 log10 lower than the expected copy number calculated by RT-qPCR standard curve. The sensitivity of the RT-qPCR and RT-qPCR array assays was found to be similar for two viruses, and better with RT-qPCR than with RT-qPCR array for eighteen viruses by a factor range of from 0.7 to 3.0 log10. Conversely, sensitivity was only 0.30 log10 better with the RT-qPCR array than with conventional RT-qPCR assays for norovirus GIV detection. Finally, the RT-qPCR array and RT-dPCR assays were successfully used together to screen clinical samples and quantify pathogenic viruses. Additionally, this method made it possible to identify co-infection in clinical samples. In conclusion, given the rapidity and potential for large numbers of viral targets, this nanofluidic RT-qPCR assay should have a major impact on human pathogenic virus surveillance and outbreak investigations and is likely to be of benefit to public health. PMID:26824897

Requirements for CEC POP Machine Protection System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pinayev, I.

2015-02-18

The requirements of CEC POP machine protection system are meant to prevent damage to a vacuum chamber by a missteered electron beam. In this example, beam energy = 22 MeV, Maximal bunch charge = 5 nC, Maximal repetition rate = 78 kHz, Normalized emittance = 5 mm mrad, Minimal β-function = 1 m. From this information the requirements of the protection system can be calculated by factoring the information into equations to find beam densities and temperature excursions.

A comparative study of digital PCR and real-time qPCR for the detection and quantification of HPV mRNA in sentinel lymph nodes of cervical cancer patients.

PubMed

Carow, Katrin; Read, Christina; Häfner, Norman; Runnebaum, Ingo B; Corner, Adam; Dürst, Matthias

2017-10-30

Qualitative analyses showed that the presence of HPV mRNA in sentinel lymph nodes of cervical cancer patients with pN0 status is associated with significantly decreased recurrence free survival. To further address the clinical potential of the strategy and to define prognostic threshold levels it is necessary to use a quantitative assay. Here, we compare two methods of quantification: digital PCR and standard quantitative PCR. Serial dilutions of 5 ng-5 pg RNA (≙ 500-0.5 cells) of the cervical cancer cell line SiHa were prepared in 5 µg RNA of the HPV-negative human keratinocyte cell line HaCaT. Clinical samples consisted of 10 sentinel lymph nodes with varying HPV transcript levels. Reverse transcription of total RNA (5 µg RNA each) was performed in 100 µl and cDNA aliquots were analyzed by qPCR and dPCR. Digital PCR was run in the RainDrop ® Digital PCR system (RainDance Technologies) using a probe-based detection of HPV E6/E7 cDNA PCR products with 11 µl template. qPCR was done using a Rotor Gene Q 5plex HRM (Qiagen) amplifying HPV E6/E7 cDNA in a SYBR Green format with 1 µl template. For the analysis of both, clinical samples and serial dilution samples, dPCR and qPCR showed comparable sensitivity. With regard to reproducibility, both methods differed considerably, especially for low template samples. Here, we found with qPCR a mean variation coefficient of 126% whereas dPCR enabled a significantly lower mean variation coefficient of 40% (p = 0.01). Generally, we saw with dPCR a substantial reduction of subsampling errors, which most likely reflects the large cDNA amounts available for analysis. Compared to real-time PCR, dPCR shows higher reliability. Thus, our HPV mRNA dPCR assay holds promise for the clinical evaluation of occult tumor cells in histologically tumor-free lymph nodes in future studies.

Properties of targeted preamplification in DNA and cDNA quantification.

PubMed

Andersson, Daniel; Akrap, Nina; Svec, David; Godfrey, Tony E; Kubista, Mikael; Landberg, Göran; Ståhlberg, Anders

2015-01-01

Quantification of small molecule numbers often requires preamplification to generate enough copies for accurate downstream enumerations. Here, we studied experimental parameters in targeted preamplification and their effects on downstream quantitative real-time PCR (qPCR). To evaluate different strategies, we monitored the preamplification reaction in real-time using SYBR Green detection chemistry followed by melting curve analysis. Furthermore, individual targets were evaluated by qPCR. The preamplification reaction performed best when a large number of primer pairs was included in the primer pool. In addition, preamplification efficiency, reproducibility and specificity were found to depend on the number of template molecules present, primer concentration, annealing time and annealing temperature. The amount of nonspecific PCR products could also be reduced about 1000-fold using bovine serum albumin, glycerol and formamide in the preamplification. On the basis of our findings, we provide recommendations how to perform robust and highly accurate targeted preamplification in combination with qPCR or next-generation sequencing.

Droplet Digital PCR for Minimal Residual Disease Detection in Mature Lymphoproliferative Disorders.

PubMed

Drandi, Daniela; Ferrero, Simone; Ladetto, Marco

2018-01-01

Minimal residual disease (MRD) detection has a powerful prognostic relevance for response evaluation and prediction of relapse in hematological malignancies. Real-time quantitative PCR (qPCR) has become the settled and standardized method for MRD assessment in lymphoid disorders. However, qPCR is a relative quantification approach, since it requires a reference standard curve. Droplet digital TM PCR (ddPCR TM ) allows a reliable absolute tumor burden quantification withdrawing the need for preparing, for each experiment, a tumor-specific standard curve. We have recently shown that ddPCR has a good concordance with qPCR and could be a feasible and reliable tool for MRD monitoring in mature lymphoproliferative disorders. In this chapter we describe the experimental workflow, from the detection of the clonal molecular marker to the MRD monitoring by ddPCR, in patients affected by multiple myeloma, mantle cell lymphoma and follicular lymphoma. However, standardization programs among different laboratories are needed in order to ensure the reliability and reproducibility of ddPCR-based MRD results.

In vitro assessment of environmental stress of persistent organic pollutants on the Indo-Pacific humpback dolphin.

PubMed

Jia, Kuntong; Ding, Liang; Zhang, Lingli; Zhang, Mei; Yi, Meisheng; Wu, Yuping

2015-12-25

Persistent organic pollutants (POPs) are detected ubiquitously and are linked to range of adverse health effects. The Indo-Pacific humpback dolphin inhabited the Pearl River Estuary (PRE), China, where high concentrations of POPs have been reported. This study evaluated the threats posed by POPs in the environment to the dolphin using an in vitro system. We selected BNF(β-naphthoflavone) and four POPs (DDTs (dichlorodiphenyltrichloroethanes), CHLs(chlorides), HCHs(hexachlorocyclohexanes) and HCB(hexachlorobenzene)) which had been accumulated in the dolphin with high concentrations to treat the cultured skin fibroblast cells (ScSF cells) of the dolphin, and investigated the expression patterns of the ecological stress biomarkers CYP1A1, AHR and HSP70 in the cell line. The results showed that CYP1A1 was up-regulated after being exposed to different concentrations of BNF, DDTs and HCHs. CHLs, HCHs and HCB promoted AHR expression. HSP70 expression was increased by high concentrations of BNF and DDTs. Moreover, comet assay experiments revealed that DDTs produced higher degree of DNA damage to ScSF cells than other POPs, implying that the Indo-Pacific humpback dolphin in the PRE has been threatened by POPs accumulated in the body, especially by DDTs. Our results provided important information to assess the risk of the Indo-Pacific humpback dolphin raised by environmental POPs in vivo. Copyright © 2015 Elsevier B.V. All rights reserved.

Selection of reference genes for RT-qPCR studies in blood of beluga whales (Delphinapterus leucas)

PubMed Central

Chen, I-Hua; Wang, Jiann-Hsiung; Chou, Shih-Jen; Wu, Yeong-Huey; Li, Tsung-Hsien; Leu, Ming-Yih; Chang, Wen-Been

2016-01-01

Reverse transcription quantitative PCR (RT-qPCR) is used for research in gene expression, and it is vital to choose appropriate housekeeping genes (HKGs) as reference genes to obtain correct results. The purpose of this study is to determine stably expressed HKGs in blood of beluga whales (Delphinapterus leucas) that can be the appropriate reference genes in relative quantification in gene expression research. Sixty blood samples were taken from four beluga whales. Thirteen candidate HKGs (ACTB, B2M, GAPDH, HPRT1, LDHB, PGK1, RPL4, RPL8, RPL18, RPS9, RPS18, TFRC, YWHAZ) were tested using RT-qPCR. The stability values of the HKGs were determined by four different algorithms. Comprehensive analysis of the results revealed that RPL4, PGK1 and ACTB are strongly recommended for use in future RT-qPCR studies in beluga blood samples. This research provides recommendation of reference gene selection, which may contribute to further mRNA relative quantification research in the peripheral blood leukocytes in captive cetaceans. The gene expression assessment of the immune components in blood have the potential to serve as an important approach to evaluating cetacean health influenced by environmental insults. PMID:26998411

Selection of reference genes for RT-qPCR studies in blood of beluga whales (Delphinapterus leucas).

PubMed

Chen, I-Hua; Wang, Jiann-Hsiung; Chou, Shih-Jen; Wu, Yeong-Huey; Li, Tsung-Hsien; Leu, Ming-Yih; Chang, Wen-Been; Yang, Wei Cheng

2016-01-01

Reverse transcription quantitative PCR (RT-qPCR) is used for research in gene expression, and it is vital to choose appropriate housekeeping genes (HKGs) as reference genes to obtain correct results. The purpose of this study is to determine stably expressed HKGs in blood of beluga whales (Delphinapterus leucas) that can be the appropriate reference genes in relative quantification in gene expression research. Sixty blood samples were taken from four beluga whales. Thirteen candidate HKGs (ACTB, B2M, GAPDH, HPRT1, LDHB, PGK1, RPL4, RPL8, RPL18, RPS9, RPS18, TFRC, YWHAZ) were tested using RT-qPCR. The stability values of the HKGs were determined by four different algorithms. Comprehensive analysis of the results revealed that RPL4, PGK1 and ACTB are strongly recommended for use in future RT-qPCR studies in beluga blood samples. This research provides recommendation of reference gene selection, which may contribute to further mRNA relative quantification research in the peripheral blood leukocytes in captive cetaceans. The gene expression assessment of the immune components in blood have the potential to serve as an important approach to evaluating cetacean health influenced by environmental insults.

Popping rocks from the Mid-Atlantic Ridge: Insights into mantle volatile concentrations and degassing dynamics

NASA Astrophysics Data System (ADS)

Jones, M.; Soule, S. A.; Kurz, M. D.; Wanless, V. D.; Le Roux, V.; Klein, F.; Mittelstaedt, E. L.; Curtice, J.

2016-12-01

During a 1985 cruise, the Mid-Atlantic Ridge (MAR) near 14°N yielded an unusually vesicular mid-ocean ridge (MOR) basalt that popped upon recovery from the seafloor due to the release of trapped volatiles. This `popping rock' has been inferred to be representative of primitive, undegassed magmas from the upper mantle due to its high volatile concentrations. Thus, the sample has been used to constrain CO2 flux from the MOR system, upper mantle volatile concentrations, and magma degassing dynamics. However, the lack of geologic context for the original popping rock raises questions about whether it truly reflects the volatile content of its mantle source. Here, we present results from a 2016 cruise to the MAR aimed at characterizing the geologic context of popping rocks and understanding their origins. The newly recovered samples display differences in volatile concentrations and vesicularities between popping and non-popping rocks. These differences may be related to geologic setting and eruption dynamics with potential implications for mantle volatile concentrations. Volatile concentrations in the outer quenched margin of new samples were measured by ion microprobe to elucidate degassing systematics, brine/magma interactions, and popping rock formation. The large variability in dissolved H2O (0.05-0.77 wt%) can be attributed to spatially variable brine contamination. Dissolved CO2 concentrations (153-356 ppm) are likely controlled by initial volatile concentrations and variable degrees of degassing. The subset of popping samples display low dissolved CO2 concentrations (161-178 ppm) and moderate dissolved H2O concentrations (.44-.50 wt%) and are at equilibrium with their eruption depth based on solubility calculations. X-ray microtomography reveals vesicularity in newly collected popping rocks exceeding 19%, making these samples the most highly vesicular recovered from the MAR. The total gas contents in the basaltic glasses are inferred from dissolved volatile concentrations and vesicularity. These calculations are aided by analysis of gas contents in vesicles by confocal Raman spectroscopy and vacuum crushing experiments. The preliminary results and seafloor observations allow an evaluation of the origins of popping rocks and their implications for mantle volatile concentrations.

Update on the CeC PoP 704 MHz 5-cell cavity cryomodule design and fabrication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brutus, J. C.; Belomestnykh, S.; Ben-Zvi, I.

2015-05-03

A 5-cell SRF cavity operating at 704 MHz will be used for the Coherent Electron Cooling Proof of Principle (CeC PoP) system under development for the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. The CeC PoP experiment will demonstrate the new technique of cooling proton and ion beams that may increase the beam luminosity in certain cases, by as much as tenfold. The 704 MHz cavity will accelerate 2 MeV electrons from a 112 MHz SRF gun up to 22MeV. This paper provides an overview of the design, the project status and schedule of the 704 MHz 5-cellmore » SRF for CeC PoP experiment.« less

PopHR: a knowledge-based platform to support integration, analysis, and visualization of population health data.

PubMed

Shaban-Nejad, Arash; Lavigne, Maxime; Okhmatovskaia, Anya; Buckeridge, David L

2017-01-01

Population health decision makers must consider complex relationships between multiple concepts measured with differential accuracy from heterogeneous data sources. Population health information systems are currently limited in their ability to integrate data and present a coherent portrait of population health. Consequentially, these systems can provide only basic support for decision makers. The Population Health Record (PopHR) is a semantic web application that automates the integration and extraction of massive amounts of heterogeneous data from multiple distributed sources (e.g., administrative data, clinical records, and survey responses) to support the measurement and monitoring of population health and health system performance for a defined population. The design of the PopHR draws on the theories of the determinants of health and evidence-based public health to harmonize and explicitly link information about a population with evidence about the epidemiology and control of chronic diseases. Organizing information in this manner and linking it explicitly to evidence is expected to improve decision making related to the planning, implementation, and evaluation of population health and health system interventions. In this paper, we describe the PopHR platform and discuss the architecture, design, key modules, and its implementation and use. © 2016 New York Academy of Sciences.

Enhanced presurgical pain temporal summation response predicts post-thoracotomy pain intensity during the acute postoperative phase.

PubMed

Weissman-Fogel, Irit; Granovsky, Yelena; Crispel, Yonathan; Ben-Nun, Alon; Best, Lael Anson; Yarnitsky, David; Granot, Michal

2009-06-01

Recent evidence points to an association between experimental pain measures obtained preoperatively and acute postoperative pain (POP). We hypothesized that pain temporal summation (TS) might be an additional predictor for POP insofar as it represents the neuroplastic changes that occur in the central nervous system following surgery. Therefore, a wide range of psychophysical tests (TS to heat and mechanical repetitive stimuli, pain threshold, and suprathreshold pain estimation) and personality tests (pain catastrophizing and anxiety levels) were administered prior to thoracotomy in 84 patients. POP ratings were evaluated on the 2nd and 5th days after surgery at rest (spontaneous pain) and in response to activity (provoked pain). Linear regression models revealed that among all assessed variables, enhanced TS and higher pain scores for mechanical stimulation were significantly associated with greater provoked POP intensity (overall r2 = 0.225, P = .008). Patients who did not demonstrate TS to both modalities reported lower scores of provoked POP as compared with patients who demonstrated TS in response to at least 1 modality (F = 4.59 P = .013). Despite the moderate association between pain catastrophizing and rest POP, none of the variables predicted the spontaneous POP intensity. These findings suggest that individual susceptibility toward a greater summation response may characterize patients who are potentially vulnerable to augmented POP. This study proposed the role of pain temporal summation assessed preoperatively as a significant psychophysical predictor for acute postoperative pain intensity. The individual profile of enhanced pain summation is associated with the greater likelihood of higher postoperative pain scores.

Planned and ongoing projects (pop) database: development and results.

PubMed

Wild, Claudia; Erdös, Judit; Warmuth, Marisa; Hinterreiter, Gerda; Krämer, Peter; Chalon, Patrice

2014-11-01

The aim of this study was to present the development, structure and results of a database on planned and ongoing health technology assessment (HTA) projects (POP Database) in Europe. The POP Database (POP DB) was set up in an iterative process from a basic Excel sheet to a multifunctional electronic online database. The functionalities, such as the search terminology, the procedures to fill and update the database, the access rules to enter the database, as well as the maintenance roles, were defined in a multistep participatory feedback loop with EUnetHTA Partners. The POP Database has become an online database that hosts not only the titles and MeSH categorizations, but also some basic information on status and contact details about the listed projects of EUnetHTA Partners. Currently, it stores more than 1,200 planned, ongoing or recently published projects of forty-three EUnetHTA Partners from twenty-four countries. Because the POP Database aims to facilitate collaboration, it also provides a matching system to assist in identifying similar projects. Overall, more than 10 percent of the projects in the database are identical both in terms of pathology (indication or disease) and technology (drug, medical device, intervention). In addition, approximately 30 percent of the projects are similar, meaning that they have at least some overlap in content. Although the POP DB is successful concerning regular updates of most national HTA agencies within EUnetHTA, little is known about its actual effects on collaborations in Europe. Moreover, many non-nationally nominated HTA producing agencies neither have access to the POP DB nor can share their projects.

Self-digitization microfluidic chip for absolute quantification of mRNA in single cells.

PubMed

Thompson, Alison M; Gansen, Alexander; Paguirigan, Amy L; Kreutz, Jason E; Radich, Jerald P; Chiu, Daniel T

2014-12-16

Quantification of mRNA in single cells provides direct insight into how intercellular heterogeneity plays a role in disease progression and outcomes. Quantitative polymerase chain reaction (qPCR), the current gold standard for evaluating gene expression, is insufficient for providing absolute measurement of single-cell mRNA transcript abundance. Challenges include difficulties in handling small sample volumes and the high variability in measurements. Microfluidic digital PCR provides far better sensitivity for minute quantities of genetic material, but the typical format of this assay does not allow for counting of the absolute number of mRNA transcripts samples taken from single cells. Furthermore, a large fraction of the sample is often lost during sample handling in microfluidic digital PCR. Here, we report the absolute quantification of single-cell mRNA transcripts by digital, one-step reverse transcription PCR in a simple microfluidic array device called the self-digitization (SD) chip. By performing the reverse transcription step in digitized volumes, we find that the assay exhibits a linear signal across a wide range of total RNA concentrations and agrees well with standard curve qPCR. The SD chip is found to digitize a high percentage (86.7%) of the sample for single-cell experiments. Moreover, quantification of transferrin receptor mRNA in single cells agrees well with single-molecule fluorescence in situ hybridization experiments. The SD platform for absolute quantification of single-cell mRNA can be optimized for other genes and may be useful as an independent control method for the validation of mRNA quantification techniques.

Multiplex quantification of 12 European Union authorized genetically modified maize lines with droplet digital polymerase chain reaction.

PubMed

Dobnik, David; Spilsberg, Bjørn; Bogožalec Košir, Alexandra; Holst-Jensen, Arne; Žel, Jana

2015-08-18

Presence of genetically modified organisms (GMO) in food and feed products is regulated in many countries. The European Union (EU) has implemented a threshold for labeling of products containing more than 0.9% of authorized GMOs per ingredient. As the number of GMOs has increased over time, standard-curve based simplex quantitative polymerase chain reaction (qPCR) analyses are no longer sufficiently cost-effective, despite widespread use of initial PCR based screenings. Newly developed GMO detection methods, also multiplex methods, are mostly focused on screening and detection but not quantification. On the basis of droplet digital PCR (ddPCR) technology, multiplex assays for quantification of all 12 EU authorized GM maize lines (per April first 2015) were developed. Because of high sequence similarity of some of the 12 GM targets, two separate multiplex assays were needed. In both assays (4-plex and 10-plex), the transgenes were labeled with one fluorescence reporter and the endogene with another (GMO concentration = transgene/endogene ratio). It was shown that both multiplex assays produce specific results and that performance parameters such as limit of quantification, repeatability, and trueness comply with international recommendations for GMO quantification methods. Moreover, for samples containing GMOs, the throughput and cost-effectiveness is significantly improved compared to qPCR. Thus, it was concluded that the multiplex ddPCR assays could be applied for routine quantification of 12 EU authorized GM maize lines. In case of new authorizations, the events can easily be added to the existing multiplex assays. The presented principle of quantitative multiplexing can be applied to any other domain.

Rapid Identification and Quantification of Aureococcus anophagefferens by qPCR Method (Taqman) in the Qinhuangdao Coastal Area: A Region for Recurrent Brown Tide Breakout in China.

PubMed

Wang, Li-Ping; Lei, Kun

2016-12-01

Since 2009, Aureococcus anophagefferens has caused brown tide to occur recurrently in Qinhuangdao coastal area, China. Because the algal cells of A. anophagefferens are so tiny (~3 µm) that it is very hard to identify exactly under a microscope for natural water samples, it is very urgent to develop a method for efficient and continuous monitoring. Here specific primers and Taqman probe are designed to develop a real-time quantitative PCR (qPCR) method for identification and quantification continually. The algal community and cell abundance of A. anophagefferens in the study area (E 119°20'-119°50' and N 39°30'-39°50') from April to October in 2013 are detected by pyrosequencing, and are used to validate the specification and precision of qPCR method for natural samples. Both pyrosequencing and qPCR shows that the targeted cells are present only in May, June and July, and the cell abundance are July > June > May. Although there are various algal species including dinoflagellata, diatom, Cryptomonadales, Chrysophyceae and Chlorophyta living in the natural seawater simultaneously, no disturbance happens to qPCR method. This qPCR method could detect as few as 10 targeted cells, indicating it is able to detect the algal cells at pre-bloom levels. Therefore, qPCR with Taqman probe provides a powerful and sensitive method to monitor the brown tide continually in Qinhuangdao coastal area, China. The results provide a necessary technology support for forecasting the brown tide initiation, in China.

Metallated porphyrin based porous organic polymers as efficient electrocatalysts

NASA Astrophysics Data System (ADS)

Lu, Guolong; Zhu, Youlong; Xu, Kongliang; Jin, Yinghua; Ren, Zhiyong Jason; Liu, Zhenning; Zhang, Wei

2015-10-01

Developing efficient, stable and low-cost catalysts for Oxygen Reduction Reaction (ORR) is of great significance to many emerging technologies including fuel cells and metal-air batteries. Herein, we report the development of a cobalt(ii) porphyrin based porous organic polymer (CoPOP) and its pyrolyzed derivatives as highly active ORR catalysts. The as-synthesized CoPOP exhibits high porosity and excellent catalytic performance stability, retaining ~100% constant ORR current over 50 000 s in both alkaline and acidic media. Pyrolysis of CoPOP at various temperatures (600 °C, 800 °C, and 1000 °C) yields the materials consisting of graphitic carbon layers and cobalt nanoparticles, which show greatly enhanced catalytic activity compared to the as-synthesized CoPOP. Among them, CoPOP-800/C pyrolyzed at 800 °C shows the highest specific surface area and ORR activity, displaying the most positive half-wave potential (0.825 V vs. RHE) and the largest limited diffusion current density (5.35 mA cm-2) in an alkaline medium, which are comparable to those of commercial Pt/C (20 wt%) (half-wave potential 0.829 V vs. RHE, limited diffusion current density 5.10 mA cm-2). RDE and RRDE experiments indicate that CoPOP-800/C directly reduces molecular oxygen to water through a 4-e- pathway in both alkaline and acidic media. More importantly, CoPOP-800/C exhibits excellent durability and methanol-tolerance under acidic and alkaline conditions, which surpass the Pt/C (20 wt%) system.Developing efficient, stable and low-cost catalysts for Oxygen Reduction Reaction (ORR) is of great significance to many emerging technologies including fuel cells and metal-air batteries. Herein, we report the development of a cobalt(ii) porphyrin based porous organic polymer (CoPOP) and its pyrolyzed derivatives as highly active ORR catalysts. The as-synthesized CoPOP exhibits high porosity and excellent catalytic performance stability, retaining ~100% constant ORR current over 50 000 s in both alkaline and acidic media. Pyrolysis of CoPOP at various temperatures (600 °C, 800 °C, and 1000 °C) yields the materials consisting of graphitic carbon layers and cobalt nanoparticles, which show greatly enhanced catalytic activity compared to the as-synthesized CoPOP. Among them, CoPOP-800/C pyrolyzed at 800 °C shows the highest specific surface area and ORR activity, displaying the most positive half-wave potential (0.825 V vs. RHE) and the largest limited diffusion current density (5.35 mA cm-2) in an alkaline medium, which are comparable to those of commercial Pt/C (20 wt%) (half-wave potential 0.829 V vs. RHE, limited diffusion current density 5.10 mA cm-2). RDE and RRDE experiments indicate that CoPOP-800/C directly reduces molecular oxygen to water through a 4-e- pathway in both alkaline and acidic media. More importantly, CoPOP-800/C exhibits excellent durability and methanol-tolerance under acidic and alkaline conditions, which surpass the Pt/C (20 wt%) system. Electronic supplementary information (ESI) available: Details of the experimental section, powder X-ray diffraction (PXRD) data, scanning electron microscopy (FE-SEM) images, Fourier transform infrared spectroscopy (FT-IR) data, and additional electrochemical data. See DOI: 10.1039/c5nr05324b

A multiplex real-time PCR assay, based on invA and pagC genes, for the detection and quantification of Salmonella enterica from cattle lymph nodes.

PubMed

Bai, Jianfa; Trinetta, Valentina; Shi, Xiaorong; Noll, Lance W; Magossi, Gabriela; Zheng, Wanglong; Porter, Elizabeth P; Cernicchiaro, Natalia; Renter, David G; Nagaraja, Tiruvoor G

2018-05-01

Cattle lymph nodes can harbor Salmonella and potentially contaminate beef products. We have developed and validated a new real-time PCR (qPCR) assay for the detection and quantification of Salmonella enterica in cattle lymph nodes. The assay targets both the invA and pagC genes, the most conserved molecular targets in Salmonella enterica. An 18S rRNA gene assay that amplifies from cattle and other animal species was also included as an internal control. Available DNA sequences for invA, pagC and 18S rRNA genes were used for primer and probe selections. Three Salmonella serotypes, S. Typhimurium, S. Anatum, and S. Montevideo, were used to assess the assay's analytical sensitivity. Correlation coefficients of standard curves generated for each target and for all three serotypes were >99% and qPCR amplification efficiencies were between 93% and 110%. Assay sensitivity was also determined using standard curve data generated from Salmonella-negative cattle lymph nodes spiked with 10-fold dilutions of the three Salmonella serotypes. Assay specificity was determined using Salmonella culture method, and qPCR testing on 36 Salmonella strains representing 33 serotypes, 38 Salmonella strains of unknown serotypes, 252 E. coli strains representing 40 serogroups, and 31 other bacterial strains representing 18 different species. A collection of 647 cattle lymph node samples from steers procured from the Midwest region of the US were tested by the qPCR, and compared to culture-method of detection. Salmonella prevalence by qPCR for pre-enriched and enriched lymph nodes was 19.8% (128/647) and 94.9% (614/647), respectively. A majority of qPCR positive pre-enriched samples (105/128) were at concentrations between 10 4 and 10 5  CFU/mL. Culture method detected Salmonella in 7.7% (50/647) and 80.7% (522/647) of pre- and post-enriched samples, respectively; 96.0% (48/50) of pre-enriched and 99.4% (519/522) of post-enriched culture-positive samples were also positive by qPCR. More samples tested positive by qPCR than by culture method, indicating that the real-time PCR assay was more sensitive. Our data indicate that this triplex qPCR can be used to accurately detect and quantify Salmonella enterica strains from cattle lymph node samples. The assay may serve as a useful tool to monitor the prevalence of Salmonella in beef production systems. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of PMA real-time PCR method to quantify viable cells of Pantoea agglomerans CPA-2, an antagonist to control the major postharvest diseases on oranges.

PubMed

Soto-Muñoz, Lourdes; Teixidó, Neus; Usall, Josep; Viñas, Inmaculada; Crespo-Sempere, Ana; Torres, Rosario

2014-06-16

Dilution plating is the quantification method commonly used to estimate the population level of postharvest biocontrol agents, but this method does not permit a distinction among introduced and indigenous strains. Recently, molecular techniques based on DNA amplification such as quantitative real-time PCR (qPCR) have been successfully applied for their high strain-specific detection level. However, the ability of qPCR to distinguish viable and nonviable cells is limited. A promising strategy to avoid this issue relies on the use of nucleic acid intercalating dyes, such as propidium monoazide (PMA), as a sample pretreatment prior to the qPCR. The objective of this study was to optimize a protocol based on PMA pre-treatment samples combined with qPCR to distinguish and quantify viable cells of the biocontrol agent P. agglomerans CPA-2 applied as a postharvest treatment on orange. The efficiency of PMA-qPCR method under the established conditions (30μM PMA for 20min of incubation followed by 30min of LED light exposure) was evaluated on an orange matrix. Results showed no difference in CFU or cells counts of viable cells between PMA-qPCR and dilution plating. Samples of orange matrix inoculated with a mixture of viable/dead cells showed 5.59log10 CFU/ml by dilution plating, 8.25log10 cells/ml by qPCR, and 5.93log10 cells/ml by PMA-qPCR. Furthermore, samples inoculated with heat-killed cells were not detected by dilution plating and PMA-qPCR, while by qPCR was of 8.16log10 cells/ml. The difference in quantification cycles (Cq) among qPCR and PMA-qPCR was approximately 16cycles, which means a reduction of 65,536 fold of the dead cells detected. In conclusion, PMA-qPCR method is a suitable tool for quantify viable CPA-2 cells, which could be useful to estimate the ability of this antagonist to colonize the orange surface. Copyright © 2014 Elsevier B.V. All rights reserved.

Dose/Exposure‐Response Modeling to Support Dosing Recommendation for Phase III Development of Baricitinib in Patients with Rheumatoid Arthritis

PubMed Central

Chua, Laiyi; Ernest, Charles; Macias, William; Rooney, Terence; Tham, Lai San

2017-01-01

Baricitinib is an oral inhibitor of Janus kinases (JAKs), selective for JAK1 and 2. It demonstrated dose‐dependent efficacy in patients with moderate‐to‐severe rheumatoid arthritis (RA) in a phase IIb study up to 24 weeks. Population pharmacokinetic/pharmacodynamic (PopPK/PD) models were developed to characterize concentration‐time profiles and dose/exposure‐response (D/E‐R) relationships for the key efficacy (proportion of patients achieving American College of Rheumatology 20%, 50%, or 70% response rate) and safety endpoints (incidence of anemia) for the phase IIb study. The modeling suggested that 4 mg q.d. was likely to offer the optimum risk/benefit balance, whereas 2 mg q.d. had the potential for adequate efficacy. In addition, at the same total daily dose, a twice‐daily regimen is not expected to provide an advantage over q.d. dosing for the efficacy or safety endpoints. The model‐based simulations formed the rationale for key aspects of dosing, such as dose levels and dosing frequency for phase III development. PMID:28891251

Viability-qPCR for detecting Legionella: Comparison of two assays based on different amplicon lengths.

PubMed

Ditommaso, Savina; Giacomuzzi, Monica; Ricciardi, Elisa; Zotti, Carla M

2015-08-01

Two different real-time quantitative PCR (PMA-qPCR) assays were applied for quantification of Legionella spp. by targeting a long amplicon (approx 400 bp) of 16S rRNA gene and a short amplicon (approx. 100 bp) of 5S rRNA gene. Purified DNA extracts from pure cultures of Legionella spp. and from environmental water samples were quantified. Application of the two assays to quantify Legionella in artificially contaminated water achieved that both assays were able to detect Legionella over a linear range of 10 to 10(5) cells ml(-1). A statistical analysis of the standard curves showed that both assays were linear with a good correlation coefficient (R(2) = 0.99) between the Ct and the copy number. Amplification with the reference assay was the most effective for detecting low copy numbers (1 bacterium per PCR mixture). Using selective quantification of viable Legionella by the PMA-qPCR method we obtained a greater inhibition of the amplification of the 400-bp 16S gene fragment (Δlog(10) = 3.74 ± 0.39 log(10) GU ml(-1)). A complete inhibition of the PCR signal was obtained when heat-killed cells in a concentration below 1 × 10(5) cells ml(-1) were pretreated with PMA. Analysing short amplicon sizes led to only 2.08 log reductions in the Legionella dead-cell signal. When we tested environmental water samples, the two qPCR assays were in good agreement according to the kappa index (0.741). Applying qPCR combined with PMA treatment, we also obtained a good agreement (kappa index 0.615). The comparison of quantitative results shows that both assays yielded the same quantification sensitivity (mean log = 4.59 vs mean log = 4.31). Copyright © 2015 Elsevier Ltd. All rights reserved.

O How Wondrous Is E-Mail!

ERIC Educational Resources Information Center

Buchanan, Larry

1998-01-01

Addresses the use of e-mail for communication and collaborative projects in schools. Discusses the effectiveness of an e-mail system based on a UNIX host; problems with POP (post office protocol) client programs; and the new Internet Mail Access Protocol (IMAP) which addresses most of the shortcomings of the POP protocol while keeping advantages…

Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA.

PubMed

Jann, Johann-Christoph; Nowak, Daniel; Nolte, Florian; Fey, Stephanie; Nowak, Verena; Obländer, Julia; Pressler, Jovita; Palme, Iris; Xanthopoulos, Christina; Fabarius, Alice; Platzbecker, Uwe; Giagounidis, Aristoteles; Götze, Katharina; Letsch, Anne; Haase, Detlef; Schlenk, Richard; Bug, Gesine; Lübbert, Michael; Ganser, Arnold; Germing, Ulrich; Haferlach, Claudia; Hofmann, Wolf-Karsten; Mossner, Maximilian

2017-09-01

Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings. For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers. Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77-0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring. In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Population III Gamma-ray Burst Afterglows: Constraints on Stellar Masses and External Medium Densities

NASA Astrophysics Data System (ADS)

Toma, Kenji; Sakamoto, Takanori; Mészáros, Peter

2011-04-01

Population (Pop.) III stars are theoretically expected to be prominent around redshifts z ~ 20, consisting of mainly very massive stars with M * >~ 100 M sun, though there is no direct observational evidence for these objects. They may produce collapsar gamma-ray bursts (GRBs), with jets driven by magnetohydrodynamic processes, whose total isotropic-equivalent energy could be as high as E iso >~ 1057 erg over a cosmological-rest-frame duration of td >~ 104 s, depending on the progenitor mass. Here, we calculate the afterglow spectra of such Pop. III GRBs based on the standard external shock model and show that they will be detectable with the Swift Burst Alert Telescope (BAT)/XRT and Fermi Large Area Telescope (LAT) instruments. We find that in some cases a spectral break due to electron-positron pair creation will be observable in the LAT energy range, which can put constraints on the ambient density of the pre-collapse Pop. III star. Thus, high-redshift GRB afterglow observations could be unique and powerful probes of the properties of Pop. III stars and their environments. We examine the trigger threshold of the BAT instrument in detail, focusing on the image trigger system, and show that the prompt emission of Pop. III GRBs could also be detected by BAT. Finally we briefly show that the late-time radio afterglows of Pop. III GRBs for typical parameters, despite the large distances, can be very bright: ~= 140 mJy at 1 GHz, which may lead to a constraint on the Pop. III GRB rate from the current radio survey data, and ~= 2.4 mJy at 70 MHz, which implies that Pop. III GRB radio afterglows could be interesting background source candidates for 21 cm absorption line detections.

Predominant Lactobacillus species types of vaginal microbiota in pregnant Korean women: quantification of the five Lactobacillus species and two anaerobes.

PubMed

Kim, Jeong Hyun; Yoo, Seung Min; Sohn, Yong Hak; Jin, Chan Hee; Yang, Yun Suk; Hwang, In Taek; Oh, Kwan Young

2017-10-01

To investigate the predominant Lactobacillus species types (LSTs) of vaginal microbiota in pregnant Korean women by quantifying five Lactobacillus species and two anaerobes. In all, 168 pregnant Korean women under antenatal care at Eulji University Hospital and local clinics were enrolled in the prospective cohort study during pregnancy (10-14 weeks). Vaginal samples were collected with Eswab for Quantitative polymerase chain reaction (qPCR) and stored in a -80 °C freezer. qPCR was performed for five Lactobacillus species and two anaerobes. To identify the predominant LSTs, quantifications were analyzed by the Cluster and Tree View programs of Eisen Lab. Also the quantifications were compared among classified groups. L. crispatus and L. iners were most commonly found in pregnant Korean women, followed by L. gasseri and L. jensenii; L. vaginalis was nearly absent. Five types (four predominant LSTs and one predominant anaerobe type without predominant Lactobacillus species) were classified. Five predominant LSTs were identified in vaginal microbiota of pregnant Korean women. L. crispatus and L. iners predominant types comprised a large proportion.

Contribution of Persistent Organic Pollutant Exposure to the Adipose Tissue Oxidative Microenvironment in an Adult Cohort: A Multipollutant Approach.

PubMed

Artacho-Cordón, Francisco; León, Josefa; Sáenz, José M; Fernández, Mariana F; Martin-Olmedo, Piedad; Olea, Nicolás; Arrebola, Juan P

2016-12-20

Despite growing in vitro and in vivo evidence of the putative role of persistent organic pollutants (POPs) in the induction of oxidative damage in cell structures, this issue has been poorly addressed from an epidemiologic perspective. The aim of this study was to explore associations between adipose tissue POP concentrations and the in situ oxidative microenvironment. A cross-sectional study was conducted in a subsample (n = 271) of a previously established cohort, quantifying levels of eight POPs and four groups of oxidative stress biomarkers in adipose tissue. Associations were explored using multivariate linear regression analyses adjusted for potential confounders. We assessed the combined effect of POPs on oxidative stress/glutathione system biomarkers using weighted quantile sum regression (WQS). Increased concentrations of p,p'-DDE, HCB, β-HCH, dicofol, and PCBs (congeners -138, -153, and -180) were predominantly associated with higher lipid peroxidation (TBARS) [exp(β) = 1.09-1.78, p < 0.01-0.04)] and SOD activity [exp(β) = 1.13-1.48, p < 0.01-0.05)] levels. However, only a few associations were observed with glutathione system biomarkers, e.g., PCB-180 with total glutathione [exp(β) = 1.98, p = 0.03]. The WQS index was found to be positively associated with SOD activity, and PCB-138, PCB-180, and β-HCH were the main contributors to the index. Likewise, the WQS index was positively associated with TBARS levels, with the three PCBs acting as the main contributors. This is the first epidemiological evidence of the putative disruption by POPs of the adipose tissue oxidative microenvironment. Our results indicate that POP exposure may enhance alternative pathways to the glutathione detoxification route, which might result in tissue damage. Further research is warranted to fully elucidate the potential health implications.

A theoretical introduction to "combinatory SYBRGreen qPCR screening", a matrix-based approach for the detection of materials derived from genetically modified plants.

PubMed

Van den Bulcke, Marc; Lievens, Antoon; Barbau-Piednoir, Elodie; MbongoloMbella, Guillaume; Roosens, Nancy; Sneyers, Myriam; Casi, Amaya Leunda

2010-03-01

The detection of genetically modified (GM) materials in food and feed products is a complex multi-step analytical process invoking screening, identification, and often quantification of the genetically modified organisms (GMO) present in a sample. "Combinatory qPCR SYBRGreen screening" (CoSYPS) is a matrix-based approach for determining the presence of GM plant materials in products. The CoSYPS decision-support system (DSS) interprets the analytical results of SYBRGREEN qPCR analysis based on four values: the C(t)- and T(m) values and the LOD and LOQ for each method. A theoretical explanation of the different concepts applied in CoSYPS analysis is given (GMO Universe, "Prime number tracing", matrix/combinatory approach) and documented using the RoundUp Ready soy GTS40-3-2 as an example. By applying a limited set of SYBRGREEN qPCR methods and through application of a newly developed "prime number"-based algorithm, the nature of subsets of corresponding GMO in a sample can be determined. Together, these analyses provide guidance for semi-quantitative estimation of GMO presence in a food and feed product.

Factors affecting the productivity of urban parks

Treesearch

Thomas A. More; Thomas A. More

1990-01-01

The park system of two Massachusetts cities-Holyoke (pop. 44,819) and Fitchburg (pop. 39,332)-produced an estimated 605,608 visitor-hours of use during the summer of 1979. The average park produced 7,877 visitor-hours in Holyoke and 9,624 in Fitchburg, though use varied widely. Contrary to original expectations, neighborhood characteristics had little influence on use...

SNPase-ARMS qPCR: Ultrasensitive Mutation-Based Detection of Cell-Free Tumor DNA in Melanoma Patients

PubMed Central

Stadler, Julia; Eder, Johanna; Pratscher, Barbara; Brandt, Sabine; Schneller, Doris; Müllegger, Robert; Vogl, Claus; Trautinger, Franz; Brem, Gottfried; Burgstaller, Joerg P.

2015-01-01

Cell-free circulating tumor DNA in the plasma of cancer patients has become a common point of interest as indicator of therapy options and treatment response in clinical cancer research. Especially patient- and tumor-specific single nucleotide variants that accurately distinguish tumor DNA from wild type DNA are promising targets. The reliable detection and quantification of these single-base DNA variants is technically challenging. Currently, a variety of techniques is applied, with no apparent “gold standard”. Here we present a novel qPCR protocol that meets the conditions of extreme sensitivity and specificity that are required for detection and quantification of tumor DNA. By consecutive application of two polymerases, one of them designed for extreme base-specificity, the method reaches unprecedented sensitivity and specificity. Three qPCR assays were tested with spike-in experiments, specific for point mutations BRAF V600E, PTEN T167A and NRAS Q61L of melanoma cell lines. It was possible to detect down to one copy of tumor DNA per reaction (Poisson distribution), at a background of up to 200 000 wild type DNAs. To prove its clinical applicability, the method was successfully tested on a small cohort of BRAF V600E positive melanoma patients. PMID:26562020

Direct qPCR quantification using the Quantifiler(®) Trio DNA quantification kit.

PubMed

Liu, Jason Yingjie

2014-11-01

The effectiveness of a direct quantification assay is essential to the adoption of the combined direct quantification/direct STR workflow. In this paper, the feasibility of using the Quantifiler(®) Trio DNA quantification kit for the direct quantification of forensic casework samples was investigated. Both low-level touch DNA samples and blood samples were collected on PE swabs and quantified directly. The increased sensitivity of the Quantifiler(®) Trio kit enabled the detection of less than 10pg of DNA in unprocessed touch samples and also minimizes the stochastic effect experienced by different targets in the same sample. The DNA quantity information obtained from a direct quantification assay using the Quantifiler(®) Trio kit can also be used to accurately estimate the optimal input DNA quantity for a direct STR amplification reaction. The correlation between the direct quantification results (Quantifiler(®) Trio kit) and the direct STR results (GlobalFiler™ PCR amplification kit(*)) for low-level touch DNA samples indicates that direct quantification using the Quantifiler(®) Trio DNA quantification kit is more reliable than the Quantifiler(®) Duo DNA quantification kit for predicting the STR results of unprocessed touch DNA samples containing less than 10pg of DNA. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Quantification of viable Legionella pneumophila cells using propidium monoazide combined with quantitative PCR.

PubMed

Yáñez, M Adela; Nocker, Andreas; Soria-Soria, Elena; Múrtula, Raquel; Martínez, Lorena; Catalán, Vicente

2011-05-01

One of the greatest challenges of implementing fast molecular detection methods as part of Legionella surveillance systems is to limit detection to live cells. In this work, a protocol for sample treatment with propidium monoazide (PMA) in combination with quantitative PCR (qPCR) has been optimized and validated for L. pneumophila as an alternative of the currently used time-consuming culture method. Results from PMA-qPCR were compared with culture isolation and traditional qPCR. Under the conditions used, sample treatment with 50 μM PMA followed by 5 min of light exposure were assumed optimal resulting in an average reduction of 4.45 log units of the qPCR signal from heat-killed cells. When applied to environmental samples (including water from cooling water towers, hospitals, spas, hot water systems in hotels, and tap water), different degrees of correlations between the three methods were obtained which might be explained by different matrix properties, but also varying degrees of non-culturable cells. It was furthermore shown that PMA displayed substantially lower cytotoxicity with Legionella than the alternative dye ethidium monoazide (EMA) when exposing live cells to the dye followed by plate counting. This result confirmed the findings with other species that PMA is less membrane-permeant and more selective for the intact cells. In conclusion, PMA-qPCR is a promising technique for limiting detection to intact cells and makes Legionella surveillance data substantially more relevant in comparison with qPCR alone. For future research it would be desirable to increase the method's capacity to exclude signals from dead cells in difficult matrices or samples containing high numbers of dead cells. Copyright © 2011 Elsevier B.V. All rights reserved.

Comprehensive Multiplex One-Step Real-Time TaqMan qRT-PCR Assays for Detection and Quantification of Hemorrhagic Fever Viruses

PubMed Central

Li, Jiandong; Qu, Jing; He, Chengcheng; Zhang, Shuo; Li, Chuan; Zhang, Quanfu; Liang, Mifang; Li, Dexin

2014-01-01

Background Viral hemorrhagic fevers (VHFs) are a group of animal and human illnesses that are mostly caused by several distinct families of viruses including bunyaviruses, flaviviruses, filoviruses and arenaviruses. Although specific signs and symptoms vary by the type of VHF, initial signs and symptoms are very similar. Therefore rapid immunologic and molecular tools for differential diagnosis of hemorrhagic fever viruses (HFVs) are important for effective case management and control of the spread of VHFs. Real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assay is one of the reliable and desirable methods for specific detection and quantification of virus load. Multiplex PCR assay has the potential to produce considerable savings in time and resources in the laboratory detection. Results Primers/probe sets were designed based on appropriate specific genes for each of 28 HFVs which nearly covered all the HFVs, and identified with good specificity and sensitivity using monoplex assays. Seven groups of multiplex one-step real-time qRT-PCR assays in a universal experimental system were then developed by combining all primers/probe sets into 4-plex reactions and evaluated with serial dilutions of synthesized viral RNAs. For all the multiplex assays, no cross-reactivity with other HFVs was observed, and the limits of detection were mainly between 45 and 150 copies/PCR. The reproducibility was satisfactory, since the coefficient of variation of Ct values were all less than 5% in each dilution of synthesized viral RNAs for both intra-assays and inter-assays. Evaluation of the method with available clinical serum samples collected from HFRS patients, SFTS patients and Dengue fever patients showed high sensitivity and specificity of the related multiplex assays on the clinical specimens. Conclusions Overall, the comprehensive multiplex one-step real-time qRT-PCR assays were established in this study, and proved to be specific, sensitive, stable and easy to serve as a useful tool for rapid detection of HFVs. PMID:24752452

SecPop Version 4: Sector Population Land Fraction and Economic Estimation Program: Users? Guide Model Manual and Verification Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Scott; Bixler, Nathan E.; McFadden, Katherine Letizia

In 1973 the U.S. Environmental Protection Agency (EPA) developed SecPop to calculate population estimates to support a study on air quality. The Nuclear Regulatory Commission (NRC) adopted this program to support siting reviews for nuclear power plant construction and license applications. Currently SecPop is used to prepare site data input files for offsite consequence calculations with the MELCOR Accident Consequence Code System (MACCS). SecPop enables the use of site-specific population, land use, and economic data for a polar grid defined by the user. Updated versions of SecPop have been released to use U.S. decennial census population data. SECPOP90 was releasedmore » in 1997 to use 1990 population and economic data. SECPOP2000 was released in 2003 to use 2000 population data and 1997 economic data. This report describes the current code version, SecPop version 4.3, which uses 2010 population data and both 2007 and 2012 economic data. It is also compatible with 2000 census and 2002 economic data. At the time of this writing, the current version of SecPop is 4.3.0, and that version is described herein. This report contains guidance for the installation and use of the code as well as a description of the theory, models, and algorithms involved. This report contains appendices which describe the development of the 2010 census file, 2007 county file, and 2012 county file. Finally, an appendix is included that describes the validation assessments performed.« less

Reference gene identification for reliable normalisation of quantitative RT-PCR data in Setaria viridis.

PubMed

Nguyen, Duc Quan; Eamens, Andrew L; Grof, Christopher P L

2018-01-01

Quantitative real-time polymerase chain reaction (RT-qPCR) is the key platform for the quantitative analysis of gene expression in a wide range of experimental systems and conditions. However, the accuracy and reproducibility of gene expression quantification via RT-qPCR is entirely dependent on the identification of reliable reference genes for data normalisation. Green foxtail ( Setaria viridis ) has recently been proposed as a potential experimental model for the study of C 4 photosynthesis and is closely related to many economically important crop species of the Panicoideae subfamily of grasses, including Zea mays (maize), Sorghum bicolor (sorghum) and Sacchurum officinarum (sugarcane). Setaria viridis (Accession 10) possesses a number of key traits as an experimental model, namely; (i) a small sized, sequenced and well annotated genome; (ii) short stature and generation time; (iii) prolific seed production, and; (iv) is amendable to Agrobacterium tumefaciens -mediated transformation. There is currently however, a lack of reference gene expression information for Setaria viridis ( S. viridis ). We therefore aimed to identify a cohort of suitable S. viridis reference genes for accurate and reliable normalisation of S. viridis RT-qPCR expression data. Eleven putative candidate reference genes were identified and examined across thirteen different S. viridis tissues. Of these, the geNorm and NormFinder analysis software identified SERINE / THERONINE - PROTEIN PHOSPHATASE 2A ( PP2A ), 5 '- ADENYLYLSULFATE REDUCTASE 6 ( ASPR6 ) and DUAL SPECIFICITY PHOSPHATASE ( DUSP ) as the most suitable combination of reference genes for the accurate and reliable normalisation of S. viridis RT-qPCR expression data. To demonstrate the suitability of the three selected reference genes, PP2A , ASPR6 and DUSP , were used to normalise the expression of CINNAMYL ALCOHOL DEHYDROGENASE ( CAD ) genes across the same tissues. This approach readily demonstrated the suitably of the three selected reference genes for the accurate and reliable normalisation of S. viridis RT-qPCR expression data. Further, the work reported here forms a highly useful platform for future gene expression quantification in S. viridis and can also be potentially directly translatable to other closely related and agronomically important C 4 crop species.

Quantitative PCR estimates Angiostrongylus cantonensis (rat lungworm) infection levels in semi-slugs (Parmarion martensi)

PubMed Central

Jarvi, Susan I.; Farias, Margaret E.M.; Howe, Kay; Jacquier, Steven; Hollingsworth, Robert; Pitt, William

2013-01-01

The life cycle of the nematode Angiostrongylus cantonensis involves rats as the definitive host and slugs and snails as intermediate hosts. Humans can become infected upon ingestion of intermediate or paratenic (passive carrier) hosts containing stage L3 A. cantonensis larvae. Here, we report a quantitative PCR (qPCR) assay that provides a reliable, relative measure of parasite load in intermediate hosts. Quantification of the levels of infection of intermediate hosts is critical for determining A. cantonensis intensity on the Island of Hawaii. The identification of high intensity infection ‘hotspots’ will allow for more effective targeted rat and slug control measures. qPCR appears more efficient and sensitive than microscopy and provides a new tool for quantification of larvae from intermediate hosts, and potentially from other sources as well. PMID:22902292

Creation of a bovine herpes virus 1 (BoHV-1) quantitative particle standard by transmission electron microscopy and comparison with established standards for use in real-time PCR.

PubMed

Hoferer, Marc; Braun, Anne; Sting, Reinhard

2017-07-01

Standards are pivotal for pathogen quantification by real-time PCR (qPCR); however, the creation of a complete and universally applicable virus particle standard is challenging. In the present study a procedure based on purification of bovine herpes virus type 1 (BoHV-1) and subsequent quantification by transmission electron microscopy (TEM) is described. Accompanying quantitative quality controls of the TEM preparation procedure using qPCR yielded recovery rates of more than 95% of the BoHV-1 virus particles on the grid used for virus counting, which was attributed to pre-treatment of the grid with 5% bovine albumin. To compare the value of the new virus particle standard for use in qPCR, virus counter based quantification and established pure DNA standards represented by a plasmid and an oligonucleotide were included. It could be shown that the numbers of virus particles, plasmid and oligonucleotide equivalents were within one log10 range determined on the basis of standard curves indicating that different approaches provide comparable quantitative values. However, only virus particles represent a complete, universally applicable quantitative virus standard that meets the high requirements of an RNA and DNA virus gold standard. In contrast, standards based on pure DNA have to be considered as sub-standard due to limited applications. Copyright © 2017 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

Identification of suitable internal controls to study expression of a Staphylococcus aureus multidrug resistance system by quantitative real-time PCR.

PubMed

Theis, Torsten; Skurray, Ronald A; Brown, Melissa H

2007-08-01

Quantitative real-time PCR (qRT-PCR) has become a routine technique for gene expression analysis. Housekeeping genes are customarily used as endogenous references for the relative quantification of genes of interest. The aim of this study was to develop a quantitative real-time PCR assay to analyze gene expression in multidrug resistant Staphylococcus aureus in the presence of cationic lipophilic substrates of multidrug transport proteins. Eleven different housekeeping genes were analyzed for their expression stability in the presence of a range of concentrations of four structurally different antimicrobial compounds. This analysis demonstrated that the genes rho, pyk and proC were least affected by rhodamine 6G and crystal violet, whereas fabD, tpiA and gyrA or fabD, proC and pyk were stably expressed in cultures grown in the presence of ethidium or berberine, respectively. Subsequently, these housekeeping genes were used as internal controls to analyze expression of the multidrug transport protein QacA and its transcriptional regulator QacR in the presence of the aforementioned compounds. Expression of qacA was induced by all four compounds, whereas qacR expression was found to be unaffected, reduced or enhanced. This study demonstrates that staphylococcal gene expression, including housekeeping genes previously used to normalize qRT-PCR data, is affected by growth in the presence of different antimicrobial compounds. Thus, identification of suitable genes usable as a control set requires rigorous testing. Identification of a such a set enabled them to be utilized as internal standards for accurate quantification of transcripts of the qac multidrug resistance system from S. aureus grown under different inducing conditions. Moreover, the qRT-PCR assay presented in this study may also be applied to gene expression studies of other multidrug transporters from S. aureus.

Digital PCR: A Sensitive and Precise Method for KIT D816V Quantification in Mastocytosis.

PubMed

Greiner, Georg; Gurbisz, Michael; Ratzinger, Franz; Witzeneder, Nadine; Simonitsch-Klupp, Ingrid; Mitterbauer-Hohendanner, Gerlinde; Mayerhofer, Matthias; Müllauer, Leonhard; Sperr, Wolfgang R; Valent, Peter; Hoermann, Gregor

2018-03-01

The analytically sensitive detection of KIT D816V in blood and bone marrow is important for diagnosing systemic mastocytosis (SM). Additionally, precise quantification of the KIT D816V variant allele fraction (VAF) is relevant clinically because it helps to predict multilineage involvement and prognosis in cases of advanced SM. Digital PCR (dPCR) is a promising new method for sensitive detection and accurate quantification of somatic mutations. We performed a validation study of dPCR for KIT D816V on 302 peripheral blood and bone marrow samples from 156 patients with mastocytosis for comparison with melting curve analysis after peptide nucleic acid-mediated PCR clamping (clamp-PCR) and allele-specific quantitative real-time PCR (qPCR). dPCR showed a limit of detection of 0.01% VAF with a mean CV of 8.5% and identified the mutation in 90% of patients compared with 70% for clamp-PCR ( P < 0.001). Moreover, dPCR for KIT D816V was highly concordant with qPCR without systematic deviation of results, and confirmed the clinical value of KIT D816V VAF measurements. Thus, patients with advanced SM showed a significantly higher KIT D816V VAF (median, 2.43%) compared with patients with indolent SM (median, 0.14%; P < 0.001). Moreover, dPCR confirmed the prognostic significance of a high KIT D816V VAF regarding survival ( P < 0.001). dPCR for KIT D816V provides a high degree of precision and sensitivity combined with the potential for interlaboratory standardization, which is crucial for the implementation of KIT D816V allele burden measurement. Thus, dPCR is suitable as a new method for KIT D816V testing in patients with mastocytosis. © 2017 American Association for Clinical Chemistry.

Chlorinated Persistent Organic Pollutants, Obesity, and Type 2 Diabetes

PubMed Central

Porta, Miquel; Jacobs, David R.; Vandenberg, Laura N.

2014-01-01

Persistent organic pollutants (POPs) are lipophilic compounds that travel with lipids and accumulate mainly in adipose tissue. Recent human evidence links low-dose POPs to an increased risk of type 2 diabetes (T2D). Because humans are contaminated by POP mixtures and POPs possibly have nonmonotonic dose-response relations with T2D, critical methodological issues arise in evaluating human findings. This review summarizes epidemiological results on chlorinated POPs and T2D, and relevant experimental evidence. It also discusses how features of POPs can affect inferences in humans. The evidence as a whole suggests that, rather than a few individual POPs, background exposure to POP mixtures—including organochlorine pesticides and polychlorinated biphenyls—can increase T2D risk in humans. Inconsistent statistical significance for individual POPs may arise due to distributional differences in POP mixtures among populations. Differences in the observed shape of the dose-response curves among human studies may reflect an inverted U-shaped association secondary to mitochondrial dysfunction or endocrine disruption. Finally, we examine the relationship between POPs and obesity. There is evidence in animal studies that low-dose POP mixtures are obesogenic. However, relationships between POPs and obesity in humans have been inconsistent. Adipose tissue plays a dual role of promoting T2D and providing a relatively safe place to store POPs. Large prospective studies with serial measurements of a broad range of POPs, adiposity, and clinically relevant biomarkers are needed to disentangle the interrelationships among POPs, obesity, and the development of T2D. Also needed are laboratory experiments that more closely mimic real-world POP doses, mixtures, and exposure duration in humans. PMID:24483949

Lower limb intracast pressures generated by different types of immobilisation casts.

PubMed

Chaudhury, Salma; Hazlerigg, Alexandra; Vusirikala, Anuhya; Nguyen, Joseph; Matthews, Stuart

2017-02-18

To determine if complete, split casts and backslabs [plaster of Paris (POP) and fiberglass] generate different intracast pressures and pain. Increased swelling within casts was modeled by a closed water system attached to an expandable bag placed directly under different types of casts applied to a healthy lower limb. Complete fiberglass and POP casts, split casts and backslabs were applied. Twenty-five milliliter aliquots of saline were injected into the system and the generated intracast pressures were measured using a sphygmomanometer. The subject was blinded to the pressure scores to avoid bias. All casts were applied to the same right limb on the same subject to avoid the effects of variations in anatomy or physiology on intracast pressures. Pain levels were evaluated using the Visual Analogue Score after each sequential saline injection. Each type of cast was reapplied four times and the measurements were repeated on four separate occasions. Sample sizes were determined by a pre-study 90% power calculation to detect a 20% difference in intracast pressures between cast groups. A significant difference between the various types of casts was noted when the saline volume was greater than 100 mL ( P = 0.009). The greatest intracast pressure was generated by complete fiberglass casts, which were significantly higher than complete POP casts or backslabs ( P = 0.018 and P = 0.008 respectively) at intracast saline volumes of 100 mL and higher. Backslabs produced a significantly lower intracast pressure compared to complete POP only once the saline volume within casts exceeded 225 mL ( P = 0.009). Intracast pressures were significantly lower in split casts ( P = 0.003). Split POP and fiberglass casts produced the lowest intracast pressures, even compared to backslabs ( P = 0.009). Complete fiberglass casts generated the highest pain levels at manometer pressures of 75 mmHg and greater ( P = 0.001). Split fiberglass casts had significantly reduced pain levels ( P = 0.001). In contrast, a split complete POP cast did not produce significantly reduced pain levels at pressures between 25-150 mmHg. There was no difference in pain generated by complete POP and backslabs at manometer pressures of 200 mmHg and lower. Fibreglass casts generate significantly higher intracast pressures and pain than POP casts. Split casts cause lower intracast pressures regardless of material, than complete casts and backslabs.

Biluminescence via Fluorescence and Persistent Phosphorescence in Amorphous Organic Donor(D4)-Acceptor(A) Conjugates, and Application in Data Security Protection.

PubMed

Bhatia, Harsh; Bhattacharjee, Indranil; Ray, Debdas

2018-06-25

Purely organic biluminescent materials are of great interest due to the involvement of both singlet and long-lived triplet emissions, which have been used in bio-imaging and organic light-emitting diodes. We show two molecules 3,4,5,6-tetraphenyloxy-phthlonitrile (POP) and 3,4,5,6-tetrakis-p-tolyloxy-phthalonitrile (TOP), in which POP was found to exhibit fluorescence and persistent room-temperature green phosphorescence (pRTGP) in the amorphous and crystal states. Both POP and TOP show aggregation induced emission in tetrahydrofuran-water mixture. We found in single crystal X-ray analysis that intra-and inter molecular lp(O)•••π interactions along with (π(C=C)•••π(C≡N), hydrogen bond (H-B), and C-H•••π interactions induce head-to-tail slipped-stacked arrangement in POP. In addition, X-ray structure of TOP with slipped-stack arrangement induced by only (π(C=C)•••π(C≡N) and H-B interactions, shows dim afterglow only in crystals. These indicate that more number of non-covalent interactions may reinforce relatively efficient inter system crossing that leads to pRTGP even in the amorphous state of POP. Given the unique green afterglow feature in amorphous state of POP, document security protection application is achievable.

IAC-POP: FINDING THE STAR FORMATION HISTORY OF RESOLVED GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aparicio, Antonio; Hidalgo, Sebastian L.

2009-08-15

IAC-pop is a code designed to solve the star formation history (SFH) of a complex stellar population system, like a galaxy, from the analysis of the color-magnitude diagram (CMD). It uses a genetic algorithm to minimize a {chi}{sup 2} merit function comparing the star distributions in the observed CMD and the CMD of a synthetic stellar population. A parameterization of the CMDs is used, which is the main input of the code. In fact, the code can be applied to any problem in which a similar parameterization of an experimental set of data and models can be made. The method'smore » internal consistency and robustness against several error sources, including observational effects, data sampling, and stellar evolution library differences, are tested. It is found that the best stability of the solution and the best way to estimate errors are obtained by several runs of IAC-pop with varying the input data parameterization. The routine MinnIAC is used to control this process. IAC-pop is offered for free use and can be downloaded from the site http://iac-star.iac.es/iac-pop. The routine MinnIAC is also offered under request, but support cannot be provided for its use. The only requirement for the use of IAC-pop and MinnIAC is referencing this paper and crediting as indicated in the site.« less

Evolution of large amplitude Alfven waves in solar wind plasmas: Kinetic-fluid models

NASA Astrophysics Data System (ADS)

Nariyuki, Y.

2014-12-01

Large amplitude Alfven waves are ubiquitously observed in solar wind plasmas. Mjolhus(JPP, 1976) and Mio et al(JPSJ, 1976) found that nonlinear evolution of the uni-directional, parallel propagating Alfven waves can be described by the derivative nonlinear Schrodinger equation (DNLS). Later, the multi-dimensional extension (Mjolhus and Wyller, JPP, 1988; Passot and Sulem, POP, 1993; Gazol et al, POP, 1999) and ion kinetic modification (Mjolhus and Wyller, JPP, 1988; Spangler, POP, 1989; Medvedev and Diamond, POP, 1996; Nariyuki et al, POP, 2013) of DNLS have been reported. Recently, Nariyuki derived multi-dimensional DNLS from an expanding box model of the Hall-MHD system (Nariyuki, submitted). The set of equations including the nonlinear evolution of compressional wave modes (TDNLS) was derived by Hada(GRL, 1993). DNLS can be derived from TDNLS by rescaling of the variables (Mjolhus, Phys. Scr., 2006). Nariyuki and Hada(JPSJ, 2007) derived a kinetically modified TDNLS by using a simple Landau closure (Hammet and Perkins, PRL, 1990; Medvedev and Diamond, POP, 1996). In the present study, we revisit the ion kinetic modification of multi-dimensional TDNLS through more rigorous derivations, which is consistent with the past kinetic modification of DNLS. Although the original TDNLS was derived in the multi-dimensional form, the evolution of waves with finite propagation angles in TDNLS has not been paid much attention. Applicability of the resultant models to solar wind turbulence is discussed.

GENASIS national and international monitoring networks for persistent organic pollutants

NASA Astrophysics Data System (ADS)

Brabec, Karel; Dušek, Ladislav; Holoubek, Ivan; Hřebíček, Jiří; Kubásek, Miroslav; Urbánek, Jaroslav

2010-05-01

Persistent organic pollutants (POPs) remain in the centre of scientific attention due to their slow rates of degradation, their toxicity, and potential for both long-range transport and bioaccumulation in living organisms. This group of compounds covers large number of various chemicals from industrial products, such as polychlorinated biphenyls, etc. The GENASIS (Global Environmental Assessment and Information System) information system utilizes data from national and international monitoring networks to obtain as-complete-as-possible set of information and a representative picture of environmental contamination by persistent organic pollutants (POPs). There are data from two main datasets on POPs monitoring: 1.Integrated monitoring of POPs in Košetice Observatory (Czech Republic) which is a long term background site of the European Monitoring and Evaluation Programme (EMEP) for the Central Europe; the data reveals long term trends of POPs in all environmental matrices. The Observatory is the only one in Europe where POPs have been monitored not only in ambient air, but also in wet atmospheric deposition, surface waters, sediments, soil, mosses and needles (integrated monitoring). Consistent data since the year 1996 are available, earlier data (up to 1998) are burdened by high variability and high detection limits. 2.MONET network is ambient air monitoring activities in the Central and Eastern European region (CEEC), Central Asia, Africa and Pacific Islands driven by RECETOX as the Regional Centre of the Stockholm Convention for the region of Central and Eastern Europe under the common name of the MONET networks (MONitoring NETwork). For many of the participating countries these activities generated first data on the atmospheric levels of POPs. The MONET network uses new technologies of air passive sampling, which was developed, tested, and calibrated by RECETOX in cooperation with Environment Canada and Lancaster University, and was originally launched as a model monitoring network providing public administration, private subject, and general public information about air pollution by POPs that had not been previously regularly monitored and whose measurement is further required by global monitoring plan of the Stockholm Convention. The MONET network is international project with many participants. Monitoring in the MONET-CZ network started in 2004 with the pilot project and continues to the current days, MONET CEEC started in 2006 and continues nowadays, MONET Africa started in 2008. The database of the GENASIS systems currently covers MONET-CZ data until the year 2008. The MONET network currently covers 37 countries in the Europe, Asia and Africa with more than 350 sampling sites. The paper will discuss about following topics * Data Fusion in GENASIS: how can GENASIS maximize the value and accuracy of the information gathered from heterogeneous data sources? * Sensor types in GENASIS: which POPs can be measured; what are the physical limitations to achievable accuracy, reliability, and long-term stability of miniaturized sensors; which applications can (not) be realized within these limitations?

Effects of Pop III to PopII transition on the lowest metallicity stars in dwarf galaxies

NASA Astrophysics Data System (ADS)

Zhang, Yimiao; Keres, Dusan; FIRE Team

2018-01-01

We examine the effects of the enrichments from Population III (Pop III) stars on the formation and properties of the first generation of the Population II (Pop II) stars. Pop III stars begin to transition towards Pop II stars when the metals dispersed in Pop III supernovae pollute the nearby gas. However, details of this transition are still largely unknown. We use dwarf galaxy simulations from the Feedback In Realistic Environments (FIRE) project to identify the star-forming gas that is likely to be pre-enriched by Pop III supernovae and follow the stars that form in such gas. This pre-enrichment will leave the signature in the lowest metallicity stars that can be used to better constrain the details of the Pop III-to-Pop II transition.

PERINEAL BODY STRETCH DURING LABOR DOES NOT PREDICT PERINEAL LACERATION, POSTPARTUM INCONTINENCE, OR POSTPARTUM SEXUAL FUNCTION: A COHORT STUDY

PubMed Central

MERIWETHER, Kate V.; ROGERS, Rebecca G.; DUNIVAN, Gena C.; ALLDREDGE, Jill K.; QUALLS, Clifford; MIGLIACCIO, Laura; LEEMAN, Lawrence

2017-01-01

Introduction The perineum stretches naturally during obstetrical labor, but it is unknown if this stretch has a negative impact on pelvic floor outcomes after a vaginal birth (VB). We aimed to evaluate whether perineal stretch was associated with postpartum pelvic floor dysfunction. Materials and Methods This was a prospective cohort study of primiparous women who had a VB. Perineal body (PB) length was measured antepartum, during labor, and 6 months postpartum. We determined the maximum PB (PB Max) measurements during the second stage of labor and PB change (ΔPB) between time points. Women completed functional questionnaires and had a POP-Q exam 6 months postpartum. We analyzed the relationship of PB measurements to perineal lacerations and postpartum outcomes including urinary, anal, or fecal incontinence, sexual activity and function, and POP-Q measurements. Results 448 women with VB had a mean age of 24 ± 5.0 years and rare (5%) third or fourth degree lacerations. During the second stage of labor, 270/448 (60%) had perineal measurements. Mean antepartum PB length was 3.7 ± 0.8 cm with a maximum mean PB length (PB Max) during the second stage of 6.1 ± 1.5 cm, an increase of 65%. The change in PB length (ΔPB) from antepartum to 6 months postpartum was a net decrease (−0.39 ± 1.02 cm). PB at any time point and PB Max were not associated with perineal lacerations or outcomes postpartum (all p>0.05). Discussion PB stretch during labor is unrelated to perineal laceration or postpartum incontinence, sexual activity, or sexual function. PMID:26874524

A Multi-Compartment 3-D Finite Element Model of Rectocele and Its Interaction with Cystocele

PubMed Central

Luo, Jiajia; Chen, Luyun; Fenner, Dee E.; Ashton-Miller, James A.; DeLancey, John O. L.

2015-01-01

We developed a subject-specific 3-D finite element model to understand the mechanics underlying formation of female pelvic organ prolapse, specifically a rectocele and its interaction with a cystocele. The model was created from MRI 3-D geometry of a healthy 45 year-old multiparous woman. It included anterior and posterior vaginal walls, levator ani muscle, cardinal and uterosacral ligaments, anterior and posterior arcus tendineus fascia pelvis, arcus tendineus levator ani, perineal body, perineal membrane and anal sphincter. Material properties were mostly from the literature. Tissue impairment was modeled as decreased tissue stiffness based on previous clinical studies. Model equations were solved using Abaqus v 6.11. The sensitivity of anterior and posterior vaginal wall geometry was calculated for different combinations tissue impairments under increasing intraabdominal pressure. Prolapse size was reported as POP-Q point at point Bp for rectocele and point Ba for cystocele. Results show that a rectocele resulted from impairments of the levator ani and posterior compartment support. For 20% levator and 85% posterior support impairments, simulated rectocele size (at POP-Q point: Bp) increased 0.29 mm/cm H2O without apical impairment and 0.36 mm/cm H2O with 60% apical impairment, as intraabdominal pressures increased from 0 to 150 cm H2O. Apical support impairment could result in the development of either a cystocele or rectocele. Simulated repair of posterior compartment support decreased rectocele but increased a preexisting cystocele. We conclude that development of rectocele and cystocele depend on the presence of anterior, posterior, levator and/or or apical support impairments, as well as the interaction of the prolapse with the opposing compartment. PMID:25757664

Evaluating statistical consistency in the ocean model component of the Community Earth System Model (pyCECT v2.0)

NASA Astrophysics Data System (ADS)

Baker, Allison H.; Hu, Yong; Hammerling, Dorit M.; Tseng, Yu-heng; Xu, Haiying; Huang, Xiaomeng; Bryan, Frank O.; Yang, Guangwen

2016-07-01

The Parallel Ocean Program (POP), the ocean model component of the Community Earth System Model (CESM), is widely used in climate research. Most current work in CESM-POP focuses on improving the model's efficiency or accuracy, such as improving numerical methods, advancing parameterization, porting to new architectures, or increasing parallelism. Since ocean dynamics are chaotic in nature, achieving bit-for-bit (BFB) identical results in ocean solutions cannot be guaranteed for even tiny code modifications, and determining whether modifications are admissible (i.e., statistically consistent with the original results) is non-trivial. In recent work, an ensemble-based statistical approach was shown to work well for software verification (i.e., quality assurance) on atmospheric model data. The general idea of the ensemble-based statistical consistency testing is to use a qualitative measurement of the variability of the ensemble of simulations as a metric with which to compare future simulations and make a determination of statistical distinguishability. The capability to determine consistency without BFB results boosts model confidence and provides the flexibility needed, for example, for more aggressive code optimizations and the use of heterogeneous execution environments. Since ocean and atmosphere models have differing characteristics in term of dynamics, spatial variability, and timescales, we present a new statistical method to evaluate ocean model simulation data that requires the evaluation of ensemble means and deviations in a spatial manner. In particular, the statistical distribution from an ensemble of CESM-POP simulations is used to determine the standard score of any new model solution at each grid point. Then the percentage of points that have scores greater than a specified threshold indicates whether the new model simulation is statistically distinguishable from the ensemble simulations. Both ensemble size and composition are important. Our experiments indicate that the new POP ensemble consistency test (POP-ECT) tool is capable of distinguishing cases that should be statistically consistent with the ensemble and those that should not, as well as providing a simple, subjective and systematic way to detect errors in CESM-POP due to the hardware or software stack, positively contributing to quality assurance for the CESM-POP code.

A comparative uncertainty study of the calibration of macrolide antibiotic reference standards using quantitative nuclear magnetic resonance and mass balance methods.

PubMed

Liu, Shu-Yu; Hu, Chang-Qin

2007-10-17

This study introduces the general method of quantitative nuclear magnetic resonance (qNMR) for the calibration of reference standards of macrolide antibiotics. Several qNMR experimental conditions were optimized including delay, which is an important parameter of quantification. Three kinds of macrolide antibiotics were used to validate the accuracy of the qNMR method by comparison with the results obtained by the high performance liquid chromatography (HPLC) method. The purities of five common reference standards of macrolide antibiotics were measured by the 1H qNMR method and the mass balance method, respectively. The analysis results of the two methods were compared. The qNMR is quick and simple to use. In a new medicine research and development process, qNMR provides a new and reliable method for purity analysis of the reference standard.

CometQ: An automated tool for the detection and quantification of DNA damage using comet assay image analysis.

PubMed

Ganapathy, Sreelatha; Muraleedharan, Aparna; Sathidevi, Puthumangalathu Savithri; Chand, Parkash; Rajkumar, Ravi Philip

2016-09-01

DNA damage analysis plays an important role in determining the approaches for treatment and prevention of various diseases like cancer, schizophrenia and other heritable diseases. Comet assay is a sensitive and versatile method for DNA damage analysis. The main objective of this work is to implement a fully automated tool for the detection and quantification of DNA damage by analysing comet assay images. The comet assay image analysis consists of four stages: (1) classifier (2) comet segmentation (3) comet partitioning and (4) comet quantification. Main features of the proposed software are the design and development of four comet segmentation methods, and the automatic routing of the input comet assay image to the most suitable one among these methods depending on the type of the image (silver stained or fluorescent stained) as well as the level of DNA damage (heavily damaged or lightly/moderately damaged). A classifier stage, based on support vector machine (SVM) is designed and implemented at the front end, to categorise the input image into one of the above four groups to ensure proper routing. Comet segmentation is followed by comet partitioning which is implemented using a novel technique coined as modified fuzzy clustering. Comet parameters are calculated in the comet quantification stage and are saved in an excel file. Our dataset consists of 600 silver stained images obtained from 40 Schizophrenia patients with different levels of severity, admitted to a tertiary hospital in South India and 56 fluorescent stained images obtained from different internet sources. The performance of "CometQ", the proposed standalone application for automated analysis of comet assay images, is evaluated by a clinical expert and is also compared with that of a most recent and related software-OpenComet. CometQ gave 90.26% positive predictive value (PPV) and 93.34% sensitivity which are much higher than those of OpenComet, especially in the case of silver stained images. The results are validated using confusion matrix and Jaccard index (JI). Comet assay images obtained after DNA damage repair by incubation in the nutrient medium were also analysed, and CometQ showed a significant change in all the comet parameters in most of the cases. Results show that CometQ is an accurate and efficient tool with good sensitivity and PPV for DNA damage analysis using comet assay images. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes.

PubMed

Hoshino, Tatsuhiko; Inagaki, Fumio

2017-01-01

Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA. To address this issue, we applied stochastic labeling approach with random-tag sequences and developed a NGS-based quantification protocol, which enables simultaneous sequencing and quantification of the targeted DNA. This quantitative sequencing (qSeq) is initiated from single-primer extension (SPE) using a primer with random tag adjacent to the 5' end of target-specific sequence. During SPE, each DNA molecule is stochastically labeled with the random tag. Subsequently, first-round PCR is conducted, specifically targeting the SPE product, followed by second-round PCR to index for NGS. The number of random tags is only determined during the SPE step and is therefore not affected by the two rounds of PCR that may introduce amplification biases. In the case of 16S rRNA genes, after NGS sequencing and taxonomic classification, the absolute number of target phylotypes 16S rRNA gene can be estimated by Poisson statistics by counting random tags incorporated at the end of sequence. To test the feasibility of this approach, the 16S rRNA gene of Sulfolobus tokodaii was subjected to qSeq, which resulted in accurate quantification of 5.0 × 103 to 5.0 × 104 copies of the 16S rRNA gene. Furthermore, qSeq was applied to mock microbial communities and environmental samples, and the results were comparable to those obtained using digital PCR and relative abundance based on a standard sequence library. We demonstrated that the qSeq protocol proposed here is advantageous for providing less-biased absolute copy numbers of each target DNA with NGS sequencing at one time. By this new experiment scheme in microbial ecology, microbial community compositions can be explored in more quantitative manner, thus expanding our knowledge of microbial ecosystems in natural environments.

Absolute determination of single-stranded and self-complementary adeno-associated viral vector genome titers by droplet digital PCR.

PubMed

Lock, Martin; Alvira, Mauricio R; Chen, Shu-Jen; Wilson, James M

2014-04-01

Accurate titration of adeno-associated viral (AAV) vector genome copies is critical for ensuring correct and reproducible dosing in both preclinical and clinical settings. Quantitative PCR (qPCR) is the current method of choice for titrating AAV genomes because of the simplicity, accuracy, and robustness of the assay. However, issues with qPCR-based determination of self-complementary AAV vector genome titers, due to primer-probe exclusion through genome self-annealing or through packaging of prematurely terminated defective interfering (DI) genomes, have been reported. Alternative qPCR, gel-based, or Southern blotting titering methods have been designed to overcome these issues but may represent a backward step from standard qPCR methods in terms of simplicity, robustness, and precision. Droplet digital PCR (ddPCR) is a new PCR technique that directly quantifies DNA copies with an unparalleled degree of precision and without the need for a standard curve or for a high degree of amplification efficiency; all properties that lend themselves to the accurate quantification of both single-stranded and self-complementary AAV genomes. Here we compare a ddPCR-based AAV genome titer assay with a standard and an optimized qPCR assay for the titration of both single-stranded and self-complementary AAV genomes. We demonstrate absolute quantification of single-stranded AAV vector genomes by ddPCR with up to 4-fold increases in titer over a standard qPCR titration but with equivalent readout to an optimized qPCR assay. In the case of self-complementary vectors, ddPCR titers were on average 5-, 1.9-, and 2.3-fold higher than those determined by standard qPCR, optimized qPCR, and agarose gel assays, respectively. Droplet digital PCR-based genome titering was superior to qPCR in terms of both intra- and interassay precision and is more resistant to PCR inhibitors, a desirable feature for in-process monitoring of early-stage vector production and for vector genome biodistribution analysis in inhibitory tissues.

Characterization of vaginal Lactobacillus species by rplK -based multiplex qPCR in Russian women.

PubMed

Demkin, Vladimir V; Koshechkin, Stanislav I

2017-10-01

We describe a multiplex qPCR assay for identification and quantitative assessment of a set of vaginal Lactobacillus species, including L. acidophilus, L. crispatus, L. gasseri, L. helveticus, L. iners, and L. jensenii. The assay extends the previously developed qPCR method for Lactobacillus detection and total quantification based on targeting the rplK gene. Both assays use only single pair of primers and a set of probes combined in three reactions, comprising a vaginal Lactobacillus diagnostic assay panel. The utility of the diagnostic panel was evaluated by analyzing of vaginal swab specimens from 145 patients with different status of vaginal health. Most frequently, only one Lactobacillus species was dominant (68,9%), mostly L. crispatus (18,6%) or L. iners (33,1%), but two or three Lactobacillus species were also being simultaneously detected (24,9%). The diagnostic panel will facilitate investigations of the role of Lactobacillus species in the health of the female reproductive system and promote studies of variability of the vaginal microbiota. Copyright © 2017 Elsevier Ltd. All rights reserved.

Innovative qPCR using interfacial effects to enable low threshold cycle detection and inhibition relief

PubMed Central

Harshman, Dustin K.; Rao, Brianna M.; McLain, Jean E.; Watts, George S.; Yoon, Jeong-Yeol

2015-01-01

Molecular diagnostics offers quick access to information but fails to operate at a speed required for clinical decision-making. Our novel methodology, droplet-on-thermocouple silhouette real-time polymerase chain reaction (DOTS qPCR), uses interfacial effects for droplet actuation, inhibition relief, and amplification sensing. DOTS qPCR has sample-to-answer times as short as 3 min 30 s. In infective endocarditis diagnosis, DOTS qPCR demonstrates reproducibility, differentiation of antibiotic susceptibility, subpicogram limit of detection, and thermocycling speeds of up to 28 s/cycle in the presence of tissue contaminants. Langmuir and Gibbs adsorption isotherms are used to describe the decreasing interfacial tension upon amplification. Moreover, a log-linear relationship with low threshold cycles is presented for real-time quantification by imaging the droplet-on-thermocouple silhouette with a smartphone. DOTS qPCR resolves several limitations of commercially available real-time PCR systems, which rely on fluorescence detection, have substantially higher threshold cycles, and require expensive optical components and extensive sample preparation. Due to the advantages of low threshold cycle detection, we anticipate extending this technology to biological research applications such as single cell, single nucleus, and single DNA molecule analyses. Our work is the first demonstrated use of interfacial effects for sensing reaction progress, and it will enable point-of-care molecular diagnosis of infections. PMID:26601245

Single versus successive pop-in modes in nanoindentation tests of single crystals

DOE PAGES

Xia, Yuzhi; Gao, Yanfei; Pharr, George M.; ...

2016-05-24

From recent nanoindentation experiments, two types of pop-in modes have been identified: a single pop-in with a large displacement excursion, or a number of pop-ins with comparable and small displacement excursions. Theoretical analyses are developed here to study the roles played by indenter tip radius, pre-existing defect density, heterogeneous nucleation source type, and lattice resistance on the pop-in modes. The evolution of dislocation structures in earlier pop-ins provides input to modeling a stochastic, heterogeneous mechanism that may be responsible for the subsequent pop-ins. It is found that when the first pop-in occurs near theoretical shear stress, the pop-in mode ismore » determined by the lattice resistance and tip radius. When the first pop-in occurs at low shear stress, whether the successive pop-in mode occurs depends on how the heterogeneous dislocation nucleation source density increases as compared to the increase of the total dislocation density. Lastly, the above transitions are found to correlate well with the ratio of indenter tip radius to the mean spacing of dislocation nucleation sources.« less

A tool for design of primers for microRNA-specific quantitative RT-qPCR.

PubMed

Busk, Peter K

2014-01-28

MicroRNAs are small but biologically important RNA molecules. Although different methods can be used for quantification of microRNAs, quantitative PCR is regarded as the reference that is used to validate other methods. Several commercial qPCR assays are available but they often come at a high price and the sequences of the primers are not disclosed. An alternative to commercial assays is to manually design primers but this work is tedious and, hence, not practical for the design of primers for a larger number of targets. I have developed the software miRprimer for automatic design of primers for the method miR-specific RT-qPCR, which is one of the best performing microRNA qPCR methods available. The algorithm is based on an implementation of the previously published rules for manual design of miR-specific primers with the additional feature of evaluating the propensity of formation of secondary structures and primer dimers. Testing of the primers showed that 76 out of 79 primers (96%) worked for quantification of microRNAs by miR-specific RT-qPCR of mammalian RNA samples. This success rate corresponds to the success rate of manual primer design. Furthermore, primers designed by this method have been distributed to several labs and used successfully in published studies. The software miRprimer is an automatic and easy method for design of functional primers for miR-specific RT-qPCR. The application is available as stand-alone software that will work on the MS Windows platform and in a developer version written in the Ruby programming language.

Optimization, validation, and application of a real-time PCR protocol for quantification of viable bacterial cells in municipal sewage sludge and biosolids using reporter genes and Escherichia coli.

PubMed

van Frankenhuyzen, Jessica K; Trevors, Jack T; Flemming, Cecily A; Lee, Hung; Habash, Marc B

2013-11-01

Biosolids result from treatment of sewage sludge to meet jurisdictional standards, including pathogen reduction. Once government regulations are met, materials can be applied to agricultural lands. Culture-based methods are used to enumerate pathogen indicator microorganisms but may underestimate cell densities, which is partly due to bacteria existing in a viable but non-culturable physiological state. Viable indicators can also be quantified by realtime polymerase chain reaction (qPCR) used with propidium monoazide (PMA), a dye that inhibits amplification of DNA found extracellularly or in dead cells. The objectives of this study were to test an optimized PMA-qPCR method for viable pathogen detection in wastewater solids and to validate it by comparing results to data obtained by conventional plating. Reporter genes from genetically marked Pseudomonas sp. UG14Lr and Agrobacterium tumefaciens 542 cells were spiked into samples of primary sludge, and anaerobically digested and Lystek-treated biosolids as cell-free DNA, dead cells, viable cells, and mixtures of live and dead cells, followed by DNA extraction with and without PMA, and qPCR. The protocol was then used for Escherichia coli quantification in the three matrices, and results compared to plate counts. PMA-qPCR selectively detected viable cells, while inhibiting signals from cell-free DNA and DNA found in membrane-compromised cells. PMA-qPCR detected 0.5-1 log unit more viable E. coli cells in both primary solids and dewatered biosolids than plate counts. No viable E. coli was found in Lystek-treated biosolids. These data suggest PMA-qPCR may more accurately estimate pathogen cell numbers than traditional culture methods.

Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

PubMed Central

May, Megan K.; Kevorkian, Richard T.; Steen, Andrew D.

2013-01-01

There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined “yield” to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly. PMID:24096423

Real-time PCR assays for detection and quantification of aflatoxin-producing molds in foods.

PubMed

Rodríguez, Alicia; Rodríguez, Mar; Luque, M Isabel; Martín, Alberto; Córdoba, Juan J

2012-08-01

Aflatoxins are among the most toxic mycotoxins. Early detection and quantification of aflatoxin-producing species is crucial to improve food safety. In the present work, two protocols of real-time PCR (qPCR) based on SYBR Green and TaqMan were developed, and their sensitivity and specificity were evaluated. Primers and probes were designed from the o-methyltransferase gene (omt-1) involved in aflatoxin biosynthesis. Fifty-three mold strains representing aflatoxin producers and non-producers of different species, usually reported in food products, were used as references. All strains were tested for aflatoxins production by high-performance liquid chromatography-mass spectrometry (HPLC-MS). The functionality of the proposed qPCR method was demonstrated by the strong linear relationship of the standard curves constructed with the omt-1 gene copy number and Ct values for the different aflatoxin producers tested. The ability of the qPCR protocols to quantify aflatoxin-producing molds was evaluated in different artificially inoculated foods. A good linear correlation was obtained over the range 4 to 1 log cfu/g per reaction for all qPCR assays in the different food matrices (peanuts, spices and dry-fermented sausages). The detection limit in all inoculated foods ranged from 1 to 2 log cfu/g for SYBR Green and TaqMan assays. No significant effect was observed due to the different equipment, operator, and qPCR methodology used in the tests of repeatability and reproducibility for different foods. The proposed methods quantified with high efficiency the fungal load in foods. These qPCR protocols are proposed for use to quantify aflatoxin-producing molds in food products. Copyright © 2012 Elsevier Ltd. All rights reserved.

A quantitative TaqMan PCR assay for the detection of Ureaplasma diversum.

PubMed

Marques, Lucas M; Amorim, Aline T; Martins, Hellen Braga; Rezende, Izadora Souza; Barbosa, Maysa Santos; Lobão, Tassia Neves; Campos, Guilherme B; Timenetsky, Jorge

2013-12-27

Ureaplasma diversum in veterinary studies is an undesirable microbe, which may cause infection in bulls and may result in seminal vesiculitis, balanopostitis, and alterations in spermatozoids, whereas in cows, it may cause placentitis, fetal alveolitis, abortion, and birth of weak calves. U. diversum is released through organic secretions, especially semen, preputial and vaginal mucus, conjunctival secretion, and milk. The aim of the present study was to develop a TaqMan probe, highly sensitive and specific quantitative PCR (qPCR) assay for the detection and quantification of U. diversum from genital swabs of bovines. Primers and probes specific to U. diversum 16S rRNA gene were designed. The specificity, detection limit, intra- and inter-assay variability of qPCR to detect this ureaplasma was compared with the results of the conventional PCR assay (cPCR). Swabs of vaginal mucus from 169 cows were tested. The qPCR assay detected as few as 10 copies of U. diversum and was 100-fold more sensitive than the cPCR. No cross-reactivity with other Mollicutes or eubacteria was observed. U. diversum was detected in 79 swabs (46.42%) by qPCR, while using cPCR it was detected in 42 (25%) samples. The difference in cPCR and qPCR ureaplasma detection between healthy and sick animals was not statistically significant. But the U. diversum load in samples from animals with genital disorders was higher than in healthy animals. The qPCR assay developed herein is highly sensitive and specific for the detection and quantification of U. diversum in vaginal bovine samples. Copyright © 2013. Published by Elsevier B.V.

Multiplex real-time PCR for detection, identification and quantification of 'Candidatus Liberibacter solanacearum' in potato plants with zebra chip.

PubMed

Li, Wenbin; Abad, Jorge A; French-Monar, Ronald D; Rascoe, John; Wen, Aimin; Gudmestad, Neil C; Secor, Gary A; Lee, Ing-Ming; Duan, Yongping; Levy, Laurene

2009-07-01

The new Liberibacter species, 'Candidatus Liberibacter solanacearum' (Lso) recently associated with potato/tomato psyllid-transmitted diseases in tomato and capsicum in New Zealand, was found to be consistently associated with a newly emerging potato zebra chip (ZC) disease in Texas and other southwestern states in the USA. A species-specific primer LsoF was developed for both quantitative real-time PCR (qPCR) and conventional PCR (cPCR) to detect and quantify Lso in infected samples. In multiplex qPCR, a plant cytochrome oxidase (COX)-based probe-primer set was used as a positive internal control for host plants, which could be used to reliably access the DNA extraction quality and to normalize qPCR data for accurate quantification of the bacterial populations in environment samples. Neither the qPCR nor the cPCR using the primer and/or probe sets with LsoF reacted with other Liberibacter species infecting citrus or other potato pathogens. The low detection limit of the multiplex qPCR was about 20 copies of the target 16S rDNA templates per reaction for field samples. Lso was readily detected and quantified in various tissues of ZC-affected potato plants collected from fields in Texas. A thorough but uneven colonization of Lso was revealed in various tissues of potato plants. The highest Lso populations were about 3x10(8) genomes/g tissue in the root, which were 3-order higher than those in the above-ground tissues of potato plants. The Lso bacterial populations were normally distributed across the ZC-affected potato plants collected from fields in Texas, with 60% of ZC-affected potato plants harboring an average Lso population from 10(5) to 10(6) genomes/g tissue, 4% of plants hosting above 10(7) Lso genomes/g tissue, and 8% of plants holding below 10(3) Lso genomes/g tissue. The rapid, sensitive, specific and reliable multiplex qPCR showed its potential to become a powerful tool for early detection and quantification of the new Liberibacter species associated with potato ZC, and will be very useful for the potato quarantine programs and seed potato certification programs to ensure the availability of clean seed potato stocks and also for epidemiological studies on the disease.

Visualization and Quantification of Rotor Tip Vortices in Helicopter Flows

NASA Technical Reports Server (NTRS)

Kao, David L.; Ahmad, Jasim U.; Holst, Terry L.

2015-01-01

This paper presents an automated approach for effective extraction, visualization, and quantification of vortex core radii from the Navier-Stokes simulations of a UH-60A rotor in forward flight. We adopt a scaled Q-criterion to determine vortex regions and then perform vortex core profiling in these regions to calculate vortex core radii. This method provides an efficient way of visualizing and quantifying the blade tip vortices. Moreover, the vortices radii are displayed graphically in a plane.

The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis.

PubMed

Devonshire, Alison S; O'Sullivan, Denise M; Honeyborne, Isobella; Jones, Gerwyn; Karczmarczyk, Maria; Pavšič, Jernej; Gutteridge, Alice; Milavec, Mojca; Mendoza, Pablo; Schimmel, Heinz; Van Heuverswyn, Fran; Gorton, Rebecca; Cirillo, Daniela Maria; Borroni, Emanuele; Harris, Kathryn; Barnard, Marinus; Heydenrych, Anthenette; Ndusilo, Norah; Wallis, Carole L; Pillay, Keshree; Barry, Thomas; Reddington, Kate; Richter, Elvira; Mozioğlu, Erkan; Akyürek, Sema; Yalçınkaya, Burhanettin; Akgoz, Muslum; Žel, Jana; Foy, Carole A; McHugh, Timothy D; Huggett, Jim F

2016-08-03

Real-time PCR (qPCR) based methods, such as the Xpert MTB/RIF, are increasingly being used to diagnose tuberculosis (TB). While qualitative methods are adequate for diagnosis, the therapeutic monitoring of TB patients requires quantitative methods currently performed using smear microscopy. The potential use of quantitative molecular measurements for therapeutic monitoring has been investigated but findings have been variable and inconclusive. The lack of an adequate reference method and reference materials is a barrier to understanding the source of such disagreement. Digital PCR (dPCR) offers the potential for an accurate method for quantification of specific DNA sequences in reference materials which can be used to evaluate quantitative molecular methods for TB treatment monitoring. To assess a novel approach for the development of quality assurance materials we used dPCR to quantify specific DNA sequences in a range of prototype reference materials and evaluated accuracy between different laboratories and instruments. The materials were then also used to evaluate the quantitative performance of qPCR and Xpert MTB/RIF in eight clinical testing laboratories. dPCR was found to provide results in good agreement with the other methods tested and to be highly reproducible between laboratories without calibration even when using different instruments. When the reference materials were analysed with qPCR and Xpert MTB/RIF by clinical laboratories, all laboratories were able to correctly rank the reference materials according to concentration, however there was a marked difference in the measured magnitude. TB is a disease where the quantification of the pathogen could lead to better patient management and qPCR methods offer the potential to rapidly perform such analysis. However, our findings suggest that when precisely characterised materials are used to evaluate qPCR methods, the measurement result variation is too high to determine whether molecular quantification of Mycobacterium tuberculosis would provide a clinically useful readout. The methods described in this study provide a means by which the technical performance of quantitative molecular methods can be evaluated independently of clinical variability to improve accuracy of measurement results. These will assist in ultimately increasing the likelihood that such approaches could be used to improve patient management of TB.

Characterization of brominated flame retardants in construction and demolition waste components: HBCD and PBDEs.

PubMed

Duan, Huabo; Yu, Danfeng; Zuo, Jian; Yang, Bo; Zhang, Yukui; Niu, Yongning

2016-12-01

The vast majority of construction material is inert and can be managed as nonhazardous. However, structures may have either been built with some environmentally unfriendly substances such as brominated flame retardants (BFRs), or have absorbed harmful elements such as heavy metals. This study focuses on end-of-life construction materials, i.e. construction and demolition (C&D) waste components. The aim was to characterize the concentration of extremely harmful substances, primarily BFRs, including hexabromocyclododecane (HBCD) and polybrominateddiphenyl ethers (PBDEs). Results revealed extremely high contents of HBCD and PBDEs in typical C&D waste components, particularly polyurethane foam materials. Policies should therefore be developed for the proper management of C&D waste, with priority for POP-containing debris. The first priority is to develop a classification system and procedures to separate out the harmful materials for more extensive processing. Additionally, identification and quantification of the environmental implications associated with dumping-dominated disposal of these wastes are required. Finally, more sustainable materials should be selected for use in the construction industry. Copyright © 2016 Elsevier B.V. All rights reserved.

Levator hiatal area as a risk factor for cystocele recurrence after surgery: a prospective study.

PubMed

Vergeldt, T F M; Notten, K J B; Weemhoff, M; van Kuijk, S M J; Mulder, F E M; Beets-Tan, R G; Vliegen, R F A; Gondrie, E T C M; Bergmans, M G M; Roovers, J P W R; Kluivers, K B

2015-07-01

To investigate whether increased levator hiatal area, measured preoperatively, was independently associated with anatom-ical cystocele recurrence 12 months after anterior colporrhaphy. Multicentre prospective cohort study. Nine teaching hospitals in the Netherlands. Women planned for conventional anterior colporrhaphy without mesh. Women underwent physical examination, translabial three-dimensional (3D) ultrasound and magnetic resonance imaging (MRI) prior to surgery. At 12 months after surgery the physical examination was repeated. Women with and without anatomical cystocele recurrence were compared to assess the association with levator hiatal area on 3D ultrasound, levator hiatal area on MRI, and potential confounding factors. The receiver operating characteristic (ROC) curve was created to quantify the discriminative ability of using levator hiatal area to predict anatomical cystocele recurrence. Of 139 included women, 76 (54.7%) had anatomical cystocele recurrence. Preoperative stage 3 or 4 and increased levator hiatal area during Valsalva on ultrasound were significantly associated with cystocele recurrence, with odds ratios of 3.47 (95% confidence interval, 95% CI 1.66-7.28) and 1.06 (95% CI 1.01-1.11) respectively. The area under the ROC curve was 0.60 (95% CI 0.51-0.70) for levator hiatal area during Valsalva on ultrasound, and 0.65 (95% CI 0.55-0.71) for preoperative Pelvic Organ Prolapse Quantification (POP-Q) stage. Increased levator hiatal area during Valsalva on ultrasound prior to surgery and preoperative stage 3 or 4 are independent risk factors for anatomical cystocele recurrence after anterior colporrhaphy; however, increased levator hiatal area as the sole factor for predicting anatomical cystocele recurrence after surgery shows poor test characteristics. © 2015 Royal College of Obstetricians and Gynaecologists.

Three-dimensional translabial ultrasound assessment of urethral supports and the urethral sphincter complex in stress urinary incontinence.

PubMed

Cassadó Garriga, Jordi; Pessarrodona Isern, Antoni; Rodríguez Carballeira, Monica; Pallarols Badia, Mar; Moya Del Corral, Manuela; Valls Esteve, Marta; Huguet Galofré, Eva

2017-09-01

The pathophysiological mechanism of incontinence is multifactorial. We evaluated the role of 3D-4D ultrasound in the assessment of the fascial supports of the urethra and the urethral sphincter complex (USC) for diagnosing stress urinary incontinence. Observational case-control study in women with and without stress urinary incontinence attending a urogynecology service and a general gynecology service. All women were interviewed, examined, and classified according to the Pelvic Organ Prolapse Quantification (POP-Q) and underwent a 3D-4D translabial ultrasound. Fascial supports of the urethra were assessed by tomographic ultrasound and were considered to be intact or absent if it was possible to identify them at eight levels on each side, urethral mobility was assessed on maximal Valsalva in sagittal section and the length and volume of the USC at rest and on maximal Valsalva were determined using the Virtual Organ Computer-aided Analysis (VOCAL) program. Variables were compared between continent and incontinent women. A total of 173 women were examined, 78 continent and 95 incontinent. There was a significant difference in urethral mobility between continent and incontinent women (12.82 mm vs. 21.85 mm, P < 0.001), but there was no significant difference in the percentage of supports affected (43.27% vs. 35.94%, P < 0.070). The length of the USC at rest was significantly shorter (P < 0.001) ​​in incontinent patients. Ultrasound evaluation of urethral supports does not discriminate between continent and incontinent women. However, the length of the USC at rest was shorter and urethral mobility was higher in incontinent women. Neurourol. Urodynam. 9999:XX-XX, 2016. © 2016 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Identification and quantification of flavonoids and chromes in Baeckea frutescens by using HPLC coupled with diode-array detection and quadruple time-of-flight mass spectrometry.

PubMed

Jia, Bei-Xi; Huangfu, Qian-Qian; Ren, Feng-Xiao; Jia, Lu; Zhang, Yan-Bing; Liu, Hong-Min; Yang, Jie; Wang, Qiang

2015-01-01

This article marks the first report on high-performance liquid chromatography (HPLC) coupled with diode-array detection (DAD) and quadruple time-of-flight mass spectrometry (Q-TOF/MS) for the identification and quantification of main bioactive constituents in Baeckea frutescens. In total, 24 compounds were identified or tentatively characterised based on their retention behaviours, UV profiles and MS fragment information. Furthermore, a validated method with good linearity, sensitivity, precision, stability, repeatability and accuracy was successfully applied for simultaneous determination of five flavonoids and one chromone in different plant parts of B. frutescens collected at different harvest times, and their dynamic contents revealed the appropriate harvest times. The established HPLC-DAD-Q-TOF/MS using multi-bioactive markers was proved to be a validated strategy for the quality evaluation on both raw materials and related products of B. frutescens.

Detection and quantification of Spirocerca lupi by HRM qPCR in fecal samples from dogs with spirocercosis.

PubMed

Rojas, Alicia; Segev, Gilad; Markovics, Alex; Aroch, Itamar; Baneth, Gad

2017-09-19

Spirocerca lupi, the dog oesophageal nematode, causes a potentially fatal disease in domestic dogs, and is currently clinically diagnosed by coproscopy and oesophagoscopy. To date, a single molecular method, a semi-nested PCR, targeting the cox1 gene, has been developed to aid in the diagnosis of spirocercosis. The present study describes three novel high-resolution melt (HRM) quantitative PCR (qPCR) assays targeting fragments of the ITS1, 18S and cytb loci of S. lupi. The performance of these molecular assays in feces was compared to fecal flotation and to the previously described cox1 gene semi-nested PCR in 18 fecal samples from dogs with clinical oesophageal spirocercosis diagnosed by oesophagoscopy. The HRM qPCR for ITS1 and 18S were both able to detect 0.2 S. lupi eggs per gram (epg), while the HRM qPCR for the cytb and the semi-nested PCR for the cox1 detected 6 epg and 526 epg, respectively. Spirocerca lupi was detected in 61.1%, 44.4%, 27.8%, 11.1% and 5.6% of the fecal samples of dogs diagnosed with spirocercosis by using the ITS1 and 18S HRM qPCR assays, fecal flotation, cytb HRM qPCR and cox1 semi-nested PCR, respectively. All dogs positive by fecal flotation were also positive by ITS1 and 18S HRM qPCRs. Quantification of S. lupi eggs was successfully achieved in the HRM qPCRs and compared to the fecal flotation with no significant difference in the calculated concentrations between the HRM qPCRs that detected the 18S and ITS1 loci and the fecal flotation. The HRM qPCR for the 18S cross-amplified DNA from Toxocara canis and Toxascaris leonina. In contrast, the HRM qPCR for ITS1 did not cross-amplify DNA from other canine gastrointestinal parasites. This study presents two new molecular assays with significantly increased sensitivity for confirming and quantifying fecal S. lupi eggs. Of these, the HRM qPCR for ITS1 showed the best performance in terms of the limit of detection and absence of cross-amplification with other parasites. These assays will be useful in detecting infection and for follow-up during therapy.

Sorption, transport and biodegradation - An insight into bioavailability of persistent organic pollutants in soil.

PubMed

Ren, Xiaoya; Zeng, Guangming; Tang, Lin; Wang, Jingjing; Wan, Jia; Liu, Yani; Yu, Jiangfang; Yi, Huan; Ye, Shujing; Deng, Rui

2018-01-01

Contamination of soils with persistent organic pollutants (POPs), such as organochlorine pesticide, polybrominated diphenyl ethers, halohydrocarbon, polycyclic aromatic hydrocarbons (PAHs) is of increasing concern. Microbial degradation is potential mechanism for the removal of POPs, but it is often restricted by low bioavailability of POPs. Thus, it is important to enhance bioavailability of POPs in soil bioremediation. A series of reviews on bioavailability of POPs has been published in the past few years. However, bioavailability of POPs in relation to soil organic matter, minerals and soil microbes has been little studied. To fully understand POPs bioavailability in soil, research on interactions of POPs with soil components and microbial responses in bioavailability limitation conditions are needed. This review focuses on bioavailability mechanisms of POPs in terms of sorption, transport and microbial adaptation, which is particularly novel. In consideration of the significance of bioavailability, further studies should investigate the influence of various bioremediation strategies on POPs bioavailability. Copyright © 2017 Elsevier B.V. All rights reserved.

Interactions between subunits of Saccharomyces cerevisiae RNase MRP support a conserved eukaryotic RNase P/MRP architecture.

PubMed

Aspinall, Tanya V; Gordon, James M B; Bennett, Hayley J; Karahalios, Panagiotis; Bukowski, John-Paul; Walker, Scott C; Engelke, David R; Avis, Johanna M

2007-01-01

Ribonuclease MRP is an endonuclease, related to RNase P, which functions in eukaryotic pre-rRNA processing. In Saccharomyces cerevisiae, RNase MRP comprises an RNA subunit and ten proteins. To improve our understanding of subunit roles and enzyme architecture, we have examined protein-protein and protein-RNA interactions in vitro, complementing existing yeast two-hybrid data. In total, 31 direct protein-protein interactions were identified, each protein interacting with at least three others. Furthermore, seven proteins self-interact, four strongly, pointing to subunit multiplicity in the holoenzyme. Six protein subunits interact directly with MRP RNA and four with pre-rRNA. A comparative analysis with existing data for the yeast and human RNase P/MRP systems enables confident identification of Pop1p, Pop4p and Rpp1p as subunits that lie at the enzyme core, with probable addition of Pop5p and Pop3p. Rmp1p is confirmed as an integral subunit, presumably associating preferentially with RNase MRP, rather than RNase P, via interactions with Snm1p and MRP RNA. Snm1p and Rmp1p may act together to assist enzyme specificity, though roles in substrate binding are also indicated for Pop4p and Pop6p. The results provide further evidence of a conserved eukaryotic RNase P/MRP architecture and provide a strong basis for studies of enzyme assembly and subunit function.

Visual pop-out in barn owls: Human-like behavior in the avian brain.

PubMed

Orlowski, Julius; Beissel, Christian; Rohn, Friederike; Adato, Yair; Wagner, Hermann; Ben-Shahar, Ohad

2015-01-01

Visual pop-out is a phenomenon by which the latency to detect a target in a scene is independent of the number of other elements, the distractors. Pop-out is an effective visual-search guidance that occurs typically when the target is distinct in one feature from the distractors, thus facilitating fast detection of predators or prey. However, apart from studies on primates, pop-out has been examined in few species and demonstrated thus far in rats, archer fish, and pigeons only. To fill this gap, here we study pop-out in barn owls. These birds are a unique model system for such exploration because their lack of eye movements dictates visual behavior dominated by head movements. Head saccades and interspersed fixation periods can therefore be tracked and analyzed with a head-mounted wireless microcamera--the OwlCam. Using this methodology we confronted two owls with scenes containing search arrays of one target among varying numbers (15-63) of similar looking distractors. We tested targets distinct either by orientation (Experiment 1) or luminance contrast (Experiment 2). Search time and the number of saccades until the target was fixated remained largely independent of the number of distractors in both experiments. This suggests that barn owls can exhibit pop-out during visual search, thus expanding the group of species and brain structures that can cope with this fundamental visual behavior. The utility of our automatic analysis method is further discussed for other species and scientific questions.

Evaluation of propidium monoazide (PMA) treatment directly on membrane filter for the enumeration of viable but non cultivable Legionella by qPCR.

PubMed

Slimani, Sami; Robyns, Audrey; Jarraud, Sophie; Molmeret, Maëlle; Dusserre, Eric; Mazure, Céline; Facon, Jean Pierre; Lina, Gérard; Etienne, Jerome; Ginevra, Christophe

2012-02-01

A PMA (propidium monoazide) pretreatment protocol, in which PMA is applied directly to membrane filters, was developed for the PCR-based quantification (PMA-qPCR) of viable Legionella pneumophila. Using this method, the amplification of DNA from membrane-damaged L. pneumophila was strongly inhibited for samples containing a small number of dead bacteria. Copyright © 2011 Elsevier B.V. All rights reserved.

New approaches for the standardization and validation of a real-time qPCR assay using TaqMan probes for quantification of yellow fever virus on clinical samples with high quality parameters

PubMed Central

Fernandes-Monteiro, Alice G; Trindade, Gisela F; Yamamura, Anna MY; Moreira, Otacilio C; de Paula, Vanessa S; Duarte, Ana Cláudia M; Britto, Constança; Lima, Sheila Maria B

2015-01-01

The development and production of viral vaccines, in general, involve several steps that need the monitoring of viral load throughout the entire process. Applying a 2-step quantitative reverse transcription real time PCR assay (RT-qPCR), viral load can be measured and monitored in a few hours. In this context, the development, standardization and validation of a RT-qPCR test to quickly and efficiently quantify yellow fever virus (YFV) in all stages of vaccine production are extremely important. To serve this purpose we used a plasmid construction containing the NS5 region from 17DD YFV to generate the standard curve and to evaluate parameters such as linearity, precision and specificity against other flavivirus. Furthermore, we defined the limits of detection as 25 copies/reaction, and quantification as 100 copies/reaction for the test. To ensure the quality of the method, reference controls were established in order to avoid false negative results. The qRT-PCR technique based on the use of TaqMan probes herein standardized proved to be effective for determining yellow fever viral load both in vivo and in vitro, thus becoming a very important tool to assure the quality control for vaccine production and evaluation of viremia after vaccination or YF disease. PMID:26011746

New approaches for the standardization and validation of a real-time qPCR assay using TaqMan probes for quantification of yellow fever virus on clinical samples with high quality parameters.

PubMed

Fernandes-Monteiro, Alice G; Trindade, Gisela F; Yamamura, Anna M Y; Moreira, Otacilio C; de Paula, Vanessa S; Duarte, Ana Cláudia M; Britto, Constança; Lima, Sheila Maria B

2015-01-01

The development and production of viral vaccines, in general, involve several steps that need the monitoring of viral load throughout the entire process. Applying a 2-step quantitative reverse transcription real time PCR assay (RT-qPCR), viral load can be measured and monitored in a few hours. In this context, the development, standardization and validation of a RT-qPCR test to quickly and efficiently quantify yellow fever virus (YFV) in all stages of vaccine production are extremely important. To serve this purpose we used a plasmid construction containing the NS5 region from 17DD YFV to generate the standard curve and to evaluate parameters such as linearity, precision and specificity against other flavivirus. Furthermore, we defined the limits of detection as 25 copies/reaction, and quantification as 100 copies/reaction for the test. To ensure the quality of the method, reference controls were established in order to avoid false negative results. The qRT-PCR technique based on the use of TaqMan probes herein standardized proved to be effective for determining yellow fever viral load both in vivo and in vitro, thus becoming a very important tool to assure the quality control for vaccine production and evaluation of viremia after vaccination or YF disease.

Enantioselective induction of cytotoxicity by o,p'-DDD in PC12 cells: implications of chirality in risk assessment of POPs metabolites.

PubMed

Wang, Cui; Li, Zhuoyu; Zhang, Quan; Zhao, Meirong; Liu, Weiping

2013-04-16

The increased release of chiral persistent organic pollutants (POPs) into the environment has resulted in more attention to the role of enantioselectivity in the fate and ecotoxicological effects of these compounds. Although the enantioselectivity of chiral POPs has been considered in previous studies, little effort has been expended to discern the enantiospecific effects of chiral POPs metabolites, which may impede comprehensive risk assessments of these chemicals. In the present study, o,p'-DDD, the chiral metabolite of o,p'-DDT, was used as a model chiral metabolite. First, a preferential chiral separation at 100% ethanol was employed to obtain a pure enantiomer. The enantioselective cytotoxicity of o,p'-DDD in rat cells (PC12) was evaluated by detecting activation of the cellular apoptosis and oxidative stress systems and microarray analysis. We have documented for the first time that R-(+)-o,p'-DDD increases apoptosis by selectively disturbing the oxidative system (enzymes and molecules) and regulating the transcription of Aven, Bid, Cideb and Tp53. By comparing the data from the present study to data derived from the parent compound, we concluded that the R-enantiomer is the more detrimental stereostructure for both o,p'-DDT and o,p'-DDD. This observed stereostructural effect is in line with the structure-activity relationship formulated at other structural levels. Biological activities of the chiral metabolites are likely to occur in the same absolute configuration between chiral POPs and their metabolites provided that they have the similar stereostructures.

Quantification and risks associated with bacterial aerosols near domestic greywater-treatment systems.

PubMed

Benami, Maya; Busgang, Allison; Gillor, Osnat; Gross, Amit

2016-08-15

Greywater (GW) reuse can alleviate water stress by lowering freshwater consumption. However, GW contains pathogens that may compromise public health. During the GW-treatment process, bioaerosols can be produced and may be hazardous to human health if inhaled, ingested, or come in contact with skin. Using air-particle monitoring, BioSampler®, and settle plates we sampled bioaerosols emitted from recirculating vertical flow constructed wetlands (RVFCW) - a domestic GW-treatment system. An array of pathogens and indicators were monitored using settle plates and by culturing the BioSampler® liquid. Further enumeration of viable pathogens in the BioSampler® liquid utilized a newer method combining the benefits of enrichment with molecular detection (MPN-qPCR). Additionally, quantitative microbial risk assessment (QMRA) was applied to assess risks of infection from a representative skin pathogen, Staphylococcus aureus. According to the settle-plate technique, low amounts (0-9.7×10(4)CFUm(-2)h(-1)) of heterotrophic bacteria, Staphylococcus spp., Pseudomonas spp., Klebsiella pneumoniae, Enterococcus spp., and Escherichia coli were found to aerosolize up to 1m away from the GW systems. At the 5m distance amounts of these bacteria were not statistically different (p>0.05) from background concentrations tested over 50m away from the systems. Using the BioSampler®, no bacteria were detected before enrichment of the GW-aerosols. However, after enrichment, using an MPN-qPCR technique, viable indicators and pathogens were occasionally detected. Consequently, the QMRA results were below the critical disability-adjusted life year (DALY) safety limits, a measure of overall disease burden, for S. aureus under the tested exposure scenarios. Our study suggests that health risks from aerosolizing pathogens near RVFCW GW-treatment systems are likely low. This study also emphasizes the growing need for standardization of bioaerosol-evaluation techniques to provide more accurate quantification of small amounts of viable, aerosolized bacterial pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.

Failure to pop out: Feature singletons do not capture attention under low signal-to-noise ratio conditions.

PubMed

Rangelov, Dragan; Müller, Hermann J; Zehetleitner, Michael

2017-05-01

Pop-out search implies that the target is always the first item selected, no matter how many distractors are presented. However, increasing evidence indicates that search is not entirely independent of display density even for pop-out targets: search is slower with sparse (few distractors) than with dense displays (many distractors). Despite its significance, the cause of this anomaly remains unclear. We investigated several mechanisms that could slow down search for pop-out targets. Consistent with the assumption that pop-out targets frequently fail to pop out in sparse displays, we observed greater variability of search duration for sparse displays relative to dense. Computational modeling of the response time distributions also supported the view that pop-out targets fail to pop out in sparse displays. Our findings strongly question the classical assumption that early processing of pop-out targets is independent of the distractors. Rather, the density of distractors critically influences whether or not a stimulus pops out. These results call for new, more reliable measures of pop-out search and potentially a reinterpretation of studies that used relatively sparse displays. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Real-Time Reverse-Transcription Quantitative Polymerase Chain Reaction Assay Is a Feasible Method for the Relative Quantification of Heregulin Expression in Non-Small Cell Lung Cancer Tissue.

PubMed

Kristof, Jessica; Sakrison, Kellen; Jin, Xiaoping; Nakamaru, Kenji; Schneider, Matthias; Beckman, Robert A; Freeman, Daniel; Spittle, Cindy; Feng, Wenqin

2017-01-01

In preclinical studies, heregulin ( HRG ) expression was shown to be the most relevant predictive biomarker for response to patritumab, a fully human anti-epidermal growth factor receptor 3 monoclonal antibody. In support of a phase 2 study of erlotinib ± patritumab in non-small cell lung cancer (NSCLC), a reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay for relative quantification of HRG expression from formalin-fixed paraffin-embedded (FFPE) NSCLC tissue samples was developed and validated and described herein. Test specimens included matched FFPE normal lung and NSCLC and frozen NSCLC tissue, and HRG -positive and HRG -negative cell lines. Formalin-fixed paraffin-embedded tissue was examined for functional performance. Heregulin distribution was also analyzed across 200 NSCLC commercial samples. Applied Biosystems TaqMan Gene Expression Assays were run on the Bio-Rad CFX96 real-time PCR platform. Heregulin RT-qPCR assay specificity, PCR efficiency, PCR linearity, and reproducibility were demonstrated. The final assay parameters included the Qiagen FFPE RNA Extraction Kit for RNA extraction from FFPE NSCLC tissue, 50 ng of RNA input, and 3 reference (housekeeping) genes ( HMBS, IPO8 , and EIF2B1 ), which had expression levels similar to HRG expression levels and were stable among FFPE NSCLC samples. Using the validated assay, unimodal HRG distribution was confirmed across 185 evaluable FFPE NSCLC commercial samples. Feasibility of an RT-qPCR assay for the quantification of HRG expression in FFPE NSCLC specimens was demonstrated.

An optimized method for neurotransmitters and their metabolites analysis in mouse hypothalamus by high performance liquid chromatography-Q Exactive hybrid quadrupole-orbitrap high-resolution accurate mass spectrometry.

PubMed

Yang, Zong-Lin; Li, Hui; Wang, Bing; Liu, Shu-Ying

2016-02-15

Neurotransmitters (NTs) and their metabolites are known to play an essential role in maintaining various physiological functions in nervous system. However, there are many difficulties in the detection of NTs together with their metabolites in biological samples. A new method for NTs and their metabolites detection by high performance liquid chromatography coupled with Q Exactive hybrid quadruple-orbitrap high-resolution accurate mass spectrometry (HPLC-HRMS) was established in this paper. This method was a great development of the applying of Q Exactive MS in the quantitative analysis. This method enabled a rapid quantification of ten compounds within 18min. Good linearity was obtained with a correlation coefficient above 0.99. The concentration range of the limit of detection (LOD) and the limit of quantitation (LOQ) level were 0.0008-0.05nmol/mL and 0.002-25.0nmol/mL respectively. Precisions (relative standard deviation, RSD) of this method were at 0.36-12.70%. Recovery ranges were between 81.83% and 118.04%. Concentrations of these compounds in mouse hypothalamus were detected by Q Exactive LC-MS technology with this method. Copyright © 2016 Elsevier B.V. All rights reserved.

Identification of Lactobacillus delbrueckii and Streptococcus thermophilus Strains Present in Artisanal Raw Cow Milk Cheese Using Real-time PCR and Classic Plate Count Methods.

PubMed

Stachelska, Milena A

2017-12-04

The aim of this paper was to detect Lactobacillus delbrueckii and Streptococcus thermophilus using real-time quantitative PCR assay in 7-day ripening cheese produced from unpasteurised milk. Real-time quantitative PCR assays were designed to identify and enumerate the chosen species of lactic acid bacteria (LAB) in ripened cheese. The results of molecular quantification and classic bacterial enumeration showed a high level of similarity proving that DNA extraction was carried out in a proper way and that genomic DNA solutions were free of PCR inhibitors. These methods revealed the presence of L. delbrueckii and S. thermophilus. The real-time PCR enabled quantification with a detection of 101-103 CFU/g of product. qPCR-standard curves were linear over seven log units down to 101 copies per reaction; efficiencies ranged from 77.9% to 93.6%. Cheese samples were analysed with plate count method and qPCR in parallel. Compared with the classic plate count method, the newly developed qPCR method provided faster and species specific identification of two dairy LAB and yielded comparable quantitative results.

Characterization of the efficiency and uncertainty of skimmed milk flocculation for the simultaneous concentration and quantification of water-borne viruses, bacteria and protozoa.

PubMed

Gonzales-Gustavson, Eloy; Cárdenas-Youngs, Yexenia; Calvo, Miquel; da Silva, Marcelle Figueira Marques; Hundesa, Ayalkibet; Amorós, Inmaculada; Moreno, Yolanda; Moreno-Mesonero, Laura; Rosell, Rosa; Ganges, Llilianne; Araujo, Rosa; Girones, Rosina

2017-03-01

In this study, the use of skimmed milk flocculation (SMF) to simultaneously concentrate viruses, bacteria and protozoa was evaluated. We selected strains of faecal indicator bacteria and pathogens, such as Escherichia coli and Helicobacter pylori. The viruses selected were adenovirus (HAdV 35), rotavirus (RoV SA-11), the bacteriophage MS2 and bovine viral diarrhoea virus (BVDV). The protozoa tested were Acanthamoeba, Giardia and Cryptosporidium. The mean recoveries with q(RT)PCR were 66% (HAdV 35), 24% (MS2), 28% (RoV SA-11), 15% (BVDV), 60% (E. coli), 30% (H. pylori) and 21% (Acanthamoeba castellanii). When testing the infectivity, the mean recoveries were 59% (HAdV 35), 12% (MS2), 26% (RoV SA-11) and 0.7% (BVDV). The protozoa Giardia lamblia and Cryptosporidium parvum were studied by immunofluorescence with recoveries of 18% and 13%, respectively. Although q(RT)PCR consistently showed higher quantification values (as expected), q(RT)PCR and the infectivity assays showed similar recoveries for HAdV 35 and RoV SA-11. Additionally, we investigated modelling the variability and uncertainty of the recovery with this method to extrapolate the quantification obtained by q(RT)PCR and estimate the real concentration. The 95% prediction intervals of the real concentration of the microorganisms inoculated were calculated using a general non-parametric bootstrap procedure adapted in our context to estimate the technical error of the measurements. SMF shows recoveries with a low variability that permits the use of a mathematical approximation to predict the concentration of the pathogen and indicator with acceptable low intervals. The values of uncertainty may be used for a quantitative microbial risk analysis or diagnostic purposes. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Elevate and Uterine Preservation: Two-Year Results.

PubMed

Stanford, Edward J; Moore, Robert D; Roovers, Jan-Paul W R; VanDrie, Douglas M; Giudice, Thomas P; Lukban, James C; Bataller, Eduardo; Sutherland, Suzette E

2015-01-01

To evaluate efficacy of the Elevate Anterior and Apical (EAA) in the repair of pelvic organ prolapse (POP) when performed after previous hysterectomy and with or without uterine preservation during POP surgery. One hundred forty-two women with anterior vaginal prolapse and/or apical descent ≥ stage II were enrolled. The primary outcome was treatment failure defined as > stage II POP-Q during follow-up using the Last observed Failure Carried Forward method. Three sub-groups were analysed: baseline previous hysterectomy (N = 61); concomitant hysterectomy (N = 29), and preserved uterus/no hysterectomy (N = 51). Demographics, primary and secondary outcomes, and extrusion were compared between the groups. A P value less than 0.05 was considered statistically significant. Anatomic success shows significant and durable improvement at 24 months. The success for the apical compartment ranged between 93.8% and 100%. Success was slightly lower for the anterior compartment (70.8-89.1%). No statistically significant difference between the 3 subgroups. Age was the only patient characteristic to be found different between the 3 subgroups. In addition, there was no difference in overall intraoperative complications (P = 0.263). Mesh extrusion was found in all groups: 3 of 61 (4.9%) had previous hysterectomy; 4 of 29 (13.8%) had concomitant hysterectomy; and 1 of 51 (2.0%) had uterus preserved (P = 0.094). There appears to be a trend toward higher extrusion when a hysterectomy was performed with the EAA. Anatomic success and complications for the EAA do not appear to be significantly impacted when the uterus is removed before or during surgery or preserved. There may be a trend toward increased mesh extrusion when a hysterectomy is performed. However, larger cohort studies are needed to determine if concomitant hysterectomy impact extrusion.

[Study of New Micropore RF system on Lesion Formation and Complications].

PubMed

Song, Yuwen; Xu, Xiulin; Cai, Yameng

2017-07-30

To study the safety and effectiveness of a new type of micropore ablation catheter in vitro ablation system, and to provide reference for clinical practice. To evaluate two kinds of catheter in cardiac tissue ablation depth, tissue temperature and thrombosis situation by the same RF system. The power set 25 W, There was no significant difference in ablation depth between the two groups, and no Pop and thrombosis occurred. When the power is more than 40 W, two groups occurred more Pop and thrombosis. When using high power for Cardiac RF ablation, doctors should pay more attention to complications and thrombosis.

Active Yeast Telomerase Shares Subunits with Ribonucleoproteins RNase P and RNase MRP.

PubMed

Lemieux, Bruno; Laterreur, Nancy; Perederina, Anna; Noël, Jean-François; Dubois, Marie-Line; Krasilnikov, Andrey S; Wellinger, Raymund J

2016-05-19

Telomerase is the ribonucleoprotein enzyme that replenishes telomeric DNA and maintains genome integrity. Minimally, telomerase activity requires a templating RNA and a catalytic protein. Additional proteins are required for activity on telomeres in vivo. Here, we report that the Pop1, Pop6, and Pop7 proteins, known components of RNase P and RNase MRP, bind to yeast telomerase RNA and are essential constituents of the telomerase holoenzyme. Pop1/Pop6/Pop7 binding is specific and involves an RNA domain highly similar to a protein-binding domain in the RNAs of RNase P/MRP. The results also show that Pop1/Pop6/Pop7 function to maintain the essential components Est1 and Est2 on the RNA in vivo. Consistently, addition of Pop1 allows for telomerase activity reconstitution with wild-type telomerase RNA in vitro. Thus, the same chaperoning module has allowed the evolution of functionally and, remarkably, structurally distinct RNPs, telomerase, and RNases P/MRP from unrelated progenitor RNAs. Copyright © 2016 Elsevier Inc. All rights reserved.

Critical assessment of digital PCR for the detection and quantification of genetically modified organisms.

PubMed

Demeke, Tigst; Dobnik, David

2018-07-01

The number of genetically modified organisms (GMOs) on the market is steadily increasing. Because of regulation of cultivation and trade of GMOs in several countries, there is pressure for their accurate detection and quantification. Today, DNA-based approaches are more popular for this purpose than protein-based methods, and real-time quantitative PCR (qPCR) is still the gold standard in GMO analytics. However, digital PCR (dPCR) offers several advantages over qPCR, making this new technique appealing also for GMO analysis. This critical review focuses on the use of dPCR for the purpose of GMO quantification and addresses parameters which are important for achieving accurate and reliable results, such as the quality and purity of DNA and reaction optimization. Three critical factors are explored and discussed in more depth: correct classification of partitions as positive, correctly determined partition volume, and dilution factor. This review could serve as a guide for all laboratories implementing dPCR. Most of the parameters discussed are applicable to fields other than purely GMO testing. Graphical abstract There are generally three different options for absolute quantification of genetically modified organisms (GMOs) using digital PCR: droplet- or chamber-based and droplets in chambers. All have in common the distribution of reaction mixture into several partitions, which are all subjected to PCR and scored at the end-point as positive or negative. Based on these results GMO content can be calculated.

A Simple, Visually Oriented Communication System to Improve Postoperative Care Following Microvascular Free Tissue Transfer: Development, Results, and Implications.

PubMed

Henderson, Peter W; Landford, Wilmina; Gardenier, Jason; Otterburn, David M; Rohde, Christine H; Spector, Jason A

2016-07-01

Background Communication, particularly transmission of information between the surgical and nursing teams, has been identified as one of the most crucial determinants of patient outcomes. Nonetheless, transfer of information among and between the physician and nursing teams in the immediate postoperative period is often informal, verbal, and inconsistent. Methods An iterative process of multidisciplinary information gathering was undertaken to create a novel postoperative communication system (the "Pop-form"). Once developed, nurses were surveyed on multiple measures regarding the perceived likelihood that it would improve their ability to provide directed patient care. Data were quantified using a Likert scale (0-10), and statistically analyzed. Results The Pop-form records and transfers operative details, specific anatomic monitoring parameters, and senior physician contact information. Sixty-eight nurses completed surveys. The perceived usefulness of different components of the Pop-form system was as follows: 8.9 for the description of the procedure; 9.3 for the operative diagram; 9.4 for the monitoring details and parameters; and 9.4 for the direct contact information for the appropriate surgical team member. All respondents were in favor of widespread adoption of the Pop-form. Conclusion This uniform, visual communication system requires less than 1 minute to compose, yet formalizes and standardizes inter-team communication, and therefore shows promise for improving outcomes following microvascular free tissue transfer. We believe that this simple, innovative communication tool has the potential to be more broadly applied to many other health care settings. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Popcorn: critical temperature, jump and sound.

PubMed

Virot, Emmanuel; Ponomarenko, Alexandre

2015-03-06

Popcorn bursts open, jumps and emits a 'pop' sound in some hundredths of a second. The physical origin of these three observations remains unclear in the literature. We show that the critical temperature 180°C at which almost all of popcorn pops is consistent with an elementary pressure vessel scenario. We observe that popcorn jumps with a 'leg' of starch which is compressed on the ground. As a result, popcorn is midway between two categories of moving systems: explosive plants using fracture mechanisms and jumping animals using muscles. By synchronizing video recordings with acoustic recordings, we propose that the familiar 'pop' sound of the popcorn is caused by the release of water vapour. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Advantageous Direct Quantification of Viable Closely Related Probiotics in Petit-Suisse Cheeses under In Vitro Gastrointestinal Conditions by Propidium Monoazide - qPCR

PubMed Central

Villarreal, Martha Lissete Morales; Padilha, Marina; Vieira, Antonio Diogo Silva; Franco, Bernadette Dora Gombossy de Melo; Martinez, Rafael Chacon Ruiz; Saad, Susana Marta Isay

2013-01-01

Species-specific Quantitative Real Time PCR (qPCR) alone and combined with the use of propidium monoazide (PMA) were used along with the plate count method to evaluate the survival of the probiotic strains Lactobacillus acidophilus La-5 and Bifidobacterium animalis subsp. lactis Bb-12, and the bacteriocinogenic and potentially probiotic strain Lactobacillus sakei subsp. sakei 2a in synbiotic (F1) and probiotic (F2) petit-suisse cheeses exposed throughout shelf-life to in vitro simulated gastrointestinal tract conditions. The three strains studied showed a reduction in their viability after the 6 h assay. Bb-12 displayed the highest survival capacity, above 72.6 and 74.6% of the initial populations, respectively, by plate count and PMA-qPCR, maintaining population levels in the range or above 6 log CFU/g. The prebiotic mix of inulin and FOS did not offer any additional protection for the strains against the simulated gastrointestinal environment. The microorganisms' populations were comparable among the three methods at the initial time of the assay, confirming the presence of mainly viable and culturable cells. However, with the intensification of the stress induced throughout the various stages of the in vitro test, the differences among the methods increased. The qPCR was not a reliable enumeration method for the quantification of intact bacterial populations, mixed with large numbers of injured and dead bacteria, as confirmed by the scanning electron microscopy results. Furthermore, bacteria plate counts were much lower (P<0.05) than with the PMA-qPCR method, suggesting the accumulation of stressed or dead microorganisms unable to form colonies. The use of PMA overcame the qPCR inability to differentiate between dead and alive cells. The combination of PMA and species-specific qPCR in this study allowed a quick and unequivocal way of enumeration of viable closely related species incorporated into probiotic and synbiotic petit-suisse cheeses and under stress conditions. PMID:24358142

[Study on reductive surgery for pelvic organ prolapse concomitant with anti-incontinence sling for treatment of occult stress urinary incontinence].

PubMed

Zhang, Xiaolong; Lu, Yongxian; Shen, Wenjie; Liu, Jingxia; Ge, Jing; Liu, Xin; Zhao, Ying; Niu, Ke; Zhang, Yinghui; Wang, Wenying; Qiu, Chengli

2014-06-01

To evaluate the clinical outcome of anti-incontinence sling in the treatment of occult stress urinary incontinence (OSUI) during reductive surgery for advanced pelvic organ prolapse (POP). From Jun. 2003 to Dec. 2012, 78 patients with OSUI underwent reductive surgery for advanced POP such as high uterosacral ligament suspension, sacrospinous ligament suspension and sacral colpopexy in the First Affiliated Hospital, General Hospital of People's Liberation Army. Among them, 41 patients received reductive surgery alone was enrolled in non-concomitant anti-incontinence group and the other 37 patients who underwent same surgery with tension-free vaginal tape (TVT) or tension-free vaginal tape-obturator technique (TVT-O) was in anti-incontinence group. The patient's demography, objective and subjective outcomes, as well as complications and injures were compared between the two groups. The pelvic organ prolapse quantitation (POP-Q) was used to evaluate the objective outcomes of POP. Urinary distress inventory (UDI-6) and incontinence impact questionnaire short form (IIQ-7) were used to evaluate the subjective outcomes of stress urinary incontinence (SUI). Compared with the non-concomitant anti-incontinence group, the objective outcomes of reductive surgery exhibited no significant differences (100%, 78/78), and only the operation time of anti-incontinence group slightly increased 16 minutes. The occurrence rate of postoperative SUI was 12% (5/41), 15% (6/41), 17% (7/41) respectively after the operation at 2-month, 6-month and 12-month follow up in the non-concomitant anti-incontinence group; and the occurrence rate of the anti-incontinence group was 3% (1/37), 3% (1/37), 3% (1/37); but none of patients in the two groups require further surgery for stress urinary incontinence. Mean score of UDI-6 and IIQ-7 in all the patients decreased significantly after operation at 2-month, 6-month and 12-month follow up (all P < 0.01). However, there was no statistic difference between the two groups (P > 0.05). It is still difficult to make decision for concomitant anti-incontinence procedure in those patients with OSUI, who are undergoing reductive surgery because of advanced POP. Whether the patients will benefit more from anti-incontinence sling depends largely on strict preoperative evaluation for the severity of SUI. The patients with severe SUI are supposed to benefit most from anti-incontinence sling. However, a two-step approach to correct the postoperative stress urinary incontinence is also reasonable.

A translocator-specific export signal establishes the translocator-effector secretion hierarchy that is important for type III secretion system function

PubMed Central

Tomalka, Amanda G.; Stopford, Charles M.; Lee, Pei-Chung; Rietsch, Arne

2012-01-01

Summary Type III secretion systems are used by many Gram-negative pathogens to directly deliver effector proteins into the cytoplasm of host cells. To accomplish this, bacteria secrete translocator proteins that form a pore in the host-cell membrane through which the effector proteins are then introduced into the host cell. Evidence from multiple systems indicates that the pore-forming translocator proteins are exported before effectors, but how this secretion hierarchy is established is unclear. Here we used the P. aeruginosa translocator protein PopD as a model to identify its export signals. The amino-terminal secretion signal and chaperone, PcrH, are required for export under all conditions. Two novel signals in PopD, one proximal to the chaperone-binding site and one at the very C-terminus of the protein, are required for export of PopD before effector proteins. These novel export signals establish the translocator-effector secretion hierarchy, which in turn, is critical for the delivery of effectors into host cells. PMID:23121689

Constraining the Statistics of Population III Binaries

NASA Technical Reports Server (NTRS)

Stacy, Athena; Bromm, Volker

2012-01-01

We perform a cosmological simulation in order to model the growth and evolution of Population III (Pop III) stellar systems in a range of host minihalo environments. A Pop III multiple system forms in each of the ten minihaloes, and the overall mass function is top-heavy compared to the currently observed initial mass function in the Milky Way. Using a sink particle to represent each growing protostar, we examine the binary characteristics of the multiple systems, resolving orbits on scales as small as 20 AU. We find a binary fraction of approx. 36, with semi-major axes as large as 3000 AU. The distribution of orbital periods is slightly peaked at approx. < 900 yr, while the distribution of mass ratios is relatively flat. Of all sink particles formed within the ten minihaloes, approx. 50 are lost to mergers with larger sinks, and 50 of the remaining sinks are ejected from their star-forming disks. The large binary fraction may have important implications for Pop III evolution and nucleosynthesis, as well as the final fate of the first stars.

The Effects of Pop-up Harm Minimisation Messages on Electronic Gaming Machine Gambling Behaviour in New Zealand.

PubMed

Palmer du Preez, Katie; Landon, Jason; Bellringer, Maria; Garrett, Nick; Abbott, Max

2016-12-01

In New Zealand a simple pop-up message feature that provides gambling session information and forces a break in play is mandatory on all electronic gaming machines in all venues (EGMs). Previous research has demonstrated small effects of more sophisticated pop-up messages tested predominantly in laboratory environments. The present research examined gambler engagement with and views on the New Zealand pop-up messages and on the relationship between pop-up messages and EGM expenditure. A sample of gamblers was recruited at casino and non-casino (pub) EGM venues. Most participants were aware of pop-up messages (57 %) and many saw them often (38 %). Among gamblers who reported seeing pop-up messages, half read the message content, and a quarter believed that pop-up messages helped them control the amount of money they spend on gambling. Participants who reported being likely to stop gambling in response to pop-up messages spent significantly less money on gambling when variables that were independently associated with EGM expenditure were controlled for. A modest harm minimisation effect of the pop-up message feature that has been operating in New Zealand for 5 years was evident. Suggestions for improvement of the harm minimisation potential of the current pop-up message feature are discussed.

Installation Restoration Program. Phase 2. Confirmation/Quantification. Stage 1 Report for Beale AFB, Marysville, California. Volume 2.

DTIC Science & Technology

1987-05-01

Maintarer.e ground water 2 scil borinF 8 hand auger 12 Disna:-e Area No. 10 (DA-10) - Entomology Bldg UO soil boring 6 13 Landfil: Nc. 1 (LF-1) ground...l’JSZIL I ’ SCIL SO V ; 7 ILill ( oi[ ;Q0 SO IL. $;I 60 . *O (3 .1 *, W i ; Q,. t.t WLi it hI OX aoPit IV 3 ’ Table F-1 (Cont.) 6OIOOtO LAB WPLIAT

Real-time PCR for the Early Detection and Quantification of Coxiella burnetii as an Alternative to the Murine Bioassay

DTIC Science & Technology

2009-01-01

that chronic disease resulting from C. burnetii infection may be the first time Q fever is diagnosed in some patients. Although endocarditis is the most...Microbiol 2006;6:2. [13] Fenollar F, Fournier PE, Raoult D. Molecular detection of Coxiella burnetii in the sera of patients with Q fever endocarditis ...automated DNA preparation. BMC Microbiol 2008;8:77. [33] Ghassemi M, Agger WA, Vanscoy RE, Howe GB. Chronic sternal wound infection and endocarditis with

Pop-Up Constructions Motivate and Reinforce Science Learning for Upper Elementary Students

ERIC Educational Resources Information Center

Olsen, Benjamin D.; Zhbanova, Ksenia S.; Parpucu, Harun; Alkouri, Zaid; Rule, Audrey C.

2013-01-01

Pop-up boxes and folder constructions support student inquiry while integrating art, craft, spatial, and creativity skills. Step-by-step illustrated directions for constructing pop-up boxes are provided with example images of pop-up boxes focused on ecological issues. Teachers used these pop-up constructions to assist fourth- and fifth-grade…

Laparoscopic hysteropexy: the initial results of a uterine suspension procedure for uterovaginal prolapse.

PubMed

Price, Natalia; Slack, A; Jackson, S R

2010-01-01

The aim of this study was to evaluate the outcome of laparoscopic hysteropexy, a surgical technique for the management of uterine prolapse, involving suspension of the uterus from the sacral promontory using bifurcated polypropylene mesh. The investigation was designed as a prospective observational study (clinical audit). The study was undertaken at a tertiary referral urogynaecology unit in the UK. The participants comprised 51 consecutive women with uterovaginal prolapse, who chose laparoscopic hysteropexy as one of the available surgical options. The hysteropexy was conducted laparoscopically in all cases. A bifurcated polypropylene mesh was used to suspend the uterus from the sacral promontory. The two arms of the mesh were introduced through bilateral windows created in the broad ligaments, and were sutured to the anterior cervix; the mesh was then fixed to the anterior longitudinal ligament over the sacral promontory, to elevate the uterus. Cure of the uterine prolapse was evaluated subjectively using the International Consultation on Incontinence Questionnaire for vaginal symptoms (ICIQ-VS), and objectively by vaginal examination using the Baden-Walker halfway system and the pelvic organ prolapse quantification (POP-Q) scale. Operative and postoperative complications were also assessed. The mean age of the 51 women was 52.5 years (range 19-71 years). All were sexually active, and at least three of them expressed a strong desire to have children in the future. All were available for follow-up in clinic at 10 weeks, and 38 have completed the questionnaires. In 50 out of 51 women the procedure was successful, with no objective evidence of uterine prolapse on examination at follow-up; there was one failure. Significant subjective improvements in prolapse symptoms, sexual wellbeing and related quality of life were observed, as detected by substantial reductions in the respective questionnaire scores. Laparoscopic hysteropexy is both a feasible and an effective procedure for correcting uterine prolapse without recourse to hysterectomy. It allows restoration of the length of the vagina without compromising its calibre, and is therefore likely to have a favourable functional outcome.

Quantification by real-time PCR of Trypanosoma cruzi DNA in samples of Triatoma infestans used in xenodiagnosis of chronic Chagas disease patients.

PubMed

Saavedra, Miguel; Zulantay, Inés; Apt, Werner; Castillo, Juan; Araya, Eduardo; Martínez, Gabriela; Rodríguez, Jorge

2016-07-04

Trypanosoma cruzi multiplies and differentiates in the digestive tract of triatomine insects. Xenodiagnosis (XD) is a parasitological tool in which the insect vectors acts as a biological culture medium to amplify and detect T. cruzi infection in mammals. The sensitivity of XD has been overcome by the application of PCR in fecal samples (FS) of XD (PCR-XD). In this study, T. cruzi amplified in Triatoma infestans fed by XD on individuals with chronic Chagas disease (CChD) is quantified by real-time PCR (qPCR-XD). Under informed consent, 100 individuals were evaluated. In 21 of them XD, PCR-XD and qPCR-XD were positive. For the contrary, 79 were negative XD. In 58 (73.4 %) and 66 cases (83.5 %) of them, PCR-XD (Fisher's exact test P = 0.005) and qPCR-XD (Fisher's exact test: P = 0.037) respectively, were positive. In cases with positive XD, qPCR-XD allowed to establish that in 9/21 cases (42.9 %) the parasite burden fluctuated between 100 and 1,000 par. eq./ml. Otherwise, in 32/79 (40.5 %) cases with negative XD, a parasite burden between 1 and 10 par. eq./ml was determined. All samples showed amplification of exogenous internal control (X12, Ct average: 31.8), so problems in the DNA extraction (excess or loss of genetic material), unspecific amplification and/or inhibition in qPCR-XD reactions were ruled out. Additionally, in all the patients qPCR in blood (qPCR-B) was performed. In the cases with positive XD, the concordance between the positivity of qPCR-XD and qPCR-B was 100 %, nevertheless, the parasite burden in blood was lower and different than XD (Chi-square test: χ (2)  = 91.82, df = 5, P = 0.0001). In the cases with negative XD the ranges of qPCR-XD and qPCR-B were similar (Chi-square test: χ (2)  = 6.71, df = 5, P = 0.1520). This study allowed the detection and quantification of T. cruzi by qPCR-XD in FS of Tr. infestans fed on patients with CChD. The highest parasite burden was observed in positive XD cases. qPCR-XD could be used in different studies related with the complex T. cruzi-vector-host interactions.

Development of a Singlet Oxygen Absorption Capacity (SOAC) Assay Method. Measurements of the SOAC Values for Carotenoids and α-Tocopherol in an Aqueous Triton X-100 Micellar Solution.

PubMed

Mukai, Kazuo; Ouchi, Aya; Azuma, Nagao; Takahashi, Shingo; Aizawa, Koichi; Nagaoka, Shin-Ichi

2017-02-01

Recently, a new assay method for the quantification of the singlet oxygen absorption capacity (SOAC) of antioxidants (AOs) and food extracts in homogeneous organic solvents was proposed. In this study, second-order rate constants (k Q ) for the reaction of singlet oxygen ( 1 O 2 ) with eight different carotenoids (Cars) and α-tocopherol (α-Toc) were measured in an aqueous Triton X-100 (5.0 wt %) micellar solution (pH 7.4, 35 °C), which was used as a simple model of biomembranes. The k Q and relative SOAC values were measured using ultraviolet-visible (UV-vis) spectroscopy. The UV-vis absorption spectra of Cars and α-Toc were measured in both a micellar solution and chloroform, to investigate the effect of solvent on the k Q and SOAC values. Furthermore, decay rates (k d ) of 1 O 2 were measured in 0.0, 1.0, 3.0, and 5.0 wt % micellar solutions (pH 7.4), using time-resolved near-infrared fluorescence spectroscopy, to determine the absolute k Q values of the AOs. The results obtained demonstrate that the k Q values of AOs in homogeneous and heterogeneous solutions vary notably depending on (i) the polarity [dielectric constant (ε)] of the reaction field between AOs and 1 O 2 , (ii) the local concentration of AOs, and (iii) the mobility of AOs in solution. In addition, the k Q and relative SOAC values obtained for the Cars in a heterogeneous micellar solution differ remarkably from those in homogeneous organic solvents. Measurements of k Q and SOAC values in a micellar solution may be useful for evaluating the 1 O 2 quenching activity of AOs in biological systems.

Detection of the KIT D816V mutation in peripheral blood of systemic mastocytosis: diagnostic implications.

PubMed

Jara-Acevedo, Maria; Teodosio, Cristina; Sanchez-Muñoz, Laura; Álvarez-Twose, Ivan; Mayado, Andrea; Caldas, Carolina; Matito, Almudena; Morgado, José M; Muñoz-González, Javier I; Escribano, Luis; Garcia-Montero, Andrés C; Orfao, Alberto

2015-08-01

Recent studies have found the KIT D816V mutation in peripheral blood of virtually all adult systemic mastocytosis patients once highly sensitive PCR techniques were used; thus, detection of the KIT D816V mutation in peripheral blood has been proposed to be included in the diagnostic work-up of systemic mastocytosis algorithms. However, the precise frequency of the mutation, the biological significance of peripheral blood-mutated cells and their potential association with involvement of bone marrow hematopoietic cells other than mast cells still remain to be investigated. Here, we determined the frequency of peripheral blood involvement by the KIT D816V mutation, as assessed by two highly sensitive PCR methods, and investigated its relationship with multilineage involvement of bone marrow hematopoiesis. Overall, our results confirmed the presence of the KIT D816V mutation in peripheral blood of most systemic mastocytosis cases (161/190; 85%)--with an increasing frequency from indolent systemic mastocytosis without skin lesions (29/44; 66%) to indolent systemic mastocytosis with skin involvement (124/135; 92%), and more aggressive disease subtypes (11/11; 100%)--as assessed by the allele-specific oligonucleotide-qPCR method, which was more sensitive (P<.0001) than the peptide nucleic acid-mediated PCR approach (84/190; 44%). Although the presence of the KIT mutation in peripheral blood, as assessed by the allele-specific oligonucleotide-qPCR technique, did not accurately predict for multilineage bone marrow involvement of hematopoiesis, the allele-specific oligonucleotide-qPCR allele burden and the peptide nucleic acid-mediated-PCR approach did. These results suggest that both methods provide clinically useful and complementary information through the identification and/or quantification of the KIT D816V mutation in peripheral blood of patients suspected of systemic mastocytosis.

Cumulative Incidence of a Subsequent Surgery After Stress Urinary Incontinence and Pelvic Organ Prolapse Procedure.

PubMed

Wu, Jennifer M; Dieter, Alexis A; Pate, Virginia; Jonsson Funk, Michele

2017-06-01

To assess the 5-year risk and timing of repeat stress urinary incontinence (SUI) and pelvic organ prolapse (POP) procedures. We conducted a retrospective cohort study using a nationwide database, the 2007-2014 MarketScan Commercial Claims and Encounters and Medicare Supplemental Databases (Truven Health Analytics), which contain deidentified health care claims data from approximately 150 employer-based insurance plans across the United States. We included women aged 18-84 years and used Current Procedural Terminology codes to identify surgeries for SUI and POP. We identified index procedures for SUI or POP after at least 3 years of continuous enrollment without a prior procedure. We defined three groups of women based on the index procedure: 1) SUI surgery only; 2) POP surgery only; and 3) Both SUI+POP surgery. We assessed the occurrence of a subsequent SUI or POP procedure over time for women younger than 65 years and 65 years or older with a median follow-up time of 2 years (interquartile range 1-4). We identified a total of 138,003 index procedures: SUI only n=48,196, POP only n=49,120, and both SUI+POP n=40,687. The overall cumulative incidence of a subsequent SUI or POP surgery within 5 years after any index procedure was 7.8% (95% confidence interval [CI] 7.6-8.1) for women younger than 65 years and 9.9% (95% CI 9.4-10.4) for women 65 years or older. The cumulative incidence was lower if the initial surgery was SUI only and higher if an initial POP procedure was performed, whether POP only or SUI+POP. The 5-year risk of undergoing a repeat SUI or POP surgery was less than 10% with higher risks for women 65 years or older and for those who underwent an initial POP surgery.

Article "403. Toxicology of Persistent Organic Pollutants (POPs)"

EPA Science Inventory

Persistent Organic Pollutants (POPs) are all synthetic chemicals, either intentionally or unintentionally produced/released. Some POPs are pesticides. Others are industrial products or unintended by-products resulting from industrial processes or combustions (see figure 1). POPs ...

Tissue response to collagen containing polypropylene meshes in an ovine vaginal repair model.

PubMed

Darzi, Saeedeh; Urbankova, Iva; Su, Kai; White, Jacinta; Lo, Camden; Alexander, David; Werkmeister, Jerome A; Gargett, Caroline E; Deprest, Jan

2016-07-15

Pelvic Organ Prolapse (POP) is the herniation of pelvic organs into the vagina. Despite broad acceptance of mesh use in POP surgical repair, the complication rate is unacceptable. We hypothesized that collagen-containing polypropylene (PP) mesh types could modulate mesh-tissue integration and reduce long-term inflammation, thereby reducing mesh-associated complications. This study compared the long-term tissue response to an unmodified PP mesh and two collagen containing meshes in an ovine model which has similar pelvic anatomy and vaginal size to human. Three commercially available macroporous PP meshes, uncoated PP mesh (Avaulta Solo) (PP), the same textile PP mesh layered with a sheet of cross-linked porcine acellular matrix (Avaulta Plus) (PP-ACM) and a different yet also macroporous PP (Sofradim) mesh coated with solubilized atelocollagen (Ugytex) (PP-sCOL) were implanted in the ovine vagina and tissue explanted after 60 and 180days. The macrophage phenotype and response to implanted meshes, and vascularity were quantified by immunostaining and morphometry. We quantified changes in extracellular matrix composition biochemically and collagen organisation and percentage area around the interface of the mesh implants by Sirius Red birefringence and morphometry. PP-ACM induced a more sustained inflammatory response, indicated by similar CD45(+) leukocytes but reduced CD163(+) M2 macrophages at 60days (P<0.05). PP-sCOL increased Von Willebrand Factor (vWF)-immunoreactive vessel profiles after 60days. At the micro-molecular level, collagen birefringence quantification revealed significantly fewer mature collagen fibrils (red, thick fibrils) at the mesh-tissue interface than control tissue for all mesh types (P<0.001) but still significantly greater than the proportion of immature (green thin fibrils) at 60days (P<0.05). The proportion of mature collagen fibrils increased with time around the mesh filaments, particularly those containing collagen. The total collagen percent area at the mesh interface was greatest around the PP-ACM mesh at 60days (P<0.05). By 180days the total mature and immature collagen fibres at the interface of the mesh filaments resembled that of native tissue. In particular, these results suggest that both meshes containing collagen evoke different types of tissue responses at different times during the healing response yet both ultimately lead to physiological tissue formation approaching that of normal tissue. Pelvic organ prolapse (POP) is the descent of the pelvic organs to the vagina. POP affects more than 25% of all women and the lifetime risk of undergoing POP surgery is 19%. Although synthetic polypropylene (PP) meshes have improved the outcome of the surgical treatment for POP, there was an unacceptable rate of adverse events including mesh exposure and contracture. It is hypothesized that coating the PP meshes with collagen would provide a protective effect by preventing severe mesh adhesions to the wound, resulting in a better controlled initial inflammatory response, and diminished risk of exposure. In this study we assessed the effect of two collagen-containing PP meshes on the long-term vaginal tissue response using new techniques to quantify these tissue responses. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Development and inter-laboratory assessment of droplet digital PCR assays for multiplex quantification of 15 genetically modified soybean lines.

PubMed

Košir, Alexandra Bogožalec; Spilsberg, Bjørn; Holst-Jensen, Arne; Žel, Jana; Dobnik, David

2017-08-17

Quantification of genetically modified organisms (GMOs) in food and feed products is often required for their labelling or for tolerance thresholds. Standard-curve-based simplex quantitative polymerase chain reaction (qPCR) is the prevailing technology, which is often combined with screening analysis. With the rapidly growing number of GMOs on the world market, qPCR analysis becomes laborious and expensive. Innovative cost-effective approaches are therefore urgently needed. Here, we report the development and inter-laboratory assessment of multiplex assays to quantify GMO soybean using droplet digital PCR (ddPCR). The assays were developed to facilitate testing of foods and feed for compliance with current GMO regulations in the European Union (EU). Within the EU, the threshold for labelling is 0.9% for authorised GMOs per ingredient. Furthermore, the EU has set a technical zero tolerance limit of 0.1% for certain unauthorised GMOs. The novel multiplex ddPCR assays developed target 11 GMO soybean lines that are currently authorised, and four that are tolerated, pending authorisation in the EU. Potential significant improvements in cost efficiency are demonstrated. Performance was assessed for the critical parameters, including limits of detection and quantification, and trueness, repeatability, and robustness. Inter-laboratory performance was also determined on a number of proficiency programme and real-life samples.

Modeling magnetization transfer effects of Q2TIPS bolus saturation in multi-TI pulsed arterial spin labeling.

PubMed

Petr, Jan; Schramm, Georg; Hofheinz, Frank; Langner, Jens; van den Hoff, Jörg

2014-10-01

To estimate the relaxation time changes during Q2TIPS bolus saturation caused by magnetization transfer effects and to propose and evaluate an extended model for perfusion quantification which takes this into account. Three multi inversion-time pulsed arterial spin labeling sequences with different bolus saturation duration were acquired for five healthy volunteers. Magnetization transfer exchange rates in tissue and blood were obtained from control image saturation recovery. Cerebral blood flow (CBF) obtained using the extended model and the standard model was compared. A decrease of obtained CBF of 6% (10%) was observed in grey matter when the duration of bolus saturation increased from 600 to 900 ms (1200 ms). This decrease was reduced to 1.6% (2.8%) when the extended quantification model was used. Compared with the extended model, the standard model underestimated CBF in grey matter by 9.7, 15.0, and 18.7% for saturation durations 600, 900, and 1200 ms, respectively. Results for simulated single inversion-time data showed 5-16% CBF underestimation depending on blood arrival time and bolus saturation duration. Magnetization transfer effects caused by bolus saturation pulses should not be ignored when performing quantification as they can cause appreciable underestimation of the CBF. Copyright © 2013 Wiley Periodicals, Inc.

Determination of the purity of pharmaceutical reference materials by 1H NMR using the standardless PULCON methodology.

PubMed

Monakhova, Yulia B; Kohl-Himmelseher, Matthias; Kuballa, Thomas; Lachenmeier, Dirk W

2014-11-01

A fast and reliable nuclear magnetic resonance spectroscopic method for quantitative determination (qNMR) of targeted molecules in reference materials has been established using the ERETIC2 methodology (electronic reference to access in vivo concentrations) based on the PULCON principle (pulse length based concentration determination). The developed approach was validated for the analysis of pharmaceutical samples in the context of official medicines control, including ibandronic acid, amantadine, ambroxol and lercanidipine. The PULCON recoveries were above 94.3% and coefficients of variation (CVs) obtained by quantification of different targeted resonances ranged between 0.7% and 2.8%, demonstrating that the qNMR method is a precise tool for rapid quantification (approximately 15min) of reference materials and medicinal products. Generally, the values were within specification (certified values) provided by the manufactures. The results were in agreement with NMR quantification using an internal standard and validated reference HPLC analysis. The PULCON method was found to be a practical alternative with competitive precision and accuracy to the classical internal reference method and it proved to be applicable to different solvent conditions. The method can be recommended for routine use in medicines control laboratories, especially when the availability and costs of reference compounds are problematic. Copyright © 2014 Elsevier B.V. All rights reserved.

Digital PCR for detection of citrus pathogens

USDA-ARS?s Scientific Manuscript database

Citrus trees are often infected with multiple pathogens of economic importance, especially those with insect or mite vectors. Real-time/quantitative PCR (qPCR) has been used for high-throughput detection and relative quantification of pathogens; however, target reference or standards are required. I...

An innovative ultrasound assisted extraction micro-scale cell combined with gas chromatography/mass spectrometry in negative chemical ionization to determine persistent organic pollutants in air particulate matter.

PubMed

Beristain-Montiel, E; Villalobos-Pietrini, R; Arias-Loaiza, G E; Gómez-Arroyo, S L; Amador-Muñoz, O

2016-12-16

New clean technologies are needed to determine concentration of organic pollutants without generating more pollution. A method to extract Persistent Organic Pollutants (POPs) from airborne particulate matter was developed using a novel technology recently patented called ultrasound assisted extraction micro-scale cell (UAE-MSC). This technology extracts, filters, collects the sample, and evaporates the solvent, on-line. No sample transfer is needed. The cell minimizes sample manipulation, solvent consumption, waste generation, time, and energy; fulfilling most of the analytical green chemistry protocol. The methodology was optimized applying a centred 2 3 factorial experimental design. Optimum conditions were used to validate and determine concentration of 16 organochlorine pesticides (OCls) and 6 polybrominated diphenyl ethers (PBDEs). The best conditions achieved were 2 extractions with 5mL (each) of dichloromethane over 5min (each) at 60°C and 80% ultrasound potency. POPs were determined by gas chromatography/mass spectrometry in negative chemical ionization (GC/MS-NCI). Analytical method validation was carried out on airborne particles spiked with POPs at seven concentration levels between 0.5 and 26.9pgm -3 . This procedure was done by triplicate (N=21). Recovery, ranged between 65.5±2.3% and 107.5±3.0% for OCls and between 79.1±6.5% and 105.2±3.8% for PBDEs. Linearity (r 2 ) was ≥0.94 for all compounds. Method detection limits, ranged from 0.5 to 2.7pgm -3 , while limits of quantification (LOQ), ranged from 1.7 to 9.0pgm -3 . A Bias from -18.6% to 9% for PBDEs was observed in the Standard Reference Material (SRM) 2787. SRM 2787 did not contain OCls. OCls recoveries were equivalent by UAE-MSC and Soxhlet methods UAE-MSC optimized extraction conditions reduced 30 times less solvent and decreased the extraction time from several hours to ten minutes, respect to Soxhlet. UAE-MSC was applied to 15 samples of particles less than 2.5μm (PM 2.5 ) from three seasons (warm dry, rainy, and cold dry) collected in five sites around Mexico City. OCls (4,4'-DDE and endrin aldehyde) concentrations ranged from

'Pop-Up' Governance: developing internal governance frameworks for consortia: the example of UK10K.

PubMed

Kaye, Jane; Muddyman, Dawn; Smee, Carol; Kennedy, Karen; Bell, Jessica

2015-01-01

Innovations in information technologies have facilitated the development of new styles of research networks and forms of governance. This is evident in genomics where increasingly, research is carried out by large, interdisciplinary consortia focussing on a specific research endeavour. The UK10K project is an example of a human genomics consortium funded to provide insights into the genomics of rare conditions, and establish a community resource from generated sequence data. To achieve its objectives according to the agreed timetable, the UK10K project established an internal governance system to expedite the research and to deal with the complex issues that arose. The project's governance structure exemplifies a new form of network governance called 'pop-up' governance. 'Pop-up' because: it was put together quickly, existed for a specific period, was designed for a specific purpose, and was dismantled easily on project completion. In this paper, we use UK10K to describe how 'pop-up' governance works on the ground and how relational, hierarchical and contractual governance mechanisms are used in this new form of network governance.

Biomonitoring persistent organic pollutants in the atmosphere with mosses: performance and application.

PubMed

Wu, Qimei; Wang, Xin; Zhou, Qixing

2014-05-01

Persistent organic pollutants (POPs) have aroused environmentalists and public concerns due to their toxicity, bioaccumulation and persistency in the environment. However, monitoring atmospheric POPs using conventional instrumental methods is difficult and expensive, and POP levels in air samples represent an instantaneous value at a sampling time. Biomonitoring methods can overcome this limitation, because biomonitors can accumulate POPs, serve as long-term integrators of POPs and provide reliable information to assess the impact of pollutants on the biota and various ecosystems. Recently, mosses are increasingly employed to monitor atmospheric POPs. Mosses have been applied to indicate POP pollution levels in the remote continent of Antarctica, trace distribution of POPs in the vicinity of pollution sources, describe the spatial patterns at the regional scale, and monitor the changes in the pollution intensity along time. In the future, many aspects need to be improved and strengthened: (i) the relationship between the concentrations of POPs in mosses and in the atmosphere (different size particulates and vapor phases); and (ii) the application of biomonitoring with mosses in human health studies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Specific binding of a Pop6/Pop7 heterodimer to the P3 stem of the yeast RNase MRP and RNase P RNAs.

PubMed

Perederina, Anna; Esakova, Olga; Koc, Hasan; Schmitt, Mark E; Krasilnikov, Andrey S

2007-10-01

Pop6 and Pop7 are protein subunits of Saccharomyces cerevisiae RNase MRP and RNase P. Here we show that bacterially expressed Pop6 and Pop7 form a soluble heterodimer that binds the RNA components of both RNase MRP and RNase P. Footprint analysis of the interaction between the Pop6/7 heterodimer and the RNase MRP RNA, combined with gel mobility assays, demonstrates that the Pop6/7 complex binds to a conserved region of the P3 domain. Binding of these proteins to the MRP RNA leads to local rearrangement in the structure of the P3 loop and suggests that direct interaction of the Pop6/7 complex with the P3 domain of the RNA components of RNases MRP and P may mediate binding of other protein components. These results suggest a role for a key element in the RNase MRP and RNase P RNAs in protein binding, and demonstrate the feasibility of directly studying RNA-protein interactions in the eukaryotic RNases MRP and P complexes.

Viability PCR, a Culture-Independent Method for Rapid and Selective Quantification of Viable Legionella pneumophila Cells in Environmental Water Samples▿

PubMed Central

Delgado-Viscogliosi, Pilar; Solignac, Lydie; Delattre, Jean-Marie

2009-01-01

PCR-based methods have been developed to rapidly screen for Legionella pneumophila in water as an alternative to time-consuming culture techniques. However, these methods fail to discriminate between live and dead bacteria. Here, we report a viability assay (viability PCR [v-PCR]) for L. pneumophila that combines ethidium monoazide bromide with quantitative real-time PCR (qPCR). The ability of v-PCR to differentiate viable from nonviable L. pneumophila cells was confirmed with permeabilizing agents, toluene, or isopropanol. v-PCR suppressed more than 99.9% of the L. pneumophila PCR signal in nonviable cultures and was able to discriminate viable cells in mixed samples. A wide range of physiological states, from culturable to dead cells, was observed with 64 domestic hot-water samples after simultaneous quantification of L. pneumophila cells by v-PCR, conventional qPCR, and culture methods. v-PCR counts were equal to or higher than those obtained by culture and lower than or equal to conventional qPCR counts. v-PCR was used to successfully monitor in vitro the disinfection efficacy of heating to 70°C and glutaraldehyde and chlorine curative treatments. The v-PCR method appears to be a promising and rapid technique for enumerating L. pneumophila bacteria in water and, in comparison with conventional qPCR techniques used to monitor Legionella, has the advantage of selectively amplifying only viable cells. PMID:19363080

A new retrospective, multi-evidence veterinary drug screening method using drift tube ion mobility mass spectrometry.

PubMed

Xu, Zhenzhen; Li, Jianzhong; Chen, Ailiang; Ma, Xin; Yang, Shuming

2018-05-03

The retrospectivity (the ability to retrospect to a previously unknown compound in raw data) is very meaningful for food safety and risk assessment when facing new emerging drugs. Accurate mass and retention time based screening may lead false positive and false negative results so new retrospective, reliable platform is desirable. Different concentration levels of standards with and without matrix were analyzed using ion mobility (IM)-quadrupole-time-of-flight (Q-TOF) for collecting retrospective accurate mass, retention time, drift time and tandem MS evidence for identification in a single experiment. The isomer separation ability of IM and the four-dimensional (4D) feature abundance quantification abilities were evaluated for veterinary drugs for the first time. The sensitivity of the IM-Q-TOF workflow was obviously higher than that of the traditional database searching algorithm [find by formula (FbF) function] for Q-TOF. In addition, the IM-Q-TOF workflow contained most of the results from FbF and removed the false positive results. Some isomers were separated by IM and the 4D feature abundance quantitation removed interference with similar accurate mass and showed good linearity. A new retrospective, multi-evidence platform was built for veterinary drug screening in a single experiment. The sensitivity was significantly improved and the data can be used for quantification. The platform showed its potential to be used for food safety and risk assessment. This article is protected by copyright. All rights reserved.

Development and characterization of a synthetic DNA, NUversa, to be used as a standard in quantitative polymerase chain reactions for molecular pneumococcal serotyping.

PubMed

Sakai, Fuminori; Sonaty, Griffin; Watson, David; Klugman, Keith P; Vidal, Jorge E

2017-09-15

Identification of Streptococcus pneumoniae and its more than 90 serotypes is routinely conducted by culture and Quellung reactions. Quantitative polymerase chain reactions (qPCRs) have been developed for molecular detection, including a pan-pneumococcus lytA assay, and assays targeting 79 serotypes. Reactions require genomic DNA from every target to prepare standards, which can be time consuming. In this study, we have developed a synthetic DNA molecule as a surrogate for genomic DNA and present new single-plex qPCR reactions to increase molecular detection to 94 pneumococcal serotypes. Specificity of these new reactions was confirmed with a limit of detection between 2 and 20 genome equivalents/reaction. A synthetic DNA (NUversa, ∼8.2 kb) was then engineered to contain all available qPCR targets for serotyping and lytA. NUversa was cloned into pUC57-Amp-modified to generate pNUversa (∼10.2 kb). Standards prepared from pNUversa and NUversa were compared against standards made out of genomic DNA. Linearity [NUversa (R2 > 0.982); pNUversa (R2 > 0.991)] and efficiency of qPCR reactions were similar to those utilizing chromosomal DNA (R2 > 0.981). Quantification with plasmid pNUversa was affected, however, whereas quantification with synthetic NUversa was comparable to that of genomic DNA. Therefore, NUversa may be utilized as DNA standard in single-plex assays of the currently known 94 pneumococcal serotypes. © FEMS 2017.

Determination of eight nitrosamines in water at the ng L(-1) levels by liquid chromatography coupled to atmospheric pressure chemical ionization tandem mass spectrometry.

PubMed

Ripollés, Cristina; Pitarch, Elena; Sancho, Juan V; López, Francisco J; Hernández, Félix

2011-09-19

In this work, we have developed a sensitive method for detection and quantification of eight N-nitrosamines, N-nitrosodimethylamine (NDMA), N-nitrosomorpholine (NMor), N-nitrosomethylethylamine (NMEA), N-nitrosopirrolidine (NPyr), N-nitrosodiethylamine (NDEA), N-nitrosopiperidine (NPip), N-nitroso-n-dipropylamine (NDPA) and N-nitrosodi-n-butylamine (NDBA) in drinking water. The method is based on liquid chromatography coupled to tandem mass spectrometry, using atmospheric pressure chemical ionization (APCI) in positive mode with a triple quadrupole analyzer (QqQ). The simultaneous acquisition of two MS/MS transitions in selected reaction monitoring mode (SRM) for each compound, together with the evaluation of their relative intensity, allowed the simultaneous quantification and reliable identification in water at ppt levels. Empirical formula of the product ions selected was confirmed by UHPLC-(Q)TOF MS accurate mass measurements from reference standards. Prior to LC-MS/MS QqQ analysis, a preconcentration step by off-line SPE using coconut charcoal EPA 521 cartridges (by passing 500 mL of water sample) was necessary to improve the sensitivity and to meet regulation requirements. For accurate quantification, two isotope labelled nitrosamines (NDMA-d(6) and NDPA-d(14)) were added as surrogate internal standards to the samples. The optimized method was validated at two concentration levels (10 and 100 ng L(-1)) in drinking water samples, obtaining satisfactory recoveries (between 90 and 120%) and precision (RSD<20%). Limits of detection were found to be in the range of 1-8 ng L(-1). The described methodology has been applied to different types of water samples: chlorinated from drinking water and wastewater treatment plants (DWTP and WWTP, respectively), wastewaters subjected to ozonation and tap waters. Copyright © 2011 Elsevier B.V. All rights reserved.

Commissioning of the 112 MHz SRF Gun and 500 MHz bunching cavities for the CeC PoP Linac

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belomestnykh, S.; Ben-Zvi, I.; Brutus, J. C.

The Coherent electron Cooling Proof-of-Principle (CeC PoP) experiment at BNL includes a short electron linac. During Phase 1, a 112 MHz superconducting RF photo-emission gun and two 500 MHz normal conducting bunching cavities were installed and are under commissioning. The paper describes the Phase1 linac layout and presents commissioning results for the cavities and associated RF, cryogenic and other sub-systems

Reforming the Military Health Care System

DTIC Science & Technology

1988-01-01

Population Model and its Application ," International Journal of Health Services, vol. 10, no. 4 (1980). 7. "Understanding Variations in the Use of... Financial Management (November 1986), pp. 26- 34. 21. Based on the following multiple regression equation: OP/NOR= 0.51 + 0.35x(POP/NOR)-6.84x(CIV/NORxPOP) (t...Military Beneficiary Health Care Survey 95 B Actual and Expected Admission Rates 99 C The Statistical Model of Family Use 103 D The Capitation Budgeting

Proof-of-principle contraband detection system for nonintrusive inspection

NASA Astrophysics Data System (ADS)

Sredniawski, Joseph J.; Debiak, T.; Kamykowski, E.; Rathke, John E.; Schmor, P.; Milton, Bill; Stanford, G.; Rogers, Joel; Boyd, J.; Brondo, J.

1997-02-01

A proof-of-principle (POP) contraband detection system (CDS), is under construction at Northrop Grumman's Advanced Technology and Development Center. We employ gamma resonance absorption to detect nitrogen or chlorine in explosives and certain forms of illegal drugs. Using tomography, 3D images of the total density and selected element density are generated. These characteristics together may be utilized with considerable confidence in determining if contraband is present in baggage or cargo. The CDS employs a high current DC electrostatic accelerator that provides a beam of proton sat either 1.75 or 1.89 MeV. These high energy particles impinge upon a target coated with 13C or 34S. The resultant resonant gamma rays are preferentially absorbed in either 14N or 35Cl. Because of the penetrating power of the gamma rays, this approach can be utilized for inspection of fully loaded aircraft containers such as the LD3. With proper design for handling baggage and with certain CDS design features not present in the POP, throughputs approaching 2000 bags/hour are estimated. Furthermore, the technology being developed for the CDS accelerator may have other applications such as for Boron Neutron Capture Therapy or Neutron Radiography. Our current program calls for testing of the POP CDS by late 1996. This paper presents the overall design, and characteristics of the CDS POP and the status of the program.

Molecular diagnostic toolkit for Rhizophagus irregularis isolate DAOM-197198 using quantitative PCR assay targeting the mitochondrial genome.

PubMed

Badri, Amine; Stefani, Franck O P; Lachance, Geneviève; Roy-Arcand, Line; Beaudet, Denis; Vialle, Agathe; Hijri, Mohamed

2016-10-01

Rhizophagus irregularis (previously named Glomus irregulare) is one of the most widespread and common arbuscular mycorrhizal fungal (AMF) species. It has been recovered worldwide in agricultural and natural soils, and the isolate DAOM-197198 has been utilized as a commercial inoculant for two decades. Despite the ecological and economical importance of this taxon, specific markers for quantification of propagules by quantitative real-time PCR (qPCR) are extremely limited and none have been rigorously validated for quality control of manufactured products such as biofertilizers. From the sequencing of 14 complete AMF mitochondrial (mt) genomes, a qPCR assay using a hydrolysis probe designed in the single copy cox3-rnl intergenic region was tested and validated to specifically and accurately quantify the spores of R. irregularis isolate DAOM-197198. Specificity tests were performed using standard PCR and qPCR, and results clearly showed that the primers specifically amplified the isolate DAOM-197198, yielding a PCR product of 106 bp. According to the qPCR analyses on spores produced in vitro, the average copy number of mt genomes per spore was 3172 ± 304 SE (n = 6). Quantification assays were successfully undertaken on known and unknown samples in liquid suspensions and commercial dry formulations to show the accuracy, precision, robustness, and reproducibility of the qPCR assay. This study provides a powerful molecular toolkit specifically designed to quantify spores of the model AMF isolate DAOM-197198. The approach of molecular toolkit used in our study could be applied to other AMF taxa and will be useful to research institutions and governmental and industrial laboratories running routine quality control of AMF-based products.

A Novel Triplex Quantitative PCR Strategy for Quantification of Toxigenic and Nontoxigenic Vibrio cholerae in Aquatic Environments

PubMed Central

Bliem, Rupert; Schauer, Sonja; Plicka, Helga; Obwaller, Adelheid; Sommer, Regina; Steinrigl, Adolf; Alam, Munirul; Reischer, Georg H.; Farnleitner, Andreas H.

2015-01-01

Vibrio cholerae is a severe human pathogen and a frequent member of aquatic ecosystems. Quantification of V. cholerae in environmental water samples is therefore fundamental for ecological studies and health risk assessment. Beside time-consuming cultivation techniques, quantitative PCR (qPCR) has the potential to provide reliable quantitative data and offers the opportunity to quantify multiple targets simultaneously. A novel triplex qPCR strategy was developed in order to simultaneously quantify toxigenic and nontoxigenic V. cholerae in environmental water samples. To obtain quality-controlled PCR results, an internal amplification control was included. The qPCR assay was specific, highly sensitive, and quantitative across the tested 5-log dynamic range down to a method detection limit of 5 copies per reaction. Repeatability and reproducibility were high for all three tested target genes. For environmental application, global DNA recovery (GR) rates were assessed for drinking water, river water, and water from different lakes. GR rates ranged from 1.6% to 76.4% and were dependent on the environmental background. Uncorrected and GR-corrected V. cholerae abundances were determined in two lakes with extremely high turbidity. Uncorrected abundances ranged from 4.6 × 102 to 2.3 × 104 cell equivalents liter−1, whereas GR-corrected abundances ranged from 4.7 × 103 to 1.6 × 106 cell equivalents liter−1. GR-corrected qPCR results were in good agreement with an independent cell-based direct detection method but were up to 1.6 log higher than cultivation-based abundances. We recommend the newly developed triplex qPCR strategy as a powerful tool to simultaneously quantify toxigenic and nontoxigenic V. cholerae in various aquatic environments for ecological studies as well as for risk assessment programs. PMID:25724966

An Improved Quantitative Real-Time PCR Assay for the Enumeration of Heterosigma akashiwo (Raphidophyceae) Cysts Using a DNA Debris Removal Method and a Cyst-Based Standard Curve.

PubMed

Kim, Joo-Hwan; Kim, Jin Ho; Wang, Pengbin; Park, Bum Soo; Han, Myung-Soo

2016-01-01

The identification and quantification of Heterosigma akashiwo cysts in sediments by light microscopy can be difficult due to the small size and morphology of the cysts, which are often indistinguishable from those of other types of algae. Quantitative real-time PCR (qPCR) based assays represent a potentially efficient method for quantifying the abundance of H. akashiwo cysts, although standard curves must be based on cyst DNA rather than on vegetative cell DNA due to differences in gene copy number and DNA extraction yield between these two cell types. Furthermore, qPCR on sediment samples can be complicated by the presence of extracellular DNA debris. To solve these problems, we constructed a cyst-based standard curve and developed a simple method for removing DNA debris from sediment samples. This cyst-based standard curve was compared with a standard curve based on vegetative cells, as vegetative cells may have twice the gene copy number of cysts. To remove DNA debris from the sediment, we developed a simple method involving dilution with distilled water and heating at 75°C. A total of 18 sediment samples were used to evaluate this method. Cyst abundance determined using the qPCR assay without DNA debris removal yielded results up to 51-fold greater than with direct counting. By contrast, a highly significant correlation was observed between cyst abundance determined by direct counting and the qPCR assay in conjunction with DNA debris removal (r2 = 0.72, slope = 1.07, p < 0.001). Therefore, this improved qPCR method should be a powerful tool for the accurate quantification of H. akashiwo cysts in sediment samples.

Development of a multiplex qPCR in real time for quantification and differential diagnosis of Salmonella Gallinarum and Salmonella Pullorum.

PubMed

Rubio, Marcela da Silva; Penha Filho, Rafael Antonio Casarin; Almeida, Adriana Maria de; Berchieri, Angelo

2017-12-01

Currently there are 2659 Salmonella serovars. The host-specific biovars Salmonella Pullorum and Salmonella Gallinarum cause systemic infections in food-producing and wild birds. Fast diagnosis is crucial to control the dissemination in avian environments. The present work describes the development of a multiplex qPCR in real time using a low-cost DNA dye (SYBr Green) to identify and quantify these biovars. Primers were chosen based on genomic regions of difference (RoD) and optimized to control dimers. Primers pSGP detect both host-specific biovars but not other serovars and pSG and pSP differentiate biovars. Three amplicons showed different melting temperatures (Tm), allowing differentiation. The pSGP amplicon (97 bp) showed Tm of 78°C for both biovars. The pSG amplicon (273 bp) showed a Tm of 86.2°C for S. Gallinarum and pSP amplicon (260 bp) dissociated at 84.8°C for S. Pullorum identification. The multiplex qPCR in real time showed high sensitivity and was capable of quantifying 10 8 -10 1 CFU of these biovars.

Testing normative and self-appraisal feedback in an online slot-machine pop-up in a real-world setting

PubMed Central

Auer, Michael M.; Griffiths, Mark D.

2015-01-01

Over the last few years, there have been an increasing number of gaming operators that have incorporated on-screen pop-up messages while gamblers play on slot machines and/or online as one of a range of tools to help encourage responsible gambling. Coupled with this, there has also been an increase in empirical research into whether such pop-up messages are effective, particularly in laboratory settings. However, very few studies have been conducted on the utility of pop-up messages in real-world gambling settings. The present study investigated the effects of normative and self-appraisal feedback in a slot machine pop-up message compared to a simple (non-enhanced) pop-up message. The study was conducted in a real-world gambling environment by comparing the behavioral tracking data of two representative random samples of 800,000 gambling sessions (i.e., 1.6 million sessions in total) across two conditions (i.e., simple pop-up message versus an enhanced pop-up message). The results indicated that the additional normative and self-appraisal content doubled the number of gamblers who stopped playing after they received the enhanced pop-up message (1.39%) compared to the simple pop-up message (0.67%). The data suggest that pop-up messages influence only a small number of gamblers to cease long playing sessions and that enhanced messages are slightly more effective in helping gamblers to stop playing in-session. PMID:25852630

The relationship between surface temperature, tissue temperature, microbubble formation, and steam pops.

PubMed

Thompson, Nathaniel; Lustgarten, Daniel; Mason, Bryan; Mueller, Enkhtuyaa; Calame, James; Bell, Stephen; Spector, Peter

2009-07-01

It has been proposed that microbubble (MB) monitoring can be used to safely titrate radiofrequency (RF) power. However, MB formation has been found to be an insensitive indicator of tissue temperature during RF delivery. We hypothesized that MB formation corresponds to surface-not tissue--temperature, and therefore would be an insensitive predictor of steam pops. An in vitro bovine heart model was used to measure surface and tissue temperatures during RF delivery under conditions designed to cause steam pops. Sensitivity of type II MB (MBII) formation as a predictor of steam pops and for surface temperatures more than 80 degrees C was calculated. Of 105 lesions delivered, 99 steam pops occurred. Twenty-one steam pops were preceded by MBII. MBII were seen in 26 lesions, five of which were not associated with steam pop. Surface temperature at onset of MBII was 87 +/- 9 degrees C versus a tissue temperature of 78 +/- 23 degrees C (P = 0.044). Surface temperature at the time of steam pops was 71 +/- 17 degrees C versus a tissue temperature of 102 +/- 17 degrees C (P < 0.0001). The sensitivity of MBII for steam pops was 21%, and 58% for detecting surface temperature in excess of 80 degrees C. MBII correlated better with surface temperature than with tissue temperature; steam pops, on the other hand, correlated better with tissue temperature. MBII was an insensitive marker of steam pops and surface temperature in excess of 80 degrees C. Therefore, MBII should not be used to titrate RF power.

Alteration of apoptosis-related genes in postmenopausal women with uterine prolapse.

PubMed

Saatli, Bahadir; Kizildag, Sefa; Cagliyan, Erkan; Dogan, Erbil; Saygili, Ugur

2014-07-01

We aimed to compare expression levels of antiapoptotic and proapoptotic genes in parametrial and vaginal tissues from postmenopausal women with and without pelvic organ prolapse (POP). We hypothesized that the expression of genes that induce apoptosis may be altered in vaginal and parametrial tissues in postmenopausal women with POP. Samples of vaginal and parametrial tissues were obtained from postmenopausal women with (n = 10) and without (n = 10) POP who underwent vaginal or abdominal hysterectomy. Expression levels of antiapoptotic (BCL-2, BCL-XL) and proapoptotic (BAX, BAD) genes were studied by real-time reverse-transcription polymerase chain reaction (RT-PCR). Gene expression levels of BCL-2 (P < 0.001), BCL-XL (P < 0.001), BAX (p = 0.001), and BAD (p = 0.004) were all higher in vaginal tissues from the POP group compared with the non-POP group. Similarly, gene expression levels of BCL-2 (p < 0.001), BCL-XL (p < 0.001), BAX (p < 0.001), and BAD (p < 0.001) in parametrial tissues were also significantly higher in the POP group compared with the non-POP group. Additionally, expression levels of BCL-2 (p = 0.05), BCL-XL (p < 0.05), BAX (p = 0.05), and BAD (p = 0.07) in the POP group were higher in parametrial tissue than in vaginal tissue samples. Antiapoptotic and proapoptotic gene expression levels differed significantly between postmenopausal women with and without POP. Bcl-2 family genes were overexpressed in the parametrium of patients with POP compared with vaginal tissue, suggesting that the processes responsible for POP have a greater effect on parametrial tissue than vaginal tissue during the development of POP.

Trocar-guided trans-vaginal mesh surgery for pelvic organ prolapse: effects on urinary continence and anatomical and functional outcomes. A prospective observational study.

PubMed

Natale, F; Costantini, E; La Penna, C; Illiano, E; Balsamo, R; Carbone, A; Cervigni, M

2017-03-01

Primary objective of this study was to assess the effects of trocar-guided transvaginal mesh surgery (TVM) on cure and prevention rates for incontinence, without concomitant surgery for Stress Urinary Incontinence (SUI). Our secondary objectives were anatomical outcomes, relief of symptoms and effect on quality of life (QoL). This prospective observational study evaluated women who underwent TVM for symptomatic stage >2 Pelvic Organ Prolapse (POP). SUI was evaluated objectively using the cough stress test with prolapse reduced. SUI and urge urinary incontinence (UUI) were subjectively evaluated using ICIQ-SF. Anatomical cure was defined as stage <2 at POP-Q. McNemar chi-square test; paired t-test; Mann-Whitney test. Seventy-two patients reached final evaluation (mean follow-up 72 months). In the 40 pre-op continent patients, 34 (85%) remained continent postoperatively and 6 (15%) showed de novo SUI. Only 1 patient chose to undergo subsequent TVT. The number needed to treat was 6 to prevent 1 women developing de novo objective SUI and 39 to prevent 1 woman having to undergo SUI surgery. In the 32 pre-op incontinent patients, 18 (56.3%) became continent postoperatively. Only 1 patient chose to undergo subsequent TVT. UUI was present in 44 patients pre-operatively and 15 (20.8%) post-operatively (1 de novo). Forty-four patients (61.1%) were continent post-operatively for SUI and UUI. We observed a significant improvement in storage, voiding, post-micturition and prolapse-related symptoms. The anatomical cure rate was 87.5% for the anterior compartment and 90.3%.for the apical segment. The apical recurrence was 8.3% in the patients previously hysterectomised, 18.8% in the patients with uterus preservation and 0% in the patients with concomitant hysterectomy. QoL scores improved in all domains except sleep and personal relationships. We observed mesh exposure in 10 patients (13.9%), in 5 of whom it was associated with a concomitant hysterectomy CONCLUSIONS: TVM showed excellent results in terms of continence and can be performed without contemporary anti-incontinence surgery, for both continent and incontinent women. Patients should have pre-operative counselling before POP surgery. For severe uterine prolapse the Perigee™ System should be employed with concomitant hysterectomy because uterus preservation is associated with significantly higher apical recurrence rates. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Point-of-purchase health information encourages customers to purchase vegetables: objective analysis by using a point-of-sales system.

PubMed

Ogawa, Yoshiko; Tanabe, Naohito; Honda, Akiko; Azuma, Tomoko; Seki, Nao; Suzuki, Tsubasa; Suzuki, Hiroshi

2011-07-01

Point-of-purchase (POP) information at food stores could help promote healthy dietary habits. However, it has been difficult to evaluate the effects of such intervention on customers' behavior. We objectively evaluated the usefulness of POP health information for vegetables in the modification of customers' purchasing behavior by using the database of a point-of-sales (POS) system. Two supermarket stores belonging to the same chain were assigned as the intervention store (store I) and control store (store C). POP health information for vegetables was presented in store I for 60 days. The percent increase in daily sales of vegetables over the sales on the same date of the previous year was compared between the stores by using the database of the POS system, adjusting for the change in monthly visitors from the previous year (adjusted ∆sales). The adjusted ∆sales significantly increased during the intervention period (Spearman's ρ = 0.258, P for trend = 0.006) at store I but did not increase at store C (ρ = -0.037, P for trend = 0.728). The growth of the mean adjusted ∆sales of total vegetables from 30 days before the intervention period through the latter half of the intervention period was estimated to be greater at store I than at store C by 18.7 percentage points (95% confidence interval 1.6-35.9). Health-related POP information for vegetables in supermarkets can encourage customers to purchase and, probably, consume vegetables.

USEPA Approach for the Detection and Quantification of Enterococcus by qPCR

EPA Science Inventory

The Beach Act 2000 specified that EPA should develop: Appropriate and effective indicators for improviding detection in a timely manner of pathogens in coastal waters Appropriate, accurate, expeditious and cost-effective methods for the timely detection of pathogens in coas...

Side effects unrelated to disease activity and acceptability of highly effective contraceptive methods in women with systemic lupus erythematosus: a randomized, clinical trial.

PubMed

Cravioto, María-del-Carmen; Jiménez-Santana, Luisa; Mayorga, Julio; Seuc, Armando H

2014-08-01

To assess the side effects unrelated to disease activity and the acceptability of combined oral contraceptives (COCs), progestin-only pills (POPs) and copper-releasing intrauterine devices (IUDs) in women with systemic lupus erythematosus (SLE). A randomized clinical trial including 162 women with SLE, assigned to COC (n=54), POP (n=54) or IUD (n=54). Follow-up visits were conducted after 1, 2, 3, 6, 9 and 12 months of treatment to monitor the presence of symptoms, changes in body weight and blood pressure as well as the development of health problems other than those relating to lupus. Reasons for discontinuation and satisfaction with the use of the assigned method were recorded at the end of treatment. Statistical analysis included descriptive statistics, repeated measure analyses and Kaplan-Meier curves. Significantly different discontinuation rates due to any reason [35%, 55%, 29% (p<0.01)] or nonmedical reasons [(11%, 31%, 4% (p<0.05)] were observed among the COC, POP and IUD groups. Nausea was most frequent among COC users, dysmenorrhea among IUD users and acne and hirsutism among POP users. Mean blood pressures remained unchanged. Mild increases in body weight were observed over time in all treatment groups. Most women were satisfied with the use of the assigned contraceptive method. Oral contraceptives and IUD are acceptable birth control methods for patients with lupus, when counseling and specialized health attention are provided; however, the acceptability of POP appears to be inferior. Side effects unrelated to lupus disease activity are not frequent reasons to discontinue the contraceptive methods. This study delves into an area that has not been explored among patients with lupus. Our findings on the associated side effects and reasons for discontinuing COCs, POPs or copper-bearing IUDs may be useful in improving contraceptive counseling for women with lupus. Furthermore, they also heighten our knowledge on the reasons that may preclude the widespread use of effective contraceptives among lupus patients. Copyright © 2014. Published by Elsevier Inc.

Absolute quantification of olive oil DNA by droplet digital-PCR (ddPCR): Comparison of isolation and amplification methodologies.

PubMed

Scollo, Francesco; Egea, Leticia A; Gentile, Alessandra; La Malfa, Stefano; Dorado, Gabriel; Hernandez, Pilar

2016-12-15

Olive oil is considered a premium product for its nutritional value and health benefits, and the ability to define its origin and varietal composition is a key step towards ensuring the traceability of the product. However, isolating the DNA from such a matrix is a difficult task. In this study, the quality and quantity of olive oil DNA, isolated using four different DNA isolation protocols, was evaluated using the qRT-PCR and ddPCR techniques. The results indicate that CTAB-based extraction methods were the best for unfiltered oil, while Nucleo Spin-based extraction protocols showed greater overall reproducibility. The use of both qRT-PCR and ddPCR led to the absolute quantification of the DNA copy number. The results clearly demonstrate the importance of the choice of DNA-isolation protocol, which should take into consideration the qualitative aspects of DNA and the evaluation of the amplified DNA copy number. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Next-Generation PCR-Based Quantification Method for Ambient Waters: Digital PCR.

PubMed

Cao, Yiping; Griffith, John F; Weisberg, Stephen B

2016-01-01

Real-time quantitative PCR (qPCR) is increasingly being used for ambient water monitoring, but development of digital polymerase chain reaction (digital PCR) has the potential to further advance the use of molecular techniques in such applications. Digital PCR refines qPCR by partitioning the sample into thousands to millions of miniature reactions that are examined individually for binary endpoint results, with DNA density calculated from the fraction of positives using Poisson statistics. This direct quantification removes the need for standard curves, eliminating the labor and materials associated with creating and running standards with each batch, and removing biases associated with standard variability and mismatching amplification efficiency between standards and samples. Confining reactions and binary endpoint measurements to small partitions also leads to other performance advantages, including reduced susceptibility to inhibition, increased repeatability and reproducibility, and increased capacity to measure multiple targets in one analysis. As such, digital PCR is well suited for ambient water monitoring applications and is particularly advantageous as molecular methods move toward autonomous field application.

Fluorescence acquisition during hybridization phase in quantitative real-time PCR improves specificity and signal-to-noise ratio.

PubMed

Mehndiratta, Mohit; Palanichamy, Jayanth Kumar; Ramalingam, Pradeep; Pal, Arnab; Das, Prerna; Sinha, Subrata; Chattopadhyay, Parthaprasad

2008-12-01

Quantitative real-time PCR (qPCR) is a standard method used for quantification of specific gene expression. This utilizes either dsDNA binding dyes or probe based chemistry. While dsDNA binding dyes have the advantage of low cost and flexibility, fluorescence due to primer dimers also interferes with the fluorescence of the specific product. Sometimes it is difficult, if not impossible, to standardize conditions and redesign primers in such a way that only specific fluorescence of the products of test and reference genes are acquired. Normally, the fluorescence acquisition in qPCR using dsDNA binding dyes is done during the melting phase of the PCR at a temperature between the melting points of primer dimers and the specific product. We have modified the protocol to acquire fluorescence during the hybridization phase. This significantly increased the signal-to-noise ratio and enabled the use of dsDNA binding dyes for mRNA quantification in situations where it was not possible when measurement was done in the melting phase. We have demonstrated it for three mRNAs, E6, E7, and DNMT1 with beta-actin as the reference gene, and for two miRNAs. This modification broadens the scope of qPCR using dsDNA binding dyes.

Comparison of the QuantiGene 2.0 Assay and Real-Time RT-PCR in the Detection of p53 Isoform mRNA Expression in Formalin-Fixed Paraffin-Embedded Tissues- A Preliminary Study

PubMed Central

Morten, Brianna C.; Scott, Rodney J.; Avery-Kiejda, Kelly A.

2016-01-01

p53 is expressed as multiple smaller isoforms whose functions in cancer are not well understood. The p53 isoforms demonstrate abnormal expression in different cancers, suggesting they are important in modulating the function of full-length p53 (FLp53). The quantification of relative mRNA expression has routinely been performed using real-time PCR (qPCR). However, there are serious limitations when detecting p53 isoforms using this method, particularly for formalin-fixed paraffin-embedded (FFPE) tissues. The use of FFPE tumours would be advantageous to correlate expression of p53 isoforms with important clinical features of cancer. One alternative method of RNA detection is the hybridization-based QuantiGene 2.0 Assay, which has been shown to be advantageous for the detection of RNA from FFPE tissues. In this pilot study, we compared the QuantiGene 2.0 Assay to qPCR for the detection of FLp53 and its isoform Δ40p53 in matched fresh frozen (FF) and FFPE breast tumours. FLp53 mRNA expression was detected using qPCR in FF and FFPE tissues, but Δ40p53 mRNA was only detectable in FF tissues. Similar results were obtained for the QuantiGene 2.0 Assay. FLp53 relative mRNA expression was shown to be strongly correlated between the two methods (R2 = 0.9927, p = 0.0031) in FF tissues, however Δ40p53 was not (R2 = 0.4429, p = 0.3345). When comparing the different methods for the detection of FLp53 mRNA from FFPE and FF samples, no correlation (R2 = 0.0002, p = 0.9863) was shown using the QuantiGene 2.0 Assay, and in contrast, the level of expression was highly correlated between the two tissues using qPCR (R2 = 0.8753, p = 0.0644). These results suggest that both the QuantiGene 2.0 Assay and qPCR methods are inadequate for the quantification of Δ40p53 mRNA in FFPE tissues. Therefore, alternative methods of RNA detection and quantification are required to study the relative expression of Δ40p53 in FFPE samples. PMID:27832134

Transplacental transfer of persistent organic pollutants in La Plata dolphins (Pontoporia blainvillei; Cetartiodactyla, Pontoporiidae).

PubMed

Barbosa, Ana Paula Moreno; Méndez-Fernandez, Paula; Dias, Patrick Simões; Santos, Marcos César Oliveira; Taniguchi, Satie; Montone, Rosalinda Carmela

2018-08-01

Persistent organic pollutants (POPs) accumulate in the fat tissue of living organisms and are found in relatively high concentrations in animals at the top of the food chain, such as dolphins. The ability of these compounds to interact with the endocrine system of marine mammals constitutes a risk for the reproduction and conservation of species. The La Plata dolphin, Pontoporia blainvillei, is exclusive to the southwestern Atlantic Ocean and is classified on the IUCN red list as a vulnerable species. Blubber, liver, kidney and muscle samples from four P. blainvillei mother-fetus pairs were analyzed to evaluate the transfer of POPs to fetal tissues through the placenta. The presence of POPs in fetal tissues indicates the maternal transfer of compounds. In the pregnant females, blubber was the tissue with POP highest concentration, followed by the liver, kidneys and muscles. In the fetuses, POP accumulation mainly occurred in the blubber followed by the muscles, liver and kidneys. Polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDTs) were found in all tissues analyzed and had the highest concentrations among all compounds. The main PCB congeners in the fetal samples had five to seven chlorine atoms. The only polybrominated diphenyl ether (PBDE) in the fetal samples was 47 and was found only in blubber. The main DDT metabolite in the fetuses was p,p'-DDE. POP transfer via the placenta occurs in the first months of gestation and increases with fetal development, according to fetus/mother (F/M) ratio: HCB>DDT>PCB>PBDE>Mirex, which may follow the order of the octanol/water partition coefficient (K ow ) values. Copyright © 2018 Elsevier B.V. All rights reserved.

Design of primers and probes for quantitative real-time PCR methods.

PubMed

Rodríguez, Alicia; Rodríguez, Mar; Córdoba, Juan J; Andrade, María J

2015-01-01

Design of primers and probes is one of the most crucial factors affecting the success and quality of quantitative real-time PCR (qPCR) analyses, since an accurate and reliable quantification depends on using efficient primers and probes. Design of primers and probes should meet several criteria to find potential primers and probes for specific qPCR assays. The formation of primer-dimers and other non-specific products should be avoided or reduced. This factor is especially important when designing primers for SYBR(®) Green protocols but also in designing probes to ensure specificity of the developed qPCR protocol. To design primers and probes for qPCR, multiple software programs and websites are available being numerous of them free. These tools often consider the default requirements for primers and probes, although new research advances in primer and probe design should be progressively added to different algorithm programs. After a proper design, a precise validation of the primers and probes is necessary. Specific consideration should be taken into account when designing primers and probes for multiplex qPCR and reverse transcription qPCR (RT-qPCR). This chapter provides guidelines for the design of suitable primers and probes and their subsequent validation through the development of singlex qPCR, multiplex qPCR, and RT-qPCR protocols.

A common base method for analysis of qPCR data and the application of simple blocking in qPCR experiments.

PubMed

Ganger, Michael T; Dietz, Geoffrey D; Ewing, Sarah J

2017-12-01

qPCR has established itself as the technique of choice for the quantification of gene expression. Procedures for conducting qPCR have received significant attention; however, more rigorous approaches to the statistical analysis of qPCR data are needed. Here we develop a mathematical model, termed the Common Base Method, for analysis of qPCR data based on threshold cycle values (C q ) and efficiencies of reactions (E). The Common Base Method keeps all calculations in the logscale as long as possible by working with log 10 (E) ∙ C q , which we call the efficiency-weighted C q value; subsequent statistical analyses are then applied in the logscale. We show how efficiency-weighted C q values may be analyzed using a simple paired or unpaired experimental design and develop blocking methods to help reduce unexplained variation. The Common Base Method has several advantages. It allows for the incorporation of well-specific efficiencies and multiple reference genes. The method does not necessitate the pairing of samples that must be performed using traditional analysis methods in order to calculate relative expression ratios. Our method is also simple enough to be implemented in any spreadsheet or statistical software without additional scripts or proprietary components.

Self-rated health and chronic conditions are associated with blood concentrations of persistent organic pollutants in the general population of Catalonia, Spain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gasull, Magda; Pallarès, Natàlia; CIBER de Epidemiología y Salud Pública

Background: Self-rated health (SRH) is a powerful predictor of mortality, morbidity, and need for health services. SRH generally increases with educational level, and decreases with age, number of chronic conditions, and body mass index (BMI). Because human concentrations of most persistent organic pollutants (POPs) also vary by age, education, and BMI, and because of the physiological and clinical effects of POPs, we hypothesized that body concentrations of POPs are inversely associated with SRH. Objectives: To analyze the relation between serum concentrations of POPs and SRH in the general population of Catalonia, Spain, taking into account sociodemographic factors and BMI, asmore » well as chronic health conditions and mental disorders, measured by the General Health Questionnaire-12 (GHQ-12). Methods: POP serum concentrations were measured by gas chromatography with electron-capture detection in 919 participants of the Catalan Health Interview Survey. Results: Individuals with higher concentrations of POPs had significantly poorer SRH; e.g., the median concentration of HCB in subjects with poor SRH was twice as high as in subjects with excellent SRH (366 ng/g vs. 169 ng/g, respectively; p-value<0.001). In crude models and in models adjusted for sex and BMI, the POPs-SRH association was often dose-dependent, and the likelihood of poor or regular SRH was 2 to 4-times higher in subjects with POP concentrations in the top quartile. In models adjusted for age or for chronic conditions virtually all ORs were near unity. No associations were found between POP levels and GHQ-12. Conclusions: Individuals with higher concentrations of POPs had significantly poorer SRH, an association likely due to age and chronic conditions, but not to sex, education, social class, BMI, or mental disorders. - Highlights: • The relation between POPs and self-rated and mental health has seldom been studied. • Subjects with higher POP levels had poorer self-rated health (SRH) (dose-dependent). • The number of chronic conditions was positively related to POP levels. • The POPs-SRH association was likely due to age (or birth cohort), and to chronic conditions. • Causal or not, the fact is that people with poorer SRH often have higher levels of POPs.« less

A UPLC-ESI-Q-TOF method for rapid and reliable identification and quantification of major indole alkaloids in Catharanthus roseus.

PubMed

Jeong, Won Tae; Lim, Heung Bin

2018-03-30

We developed a novel ultra performance liquid chromatography-quadrupole time-of-flight (UPLC-Q-TOF) mass spectrometry method that allows sensitive, rapid, and reliable detection and identification of six representative indole alkaloids (vincristine, vinblastine, ajmalicine, catharanthine, serpentine, and vindoline) that exhibit physiological activity in Catharanthus roseus (C. roseus). The alkaloids were eluted on a C18 column with acetonitrile and water containing 0.1% formic acid and 10 mM ammonium acetate, and separated with good resolution within 13 min. Electrospray ionization-Q-TOF (ESI-Q-TOF) analysis was performed to characterize the molecules and their fragment ions, and the characteristic ions and fragmentation patterns were used as to identify the alkaloids. The proposed analytical method was verified in reference to the ICH guidelines and the results showed excellent linearity (R 2  > 0.9988), limit of detection (1 ng/mL to 10 ng/mL), limit of quantification (3 ng/mL to 30 ng/mL), intra-day and inter-day precisions, and extraction recovery rates (92.8% to 104.1%) for all components. The validated UPLC-Q-TOF method was applied to the analysis of extracts from the root, stem, and leaves of C. roseus, allowing the identification of six alkaloids by comparison of retention times, molecular ions, and fragmentation patterns with those of reference compounds. Sixteen additional indole alkaloids were tentatively identified by comparison of chromatograms to chemical databases and literature reports. The contents of bis-indole alkaloids (vincristine and vinblastine) were high in the aerial parts, while the contents of mono-indole alkaloids (ajmalicine, catharanthine, serpentine, and vindoline) were high in the roots. The present results demonstrate that the proposed UPLC-Q-TOF method can be useful for the investigation of phytochemical constituents of medicinal plants. Copyright © 2018 Elsevier B.V. All rights reserved.

Latitudinal exposure to DDTs, HCB, PCBs, PBDEs and DP in giant petrels (Macronectes spp.) across the Southern Ocean

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roscales, Jose L., E-mail: jlroscales@iqog.csic.es; González-Solís, Jacob; Zango, Laura

Studies on Persistent Organic Pollutants (POPs) in Antarctic wildlife are scarce, and usually limited to a single locality. As a result, wildlife exposure to POPs across the Southern Ocean is poorly understood. In this study, we report the differential exposure of the major southern ocean scavengers, the giant petrels, to POPs across a wide latitudinal gradient. Selected POPs (PCBs, HCB, DDTs, PBDEs) and related compounds, such as Dechlorane Plus (DP), were analyzed in plasma of southern giant petrels (Macronectes giganteus) breeding on Livingston (62°S 61°W, Antarctica), Marion (46°S 37°E, sub-Antarctic), and Gough (40°S 10°W, cool temperate) islands. Northern giant petrelsmore » (Macronectes halli) from Marion Island were also studied. Stable isotope ratios of C and N (δ{sup 13}C and δ{sup 15}N) were used as dietary tracers of the marine habitat and trophic level, respectively. Breeding locality was a major factor explaining petrel exposure to POPs compared with species and sex. Significant relationships between δ{sup 13}C values and POP burdens, at both inter- and intra-population levels, support latitudinal variations in feeding grounds as a key factor in explaining petrel pollutant burdens. Overall, pollutant levels in giant petrels decreased significantly with latitude, but the relative abundance (%) of the more volatile POPs increased towards Antarctica. DP was found at negligible levels compared with legacy POPs in Antarctic seabirds. Spatial POP patterns found in giant petrels match those predicted by global distribution models, and reinforce the hypothesis of atmospheric long-range transport as the main source of POPs in Antarctica. Our results confirm that wildlife movements out of the polar region markedly increase their exposure to POPs. Therefore, strategies for Antarctic wildlife conservation should consider spatial heterogeneity in exposure to marine pollution. Of particular relevance is the need to clarify the exposure of Antarctic predators to emerging contaminants that are not yet globally regulated. - Highlights: • Latitude of petrels' foraging areas explains their exposure to legacy and emerging POPs. • Spatial patterns of POPs in giant petrels across the Southern Ocean are congener-dependent. • Overall POP burdens in giant petrels decrease southwards across the Southern Ocean. • Latitudinal patterns of POP in giant petrels agree with global distribution models. • POP patterns in giant petrels suggest long-range transport as their main source.« less

The association between the brain and mind pops: a voxel-based morphometry study in 256 Chinese college students.

PubMed

Zhang, Lei; Li, Wenfu; Wei, Dongtao; Yang, Wenjing; Yang, Ning; Qiao, Lei; Qiu, Jiang; Zuo, Xi-Nian; Zhang, Qinglin

2016-06-01

Mind pops or involuntary semantic memories refer to words, phrases, images, or melodies that suddenly pop into one's mind without any deliberate attempt to recall them. Despite their prevalence in everyday life, research on mind pops has started only recently. Notably, mind pops are very similar to clinical involuntary phenomena such as hallucinations in schizophrenia, suggesting their potential role in pathology. The present study aimed to investigate the relationship between mind pops and the brain morphometry measured in 302 healthy young adults; after exclusions, 256 participants were included in our analyses. Specifically, the Mind Popping Questionnaire (MPQ) was employed to measure the degree of individual mind pops, whereas the Voxel-Based Morphometry (VBM) was used to compute the volumes of both gray and white matter tissues. Multiple regression analyses on MPQ and VBM metrics indicated that high-frequency mind pops were significantly associated with smaller gray matter volume in the left middle temporal gyrus as well as with larger gray and white matter volume in the right medial prefrontal cortex. This increase in mind pops is also linked to higher creativity and the personality trait of 'openness'. These data not only suggest a key role of the two regions in generating self-related thoughts, but also open a possible link between brain and creativity or personality.

Orexinergic system and pathophysiology of epilepsy.

PubMed

Doreulee, N; Alania, M; Vashalomidze, G; Skhirtladze, E; Kapanadze, Ts

2010-11-01

Neuropeptids orexins, also known as the hypocretins, are expressed in the lateral hypothalamus. Orexin-containing cells project widely throughout the brains, are crucial for the regulation of wakefulness and dysfunction of this system is associated with pathophysiology of narcolepsy-cataplexy. Orexin neurons play an important role in motivation, feeding and adaptive behaviors. Distribution of orexinergic receptors in the hippocampus tended to the ideas that orexins might be involved in the functions relating to the hippocampus. Effects of neuropeptide orexin-A on epileptiform activity in hippocampal slices were investigated. 500 µm thick hippocampal slices from 8-10 week-old rodents were used. Field excitatory postsynaptic potential (pop-fEPSP) and population spike in CA1 of hippocamopus were registered using standard protocol of in vitro electrophysiological experiments. Initial slope of the fEPSP and amplitude of II pop-spike were measured. Bursting neurons in CA3 were recorded in modified saline. We have found that orexin-A decreases duration/amplitude of multiple discharges of pop-spikes and inhibits spontaneous epileptiform afterdischarges induced by bicuculline methiodide in CA1. Orexin-A also modulates the frequency of discharges of bursting neurons in CA3. Our results suggest possible involvement of orexinergic system in antiepileptic action. Supported by ISTC Grant G-1318.

Isolation and Properties of Enterococcus hirae Mutants Defective in the Potassium/Proton Antiport System

PubMed Central

Kakinuma, Yoshimi; Igarashi, Kazuei

1999-01-01

A K+/H+ antiporter regulates cytoplasmic pH in Enterococcus hirae growing at alkaline pH. Mutants defective in this antiport activity were alkaline pH sensitive. One mutant, Pop1, lacked both K+/methylamine exchange at pH 9.5 and concomitant acidification of cytoplasmic pH. Pop1 grew well at pHs below 8 but did not at pHs above 9, conditions under which cytoplasmic pH was not fully acidified. PMID:10383981

Unique Signatures of Population III Stars in the Global 21-cm Signal

NASA Astrophysics Data System (ADS)

Mirocha, Jordan; Mebane, Richard H.; Furlanetto, Steven R.; Singal, Krishma; Trinh, Donald

2018-05-01

We investigate the effects of Population III stars on the sky-averaged 21-cm background radiation, which traces the collective emission from all sources of ultraviolet and X-ray photons before reionization is complete. While UV photons from Pop III stars can in principle shift the onset of radiative coupling of the 21-cm transition - and potentially reionization - to early times, we find that the remnants of Pop III stars are likely to have a more discernible impact on the 21-cm signal than Pop III stars themselves. The X-rays from such sources preferentially heat the IGM at early times, which elongates the epoch of reheating and results in a more gradual transition from an absorption signal to emission. This gradual heating gives rise to broad, asymmetric wings in the absorption signal, which stand in contrast to the relatively sharp, symmetric signals that arise in models treating Pop II sources only. A stronger signature of Pop III, in which the position of the absorption minimum becomes inconsistent with Pop II-only models, requires extreme star-forming events that may not be physically plausible, lending further credence to predictions of relatively high frequency absorption troughs, νmin ˜ 100 MHz. As a result, though the trough location alone may not be enough to indicate the presence of Pop III, the asymmetric wings should arise even if only a few Pop III stars form in each halo before the transition to Pop II star formation occurs, provided that the Pop III IMF is sufficiently top-heavy and at least some Pop III stars form in binaries.

The Yeast PUF Protein Puf5 Has Pop2-Independent Roles in Response to DNA Replication Stress

PubMed Central

Traven, Ana; Lo, Tricia L.; Lithgow, Trevor; Heierhorst, Jörg

2010-01-01

PUFs are RNA binding proteins that promote mRNA deadenylation and decay and inhibit translation. Yeast Puf5 is the prototype for studying PUF-dependent gene repression. Puf5 binds to the Pop2 subunit of the Ccr4-Pop2-NOT mRNA deadenylase, recruiting the deadenylase and associated translational repressors to mRNAs. Here we used yeast genetics to show that Puf5 has additional roles in vivo that do not require Pop2. Deletion of PUF5 caused increased sensitivity to DNA replication stress in cells lacking Pop2, as well as in cells mutated for two activities recruited to mRNAs by the Puf5-Pop2 interaction, the deadenylase Ccr4 and the translational repressor Dhh1. A functional Puf5 RNA binding domain was required, and Puf5 cytoplasmic localisation was sufficient for resistance to replication stress, indicating posttranscriptional gene expression control is involved. In contrast to DNA replication stress, in response to the cell wall integrity pathway activator caffeine, PUF5 and POP2 acted in the same genetic pathway, indicating that functions of Puf5 in the caffeine response are mediated by Pop2-dependent gene repression. Our results support a model in which Puf5 uses multiple, Pop2-dependent and Pop2-independent mechanisms to control mRNA expression. The Pop2-independent roles for Puf5 could involve spatial control of gene expression, a proposition supported by our data indicating that the active form of Puf5 is localised to cytoplasmic foci. PMID:20498834

Direct quantification of microRNA at low pM level in sera of glioma patients using a competitive hybridization followed by amplified voltammetric detection

PubMed Central

Wang, Jianxiu; Yi, Xinyao; Tang, Hailin; Han, Hongxing; Wu, Minghua; Zhou, Feimeng

2012-01-01

MicroRNAs (miRNAs), acting as oncogenes or tumor suppressors in humans, play a key role in regulating gene expression and are believed to be important for developing novel therapeutic treatments and clinical prognoses. Due to their short lengths (17–25 nucleotides) and extremely low concentrations (typically < pM) in biological samples, quantification of miRNAs has been challenging to conventional biochemical methods, such as Northern blotting, microarray, and quantitative polymerase chain reaction (qPCR). In this work, a biotinylated miRNA (biotin-miRNA) whose sequence is the same as that of a miRNA target is introduced into samples of interest and allowed to compete with the miRNA target for the oligonucleotide (ODN) probe preimmobilized onto an electrode. Voltammetric quantification of the miRNA target was accomplished after complexation of the biotin-miRNA with ferrocene (Fc)-capped gold nanoparticle/streptavidin conjugates. The Fc oxidation current was found to be inversely proportional to the concentration of target miRNA between 10 fM and 2.0 pM. The method is highly reproducible (RSD < 5%), regenerable (at least 8 regeneration/assay cycles without discernible signal decrease) and selective (with sequence specificity down to a single nucleotide mismatch). The low detection levels (10 fM or 0.1 attomoles of miRNA in a 10-HL solution) allow the direct quantification of miRNA-182, a marker correlated to the progression of glioma in patients, to be performed in serum samples without sample pretreatment and RNA extraction and enrichment. The concentration of miRNA-182 in glioma patients was found to be 3.1 times as high as that in healthy persons, a conclusion in excellent agreement with a separate qPCR measurement of the expression level. The obviations of the requirement of an internal reference in qPCR, simplicity, and cost-effectiveness are other additional advantages of this method for detection of nucleic acids in clinical samples. PMID:22788545

Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR.

PubMed

McDermott, Geoffrey P; Do, Duc; Litterst, Claudia M; Maar, Dianna; Hindson, Christopher M; Steenblock, Erin R; Legler, Tina C; Jouvenot, Yann; Marrs, Samuel H; Bemis, Adam; Shah, Pallavi; Wong, Josephine; Wang, Shenglong; Sally, David; Javier, Leanne; Dinio, Theresa; Han, Chunxiao; Brackbill, Timothy P; Hodges, Shawn P; Ling, Yunfeng; Klitgord, Niels; Carman, George J; Berman, Jennifer R; Koehler, Ryan T; Hiddessen, Amy L; Walse, Pramod; Bousse, Luc; Tzonev, Svilen; Hefner, Eli; Hindson, Benjamin J; Cauly, Thomas H; Hamby, Keith; Patel, Viresh P; Regan, John F; Wyatt, Paul W; Karlin-Neumann, George A; Stumbo, David P; Lowe, Adam J

2013-12-03

Two years ago, we described the first droplet digital PCR (ddPCR) system aimed at empowering all researchers with a tool that removes the substantial uncertainties associated with using the analogue standard, quantitative real-time PCR (qPCR). This system enabled TaqMan hydrolysis probe-based assays for the absolute quantification of nucleic acids. Due to significant advancements in droplet chemistry and buoyed by the multiple benefits associated with dye-based target detection, we have created a "second generation" ddPCR system compatible with both TaqMan-probe and DNA-binding dye detection chemistries. Herein, we describe the operating characteristics of DNA-binding dye based ddPCR and offer a side-by-side comparison to TaqMan probe detection. By partitioning each sample prior to thermal cycling, we demonstrate that it is now possible to use a DNA-binding dye for the quantification of multiple target species from a single reaction. The increased resolution associated with partitioning also made it possible to visualize and account for signals arising from nonspecific amplification products. We expect that the ability to combine the precision of ddPCR with both DNA-binding dye and TaqMan probe detection chemistries will further enable the research community to answer complex and diverse genetic questions.

Identification of quantitative trait loci for popping traits and kernel characteristics in sorghum grain

USDA-ARS?s Scientific Manuscript database

Popped grain sorghum has developed a niche among specialty snack-food consumers. In contrast to popcorn, sorghum has not benefited from persistent selective breeding for popping efficiency and kernel expansion ratio. While recent studies have already demonstrated that popping characteristics are h...

Blacks in Pop Music: A Short Story.

ERIC Educational Resources Information Center

Rickelman, Melinda

1991-01-01

A short history of black pop music includes artists who have changed pop music or culture and highlights from the 1920s into the 1980s, from Fats Waller to Michael Jackson. In black pop music, there is a direct line of influence from the sharecropper to the current Top 40. (SLD)

Microplastics are not important for the cycling and bioaccumulation of organic pollutants in the oceans-but should microplastics be considered POPs themselves?

PubMed

Lohmann, Rainer

2017-05-01

The role of microplastic particles in the cycling and bioaccumulation of persistent organic pollutants (POPs) is discussed. Five common concepts, sometimes misconceptions, about the role of microplastics are reviewed. While there is ample evidence that microplastics accumulate high concentrations of POPs, this does not result in microplastics being important for the global dispersion of POPs. Similarly, there is scant evidence that microplastics are an important transfer vector of POPs into animals, but possibly for plastic additives (flame retardants). Last, listing microplastics as POPs could help reduce their environmental impact. Integr Environ Assess Manag 2017;13:460-465. © 2017 SETAC. © 2017 SETAC.

High-throughput telomere length quantification by FISH and its application to human population studies.

PubMed

Canela, Andrés; Vera, Elsa; Klatt, Peter; Blasco, María A

2007-03-27

A major limitation of studies of the relevance of telomere length to cancer and age-related diseases in human populations and to the development of telomere-based therapies has been the lack of suitable high-throughput (HT) assays to measure telomere length. We have developed an automated HT quantitative telomere FISH platform, HT quantitative FISH (Q-FISH), which allows the quantification of telomere length as well as percentage of short telomeres in large human sample sets. We show here that this technique provides the accuracy and sensitivity to uncover associations between telomere length and human disease.

75 FR 38412 - Safety Zone; San Diego POPS Fireworks, San Diego, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-02

...-AA00 Safety Zone; San Diego POPS Fireworks, San Diego, CA AGENCY: Coast Guard, DHS. ACTION: Temporary... waters of San Diego Bay in support of the San Diego POPS Fireworks. This safety zone is necessary to... San Diego POPS Fireworks, which will include fireworks presentations conducted from a barge in San...

Steps to achieve quantitative measurements of microRNA using two step droplet digital PCR.

PubMed

Stein, Erica V; Duewer, David L; Farkas, Natalia; Romsos, Erica L; Wang, Lili; Cole, Kenneth D

2017-01-01

Droplet digital PCR (ddPCR) is being advocated as a reference method to measure rare genomic targets. It has consistently been proven to be more sensitive and direct at discerning copy numbers of DNA than other quantitative methods. However, one of the largest obstacles to measuring microRNA (miRNA) using ddPCR is that reverse transcription efficiency depends upon the target, meaning small RNA nucleotide composition directly effects primer specificity in a manner that prevents traditional quantitation optimization strategies. Additionally, the use of reagents that are optimized for miRNA measurements using quantitative real-time PCR (qRT-PCR) appear to either cause false positive or false negative detection of certain targets when used with traditional ddPCR quantification methods. False readings are often related to using inadequate enzymes, primers and probes. Given that two-step miRNA quantification using ddPCR relies solely on reverse transcription and uses proprietary reagents previously optimized only for qRT-PCR, these barriers are substantial. Therefore, here we outline essential controls, optimization techniques, and an efficacy model to improve the quality of ddPCR miRNA measurements. We have applied two-step principles used for miRNA qRT-PCR measurements and leveraged the use of synthetic miRNA targets to evaluate ddPCR following cDNA synthesis with four different commercial kits. We have identified inefficiencies and limitations as well as proposed ways to circumvent identified obstacles. Lastly, we show that we can apply these criteria to a model system to confidently quantify miRNA copy number. Our measurement technique is a novel way to quantify specific miRNA copy number in a single sample, without using standard curves for individual experiments. Our methodology can be used for validation and control measurements, as well as a diagnostic technique that allows scientists, technicians, clinicians, and regulators to base miRNA measures on a single unit of measurement rather than a ratio of values.

Steps to achieve quantitative measurements of microRNA using two step droplet digital PCR

PubMed Central

Duewer, David L.; Farkas, Natalia; Romsos, Erica L.; Wang, Lili; Cole, Kenneth D.

2017-01-01

Droplet digital PCR (ddPCR) is being advocated as a reference method to measure rare genomic targets. It has consistently been proven to be more sensitive and direct at discerning copy numbers of DNA than other quantitative methods. However, one of the largest obstacles to measuring microRNA (miRNA) using ddPCR is that reverse transcription efficiency depends upon the target, meaning small RNA nucleotide composition directly effects primer specificity in a manner that prevents traditional quantitation optimization strategies. Additionally, the use of reagents that are optimized for miRNA measurements using quantitative real-time PCR (qRT-PCR) appear to either cause false positive or false negative detection of certain targets when used with traditional ddPCR quantification methods. False readings are often related to using inadequate enzymes, primers and probes. Given that two-step miRNA quantification using ddPCR relies solely on reverse transcription and uses proprietary reagents previously optimized only for qRT-PCR, these barriers are substantial. Therefore, here we outline essential controls, optimization techniques, and an efficacy model to improve the quality of ddPCR miRNA measurements. We have applied two-step principles used for miRNA qRT-PCR measurements and leveraged the use of synthetic miRNA targets to evaluate ddPCR following cDNA synthesis with four different commercial kits. We have identified inefficiencies and limitations as well as proposed ways to circumvent identified obstacles. Lastly, we show that we can apply these criteria to a model system to confidently quantify miRNA copy number. Our measurement technique is a novel way to quantify specific miRNA copy number in a single sample, without using standard curves for individual experiments. Our methodology can be used for validation and control measurements, as well as a diagnostic technique that allows scientists, technicians, clinicians, and regulators to base miRNA measures on a single unit of measurement rather than a ratio of values. PMID:29145448

Low-level (submicromole) environmental 14C metrology

NASA Astrophysics Data System (ADS)

Currie, L. A.; Kessler, J. D.; Marolf, J. V.; McNichol, A. P.; Stuart, D. R.; Donoghue, J. C.; Donahue, D. J.; Burr, G. S.; Biddulph, D.

2000-10-01

Accelerator mass spectrometry (AMS) measurements of environmental 14C have been employed during the past decade at the several micromole level (tens of μg carbon), but advanced research in the atmospheric and marine sciences demands still higher (μg) sensitivity, an extreme example being the determination of 14C in elemental or "black" carbon (BC) at levels of 2-10 μg per kg of Greenland snow and ice (Currie et al., 1998). A fundamental limitation for 14C AMS is Poisson counting statistics, which sets in at about 1 μg modern-C. Using the small sample (25 μg) AMS target preparation facility at NOSAMS (Pearson et al., 1998), and the microsample combustion-dilution facility at NIST, we have demonstrated an intrinsic modern-C quantification limit ( mQ) of ca. 0.9 μg, based on a 1-parameter fit to the empirical AMS variance function. (For environmental 14C, the modern carbon quantification limit is defined as that mass ( mQ) corresponding to 10% relative standard deviation (rsd) for the fraction of modern carbon, σ( fM)/ fM.) Stringent control, required for quantitative dilution factors (DL), is achieved with the NIST on-line manometric/mass spectrometry facility that compensates also for unsuspected trace impurities from vigorous chemical processing (e.g., acid digestion). Our current combustion blank is trivial (mean: 0.16 ± 0.02 μg C, n=13) but lognormally distributed (dispersion [σ]: 0.07 ± 0.01 μg). An iterative numerical expression is introduced to assess the quantitative impacts of fossil and modern carbon blank components on mQ; and a new "clean chemistry" BC processing system is described for the minimization of such blanks. For the assay of soot carbon in Greenland snow/ice, the overall processing blank has been reduced from nearly 7 μg total carbon to less than 1 μg, and is undetectable for BC.

Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci

PubMed Central

Liu, Fan; Wollstein, Andreas; Hysi, Pirro G.; Ankra-Badu, Georgina A.; Spector, Timothy D.; Park, Daniel; Zhu, Gu; Larsson, Mats; Duffy, David L.; Montgomery, Grant W.; Mackey, David A.; Walsh, Susan; Lao, Oscar; Hofman, Albert; Rivadeneira, Fernando; Vingerling, Johannes R.; Uitterlinden, André G.; Martin, Nicholas G.; Hammond, Christopher J.; Kayser, Manfred

2010-01-01

Previous studies have successfully identified genetic variants in several genes associated with human iris (eye) color; however, they all used simplified categorical trait information. Here, we quantified continuous eye color variation into hue and saturation values using high-resolution digital full-eye photographs and conducted a genome-wide association study on 5,951 Dutch Europeans from the Rotterdam Study. Three new regions, 1q42.3, 17q25.3, and 21q22.13, were highlighted meeting the criterion for genome-wide statistically significant association. The latter two loci were replicated in 2,261 individuals from the UK and in 1,282 from Australia. The LYST gene at 1q42.3 and the DSCR9 gene at 21q22.13 serve as promising functional candidates. A model for predicting quantitative eye colors explained over 50% of trait variance in the Rotterdam Study. Over all our data exemplify that fine phenotyping is a useful strategy for finding genes involved in human complex traits. PMID:20463881

Application of real-time PCR (qPCR) for characterization of microbial populations and type of milk in dairy food products.

PubMed

Agrimonti, Caterina; Bottari, Benedetta; Sardaro, Maria Luisa Savo; Marmiroli, Nelson

2017-09-08

Dairy foods represent an important sector of the food market for their nutritional qualities and their organoleptic characteristics, which are often linked to tradition and to region. These products are typically protected by labels such as PDO (Protected Designation of Origin) and PGI (Protected Geographical Indication). Real-time PCR (qPCR) is a fundamental tool in "Food Genomics;" a discipline concerned with the residual DNA in food, which, alongside traditional physical and chemical methods, is frequently used to determine product safety, quality and authenticity. Compared to conventional or "end-point" PCR, qPCR incorporates continuous monitoring of reaction progress, thereby enabling quantification of target DNA. This review describes qPCR applications to the analysis of microbiota, and to the identification of the animal species source of milk from which dairy products have been made. These are important aspects for ensuring safety and authenticity. The various applications of qPCR are discussed, as well as advantages and disadvantages in comparison with other analytical methods.

Loss of PopZAt activity in Agrobacterium tumefaciens by Deletion or Depletion Leads to Multiple Growth Poles, Minicells, and Growth Defects

PubMed Central

Grangeon, Romain; Zupan, John; Jeon, Yeonji

2017-01-01

ABSTRACT Agrobacterium tumefaciens grows by addition of peptidoglycan (PG) at one pole of the bacterium. During the cell cycle, the cell needs to maintain two different developmental programs, one at the growth pole and another at the inert old pole. Proteins involved in this process are not yet well characterized. To further characterize the role of pole-organizing protein A. tumefaciens PopZ (PopZAt), we created deletions of the five PopZAt domains and assayed their localization. In addition, we created a popZAt deletion strain (ΔpopZAt) that exhibited growth and cell division defects with ectopic growth poles and minicells, but the strain is unstable. To overcome the genetic instability, we created an inducible PopZAt strain by replacing the native ribosome binding site with a riboswitch. Cultivated in a medium without the inducer theophylline, the cells look like ΔpopZAt cells, with a branching and minicell phenotype. Adding theophylline restores the wild-type (WT) cell shape. Localization experiments in the depleted strain showed that the domain enriched in proline, aspartate, and glutamate likely functions in growth pole targeting. Helical domains H3 and H4 together also mediate polar localization, but only in the presence of the WT protein, suggesting that the H3 and H4 domains multimerize with WT PopZAt, to stabilize growth pole accumulation of PopZAt. PMID:29138309

Family history associated with pelvic organ prolapse in young women.

PubMed

Alcalay, Menachem; Stav, Kobi; Eisenberg, Vered H

2015-12-01

Pelvic organ prolapse (POP) among young women is a relatively rare disorder with a unique clinical background. The objective of our study was to investigate the relative risk factors for POP and the relationship between family history and POP development in young women. In a retrospective longitudinal study we investigated 26 young patients (age <45 years) who underwent POP surgery and compared them to a control group of 26 patients (age >55 years) who underwent similar surgery and were matched with regard to parity. All women were interviewed for family history of POP, POP surgery among first-degree relatives, and hernia repair. Family history of POP was five times more prevalent among women in the study group than in the control group (46 % vs. 8 %, P < 0.01). Moreover, POP surgery among the first-degree relatives was significantly more prevalent in the study group (23.1 % vs. 3.8 %, p < 0.05). The prevalence of a family history of POP in more than one first-degree relative (11.5 % vs. 3.84 %, p = 0.3) and the family history of hernia repair among first-degree relatives (11.5 % vs. 15.4 %) did not differ between the groups. A family history of POP is significantly more common in younger affected women than in older affected women. We suggest that future genetic studies should concentrate on this specific population.

OntoPop: An Ontology Population System for the Semantic Web

NASA Astrophysics Data System (ADS)

Thongkrau, Theerayut; Lalitrojwong, Pattarachai

The development of ontology at the instance level requires the extraction of the terms defining the instances from various data sources. These instances then are linked to the concepts of the ontology, and relationships are created between these instances for the next step. However, before establishing links among data, ontology engineers must classify terms or instances from a web document into an ontology concept. The tool for help ontology engineer in this task is called ontology population. The present research is not suitable for ontology development applications, such as long time processing or analyzing large or noisy data sets. OntoPop system introduces a methodology to solve these problems, which comprises two parts. First, we select meaningful features from syntactic relations, which can produce more significant features than any other method. Second, we differentiate feature meaning and reduce noise based on latent semantic analysis. Experimental evaluation demonstrates that the OntoPop works well, significantly out-performing the accuracy of 49.64%, a learning accuracy of 76.93%, and executes time of 5.46 second/instance.

Nanohybrids of magnetic iron-oxide particles in hydrophobic organoclays for oil recovery.

PubMed

Hsu, Ru-Siou; Chang, Wen-Hsin; Lin, Jiang-Jen

2010-05-01

Nanohybrids with magnetic iron-oxide nanoparticles (FeNPs) embedded in the multilayered silicate clay were synthesized by in situ Fe(2+)/Fe(3+) coprecipitation. The natural clay, sodium montmorillonite (Na(+)-MMT), was first modified with hydrophobic poly(oxypropylene)amine salts (POP at 2000 and 4000 g/mol M(w)). The two POP-intercalated organoclays, with a silicate interlayer expansion from 1.2 to 5.2 and 9.2 nm, respectively, are suitable for embedding FeNPs. The presence of POP organics in layered structure created the space for intercalating with FeNPs of 2-4 nm in diameter, observed by transmission electronic microscope. The synthesized nanohybrids of POP4000/MMT-FeNP was composed of 17% iron oxide and 51 wt % POP within the silicate basal spacing of 5.0 nm. In contrast, the lower molecular weight of POP2000 intercalated MMT failed to encapsulate FeNPs in a significant amount, but resulting a "crowding-out effect" that caused the silicate interlayer space to shrink from 5.2 to 1.8 nm because of the replacement of the POP salt by Fe(2+)/Fe(3+) ions. The synthesis required the use of high molecular weight POP4000 and low temperatures (<4 degrees C) for a better dispersion in the reaction medium. The presence of POP in the layered silicate facilitated a homogeneous POP/MMT in water, associating with Fe(2+)/Fe(3+) ions and spatially accommodating for the subsequently generated FeNPs. The synthesized nanostructure consisting of POP and FeNP could be used as a pollutant remedy because of its ability to adsorbing crude oil and it is maneuverable under an applied magnetism.

Popping Rocks Revealed: Investigations from 14°N on the Mid-Atlantic Ridge

NASA Astrophysics Data System (ADS)

Wanless, V. D.; Jones, M.; Kurz, M. D.; Soule, S. A.; Fornari, D. J.; Bendana, S.; Mittelstaedt, E. L.

2017-12-01

The popping rock, recovered in dredge 2πD43 in 1985, is commonly considered to be one of the most representative samples of undegassed upper mantle, based on high volatile and noble gas abundances. While this basalt is used to reconstruct mantle volatile contents and CO2 fluxes from mid-ocean ridges (MOR), the origin of the popping rock has remained ambiguous due to a lack of geologic context. Here, we present results from the first combined geochemical, geophysical, and geologic investigation of popping rocks from 14N on the Mid-Atlantic Ridge. By combining lava compositions with high-resolution bathymetric maps, we show that the popping rocks are confined to a single geographic area, at the transition between magmatic and tectonic segments. Fifteen popping rocks were collected in situ using the Alvin submersible in 2016. X-ray microtomography indicates that these lavas have variable vesicle abundances; including the highest vesicularities (>19%) recorded for any MOR basalt. Dissolved CO2 contents (163-175 ppm) are similar to proximal non-popping rocks and are in equilibrium at their eruption depths (>3600 m); however, total CO2 contents (based on vesicularity, dissolved CO2, and vesicle gas contents) are higher than non-popping rocks, ranging from 2800-14150 ppm. The popping rocks have average 3He/4He ratios of 8.17 ± 0.1 Ra and 4He concentrations of 1.84e-5 to 7.67e-5 cc/g STP. Compared to non-popping lavas, the popping rocks have a narrow range of major and trace element concentrations, suggesting little to no crystallization occurred during ascent or eruption. REE patterns and trace element ratios are indistinguishable in the popping rocks (La/Sm = 2.89 ± 0.05), indicating similar mantle sources and extents of melting. Based on lava compositions and spatial distribution, we suggest that the popping rocks at 14N were produced under similar magmatic conditions and erupted over short timescales, perhaps during a series of closely timed eruptions.

Phytosterol oxidation products (POP) in foods with added phytosterols and estimation of their daily intake: A literature review

PubMed Central

Knol, Diny; Trautwein, Elke A.

2016-01-01

1 To evaluate the content of phytosterol oxidation products (POP) of foods with added phytosterols, in total 14 studies measuring POP contents of foods with added phytosterols were systematically reviewed. In non‐heated or stored foods, POP contents were low, ranging from (medians) 0.03–3.6 mg/100 g with corresponding oxidation rates of phytosterols (ORP) of 0.03–0.06%. In fat‐based foods with 8% of added free plant sterols (FPS), plant sterol esters (PSE) or plant stanol esters (PAE) pan‐fried at 160–200°C for 5–10 min, median POP contents were 72.0, 38.1, and 4.9 mg/100 g, respectively, with a median ORP of 0.90, 0.48, and 0.06%. Hence resistance to thermal oxidation was in the order of PAE > PSE > FPS. POP formation was highest in enriched butter followed by margarine and rapeseed oil. In margarines with 7.5–10.5% added PSE oven‐heated at 140–200°C for 5–30 min, median POP content was 0.3 mg/100 g. Further heating under same temperature conditions but for 60–120 min markedly increased POP formation to 384.3 mg/100 g. Estimated daily upper POP intake was 47.7 mg/d (equivalent to 0.69 mg/kg BW/d) for foods with added PSE and 78.3 mg/d (equivalent to 1.12 mg/kg BW/d) for foods with added FPS as calculated by multiplying the advised upper daily phytosterol intake of 3 g/d with the 90% quantile values of ORP. In conclusion, heating temperature and time, chemical form of phytosterols added and the food matrix are determinants of POP formation in foods with added phytosterols, leading to an increase in POP contents. Practical applications: Phytosterol oxidation products (POP) are formed in foods containing phytosterols especially when exposed to heat treatment. This review summarising POP contents in foods with added phytosterols in their free and esterified forms reveals that heating temperature and time, the chemical form of phytosterols added and the food matrix itself are determinants of POP formation with heating temperature and time having the biggest impact. The estimated upper daily intakes of POP is 78.3 mg/d for fat‐based products with added free plant sterols and 47.7 mg/d for fat‐based products with added plant sterol esters. Phytosterols in foods are susceptible to oxidation to form phytosterol oxidation products (POP). This review summarizes literature data regarding POP contents of foods with added phytosterols that were exposed to storage and heat treatments. PMID:27812313

Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

USGS Publications Warehouse

Chase, D.M.; Elliott, D.G.; Pascho, R.J.

2006-01-01

Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

A girl with an atypical form of ataxia telangiectasia and an additional de novo 3.14 Mb microduplication in region 19q12.

PubMed

Bartsch, Oliver; Schindler, Detlev; Beyer, Vera; Gesk, Stefan; van't Slot, Ruben; Feddersen, Isa; Buijs, Arjan; Jaspers, Nicolaas G J; Siebert, Reiner; Haaf, Thomas; Poot, Martin

2012-01-01

A 9-year-old girl born to healthy parents showed manifestations suggestive of ataxia telangiectasia (AT), such as short stature, sudden short bouts of horizontal and rotary nystagmus, a weak and dysarthric voice, rolling gait, unstable posture, and atactic movements. She did not show several cardinal features typical of AT such as frequent, severe infections of the respiratory tract. In contrast, she showed symptoms not generally related to AT, including microcephaly, profound motor and mental retardation, small hands and feet, severely and progressively reduced muscle tone with slackly protruding abdomen and undue drooling, excess fat on her upper arms, and severe oligoarthritis. A cranial MRI showed no cerebellar hypoplasia and other abnormalities. In peripheral blood samples she carried a de novo duplication of 3.14 Mb in chromosomal region 19q12 containing six annotated genes, UQCRFS1, VSTM2B, POP4, PLEKHF1, CCNE1, and ZNF536, and a de novo mosaic inversion 14q11q32 (96% of metaphases). In a saliva-derived DNA sample only the duplication in 19q12 was detected, suggesting that the rearrangements in blood lymphocytes were acquired. These findings reinforced the suspicion that she had AT. AT was confirmed by strongly elevated serum AFP levels, cellular radiosensitivity and two inherited mutations in the ATM gene (c.510_511delGT; paternal origin and c.2922-50_2940del69; maternal origin). This case suggest that a defective ATM-dependent DNA damage response may entail additional stochastic genomic rearrangements. Screening for genomic rearrangements appears indicated in patients suspected of defective DNA damage responses. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Population-based versus practice-based recall for childhood immunizations: a randomized controlled comparative effectiveness trial.

PubMed

Kempe, Allison; Saville, Alison; Dickinson, L Miriam; Eisert, Sheri; Reynolds, Joni; Herrero, Diana; Beaty, Brenda; Albright, Karen; Dibert, Eva; Koehler, Vicky; Lockhart, Steven; Calonge, Ned

2013-06-01

We compared the effectiveness and cost-effectiveness of population-based recall (Pop-recall) versus practice-based recall (PCP-recall) at increasing immunizations among preschool children. This cluster-randomized trial involved children aged 19 to 35 months needing immunizations in 8 rural and 6 urban Colorado counties. In Pop-recall counties, recall was conducted centrally using the Colorado Immunization Information System (CIIS). In PCP-recall counties, practices were invited to attend webinar training using CIIS and offered financial support for mailings. The percentage of up-to-date (UTD) and vaccine documentation were compared 6 months after recall. A mixed-effects model assessed the association between intervention and whether a child became UTD. Ten of 195 practices (5%) implemented recall in PCP-recall counties. Among children needing immunizations, 18.7% became UTD in Pop-recall versus 12.8% in PCP-recall counties (P < .001); 31.8% had documented receipt of 1 or more vaccines in Pop-recall versus 22.6% in PCP-recall counties (P < .001). Relative risk estimates from multivariable modeling were 1.23 (95% confidence interval [CI] = 1.10, 1.37) for becoming UTD and 1.26 (95% CI = 1.15, 1.38) for receipt of any vaccine. Costs for Pop-recall versus PCP-recall were $215 versus $1981 per practice and $17 versus $62 per child brought UTD. Population-based recall conducted centrally was more effective and cost-effective at increasing immunization rates in preschool children.

The neural underpinnings of music listening under different attention conditions.

PubMed

Jäncke, Lutz; Leipold, Simon; Burkhard, Anja

2018-05-02

Most studies examining the neural underpinnings of music listening have no specific instruction on how to process the presented musical pieces. In this study, we explicitly manipulated the participants' focus of attention while they listened to the musical pieces. We used an ecologically valid experimental setting by presenting the musical stimuli simultaneously with naturalistic film sequences. In one condition, the participants were instructed to focus their attention on the musical piece (attentive listening), whereas in the second condition, the participants directed their attention to the film sequence (passive listening). We used two instrumental musical pieces: an electronic pop song, which was a major hit at the time of testing, and a classical musical piece. During music presentation, we measured electroencephalographic oscillations and responses from the autonomic nervous system (heart rate and high-frequency heart rate variability). During passive listening to the pop song, we found strong event-related synchronizations in all analyzed frequency bands (theta, lower alpha, upper alpha, lower beta, and upper beta). The neurophysiological responses during attentive listening to the pop song were similar to those of the classical musical piece during both listening conditions. Thus, the focus of attention had a strong influence on the neurophysiological responses to the pop song, but not on the responses to the classical musical piece. The electroencephalographic responses during passive listening to the pop song are interpreted as a neurophysiological and psychological state typically observed when the participants are 'drawn into the music'.

Properties of a hybrid plaster-fibreglass cast

PubMed Central

Charles, Mark N.; Yen, David

2000-01-01

Objective To examine the suitability of a plaster-fibreglass hybrid cast for orthopedic applications, comparing them to plaster of Paris (POP) and fibreglass constructs. Method Groups of 10 standardized hybrid, POP and fibreglass casts were studied. An Instron servo-hydraulic system was used to test the casts in 3-point bending and shear. Outcome measures Strength, stiffness, weight, thickness and cost of the 3 types of cast, and shear strength at the interface between the POP and fibreglass in the hybrid casts. Results The hybrid casts were twice as strong as the POP constructs, were stiffer and weighed 14% less but were thicker and cost 2.5 times more. They were almost as strong as and less than half the cost of the fibreglass constructs but were thicker, not as stiff, and weighed 42% more. The shear strength of the POP–fibreglass interface in the hybrid casts was higher than the 3-point bending strength of this construct by a factor of 3. Conclusions Plaster-fibreglass hybrid casts should be considered for orthopedic use on the basis of their strength, stiffness, weight and cost, combined with their acknowledged advantages of good moulding ability and water resistance. PMID:11045095

Phase behavior of binary mixture systems of saturated-unsaturated mixed-acid triacylglycerols: effects of glycerol structures and chain-chain interactions.

PubMed

Bayés-García, Laura; Calvet, Teresa; Cuevas-Diarte, Miquel Àngel; Ueno, Satoru; Sato, Kiyotaka

2015-03-26

We systematically examined the phase behavior of binary mixtures of mixed-acid triacylglycerols (TAGs) containing palmitic and oleic acid moieties 1,3-dioleoyl-2-palmitoyl-glycerol (OPO), 1,2-dipalmitoyl-3-oleoyl-rac-glycerol (PPO), and 1,2-dioleoyl-3-palmitoyl-rac-glycerol (OOP), which are widely present in natural fats and are employed in the food, pharmaceutical, and cosmetic industries. Differential scanning calorimetry and X-ray diffraction methods were applied to observe the mixing behavior of PPO/OPO, OOP/OPO, and PPO/OOP under metastable and stable conditions. The results led to three conclusions: (1) Eutectic behavior was observed in PPO/OPO. (2) Molecular compound (MC) crystals were formed in the mixtures of OOP/OPO and PPO/OOP. (3) However, the MC crystals occurred only under metastable conditions and tended to separate into component TAGs to form eutectic mixture systems after 17 months of incubation. These results were contrary to those of previous studies on 1,3-dipalmitoyl-2-oleoyl glycerol (POP)/OPO and POP/PPO in which the MC crystals were thermodynamically stable. We determined that specific molecular interactions may cause this different phase behavior (stability of POP/OPO and POP/PPO MC crystals and metastability of OOP/OPO and PPO/OOP MC crystals). All results confirm the significant effects of molecular structures of glycerol groups, interactions of fatty acid chains, and polymorphism of the component TAGs on the mixing behavior of mixed-acid TAGs.

A qPCR assay for detection and quantification of Verticillium dahliae in spinach seed.

USDA-ARS?s Scientific Manuscript database

The fungus Verticillium dahliae is the causal agent of Verticillium wilt of lettuce and other specialty crops in the Salinas Valley of California. Spinach, another major specialty crop in California, is not affected by Verticillium wilt in commercial production. However, spinach seed infected with ...

Development of a qPCR assay for quantification of verticillium dahliae in spinach seed.

USDA-ARS?s Scientific Manuscript database

Verticillium wilt, caused by the soilborne fungus Verticillium dahliae, is an important disease of lettuce and other specialty crops in the Salinas Valley of California. Although spinach is not affected by Verticillium wilt in commercial production, spinach seed infected with V. dahliae from locatio...

Inter-laboratory Comparison of Real-time PCR Methods for Quantification of General Fecal Indicator Bacteria

EPA Science Inventory

The application of quantitative real-time PCR (qPCR) technologies for the rapid identification of fecal bacteria in environmental waters is being considered for use as a national water quality metric in the United States. The transition from research tool to a standardized prot...

Interlaboratory Comparison of Real-time PCR Protocols for Quantification of General Fecal Indicator Bacteria

EPA Science Inventory

The application of quantitative real-time PCR (qPCR) technologies for the rapid identification of fecal bacteria in environmental waters is being considered for use as a national water quality metric in the United States. The transition from research tool to a standardized proto...

Measured and Calculated Volumes of Wetland Depressions

EPA Pesticide Factsheets

Measured and calculated volumes of wetland depressionsThis dataset is associated with the following publication:Wu, Q., and C. Lane. Delineation and quantification of wetland depressions in the Prairie Pothole Region of North Dakota. WETLANDS. The Society of Wetland Scientists, McLean, VA, USA, 36(2): 215-227, (2016).

Effect of platform, reference material, and quantification model on enumeration of Enterococcus by quantitative PCR methods

EPA Science Inventory

Quantitative polymerase chain reaction (qPCR) is increasingly being used for the quantitative detection of fecal indicator bacteria in beach water. QPCR allows for same-day health warnings, and its application is being considered as an optionn for recreational water quality testi...

chipPCR: an R package to pre-process raw data of amplification curves.

PubMed

Rödiger, Stefan; Burdukiewicz, Michał; Schierack, Peter

2015-09-01

Both the quantitative real-time polymerase chain reaction (qPCR) and quantitative isothermal amplification (qIA) are standard methods for nucleic acid quantification. Numerous real-time read-out technologies have been developed. Despite the continuous interest in amplification-based techniques, there are only few tools for pre-processing of amplification data. However, a transparent tool for precise control of raw data is indispensable in several scenarios, for example, during the development of new instruments. chipPCR is an R: package for the pre-processing and quality analysis of raw data of amplification curves. The package takes advantage of R: 's S4 object model and offers an extensible environment. chipPCR contains tools for raw data exploration: normalization, baselining, imputation of missing values, a powerful wrapper for amplification curve smoothing and a function to detect the start and end of an amplification curve. The capabilities of the software are enhanced by the implementation of algorithms unavailable in R: , such as a 5-point stencil for derivative interpolation. Simulation tools, statistical tests, plots for data quality management, amplification efficiency/quantification cycle calculation, and datasets from qPCR and qIA experiments are part of the package. Core functionalities are integrated in GUIs (web-based and standalone shiny applications), thus streamlining analysis and report generation. http://cran.r-project.org/web/packages/chipPCR. Source code: https://github.com/michbur/chipPCR. stefan.roediger@b-tu.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Levels and Trends of Historic POPs (PCDD/Fs and PCBs) and Newer POPs (PBDEs) in U.S. Meat and Poultry and Implications for Human Exposure

USDA-ARS?s Scientific Manuscript database

The concentrations of several historic POPs, i.e. polychlorinated dibenzo p dioxins, polychlorinated dibenzofurans, and polychlorinated biphenyls, along with a newer class of POPs, the polybrominated diphenyl ethers (PBDEs), were measured in domestic meat and poultry samples from 2002 and 2008. The ...

The Eyes Have It: Visual Pop-Out in Infants and Adults

ERIC Educational Resources Information Center

Adler, Scott A.; Orprecio, Jazmine

2006-01-01

Visual search studies with adults have shown that stimuli that contain a unique perceptual feature pop out from dissimilar distractors and are unaffected by the number of distractors. Studies with very young infants have suggested that they too might exhibit pop-out. However, infant studies have used paradigms in which pop-out is measured in…

An update on the dangers of soda pop.

PubMed

Kaplowitz, Gary J

2011-01-01

The consumption of soda pop in the United States continues to increase in alarming proportions with consequent drastic effects on the dentition of many people. Patients should be asked about how much soda pop they ingest. Parents should be counseled on the effects of soda pop demineralization and begin to limit the amounts given to children at home and in schools. The dental team has the expertise and training to intervene with diet counseling, home care instructions and professionally applied fluoride to decrease the potential ravages of soda pop.

Necessity for Establishment of Inventories for Persistent Organic Pollutants (POPs) in Landfills and Contaminated Sites for an Evaluation of Mobilisation Risk by Climate Change

NASA Astrophysics Data System (ADS)

Weber, Roland; Watson, Alan; Forter, Martin

2010-05-01

The landfilling of persistent hazardous compounds with a tendency to migrate, such as Hexachlorocyclohexane (HCH), polychlorinated biphenyls (PCBs), Hexachlorobenzene (HCB) or Hexachlorobutadiene (HCBD) is a major pollution challenge. Historic dumping and landfilling in badly engineered and unsuitably located sites has resulted in widespread contamination from the landfilling of HCH, HCB and PCB wastes around former production sites. In the case of PCBs this has been exacerbated by subsequent landfilling of contaminated products (oils, capacitors, sealants and other building residues). In most cases locations and amounts are not or vaguely known but impacts are increasingly discovered by monitoring in the most advanced countries with sophisticated monitoring schemes in place. These reveal that entire river systems are being contaminated by these old dumps and contaminated sites and that expensive remediation work is required for to reduce further contamination. In addition more recently other (halogenated) chemicals exhibiting the characteristics of POPs have emerged including e.g. brominated aromatic compounds (e.g. Polybrominated diphenylethers (PBDEs) and other brominated flame retardants) widely used as flame retardants for electronics; textiles, furniture; upholstery; insulation foam etc.) and fluorinated organic pollutants (e.g. PFOS or PFOA used in carpets, textiles, furniture, paper coating etc.). As products containing these chemicals reach the end of their life these hazardous compounds increasingly ended and end up in the waste stream. In most countries a large proportion of these wastes are disposed to landfills. In developing countries and those with economies in transition almost all this waste is landfilled. Consequently the quantities of POPs in municipal waste landfills have increased the last two decades. Therefore in addition to chemical landfills also municipal landfills increasingly become POPs deposits and sources. Because of their persistence and relative mobility, these compounds will persist in landfills for many decades and probably centuries. Over these extended time frames landfill engineering systems, including basal and capping liners, gas and leachate collection systems will inevitably degrade and loose their abilities to contain contamination. Furthermore consideration must now be given to the impacts of climate change and extreme weather events. This is likely to result in higher temperatures with increased volatalisation of semi-volatile compounds; longer dry periods with drying of surface caps; together with higher intensity rainfall events and increased flooding risks. These effects will impact on the integrity of the containment systems. It is therefore inevitable that more of the deposited POPs will leach into rivers, lakes and the larger environment via escaping leachate, ground or surface water as well as escaping to atmosphere by volatilisation. At the same time our reliance on water resources is likely to increase. In order to evaluate the associated risks for human exposure and biodiversity, inventories of deposited POPs and other PBTs need to be established, their locations comprehensively mapped and linked to future flooding scenarios for prediction of contamination of the precious water resources. This interdisciplinary task will require the cooperation between POPs experts, geotechnical engineers, contaminated site/landfill experts, water management specialists and geoscientists working on climate change and flooding.

Anthropogenic acidification effects in primeval forests in the Transcarpathian Mts., western Ukraine.

PubMed

Oulehle, F; Hleb, R; Houska, J; Samonil, P; Hofmeister, J; Hruska, J

2010-01-15

The precipitation chemistry, deposition, nutrient pools and composition of soils and soil water, as well as an estimate of historical deposition of sulphur (S) and inorganic nitrogen (N) for the period 1860-2008, were determined in primeval deciduous and coniferous forests at the sites Javornik and Pop Ivan, respectively. Measured S throughfall inputs of 10 kg ha(-1)year(-1) in 2008 were similar to those estimated for the period 1900-1950 at both sites. The highest estimated S inputs were in the 1980s. Measured bulk deposition of N in 2008 was lower at Pop Ivan (5.6 kg ha(-1)year(-1)) compared to Javornik (12 kg ha(-1)year(-1)). Significantly lower NO(3) deposition was both estimated and measured at Pop Ivan. Higher soil base cation concentrations were observed at well-buffered Javornik underlain by flysch (Ca pool of 2046 kg ha(-1) and base saturation of 29%) compared to Pop Ivan underlain by crystalline schist (Ca pool of 186 kg ha(-1) and base saturation of 6.5%). The soil pool of organic carbon (C) was higher at Pop Ivan (212 t ha(-1)) compared to Javornik (127 t ha(-1)). The C concentration was positively correlated with organic N in the soil (p<0.001) at both sites, but the mass average C/N ratio in the forest floor was lower at Javornik (22) than at Pop Ivan (26). High N leaching of 17 kg ha(-1)year(-1) at the 90 cm depth was measured in the soil water at Javornik, suggesting high mineralization and nitrification rates in old growth deciduous forests in the area. Despite relatively low Al concentrations in the soil water, a low soil water Bc/Al ratio (0.9) (Bc=Ca+Mg+K) was found in the upper mineral soil at Pop Ivan. This suggests that the spruce forest ecosystems in the area are vulnerable to anthropogenic acidification and to the adverse effects of Al on forest root systems. Copyright 2009 Elsevier B.V. All rights reserved.

An ethnographic exploration of postoperative pain experiences among Ghanaian surgical patients.

PubMed

Aziato, Lydia; Adejumo, Oluyinka

2015-05-01

The experience of pain associated with surgery has been a challenge for health care professionals for many years, and culture is said to influence pain. This study focused on patients' experiences of postoperative pain (POP) and factors that affect POP. The study employed qualitative ethnographic principles. Data were collected through individual face-to-face interviews. Data were saturated after analyzing data from 13 patients from two hospitals in Ghana. Themes that emerged were the subjective nature of pain, which described pain dimensions and communication; psycho-sociocultural factors, such as personal inclinations and sociocultural background; and health system factors, such as personnel attitudes and health financing. Health professionals need to understand the sociocultural effects of pain in order to give effective care. The study highlighted the need for patient education and the importance that health care professionals understand context-specific factors that influence POP management. © The Author(s) 2014.

Prolyl Oligopeptidase from the Blood Fluke Schistosoma mansoni: From Functional Analysis to Anti-schistosomal Inhibitors

PubMed Central

Fajtová, Pavla; Štefanić, Saša; Hradilek, Martin; Dvořák, Jan; Vondrášek, Jiří; Jílková, Adéla; Ulrychová, Lenka; McKerrow, James H.; Caffrey, Conor R.; Mareš, Michael; Horn, Martin

2015-01-01

Background Blood flukes of the genus Schistosoma cause schistosomiasis, a parasitic disease that infects over 240 million people worldwide, and for which there is a need to identify new targets for chemotherapeutic interventions. Our research is focused on Schistosoma mansoni prolyl oligopeptidase (SmPOP) from the serine peptidase family S9, which has not been investigated in detail in trematodes. Methodology/Principal Findings We demonstrate that SmPOP is expressed in adult worms and schistosomula in an enzymatically active form. By immunofluorescence microscopy, SmPOP is localized in the tegument and parenchyma of both developmental stages. Recombinant SmPOP was produced in Escherichia coli and its active site specificity investigated using synthetic substrate and inhibitor libraries, and by homology modeling. SmPOP is a true oligopeptidase that hydrolyzes peptide (but not protein) substrates with a strict specificity for Pro at P1. The inhibition profile is analogous to those for mammalian POPs. Both the recombinant enzyme and live worms cleave host vasoregulatory, proline-containing hormones such as angiotensin I and bradykinin. Finally, we designed nanomolar inhibitors of SmPOP that induce deleterious phenotypes in cultured schistosomes. Conclusions/Significance We provide the first localization and functional analysis of SmPOP together with chemical tools for measuring its activity. We briefly discuss the notion that SmPOP, operating at the host-parasite interface to cleave host bioactive peptides, may contribute to the survival of the parasite. If substantiated, SmPOP could be a new target for the development of anti-schistosomal drugs. PMID:26039195

Perioperative risk factors for postoperative pneumonia after major oral cancer surgery: A retrospective analysis of 331 cases.

PubMed

Xu, Jieyun; Hu, Jing; Yu, Pei; Wang, Weiwang; Hu, Xingxue; Hou, Jinsong; Fang, Silian; Liu, Xiqiang

2017-01-01

Postoperative pneumonia (POP) is common and results in prolonged hospital stays, higher costs, increased morbidity and mortality. However, data on the incidence and risk factors of POP after oral and maxillofacial surgery are rare. This study aims to identify perioperative risk factors for POP after major oral cancer (OC) surgery. Perioperative data and patient records of 331 consecutive subjects were analyzed in the period of April 2014 to March 2016. We individually traced each OC patient for a period to discharge from the hospital or 45 days after surgery, whichever occur later. The incidence of POP after major OC surgery with free flap construction or major OC surgery was 11.6% or 4.5%, respectively. Patient-related risk factors for POP were male sex, T stage, N stage, clinical stage and preoperative serum albumin level. Among the investigated procedure-related variables, incision grade, mandibulectomy, free flap reconstruction, tracheotomy, intraoperative blood loss, and the length of the operation were shown to be associated with the development of POP. Postoperative hospital stay was also significantly related to increased incidence of POP. Using a multivariable logistic regression model, we identified male sex, preoperative serum albumin level, operation time and postoperative hospital stay as independent risk factors for POP. Several perioperative risk factors can be identified that are associated with POP. At-risk oral cancer patients should be subjected to intensified postoperative pulmonary care.

Environment and human exposure to persistent organic pollutants (POPs) in India: a systematic review of recent and historical data.

PubMed

Sharma, Brij Mohan; Bharat, Girija K; Tayal, Shresth; Nizzetto, Luca; Cupr, Pavel; Larssen, Thorjørn

2014-05-01

Persistent organic pollutants (POPs) have been used in a wide range of agricultural and industrial commodities, resulting in vigorous deterioration of environment and human health. A number of studies on the occurrence of POPs confirm their presence in various environmental compartments and human body. In order to deal with this global concern, India has recently prepared the National Implementation Plan (NIP) of the Stockholm Convention. Common beliefs point at India as a hot spot of POP contamination and human exposure; however no systematic analysis was ever performed so far considering all available past data on POP occurrence. This review aims to examine the distribution pattern of POPs in multicompartment environment and human samples, meta-analysis of time trends in exposure levels to environment and humans, and cross country comparison of POP contamination with China. Based on this review, it can be concluded that the Indian environment and human population are highly contaminated by DDTs and HCHs; however scarcity of data on other POPs makes it challenging to assess their nationwide human and environmental exposure. No evidence of a general decline in DDT and HCH residues in the environment and human body come out from the meta-analysis of time trend. While comparing contamination levels between India and China, tendency towards decline in POP contamination is visible in China, unlike India. Copyright © 2014 Elsevier Ltd. All rights reserved.

Hepatitis E Virus (HEV) Detection and Quantification by a Real-Time Reverse Transcription-PCR Assay Calibrated to the World Health Organization Standard for HEV RNA

PubMed Central

Germer, Jeffrey J.; Ankoudinova, Irina; Belousov, Yevgeniy S.; Mahoney, Walt; Dong, Chen; Meng, Jihong; Mandrekar, Jayawant N.

2017-01-01

ABSTRACT Hepatitis E virus (HEV) has emerged as a cause of chronic hepatitis among immunocompromised patients. Molecular assays have become important tools for the diagnosis and management of these chronically infected patients. A real-time reverse transcription-quantitative PCR (RT-qPCR) assay utilizing Pleiades probe chemistry and an RNA internal control for the simultaneous detection and quantification of HEV RNA in human serum was developed based on an adaptation of a previously described and broadly reactive primer set targeting the overlapping open reading frame 2/3 (ORF2/3) nucleotide sequence of HEV. A chimeric bovine viral diarrhea virus construct containing an HEV RNA insert (SynTura HEV) was developed, value assigned with the first World Health Organization (WHO) international standard for HEV RNA (code 6329/10), and used to prepare working assay calibrators and controls, which supported an assay quantification range of 100 to 5,000,000 IU/ml. The analytical sensitivity (95% detection rate) of this assay was 25.2 IU/ml (95% confidence interval [CI], 19.2 to 44.1 IU/ml). The assay successfully amplified 16 different HEV sequences with significant nucleotide mismatching in primer/probe binding regions, while evaluation of a WHO international reference panel for HEV genotypes (code 8578/13) showed viral load results falling within the result ranges generated by WHO collaborative study participants for all panel members (genotypes 1 to 4). Broadly reactive RT-qPCR primers targeting HEV ORF2/3 were successfully adapted for use in an assay based on Pleiades probe chemistry. The availability of secondary standards calibrated to the WHO HEV international standard can improve the standardization and performance of assays for the detection and quantification of HEV RNA. PMID:28228493

Pop in a Popper

ERIC Educational Resources Information Center

Reading Teacher, 2011

2011-01-01

This article describes Pop in a Popper, an effective lesson for teaching students how to choose and use words to give their writing fluency and flair. Pop in a Popper introduces the appositive: a group of words inserted after a noun to modify that noun. In simplest terms, writers pop this group of words into a sentence to tell more about a noun.…

Public health concern behind the exposure to persistent organic pollutants and the risk of metabolic diseases.

PubMed

Ruzzin, Jérôme

2012-04-20

Persistent organic pollutants (POPs) are hazardous chemicals omnipresent in our food chain, which have been internationally regulated to ensure public health. Initially described for their potency to affect reproduction and promote cancer, recent studies have highlighted an unexpected implication of POPs in the development of metabolic diseases like type 2 diabetes and obesity. Based on this novel knowledge, this article aims at stimulating discussion and evaluating the effectiveness of current POP legislation to protect humans against the risk of metabolic diseases. Furthermore, the regulation of POPs in animal food products in the European Union (EU) is addressed, with a special focus on marine food since it may represent a major source of POP exposure to humans. There is mounting scientific evidence showing that current POP risk assessment and regulation cannot effectively protect humans against metabolic disorders. Better regulatory control of POPs in dietary products should be of high public health priority. The general population is exposed to sufficient POPs, both in term of concentration and diversity, to induce metabolic disorders. This situation should attract the greatest attention from the public health and governmental authorities.

Seasonal variation and source analysis of persistent organic pollutants in the atmosphere over the western Tibetan Plateau.

PubMed

Zhang, Jingyi; Wang, Xiaoping; Gong, Ping; Wang, Chuanfei; Sun, Dianchao

2018-06-08

Over the past few decades, the Tibetan Plateau (TP) region has become gradually contaminated by persistent organic pollutants (POPs). The picture regarding POPs is clear in the central and southern parts of the TP; however, few observational campaigns have focused on the western TP. To clarify the concentrations, seasonal trends and source regions of POPs in the western TP, a first study of POPs in Muztagh Ata (westerly region) and a long-term (5 years) monitoring program in Ngari (transect region influenced by both the Indian monsoon and westerly climate) were conducted. Except for hexachlorobenzene (HCB) and polychlorinated biphenyls (PCBs), relatively low POP levels were observed in the western TP. In Muztagh Ata, dichlorodiphenyltrichloroethanes (DDTs) showed higher concentrations in winter and lower ones in summer, whereas at Ngari, higher DDTs and hexachlorocyclohexanes (HCHs) concentrations were observed in summer as compared with winter. Source diagnosis indicated that Xinjiang and central Asia were the main source regions for POPs in Muztagh Ata and that westerly winds play a key role in transporting POPs from central Asia. No correlation was found between the height of the atmospheric boundary layer and the concentrations of POPs over the TP.

Understanding pop-ins in spherical nanoindentation

DOE PAGES

Pathak, Siddhartha; Riesterer, Jessica L.; Kalidindi, Surya R.; ...

2014-10-24

In this study, pop-ins, or sudden displacement-bursts at constant load in a nanoindentation test, are typically attributed to the difficulty of setting up potent dislocation sources in the very small indentation zones in these experiments. Such displacement (and strain) bursts would intuitively indicate a sharp drop in stress during the pop-in event itself. However, spherical indentation stress-strain curves routinely exhibit a high and stable indentation stress value during the pop-in, and the indentation stresses decrease only after a further finite amount of additional indentation displacement has been applied. In order to understand this discrepancy, we utilize a combination of interruptedmore » spherical indentation tests along with depth profiling of the residual indentation surfaces using in-situ atomic force microscopy (AFM) to study pop-ins. The AFM surface profile maps show that there is an asymmetric profile change over a limited region around the indentation contact area for a single pop-in; the asymmetry disappears upon further loading beyond the pop-in. A plausible sequence of physical processes (related to metal plasticity) occurring underneath the indenter during and immediately after the occurrence of the pop-in is proposed to explain these observations.« less

Understanding pop-ins in spherical nanoindentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pathak, Siddhartha, E-mail: pathak@lanl.gov, E-mail: siddharthapathak@gmail.com; Riesterer, Jessica L.; Michler, Johann

2014-10-20

Pop-ins, or sudden displacement-bursts at constant load in a nanoindentation test, are typically attributed to the difficulty of setting up potent dislocation sources in the very small indentation zones in these experiments. Such displacement (and strain) bursts would intuitively indicate a sharp drop in stress during the pop-in event itself. However, spherical indentation stress-strain curves routinely exhibit a high and stable indentation stress value during the pop-in, and the indentation stresses decrease only after a further finite amount of additional indentation displacement has been applied. In order to understand this discrepancy, we utilize a combination of interrupted spherical indentation testsmore » along with depth profiling of the residual indentation surfaces using in-situ atomic force microscopy (AFM) to study pop-ins. The AFM surface profile maps show that there is an asymmetric profile change over a limited region around the indentation contact area for a single pop-in; the asymmetry disappears upon further loading beyond the pop-in. A plausible sequence of physical processes (related to metal plasticity) occurring underneath the indenter during and immediately after the occurrence of the pop-in is proposed to explain these observations.« less

Plant-bacteria partnerships for the remediation of persistent organic pollutants.

PubMed

Arslan, Muhammad; Imran, Asma; Khan, Qaiser Mahmood; Afzal, Muhammad

2017-02-01

High toxicity, bioaccumulation factor and widespread dispersal of persistent organic pollutants (POPs) cause environmental and human health hazards. The combined use of plants and bacteria is a promising approach for the remediation of soil and water contaminated with POPs. Plants provide residency and nutrients to their associated rhizosphere and endophytic bacteria. In return, the bacteria support plant growth by the degradation and detoxification of POPs. Moreover, they improve plant growth and health due to their innate plant growth-promoting mechanisms. This review provides a critical view of factors that affect absorption and translocation of POPs in plants and the limitations that plant have to deal with during the remediation of POPs. Moreover, the synergistic effects of plant-bacteria interactions in the phytoremediation of organic pollutants with special reference to POPs are discussed.

Identification and accurate quantification of structurally related peptide impurities in synthetic human C-peptide by liquid chromatography-high resolution mass spectrometry.

PubMed

Li, Ming; Josephs, Ralf D; Daireaux, Adeline; Choteau, Tiphaine; Westwood, Steven; Wielgosz, Robert I; Li, Hongmei

2018-06-04

Peptides are an increasingly important group of biomarkers and pharmaceuticals. The accurate purity characterization of peptide calibrators is critical for the development of reference measurement systems for laboratory medicine and quality control of pharmaceuticals. The peptides used for these purposes are increasingly produced through peptide synthesis. Various approaches (for example mass balance, amino acid analysis, qNMR, and nitrogen determination) can be applied to accurately value assign the purity of peptide calibrators. However, all purity assessment approaches require a correction for structurally related peptide impurities in order to avoid biases. Liquid chromatography coupled to high resolution mass spectrometry (LC-hrMS) has become the key technique for the identification and accurate quantification of structurally related peptide impurities in intact peptide calibrator materials. In this study, LC-hrMS-based methods were developed and validated in-house for the identification and quantification of structurally related peptide impurities in a synthetic human C-peptide (hCP) material, which served as a study material for an international comparison looking at the competencies of laboratories to perform peptide purity mass fraction assignments. More than 65 impurities were identified, confirmed, and accurately quantified by using LC-hrMS. The total mass fraction of all structurally related peptide impurities in the hCP study material was estimated to be 83.3 mg/g with an associated expanded uncertainty of 3.0 mg/g (k = 2). The calibration hierarchy concept used for the quantification of individual impurities is described in detail. Graphical abstract ᅟ.

Legionella in water samples: how can you interpret the results obtained by quantitative PCR?

PubMed

Ditommaso, Savina; Ricciardi, Elisa; Giacomuzzi, Monica; Arauco Rivera, Susan R; Zotti, Carla M

2015-02-01

Evaluation of the potential risk associated with Legionella has traditionally been determined from culture-based methods. Quantitative polymerase chain reaction (qPCR) is an alternative tool that offers rapid, sensitive and specific detection of Legionella in environmental water samples. In this study we compare the results obtained by conventional qPCR (iQ-Check™ Quanti Legionella spp.; Bio-Rad) and by culture method on artificial samples prepared in Page's saline by addiction of Legionella pneumophila serogroup 1 (ATCC 33152) and we analyse the selective quantification of viable Legionella cells by the qPCR-PMA method. The amount of Legionella DNA (GU) determined by qPCR was 28-fold higher than the load detected by culture (CFU). Applying the qPCR combined with PMA treatment we obtained a reduction of 98.5% of the qPCR signal from dead cells. We observed a dissimilarity in the ability of PMA to suppress the PCR signal in samples with different amounts of bacteria: the effective elimination of detection signals by PMA depended on the concentration of GU and increasing amounts of cells resulted in higher values of reduction. Using the results from this study we created an algorithm to facilitate the interpretation of viable cell level estimation with qPCR-PMA. Copyright © 2014 Elsevier Ltd. All rights reserved.

Persistent organic pollutant levels in human visceral and subcutaneous adipose tissue in obese individuals—Depot differences and dysmetabolism implications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pestana, Diogo, E-mail: diogopestana@gmail.com; CINTESIS—Center for Research in Health Technologies and Information Systems, P-4200-450 Porto; Faria, Gil

Background: The role of persistent organic pollutants (POPs) with endocrine disrupting activity in the aetiology of obesity and other metabolic dysfunctions has been recently highlighted. Adipose tissue (AT) is a common site of POPs accumulation where they can induce adverse effects on human health. Objectives: To evaluate the presence of POPs in human visceral (vAT) and subcutaneous (scAT) adipose tissue in a sample of Portuguese obese patients that underwent bariatric surgery, and assess their putative association with metabolic disruption preoperatively, as well as with subsequent body mass index (BMI) reduction. Methods: AT samples (n=189) from obese patients (BMI ≥35) weremore » collected and the levels of 13 POPs were determined by gas chromatography with electron-capture detection (GC-ECD). Anthropometric and biochemical data were collected at the time of surgery. BMI variation was evaluated after 12 months and adipocyte size was measured in AT samples. Results: Our data confirm that POPs are pervasive in this obese population (96.3% of detection on both tissues), their abundance increasing with age (R{sub S}=0.310, p<0.01) and duration of obesity (R{sub S}=0.170, p<0.05). We observed a difference in AT depot POPs storage capability, with higher levels of ΣPOPs in vAT (213.9±204.2 compared to 155.1±147.4 ng/g of fat, p<0.001), extremely relevant when evaluating their metabolic impact. Furthermore, there was a positive correlation between POP levels and the presence of metabolic syndrome components, namely dysglycaemia and hypertension, and more importantly with cardiovascular risk (R{sub S}=0.277, p<0.01), with relevance for vAT (R{sub S}=0.315, p<0.01). Finally, we observed an interesting relation of higher POP levels with lower weight loss in older patients. Conclusion: Our sample of obese subjects allowed us to highlight the importance of POPs stored in AT on the development of metabolic dysfunction in a context of obesity, shifting the focus to their metabolic effects and not only for their recognition as environmental obesogens. - Highlights: • POPs are pervasive in this sample of obese patients undergoing bariatric surgery. • Distinct adipose tissues have dissimilar POPs storage capability. • Despite the presence of obesity, POPs are important for metabolic dysregulation.« less

Highly sensitive and selective analysis of urinary steroids by comprehensive two-dimensional gas chromatography combined with positive chemical ionization quadrupole mass spectrometry

PubMed Central

Zhang, Ying; Tobias, Herbert J.; Brenna, J. Thomas

2014-01-01

Comprehensive two dimensional gas chromatography (GC×GC) provides greater separation space than conventional GC. Because of fast peak elution, a time of flight mass spectrometer (TOFMS) is the usual structure-specific detector of choice. The quantitative capabilities of a novel GC×GC fast quadrupole MS were investigated with electron ionization (EI), and CH4 or NH3 positive chemical ionization (PCI) for analysis of endogenous urinary steroids targeted in anti-doping tests. Average precisions for steroid quantitative analysis from replicate urine extractions were 6% (RSD) for EI and 8% for PCI-NH3. The average limits of detection (LOD) calculated by quantification ions for 12 target steroids spiked into steroid-free urine matrix (SFUM) were 2.6 ng mL−1 for EI, 1.3 ng mL−1 for PCI-CH4, and 0.3 ng mL−1 for PCI-NH3, all in mass scanning mode. The measured limits of quantification (LOQ) with full mass scan GC×GC-qMS were comparable with the LOQ values measured by one-dimensional GC-MS in single ion monitoring (SIM) mode. PCI-NH3 yields fewer fragments and greater (pseudo)molecular ion abundances than EI or PCI-CH4. These data show a benchtop GC×GC-qMS system has the sensitivity, specificity, and resolution to analyze urinary steroids at normal urine concentrations, and that PCI-NH3, not currently available on most GC×GC-TOFMS instruments, is of particular value for generation of structure-specific ions. PMID:22606686

An event-specific method for the detection and quantification of ML01, a genetically modified Saccharomyces cerevisiae wine strain, using quantitative PCR.

PubMed

Vaudano, Enrico; Costantini, Antonella; Garcia-Moruno, Emilia

2016-10-03

The availability of genetically modified (GM) yeasts for winemaking and, in particular, transgenic strains based on the integration of genetic constructs deriving from other organisms into the genome of Saccharomyces cerevisiae, has been a reality for several years. Despite this, their use is only authorized in a few countries and limited to two strains: ML01, able to convert malic acid into lactic acid during alcoholic fermentation, and ECMo01 suitable for reducing the risk of carbamate production. In this work we propose a quali-quantitative culture-independent method for the detection of GM yeast ML01 in commercial preparations of ADY (Active Dry Yeast) consisting of efficient extraction of DNA and qPCR (quantitative PCR) analysis based on event-specific assay targeting MLC (malolactic cassette), and a taxon-specific S. cerevisiae assay detecting the MRP2 gene. The ADY DNA extraction methodology has been shown to provide good purity DNA suitable for subsequent qPCR. The MLC and MRP2 qPCR assay showed characteristics of specificity, dynamic range, limit of quantification (LOQ) limit of detection (LOD), precision and trueness, which were fully compliant with international reference guidelines. The method has been shown to reliably detect 0.005% (mass/mass) of GM ML01 S. cerevisiae in commercial preparations of ADY. Copyright © 2016 Elsevier B.V. All rights reserved.

Development of multiplex PCR assay for simultaneous detection of Salmonella genus, Salmonella subspecies I, Salm. Enteritidis, Salm. Heidelberg and Salm. Typhimurium.

PubMed

Park, S H; Ricke, S C

2015-01-01

The aim of this research was to develop multiplex PCR assay that could simultaneously detect Salmonella genus, Salmonella subsp. I, Salm. Enteritidis, Heidelberg and Typhimurium because these Salmonella serovars are the most common isolates associated with poultry products. Five primers were utilized to establish multiplex PCR and applied to Salmonella isolates from chickens and farm environments. These isolates were identified as Salmonella subsp. I and 16 of 66 isolates were classified as Salm. Enteritidis, while Heidelberg or Typhimurium was not detected. We also spiked three Salmonella strains on chicken breast meat to evaluate the specificity and sensitivity of multiplex PCR as well as qPCR to optimize quantification of Salmonella in these samples. The optimized multiplex PCR and qPCR could detect approx. 2·2 CFU of Salmonella per gram after 18 h enrichment. The multiplex PCR and qPCR would provide rapid and consistent results. Also, these techniques would be useful for the detection and quantification of Salmonella in contaminated poultry, foods and environmental samples. The strategy for the rapid detection of Salmonella serovars in poultry is needed to further reduce the incidence of salmonellosis in humans. The optimized multiplex PCR will be useful to detect prevalent Salmonella serovars in poultry products. © 2014 The Society for Applied Microbiology.

Investigating the Role of Pop Songs on Vocabulary Recall, Attitude and Retention of Iranian EFL Learners: The Case of Gender

ERIC Educational Resources Information Center

Shakerian, Pouya; Rezaei, Omid; Murnani, Zeinab Toghyani; Moeinmanesh, Hamid

2016-01-01

Pop songs are, in fact, an ideal source for incidental vocabulary learning because teenagers often spend large amounts of their free time listening to music and in particular to pop songs. Employing an experimental approach, this study attempted to investigate the role of pop songs on vocabulary recall, attitude and retention of Iranian advanced…

Increased blood levels of persistent organic pollutants (POP) in obese individuals after weight loss-A review.

PubMed

Jansen, Aina; Lyche, Jan L; Polder, Anuschka; Aaseth, Jan; Skaug, Marit Aralt

2017-01-01

Lipophilic persistent organic pollutants (POP) are stored in adipose tissue. Following rapid weight loss such as when induced by bariatric surgery, an increased release of potential harmful lipophilic compounds into the blood circulation may occur. Weight reduction is recommended for overweight and obese individuals in order to decrease risk of weight-related health problems. However, in cases of significant weight reduction POP become mobilized chemicals and consequently may adversely affect health, including endocrine disruption. The objective of the present investigation was to estimate quantitatively the level of mobilization of POP following weight loss over time. According to literature search criteria, 17 studies were identified with 2061 participants. Data from 5 of the studies with 270 participants were used to assess the change in blood levels of POP in percent per kilogram weight loss. Weight loss in the included studies varied from 4.4 to 64.8 kg. In all studies, the majority of POP concentrations in blood were found to rise following weight reduction. Blood concentrations following weight reduction were elevated by 2-4% per kilogram weight loss for most POP examined. The increased POP levels were still elevated 12 mo after intervention. Most research in this field, including animal studies, is carried out on a single compound or group of selected compounds, not taking the "cocktail effect" into consideration. This does not reflect the true range of POP to which humans are actually exposed. Few chronic investigations have been published and, in particular, few studies were available that compared the increase in POP concentrations with clinical consequences as individuals lost weight. These limitations call for caution in interpreting results. The benefits of losing weight still far outweigh the potential adverse health risks. However, further studies are recommended to determine the clinical significance of increased blood levels of POPs following rapid and excessive weight loss, particularly for women attending weight reduction treatment before pregnancy.

Pelvic floor dysfunction: women's sexual concerns unraveled.

PubMed

Roos, Anne-Marie; Thakar, Ranee; Sultan, Abdul H; Burger, Curt W; Paulus, Aggie T G

2014-03-01

Sexual function of women suffering from pelvic organ prolapse (POP) and/or urinary incontinence (UI) is adversely affected. However, our current understanding of the exact relationship between female sexual dysfunction and POP and/or UI is incomplete. A qualitative study can improve our understanding by describing what women themselves perceive as the real problem. To gain a more in-depth understanding of the impact of POP and/or UI on the different categories of female sexual dysfunction by way of a qualitative study. Qualitative semistructured interviews were conducted in 37 women scheduled for pelvic floor surgery, and one was excluded from analysis due to incomplete recordings. The impact of POP and/or UI on female sexual function. Only 17% of women were completely positive about their sex life. Both POP and UI had a negative effect on body image. Women with POP had a negative image of their vagina, which caused them to be insecure about their partner's sexual experience, while women with UI were embarrassed about their incontinence and pad use, and feared smelling of urine. Worries about the presence of POP during sexual activity, discomfort from POP, and reduced genital sensations were the most important reasons for decreased desire, arousal, and difficulty reaching an orgasm in women with POP. Fear of incontinence during intercourse affected desire, arousal, and orgasm and could be a cause for dyspareunia in women with UI. Desire was divided into two main elements: "drive" and "motivation." Although "drive," i.e., spontaneous sexual interest, was not commonly affected by POP and/or UI, a decrease in "motivation" or the willingness to engage in sexual activity was the most common sexual dysfunction mentioned. Body image plays a key role in the sexual functioning of women with POP and/or UI with the biggest impact on women's "motivation." © 2013 International Society for Sexual Medicine.

Persistent organic pollutants in fat of three species of Pacific pelagic longline caught sea turtles: Accumulation in relation to ingested plastic marine debris

USGS Publications Warehouse

Clukey, Katharine; Lepczyk, Christopher A.; Balazs, George H.; Work, Thierry M.; Li, Qing X.; Bachman, Melanie J.; Lynch, Jennifer M.

2017-01-01

In addition to eating contaminated prey, sea turtles may be exposed to persistent organic pollutants (POPs) from ingesting plastic debris that has absorbed these chemicals. Given the limited knowledge about POPs in pelagic sea turtles and how plastic ingestion influences POP exposure, our objectives were to: 1) provide baseline contaminant levels of three species of pelagic Pacific sea turtles; and 2) assess trends of contaminant levels in relation to species, sex, length, body condition and capture location. In addition, we hypothesized that if ingesting plastic is a significant source of POP exposure, then the amount of ingested plastic may be correlated to POP concentrations accumulated in fat. To address our objectives we compared POP concentrations in fat samples to previously described amounts of ingested plastic from the same turtles. Fat samples from 25 Pacific pelagic sea turtles [2 loggerhead (Caretta caretta), 6 green (Chelonia mydas) and 17 olive ridley (Lepidochelys olivacea) turtles] were analyzed for 81 polychlorinated biphenyls (PCBs), 20 organochlorine pesticides, and 35 brominated flame-retardants. The olive ridley and loggerhead turtles had higher ΣDDTs (dichlorodiphenyltrichloroethane and metabolites) than ΣPCBs, at a ratio similar to biota measured in the South China Sea and southern California. Green turtles had a ratio close to 1:1. These pelagic turtles had lower POP levels than previously reported in nearshore turtles. POP concentrations were unrelated to the amounts of ingested plastic in olive ridleys, suggesting that their exposure to POPs is mainly through prey. In green turtles, concentrations of ΣPCBs were positively correlated with the number of plastic pieces ingested, but these findings were confounded by covariance with body condition index (BCI). Green turtles with a higher BCI had eaten more plastic and also had higher POPs. Taken together, our findings suggest that sea turtles accumulate most POPs through their prey rather than marine debris.

Relationship Between Pelvic Organ Prolapse and Non-Human Papillomavirus Pap Smear Abnormalities.

PubMed

Menhaji, Kimia; Harvie, Heidi S; Cheston, Emily; Levin, Pamela J; Arya, Lily A; Andy, Uduak U

2017-07-13

The aim of this study was to determine the association between pelvic organ prolapse (POP) and non-human papillomavirus (HPV) Papanicolaou (Pap) smear abnormalities. This was a retrospective cohort study of women aged 40 to 70 years who presented for consultation at our institution between 2010 and 2015 and had results of a Pap smear and HPV test available within 5 years of their visit. We extracted demographic information, medical and social history, Pap smear, and HPV results from the electronic medical record. Associations between the presence of POP and non-HPV Pap smear abnormalities were estimated using univariable and multivariable analyses. We reviewed 1590 charts and excluded 980 women, leaving 610 women in the study: 183 with POP and 427 without POP. Women with POP were significantly older (58.2 ± 7.2 vs 55.6 ± 6.6, P < 0.01) and more likely to have a remote (>10 year) history of abnormal Pap smear (24.0% vs 14.8%, P < 0.01). The rate of non-HPV-associated abnormal Pap smears was higher in the POP group than in the non-POP group (12/183 [6.6%] vs 12/427 [2.8%], P = 0.029). In the POP group, the rate of non-HPV Pap smear abnormality was significantly associated with increasing prolapse stage (stage 1: 0/16 [0%], stage 2: 5/77 [6.5%], stage 3: 3/73 [4.1%], stage 4: 4/17 [23.5%]; P = 0.02). After controlling for age and remote history of abnormal Pap smear, the odds ratio for non-HPV Pap smear abnormalities in the POP group remained significant (2.49; 95% confidence interval, 1.08-5.79). Human papillomavirus-negative Pap smear abnormalities may be related to POP. Our findings have important implications for surgeons seeking to leave the cervix in situ in women with POP.

Adapting and Bending the Portal to the Public: Evaluation of an NSF-Funded Science Communication Model for UNAVCO's Geoscience Summer Internships

NASA Astrophysics Data System (ADS)

Dutilly, E.; Charlevoix, D. J.; Bartel, B. A.

2017-12-01

UNAVCO is a National Science Foundation (NSF) facility specializing in geodesy. As part of its education and outreach work, it operates annual summer internships. In 2016, UNAVCO joined the Portal to the Public (PoP) network and the PoP model was adapted and bent to provide science communication professional development for summer interns. PoP is one way that UNAVCO invests in and trains future generations of geoscientists. The NSF-funded PoP initiative and its network, PoPNet, is a premier outreach framework connecting scientists and public audiences for over a decade. PoPNet is a network of sixty organizations committed to using the PoP method to engage the public in face-to-face interactions with practicing scientists. The PoP initiative provides professional development to scientists focused on best practices in science communication, helps them to develop an interactive exhibit consistent with their current research, and offers them a venue for interacting with the public. No other evaluation work to date has examined how summer internships can uptake the PoP model. This presentation focuses on evaluation findings from two cohorts of summer interns across two years. Three primary domains were assessed: how demographic composition across cohorts required changes to the original PoP framework, which of the PoP professional development trainings were valued (or not) by interns, and changes to intern knowledge, attitudes, and abilities to communicate science. Analyses via surveys and interviews revealed that level of intern geoscience knowledge was a major factor in deciding the focus of the work, specifically whether to create new hands-on exhibits or use existing ones. Regarding the use of PoP trainings, there was no obvious pattern in what interns preferred. Most growth and learning for interns occurred during and after the outreach activity. Results of this evaluation can be used to inform other applications of the PoP approach in summer internships.

Following the Cosmic Evolution of Pristine Gas. II. The Search for Pop III–bright Galaxies

NASA Astrophysics Data System (ADS)

Sarmento, Richard; Scannapieco, Evan; Cohen, Seth

2018-02-01

Direct observational searches for Population III (Pop III) stars at high redshift are faced with the question of how to select the most promising targets for spectroscopic follow-up. To help answer this, we use a large-scale cosmological simulation, augmented with a new subgrid model that tracks the fraction of pristine gas, to follow the evolution of high-redshift galaxies and the Pop III stars they contain. We generate rest-frame ultraviolet (UV) luminosity functions for our galaxies and find that they are consistent with current z≥slant 7 observations. Throughout the redshift range 7≤slant z≤slant 15, we identify “Pop III–bright” galaxies as those with at least 75% of their flux coming from Pop III stars. While less than 1% of galaxies brighter than {m}UV,{AB}}=31.4 mag are Pop III–bright in the range 7≤slant z≤slant 8, roughly 17% of such galaxies are Pop III–bright at z = 9, immediately before reionization occurs in our simulation. Moving to z = 10, {m}UV,{AB}}=31.4 mag corresponds to larger, more luminous galaxies, and the Pop III–bright fraction falls off to 5%. Finally, at the highest redshifts, a large fraction (29% at z = 14 and 41% at z = 15) of all galaxies are Pop III–bright regardless of magnitude. While {m}UV,{AB}}=31.4 mag galaxies are extremely rare during this epoch, we find that 13% of galaxies at z = 14 are Pop III–bright with {m}UV,{AB}}≤slant 33 mag, a intrinsic magnitude within reach of the James Webb Space Telescope using lensing. Thus, we predict that the best redshift to search for luminous Pop III–bright galaxies is just before reionization, while lensing surveys for fainter galaxies should push to the highest redshifts possible.

Autoacetylation of the Ralstonia solanacearum effector PopP2 targets a lysine residue essential for RRS1-R-mediated immunity in Arabidopsis.

PubMed

Tasset, Céline; Bernoux, Maud; Jauneau, Alain; Pouzet, Cécile; Brière, Christian; Kieffer-Jacquinod, Sylvie; Rivas, Susana; Marco, Yves; Deslandes, Laurent

2010-11-18

Type III effector proteins from bacterial pathogens manipulate components of host immunity to suppress defence responses and promote pathogen development. In plants, host proteins targeted by some effectors called avirulence proteins are surveyed by plant disease resistance proteins referred to as "guards". The Ralstonia solanacearum effector protein PopP2 triggers immunity in Arabidopsis following its perception by the RRS1-R resistance protein. Here, we show that PopP2 interacts with RRS1-R in the nucleus of living plant cells. PopP2 belongs to the YopJ-like family of cysteine proteases, which share a conserved catalytic triad that includes a highly conserved cysteine residue. The catalytic cysteine mutant PopP2-C321A is impaired in its avirulence activity although it is still able to interact with RRS1-R. In addition, PopP2 prevents proteasomal degradation of RRS1-R, independent of the presence of an integral PopP2 catalytic core. A liquid chromatography/tandem mass spectrometry analysis showed that PopP2 displays acetyl-transferase activity leading to its autoacetylation on a particular lysine residue, which is well conserved among all members of the YopJ family. These data suggest that this lysine residue may correspond to a key binding site for acetyl-coenzyme A required for protein activity. Indeed, mutation of this lysine in PopP2 abolishes RRS1-R-mediated immunity. In agreement with the guard hypothesis, our results favour the idea that activation of the plant immune response by RRS1-R depends not only on the physical interaction between the two proteins but also on its perception of PopP2 enzymatic activity.

Self-rated health and chronic conditions are associated with blood concentrations of persistent organic pollutants in the general population of Catalonia, Spain.

PubMed

Gasull, Magda; Pallarès, Natàlia; Salcedo, Natalia; Pumarega, José; Alonso, Jordi; Porta, Miquel

2015-11-01

Self-rated health (SRH) is a powerful predictor of mortality, morbidity, and need for health services. SRH generally increases with educational level, and decreases with age, number of chronic conditions, and body mass index (BMI). Because human concentrations of most persistent organic pollutants (POPs) also vary by age, education, and BMI, and because of the physiological and clinical effects of POPs, we hypothesized that body concentrations of POPs are inversely associated with SRH. To analyze the relation between serum concentrations of POPs and SRH in the general population of Catalonia, Spain, taking into account sociodemographic factors and BMI, as well as chronic health conditions and mental disorders, measured by the General Health Questionnaire-12 (GHQ-12). POP serum concentrations were measured by gas chromatography with electron-capture detection in 919 participants of the Catalan Health Interview Survey. Individuals with higher concentrations of POPs had significantly poorer SRH; e.g., the median concentration of HCB in subjects with poor SRH was twice as high as in subjects with excellent SRH (366 ng/g vs. 169 ng/g, respectively; p-value<0.001). In crude models and in models adjusted for sex and BMI, the POPs-SRH association was often dose-dependent, and the likelihood of poor or regular SRH was 2 to 4-times higher in subjects with POP concentrations in the top quartile. In models adjusted for age or for chronic conditions virtually all ORs were near unity. No associations were found between POP levels and GHQ-12. Individuals with higher concentrations of POPs had significantly poorer SRH, an association likely due to age and chronic conditions, but not to sex, education, social class, BMI, or mental disorders. Copyright © 2015 Elsevier Inc. All rights reserved.

Abundance profiling of extremely metal-poor stars and supernova properties in the early universe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tominaga, Nozomu; Iwamoto, Nobuyuki; Nomoto, Ken'ichi, E-mail: tominaga@konan-u.ac.jp, E-mail: iwamoto.nobuyuki@jaea.go.jp, E-mail: nomoto@astron.s.u-tokyo.ac.jp

2014-04-20

After the big bang nucleosynthesis, the first heavy element enrichment in the universe was made by a supernova (SN) explosion of a population (Pop) III star (Pop III SN). The abundance ratios of elements produced from Pop III SNe are recorded in abundance patterns of extremely metal-poor (EMP) stars. The observations of the increasing number of EMP stars have made it possible to statistically constrain the explosion properties of Pop III SNe. We present Pop III SN models whose nucleosynthesis yields well reproduce, individually, the abundance patterns of 48 such metal-poor stars as [Fe/H] ≲ – 3.5. We then derivemore » relations between the abundance ratios of EMP stars and certain explosion properties of Pop III SNe: the higher [(C + N)/Fe] and [(C + N)/Mg] ratios correspond to the smaller ejected Fe mass and the larger compact remnant mass, respectively. Using these relations, the distributions of the abundance ratios of EMP stars are converted to those of the explosion properties of Pop III SNe. Such distributions are compared with those of the explosion properties of present day SNe: the distribution of the ejected Fe mass of Pop III SNe has the same peak as that of the present day SNe but shows an extended tail down to ∼10{sup –2}-10{sup –5} M {sub ☉}, and the distribution of the mass of the compact remnant of Pop III SNe is as wide as that of the present-day, stellar-mass black holes. Our results demonstrate the importance of large samples of EMP stars obtained by ongoing and future EMP star surveys and subsequent high-dispersion spectroscopic observations in clarifying the nature of Pop III SNe in the early universe.« less

Visualizing intramyocardial steam formation with a radiofrequency ablation catheter incorporating near-field ultrasound.

PubMed

Wright, Matthew; Harks, Erik; Deladi, Szabolcs; Fokkenrood, Steven; Zuo, Fei; Van Dusschoten, Anneke; Kolen, Alexander F; Belt, Harm; Sacher, Frederic; Hocini, Mélèze; Haïssaguerre, Michel; Jaïs, Pierre

2013-12-01

Steam pops are a risk of irrigated RF ablation even when limiting power delivery. There is currently no way to predict gas formation during ablation. It would be useful to visualize intramyocardial gas formation prior to a steam pop occurring using near-field ultrasound integrated into a RF ablation catheter. In an in vivo open-chest ovine model (n = 9), 86 lesions were delivered to the epicardial surface of the ventricles. Energy was delivered for 15-60 seconds, to achieve lesions with and without steam pops, based on modeling data. The ultrasound image was compared to a digital audio recording from within the pericardium by a blinded observer. Of 86 lesions, 28 resulted in an audible steam pop. For lesions that resulted in a steam pop compared to those that did not (n = 58), the mean power delivered was 8.0 ± 1.8 W versus 6.7 ± 2.0 W, P = 0.006. A change in US contrast due to gas formation in the tissue occurred in all lesions that resulted in a steam pop. In 4 ablations, a similar change in US contrast was observed in the tissue and RF delivery was stopped; in these cases, no pop occurred. The mean depth of gas formation was 0.9 ± 0.8 mm, which correlated with maximal temperature predicted by modeling. Changes in US contrast occurred 7.6 ± 7.2 seconds before the impedance rise and 7.9 ± 6.2 seconds (0.1-17.0) before an audible pop. Integrated US in an RF ablation catheter is able to visualize gas formation intramyocardially several seconds prior to a steam pop occurring. This technology may help prevent complications arising from steam pops. © 2013 Wiley Periodicals, Inc.

Ultra high performance liquid chromatography-quadrupole-time of flight analysis for the identification and the determination of resveratrol and its metabolites in mouse plasma.

PubMed

Menet, M C; Cottart, C H; Taghi, M; Nivet-Antoine, V; Dargère, D; Vibert, F; Laprévote, O; Beaudeux, J-L

2013-01-25

Resveratrol is a polyphenol that has numerous interesting biological properties, but, per os, it is quickly metabolized. Some of its metabolites are more concentrated than resveratrol, may have greater biological activities, and may act as a kind of store for resveratrol. Thus, to understand the biological impact of resveratrol on a physiological system, it is crucial to simultaneously analyze resveratrol and its metabolites in plasma. This study presents an analytical method based on UHPLC-Q-TOF mass spectrometry for the quantification of resveratrol and of its most common hydrophilic metabolites. The use of (13)C- and D-labeled standards specific to each molecule led to a linear calibration curve on a larger concentration range than described previously. The use of high resolution mass spectrometry in the full scan mode enabled simultaneous identification and quantification of some hydrophilic metabolites not previously described in mice. In addition, UHPLC separation, allowing run times lower than 10 min, can be used in studies that requiring analysis of many samples. Copyright © 2012 Elsevier B.V. All rights reserved.

Climate change and environmental concentrations of POPs: A review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nadal, Martí, E-mail: marti.nadal@urv.cat; Marquès, Montse; Mari, Montse

In recent years, the climate change impact on the concentrations of persistent organic pollutants (POPs) has become a topic of notable concern. Changes in environmental conditions such as the increase of the average temperature, or the UV-B radiation, are likely to influence the fate and behavior of POPs, ultimately affecting human exposure. The state of the art of the impact of climate change on environmental concentrations of POPs, as well as on human health risks, is here reviewed. Research gaps are also identified, while future studies are suggested. Climate change and POPs are a hot issue, for which wide attentionmore » should be paid not only by scientists, but also and mainly by policy makers. Most studies reported in the scientific literature are focused on legacy POPs, mainly polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs) and pesticides. However, the number of investigations aimed at estimating the impact of climate change on the environmental levels of polycyclic aromatic hydrocarbons (PAHs) is scarce, despite of the fact that exposure to PAHs and photodegradation byproducts may result in adverse health effects. Furthermore, no data on emerging POPs are currently available in the scientific literature. In consequence, an intensification of studies to identify and mitigate the indirect effects of the climate change on POP fate is needed to minimize the human health impact. Furthermore, being this a global problem, interactions between climate change and POPs must be addressed from an international perspective.« less

Climate change and environmental concentrations of POPs: A review.

PubMed

Nadal, Martí; Marquès, Montse; Mari, Montse; Domingo, José L

2015-11-01

In recent years, the climate change impact on the concentrations of persistent organic pollutants (POPs) has become a topic of notable concern. Changes in environmental conditions such as the increase of the average temperature, or the UV-B radiation, are likely to influence the fate and behavior of POPs, ultimately affecting human exposure. The state of the art of the impact of climate change on environmental concentrations of POPs, as well as on human health risks, is here reviewed. Research gaps are also identified, while future studies are suggested. Climate change and POPs are a hot issue, for which wide attention should be paid not only by scientists, but also and mainly by policy makers. Most studies reported in the scientific literature are focused on legacy POPs, mainly polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs) and pesticides. However, the number of investigations aimed at estimating the impact of climate change on the environmental levels of polycyclic aromatic hydrocarbons (PAHs) is scarce, despite of the fact that exposure to PAHs and photodegradation byproducts may result in adverse health effects. Furthermore, no data on emerging POPs are currently available in the scientific literature. In consequence, an intensification of studies to identify and mitigate the indirect effects of the climate change on POP fate is needed to minimize the human health impact. Furthermore, being this a global problem, interactions between climate change and POPs must be addressed from an international perspective. Copyright © 2015 Elsevier Inc. All rights reserved.

Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples

PubMed Central

2010-01-01

Background Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR) is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Results Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. Conclusions We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system. PMID:20492695

Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples.

PubMed

Mehta, Rohini; Birerdinc, Aybike; Hossain, Noreen; Afendy, Arian; Chandhoke, Vikas; Younossi, Zobair; Baranova, Ancha

2010-05-21

Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR) is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system.

Computer-Aided Acquisition and Logistic Support Gateway Development

DTIC Science & Technology

1989-09-01

The initial step integrates the current vendor interfaces (Paperless Order Processing System (POPS) and SAMXIMS Procurement by Electronic Data Exchange...Paperless Order Processing System POSIX = Portable Operating System for UNIX RFQ = Request for Quotation RS-232C = The Electronics Industries

DETECTION OF STACHYBOTRYS CHARTARUM USING rRNA, tri5, AND Β-TUBULIN PRIMERS AND DETERMINING THEIR RELATIVE COPY NUMBER BY REAL TIME PCR

EPA Science Inventory

This research utilizes the quantitative polymerase chain reaction (qPCR) to determine ribosomal copy number of fungal organisms found in unhealthy indoor environments. Knowing specific copy numbers will allow for greater accuracy in quantification when utilizing current pQCR tec...

Identification and evaluation of reliable reference genes for quantitative real-time PCR analysis in tea plant (Camellia sinensis (L.) O. Kuntze)

USDA-ARS?s Scientific Manuscript database

Quantitative real-time polymerase chain reaction (qRT-PCR) is a commonly used technique for measuring gene expression levels due to its simplicity, specificity, and sensitivity. Reliable reference selection for the accurate quantification of gene expression under various experimental conditions is a...

From the viral perspective: infectious salmon anemia virus (ISAV) transcriptome during the infective process in Atlantic salmon (Salmo salar).

PubMed

Valenzuela-Miranda, Diego; Cabrejos, María Eugenia; Yañez, José Manuel; Gallardo-Escárate, Cristian

2015-04-01

The infectious salmon anemia virus (ISAV) is a severe disease that mainly affects the Atlantic salmon (Salmo salar) aquaculture industry. Although several transcriptional studies have aimed to understand Salmon-ISAV interaction through the evaluation of host-gene transcription, none of them has focused their attention upon the viral transcriptional dynamics. For this purpose, RNA-Seq and RT-qPCR analyses were conducted in gills, liver and head-kidney of S. salar challenged by cohabitation with ISAV. Results evidence the time and tissue transcript patterns involved in the viral expression and how the transcription levels of ISAV segments are directly linked with the protein abundance found in other virus of the Orthomyxoviridae family. In addition, RT-qPCR result evidenced that quantification of ISAV through amplification of segment 3 would result in a more sensitive approach for detection and quantification of ISAV. This study offers a more comprehensive approach regarding the ISAV infective process and gives novel knowledge for its molecular detection. Copyright © 2014 Elsevier B.V. All rights reserved.

Steroids in house sparrows (Passer domesticus): Effects of POPs and male quality signalling.

PubMed

Nossen, Ida; Ciesielski, Tomasz M; Dimmen, Malene V; Jensen, Henrik; Ringsby, Thor Harald; Polder, Anuschka; Rønning, Bernt; Jenssen, Bjørn M; Styrishave, Bjarne

2016-03-15

At high trophic levels, environmental contaminants have been found to affect endocrinological processes. Less attention has been paid to species at lower trophic levels. The house sparrow (Passer domesticus) may be a useful model for investigating effects of POPs in mid-range trophic level species. In male house sparrows, ornamental traits involved in male quality signalling are important for female selection. These traits are governed by endocrinological systems, and POPs may therefore interfere with male quality signalling. The aim of the present study was to use the house sparrow as a mid-range trophic level model species to study the effects of environmental contaminants on endocrinology and male quality signalling. We analysed the levels of selected PCBs, PBDEs and OCPs and investigated the possible effects of these contaminants on circulating levels of steroid hormones (4 progestagens, 4 androgens and 3 estrogens) in male and female adult house sparrows from a population on the island Leka, Norway. Plasma samples were analysed for steroid hormones by GC-MS and liver samples were analysed for environmental contaminants by GC-ECD and GC-MS. In males, we also quantified ornament traits. It was hypothesised that POPs may have endocrine disrupting effects on the local house sparrow population and can thus interfere with the steroid hormone homeostasis. Among female house sparrows, bivariate correlations revealed negative relationships between POPs and estrogens. Among male sparrows, positive relationships between dihydrotestosterone levels and PCBs were observed. In males, positive relationships were also found between steroids and beak length, and between steroids and ornamental traits such as total badge size. This was confirmed by a significant OPLS model between beak length and steroids. Although sparrows are in the mid-range trophic levels, the present study indicates that POPs may affect steroid homeostasis in house sparrows, in particular for females. For males, circulating steroid levels appears to be more associated with biometric parameters related to ornamental traits. Copyright © 2015 Elsevier B.V. All rights reserved.

Rapid geographical clustering of wound botulism in Germany after subcutaneous and intramuscular injection of heroin.

PubMed

Galldiks, Norbert; Nolden-Hoverath, Silke; Kosinski, Christoph M; Stegelmeyer, Ulrike; Schmidt, Sylvia; Dohmen, Christian; Kuhn, Jens; Gerbershagen, Kathrin; Bewermeyer, Heiko; Walger, Peter; Biniek, Rolf; Neveling, Michael; Jacobs, Andreas H; Haupt, Walter F

2007-01-01

Wound infections due to Clostridium botulinum in Germany are rare and occur predominantly in heroin injectors, especially after subcutaneous or intramuscular injection of heroin ("skin popping"), which is contaminated with spores of C. botulinum. We report a rapid geographical clustering of cases in Germany in a region between Cologne, Bonn, and Aachen with wound botulism and consecutive systemic C. botulinum intoxication in intravenous drug users (IDUs) within 6 weeks in October and November 2005. A group of 12 IDUs with wound botulism after "skin popping." Clinical data were available in 11 (92%) of 12 patients; in 7 (58%) of the 12 cases, there was cranial nerve involvement including mydriasis, diplopia, dysarthria, and dysphagia, followed by progressing symmetric and flaccid paralysis of proximal muscles of the neck, arms, trunk, and respiratory muscles. Mechanical respiratory support was necessary. Five of the IDUs were treated with antitoxin, but mechanical respiratory support could not be avoided. The mean ventilation duration was 27.4 days (range 6-77 days). In 4 patients (33%), mechanical ventilation could be avoided; two were treated with antitoxin. This report describes rapid geographical clustering of wound botulism with severe respiratory complications in IDUs after "skin popping," which has not previously been reported either in Germany or any other European country. Based on these observations and those in other European countries, we conclude that there is a trend towards "skin popping," suggesting a change in injection practices in IDUs. Secondly, we conclude that the total number of cases with wound botulism is likely to increase because "skin popping" is the main risk factor.

40 CFR 180.438 - Lambda-cyhalothrin and an isomer gamma-cyhalothrin; tolerances for residues.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Corn, pop, grain 0.05 Corn, pop, stover 1.0 Corn, sweet, forage 6.0 Corn, sweet, kernel plus cob with..., seed 1.0 Cattle, fat 3.0 Cattle, meat 0.2 Cattle, meat byproducts 0.2 Corn, field, flour 0.15 Corn, field, forage 6.0 Corn, field, grain 0.05 Corn, field, stover 1.0 Corn, pop, grain 0.05 Corn, pop, grain...

40 CFR 180.438 - Lambda-cyhalothrin and an isomer gamma-cyhalothrin; tolerances for residues.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Corn, pop, grain 0.05 Corn, pop, stover 1.0 Corn, sweet, forage 6.0 Corn, sweet, kernel plus cob with..., seed 1.0 Cattle, fat 3.0 Cattle, meat 0.2 Cattle, meat byproducts 0.2 Corn, field, flour 0.15 Corn, field, forage 6.0 Corn, field, grain 0.05 Corn, field, stover 1.0 Corn, pop, grain 0.05 Corn, pop, grain...

40 CFR 180.438 - Lambda-cyhalothrin and an isomer gamma-cyhalothrin; tolerances for residues.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Corn, pop, grain 0.05 Corn, pop, stover 1.0 Corn, sweet, forage 6.0 Corn, sweet, kernel plus cob with..., seed 1.0 Cattle, fat 3.0 Cattle, meat 0.2 Cattle, meat byproducts 0.2 Corn, field, flour 0.15 Corn, field, forage 6.0 Corn, field, grain 0.05 Corn, field, stover 1.0 Corn, pop, grain 0.05 Corn, pop, grain...

Selecting Cooking Methods to Decrease Persistent Organic Pollutant Concentrations in Food of Animal Origin Using a Consensus Decision-Making Model.

PubMed

Tan, Xiao; Gong, Zaiwu; Huang, Minji; Wang, Zhou-Jing

2017-02-14

Persistent organic pollutants (POPs) pose serious threats to human health. Increasing attention has been paid to POPs to protect the environment and prevent disease. Humans are exposed to POPs through diet (the major route), inhaling air and dust and skin contact. POPs are very lipophilic and hydrophobic, meaning that they accumulate in fatty tissues in animals and can biomagnify. Humans can therefore be exposed to relatively high POP concentrations in food of animal origin. Cooking animal products can decrease the POP contents, and different cooking methods achieve different reduction rates. Here, a consensus decision-making model with interval preference relations is used to prioritize cooking methods for specific animal products in terms of reducing POP concentrations. Two consistency mathematical expressions ( I -consistency and I I -consistency) are defined, then the ideal interval preference relations are determined for the cooking methods with respect to different social choice principles. The objective is to minimize disparities between individual judgments and the ideal consensus judgment. Consistency is used as a constraint to determine the rationality of the consistency definitions. A numerical example indicated that baking is the best cooking method for decreasing POP concentrations in grass carp. The I -consistency results were more acceptable than the I I -consistency results.

Selecting Cooking Methods to Decrease Persistent Organic Pollutant Concentrations in Food of Animal Origin Using a Consensus Decision-Making Model

PubMed Central

Tan, Xiao; Gong, Zaiwu; Huang, Minji; Wang, Zhou-Jing

2017-01-01

Persistent organic pollutants (POPs) pose serious threats to human health. Increasing attention has been paid to POPs to protect the environment and prevent disease. Humans are exposed to POPs through diet (the major route), inhaling air and dust and skin contact. POPs are very lipophilic and hydrophobic, meaning that they accumulate in fatty tissues in animals and can biomagnify. Humans can therefore be exposed to relatively high POP concentrations in food of animal origin. Cooking animal products can decrease the POP contents, and different cooking methods achieve different reduction rates. Here, a consensus decision-making model with interval preference relations is used to prioritize cooking methods for specific animal products in terms of reducing POP concentrations. Two consistency mathematical expressions (I-consistency and II-consistency) are defined, then the ideal interval preference relations are determined for the cooking methods with respect to different social choice principles. The objective is to minimize disparities between individual judgments and the ideal consensus judgment. Consistency is used as a constraint to determine the rationality of the consistency definitions. A numerical example indicated that baking is the best cooking method for decreasing POP concentrations in grass carp. The I-consistency results were more acceptable than the II-consistency results. PMID:28216589

The possible existence of Pop III NS-BH binary and its detectability

NASA Astrophysics Data System (ADS)

Kinugawa, Tomoya; Nakamura, Takashi; Nakano, Hiroyuki

2017-02-01

In the population synthesis simulations of Pop III stars, many BH (black hole)-BH binaries with merger time less than the age of the Universe (τH) are formed, while NS (neutron star)-BH binaries are not. The reason is that Pop III stars have no metal so that no mass loss is expected. Then, in the final supernova explosion to NS, much mass is lost so that the semimajor axis becomes too large for Pop III NS-BH binaries to merge within τH . However it is almost established that the kick velocity of the order of 200 ‑500  km s‑1 exists for NS from the observation of the proper motion of the pulsar. Therefore, the semimajor axis of the half of NS-BH binaries can be smaller than that of the previous argument for Pop III NS-BH binaries to decrease the merging time. We perform population synthesis Monte Carlo simulations of Pop III NS-BH binaries including the kick of NS and find that the event rate of Pop III NS-BH merger rate is 1  Gpc‑3 yr‑1 . This suggests that there is a good chance of detecting Pop III NS-BH mergers in O2 (Observation run 2) of Advanced LIGO and Advanced Virgo from this autumn.

Research on persistent organic pollutants in China on a national scale: 10 years after the enforcement of the Stockholm Convention.

PubMed

Liu, Li-Yan; Ma, Wan-Li; Jia, Hong-Liang; Zhang, Zi-Feng; Song, Wei-Wei; Li, Yi-Fan

2016-10-01

As a signatory of the Stockholm Convention and the largest developing country, China plays a very important role in implementation of the convention to reduce and finally eliminate persistent organic pollutants (POPs) in the world. In the past ten years after the enforcement in 2004, Chinese Government and scientists have made great progress on the study of POPs. The present work aims to provide an overview on recent studies on POPs in China, with particular focus on usage/emission inventory, residue inventory, and pollution status of POPs on national scale. Several legend (old) and new target POPs were comprehensively summarized with progress on inventory. Furthermore, several national scale monitoring programs have been selected for the occurrence, spatial and temporal trends of POPs in China, which are compared with Asian data and Global data. Based on the observed results, some important scientific issues, such as the primary and secondary distribution patterns, the primary and secondary fractionations, and air-soil exchange of POPs, are also discussed. It is proposed that more studies should be carried out for the new targeted POPs in future for both the national and global interests. Copyright © 2016 Elsevier Ltd. All rights reserved.

Atlantic ocean surface waters buffer declining atmospheric concentrations of persistent organic pollutants.

PubMed

Nizzetto, Luca; Lohmann, Rainer; Gioia, Rosalinda; Dachs, Jordi; Jones, Kevin C

2010-09-15

Decreasing environmental concentrations of some persistent organic pollutants (POPs) have been observed at local or regional scales in continental areas after the implementation of international measures to curb primary emissions. A decline in primary atmospheric emissions can result in re-emissions of pollutants from the environmental capacitors (or secondary sources) such as soils and oceans. This may be part of the reason why concentrations of some POPs such as polychlorinated biphenyls (PCBs) have not declined significantly in the open oceanic areas, although re-emission of POPs from open ocean water has barely been documented. In contrast, results from this study show that several polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs) have undergone a marked decline (2-3 orders of magnitude for some homologues) over a major portion of the remote oligotrophic Atlantic Ocean. The decline appears to be faster than that observed over continental areas, implicating an important role of oceanic geochemical controls on levels and cycling of some POPs. For several lower chlorinated PCDD/Fs, we observed re-emission from surface water back to the atmosphere. An assessment of the effectiveness of the main sink processes highlights the role of degradation in surface waters as potentially key to explaining the different behavior between PCDD/Fs and PCBs and controlling their overall residence time in the ocean/atmosphere system. This study provides experimental evidence that the ocean has a buffering capacity - dependent on individual chemicals - which moderates the rate at which the system will respond to an underlying change in continental emissions.

Driver education and teen crashes and traffic violations in the first two years of driving in a graduated licensing system.

PubMed

Shell, Duane F; Newman, Ian M; Córdova-Cazar, Ana Lucía; Heese, Jill M

2015-09-01

Our primary research question was whether teens obtaining their intermediate-level provisional operators permit (POP) in a graduated driver licensing (GDL) environment through driver education differed in crashes and traffic violations from teens who obtained their POP by completing a supervised driving certification log without taking driver education. A descriptive epidemiological study examining a census of all teen drivers in Nebraska (151,880 teens, 48.6% girls, 51.4% boys) during an eight year period from 2003 to 2010 was conducted. The driver education cohort had significantly fewer crashes, injury or fatal crashes, violations, and alcohol-related violations than the certification log cohort in both years one and two of driving following receipt of the POP. Hierarchical logistic regression was conducted, controlling for gender, race/ethnicity, median household income, urban-rural residence, and age receiving the POP. In both year one and two of driving, teens in the certification log cohort had higher odds of a crash, injury or fatal crash, violation, or alcohol-related violation. Findings support that relative to a supervised driving certification log approach, teens taking driver education are less likely to be involved in crashes or to receive a traffic violation during their first two years of driving in an intermediate stage in a graduated driver licensing system. Because teen crash and fatality rates are highest at ages 16-18, these reductions are especially meaningful. Driver education appears to make a difference in teen traffic outcomes at a time when risk is highest. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Emerging Persistent Organic Pollutants in Chinese Bohai Sea and Its Coastal Regions

PubMed Central

Wang, Yawei; Pan, Yuanyuan

2014-01-01

Emerging persistent organic pollutants (POPs) have widely aroused public concern in recent years. Polybrominated diphenyl ethers (PBDEs) and perfluorooctane sulfonyl fluoride/perfluorooctane sulfonic acid (POSF/PFOS) had been newly listed in Stockholm Convention in 2009, and short chain chlorinated paraffins (SCCPs) and hexabromocyclododecanes (HBCDs) were listed as candidate POPs. Bohai Sea is located in the arms of numbers of industrial cities, the semienclosed location of which makes it an ideal sink of emerging pollutants. In the present paper, latest contamination status of emerging POPs in Bohai Sea was reviewed. According to the literature data, Bohai Sea areas are not heavily contaminated by emerging POPs (PBDE: 0.01–720 ng/g; perfluorinated compounds: 0.1–304 ng/g; SCCPs: 64.9–5510 ng/g; HBCDs: nd-634 ng/g). Therefore, humans are not likely to be under serious risk of emerging POPs exposure through consuming seafood from Bohai Sea. However, the ubiquitous occurrence of emerging POPs in Bohai Sea region might indicate that more work should be done to expand the knowledge about potential risk of emerging POPs pollution. PMID:24688410

Evaluation of Suitable Reference Genes for Normalization of qPCR Gene Expression Studies in Brinjal (Solanum melongena L.) During Fruit Developmental Stages.

PubMed

Kanakachari, Mogilicherla; Solanke, Amolkumar U; Prabhakaran, Narayanasamy; Ahmad, Israr; Dhandapani, Gurusamy; Jayabalan, Narayanasamy; Kumar, Polumetla Ananda

2016-02-01

Brinjal/eggplant/aubergine is one of the major solanaceous vegetable crops. Recent availability of genome information greatly facilitates the fundamental research on brinjal. Gene expression patterns during different stages of fruit development can provide clues towards the understanding of its biological functions. Quantitative real-time PCR (qPCR) has become one of the most widely used methods for rapid and accurate quantification of gene expression. However, its success depends on the use of a suitable reference gene for data normalization. For qPCR analysis, a single reference gene is not universally suitable for all experiments. Therefore, reference gene validation is a crucial step. Suitable reference genes for qPCR analysis of brinjal fruit development have not been investigated so far. In this study, we have selected 21 candidate reference genes from the Brinjal (Solanum melongena) Plant Gene Indices database (compbio.dfci.harvard.edu/tgi/plant.html) and studied their expression profiles by qPCR during six different fruit developmental stages (0, 5, 10, 20, 30, and 50 days post anthesis) along with leaf samples of the Pusa Purple Long (PPL) variety. To evaluate the stability of gene expression, geNorm and NormFinder analytical softwares were used. geNorm identified SAND (SAND family protein) and TBP (TATA binding protein) as the best pairs of reference genes in brinjal fruit development. The results showed that for brinjal fruit development, individual or a combination of reference genes should be selected for data normalization. NormFinder identified Expressed gene (expressed sequence) as the best single reference gene in brinjal fruit development. In this study, we have identified and validated for the first time reference genes to provide accurate transcript normalization and quantification at various fruit developmental stages of brinjal which can also be useful for gene expression studies in other Solanaceae plant species.

Combined quantification of pulmonary Pneumocystis jirovecii DNA and serum (1->3)-β-D-glucan for differential diagnosis of pneumocystis pneumonia and Pneumocystis colonization.

PubMed

Damiani, Céline; Le Gal, Solène; Da Costa, Cécilia; Virmaux, Michèle; Nevez, Gilles; Totet, Anne

2013-10-01

This study assessed a quantitative PCR (qPCR) assay for Pneumocystis jirovecii quantification in bronchoalveolar lavage (BAL) fluid samples combined with serum (1→3)-β-d-glucan (BG) level detection to distinguish Pneumocystis pneumonia (PCP) from pulmonary colonization with P. jirovecii. Forty-six patients for whom P. jirovecii was initially detected in BAL fluid samples were retrospectively enrolled. Based on clinical data and results of P. jirovecii detection, 17 and 29 patients were diagnosed with PCP and colonization, respectively. BAL fluid samples were reassayed using a qPCR assay targeting the mitochondrial large subunit rRNA gene. qPCR results and serum BG levels (from a Fungitell kit) were analyzed conjointly. P. jirovecii DNA copy numbers were significantly higher in the PCP group than in the colonization group (1.3 × 10(7) versus 3.4 × 10(3) copies/μl, P < 0.05). A lower cutoff value (1.6 × 10(3) copies/μl) achieving 100% sensitivity for PCP diagnosis and an upper cutoff value (2 × 10(4) copies/μl) achieving 100% specificity were determined. Applying these two values, 13/17 PCP patients and 19/29 colonized patients were correctly assigned to their patient groups. For the remaining 14 patients with P. jirovecii DNA copy numbers between the cutoff values, PCP and colonization could not be distinguished on the basis of qPCR results. Four of these patients who were initially assigned to the PCP group presented BG levels of ≥100 pg/ml. The other 10 patients, who were initially assigned to the colonization group, presented BG levels of <100 pg/ml. These results suggest that the combination of the qPCR assay, applying cutoff values of 1.6 × 10(3) and 2 × 10(4) copies/μl, and serum BG detection, applying a 100 pg/ml threshold, can differentiate PCP and colonization diagnoses.

Combined Quantification of Pulmonary Pneumocystis jirovecii DNA and Serum (1→3)-β-d-Glucan for Differential Diagnosis of Pneumocystis Pneumonia and Pneumocystis Colonization

PubMed Central

Le Gal, Solène; Da Costa, Cécilia; Virmaux, Michèle; Nevez, Gilles; Totet, Anne

2013-01-01

This study assessed a quantitative PCR (qPCR) assay for Pneumocystis jirovecii quantification in bronchoalveolar lavage (BAL) fluid samples combined with serum (1→3)-β-d-glucan (BG) level detection to distinguish Pneumocystis pneumonia (PCP) from pulmonary colonization with P. jirovecii. Forty-six patients for whom P. jirovecii was initially detected in BAL fluid samples were retrospectively enrolled. Based on clinical data and results of P. jirovecii detection, 17 and 29 patients were diagnosed with PCP and colonization, respectively. BAL fluid samples were reassayed using a qPCR assay targeting the mitochondrial large subunit rRNA gene. qPCR results and serum BG levels (from a Fungitell kit) were analyzed conjointly. P. jirovecii DNA copy numbers were significantly higher in the PCP group than in the colonization group (1.3 × 107 versus 3.4 × 103 copies/μl, P < 0.05). A lower cutoff value (1.6 × 103 copies/μl) achieving 100% sensitivity for PCP diagnosis and an upper cutoff value (2 × 104 copies/μl) achieving 100% specificity were determined. Applying these two values, 13/17 PCP patients and 19/29 colonized patients were correctly assigned to their patient groups. For the remaining 14 patients with P. jirovecii DNA copy numbers between the cutoff values, PCP and colonization could not be distinguished on the basis of qPCR results. Four of these patients who were initially assigned to the PCP group presented BG levels of ≥100 pg/ml. The other 10 patients, who were initially assigned to the colonization group, presented BG levels of <100 pg/ml. These results suggest that the combination of the qPCR assay, applying cutoff values of 1.6 × 103 and 2 × 104 copies/μl, and serum BG detection, applying a 100 pg/ml threshold, can differentiate PCP and colonization diagnoses. PMID:23903553

[Impact of colpocleisis on body image in women with severe pelvic organ prolapse].

PubMed

Zhang, Ying-hui; Lu, Yong-xian; Liu, Xin; Liu, Jing-xia; Shen, Wen-jie; Wang, Wen-ying; Ge, Jing; Zhao, Ying; Niu, Ke

2011-06-01

To investigate the impact of colpocleisis on body image in women with severe pelvic organ prolapse (POP). From Oct. 2005 to Feb. 2010, 60 POP patients with stage III and IV by POP quantitation system underwent total or partial colpocleisis. Patients received body image evaluation before and 1 year after operation. One year after operation, 52 (87%, 52/60) patients completed body image evaluation. Before and 1 year after operation, the ratio of answer "Not at all" of questions such as "Have you felt less physically attractive as a result of your vaginal prolapse?", "Have you been feeling less feminine as a result of your vaginal prolapse?", "Did you find it difficult to look at yourself naked?", "Have you been feeling less sexually attractive as a result of your vaginal prolapse?", "Have you felt dissatisfied with your body?" were 25% and 96% (P < 0.01), 21% and 96% (P < 0.01), 37% and 67% (P = 0.018), 29% and 96% (P < 0.01), 12% and 83% (P < 0.01), respectively, indicating significant improvement on body image after operation for patients treated by colpocleisis. Women underwent colpocleisis for severe POP could not decrease their body image as a result of the disability of vaginal intercourse.

RNase MRP RNA and RNase P activity in plants are associated with a Pop1p containing complex

PubMed Central

Krehan, Mario; Heubeck, Christian; Menzel, Nicolas; Seibel, Peter; Schön, Astrid

2012-01-01

RNase P processes the 5′-end of tRNAs. An essential catalytic RNA has been demonstrated in Bacteria, Archaea and the nuclei of most eukaryotes; an organism-specific number of proteins complement the holoenzyme. Nuclear RNase P from yeast and humans is well understood and contains an RNA, similar to the sister enzyme RNase MRP. In contrast, no protein subunits have yet been identified in the plant enzymes, and the presence of a nucleic acid in RNase P is still enigmatic. We have thus set out to identify and characterize the subunits of these enzymes in two plant model systems. Expression of the two known Arabidopsis MRP RNA genes in vivo was verified. The first wheat MRP RNA sequences are presented, leading to improved structure models for plant MRP RNAs. A novel mRNA encoding the central RNase P/MRP protein Pop1p was identified in Arabidopsis, suggesting the expression of distinct protein variants from this gene in vivo. Pop1p-specific antibodies precipitate RNase P activity and MRP RNAs from wheat extracts. Our results provide evidence that in plants, Pop1p is associated with MRP RNAs and with the catalytic subunit of RNase P, either separately or in a single large complex. PMID:22641852

RNase MRP RNA and RNase P activity in plants are associated with a Pop1p containing complex.

PubMed

Krehan, Mario; Heubeck, Christian; Menzel, Nicolas; Seibel, Peter; Schön, Astrid

2012-09-01

RNase P processes the 5'-end of tRNAs. An essential catalytic RNA has been demonstrated in Bacteria, Archaea and the nuclei of most eukaryotes; an organism-specific number of proteins complement the holoenzyme. Nuclear RNase P from yeast and humans is well understood and contains an RNA, similar to the sister enzyme RNase MRP. In contrast, no protein subunits have yet been identified in the plant enzymes, and the presence of a nucleic acid in RNase P is still enigmatic. We have thus set out to identify and characterize the subunits of these enzymes in two plant model systems. Expression of the two known Arabidopsis MRP RNA genes in vivo was verified. The first wheat MRP RNA sequences are presented, leading to improved structure models for plant MRP RNAs. A novel mRNA encoding the central RNase P/MRP protein Pop1p was identified in Arabidopsis, suggesting the expression of distinct protein variants from this gene in vivo. Pop1p-specific antibodies precipitate RNase P activity and MRP RNAs from wheat extracts. Our results provide evidence that in plants, Pop1p is associated with MRP RNAs and with the catalytic subunit of RNase P, either separately or in a single large complex.

A newly developed real-time PCR assay for detection and quantification of Fusarium oxysporum and its use in compatible and incompatible interactions with grafted melon genotypes.

PubMed

Haegi, Anita; Catalano, Valentina; Luongo, Laura; Vitale, Salvatore; Scotton, Michele; Ficcadenti, Nadia; Belisario, Alessandra

2013-08-01

A reliable and species-specific real-time quantitative polymerase chain reaction (qPCR) assay was developed for detection of the complex soilborne anamorphic fungus Fusarium oxysporum. The new primer pair, designed on the translation elongation factor 1-α gene with an amplicon of 142 bp, was highly specific to F. oxysporum without cross reactions with other Fusarium spp. The protocol was applied to grafted melon plants for the detection and quantification of F. oxysporum f. sp. melonis, a devastating pathogen of this cucurbit. Grafting technologies are widely used in melon to confer resistance against new virulent races of F. oxysporum f. sp. melonis, while maintaining the properties of valuable commercial varieties. However, the effects on the vascular pathogen colonization have not been fully investigated. Analyses were performed on 'Charentais-T' (susceptible) and 'Nad-1' (resistant) melon cultivars, both used either as rootstock and scion, and inoculated with F. oxysporum f. sp. melonis race 1 and race 1,2. Pathogen development was compared using qPCR and isolations from stem tissues. Early asymptomatic melon infections were detected with a quantification limit of 1 pg of fungal DNA. The qPCR protocol clearly showed that fungal development was highly affected by host-pathogen interaction (compatible or incompatible) and time (days postinoculation). The principal significant effect (P ≤ 0.01) on fungal development was due to the melon genotype used as rootstock, and this effect had a significant interaction with time and F. oxysporum f. sp. melonis race. In particular, the amount of race 1,2 DNA was significantly higher compared with that estimated for race 1 in the incompatible interaction at 18 days postinoculation. The two fungal races were always present in both the rootstock and scion of grafted plants in either the compatible or incompatible interaction.

Detection and quantification by PCR assay of the biocontrol agent Pantoea agglomerans CPA-2 on apples.

PubMed

Soto-Muñoz, Lourdes; Teixidó, Neus; Usall, Josep; Viñas, Inmaculada; Torres, Rosario

2014-04-03

The registration of biological control agents requires the development of monitoring systems to detect and quantify the agent in the environment. Pantoea agglomerans CPA-2 is an effective biocontrol agent for postharvest diseases of citrus and pome fruits. The monitoring of CPA-2 in postharvest semi-commercial trials was evaluated by Rodac impression plates and the colonies isolated were confirmed by conventional PCR using the SCAR primers PAGA1 and PAGB1. Samples were taken from different surfaces that had contact with CPA-2, the surrounding environment and working clothes worn by handlers. Moreover, population dynamics of the strain CPA-2 were determined on apple surfaces using both the classical plating technique and real-time quantitative PCR (qPCR). A qPCR assay using a 3'-minor groove-binding (MGB) probe was developed for the specific detection and quantification of P. agglomerans strain CPA-2. Based on the nucleotide sequence of a SCAR fragment of CPA-2, one primer set and TaqMan MGB probe were designed. The primers SP2-F/SP2-R and the TaqMan MGB probe showed a specific detection of strain CPA-2 on apple surfaces, which was verified tested against purified DNA from 17 strains of P. agglomerans, 4 related Pantoea species, and 21 bacterial strains from other genera isolated from whole and also freshly-cut fruit and vegetables. The detection level was approximately 10(3) cells per reaction, and the standard curve was linear within a range of 5log units. Results from semi-commercial trials showed that CPA-2 had a low impact. The maximum persistence of P. agglomerans CPA-2 was not longer than 5days in plastic boxes stored at 0°C. Significant differences in CPA-2 population level dynamics were observed in results obtained by qPCR and dilution plating. These differences may indicate the presence of non-degraded DNA from non-viable cells. In conclusion, qPCR is a novel potential tool to quickly and specifically monitor recent surface colonisation by CPA-2 populations on apple surfaces during large-scale experiments that could ensure efficient and successful treatments. Copyright © 2014 Elsevier B.V. All rights reserved.

Alternative Pop-Up for Surfers with Low Back Pain

PubMed Central

Loubert, Peter V.

2010-01-01

Surfing is enjoyed by many people around the world. A common problem in surfers is back pain during the “take-off,” specifically the “pop-up.” This article describes each part of the “take-off, and introduces an alternative to the “prone pop up” - called the “knee pop-up.” This alternative is a suggested technique to alleviate the stress in the lumbar spine during surfing. PMID:21509154

Pop-out in visual search of moving targets in the archer fish.

PubMed

Ben-Tov, Mor; Donchin, Opher; Ben-Shahar, Ohad; Segev, Ronen

2015-03-10

Pop-out in visual search reflects the capacity of observers to rapidly detect visual targets independent of the number of distracting objects in the background. Although it may be beneficial to most animals, pop-out behaviour has been observed only in mammals, where neural correlates are found in primary visual cortex as contextually modulated neurons that encode aspects of saliency. Here we show that archer fish can also utilize this important search mechanism by exhibiting pop-out of moving targets. We explore neural correlates of this behaviour and report the presence of contextually modulated neurons in the optic tectum that may constitute the neural substrate for a saliency map. Furthermore, we find that both behaving fish and neural responses exhibit additive responses to multiple visual features. These findings suggest that similar neural computations underlie pop-out behaviour in mammals and fish, and that pop-out may be a universal search mechanism across all vertebrates.

Effect of popping on sorghum starch digestibility and predicted glycemic index.

PubMed

Nathakattur Saravanabavan, Sanddhya; Manchanahally Shivanna, Meera; Bhattacharya, Sila

2013-04-01

Effect of popping on carbohydrate, protein, phytic acid and minerals of three varieties (pop sorghum, maldandi and red sorghum) of sorghum were studied. Significant changes (p ≤ 0.05) in the starch degradability including total and soluble amylose content, and resistant starch occurred due to popping; in-vitro protein digestibility along with the content of albumin proteins increased. Starch characteristics had substantial differences among these three varieties which are based on the nature of endosperm and amylose content. Phytic acid content had a reduction of 20%-25% after popping. Glycemic index (GI) determined from kinetic study of enzymatic hydrolysis of sorghum starch was between 85 and 92; the rate constant for hydrolysis for these three varieties were in the range of 0.025 and 0.029 min(-1). Popping helped to control phytic acid content in sorghum and enhanced protein as well as starch digestibility.

Maternal transfer of organohalogenated compounds in sharks and stingrays.

PubMed

Weijs, Liesbeth; Briels, Nathalie; Adams, Douglas H; Lepoint, Gilles; Das, Krishna; Blust, Ronny; Covaci, Adrian

2015-03-15

Elasmobranchs can bioaccumulate considerable amounts of persistent organic pollutants (POPs) and utilize several reproductive strategies thereby influencing maternal transfer of contaminants. This study provides preliminary data on the POP transfer from pregnant females to offspring of three species (Atlantic stingrays, bonnethead, blacktip sharks) with different reproduction modes (aplacental, placental viviparity). Polychlorinated biphenyl (PCB) levels were generally higher than any other POPs. Stingrays and blacktip shark embryos contained the lowest POP concentrations while bonnetheads and the blacktip adult female had the highest concentrations. Results suggest that POPs are more readily transferred from the mother to the embryo compared to what is transferred to ova in stingrays. Statistically significant differences in levels of selected POPs were found between embryos from the left and right uterus within the same litter as well as between female and male embryos within the same litter for bonnetheads, but not for the blacktip sharks. Copyright © 2015 Elsevier Ltd. All rights reserved.

Integrated standardization concept for Angelica botanicals using quantitative NMR

PubMed Central

Gödecke, Tanja; Yao, Ping; Napolitano, José G.; Nikolić, Dejan; Dietz, Birgit M.; Bolton, Judy L.; van Breemen, Richard B.; Farnsworth, Norman R.; Chen, Shao-Nong; Lankin, David C.; Pauli, Guido F.

2011-01-01

Despite numerous in vitro/vivo and phytochemical studies, the active constituents of Angelica sinensis (AS) have not been conclusively identified for the standardization to bioactive markers. Phytochemical analyses of AS extracts and fractions that demonstrate activity in a panel of in vitro bioassays, have repeatedly pointed to ligustilide as being (associated with) the active principle(s). Due to the chemical instability of ligustilide and related issues in GC/LC analyses, new methods capable of quantifying ligustilide in mixtures that do not rely on an identical reference standard are in high demand. This study demonstrates how NMR can satisfy the requirement for simultaneous, multi-target quantification and qualitative identification. First, the AS activity was concentrated into a single fraction by RP-solid-phase extraction, as confirmed by an (anti-)estrogenicity and cytotoxicity assay. Next, a quantitative 1H NMR (qHNMR) method was established and validated using standard compounds and comparing processing methods. Subsequent 1D/2D NMR and qHNMR analysis led to the identification and quantification of ligustilide and other minor components in the active fraction, and to the development of quality criteria for authentic AS preparations. The absolute and relative quantities of ligustilide, six minor alkyl phthalides, and groups of phenylpropanoids, polyynes, and poly-unsaturated fatty acids were measured by a combination of qHNMR and 2D COSY. The qNMR approach enables multi-target quality control of the bioactive fraction, and enables the integrated biological and chemical standardization of AS botanicals. This methodology can potentially be transferred to other botanicals with active principles that act synergistically, or that contain closely related and/or constituents, which have not been conclusively identified as the active principles. PMID:21907766

Development and preliminary evaluation of a real-time PCR assay for Halioticida noduliformans in abalone tissues.

PubMed

Greeff, Mariska R; Christison, Kevin W; Macey, Brett M

2012-06-13

Abalone Haliotis midae exhibiting typical clinical signs of tubercle mycosis were discovered in South African culture facilities in 2006, posing a significant threat to the industry. The fungus responsible for the outbreak was identified as a Peronosporomycete, Halioticida noduliformans. Currently, histopathology and gross observation are used to diagnose this disease, but these 2 methods are neither rapid nor sensitive enough to provide accurate and reliable diagnosis. Real-time quantitative PCR (qPCR) is a rapid and reliable method for the detection and quantification of a variety of pathogens, so therefore we aimed to develop a qPCR assay for species-specific detection and quantification of H. noduliformans. Effective extraction of H. noduliformans genomic DNA from laboratory grown cultures, as well as from spiked abalone tissues, was accomplished by grinding samples using a pellet pestle followed by heat lysis in the presence of Chelax-100 beads. A set of oligonucleotide primers was designed to specifically amplify H. noduliformans DNA in the large subunit (LSU) rRNA gene, and tested for cross-reactivity to DNA extracted from related and non-related fungi isolated from seaweeds, crustaceans and healthy abalone; no cross-amplification was detected. When performing PCR assays in an abalone tissue matrix, an environment designed to be a non-sterile simulation of environmental conditions, no amplification occurred in the negative controls. The qPCR assay sensitivity was determined to be approximately 0.28 pg of fungal DNA (~2.3 spores) in a 25 µl reaction volume. Our qPCR technique will be useful for monitoring and quantifying H. noduliformans for the surveillance and management of abalone tubercle mycosis in South Africa.

Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples

USGS Publications Warehouse

Stelzer, Erin A.; Strickler, Kriston M.; Schill, William B.

2012-01-01

During summer and early fall 2010, 15 river samples and 6 fecal-source samples were collected in West Virginia. These samples were analyzed by three laboratories for three microbial source tracking (MST) markers: AllBac, a general fecal indicator; BacHum, a human-associated fecal indicator; and BoBac, a ruminant-associated fecal indicator. MST markers were analyzed by means of the quantitative polymerase chain reaction (qPCR) method. The aim was to assess interlaboratory precision when the three laboratories used the same MST marker and shared deoxyribonucleic acid (DNA) extracts of the samples, but different equipment, reagents, and analyst experience levels. The term assay refers to both the markers and the procedure differences listed above. Interlaboratory precision was best for all three MST assays when using the geometric mean absolute relative percent difference (ARPD) and Friedman's statistical test as a measure of interlaboratory precision. Adjustment factors (one for each MST assay) were calculated using results from fecal-source samples analyzed by all three laboratories and applied retrospectively to sample concentrations to account for differences in qPCR results among labs using different standards and procedures. Following the application of adjustment factors to qPCR results, ARPDs were lower; however, statistically significant differences between labs were still observed for the BacHum and BoBac assays. This was a small study and two of the MST assays had 52 percent of samples with concentrations at or below the limit of accurate quantification; hence, more testing could be done to determine if the adjustment factors would work better if the majority of sample concentrations were above the quantification limit.

Selective pressurized liquid extraction of pesticides, polychlorinated biphenyls and polybrominated diphenyl ethers in a whale earplug (earwax): a novel method for analyzing organic contaminants in lipid-rich matrices.

PubMed

Robinson, Eleanor M; Trumble, Stephen J; Subedi, Bikram; Sanders, Rebel; Usenko, Sascha

2013-12-06

Lipid-rich matrices are often sinks for lipophilic contaminants, such as pesticides, polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs). Typically methods for contaminant extraction and cleanup for lipid-rich matrices require multiple cleanup steps; however, a selective pressurized liquid extraction (SPLE) technique requiring no additional cleanup has been developed for the simultaneous extraction and cleanup of whale earwax (cerumen; a lipid-rich matrix). Whale earwax accumulates in select whale species over their lifetime to form wax earplugs. Typically used as an aging technique in cetaceans, layers or laminae that comprise the earplug are thought to be associated with annual or semiannual migration and feeding patterns. Whale earplugs (earwax) represent a unique matrix capable of recording and archiving whales' lifetime contaminant profiles. This study reports the first analytical method developed for identifying and quantifying lipophilic persistent organic pollutants (POPs) in a whale earplug including organochlorine pesticides, polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs). The analytical method was developed using SPLE to extract contaminants from ∼0.25 to 0.5g aliquots of each lamina of sectioned earplug. The SPLE was optimized for cleanup adsorbents (basic alumina, silica gel, and Florisil(®)), adsorbent to sample ratio, and adsorbent order. In the optimized SPLE method, the earwax homogenate was placed within the extraction cell on top of basic alumina (5g), silica gel (15g), and Florisil(®) (10g) and the target analytes were extracted from the homogenate using 1:1 (v/v) dichloromethane:hexane. POPs were analyzed using gas chromatography-mass spectrometry with electron capture negative ionization and electron impact ionization. The average percent recoveries for the POPs were 91% (±6% relative standard deviation), while limits of detection and quantification ranged from 0.00057 to 0.96ngg(-1) and 0.0017 to 2.9ngg(-1), respectively. Pesticides, PCBs, and PBDEs, were measured in a single blue whale (Balaenoptera musculus) cerumen lamina at concentrations ranging from 0.11 to 150ng g(-1). Copyright © 2013 Elsevier B.V. All rights reserved.

Quantitative polymerase chain reaction based quantification of Brucella DNA in serum of pre- and post-therapeutic occupationally exposed infected human population.

PubMed

Thakur, Shalini; Bedi, Jasbir S; Singh, Randhir; Gill, Jatinder P S; Arora, Anil K; Kashyap, Neeraj

Brucellosis is one of the neglected zoonotic diseases in humans. The serological methods based on antibody detections are unable to detect the effectiveness of treatment in humans as antibodies persist for long time in humans even after therapy. Therefore, we developed qPCR technique to overcome such discrepancy and device a rapid and efficient test for both diagnosis and follow up of the brucellosis affected individuals. High risk suspected individuals with positive serology (RBPT, STAT and iELISA) and PCR were mainly analyzed for DNA quantification by qPCR assay. The bcsp-31 gene, a shared gene of Brucella species was amplified by genus specific primers and cloned to pGEMT™ easy vector and the cloned plasmid were used to construct a standard curve (R 2 =0.99, efficiency=1.98) over 7 orders of magnitude with sensitivity of ≈10 copy number. The assay was found 100% specific. Overall 85 individuals were found positive out of 188. Out of them, 23 serological, PCR and qPCR positive individuals were recommended for 45days therapy according to WHO regimen (Doxycycline and Rifampin) and each case was further followed by qPCR. The mean threshold cycle (C q ) before treatment was 26.05±0.347 (3940.5copies/μl), which increased significantly to 32.7±0.66 (259.13copies/μl) on 4th week during treatment, 35.12±3.12 (38.52copies/μl) at 6th week on day of treatment completion, 35.6±0.66 (34.21copies/μl) on 21st day after treatment depicting a significant reduction in DNA load over the course of treatment. Serological follow up showed that only 3 individuals had decreased STAT titre but no change in RBPT results. Out of 17 symptomatic individuals under therapy, 10 improved clinically, 5 improved clinically with persistent weakness and 2 had no effect of therapy. The study suggests that qPCR is more useful and rapid test to follow treated individuals than serology. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Interlaboratory comparison of real-time pcr protocols for quantification of general fecal indicator bacteria

USGS Publications Warehouse

Shanks, O.C.; Sivaganesan, M.; Peed, L.; Kelty, C.A.; Blackwood, A.D.; Greene, M.R.; Noble, R.T.; Bushon, R.N.; Stelzer, E.A.; Kinzelman, J.; Anan'Eva, T.; Sinigalliano, C.; Wanless, D.; Griffith, J.; Cao, Y.; Weisberg, S.; Harwood, V.J.; Staley, C.; Oshima, K.H.; Varma, M.; Haugland, R.A.

2012-01-01

The application of quantitative real-time PCR (qPCR) technologies for the rapid identification of fecal bacteria in environmental waters is being considered for use as a national water quality metric in the United States. The transition from research tool to a standardized protocol requires information on the reproducibility and sources of variation associated with qPCR methodology across laboratories. This study examines interlaboratory variability in the measurement of enterococci and Bacteroidales concentrations from standardized, spiked, and environmental sources of DNA using the Entero1a and GenBac3 qPCR methods, respectively. Comparisons are based on data generated from eight different research facilities. Special attention was placed on the influence of the DNA isolation step and effect of simplex and multiplex amplification approaches on interlaboratory variability. Results suggest that a crude lysate is sufficient for DNA isolation unless environmental samples contain substances that can inhibit qPCR amplification. No appreciable difference was observed between simplex and multiplex amplification approaches. Overall, interlaboratory variability levels remained low (<10% coefficient of variation) regardless of qPCR protocol. ?? 2011 American Chemical Society.

Pelvic floor symptoms and severity of pelvic organ prolapse in women seeking care for pelvic floor problems.

PubMed

Espuña-Pons, Montserrat; Fillol, Manuel; Pascual, María A; Rebollo, Pablo; Mora, Ana M

2014-06-01

The aim of the study was to estimate whether POP severity is related to lower urinary tract symptoms (LUTS) and symptoms of sexual difficulties, when evaluated with validated questionnaires. Multicentric cross-sectional study of 521 women seeking care for PFD in 35 specialized urogynecological clinics. Patients answered the EPIQ to detect symptoms of PFD. The severity of urinary incontinence and the OAB symptoms were measured by ICIQ-UI SF and BSAQ. POP anatomic severity was measured by the anatomic stage of each compartment, determined in pelvic examination in accordance with the IUGA-ICS terminology. A maximum POP stage (M-POP-S) was assigned to each patient: Group A, patients with no POP (stage 0-I); group B, M-POP-S stage II; and group C, M-POP-S stage III-IV. Pelvic examination demonstrated anatomic POP in 224 patients (stage from II to IV). 288 women (56.25%) were classified in group A (no prolapse); 102 (19.92%) group B (stage II); and 122 (28.83%) group C (stage III-IV). Several associations were found between studied variables and M-POP-S (age<55 years, menopause, number of vaginal deliveries, symptom of vaginal bulge, feeling of a bulge makes it difficult to have sexual relations, symptoms of stress urinary incontinence, nocturia and voiding difficulties), but the only variables independently associated were age, symptom of vaginal bulge and difficulty in having sexual relations due to feeling of a bulge. In patients seeking care for PFD, LUTS are not independently associated to the prolapse stage. Copyright © 2014. Published by Elsevier Ireland Ltd.

LONG-DURATION X-RAY FLASH AND X-RAY-RICH GAMMA-RAY BURSTS FROM LOW-MASS POPULATION III STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakauchi, Daisuke; Kashiyama, Kazumi; Nakamura, Takashi

2012-11-10

Recent numerical simulations suggest that Population III (Pop III) stars were born with masses not larger than {approx}100 M {sub Sun} and typically {approx}40 M {sub Sun }. By self-consistently considering the jet generation and propagation in the envelope of these low-mass Pop III stars, we find that a Pop III blue supergiant star has the possibility of giving rise to a gamma-ray burst (GRB) even though it keeps a massive hydrogen envelope. We evaluate observational characteristics of Pop III GRBs and predict that Pop III GRBs have a duration of {approx}10{sup 5} s in the observer frame and amore » peak luminosity of {approx}5 Multiplication-Sign 10{sup 50} erg s{sup -1}. Assuming that the E {sub p}-L {sub p} (or E {sub p}-E {sub {gamma},iso}) correlation holds for Pop III GRBs, we find that the spectrum peak energy falls at approximately a few keV (or {approx}100 keV) in the observer frame. We discuss the detectability of Pop III GRBs by future satellite missions such as EXIST and Lobster. If the E {sub p}-E {sub {gamma},iso} correlation holds, we have the possibility to detect Pop III GRBs at z {approx} 9 as long-duration X-ray-rich GRBs by EXIST. Conversely, if the E {sub p}-L {sub p} correlation holds, we have the possibility to detect Pop III GRBs up to z {approx} 19 as long-duration X-ray flashes by Lobster.« less

Validation of the International Consultation on Incontinence Questionnaire-Vaginal Symptoms (ICIQ-VS) in two south- Asian languages.

PubMed

Ekanayake, Chanil D; Pathmeswaran, Arunasalam; Herath, Rasika P; Perera, H Suharshi S; Patabendige, Malitha; Wijesinghe, Prasantha S

2017-12-01

The multifaceted nature of pelvic floor disorders means that a systematic evaluation is required for optimal treatment outcome. It is also generally acknowledged that a valid tool is necessary to objectively assess symptoms reported by affected women. The International Consultation on Incontinence Questionnaire-Vaginal Symptoms (ICIQ-VS) questionnaire was translated to Sinhala and Tamil and a validation study carried out among women attending gynecology clinics at North Colombo Teaching Hospital, Ragama, and the district general hospitals Mannar and Vavuniya. Content validity was assessed by the level of missing answers, which was < 4% and 2% for each item in Sinhala and Tamil, respectively. Construct validity was assessed by the ability of the questionnaire to differentiate between patients and controls. Both differentiated patients from controls on vaginal symptoms score (VSS) (p < 0.001), sexual symptoms score (SSS) (p < 0.01), and quality of life (QoL) (p < 0.001). There was a strong positive correlation between Pelvic Organ Prolapse Quantification (POP-Q) scores and VSS (Sinhala r s  = 0.64, p < 0.001, Tamil r s  = 0.65, p < 0.001), and QoL (Sinhala r s  = 0.49, p < 0.001, Tamil r s  = 0.60, p < 0.001). Internal consistency as assessed using Cronbach's coefficient alpha: 0.78 (0.76-0.78) and 0.83 (0.80-0.84) in Sinhala and Tamil, respectively. Test-retest reliability was assessed by weighted kappa scores (Sinhala 0.58-0.88 and Tamil 0.76-0.90). Both questionnaires were sensitive to change and showed that VSS and QoL improved following surgery (Wilcoxon matched-pairs signed-rank test p < 0.001). The validated Sinhala and Tamil translations of ICIQ-VS will be useful for assessing vaginal and sexual symptoms among women speaking Sinhala and Tamil.

Sensitive quantification of Clostridium perfringens in human feces by quantitative real-time PCR targeting alpha-toxin and enterotoxin genes.

PubMed

Nagpal, Ravinder; Ogata, Kiyohito; Tsuji, Hirokazu; Matsuda, Kazunori; Takahashi, Takuya; Nomoto, Koji; Suzuki, Yoshio; Kawashima, Kazunari; Nagata, Satoru; Yamashiro, Yuichiro

2015-10-19

Clostridium perfringens is a widespread pathogen, but the precise quantification of this subdominant gut microbe remains difficult due to its low fecal count (particularly in asymptomatic subjects) and also due to the presence of abundant polymerase-inhibitory substances in human feces. Also, information on the intestinal carriage of toxigenic C. perfringens strains in healthy subjects is sparse. Therefore, we developed a sensitive quantitative real-time PCR assays for quantification of C. perfringens in human feces by targeting its α-toxin and enterotoxin genes. To validate the assays, we finally observed the occurrence of α-toxigenic and enterotoxigenic C. perfringens in the fecal microbiota of healthy Japanese infants and young adults. The plc-specific qPCR assay was newly validated, while primers for 16S rRNA and cpe genes were retrieved from literature. The assays were validated for specificity and sensitivity in pre-inoculated fecal samples, and were finally applied to quantify C. perfringens in stool samples from apparently healthy infants (n 124) and young adults (n 221). The qPCR assays were highly specific and sensitive, with a minimum detection limit of 10(3) bacterial cells/g feces. Alpha-toxigenic C. perfringens was detected in 36% infants and 33% adults, with counts ranging widely (10(3)-10(7) bacterial cells/g). Intriguingly, the mean count of α-toxigenic C. perfringens was significantly higher in infants (6.0±1.5 log10 bacterial cells/g), as compared to that in adults (4.8±1.2). Moreover, the prevalence of enterotoxigenic C. perfringens was also found to be significantly higher in infants, as compared to that in adults. The mean enterotoxigenic C. perfringens count was 5.9±1.9 and 4.8±0.8 log10 bacterial cells/g in infants and adults, respectively. These data indicate that some healthy infants and young adults carry α-toxigenic and enterotoxigenic C. perfringens at significant levels, and may be predisposed to related diseases. Thus, high fecal carriage of toxigenic C. perfringens in healthy children warrants further investigation on its potential sources and clinical significance in these subjects. In summary, we present a novel qPCR assay for sensitive and accurate quantification of α-toxigenic and enterotoxigenic C. perfringens in human feces, which should facilitate prospective studies of the gut microbiota.

HUMAN HEALTH IMPACTS OF EXPOSURE TO POPS

EPA Science Inventory

The Stockholm Convention on persistent organic pollutants (POPs) was adopted in 2001 to protect human health and the environment from chemicals that are highly toxic, persistent, bioaccumulative and undergo long range transport. These POPs include 9 pesticides, polychlorinated d...

Integrated quantitative and qualitative workflow for in vivo bioanalytical support in drug discovery using hybrid Q-TOF-MS.

PubMed

Ranasinghe, Asoka; Ramanathan, Ragu; Jemal, Mohammed; D'Arienzo, Celia J; Humphreys, W Griffith; Olah, Timothy V

2012-03-01

UHPLC coupled with orthogonal acceleration hybrid quadrupole-TOF (Q-TOF)-MS is an emerging technique offering new strategies for the efficient screening of new chemical entities and related molecules at the early discovery stage within the pharmaceutical industry. In the first part of this article, we examine the main instrumental parameters that are critical for the integration of UHPLC-Q-TOF technology to existing bioanalytical workflows, in order to provide simultaneous quantitative and qualitative bioanalysis of samples generated following in vivo studies. Three modern Q-TOF mass spectrometers, including Bruker maXis™, Agilent 6540 and Sciex TripleTOF™ 5600, all interfaced with UHPLC systems, are evaluated in the second part of the article. The scope of this work is to demonstrate the potential of Q-TOF for the analysis of typical small molecules, therapeutic peptides (molecular weight <6000 Da), and enzymatically (i.e., trypsin, chymotrypsin and pepsin) cleaved peptides from larger proteins. This work focuses mainly on full-scan TOF data obtained under ESI conditions, the major mode of TOF operation in discovery bioanalytical research, where the compounds are selected based on their pharmacokinetic/pharmacodynamic behaviors using animal models prior to selecting a few desirable candidates for further development. Finally, important emerging TOF technologies that could potentially benefit bioanalytical research in the semi-quantification of metabolites without synthesized standards are discussed. Particularly, the utility of captive spray ionization coupled with TripleTOF 5600 was evaluated for improving sensitivity and providing normalized MS response for drugs and their metabolites. The workflow proposed compromises neither the efficiency, nor the quality of pharmacokinetic data in support of early drug discovery programs.

A Quantitative Polymerase Chain Reaction Assay for the Detection and Quantification of Epizootic Epitheliotropic Disease Virus (EEDV; Salmonid Herpesvirus 3).

PubMed

Glenney, Gavin W; Barbash, Patricia A; Coll, John A

2016-03-01

Epizootic epitheliotropic disease virus (EEDV; salmonid herpesvirus [SalHV3]; family Alloherpesviridae) causes a systemic disease of juvenile and yearling Lake Trout Salvelinus namaycush. No cell lines are currently available for the culture and propagation of EEDV, so primary diagnosis is limited to PCR and electron microscopy. To better understand the pervasiveness of EEDV (carrier or latent state of infection) in domesticated and wild Lake Trout populations, we developed a sensitive TaqMan quantitative PCR (qPCR) assay to detect the presence of the EEDV terminase gene in Lake Trout tissues. This assay was able to detect a linear standard curve over nine logs of plasmid dilution and was sensitive enough to detect single-digit copies of EEDV. The efficiency of the PCR assay was 99.4 ± 0.06% (mean ± SD), with a 95% confidence limit of 0.0296 (R(2) = 0.994). Methods were successfully applied to collect preliminary data from a number of species and water bodies in the states of Pennsylvania, New York, and Vermont, indicating that EEDV is more common in wild fish than previously known. In addition, through the development of this qPCR assay, we detected EEDV in a new salmonid species, the Cisco Coregonus artedi. The qPCR assay was unexpectedly able to detect two additional herpesviruses, the Atlantic Salmon papillomatosis virus (ASPV; SalHV4) and the Namaycush herpesvirus (NamHV; SalHV5), which both share high sequence identity with the EEDV terminase gene. With these unexpected findings, we subsequently designed three primer sets to confirm initial TaqMan qPCR assay positives and to differentiate among EEDV, ASPV, and NamHV by detecting the glycoprotein genes via SYBR Green qPCR. Received April 20, 2015; accepted November 10, 2015.

Longitudinal changes in persistent organic pollutants (POPs) from 2001 to 2009 in a sample of elderly Swedish men and women.

PubMed

Stubleski, Jordan; Lind, Lars; Salihovic, Samira; Lind, P Monica; Kärrman, Anna

2018-04-28

Prospective cohort studies evaluating the temporal trends of background-level persistent organic pollutants (POPs) and their potential negative health effects in humans are needed. The objectives of this study are to examine the five year longitudinal trend in chlorinated and brominated (Cl/Br) POP concentrations in a sample of elderly individuals and to investigate the relationship between gender, changes in body weight, plasma lipid levels and POP concentrations. In the population-based Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) study, plasma samples were collected from the same individuals over a 5 year period. Originally 992 subjects (all aged 70) were sampled between 2001 and 2004 and 814 returning subjects (all aged 75) were sampled again from 2006 to 2009. Plasma concentrations of 16 polychlorinated biphenyls (PCBs), 5 organochlorine pesticides (OCPs), octachlorinated dibenzo-p-dioxin (OCDD), and one polybrominated diphenylether (BDE 47) were determined using high-throughput 96-well plate solid phase extraction and gas chromatography-high resolution mass spectrometry (GC-HRMS). During the 5-year follow-up, plasma concentrations of all POPs significantly decreased (p < 0.00001). Median reductions ranged from 4% (PCB105) to 45% (PCB 99), with most reductions being in the 30-40% range. For most POPs, a larger decline was seen in men than in women. The relationship between the weight change and change in POP concentrations was generally negative, but a positive relationship between lipid levels and POP concentrations when expressed as wet-weight was observed. In general, similar changes in POP concentrations and their relationships to body weight were observed regardless of using either wet-weight (pg/mL) or lipid-normalized (ng/g lipid) concentrations. In this longitudinal cohort study, gender and minor, but varying changes in body weight and lipid levels greatly influenced the individual-based changes in POP concentrations. In general, our findings suggest that men and women with larger decreases in body weight and greater increases in lipid levels have the slowest decline in body burden of POPs. Based on the results from this study, either wet-weight or lipid normalized concentrations can be used to determine the percent change in POP concentrations and their relationships to physiological changes and differences. Copyright © 2018. Published by Elsevier Inc.

The Audible Pop from Thoracic Spine Thrust Manipulation and Its Relation to Short-Term Outcomes in Patients with Neck Pain

PubMed Central

Cleland, Joshua A.; Flynn, Timothy W.; Childs, John D.; Eberhart, Sarah

2007-01-01

Clinicians routinely consider the success of a thrust manipulation technique based on the presence or absence of an audible pop despite the lack of evidence suggesting that this pop is associated with improved outcomes. The purpose of this study was to determine the relationship between the number of audible pops with thoracic spinal manipulation and improvement in pain and function in patients with mechanical neck pain. In this prospective cohort study, 78 patients referred to physical therapy with mechanical neck pain underwent a standardized examination and thoracic spine manipulation treatment protocol. All patients were treated with a total of 6 thrust manipulation techniques directed to the thoracic spine followed by a basic cervical range of motion exercise. The treating clinician recorded the presence or absence of a pop during each manipulation. Outcomes were assessed at a 2–4 day follow-up with an 11-point numeric pain rating (NPRS), the Neck Disability Index, the patient Global Rating of Change (GROC), and measurements of cervical range of motion (CROM). The relationship between the number of pops and change scores for pain, disability, and CROM was first examined using Pearson correlation coefficients. Individuals were then categorized as having received ≤3 or >3 pops. Repeated measures analyses of variance were used to examine whether achievement of >3 pops resulted in improved outcome. Seventy-eight patients with a mean age of 42 (SD 11.3) years participated in the study. Pearson correlation coefficients revealed no significant correlation existed between the number of pops and outcomes with the exception of 3 of the 6 CROM measurements, which were inversely related. There was no significant interaction for group X time for any of the dependent measures (P>0.05). The odds ratio for patients experiencing dramatic improvement was in favor of the group experiencing ≤3 pops but this was not clinically meaningful (1.3: 95% CI 0.46, 3.7). The results of this analysis provide preliminary evidence for the hypothesis that there is no relationship between the number of audible pops during thoracic spine thrust manipulation and clinically meaningful improvements in pain, disability, or CROM in patients with mechanical neck pain. Additionally, a greater number of audible pops experienced was not associated with a dramatic improvement with manipulation treatment. PMID:19066662

Space activities and global popular music culture

NASA Astrophysics Data System (ADS)

Wessels, Allison Rae; Collins, Patrick

During the "space age" era, space activities appear increasingly as a theme in Western popular music, as they do in popular culture generally. In combination with the electronics and tele-communications revolution, "pop/rock" music has grown explosively during the space age to become an effectively global culture. From this base a number of trends are emerging in the pattern of influences that space activities have on pop music. The paper looks at the use of themes and imagery in pop music; the role of space technology in the modern "globalization" of pop music; and current and future links between space activities and pop music culture, including how public space programmes are affected by its influence on popular attitudes.

UniPOPS: Unified data reduction suite

NASA Astrophysics Data System (ADS)

Maddalena, Ronald J.; Garwood, Robert W.; Salter, Christopher J.; Stobie, Elizabeth B.; Cram, Thomas R.; Morgan, Lorrie; Vance, Bob; Hudson, Jerome

2015-03-01

UniPOPS, a suite of programs and utilities developed at the National Radio Astronomy Observatory (NRAO), reduced data from the observatory's single-dish telescopes: the Tucson 12-m, the Green Bank 140-ft, and archived data from the Green Bank 300-ft. The primary reduction programs, 'line' (for spectral-line reduction) and 'condar' (for continuum reduction), used the People-Oriented Parsing Service (POPS) as the command line interpreter. UniPOPS unified previous analysis packages and provided new capabilities; development of UniPOPS continued within the NRAO until 2004 when the 12-m was turned over to the Arizona Radio Observatory (ARO). The submitted code is version 3.5 from 2004, the last supported by the NRAO.

Increased frequency of involuntary semantic memories or mind-pops in schizophrenia: a diary study.

PubMed

Elua, Ia; Laws, Keith R; Kvavilashvili, Lia

2015-01-01

Hallucinations constitute a prominent symptom of schizophrenia and may take a variety of forms (verbal, visual, musical, or environmental noises). Interesting similarities exist between hallucinations and so-called mind-pops which refer to isolated fragments of one's semantic knowledge (e.g., a word/sentence, visual image, or a song/melody) that come to mind unexpectedly, often without any obvious triggers, and are difficult to control. The aim of the present study was to evaluate whether mind-pops may constitute the raw cognitive material from which hallucinations are constructed by studying the nature and frequency of mind-pops in the everyday life of people with schizophrenia and non-clinical controls. Eleven participants with schizophrenia and 14 non-clinical controls kept a diary of their mind-pops for seven days and completed a brief questionnaire every time they had a mind-pop. Schizophrenia participants reported significantly more verbal and image mind-pops than controls and their content was negative more often than in controls. No group differences were obtained in terms of reported triggers or ongoing activities. Data from both groups also supported the priming hypothesis by showing that stimuli encountered in one's environment or thoughts could later re-appear in the form of a mind-pop. The findings have implications for models of schizophrenia that emphasise the role of intrusive thoughts and memories in the aetiology and development of key psychotic symptoms.

Understanding traffic dynamics at a backbone POP

NASA Astrophysics Data System (ADS)

Taft, Nina; Bhattacharyya, Supratik; Jetcheva, Jorjeta; Diot, Christophe

2001-07-01

Spatial and temporal information about traffic dynamics is central to the design of effective traffic engineering practices for IP backbones. In this paper we study backbone traffic dynamics using data collected at a major POP on a tier-1 IP backbone. We develop a methodology that combines packet-level traces from access links in the POP and BGP routing information to build components of POP-to-POP traffic matrices. Our results show that there is wide disparity in the volume of traffic headed towards different egress POPs. At the same time, we find that current routing practices in the backbone tend to constrain traffic between ingress-egress POP pairs to a small number of paths. As a result, there is a wide variation in the utilization level of links in the backbone. Frequent capacity upgrades of the heavily used links are expensive; the need for such upgrades can be reduced by designing load balancing policies that will route more traffic over less utilized links. We identify traffic aggregates based on destination address prefixes and find that this set of criteria isolates a few aggregates that account for an overwhelmingly large portion of inter-POP traffic. We also demonstrate that these aggregates exhibit stability throughout the day on per-hour time scales, and thus they form a natural basis for splitting traffic over multiple paths in order to improve load balancing.

Multi-residue analysis of legacy POPs and emerging organic contaminants in Singapore's coastal waters using gas chromatography-triple quadrupole tandem mass spectrometry.

PubMed

Zhang, Hui; Bayen, Stéphane; Kelly, Barry C

2015-08-01

A gas chromatography-triple quadrupole mass spectrometry (GC-MS/MS) based method was developed for determination of 86 hydrophobic organic compounds in seawater. Solid-phase extraction (SPE) was employed for sequestration of target analytes in the dissolved phase. Ultrasound assisted extraction (UAE) and florisil chromatography were utilized for determination of concentrations in suspended sediments (particulate phase). The target compounds included multi-class hydrophobic contaminants with a wide range of physical-chemical properties. This list includes several polycyclic and nitro-aromatic musks, brominated and chlorinated flame retardants, methyl triclosan, chlorobenzenes, organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs). Spiked MilliQ water and seawater samples were used to evaluate the method performance. Analyte recoveries were generally good, with the exception of some of the more volatile target analytes (chlorobenzenes and bromobenzenes). The method is very sensitive, with method detection limits typically in the low parts per quadrillion (ppq) range. Analysis of 51 field-collected seawater samples (dissolved and particulate-bound phases) from four distinct coastal sites around Singapore showed trace detection of several polychlorinated biphenyl congeners and other legacy POPs, as well as several current-use emerging organic contaminants (EOCs). Polycyclic and nitro-aromatic musks, bromobenzenes, dechlorane plus isomers (syn-DP, anti-DP) and methyl triclosan were frequently detected at appreciable levels (2-20,000pgL(-1)). The observed concentrations of the monitored contaminants in Singapore's marine environment were generally comparable to previously reported levels in other coastal marine systems. To our knowledge, these are the first measurements of these emerging contaminants of concern in Singapore or Southeast Asia. The developed method may prove beneficial for future environmental monitoring of hydrophobic organic contaminants in marine environments. Further, the study provides novel information regarding several potentially hazardous contaminants of concern in Singapore's marine environment, which will aid future risk assessment initiatives. Copyright © 2015 Elsevier B.V. All rights reserved.

M4FT-15OR03100415 - Update on COF-based Adsorbent Survey

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayes, Richard T.; Dai, Sheng

2015-02-01

This letter report provides an update on activities focused on generating nanoporous adsorbents involving covalent organic frameworks (COF) and zeolitic imidazolium frameworks (ZIF). The adsorbents have been generated and screened in a uranyl-spiked brine (6 ppm U) to understand uranyl-binding behavior. Porous organic polymers (POP) also qualify under this title and are similar to the COF PPN-6 that is discussed herein. Seven COF/POP and one 1 ZIF were synthesized and screened for uranyl adsorption. Seawater screening is on-going via batch testing while flow screening systems are being developed at PNNL.

Effects of mechanical stretching on the morphology of extracellular polymers and the mRNA expression of collagens and small leucine-rich repeat proteoglycans in vaginal fibroblasts from women with pelvic organ prolapse.

PubMed

Wang, Sumei; Lü, Dongyuan; Zhang, Zhenyu; Jia, Xingyuan; Yang, Lei

2018-01-01

To determine the effect of mechanical stretching load and the efficacy of postmenopausal estrogen therapy (ET) on pelvic organ prolapse (POP), vaginal fibroblasts isolated from postmenopausal women with or without POP were subjected to 0.1-Hz uniaxial cyclic mechanical stretching (CS) with 10% elongation and 10-8 M 17-β-estradiol (E2) treatment. We investigated the morphological characteristics of extracellular polymers using scanning electron microscopy (SEM) and monitored the mRNA expression of type I collagen (COL I) and type III collagen (COL III) as well as the small leucine-rich proteoglycan (SLRP) family members decorin (DCN), biglycan (BGN), fibromodulin (FMO), and lumican (LUM), using real-time quantitative polymerase chain reaction (RT-PCR). Using SEM, certain viscoelastic polymers were found to be randomly distributed among fibroblasts, which for normal fibroblasts formed clusters of plum flower-like patterns under static-culture conditions and resembled stretched strips when stretched in culture, whereas polymers among POP fibroblasts resembled stretched strips under static-cultured conditions and presented broken networks when stretched in culture. RT-PCR revealed that COL I, DCN, BGN, FMO, and LUM mRNA expression was significantly higher in POP than in normal fibroblasts under static-culture condition. Following CS, COL I and BGN mRNA expression was significantly up-regulated in normal fibroblasts, and DCN and FMO mRNA expression was down-regulated in POP fibroblasts. Following concomitant CS and E2 treatment, significantly elevated COL I and DCN mRNA expression was observed in normal fibroblasts, and significantly elevated COL I and BGN mRNA expression was observed in POP fibroblasts. COL III mRNA expression was not significantly different between the POP and normal group, and CS did not significantly affect expression in either group, though COL III was down-regulated in normal fibroblasts concomitantly treated with E2 and CS. We conclude that the morphological distribution of extracellular polymers in POP fibroblasts exhibited higher sensitivity and lower tolerance to stretching loads than do normal fibroblasts. These mechanical properties were further reflected in the transcription of COL I. Defects in the compensatory function of BGN for DCN and LUM for FMO exist in POP fibroblasts, which further affect the structure and function of COL I in response to stretching load, ultimately resulting in abnormal reconstruction of pelvic supportive connective tissues and the occurrence of POP. ET can maintain stretching-induced elevations in COL I and DCN transcription in healthy women and improve stretching-induced COL I, DCN, BGN, and FMO transcriptional changes in POP women to prevent and improve POP. Only down-regulated COL III transcription was observed upon concomitant CS and E2 treatment in normal fibroblasts, which suggests that the tensile strength, not the elasticity, of the supportive connective tissues is damaged in POP and that the higher tensile strength induced by ET in healthy fibroblasts prevents POP. These findings confirm the role of higher sensitivity and lower tolerance to mechanical stretching in the pathogenesis of POP and further provide evidence supporting the use of ET to prevent and inhibit POP in postmenopausal women.

Pelvic organ prolapse (POP) surgery: the evidence for the repairs.

PubMed

Gomelsky, Alex; Penson, David F; Dmochowski, Roger R

2011-06-01

What is known on the subject? and What does the study add? Substantial experience of the outcomes has been gathered regarding the acute and sub-acute experience with various types of corrective procedures for POP. These include long-term POP correction as well as more recent recognition of improvement in functional disorders associated with POP such as UI, colorectal dysfunction, and sexual dysfunction. Long-term follow-up is available for some of the older types of interventions and current multicentre trials are being accrued with longer term follow-up for new interventions including mesh-type repairs. The study adds a condensed and summarized version of the current literature regarding the various interventions for POP and also provides an overview of the current controversies and areas where knowledge is incomplete and in need of further elaboration for definitive answers regarding optimization of surgical care for POP. Our aim is to summarise the available data on the transvaginal placement of synthetic mesh for pelvic organ prolapse (POP) repair, with a focus on the outcomes and complications of commercial POP-repair kits. As the stability and durability of autologous tissues may be questionable, nonabsorbable, synthetic materials are an attractive alternative for providing additional support during POP surgery. These materials are not novel, and most have been used for many years in surgical applications, e.g. hernia repairs. While theoretically appealing, the implantation of synthetic mesh in the pelvis may be associated with inherent adverse consequences, such as erosion, extrusion, and infection. Additionally, the routine use of these materials may carry potential long-term complications, such as dyspareunia, chronic pelvic pain, and vaginal distortion. The success and failure of mesh-augmented POP repair is related not only to the synthetic material itself, but also to patient- and surgeon-related factors. Recent warnings by the USA Food and Drug Administration and other groups regarding adverse events further complicate the decision to use synthetic mesh. © 2011 THE AUTHORS; BJU INTERNATIONAL © 2011 BJU INTERNATIONAL.

Pop-cola acids and tooth erosion: an in vitro, in vivo, electron-microscopic, and clinical report.

PubMed

Borjian, Amirfirooz; Ferrari, Claudia C F; Anouf, Antoni; Touyz, Louis Z G

2010-01-01

Introduction. Manufactured Colas are consumed universally as soft drinks. Evidence about the acid contents of Cola-beverages and its effects on teeth is rare. Aim. To assess (i) cola acidity and buffering capacity in vitro, (ii) tooth erosion after swishing with colas in vivo (iii) scanning electron microscopic effects on teeth of colas, and tooth-brush abrasion, and (iv) report a clinical case of erosion from cola consumption. Materials and Methods. (i) We measured six commercially available pop "Cola beverages", pH, and buffering capacities using a pH-Mettler Automatic Titrator, with weak solution of Sodium Hydroxide (ii) two cohorts, one with teeth, the second without teeth rinsed with aliquots of Cola for 60 seconds. Swished cola samples tested for calcium and phosphorus contents using standardized chemical analytical methods (iii) enamel, dentine, and the enamel-cemental junction from unerupted extracted wisdom teeth were examined with a scanning electron microscope after exposure to colas, and tested for tooth-brush abrasion; (iv) a clinical case of pop cola erosion presentation, are all described. Results. Comparisons among pop colas tested in vitro reveal high acidity with very low pH. Buffering capacities in millilitres of 0.5 M NaOH needed to increase one pH unit, to pH 5.5 and pH 7 are reported. Rinsing in vivo with pop cola causes leeching of calcium from teeth; SEM shows dental erosion, and pop-cola consumption induces advanced dental erosion and facilitates abrasion. Conclusions. (i) Pop-Cola acid activity is below the critical pH 5.5 for tooth dissolution, with high buffering capacities countering neutralization effects of saliva; (ii) calcium is leeched out of teeth after rinsing with pop colas; (iii) SEM evidence explains why chronic exposure to acid pop colas causes dental frangibles; (iv) a clinical case of pop-cola erosion confirms this.

PCDD, PCDF, dl-PCB and organochlorine pesticides monitoring in São Paulo City using passive air sampler as part of the Global Monitoring Plan.

PubMed

Tominaga, M Y; Silva, C R; Melo, J P; Niwa, N A; Plascak, D; Souza, C A M; Sato, M I Z

2016-11-15

The persistent organic pollutants (POPs), such as organochlorine pesticides and PCBs, are ordinarily monitored in the aquatic environment or in soil in the environmental quality monitoring programs in São Paulo, Brazil. One of the core matrices proposed in the POPs Global Monitoring Plan (GMP) from the Stockholm Convention list is the ambient air, which is not a usual matrix for POPs monitoring in the country. In this study POP levels were evaluated in the air samples from an urban site in São Paulo City over five years, starting in 2010 as a capacity building project for Latin America and the Caribbean region for POP monitoring in ambient air using passive samplers. Furthermore, after the end of the Project in 2012, the monitoring continued in the same sampling site as means to improving the analytical capacity building and contribute to the GMP data. The POPs monitored were 17 congeners of 2,3,7,8 chloro-substituted PCDDs and PCDFs, dioxin-like PCBs, indicator PCBs, organochlorine pesticides and toxaphene. The results show a slight decrease in PCDD/F, dl-PCBs and indicator PCBs levels along the five years. The organochlorine pesticide endosulfan was present at its highest concentration at the beginning of the monitoring period, but it was below detection level in the last year of the monitoring. Some other organochlorine pesticides were detected close to or below quantitation limits. The compounds identified were dieldrin, chlordane, α-HCH, γ-HCH, heptachlor, heptachlor epoxide, hexachlorobenzene and DDTs. Toxaphene congeners were not detected. These results have confirmed the efficacy of passive sampling for POP monitoring and the capacity building for POP analysis and monitoring was established. However more needs to be done, including expansion of sampling sites, new POPs and studies on sampling rates to be considered in calculating the concentration of POPs in ambient air using a passive sampler. Copyright © 2016 Elsevier B.V. All rights reserved.

The distribution and stratification of persistent organic pollutants and fatty acids in bottlenose dolphin (Tursiops truncatus) blubber.

PubMed

Ellisor, Debra; McLellan, William; Koopman, Heather; Schwacke, Lori; McFee, Wayne; Kucklick, John

2013-10-01

Blubber has been used for decades to monitor exposure of marine mammals to persistent organic pollutants (POPs). However, little is known about POP variability as a function of blubber depth and across the body of the animal. Remote blubber biopsy sampling (e.g, projectile biopsy) is the most common technique used to acquire samples from free-swimming animals, yet such techniques may result in variable sampling. It is important to understand whether blubber stratification or body location affects POP concentration or the concentration of other important blubber constituents such as fatty acids (FA). To investigate the influence of sampling depth and location on POP concentration, full depth blubber samples were taken from one stranded bottlenose dolphin (Tursiops truncatus) at six different body sites to assess variation in FA distribution and contaminant storage with body location. Three of the samples from different body locations were separated into histologically distinct layers to examine the effect of blubber depth and body location on POPs and FAs. In this individual, both POPs and FAs were heterogeneous with blubber depth and body location. POP concentrations were significantly greater in ventral (average ΣPBDEs 1350 ng/g lipid) and anterior (average ΣPCBs 28,700 ng/g lipid) body locations and greater in the superficial blubber layer (average ΣPCBs 35,500 ng/g lipid) when compared to the deep (8390 ng/g lipid) and middle (23,700 ng/g lipid) layers. Proportionally more dietary FAs were found in dorsal blubber and in middle and deep layers relative to other locations while the reverse was true for biosynthesized FAs. Stratification was further examined in blubber from the same body location in five additional stranded bottlenose dolphins. Although FAs were stratified with blubber depth, lipid-normalized POPs were not significantly different with depth, indicating that POP concentrations can vary in an individual with blubber depth though the direction of POP stratification is not consistent among individuals. Published by Elsevier B.V.

Pop-Cola Acids and Tooth Erosion: An In Vitro, In Vivo, Electron-Microscopic, and Clinical Report

PubMed Central

Borjian, Amirfirooz; Ferrari, Claudia C. F.; Anouf, Antoni; Touyz, Louis Z. G.

2010-01-01

Introduction. Manufactured Colas are consumed universally as soft drinks. Evidence about the acid contents of Cola-beverages and its effects on teeth is rare. Aim. To assess (i) cola acidity and buffering capacity in vitro, (ii) tooth erosion after swishing with colas in vivo (iii) scanning electron microscopic effects on teeth of colas, and tooth-brush abrasion, and (iv) report a clinical case of erosion from cola consumption. Materials and Methods. (i) We measured six commercially available pop “Cola beverages”, pH, and buffering capacities using a pH-Mettler Automatic Titrator, with weak solution of Sodium Hydroxide (ii) two cohorts, one with teeth, the second without teeth rinsed with aliquots of Cola for 60 seconds. Swished cola samples tested for calcium and phosphorus contents using standardized chemical analytical methods (iii) enamel, dentine, and the enamel-cemental junction from unerupted extracted wisdom teeth were examined with a scanning electron microscope after exposure to colas, and tested for tooth-brush abrasion; (iv) a clinical case of pop cola erosion presentation, are all described. Results. Comparisons among pop colas tested in vitro reveal high acidity with very low pH. Buffering capacities in millilitres of 0.5 M NaOH needed to increase one pH unit, to pH 5.5 and pH 7 are reported. Rinsing in vivo with pop cola causes leeching of calcium from teeth; SEM shows dental erosion, and pop-cola consumption induces advanced dental erosion and facilitates abrasion. Conclusions. (i) Pop-Cola acid activity is below the critical pH 5.5 for tooth dissolution, with high buffering capacities countering neutralization effects of saliva; (ii) calcium is leeched out of teeth after rinsing with pop colas; (iii) SEM evidence explains why chronic exposure to acid pop colas causes dental frangibles; (iv) a clinical case of pop-cola erosion confirms this. PMID:21151663

tRNAs as Biomarkers and Regulators for Breast Cancer

DTIC Science & Technology

2009-08-01

codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific...CONTRACTING ORGANIZATION : The University of Chicago Chicago, IL 60637 REPORT...Geslain, Q. Dai. 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT

Optimisation of techniques for quantification of Botrytis cinerea in grape berries and receptacles by quantitative polymerase chain reaction

USDA-ARS?s Scientific Manuscript database

Quantitative PCR (qPCR) can be used to detect and monitor pathogen colonization, but early attempts to apply the technology to Botrytis cinerea infection of grape berries have identified limitations to current techniques. In this study, four DNA extraction methods, two grinding methods, two grape or...

Understanding the transmission dynamics of Leishmania donovani to provide robust evidence for interventions to eliminate visceral leishmaniasis in Bihar, India

USDA-ARS?s Scientific Manuscript database

Molecular tools enable the collection of accurate estimates of human blood index (HBI) in Phlebotomus argentipes. The refinement of a metacyclic-specific qPCR assay to identify L. donovani in P. argentipes would enable quantification of the entomological inoculation rate (EIR) for the first time. Li...

Understanding the transmission dynamics of Leishmania donovani to provide robust evidence for interventions to eliminate visceral leishmaniasis in Bihar, India

USDA-ARS?s Scientific Manuscript database

Molecular tools enable the collection of accurate estimates of human blood index (HBI) in P. argentipes. The refinement of a metacyclic-specific qPCR assay to identify L. donovani in P. argentipes would enable quantification of the entomological inoculation rate (EIR) for the first time. Likewise, a...

Orthogonal analytical methods for botanical standardization: Determination of green tea catechins by qNMR and LC-MS/MS

PubMed Central

Napolitano, José G.; Gödecke, Tanja; Lankin, David C.; Jaki, Birgit U.; McAlpine, James B.; Chen, Shao-Nong; Pauli, Guido F.

2013-01-01

The development of analytical methods for parallel characterization of multiple phytoconstituents is essential to advance the quality control of herbal products. While chemical standardization is commonly carried out by targeted analysis using gas or liquid chromatography-based methods, more universal approaches based on quantitative 1H NMR (qHNMR) measurements are being used increasingly in the multi-targeted assessment of these complex mixtures. The present study describes the development of a 1D qHNMR-based method for simultaneous identification and quantification of green tea constituents. This approach utilizes computer-assisted 1H iterative Full Spin Analysis (HiFSA) and enables rapid profiling of seven catechins in commercial green tea extracts. The qHNMR results were cross-validated against quantitative profiles obtained with an orthogonal LC-MS/MS method. The relative strengths and weaknesses of both approaches are discussed, with special emphasis on the role of identical reference standards in qualitative and quantitative analyses. PMID:23870106

Behavior of POP-calcium carbonate hydrogel as bone substitute with controlled release capability: a study in rat.

PubMed

Dewi, Anne Handrini; Ana, Ika Dewi; Wolke, Joop; Jansen, John

2015-10-01

Gypsum or calcium sulfate (CS) or plaster of Paris (POP) is considered as a fast degradable material that usually resorbs before the bone defect area is completely filled by new bone. In this study, the incorporation of CaCO3 hydrogel into POP in different compositions was proposed to enhance the bone biological activity of POP and to decrease its degradability. The mechanical and degradation properties of the various materials were characterized by in vitro analysis. Subsequently, the materials were inserted into cylindrically sized bone defects as created into the femoral condyle of rats and left in situ for 1, 4, and 8 weeks. Histological analysis of the retrieved specimens indicated that the addition of CaCO3 hydrogel into POP increased bone formation, angiogenesis and collagen density and resulted into faster bone formation and maturation. It was also confirmed that the degradation rate of the POP decreased by the addition of CaCO3 hydrogel. The in vivo findings did corroborate with the in vitro analysis. In conclusion, the incorporation of CaCO3 hydrogel provides a promising technology to improve the properties of POP, the oldest biomaterial used for bone grafting. © 2015 Wiley Periodicals, Inc.

Persistent Organic Pollutants in Biotic and Abiotic Components of Antarctic Pristine Environment

NASA Astrophysics Data System (ADS)

Bhardwaj, Laxmikant; Chauhan, Abhishek; Ranjan, Anuj; Jindal, Tanu

2018-05-01

Over the past decades, research in Antarctica has built a new understanding of Antarctica, its past, present and future. Human activities and long-range pollutants are increasing on the Antarctic continent. Research on persistent organic pollutants (POPs) has been carried out internationally by several countries having their permanent research stations to explain the impact of an ever increasing range of POPs in Antarctic ecosystem. POPs have been detected in Antarctica despite its geographical isolation and almost complete absence of human settlements. The presence of POPs in different abiotic (atmosphere, water bodies, sediments, soil, sea ice) and biotic components (mosses, lichens, krill, penguins, skua, etc.) in Antarctica has been studied and documented around for decades and has either been banned or strictly regulated but is still found in the environment. This review focuses on recent research pertaining to sources and occurrence of POPs in Antarctic lake water, soil, sediment, lichen, mosses and other Antarctic marine community. This review also proposes to summarize the current state of research on POPs in Antarctica environment and draw the earliest conclusions on possible significance of POPs in Antarctica based on presently available information from related Antarctic environment.