Primary Pediatric Care Psychopharmacology: Focus on medications for ADHD, depression and anxiety

PubMed Central

Strawn, Jeffrey R.; Dobson, Eric; Giles, Lisa

2016-01-01

The evidence base for psychopharmacologic interventions in youth with depressive and anxiety disorders as well as attention/deficit hyperactivity disorder (ADHD) has dramatically increased over the past two decades. Psychopharmacologic interventions commonly utilized in the pediatric primary care setting—selective serotonin (norepinephrine) reuptake inhibitors (SSRIs/SSNRIs), stimulants and α2 agonists—are reviewed. General pharmacologic principles are summarized along with class-related side effects and tolerability concerns (e.g., suicidality and activation in antidepressant-treated youth as well as insomnia, irritability, anorexia in stimulant-treated pediatric patients). Selected landmark trials of antidepressant medications in youth with depressive disorders (Treatment of Adolescent Depression Study [TADS] and the Treatment of SSRI-Resistant Depression Study [TADS]) and anxiety disorders (Child/Adolescent Anxiety Multimodal Study [CAMS] and Child/Adolescent Anxiety Multimodal Extended Long-term Study [CAMELS]) are described in addition to the Multimodal Treatment of ADHD Study. Finally, available data are presented that are related to prediction of treatment outcomes in youth with depressive disorders, anxiety disorders and ADHD. PMID:28043839

African-American and Latino Families in TADS: Recruitment and Treatment Considerations

ERIC Educational Resources Information Center

Sweeney, Michael; Robins, Michele; Ruberu, Maryse; Jones, Jennifer

2005-01-01

The goal of this article is to review the experiences of some of the African-American and Latino families who participated in the Treatment for Adolescents With Depression Study (TADS). The importance of this article derives from the historical and current inequities in mental health care for families of color. We describe the attempts within the…

The Treatment for Adolescents with Depression Study (TADS): Demographic and Clinical Characteristics

ERIC Educational Resources Information Center

n/a; n/a

2005-01-01

Objective: The Treatment for Adolescents With Depression Study is a multicenter, randomized clinical trial sponsored by the NIMH. This study is designed to evaluate the short- and long-term effectiveness of four treatments for adolescents with major depressive disorder: fluoxetine, cognitive-behavioral therapy, their combination, and, acutely,…

Primary Pediatric Care Psychopharmacology: Focus on Medications for ADHD, Depression, and Anxiety.

PubMed

Strawn, Jeffrey R; Dobson, Eric T; Giles, Lisa L

2017-01-01

The evidence base for psychopharmacologic interventions in youth with depressive and anxiety disorders as well as attention/deficit hyperactivity disorder (ADHD) has dramatically increased over the past two decades. Psychopharmacologic interventions commonly utilized in the pediatric primary care setting-selective serotonin (norepinephrine) reuptake inhibitors (SSRIs/SSNRIs), stimulants and α 2 agonists-are reviewed. General pharmacologic principles are summarized along with class-related side effects and tolerability concerns (e.g., suicidality and activation in antidepressant-treated youth as well as insomnia, irritability, anorexia in stimulant-treated pediatric patients). Selected landmark trials of antidepressant medications in youth with depressive disorders [Treatment of Adolescent Depression Study (TADS) and the Treatment of SSRI-Resistant Depression Study (TADS)] and anxiety disorders [Child/Adolescent Anxiety Multimodal Study (CAMS) and Child/Adolescent Anxiety Multimodal Extended Long-term Study (CAMELS)] are described in addition to the Multimodal Treatment of ADHD Study. Finally, available data are presented that are related to prediction of treatment outcomes in youth with depressive disorders, anxiety disorders, and ADHD. Copyright © 2016 Mosby, Inc. All rights reserved.

Functioning and Quality of Life in the Treatment for Adolescents with Depression Study (TADS)

ERIC Educational Resources Information Center

Vitiello, Benedetto; Rohde, Paul; Silva, Susan; Wells, Karen; Casat, Charles; Waslick, Bruce; Simons, Anne; Reinecke, Mark; Weller, Elizabeth; Kratochvil, Christopher; Walkup, John; Pathak, Sanjeev; Robins, Michele; March, John

2006-01-01

Obective: To test whether 12-week treatment of major depression improved the level of functioning, global health, and quality of life of adolescents. Method: The Treatment for Adolescents With Depression Study was a multisite, randomized clinical trial of fluoxetine, cognitive-behavioral therapy (CBT), their combination (COMB), or clinical…

Remission and Recovery in the Treatment for Adolescents with Depression Study (TADS): Acute and Long-term Outcomes

PubMed Central

Kennard, Betsy D.; Silva, Susan G.; Tonev, Simon; Rohde, Paul; Hughes, Jennifer L.; Vitiello, Benedetto; Kratochvil, Christopher J.; Curry, John F.; Emslie, Graham J.; Reinecke, Mark; March, John

2010-01-01

Objective We examine remission rate probabilities, recovery rates, and residual symptoms across 36 weeks in the Treatment for Adolescents with Depression Study (TADS). Method TADS, a multisite clinical trial, randomized 439 adolescents with major depressive disorder (MDD) to 12 weeks of treatment to fluoxetine (FLX), cognitive behavioral therapy (CBT), their combination (COMB), or pill placebo (PBO). The PBO group, treated openly after week 12, was not included in the subsequent analyses. Treatment differences in remission rates and probabilities of remission over time are compared. Recovery rates in remitters at week 12 (acute phase remitters) and week 18 (continuation phase remitters) are summarized. We also examined whether residual symptoms at the end of 12 weeks of acute treatment predicted later remission. Results At Week 36, the estimated remission rates for intention-to-treat cases were: COMB: 60%, FLX: 55%; CBT: 64%; overall: 60%. Paired comparisons reveal that at week 24 all active treatments converge on remission outcomes. The recovery rate at Week 36 was 65% for acute phase remitters and 71% for continuation phase remitters, with no significant between-treatment differences in recovery rates. Residual symptoms at the end of acute treatment predicted failure to achieve remission at weeks 18 and 36. Conclusions The majority of depressed adolescents in all three treatment modalities achieved remission at the end of nine months of treatment. PMID:19127172

Remission and Recovery in the Treatment for Adolescents with Depression Study (TADS): Acute and Long-Term Outcomes

ERIC Educational Resources Information Center

Kennard, Betsy D.; Silva, Susan G.; Tonev, Simon; Rohde, Paul; Hughes, Jennifer L.; Vitiello, Benedetto; Kratochvil, Christopher J.; Curry, John F.; Emslie, Graham J.; Reinecke, Mark; March, John

2009-01-01

The remission and recovery rates of adolescent patients with depression who were treated with fluoxetine, cognitive-behavioral therapy, their combination, and placebos were examined through a multisite clinical trial. It is concluded that most depressed adolescents who received such therapies achieved remission at the end of nine months.

Striving for Effectiveness in the Treatment of Adolescent Depression: Cognitive Behavior Therapy for Multisite Community Intervention

ERIC Educational Resources Information Center

Curry, John F.; Wells, Karen C.

2005-01-01

The Treatment for Adolescents With Depression Study (TADS) was designed to compare the relative and combined effectiveness of cognitive behavior therapy (CBT) and fluoxetine, each of which had demonstrated efficacy in carefully controlled single-site studies. Models of CBT from these efficacy studies served as the foundation for the TADS…

Dysfunctional Attitudes Scale Perfectionism: A Predictor and Partial Mediator of Acute Treatment Outcome among Clinically Depressed Adolescents

ERIC Educational Resources Information Center

Jacobs, Rachel H.; Silva, Susan G.; Reinecke, Mark A.; Curry, John F.; Ginsburg, Golda S.; Kratochvil, Christopher J.; March, John S.

2009-01-01

The effect of perfectionism on acute treatment outcomes was explored in a randomized controlled trial of 439 clinically depressed adolescents (12-17 years of age) enrolled in the Treatment for Adolescents with Depression Study (TADS) who received cognitive behavior therapy (CBT), fluoxetine, a combination of CBT and FLX, or pill placebo. Measures…

Factors Associated with Recruitment and Screening in the Treatment for Adolescents with Depression Study (TADS)

ERIC Educational Resources Information Center

May, Diane E.; Hallin, Mary J.; Kratochvil, Christopher J.; Puumala, Susan E.; Smith, Lynette S.; Reinecke, Mark A.; Silva, Susan G.; Weller, Elizabeth B.; Vitiello, Benedetto; Breland-Noble, Alfiee; March, John S.

2007-01-01

Objective: To examine factors associated with eligibility and randomization and consider the efficiency of recruitment methods. Method: Adolescents, ages 12 to 17 years, were telephone screened (N = 2,804) followed by in-person evaluation (N = 1,088) for the Treatment for Adolescents With Depression Study. Separate logistic regression models,…

Treatment for Adolescents with Depression Study (TADS): Safety Results

ERIC Educational Resources Information Center

Emslie, Graham; Kratochvil, Christopher; Vitiello, Benedetto; Silva, Susan; Mayes, Taryn; McNulty, Steven; Weller, Elizabeth; Waslick, Bruce; Casat, Charles; Walkup, John; Pathak, Sanjeev; Rohde, Paul; Posner, Kelly; March, John

2006-01-01

Objective: To compare the rates of physical, psychiatric, and suicide-related events in adolescents with MDD treated with fluoxetine alone (FLX), cognitive-behavioral therapy (CBT), combination treatment (COMB), or placebo (PBO). Method: Safety assessments included adverse events (AEs) collected by spontaneous report, as well as systematic…

Relative Cost-Effectiveness of Treatments for Adolescent Depression: 36-Week Results from the TADS Randomized Trial

ERIC Educational Resources Information Center

Domino, Marisa Elena; Foster, E. Michael; Vitiello, Benedetto; Kratochvil, Christopher J.; Burns, Barbara J.; Silva, Susan G.; Reinecke, Mark A.; March, John S.

2009-01-01

Randomized controlled trials that involve 327 participants aged 12 to 18 who were diagnosed with major depression were given either fluoxetine alone, cognitive-behavioral therapy, or a combination of both. Cost-effectiveness acceptability curves suggest that combination treatment is highly likely to be the most cost-effective treatment than…

Predictors of hopelessness among clinically depressed youth.

PubMed

Becker-Weidman, Emily G; Reinecke, Mark A; Jacobs, Rachel H; Martinovich, Zoran; Silva, Susan G; March, John S

2009-05-01

Factors that distinguish depressed individuals who become hopeless from those who do not are poorly understood. In this study, predictors of hopelessness were examined in a sample of 439 clinically depressed adolescents participating in the Treatment for Adolescents with Depression Study (TADS). The total score of the Beck Hopelessness Scale (BHS) was used to assess hopelessness at baseline. Multiple regression and logistic regression analyses were conducted to evaluate the extent to which variables were associated with hopelessness and determine which cluster of measures best predicted clinically significantly hopelessness. Hopelessness was associated with greater depression severity, poor social problem-solving, cognitive distortions, and family conflict. View of self, view of the world, internal attributional style, need for social approval, positive problem-solving orientation, and family problems consistently emerged as the best predictors of hopelessness in depressed youth. Cognitive and familial factors predict those depressed youth who have high levels of hopelessness.

HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions

PubMed Central

Wang, Xiao-Tao; Cui, Wang

2017-01-01

Abstract A current question in the high-order organization of chromatin is whether topologically associating domains (TADs) are distinct from other hierarchical chromatin domains. However, due to the unclear TAD definition in tradition, the structural and functional uniqueness of TAD is not well studied. In this work, we refined TAD definition by further constraining TADs to the optimal separation on global intra-chromosomal interactions. Inspired by this constraint, we developed a novel method, called HiTAD, to detect hierarchical TADs from Hi-C chromatin interactions. HiTAD performs well in domain sensitivity, replicate reproducibility and inter cell-type conservation. With a novel domain-based alignment proposed by us, we defined several types of hierarchical TAD changes which were not systematically studied previously, and subsequently used them to reveal that TADs and sub-TADs differed statistically in correlating chromosomal compartment, replication timing and gene transcription. Finally, our work also has the implication that the refinement of TAD definition could be achieved by only utilizing chromatin interactions, at least in part. HiTAD is freely available online. PMID:28977529

Dysfunctional Attitudes Scale Perfectionism: A Predictor and Partial Mediator of Acute Treatment Outcome among Clinically Depressed Adolescents

PubMed Central

Jacobs, Rachel H.; Silva, Susan G.; Reinecke, Mark A.; Curry, John F.; Ginsburg, Golda S.; Kratochvil, Christopher J.; March, John S.

2009-01-01

The effect of perfectionism on acute treatment outcomes was explored in a randomized controlled trial of 439 clinically depressed adolescents (12–17 years of age) enrolled in the Treatment for Adolescents with Depression Study (TADS) who received cognitive behavior therapy (CBT), fluoxetine, a combination of CBT and FLX, or pill placebo. Measures included the Children’s Depression Rating Scale–Revised, the Suicidal Ideation Questionnaire–Grades 7–9, and the perfectionism subscale from the Dysfunctional Attitudes Scale (DAS). Predictor results indicate that adolescents with higher versus lower DAS perfectionism scores at baseline, regardless of treatment, continued to demonstrate elevated depression scores across the acute treatment period. In the case of suicidality, DAS perfectionism impeded improvement. Treatment outcomes were partially mediated by the change in DAS perfectionism across the 12-week period. PMID:20183664

Association between thoracic aortic disease and inguinal hernia.

PubMed

Olsson, Christian; Eriksson, Per; Franco-Cereceda, Anders

2014-08-21

The study hypothesis was that thoracic aortic disease (TAD) is associated with a higher-than-expected prevalence of inguinal hernia. Such an association has been reported for abdominal aortic aneurysm (AAA) and hernia. Unlike AAA, TAD is not necessarily detectable with clinical examination or ultrasound, and there are no population-based screening programs for TAD. Therefore, conditions associated with TAD, such as inguinal hernia, are of particular clinical relevance. The prevalence of inguinal hernia in subjects with TAD was determined from nation-wide register data and compared to a non-TAD group (patients with isolated aortic stenosis). Groups were balanced using propensity score matching. Multivariable statistical analysis (logistic regression) was performed to identify variables independently associated with hernia. Hernia prevalence was 110 of 750 (15%) in subjects with TAD versus 29 of 301 (9.6%) in non-TAD, P=0.03. This statistically significant difference remained after propensity score matching: 21 of 159 (13%) in TAD versus 14 of 159 (8.9%) in non-TAD, P<0.001. Variables independently associated with hernia in multivariable analysis were male sex (odds ratio [OR] with 95% confidence interval [95% CI]) 3.4 (2.1 to 5.4), P<0.001; increased age, OR 1.02/year (1.004 to 1.04), P=0.014; and TAD, OR 1.8 (1.1 to 2.8), P=0.015. The prevalence of inguinal hernia (15%) in TAD is higher than expected in a general population and higher in TAD, compared to non-TAD. TAD is independently associated with hernia in multivariable analysis. Presence or history of hernia may be of importance in detecting TAD, and the association warrants further study. © 2014 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Thoracic aortic dissection and rupture in conotruncal cardiac defects: A population-based study.

PubMed

Frischhertz, Benjamin P; Shamszad, Pirouz; Pedroza, Claudia; Milewicz, Dianna M; Morris, Shaine A

2015-04-01

Although the risk of thoracic aortic dissection and rupture (TAD) is well-known in bicuspid aortic valve (BAV), the risk of TAD in other congenital heart diseases (CHD), particularly conotruncal lesions like tetralogy of Fallot (TOF), truncus arteriosus, D-transposition of the great arteries (D-TGA), and double outlet right ventricle is currently unknown. The primary purpose of this study was to describe TAD in conotruncal CHD, and the secondary purpose was to explore whether an association exists between TAD and conotruncal CHD. Using the Texas Inpatient Public Use Data File, an administrative database of all Texas hospitalizations, including >37.9 million hospitalizations from January 1999 through June 2012, 12,016 cases of TAD and 214 cases of TAD in CHD were identified. The most common lesions were BAV (42%), atrial septal defect (21%), aortic coarctation (7%), ventricular septal defect (6%), and patent ductus arteriosus (4%). Three patients with TOF, 2 with D-TGA, and 1 with truncus arteriosus were admitted with TAD. An exploratory case-control study in patients older than 1 year using multilevel logistic regression models to evaluate the association between CHD and TAD that controlled for known TAD risk factors demonstrated a significant association between TAD and BAV (OR 10, 95% CI 8.2-13) but not coarctation of the aorta or any conotruncal lesion. TAD in conotruncal CHD is exquisitely rare. In our hospitalized population, there was no increased occurrence of TAD in conotruncal CHD above what would be expected in the rest of the hospitalized population. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Aortic elongation and the risk for dissection: the Tübingen Aortic Pathoanatomy (TAIPAN) project†.

PubMed

Krüger, Tobias; Oikonomou, Alexandre; Schibilsky, David; Lescan, Mario; Bregel, Katharina; Vöhringer, Luise; Schneider, Wilke; Lausberg, Henning; Blumenstock, Gunnar; Bamberg, Fabian; Schlensak, Christian

2017-06-01

We measured aortic dimensions, particularly length parameters, using 3D imaging with the aim of refining the risk-morphology for Stanford type A aortic dissection (TAD). Computer tomography angiography studies were analysed using the curved multiplanar reformats. At defined landmarks, the diameters and lengths of aortic segments were recorded. Three groups were compared retrospectively: patients actually suffering from a TAD (TAD-group; n  = 150), patients before suffering a TAD (preTAD-group n  = 15) and a healthy control group ( n  = 215). Receiver operating characteristic curves (ROCs) were analysed (control versus preTAD) to study the diagnostic value of the individual variables. Median diameters of preTAD (43 mm) and TAD (50 mm) aortas were significantly ( P  < 0.001) larger than those of the control group (35 mm). Ninety-three percent of preTAD and 68% of TAD aortas were less than 55 mm in the mid-ascending aorta. The ascending aorta and the aortic arch were significantly longer in both preTAD and TAD aortas compared to control aortas ( P  < 0.001); in the control aortas the central line distance from the aortic valve to the brachiocephalic trunk was 93 mm. In preTAD aortas, it was 111 mm, and it was 117 mm in TAD aortas ( P  < 0.001). In ROC analysis, the area under the curve was 0.912 for the ascending diameter and 0.787 for the ascending and arch lengths. TAD-prediction based on the aortic diameter is ineffective. Besides circumferential dilatation, ascending aorta elongation precedes TAD and appears to be a useful additional parameter for prognostication. We propose a diagnostic score involving ascending aorta diameter and length. © The Author 2017. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

TAD disruption as oncogenic driver

PubMed Central

Valton, Anne-Laure; Dekker, Job

2016-01-01

Topologically Associating Domains (TADs) are conserved during evolution and play roles in guiding and constraining long-range regulation of gene expression. Disruption of TAD boundaries results in aberrant gene expression by exposing genes to inappropriate regulatory elements. Recent studies have shown that TAD disruption is often found in cancer cells and contributes to oncogenesis through two mechanisms. One mechanism locally disrupts domains by deleting or mutating a TAD boundary leading to fusion of the two adjacent TADs. The other mechanism involves genomic rearrangements that break up TADs and creates new ones without directly affecting TAD boundaries. Understanding the mechanisms by which TADs form and control long-range chromatin interactions will therefore not only provide insights into the mechanism of gene regulation in general, but will also reveal how genomic rearrangements and mutations in cancer genomes can lead to misregulation of oncogenes and tumor suppressors. PMID:27111891

Role and Regulation of the Flp/Tad Pilus in the Virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193

PubMed Central

Nykyri, Johanna; Mattinen, Laura; Niemi, Outi; Adhikari, Satish; Kõiv, Viia; Somervuo, Panu; Fang, Xin; Auvinen, Petri; Mäe, Andres; Palva, E. Tapio; Pirhonen, Minna

2013-01-01

In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers. PMID:24040039

Role and regulation of the Flp/Tad pilus in the virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193.

PubMed

Nykyri, Johanna; Mattinen, Laura; Niemi, Outi; Adhikari, Satish; Kõiv, Viia; Somervuo, Panu; Fang, Xin; Auvinen, Petri; Mäe, Andres; Palva, E Tapio; Pirhonen, Minna

2013-01-01

In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers.

Validation of a new radiographic measurement of acetabular version: the transverse axis distance (TAD).

PubMed

Nitschke, Ashley; Lambert, Jeffery R; Glueck, Deborah H; Jesse, Mary Kristen; Mei-Dan, Omer; Strickland, Colin; Petersen, Brian

2015-11-01

This study has three aims: (1) validate a new radiographic measure of acetabular version, the transverse axis distance (TAD) by showing equivalent TAD accuracy in predicting CT equatorial acetabular version when compared to a previously validated, but more cumbersome, radiographic measure, the p/a ratio; (2) establish predictive equations of CT acetabular version from TAD; (3) calculate a sensitive and specific cut point for predicting excessive CT acetabular anteversion using TAD. A 14-month retrospective review was performed of patients who had undergone a dedicated MSK CT pelvis study and who also had a technically adequate AP pelvis radiograph. Two trained observers measured the radiographic p/a ratio, TAD, and CT acetabular equatorial version for 110 hips on a PACS workstation. Mixed model analysis was used to find prediction equations, and ROC analysis was used to evaluate the diagnostic accuracy of p/a ratio and TAD. CT equatorial acetabular version can accurately be predicted from either p/a ratio (p < 0.001) or TAD (p < 0.001). The diagnostic accuracies of p/a ratio and TAD are comparable (p =0.46). Patients whose TAD is higher than 17 mm may have excessive acetabular anteversion. For that cutpoint, the sensitivity of TAD is 0.73, with specificity of 0.82. TAD is an accurate radiographic predictor of CT acetabular anteversion and provides an easy-to-use and intuitive point-of-care assessment of acetabular version in patients with hip pain.

The 9aaTAD Transactivation Domains: From Gal4 to p53.

PubMed

Piskacek, Martin; Havelka, Marek; Rezacova, Martina; Knight, Andrea

2016-01-01

The family of the Nine amino acid Transactivation Domain, 9aaTAD family, comprises currently over 40 members. The 9aaTAD domains are universally recognized by the transcriptional machinery from yeast to man. We had identified the 9aaTAD domains in the p53, Msn2, Pdr1 and B42 activators by our prediction algorithm. In this study, their competence to activate transcription as small peptides was proven. Not surprisingly, we elicited immense 9aaTAD divergence in hundreds of identified orthologs and numerous examples of the 9aaTAD species' convergence. We found unforeseen similarity of the mammalian p53 with yeast Gal4 9aaTAD domains. Furthermore, we identified artificial 9aaTAD domains generated accidentally by others. From an evolutionary perspective, the observed easiness to generate 9aaTAD transactivation domains indicates the natural advantage for spontaneous generation of transcription factors from DNA binding precursors.

TAD disruption as oncogenic driver.

PubMed

Valton, Anne-Laure; Dekker, Job

2016-02-01

Topologically Associating Domains (TADs) are conserved during evolution and play roles in guiding and constraining long-range regulation of gene expression. Disruption of TAD boundaries results in aberrant gene expression by exposing genes to inappropriate regulatory elements. Recent studies have shown that TAD disruption is often found in cancer cells and contributes to oncogenesis through two mechanisms. One mechanism locally disrupts domains by deleting or mutating a TAD boundary leading to fusion of the two adjacent TADs. The other mechanism involves genomic rearrangements that break up TADs and creates new ones without directly affecting TAD boundaries. Understanding the mechanisms by which TADs form and control long-range chromatin interactions will therefore not only provide insights into the mechanism of gene regulation in general, but will also reveal how genomic rearrangements and mutations in cancer genomes can lead to misregulation of oncogenes and tumor suppressors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genetic variants in FBN-1 and risk for thoracic aortic aneurysm and dissection.

PubMed

Iakoubova, Olga A; Tong, Carmen H; Rowland, Charles M; Luke, May M; Garcia, Veronica E; Catanese, Joseph J; Moomiaie, Remo M; Sotonyi, Peter; Ascady, Gyorgy; Nikas, Demitrios; Dedelias, Panagiotis; Tranquilli, Maryann; Elefteriades, John A

2014-01-01

A recent genome wide association study (GWAS) by LeMaire et al. found that two single nucleotide polymorphisms (SNPs), rs2118181 and rs10519177 in the FBN-1 gene (encoding Fibrillin-1), were associated with thoracic aortic dissection (TAD), non-dissecting thoracic aortic aneurysm (TAA), and thoracic aortic aneurysm or dissection (TAAD); the largest effect was observed for the association of rs2118181 with TAD. We investigated whether rs2118181 and rs10519177 were associated with TAD, TAA, and TAAD in the Yale study. The genotypes of rs2118181 and rs10519177 were determined for participants in the Yale study: 637 TAAD cases (140 TAD, 497 TAA) and 275 controls from the United States, Hungary, and Greece. The association of the genotypes with TAD, TAA and TAAD were assessed using logistic regression models adjusted for sex, age, study center and hypertension. In the Yale study, rs2118181 was associated with TAD: compared with non-carriers, carriers of the risk allele had an unadjusted odds ratio for TAD of 1.80 (95% CI 1.15-2.80) and they had odds ratio for TAD of 1.87 (95% CI 1.09-3.20) after adjusting for sex, age, study center and hypertension. We did not find significant differences in aortic size, a potential confounder for TAD, between rs2118181 risk variant carriers and non-carriers: mean aortic size was 5.56 (95% CI: 5.37-5.73) for risk variant carriers (CC+CT) and was 5.48 (95% CI: 5.36-5.61) for noncarriers (TT) (p = 0.56). rs2118181 was not associated with TAA or TAAD. rs10519177 was not associated with TAD, TAA, or TAAD in the Yale study. Thus, the Yale study provided further support for the association of the FBN-1 rs2118181SNP with TAD.

ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data.

PubMed

Oluwadare, Oluwatosin; Cheng, Jianlin

2017-11-14

With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-C technique can generate genome-wide chromosomal interaction (contact) data, which can be used to investigate the higher-level organization of chromosomes, such as Topologically Associated Domains (TAD), i.e., locally packed chromosome regions bounded together by intra chromosomal contacts. The identification of the TADs for a genome is useful for studying gene regulation, genomic interaction, and genome function. Here, we formulate the TAD identification problem as an unsupervised machine learning (clustering) problem, and develop a new TAD identification method called ClusterTAD. We introduce a novel method to represent chromosomal contacts as features to be used by the clustering algorithm. Our results show that ClusterTAD can accurately predict the TADs on a simulated Hi-C data. Our method is also largely complementary and consistent with existing methods on the real Hi-C datasets of two mouse cells. The validation with the chromatin immunoprecipitation (ChIP) sequencing (ChIP-Seq) data shows that the domain boundaries identified by ClusterTAD have a high enrichment of CTCF binding sites, promoter-related marks, and enhancer-related histone modifications. As ClusterTAD is based on a proven clustering approach, it opens a new avenue to apply a large array of clustering methods developed in the machine learning field to the TAD identification problem. The source code, the results, and the TADs generated for the simulated and real Hi-C datasets are available here: https://github.com/BDM-Lab/ClusterTAD .

Can TAD and CalTAD predict cut-out after extra-medullary fixation with new generation devices of proximal femoral fractures? A retrospective study.

PubMed

Caruso, Gaetano; Andreotti, Mattia; Pari, Carlotta; Soldati, Francesco; Gildone, Alessandro; Lorusso, Vincenzo; Massari, Leo

2017-01-01

Intramedullary and extramedullary strategies of pertrochanteric fracture fixation are still controversial, but new percutaneous devices may give advantages regarding operative time, blood loss and rate of cardiovascular complications. We retrospectively analyze our cases regarding Anteversa ® plate (Intrauma, Turin, Italy) fixation of pertrochanteric femoral fractures, focusing on the correlation between two radiographical parameters (tip-apex distance "TAD" and calcar referenced tip-apex distance "CalTAD") and the occurrence of cut-out. The purpose of this study was to determine if these predicting factors of cut-out are reliable in the treatment of proximal femoral fractures with the Anteversa plate. A series of 77 patients with 53 31-A1 fracture types and 24-A2 fractures completed a 12-month-follow-up. Clinical outcomes were evaluated according to Parker-Palmer Mobility Score at the final follow-up. TAD and CalTAD were considered to determine their correlation with cut-out events. The mean Parker-Palmer Score was 6.94 in A1 group and 7.41 in A2 group ( p  = 0.47). Mean value of TAD index was 29.58, 29.81 in the A1 group and 29.08 in the A2 group, and mean value of CalTAD index was 30.87, 31.03 in the A1 group and 30.50 in the A2 group. We observed 3 cases of implant cut-out. We shared our sample in two groups, one group with TAD and CalTAD indices lower than 25 mm and another group higher than 25 mm to evaluate how the Palmer Parker score changed and no statistical differences were found between the two groups. Taking into consideration that good clinical results were obtained for TAD and CalTAD values superior to 25 mm, the prognostic value of 25 mm of TAD and CalTAD indices might not be appropriate to this new percutaneous plate.

Generation of traveling atmospheric disturbances during pulsating geomagnetic storms

NASA Astrophysics Data System (ADS)

Gardner, Larry; Schunk, Robert

Traveling Atmospheric Disturbances (TADs) are effective in transporting momentum and en-ergy deposited at high latitudes to the mid and low latitude regions of the thermosphere. They also act to transport momentum and energy from the lower thermosphere into the upper ther-mosphere. Previously, model studies have been conducted to determine the characteristics of isolated, single-pulse TADs, but the generation of multiple TADs excited during pulsating storms have not been considered before. Here, a high-resolution global thermosphere-ionosphere model was used to study the basic characteristic of multiple TADs excited during pulsating storms, including idealized weak and strong pulsating storms, and an approximation of the May 4, 1998 pulsating storm. For all three pulsating storm simulations, multiple TADs were excited that propagated away form the auroral oval both toward the poles and toward the equator at all longitudes, with the maximum amplitudes between midnight and dawn. The TAD amplitudes were a maximum near the poles, diminished towards the equator and were larger on the nightside than on the dayside. The TADs propagated at a slight upward angle to the horizontal, with the result that the lower boundary of the TADs increased with decreas-ing latitude. The TADs crossed the equator and propagated to mid-latitudes in the opposite hemisphere, where wave interference occurred for the strong pulsating storm cases. The TAD wavelengths vary from 2500-3000 km and the phase speeds from 800-1000 m/s. The maximum TAD perturbations are 20% for the mass density 14% for the neutral temperature and 100 m/s for the winds.

Generation of traveling atmospheric disturbances during pulsating geomagnetic storms

NASA Astrophysics Data System (ADS)

Gardner, L. C.; Schunk, R. W.

2010-08-01

Traveling atmospheric disturbances (TADs) are effective in transporting momentum and energy deposited at high latitudes to the midlatitude and low-latitude regions of the thermosphere. They also act to transport momentum and energy from the lower thermosphere into the upper thermosphere. Previously, model studies have been conducted to determine the characteristics of isolated, single-pulse TADs, but the generation of multiple TADs excited during pulsating storms have not been considered before. Here a high-resolution global thermosphere-ionosphere model was used to study the basic characteristics of multiple TADs excited during pulsating storms, including idealized weak and strong pulsating storms, and an approximation of the 4 May 1998 pulsating storm. For all three pulsating storm simulations, multiple TADs that propagated away from the auroral oval toward both the poles and the equator at all longitudes, with the maximum amplitudes between midnight and dawn, were excited. The TAD amplitudes were at maximum near the poles and diminished toward the equator and were larger on the nightside than on the dayside. The TADs propagated at a slightly upward angle to the horizontal, with the result that the lower boundary of the TADs increased with decreasing latitude. The TADs crossed the equator and propagated to midlatitudes in the opposite hemisphere, where wave interference occurred for the strong pulsating storm cases. The TAD wavelengths vary from 2500 to 3000 km and the phase speeds vary from 800 to 1000 m/s. The maximum TAD perturbations are 20% for the mass density, 14% for the neutral temperature, and 100 m/s for the winds.

Generating relevant kinetic Monte Carlo catalogs using temperature accelerated dynamics with control over the accuracy

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

Chatterjee, Abhijit; Voter, Arthur

2009-01-01

We develop a variation of the temperature accelerated dynamics (TAD) method, called the p-TAD method, that efficiently generates an on-the-fly kinetic Monte Carlo (KMC) process catalog with control over the accuracy of the catalog. It is assumed that transition state theory is valid. The p-TAD method guarantees that processes relevant at the timescales of interest to the simulation are present in the catalog with a chosen confidence. A confidence measure associated with the process catalog is derived. The dynamics is then studied using the process catalog with the KMC method. Effective accuracy of a p-TAD calculation is derived when amore » KMC catalog is reused for conditions different from those the catalog was originally generated for. Different KMC catalog generation strategies that exploit the features of the p-TAD method and ensure higher accuracy and/or computational efficiency are presented. The accuracy and the computational requirements of the p-TAD method are assessed. Comparisons to the original TAD method are made. As an example, we study dynamics in sub-monolayer Ag/Cu(110) at the time scale of seconds using the p-TAD method. It is demonstrated that the p-TAD method overcomes several challenges plaguing the conventional KMC method.« less

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

PubMed Central

Ulianov, Sergey V.; Khrameeva, Ekaterina E.; Gavrilov, Alexey A.; Flyamer, Ilya M.; Kos, Pavel; Mikhaleva, Elena A.; Penin, Aleksey A.; Logacheva, Maria D.; Imakaev, Maxim V.; Chertovich, Alexander; Gelfand, Mikhail S.; Shevelyov, Yuri Y.; Razin, Sergey V.

2016-01-01

Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster, we performed Hi-C and poly(A)+ RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin. PMID:26518482

Inflammatory Cell Infiltrates in Acute and Chronic Thoracic Aortic Dissection.

PubMed

Wu, Darrell; Choi, Justin C; Sameri, Aryan; Minard, Charles G; Coselli, Joseph S; Shen, Ying H; LeMaire, Scott A

2013-12-01

Thoracic aortic dissection (TAD) is a highly lethal cardiovascular disease. Injury to the intima and media allows pulsatile blood to enter the media, leading to dissection formation. Inflammatory cells then infiltrate the site of aortic injury to clear dead cells and damaged tissue. This excessive inflammation may play a role in aneurysm formation after dissection. Using immunohistochemistry, we compared aortic tissues from patients with acute TAD (n = 11), patients with chronic TAD (n = 35), and donor controls (n = 20) for the presence of CD68+ macrophages, neutrophils, mast cells, and CD3+ T lymphocytes. Tissue samples from patients with acute or chronic TAD generally had significantly more inflammatory cells in both the medial and adventitial layers than did the control samples. In tissues from patients with acute TAD, the adventitia had more of the inflammatory cells studied than did the media. The pattern of increase in inflammatory cells was similar in chronic and acute TAD tissues, except for macrophages, which were seen more frequently in the adventitial layer of acute TAD tissue than in the adventitia of chronic TAD tissue. The inflammatory cell content of both acute and chronic TAD tissue was significantly different from that of control tissue. However, the inflammatory cell profile of aneurysmal chronic TAD was similar to that of acute TAD. This may reflect a sustained injury response that contributes to medial degeneration and aneurysm formation.

The cold-induced defensin TAD1 confers resistance against snow mold and Fusarium head blight in transgenic wheat.

PubMed

Sasaki, Kentaro; Kuwabara, Chikako; Umeki, Natsuki; Fujioka, Mari; Saburi, Wataru; Matsui, Hirokazu; Abe, Fumitaka; Imai, Ryozo

2016-06-20

TAD1 (Triticum aestivum defensin 1) is induced during cold acclimation in winter wheat and encodes a plant defensin with antimicrobial activity. In this study, we demonstrated that recombinant TAD1 protein inhibits hyphal growth of the snow mold fungus, Typhula ishikariensis in vitro. Transgenic wheat plants overexpressing TAD1 were created and tested for resistance against T. ishikariensis. Leaf inoculation assays revealed that overexpression of TAD1 confers resistance against the snow mold. In addition, the TAD1-overexpressors showed resistance against Fusarium graminearum, which causes Fusarium head blight, a devastating disease in wheat and barley. These results indicate that TAD1 is a candidate gene to improve resistance against multiple fungal diseases in cereal crops. Copyright © 2016 Elsevier B.V. All rights reserved.

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries.

PubMed

Gong, Yixiao; Lazaris, Charalampos; Sakellaropoulos, Theodore; Lozano, Aurelie; Kambadur, Prabhanjan; Ntziachristos, Panagiotis; Aifantis, Iannis; Tsirigos, Aristotelis

2018-02-07

The metazoan genome is compartmentalized in areas of highly interacting chromatin known as topologically associating domains (TADs). TADs are demarcated by boundaries mostly conserved across cell types and even across species. However, a genome-wide characterization of TAD boundary strength in mammals is still lacking. In this study, we first use fused two-dimensional lasso as a machine learning method to improve Hi-C contact matrix reproducibility, and, subsequently, we categorize TAD boundaries based on their insulation score. We demonstrate that higher TAD boundary insulation scores are associated with elevated CTCF levels and that they may differ across cell types. Intriguingly, we observe that super-enhancers are preferentially insulated by strong boundaries. Furthermore, we demonstrate that strong TAD boundaries and super-enhancer elements are frequently co-duplicated in cancer patients. Taken together, our findings suggest that super-enhancers insulated by strong TAD boundaries may be exploited, as a functional unit, by cancer cells to promote oncogenesis.

[Interest of tricuspid annular displacement (TAD) in evaluation of right ventricular ejection fraction].

PubMed

Hugues, T; Ducreux, D; Bertora, D; Berthier, F; Lemoigne, F; Padovani, B; Gibelin, P

2010-04-01

The ultrasound assessment of RV structure and function is often sub-optimal. The range of excursions of the mitral or tricuspid annulus measured in millimetre by 2D or TM-mode in centimetre per second by DTI-mode echocardiography has been shown to reflect the systolic function of both ventricles. We studied a new technique based on a tissue tracking algorithm that is ultrasound beam angle independent for automated detection of tricuspid annular displacement (TAD) (QLAB, Philips Medical Imaging). Twenty-six patients (pts) referred for magnetic resonance imaging (MRI) and 44 control subjects underwent a complete transthoracic echocardiography. MRI of the right ventricular ejection fraction (RVEF) was correlated by linear regression with TAD. Sixteen pts (61.5%) exhibited right ventricular systolic dysfunction (MRI RVEF<40%). The MRI RVEF was positively correlated with TAD (R(2)=0,65; p<0,0001). A value of TAD <14mm predicted right ventricular dysfunction with a sensitivity of 87.5% and a specificity of 90%. Most of (90%) healthy subjects exhibited TAD values exceeding this cut-off point (mean: 16.9+/-1.64mm; range: 13.3 to 24.8mm). Negative correlation was found between TAD and age (R(2)=0,36; p<0,0001). Our study is the first to correlate TAD with MRI RVEF. TAD is a simple, rapid, and non-invasive tool for right ventricular systolic function assessment.

Aortic elongation in aortic aneurysm and dissection: the Tübingen Aortic Pathoanatomy (TAIPAN) project.

PubMed

Krüger, Tobias; Sandoval Boburg, Rodrigo; Lescan, Mario; Oikonomou, Alexandre; Schneider, Wilke; Vöhringer, Luise; Lausberg, Henning; Bamberg, Fabian; Blumenstock, Gunnar; Schlensak, Christian

2018-01-24

To study the lengths and diameters of aortic segments in healthy and diseased aortas and to assess the role of aortic elongation in Type A aortic dissection (TAD) prediction. Ectasia and aneurysm were defined by ascending aorta diameters of 45-54 mm and ≥55 mm, respectively. Computed tomography angiography studies of 256 healthy, 102 ectasia, 38 aneurysm, 17 pre-TAD and 166 TAD aortas were analysed using curved multiplanar reformats. The study groups were structurally equal. The diameter of the ascending aorta was 35 mm in the control group and was larger (P < 0.001) in the pre-TAD (43 mm) and TAD (56 mm) groups. The length of the ascending aorta from the aortic annulus to the brachiocephalic trunk was 92 mm in the control group, 113 mm in the ectasia group, 120 mm in the aneurysm group and 111 mm and 118 mm in the pre-TAD and TAD groups (all P < 0.001 compared with the control group). An ascending aorta length of 120 mm was exceeded in 2% of the control group, 31% of the ectasia group, 50% of the aneurysm group, 24% of the pre-TAD group and 48% of the TAD group. The correlation between the diameter and the length of the ascending aorta was r = 0.752; therefore, both parameters must be examined separately. A score considering both parameters identified 23.5% of pre-TAD patients, significantly more than the diameter alone, and 31.4% of ectasia aortas were elongated. Patients with ectatic (45-54 mm diameter) and elongated (≥120 mm) ascending aortas represent a high-risk subpopulation for TAD. © The Author(s) 2018. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Formation of chromosomal domains in interphase by loop extrusion

NASA Astrophysics Data System (ADS)

Fudenberg, Geoffrey

While genomes are often considered as one-dimensional sequences, interphase chromosomes are organized in three dimensions with an essential role for regulating gene expression. Recent studies have shown that Topologically Associating Domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes. Despite observations that architectural proteins, including CTCF, demarcate and maintain the borders of TADs, the mechanisms underlying TAD formation remain unknown. Here we propose that loop extrusion underlies the formation TADs. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops, but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. This process dynamically forms loops of various sizes within but not between TADs. Using polymer simulations, we find that loop extrusion can produce TADs as determined by our analyses of the highest-resolution experimental data. Moreover, we find that loop extrusion can explain many diverse experimental observations, including: the preferential orientation of CTCF motifs and enrichments of architectural proteins at TAD boundaries; TAD boundary deletion experiments; and experiments with knockdown or depletion of CTCF, cohesin, and cohesin-loading factors. Together, the emerging picture from our work is that TADs are formed by rapidly associating, growing, and dissociating loops, presenting a clear framework for understanding interphase chromosomal organization.

A refined definition improves the measurement reliability of the tip-apex distance.

PubMed

Sakagoshi, Daigo; Sawaguchi, Takeshi; Shima, Yosuke; Inoue, Daisuke; Oshima, Takeshi; Goldhahn, Sabine

2016-07-01

Tip-apex distance (TAD) is reported as a good predictor for cut-outs of lag screws and spiral blades in the treatment of intertrochanteric fractures, and surgeons are advised to strive for TAD within 20 mm. However, the femoral neck axis and the position of the lower limb in the lateral radiograph are not clearly defined and can lead to measurement errors. We propose a refined TAD by defining these factors. The objective of this study was to analyze the reliability of this refined TAD. The radiographs of 130 prospective cases with unstable trochanteric fractures were used for the analysis of the refined TAD. The refined TAD was independently measured by 2 raters with clinical experience of more than 10 years (rater 1, 2) and 2 raters with much less clinical experience (rater 3, 4) after they received a training about the new measurement method. Intraclass correlation coefficient (ICC [2,4]) was calculated to assess the interrater reliability. The mean refined TADs were 18.2:18.4:18.2:18.2 mm for rater 1:2:3:4. There was a strong correlation among all four raters (ICC 0.998, (95% CI: 0.998, 0.999). Regardless of the clinical experience of raters, the refined TAD is a reliable tool and can be used to develop new TAD recommendations for predicting failure of fixation. Future studies with larger samples are needed to evaluate the predictive value of the refined TAD. Copyright © 2016 The Japanese Orthopaedic Association. Published by Elsevier B.V. All rights reserved.

TADs are 3D structural units of higher-order chromosome organization in Drosophila

PubMed Central

Szabo, Quentin; Jost, Daniel; Chang, Jia-Ming; Cattoni, Diego I.; Papadopoulos, Giorgio L.; Bonev, Boyan; Sexton, Tom; Gurgo, Julian; Jacquier, Caroline; Nollmann, Marcelo; Bantignies, Frédéric; Cavalli, Giacomo

2018-01-01

Deciphering the rules of genome folding in the cell nucleus is essential to understand its functions. Recent chromosome conformation capture (Hi-C) studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus or whether they reflect statistical frequencies of measured interactions within cell populations is unclear. Using a combination of Hi-C, three-dimensional (3D) fluorescent in situ hybridization, super-resolution microscopy, and polymer modeling, we provide an integrative view of chromatin folding in Drosophila. We observed that repressed TADs form a succession of discrete nanocompartments, interspersed by less condensed active regions. Single-cell analysis revealed a consistent TAD-based physical compartmentalization of the chromatin fiber, with some degree of heterogeneity in intra-TAD conformations and in cis and trans inter-TAD contact events. These results indicate that TADs are fundamental 3D genome units that engage in dynamic higher-order inter-TAD connections. This domain-based architecture is likely to play a major role in regulatory transactions during DNA-dependent processes. PMID:29503869

Social problem-solving among adolescents treated for depression.

PubMed

Becker-Weidman, Emily G; Jacobs, Rachel H; Reinecke, Mark A; Silva, Susan G; March, John S

2010-01-01

Studies suggest that deficits in social problem-solving may be associated with increased risk of depression and suicidality in children and adolescents. It is unclear, however, which specific dimensions of social problem-solving are related to depression and suicidality among youth. Moreover, rational problem-solving strategies and problem-solving motivation may moderate or predict change in depression and suicidality among children and adolescents receiving treatment. The effect of social problem-solving on acute treatment outcomes were explored in a randomized controlled trial of 439 clinically depressed adolescents enrolled in the Treatment for Adolescents with Depression Study (TADS). Measures included the Children's Depression Rating Scale-Revised (CDRS-R), the Suicidal Ideation Questionnaire--Grades 7-9 (SIQ-Jr), and the Social Problem-Solving Inventory-Revised (SPSI-R). A random coefficients regression model was conducted to examine main and interaction effects of treatment and SPSI-R subscale scores on outcomes during the 12-week acute treatment stage. Negative problem orientation, positive problem orientation, and avoidant problem-solving style were non-specific predictors of depression severity. In terms of suicidality, avoidant problem-solving style and impulsiveness/carelessness style were predictors, whereas negative problem orientation and positive problem orientation were moderators of treatment outcome. Implications of these findings, limitations, and directions for future research are discussed. Copyright 2009 Elsevier Ltd. All rights reserved.

Greater rate of cephalic screw mobilisation following proximal femoral nailing in hip fractures with a tip-apex distance (TAD) and a calcar referenced TAD greater than 25 mm.

PubMed

Aicale, Rocco; Maffulli, Nicola

2018-05-02

To ascertain whether the tip-apex distance (TAD), calcar referenced TAD (CalTAD), and the sum of both (TADcalTAD) are predictive measurements of mobilisation of the cephalic screw in patients with trochanteric hip fractures. Between 2014 and 2015, 68 patients (mean age 86 years, 45 females, 23 males) with a trochanteric hip fracture underwent intramedullary nailing. The TAD and CalTAD were measured, and for each parameter, we calculated sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). There is evidence of a statistically significant association between a TAD and CalTAD greater than 25 mm and a TADcalTAD greater than 50 mm and mobilisation of the cephalic screw. All measurements have similar sensitivity, but the TAD presents the highest specificity (p < 0.01). To avoid the risk of mobilisation of the cephalic screw and possible subsequent failure of the construct, surgeons should strive for a TAD and CalTAD less than 25 mm and a TADcalTAD less than 50 mm when using intramedullary fixation.

Computational characterization of chromatin domain boundary-associated genomic elements

PubMed Central

Hong, Seungpyo

2017-01-01

Abstract Topologically associated domains (TADs) are 3D genomic structures with high internal interactions that play important roles in genome compaction and gene regulation. Their genomic locations and their association with CCCTC-binding factor (CTCF)-binding sites and transcription start sites (TSSs) were recently reported. However, the relationship between TADs and other genomic elements has not been systematically evaluated. This was addressed in the present study, with a focus on the enrichment of these genomic elements and their ability to predict the TAD boundary region. We found that consensus CTCF-binding sites were strongly associated with TAD boundaries as well as with the transcription factors (TFs) Zinc finger protein (ZNF)143 and Yin Yang (YY)1. TAD boundary-associated genomic elements include DNase I-hypersensitive sites, H3K36 trimethylation, TSSs, RNA polymerase II, and TFs such as Specificity protein 1, ZNF274 and SIX homeobox 5. Computational modeling with these genomic elements suggests that they have distinct roles in TAD boundary formation. We propose a structural model of TAD boundaries based on these findings that provides a basis for studying the mechanism of chromatin structure formation and gene regulation. PMID:28977568

Transcriptional regulation of the tad locus in Aggregatibacter actinomycetemcomitans: a termination cascade.

PubMed

Kram, Karin E; Hovel-Miner, Galadriel A; Tomich, Mladen; Figurski, David H

2008-06-01

The tad (tight adherence) locus of Aggregatibacter actinomycetemcomitans includes genes for the biogenesis of Flp pili, which are necessary for bacterial adhesion to surfaces, biofilm formation, and pathogenesis. Although studies have elucidated the functions of some of the Tad proteins, little is known about the regulation of the tad locus in A. actinomycetemcomitans. A promoter upstream of the tad locus was previously identified and shown to function in Escherichia coli. Using a specially constructed reporter plasmid, we show here that this promoter (tadp) functions in A. actinomycetemcomitans. To study expression of the pilin gene (flp-1) relative to that of tad secretion complex genes, we used Northern hybridization analysis and a lacZ reporter assay. We identified three terminators, two of which (T1 and T2) can explain flp-1 mRNA abundance, while the third (T3) is at the end of the locus. T1 and T3 have the appearance and behavior of intrinsic terminators, while T2 has a different structure and is inhibited by bicyclomycin, indicating that T2 is probably Rho dependent. To help achieve the appropriate stoichiometry of the Tad proteins, we show that a transcriptional-termination cascade is important to the proper expression of the tad genes. These data indicate a previously unreported mechanism of regulation in A. actinomycetemcomitans and lead to a more complete understanding of its Flp pilus biogenesis.

Involvement of NO-cGMP pathway in anti-hyperalgesic effect of PDE5 inhibitor tadalafil in experimental hyperalgesia.

PubMed

Otari, K V; Upasani, C D

2015-08-01

The association of elevated level of cyclic guanosine monophosphate (cGMP) with inhibition of hyperalgesia and involvement of nitric oxide (NO)-cGMP pathway in the modulation of pain perception was previously reported. Phosphodiesterases 5 (PDE5) inhibitors, sildenafil and tadalafil (TAD) used in erectile dysfunction, are known to act via the NO-cGMP pathway. TAD exerts its action by increasing the levels of intracellular cGMP. Hence, the present study investigated the effect of TAD 5, 10, or 20 mg/kg, per os (p.o.) or L-NAME 20 mg/kg, intraperitoneally (i.p.) and TAD (20 mg/kg, p.o.) in carrageenan- and diabetes-induced hyperalgesia in rats using hot plate test at 55 ± 2 °C. In carrageenan- and diabetes-induced hyperalgesia, TAD (10 and 20 mg/kg, p.o.) significantly increased paw withdrawal latencies (PWLs) as compared to the control group. L-NAME significantly decreased PWLs as compared to the normal group and aggravated the hyperalgesia. Moreover, significant difference in PWLs of L-NAME and TAD 20 was evident. Co-administration of L-NAME (20 mg/kg) with TAD (20 mg/kg) showed significant difference in PWLs as compared to the TAD (20 mg/kg), indicating L-NAME reversed and antagonized TAD-induced anti-hyperalgesia. This suggested an important role of NO-cGMP pathway in TAD-induced anti-hyperalgesic effect.

Association of TNF-α gene variations with thoracic aortic dissection risk in a Chinese Han population.

PubMed

DU, Xiao M; Liu, Li W; DU, Zhan K; Gu, Ruo X; Han, Ya L; Wang, Xiao Z

2016-08-01

Chronic inflammation may be involved in pathogenesis of thoracic aortic dissection (TAD). Tumor necrosis factor-alpha (TNF-α) is a proinflammatory cytokine that plays an important role in pathological TAD progression. In this study, we determined wether genetic variants of TNF-α were associated with TAD. Frequency distributions of TNF-α promoter polymorphisms (-1031C/T,-857C/T,-308G/A, and -238G/A) were determined by direct sequencing. TNF-α plasma levels were measured by enzyme-linked immunosorbent assay. Plasma levels of TNF-α mRNA in peripheral-blood mononuclear cells were analyzed by real-time quantitative polymerase chain reaction amplification. We found the TNF-α promoter -857C/T polymorphism is associated with disease progression susceptibility in TAD patients. The CC homozygote of TAD patients had a significantly higher risk of TAD than did T allele carriers (P< 0.05). Plasma TNF-α concentrations were also significantly higher in TAD patients than control subjects (P<0.05), and CC genotype carriers showed increased TNF-α levels compared with T allele carriers (P<0.05). Moreover, peripheral-blood mononuclear cells carrying the CC genotype showed increased TNF-α mRNA levels compared with cells carrying the T allele. The -857C/T polymorphism of TNF-α promoter plays a role in the genetic variation underlying susceptibility of individuals to TAD progression. The CC genotype is associated with increased TNF-α expression in TAD patients, and may be an independent predictive factor for TAD.

Effects of tadalafil on ischemia/reperfusion injury in rat brain.

PubMed

Altaş, Murat; Aras, M; Meydan, S; Nacar, E; Ulutaş, K T; Serarslan, Y; Yılmaz, N

2014-03-01

Cerebral ischemia-reperfusion (I/R) injury is caused by lack of blood supply to the brain. The accumulation of toxic products such as reactive oxygen species (ROS) occurs on reperfusion, when the occlusion is removed. The resulting oxidative stress results in the initiation of pathways leading to necrotic and apoptotic cell death. Tadalafil (TAD) prevents the accumulation of ROS and increases antioxidant cellular protective mechanisms. The aim of this study was to investigate the effect of TAD treatment against short-term global brain I/R injury in rats. The study was carried out on 30 Wistar-albino rats, which were divided into three groups including a control group (n = 10), an I/R group (n = 10) and an I/R + TAD group (n = 10) (2 mg/kg/day for 4 days before ischemia). At the end of the experiment, tissue samples were collected for both biochemical and histopathological analyses. Malondialdehyde was significantly lower in the TAD-administered group (9.06 ± 0.15) than in the I/R group (p < 0.05). However, no significant difference was observed in nitric oxide levels in the TAD-administered group compared to the I/R group. The mean superoxide dismutase level was significantly higher in the I/R-TAD group than the I/R group. There was no statistically significant difference in glutathione peroxidase levels in I/R + TAD group compared to I/R group. Histopathologically, TAD-administered group provided significant morphological improvement compared to the I/R group. We concluded that TAD prevented I/R-induced neurotoxicity as shown by obtained biochemical and histopathological findings.

5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells

PubMed Central

Malashchuk, Igor; Lajoie, Brian R.; Mardaryev, Andrei N.; Gdula, Michal R.; Sharov, Andrey A.; Kohwi-Shigematsu, Terumi; Fessing, Michael Y.

2017-01-01

Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C) technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC) locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac) revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene promoters and enhancers at the multi-TAD EDC locus in skin epithelial cells are cell type-specific and involve extensive contacts within TADs as well as between different gene-rich TADs, forming the framework for lineage-specific transcription. PMID:28863138

Titanium alloy vs. stainless steel miniscrews: an in vivo split-mouth study.

PubMed

Bollero, P; Di Fazio, V; Pavoni, C; Cordaro, M; Cozza, P; Lione, R

2018-04-01

To compare in vivo Titanium Alloy (TiA) with Stainless Steel (SS) miniscrews Temporary Anchorage Devices (TADs) using removal torque and Scanning Electron Microscopic (SEM) analysis. 15 subjects (6 males and 9 females) who required maximum anchorage were recruited. For each patient, a TiA TAD and a SS TAD with same length and width were implanted following a randomized split-mouth study design. Retraction was carried out with nickel-titanium spring ligated directly from the anterior hooks of the archwire to the TADs to produce 90 to 100 g of force. When no further anchorage supplementation was needed, the TADs were removed. The removal torque values were registered with a digital screwdriver. After removal, the TADs were collected in a fixed solution and examined using SEM and X-ray microanalysis. All TADs remained intact, with a 100% success rate. There was no difference in removal torque between TiA and SS miniscrews (4.4 ± 1.3 N-cm and 5.1 ± 0.7 N-cm, respectively). All specimens' loss of gloss with signs of biological contaminations resulted in a dull implant surface. SEM photomicrographs of TiA miniscrews showed predominantly blood cells while SS miniscrews showed the precipitation of an amorphous layer with low cellular component. There was no difference in spectroscopic analysis between TiA and SS miniscrews. TiA and SS miniscrews had comparable removal torque values. SEM photomicrographs showed no evidence of osseointegration with both TADs having similar biological responses.

Increased interleukin-11 levels in thoracic aorta and plasma from patients with acute thoracic aortic dissection.

PubMed

Xu, Yao; Ye, Jing; Wang, Menglong; Wang, Yuan; Ji, Qingwei; Huang, Ying; Zeng, Tao; Wang, Zhen; Ye, Di; Jiang, Huimin; Liu, Jianfang; Lin, Yingzhong; Wan, Jun

2018-06-01

Interleukin (IL) 11 is closely related to tumor and hematological system diseases. Recent studies have demonstrated that IL-11 also participates in cardiovascular diseases, including ischemia-reperfusion mediated heart injury and acute myocardial infarction. This study aimed to investigate whether IL-11 is involved in acute thoracic aortic dissection (TAD). Aortic tissue samples from normal donors and acute TAD patients were collected, and the expression of IL-11 in all aortic tissue was analyzed. In addition, blood samples from patients with chest pain were collected and divided into a non-AD (NAD) group and a TAD group according to the results of computed tomography angiography of the thoracic aorta. The plasma IL-11, IL-17 and interferon (IFN) γ in all blood samples were measured. Compared with aortic tissue of normal controls, IL-11 was significantly increased in aortic tissue of acute TAD patients, especially in the torn section. The IL-11 was derived from aorta macrophages in TAD. In addition, the plasma IL-11, IL-17 and IFN-γ were significantly higher in acute TAD patients than in NAD patients, and the correlation analysis showed that IL-11 levels were positively correlated with levels of IFN-γ, IL-17, glucose, systolic blood pressure, diastolic blood pressure, white blood cells, C-reactive proteins and D-dimers. Binary logistic regression analyses showed that elevated IL11 in patients who may have diagnostic value of TAD, but less that D-dimer. IL-11 was increased in thoracic aorta and plasma of TAD patients and may be a promising biomarker for diagnosis in patients with TAD. Copyright © 2018. Published by Elsevier B.V.

c-Myc plays a key role in TADs-induced apoptosis and cell cycle arrest in human hepatocellular carcinoma cells.

PubMed

Zhang, Dongdong; Qi, Junpeng; Liu, Rui; Dai, Bingling; Ma, Weina; Zhan, Yingzhuan; Zhang, Yanmin

2015-01-01

Cancer cell growth is complicated progression which is regulated and controlled by multiple factors including cell cycle, migration and apoptosis. In present study, we report that TADs, a novel derivative of taspine, has an essential role in resisting hepatocellular carcinoma growth (including arrest cell cycle) and migration, and inducing cell apoptosis. Our findings demonstrated that the TADs showed good inhibition on the hepatoma cell growth and migration, and good action on apoptosis induction. Using genome-wide microarray analysis, we found the down-regulated growth and apoptosis factors, and selected down-regulated genes were confirmed by Western blot. Knockdown of a checkpoint c-Myc by siRNA significantly attenuated tumor inhibition and apoptosis effects of TADs. Moreover, our results indicated TADs could simultaneously increase cyclin D1 protein levels and decrease amount of cyclin E, cyclin B1 and cdc2 of the cycle proteins, and also TADs reduced Bcl-2 expression, and upregulated Bad, Bak and Bax activities. In conclusion, these results illustrated that TADs is a key factor in growth and apoptosis signaling inhibitor, has potential in cancer therapy.

Global Conformational Selection and Local Induced Fit for the Recognition between Intrinsic Disordered p53 and CBP

PubMed Central

Yu, Qingfen; Ye, Wei; Wang, Wei; Chen, Hai-Feng

2013-01-01

The transactivation domain (TAD) of tumor suppressor p53 can bind with the nuclear coactivator binding domain (NCBD) of cyclic-AMP response element binding protein (CBP) and activate transcription. NMR experiments demonstrate that both apo-NCBD and TAD are intrinsic disordered and bound NCBD/TAD undergoes a transition to well folded. The recognition mechanism between intrinsic disordered proteins is still hotly debated. Molecular dynamics (MD) simulations in explicit solvent are used to study the recognition mechanism between intrinsic disordered TAD and NCBD. The average RMSD values between bound and corresponding apo states and Kolmogorov-Smirnov P test analysis indicate that TAD and NCBD may follow an induced fit mechanism. Quantitative analysis indicates there is also a global conformational selection. In summary, the recognition of TAD and NCBD might obey a local induced fit and global conformational selection. These conclusions are further supported by high-temperature unbinding kinetics and room temperature landscape analysis. These methods can be used to study the recognition mechanism of other intrinsic disordered proteins. PMID:23555731

Comparative efficacy of tadalafil once daily in men with erectile dysfunction who demonstrated previous partial responses to as-needed sildenafil, tadalafil, or vardenafil.

PubMed

Kim, Edward; Seftel, Allen; Goldfischer, Evan; Baygani, Simin; Burns, Patrick

2015-02-01

Phosphodiesterase type-5 inhibitors (PDE5Is) are first-line therapies for erectile dysfunction (ED). Sildenafil (SIL) and vardenafil (VAR) are approved for as-needed (PRN) dosing; tadalafil (TAD) is approved for both PRN and once-a-day (OaD) dosing for ED. Recent evidence suggests that TAD-OaD may be effective as therapy in men with an incomplete response to PRN-PDE5I therapy. This study evaluated whether TAD-OaD provides similar efficacy in men with ED who had previously demonstrated a partial response to PRN-PDE5I therapy. In this randomized, double-blind, placebo-controlled trial, men with a ≥3 month ED history received SIL 100 mg, TAD 20 mg, or VAR 20 mg during a 4 week open-label lead-in period. Those with International Index of Erectile Function - Erectile Function (IIEF-EF) domain scores <26 following lead-in treatment completed a 4 week washout period, then randomized to TAD 2.5 mg up-titrated to 5 mg, TAD 5 mg, or placebo (PBO) OaD for 12 weeks. MAIN OUTCOME MEASURES obtained from patients treated with TAD-OaD were compared to PBO-treated patients. Additionally, results of treatment with TAD-OaD were compared to results obtained from 4 week PRN-PDE5I therapy to determine whether OaD and PRN regimens provided comparable efficacy. NCT01130532. International Index of Erectile Function (IIEF) domain scores; Sexual Encounter Profile (SEP) questions 2-5. Endpoint data was obtained from 590 men (391 TAD; 199 PBO). RESULTS for all IIEF and SEP measures were significantly better for TAD-OaD (p < 0.001 for all) compared to PBO and were comparable to those observed during PRN-PDE5I treatment. TAD 2.5 mg and TAD 5 mg OaD therapy were safe and generally well tolerated. Tadalafil once daily is a viable alternative to as-needed PDE5I therapy in men with ED. Key limitations include the lack of a PRN PDE5I study group during the double-blind period, and that many more patients took tadalafil than sildenafil or vardenafil during the PRN period.

Identification of hierarchical chromatin domains

PubMed Central

Weinreb, Caleb; Raphael, Benjamin J.

2016-01-01

Motivation: The three-dimensional structure of the genome is an important regulator of many cellular processes including differentiation and gene regulation. Recently, technologies such as Hi-C that combine proximity ligation with high-throughput sequencing have revealed domains of self-interacting chromatin, called topologically associating domains (TADs), in many organisms. Current methods for identifying TADs using Hi-C data assume that TADs are non-overlapping, despite evidence for a nested structure in which TADs and sub-TADs form a complex hierarchy. Results: We introduce a model for decomposition of contact frequencies into a hierarchy of nested TADs. This model is based on empirical distributions of contact frequencies within TADs, where positions that are far apart have a greater enrichment of contacts than positions that are close together. We find that the increase in contact enrichment with distance is stronger for the inner TAD than for the outer TAD in a TAD/sub-TAD pair. Using this model, we develop the TADtree algorithm for detecting hierarchies of nested TADs. TADtree compares favorably with previous methods, finding TADs with a greater enrichment of chromatin marks such as CTCF at their boundaries. Availability and implementation: A python implementation of TADtree is available at http://compbio.cs.brown.edu/software/ Contact: braphael@cs.brown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26315910

[Usefulness of tricuspid annular displacement (TAD) to identify right ventricular dysfunction in normotensive patients with acute pulmonary embolism].

PubMed

Hugues, T; Yaici, K; Latcu, D-G; Rinaldi, J-P; Zarqane, N; Saoudi, N; Gibelin, P

2011-02-01

Echocardiographic criteria of right ventricular dysfunction (RVD) in acute pulmonary embolism (PE) differ among published studies. Assessment of RV systolic function remains difficult because of the RV's complex shape. We aimed to evaluate RV systolic function with TAD in patients (pts) with acute PE. TAD (QLAB, Philips Medical Imaging) was based on a tissue-tracking algorithm that is ultrasound beam angle independent for automated detection of tricuspid annular displacement. Prospective and observational study. All adults' pts who were diagnosed with PE from December 2008 to December 2009 at Princess Grace Hospital, Monaco were eligible for this study after exclusion of history of heart failure. We evaluated 36 consecutive pts with PE (18 male, mean age 62.7 years), which underwent echocardiography, plasma BNP titration during the first day after admission, and a second echocardiography obtained within 48 hours before discharge. TAD value were significantly lower in pts with abnormal RV function by echocardiogram (15.9 ± 0.3 vs. 12.7 ± 0.2 ; P = 0.026). Pts with a normal BNP (<80 pg/ml) had an elevated TAD (16.4 ± 0.2 vs. 11.2 ± 0.3 mm ; P < 0.0001). At discharge, echocardiographic data were obtained from 33 pts (mean: 8.3 ± 3.5 days). RV end diastolic diameter, RV to LV diameter, pulmonary arterial systolic pressure, mean pulmonic valve acceleration time, RV FAC, Sa and TAD were significantly improved. There was no difference between TAD among pts with echocardiographic RVD at baseline vs. pts without RVD (14.9 ± 3.7 vs. 16.1 ± 2.9 mm ; P = 0.3). Four pts who deteriorated during short-term observation had substantially lower TAD values than those with uncomplicated courses (7.7 ± 0.4mm vs. 14.6 ± 0.2 mm ; P = 0.001). In conclusion, impaired TAD was associated with decreased RV systolic function in pts with acute PE. To identify the clinical meaning of decreased TAD, larger trials with longer follow-up periods are needed. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

Improved Performance and Reproducibility of Perovskite Solar Cells by Well-Soluble Tris(pentafluorophenyl)borane as a p-Type Dopant.

PubMed

Ye, Tengling; Wang, Junhai; Chen, Wenbo; Yang, Yulin; He, Dongqing

2017-05-31

In this work, well-soluble tris(pentafluorophenyl)borane (BCF) is introduced for the first time into 2,2',7,7'-tetrakis(N,N'-di-p-methoxyphenylamine)-9,9'-spirobifluorene (spiro-OMeTAD) as a p-dopant. The conductivity of spiro-OMeTAD films is dramatically enhanced. When the BCF-doped spiro-OMeTAD film is used as a hole-transport layer (HTL) in perovskite solar cells (PSCs), nearly double increase in power conversion efficiency (PCE) is obtained compared to that of the PSCs based on a pristine spiro-OMeTAD HTL. By the introduction of lithium bis(trifluoromethanesulfonyl)imide and 4-tert-butylpyridine into the BCF-doped spiro-OMeTAD film, the conductivity of spiro-OMeTAD film can be further enhanced, and an optimum PCE of 14.65% is obtained. In addition, the average efficiency of the device and the reproducibility of BCF-based PSCs are better than those of FK209-based PSCs. The working mechanism of the BCF doping effect on spiro-OMeTAD is studied in detail. The strong electron-accepting ability, excellent solubility in common organic solvents, and the low cost make BCF a very attractive p-type dopant for spiro-OMeTAD.

Synthesis and reactivity of TADDOL-based chiral Fe(II) PNP pincer complexes-solution equilibria between κ(2)P,N- and κ(3)P,N,P-bound PNP pincer ligands.

PubMed

Holzhacker, Christian; Stöger, Berthold; Carvalho, Maria Deus; Ferreira, Liliana P; Pittenauer, Ernst; Allmaier, Günter; Veiros, Luis F; Realista, Sara; Gil, Adrià; Calhorda, Maria José; Müller, Danny; Kirchner, Karl

2015-08-07

Treatment of anhydrous FeX2 (X = Cl, Br) with 1 equiv. of the asymmetric chiral PNP pincer ligands PNP-R,TAD (R = iPr, tBu) with an R,R-TADDOL (TAD) moiety afforded complexes of the general formula [Fe(PNP)X2]. In the solid state these complexes adopt a tetrahedral geometry with the PNP ligand coordinated in κ(2)P,N-fashion, as shown by X-ray crystallography and Mössbauer spectroscopy. Magnetization studies led to a magnetic moment very close to 4.9μB reflecting the expected four unpaired d-electrons (quintet ground state). In solution there are equilibria between [Fe(κ(3)P,N,P-PNP-R,TAD)X2] and [Fe(κ(2)P,N-PNP-R,TAD)X2] complexes, i.e., the PNP-R,TAD ligand is hemilabile. At -50 °C these equilibria are slow and signals of the non-coordinated P-TAD arm of the κ(2)P,N-PNP-R,TAD ligand can be detected by (31)P{(1)H} NMR spectroscopy. Addition of BH3 to a solution of [Fe(PNP-iPr,TAD)Cl2] leads to selective boronation of the pendant P-TAD arm shifting the equilibrium towards the four-coordinate complex [Fe(κ(2)P,N-PNP-iPr,TAD(BH3))Cl2]. DFT calculations corroborate the existence of equilibria between four- and five-coordinated complexes. Addition of CO to [Fe(PNP-iPr,TAD)X2] in solution yields the diamagnetic octahedral complexes trans-[Fe(κ(3)P,N,P-PNP-iPr,TAD)(CO)X2], which react further with Ag(+) salts in the presence of CO to give the cationic complexes trans-[Fe(κ(3)P,N,P-PNP-iPr,TAD)(CO)2X](+). CO addition most likely takes place at the five coordinate complex [Fe(κ(3)P,N,P-PNP-iPr,TAD)X2]. The mechanism for the CO addition was also investigated by DFT and the most favorable path obtained corresponds to the rearrangement of the pincer ligand first from a κ(2)P,N- to a κ(3)P,N,P-coordination mode followed by CO coordination to [Fe(κ(3)P,N,P-PNP-iPr,TAD)X2]. Complexes bearing tBu substituents do not react with CO. Moreover, in the solid state none of the tetrahedral complexes are able to bind CO.

Oral immunisation of laying hens with the live vaccine strains of TAD Salmonella vac E and TAD Salmonella vac T reduces internal egg contamination with Salmonella Enteritidis.

PubMed

Gantois, Inne; Ducatelle, Richard; Timbermont, Leen; Boyen, Filip; Bohez, Lotte; Haesebrouck, Freddy; Pasmans, Frank; van Immerseel, Filip

2006-09-11

Eggs are a major source of human infections with Salmonella. Therefore controlling egg contamination in laying hen flocks is one of the main targets for control programmes. A study was carried out to assess the effect of oral vaccination with TAD Salmonella vac E, TAD Salmonella vac T and with both vaccines TAD Salmonella vac E and TAD Salmonella vac T, on colonization of the reproductive tract and internal egg contamination of laying hens with Salmonella Enteritidis. Three groups of 30 laying hens were vaccinated at 1 day, 6 weeks and 16 weeks of age with either one of the vaccine strains, or a combination of both vaccine strains, while a fourth group was left unvaccinated. At 24 weeks of age, the birds were intravenously challenged with 0.5 ml containing 5 x 10(7)cfu Salmonella Enteritidis PT4 S1400/94. The number of oviducts from which Salmonella was isolated, was significantly lower in the vaccinated than in the non-vaccinated hens at 3 weeks post-challenge. Significantly less egg contents were Salmonella positive in the birds vaccinated with TAD Salmonella vac E or TAD Salmonella vac T (12/105 batches of eggs in both groups) than in the unvaccinated birds (28/105 batches of eggs). Internal egg contamination in the hens vaccinated with both TAD Salmonella vac E and TAD Salmonella vac T was even more reduced, as over the whole experiment, only one batch of eggs was positive. In conclusion, these data indicate that vaccination of laying hens with these live vaccines could be considered as a valuable tool in controlling internal egg contamination.

Cardioprotective role of tadalafil against cisplatin-induced cardiovascular damage in rats.

PubMed

Saleh, Rasha M; Awadin, Walaa F; El-Shafei, Reham A; Elseady, Yousef Y; Wehaish, Faheim E; Elshal, Mohamed F

2015-10-15

The present study investigated the possible cardioprotective effect of tadalafil (Tad) on cisplatin (CDDP)-induced cardiac and vascular damages in rats. A total number of seventy two healthy male albino rats initially weighting between 200 and 220 g were used and randomly divided into four groups,18 rats in each. The control group received no treatment; CDDP group received a single dose of CDDP (4 mg/kg) intraperitoneal (i.p.) per week for 4 weeks the duration of the experiment; Tad group received 0.4 mg/kg BW Tad i.p. daily and Tad +CDDP group received 0.4 mg/kg BW Tad i.p. +4 mg/kg BW CDDP i.p. The results showed that Tad was able to decrease blood pressure, heart rate, levels of serum cardiac troponin (cTn-I), malondialdehyde (MDA) and increased levels of reduced glutathione (GSH) and nitric oxide (NO) in the heart homogenate sample from CDDP treated rats. Semi-quantitative analysis showed that Tad was able to decrease the histopathological scores of cardiac muscular hyalinzation and fibrosis in three sacrifices in CDDP treated rats. CDDP treated rats showed significantly increased thickening in wall of aorta with an irregular luminal layer of endothelial cell linings in three sacrifices when it was compared to other groups. Moreover, immunohistochemical labeling of α- smooth muscle actin (α-SMA) in aorta revealed significant lower scores in Tad +CDDP group when they were compared to CDDP group. In conclusion, Tad alone did not induce any harmful effects on blood pressure, selective antioxidant, peroxidation markers or cardiac histology, in addition, Tad has a cardio-protective role against CDDP. Copyright © 2015 Elsevier B.V. All rights reserved.

DNA methylation inhibits expression and transposition of the Neurospora Tad retrotransposon.

PubMed

Zhou, Y; Cambareri, E B; Kinsey, J A

2001-06-01

Tad is a LINE-like retrotransposon of the filamentous fungus Neurospora crassa. We have analyzed both expression and transposition of this element using strains with a single copy of Tad located in the 5' noncoding sequences of the am (glutamate dehydrogenase) gene. Tad in this position has been shown to carry a de novo cytosine methylation signal which causes reversible methylation of both Tad and am upstream sequences. Here we find that methylation of the Tad sequences inhibits both Tad expression and transposition. This inhibition can be relieved by the use of 5-azacytidine, a drug which reduces cytosine methylation, or by placing the Tad/am sequences in a dim-2 genetic background.

Enhanced cephalomedullary nail lag screw placement and intraoperative tip-apex distance measurement with a novel computer assisted surgery system.

PubMed

Kuhl, Mitchell; Beimel, Claudia

2016-10-01

The goal of this study was to evaluate the ability of a novel computer assisted surgery system to guide ideal placement of a lag screw during cephalomedullary nailing and then accurately measure the tip-apex distance (TAD) measurement intraoperatively. Retrospective case review. Level II trauma hospital. The initial 98 consecutive clinical cases treated with a cephalomedullary nail in conjunction with a novel computer assisted surgery system were retrospectively reviewed. A novel computer assisted surgery system was utilized to enhance lag screw placement during cephalomedullary nailing procedures. The computer assisted surgery system calculates the TAD intraoperatively after final lag screw placement. The ideal TAD was considered to be within a range of 5mm-20mm. The ability of the computer assisted surgery system (CASS) to assist in placement of a lag screw within the ideal TAD was evaluated. Intraoperative TAD measurements provided by the computer assisted surgery system were then compared to standard postoperative TAD measurements on PACS (picture archiving and communication system) images to determine whether these measurements are equivalent. 79 cases (80.6%) were available with complete information for a retrospective review. All cases had CASS TAD and PACS TAD measurements >5mm and<20mm. In addition, no significant difference could be detected between the intraoperative CASS TAD and the postoperative PACS TAD (p=0.374, Wilcoxon Test; p=0.174, paired T-Test). A cut-out rate of 0% was observed in all patients who were treated with CASS in this case series (95% CI: 0 - 3.01%). The novel computer assisted surgery system tested here is an effective and reliable adjunct that can be utilized for optimal lag screw placement in cephalomedullary nailing procedures. The computer assisted surgery system provides an accurate intraoperative TAD measurement that is equivalent to the standard postoperative measurement utilizing PACS images. Therapeutic Level IV. Copyright © 2016 Elsevier Ltd. All rights reserved.

SpecTAD

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

Zamora, Richard; Voter, Arthur; Uberuaga, Bla

2017-10-23

The SpecTAD software represents a refactoring of the Temperature Accelerated Dynamics (TAD2) code authored by Arthur F. Voter and Blas P. Uberuaga (LA-CC-02-05). SpecTAD extends the capabilities of TAD2, by providing algorithms for both temporal and spatial parallelism. The novel algorithms for temporal parallelism include both speculation and replication based techniques. SpecTAD also offers the optional capability to dynamically link to the open-source LAMMPS package.

Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells.

PubMed

Wang, Qi; Sun, Qiu; Czajkowsky, Daniel M; Shao, Zhifeng

2018-01-15

Topologically associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. However, recent studies suggest that the insulating complexes, CTCF/cohesin, present at TAD borders in mammals are absent from those in Drosophila melanogaster, raising the possibility that border elements are not conserved among metazoans. Using in situ Hi-C with sub-kb resolution, here we show that the D. melanogaster genome is almost completely partitioned into >4000 TADs, nearly sevenfold more than previously identified. The overwhelming majority of these TADs are demarcated by the insulator complexes, BEAF-32/CP190, or BEAF-32/Chromator, indicating that these proteins may play an analogous role in flies as that of CTCF/cohesin in mammals. Moreover, extended regions previously thought to be unstructured are shown to consist of small contiguous TADs, a property also observed in mammals upon re-examination. Altogether, our work demonstrates that fundamental features associated with the higher-order folding of the genome are conserved from insects to mammals.

c-Myc plays a key role in TADs-induced apoptosis and cell cycle arrest in human hepatocellular carcinoma cells

PubMed Central

Zhang, Dongdong; Qi, Junpeng; Liu, Rui; Dai, Bingling; Ma, Weina; Zhan, Yingzhuan; Zhang, Yanmin

2015-01-01

Cancer cell growth is complicated progression which is regulated and controlled by multiple factors including cell cycle, migration and apoptosis. In present study, we report that TADs, a novel derivative of taspine, has an essential role in resisting hepatocellular carcinoma growth (including arrest cell cycle) and migration, and inducing cell apoptosis. Our findings demonstrated that the TADs showed good inhibition on the hepatoma cell growth and migration, and good action on apoptosis induction. Using genome-wide microarray analysis, we found the down-regulated growth and apoptosis factors, and selected down-regulated genes were confirmed by Western blot. Knockdown of a checkpoint c-Myc by siRNA significantly attenuated tumor inhibition and apoptosis effects of TADs. Moreover, our results indicated TADs could simultaneously increase cyclin D1 protein levels and decrease amount of cyclin E, cyclin B1 and cdc2 of the cycle proteins, and also TADs reduced Bcl-2 expression, and upregulated Bad, Bak and Bax activities. In conclusion, these results illustrated that TADs is a key factor in growth and apoptosis signaling inhibitor, has potential in cancer therapy. PMID:26045987

Expression of platelet-derived growth factor B is upregulated in patients with thoracic aortic dissection.

PubMed

Meng, Weixin; Liu, Shangdian; Li, Dandan; Liu, Zonghong; Yang, Hui; Sun, Bo; Liu, Hongyu

2018-04-20

Thoracic aortic dissection (TAD) is a serious condition requiring urgent treatment to avoid catastrophic consequences. The inflammatory response is involved in the occurrence and development of TAD, possibly potentiated by platelet-derived growth factors (PDGFs). This study aimed to determine whether expression of PDGF-B (a subunit of PDGF-BB) was increased in TAD patients and to explore the factors responsible for its upregulation and subsequent effects on TAD. Full-thickness ascending aorta wall specimens from TAD patients (n = 15) and control patients (n = 10) were examined for expression of PDGF-B and its receptor (PDGFRB) and in terms of morphology, inflammation, and fibrosis. Blood samples from TAD and control patients were collected to detect plasma levels of PDGF-BB and soluble elastins. Expression levels of PDGF-B, PDGFRB, and collagen I were significantly enhanced in ascending aorta wall specimens from TAD patients compared with controls. Furthermore, soluble elastic fragments and PDGF-BB were significantly increased in plasma from TAD patients compared with controls, and numerous irregular elastic fibers and macrophages were seen in the ascending aorta wall in TAD patients. An increase in elastic fragments in the aorta wall might be responsible for inducing the activation and migration of macrophages to injured sites, leading to elevated expression of PDGF-B, which in turn induces deposition of collagen, disrupts extracellular matrix homeostasis, and increases the stiffness of the aorta wall, resulting in compromised aorta compliance. Copyright © 2018 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver

PubMed Central

2018-01-01

CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present and validate a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues. We propose that intra-TAD loops form by the same loop extrusion mechanism as the larger TAD loops, and that their shorter length enables finer regulatory control in restricting enhancer-promoter interactions, which enables selective, high-level expression of gene targets of super-enhancers and genes located within repressive nuclear compartments. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization associated with widespread insulation of distal enhancer activity. PMID:29757144

Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver.

PubMed

Matthews, Bryan J; Waxman, David J

2018-05-14

CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present and validate a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues. We propose that intra-TAD loops form by the same loop extrusion mechanism as the larger TAD loops, and that their shorter length enables finer regulatory control in restricting enhancer-promoter interactions, which enables selective, high-level expression of gene targets of super-enhancers and genes located within repressive nuclear compartments. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization associated with widespread insulation of distal enhancer activity. © 2018, Matthews et al.

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

PubMed Central

Smith, Emily M.; Lajoie, Bryan R.; Jain, Gaurav; Dekker, Job

2016-01-01

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. PMID:26748519

Disturbed P53-MDM2 Feedback Loop Contributes to Thoracic Aortic Dissection Formation and May be a Result of TRIM25 Overexpression.

PubMed

Gong, Bin; Wang, Zhiwei; Zhang, Min; Hu, Zhipeng; Ren, Zongli; Tang, Zheng; Jiang, Wanli; Cheng, Lianghao; Huang, Jun; Ren, Wei; Wang, Qingtao

2017-04-01

The development of thoracic aortic dissection (TAD) is attributed to a broad range of degenerative, genetic, structural, oxidative, apoptotic, and acquired disease states. In this study, we examined the role of the disturbed p53-MDM2 (murine double minute 2) feedback loop in the formation of TAD, and one of a potential feedback loop regulator, TRIM25 (tripartite motif protein-25). Surgical specimens of the aorta from TAD patients (n = 10) and controls (n = 10) were tested for α-smooth muscle actin (α-SMA), p53, MDM2, and TRIM25 by western blot, immunohistochemical staining, and quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR), respectively. When compared with controls, western blot shows that the protein levels of p53, MDM2, and TRIM25 were increased significantly in the aortic media of TAD patients. qRT-PCR further verified that the mRNA expression of MDM2 and TRIM25 was also increased 6- and 4-folds, respectively, in the TAD media of the aortic wall. Immunohistochemistry results showed significantly decreased staining of α-SMA, smooth muscle cells, and more collagen deposition in the media of the aortic wall from patients with TAD. This study provided a new insight into the disturbed p53-MDM2 feedback loop in the pathogenesis of TAD, and this may be because of the TRIM25 overexpression. Copyright © 2016 Elsevier Inc. All rights reserved.

Comparison of in-vivo failure of single-thread and dual-thread temporary anchorage devices over 18 months: A split-mouth randomized controlled trial.

PubMed

Durrani, Owais Khalid; Shaheed, Sohrab; Khan, Arsalan; Bashir, Ulfat

2017-10-01

The purpose of this study was to compare the in-vivo failure rates of single-thread and dual-thread temporary anchorage device (TAD) designs over 18 months. Thirty patients with skeletal Class II Division 1 malocclusion requiring anchorage from TADs for retraction of maxillary incisors into the extracted premolar space were recruited in this parallel group, split-mouth, randomized controlled trial. A block randomization sequence was generated with Random Allocation Software (version 2.0; Isfahan, Iran) with the allocations concealed in sequentially numbered, opaque, sealed envelopes. A total of 60 TADs (diameter, 2 mm; length, 10 mm) were placed in the maxillary arches of these patients with random allocation of the 2 types to the left and the right sides in a 1:1 ratio. All TADs were placed between the roots of the second premolar and the first molar and were immediately loaded. Patients were followed for a minimum of 12 months and a maximum of 18 months for the failure of the TADs. Data were analyzed blindly on an intention-to-treat basis. Four TADs (13.3%) failed in the single-thread group, and 6 TADs (20%) failed in the dual-thread group. The McNemar test showed an insignificant difference (P = 0.72) between the 2 groups. An odds ratio of 1.6 (95% confidence interval, 0.39-6.97) showed no significant associations among the variables. Most TADs failed in the first month after insertion (50%). The failure rate of dual-thread TADs compared with single-thread TADs is statistically insignificant when placed in the maxilla for retraction of the anterior segment. Registration: The trial was not registered before commencement. The protocol was not published before the trial. Copyright © 2016 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Dynamic autophagic activity affected the development of thoracic aortic dissection by regulating functional properties of smooth muscle cells

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

Wang, Yang; Zhao, Zhi-Min; Zhang, Guan-Xin

The aortic medial degeneration is the key histopathologic feature of Thoracic aortic dissection (TAD). The aim of this study was to identify the change of autophagic activity in the aortic wall during TAD development, and to explore the roles of autophagy on regulating functional properties of smooth muscle cells (SMCs). Firstly, compared with control group (n = 11), the increased expression of autophagic markers Beclin1 and LC3 was detected in the aortic wall from TAD group (n = 23) by immunochemistry and western blot. We found that more autophagic vacuoles were present in the aortic wall of TAD patients using Transmission electron microscopy. Next,more » autophagic activity was examined in AD mice model established by β-aminopropionitrile fumarate (BAPN) and angiotensin II. Immunochemistry proved that autophagic activity was dynamically changed during AD development. Beclin1 and LC3 were detected up-regulated in the aortic wall in the second week after BAPN feeding, earlier than the fragmentation or loss of elastic fibers. When AD occurred in the 4th week, the expression of Beclin1 and LC3 began to decrease, but still higher than the control. Furthermore, autophagy was found to inhibit starvation-induced apoptosis of SMCs. Meanwhile, blockage of autophagy could suppress PDGF-induced phenotypic switch of SMCs. Taken together, autophagic activity was dynamically changed in the aortic wall during TAD development. The abnormal autophagy could regulate the functional properties of aortic SMCs, which might be the potential pathogenesis of TAD. - Highlights: • Autophagy is up-regulated in aorta wall from thoracic aorta dissection (TAD) patient. • Autophagic activity is dynamically changed during TAD development. • Dynamically change of autophagy is associated with pathological process of TAD. • Autophagy participate in the development of TAD by regulating function of SMCs.« less

Relationship between ion migration and interfacial degradation of CH3NH3PbI3 perovskite solar cells under thermal conditions.

PubMed

Kim, Seongtak; Bae, Soohyun; Lee, Sang-Won; Cho, Kyungjin; Lee, Kyung Dong; Kim, Hyunho; Park, Sungeun; Kwon, Guhan; Ahn, Seh-Won; Lee, Heon-Min; Kang, Yoonmook; Lee, Hae-Seok; Kim, Donghwan

2017-04-26

Organic-inorganic hybrid perovskite solar cells (PSCs) have been extensively studied because of their outstanding performance: a power conversion efficiency exceeding 22% has been achieved. The most commonly used PSCs consist of CH 3 NH 3 PbI 3 (MAPbI 3 ) with a hole-selective contact, such as 2,2',7,7'-tetrakis(N,N-di-p-methoxyphenylamine)-9,9-spiro-bifluorene (spiro-OMeTAD), for collecting holes. From the perspective of long-term operation of solar cells, the cell performance and constituent layers (MAPbI 3 , spiro-OMeTAD, etc.) may be influenced by external conditions like temperature, light, etc. Herein, we report the effects of temperature on spiro-OMeTAD and the interface between MAPbI 3 and spiro-OMeTAD in a solar cell. It was confirmed that, at high temperatures (85 °C), I - and CH 3 NH 3 + (MA + ) diffused into the spiro-OMeTAD layer in the form of CH 3 NH 3 I (MAI). The diffused I - ions prevented oxidation of spiro-OMeTAD, thereby degrading the electrical properties of spiro-OMeTAD. Since ion diffusion can occur during outdoor operation, the structural design of PSCs must be considered to achieve long-term stability.

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.

PubMed

Smith, Emily M; Lajoie, Bryan R; Jain, Gaurav; Dekker, Job

2016-01-07

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

TADS: A CFD-based turbomachinery and analysis design system with GUI. Volume 1: Method and results

NASA Technical Reports Server (NTRS)

Topp, D. A.; Myers, R. A.; Delaney, R. A.

1995-01-01

The primary objective of this study was the development of a computational fluid dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a graphical user interface (GUI). The computer codes resulting from this effort are referred to as the Turbomachinery Analysis and Design System (TADS). This document describes the theoretical basis and analytical results from the TADS system. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) in an interactive package. Throughflow analysis capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of various programs was done in a way that alternative solvers or grid generators could be easily incorporated into the TADS framework. Results of aerodynamic calculations using the TADS system are presented for a highly loaded fan, a compressor stator, a low-speed turbine blade, and a transonic turbine vane.

Outer membrane components of the Tad (tight adherence) secreton of Aggregatibacter actinomycetemcomitans.

PubMed

Clock, Sarah A; Planet, Paul J; Perez, Brenda A; Figurski, David H

2008-02-01

Prokaryotic secretion relies on proteins that are widely conserved, including NTPases and secretins, and on proteins that are system specific. The Tad secretion system in Aggregatibacter actinomycetemcomitans is dedicated to the assembly and export of Flp pili, which are needed for tight adherence. Consistent with predictions that RcpA forms the multimeric outer membrane secretion channel (secretin) of the Flp pilus biogenesis apparatus, we observed the RcpA protein in multimers that were stable in the presence of detergent and found that rcpA and its closely related homologs form a novel and distinct subfamily within a well-supported gene phylogeny of the entire secretin gene superfamily. We also found that rcpA-like genes were always linked to Aggregatibacter rcpB- or Caulobacter cpaD-like genes. Using antisera, we determined the localization and gross abundances of conserved (RcpA and TadC) and unique (RcpB, RcpC, and TadD) Tad proteins. The three Rcp proteins (RcpA, RcpB, and RcpC) and TadD, a putative lipoprotein, localized to the bacterial outer membrane. RcpA, RcpC, and TadD were also found in the inner membrane, while TadC localized exclusively to the inner membrane. The RcpA secretin was necessary for wild-type abundances of RcpB and RcpC, and TadC was required for normal levels of all three Rcp proteins. TadC abundance defects were observed in rcpA and rcpC mutants. TadD production was essential for wild-type RcpA and RcpB abundances, and RcpA did not multimerize or localize to the outer membrane without the expression of TadD. These data indicate that membrane proteins TadC and TadD may influence the assembly, transport, and/or function of individual outer membrane Rcp proteins.

Formation of new chromatin domains determines pathogenicity of genomic duplications.

PubMed

Franke, Martin; Ibrahim, Daniel M; Andrey, Guillaume; Schwarzer, Wibke; Heinrich, Verena; Schöpflin, Robert; Kraft, Katerina; Kempfer, Rieke; Jerković, Ivana; Chan, Wing-Lee; Spielmann, Malte; Timmermann, Bernd; Wittler, Lars; Kurth, Ingo; Cambiaso, Paola; Zuffardi, Orsetta; Houge, Gunnar; Lambie, Lindsay; Brancati, Francesco; Pombo, Ana; Vingron, Martin; Spitz, Francois; Mundlos, Stefan

2016-10-13

Chromosome conformation capture methods have identified subchromosomal structures of higher-order chromatin interactions called topologically associated domains (TADs) that are separated from each other by boundary regions. By subdividing the genome into discrete regulatory units, TADs restrict the contacts that enhancers establish with their target genes. However, the mechanisms that underlie partitioning of the genome into TADs remain poorly understood. Here we show by chromosome conformation capture (capture Hi-C and 4C-seq methods) that genomic duplications in patient cells and genetically modified mice can result in the formation of new chromatin domains (neo-TADs) and that this process determines their molecular pathology. Duplications of non-coding DNA within the mouse Sox9 TAD (intra-TAD) that cause female to male sex reversal in humans, showed increased contact of the duplicated regions within the TAD, but no change in the overall TAD structure. In contrast, overlapping duplications that extended over the next boundary into the neighbouring TAD (inter-TAD), resulted in the formation of a new chromatin domain (neo-TAD) that was isolated from the rest of the genome. As a consequence of this insulation, inter-TAD duplications had no phenotypic effect. However, incorporation of the next flanking gene, Kcnj2, in the neo-TAD resulted in ectopic contacts of Kcnj2 with the duplicated part of the Sox9 regulatory region, consecutive misexpression of Kcnj2, and a limb malformation phenotype. Our findings provide evidence that TADs are genomic regulatory units with a high degree of internal stability that can be sculptured by structural genomic variations. This process is important for the interpretation of copy number variations, as these variations are routinely detected in diagnostic tests for genetic disease and cancer. This finding also has relevance in an evolutionary setting because copy-number differences are thought to have a crucial role in the evolution of genome complexity.

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

PubMed Central

Le Dily, François; Baù, Davide; Pohl, Andy; Vicent, Guillermo P.; Serra, François; Soronellas, Daniel; Castellano, Giancarlo; Wright, Roni H.G.; Ballare, Cecilia; Filion, Guillaume; Marti-Renom, Marc A.

2014-01-01

The human genome is segmented into topologically associating domains (TADs), but the role of this conserved organization during transient changes in gene expression is not known. Here we describe the distribution of progestin-induced chromatin modifications and changes in transcriptional activity over TADs in T47D breast cancer cells. Using ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing), Hi-C (chromosome capture followed by high-throughput sequencing), and three-dimensional (3D) modeling techniques, we found that the borders of the ∼2000 TADs in these cells are largely maintained after hormone treatment and that up to 20% of the TADs could be considered as discrete regulatory units where the majority of the genes are either transcriptionally activated or repressed in a coordinated fashion. The epigenetic signatures of the TADs are homogeneously modified by hormones in correlation with the transcriptional changes. Hormone-induced changes in gene activity and chromatin remodeling are accompanied by differential structural changes for activated and repressed TADs, as reflected by specific and opposite changes in the strength of intra-TAD interactions within responsive TADs. Indeed, 3D modeling of the Hi-C data suggested that the structure of TADs was modified upon treatment. The differential responses of TADs to progestins and estrogens suggest that TADs could function as “regulons” to enable spatially proximal genes to be coordinately transcribed in response to hormones. PMID:25274727

A critical assessment of topologically associating domain prediction tools

PubMed Central

Dali, Rola

2017-01-01

Abstract Topologically associating domains (TADs) have been proposed to be the basic unit of chromosome folding and have been shown to play key roles in genome organization and gene regulation. Several different tools are available for TAD prediction, but their properties have never been thoroughly assessed. In this manuscript, we compare the output of seven different TAD prediction tools on two published Hi-C data sets. TAD predictions varied greatly between tools in number, size distribution and other biological properties. Assessed against a manual annotation of TADs, individual TAD boundary predictions were found to be quite reliable, but their assembly into complete TAD structures was much less so. In addition, many tools were sensitive to sequencing depth and resolution of the interaction frequency matrix. This manuscript provides users and designers of TAD prediction tools with information that will help guide the choice of tools and the interpretation of their predictions. PMID:28334773

Topologically Associating Domains: An invariant framework or a dynamic scaffold?

PubMed

Cubeñas-Potts, Caelin; Corces, Victor G

2015-01-01

Metazoan genomes are organized into regions of topologically associating domains (TADs). TADs are demarcated by border elements, which are enriched for active genes and high occupancy architectural protein binding sites. We recently demonstrated that 3D chromatin architecture is dynamic in response to heat shock, a physiological stress that downregulates transcription and causes a global redistribution of architectural proteins. We utilized a quantitative measure of border strength after heat shock, transcriptional inhibition, and architectural protein knockdown to demonstrate that changes in both transcription and architectural protein occupancy contribute to heat shock-induced TAD dynamics. Notably, architectural proteins appear to play a more important role in altering 3D chromatin architecture. Here, we discuss the implications of our findings on previous studies evaluating the dynamics of TAD structure during cellular differentiation. We propose that the subset of variable TADs observed after differentiation are representative of cell-type specific gene expression and are biologically significant.

TADS: A CFD-based turbomachinery and analysis design system with GUI. Volume 2: User's manual

NASA Technical Reports Server (NTRS)

Myers, R. A.; Topp, D. A.; Delaney, R. A.

1995-01-01

The primary objective of this study was the development of a computational fluid dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a graphical user interface (GUI). The computer codes resulting from this effort are referred to as the Turbomachinery Analysis and Design System (TADS). This document is intended to serve as a user's manual for the computer programs which comprise the TADS system. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) in an interactive package. Throughflow analysis capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of various programs was done in a way that alternative solvers or grid generators could be easily incorporated into the TADS framework.

Properties of traveling atmospheric disturbances (TADs) inferred from CHAMP accelerometer observations

NASA Astrophysics Data System (ADS)

Bruinsma, Sean L.; Forbes, Jeffrey M.

2009-02-01

Densities derived from accelerometer measurements on the CHAMP satellite near 400 km are used to statistically establish characteristics of large-scale (>1000 km) traveling atmospheric disturbances (TADs). Only TADs that at least propagate from the auroral zone to the equator are analyzed here, and a total of 21 identifiable events are found over the years 2001 2007. The average speed of all TADs, regardless of local time, is 646 ± 122 ms-1. The average speeds on the dayside and nightside are 595 ± 127 ms-1 and 685 ± 106 ms-1, respectively, i.e., the speed appears to be 10% higher on average on the nightside. On six occasions TADs were only detected on the night side; however, TADs on the dayside often appear more distinctly in the data. Moreover, contrary to some theoretical expectations, dayside TADs do not dissipate more readily than night side TADs, although much less are detected between 8 20 solar local time. No clear dependence of TAD amplitude or phase speed with respect to Kp, or rate of increase of Kp, is found.

The prognostic value of tip-to-apex distance (TAD index) in intertrochanteric fractures fixed by dynamic hip screw.

PubMed

Sedighi, Ali; Sales, Jafar Ganjpour; Alavi, Sahar

2012-11-02

Intertrochanteric fractures (ITFs) are the most common type of fractures requiring surgical intervention. They also have the highest surgical mortality among orthopedic operations. Among the many different techniques used for fixation of this type of fracture, use of the Dynamic Hip Screw (DHS) has gained wide acceptance. This current study was designed to assess positive predictive value of tip-to-apex distance (TAD) index in the prognosis of patients treated with DHS. The study was designed according to a descriptive-analytic protocol, made up of 100 cases of ITFs caused by falling, treated in the Shohada Orthopedic Center, Tabriz, Iran. All patients underwent lateral and antero-posterior hip X-ray to measure TAD index. The cohort was followed for three months after DHS placement. Of a total of 100 cases (53 male, 47 female) with a mean age of 76.7 years (range 29-100 years), 43% had grade 4, 29% grade 3, 21% grade 5, 5% grade 2 and 2% grade 6 osteoporosis. The screw position was postero-inferior in 57%, central in 40% and superior in 3% of patients. Minimum and maximum TAD index were 20 and 28 mm, respectively. Mean TAD was 23.5 mm. There were no post-operative complications in 84% of cases. Screw failure was the most common complication in the remaining 16% of patients. The study shows a statistically significant correlation between TAD index and cut-off rate in patients with intertrochanteric fractures of femoral bone treated by DHS. This validates the use of TAD index in determining the prognosis of patients treated by DHS.

Elimination of active tad elements during the sexual phase of the Neurospora crassa life cycle.

PubMed

Anderson, C; Tang, Q; Kinsey, J A

2001-06-01

Tad is an active LINE-like retrotransposon isolated from the Adiopodoumé strain of Neurospora crassa. Extensive analysis of other Neurospora strains has revealed no other strain with active Tad, but all strains tested have multiple copies of defective Tad elements. We have examined the ability of Tad to survive during the sexual cycle of Neurospora and find that active Tad is rapidly eliminated. The characteristics of this elimination suggest that the repeat-induced point mutation (RIP) mechanism was responsible. By the use of transformation to switch the mating type of the Adiopodoumé strain we concluded that this strain is not defective in the RIP process. Analysis of defective Tad elements isolated from a variety of strains indicates that the major difference between these elements and active Tad is due to the presence of a large number of G-C to A-T transition mutations. This would be expected if the changes were due primarily to the RIP process. Mapping of a selection of defective Tad elements reveals that they are present on all of the chromosomes; however, many of the elements are not widely shared among strains. This suggests that repeated introduction and elimination of Tad elements has occurred. Mechanisms that might be responsible for this repeated introduction are discussed. Copyright 2001 Academic Press.

Interaction of the Transactivation Domain of B-Myb with the TAZ2 Domain of the Coactivator p300: Molecular Features and Properties of the Complex

PubMed Central

Oka, Ojore; Waters, Lorna C.; Strong, Sarah L.; Dosanjh, Nuvjeevan S.; Veverka, Vaclav; Muskett, Frederick W.; Renshaw, Philip S.; Klempnauer, Karl-Heinz; Carr, Mark D.

2012-01-01

The transcription factor B-Myb is a key regulator of the cell cycle in vertebrates, with activation of transcription involving the recognition of specific DNA target sites and the recruitment of functional partner proteins, including the coactivators p300 and CBP. Here we report the results of detailed studies of the interaction between the transactivation domain of B-Myb (B-Myb TAD) and the TAZ2 domain of p300. The B-Myb TAD was characterized using circular dichroism, fluorescence and NMR spectroscopy, which revealed that the isolated domain exists as a random coil polypeptide. Pull-down and spectroscopic experiments clearly showed that the B-Myb TAD binds to p300 TAZ2 to form a moderately tight (Kd ∼1.0–10 µM) complex, which results in at least partial folding of the B-Myb TAD. Significant changes in NMR spectra of p300 TAZ2 suggest that the B-Myb TAD binds to a relatively large patch on the surface of the domain (∼1200 Å2). The apparent B-Myb TAD binding site on p300 TAZ2 shows striking similarity to the surface of CBP TAZ2 involved in binding to the transactivation domain of the transcription factor signal transducer and activator of transcription 1 (STAT1), which suggests that the structure of the B-Myb TAD-p300 TAZ2 complex may share many features with that reported for STAT1 TAD-p300 TAZ2. PMID:23300815

Impact of the telephone assistive device (TAD) on stuttering severity while speaking on the telephone.

PubMed

Chambers, Nola

2009-01-01

There is extensive experimental evidence that altered auditory feedback (AAF) can have a clinically significant effect on the severity of speech symptoms in people who stutter. However, there is less evidence regarding whether these experimental effects can be observed in naturalistic everyday settings particularly when using the telephone. This study aimed to investigate the effectiveness of the Telephone Assistive Device (TAD), which is designed to provide AAF on the telephone to people who stutter, on reducing stuttering severity. Nine adults participated in a quasi-experimental study. Stuttering severity was measured first without and then with the device in participants' naturalistic settings while making and receiving telephone calls (immediate benefit). Participants were then allowed a week of repeated use of the device following which all measurements were repeated (delayed benefit). Overall, results revealed significant immediate benefits from the TAD in all call conditions. Delayed benefits in received and total calls were also significant. There was substantial individual variability in response to the TAD but none of the demographic or speech-related factors measured in the study were found to significantly impact the benefit (immediate or delayed) derived from the TAD. Results have implications for clinical decision making for adults who stutter.

Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing

PubMed Central

Li, Li; Lyu, Xiaowen; Hou, Chunhui; Takenaka, Naomi; Nguyen, Huy Q.; Ong, Chin-Tong; Cubeñas-Potts, Caelin; Hu, Ming; Lei, Elissa P.; Bosco, Giovanni; Qin, Zhaohui S.; Corces, Victor G.

2015-01-01

SUMMARY Chromosomes of metazoan organisms are partitioned in the interphase nucleus into discrete topologically associating domains (TADs). Borders between TADs are formed in regions containing active genes and clusters of architectural protein binding sites. Transcription of most genes is repressed after temperature stress in Drosophila. Here we show that temperature stress induces relocalization of architectural proteins from TAD borders to inside TADs, and this is accompanied by a dramatic rearrangement in the 3D organization of the nucleus. TAD border strength declines, allowing for an increase in long-distance inter-TAD interactions. Similar but quantitatively weaker effects are observed upon inhibition of transcription or depletion of individual architectural proteins. Heat shock-induced inter-TAD interactions result in increased contacts among enhancers and promoters of silenced genes, which recruit Pc and form Pc bodies in the nucleolus. These results suggest that the TAD organization of metazoan genomes is plastic and can be quickly reconfigured. PMID:25818644

A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus.

PubMed

Barutcu, A Rasim; Maass, Philipp G; Lewandowski, Jordan P; Weiner, Catherine L; Rinn, John L

2018-04-13

The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genome into TADs are not fully understood. Here we test the effects of deleting a CTCF-rich locus on TAD boundary formation. Using genome-wide chromosome conformation capture (Hi-C), we focus on one TAD boundary on chromosome X harboring ~ 15 CTCF binding sites and located at the long non-coding RNA (lncRNA) locus Firre. Specifically, this TAD boundary is invariant across evolution, tissues, and temporal dynamics of X-chromosome inactivation. We demonstrate that neither the deletion of this locus nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter TADs in a sex-specific or allele-specific manner. In contrast, Firre's deletion disrupts the chromatin super-loop formation of the inactive X-chromosome. Collectively, our findings suggest that apart from CTCF binding, additional mechanisms may play roles in establishing TAD boundary formation.

6-Thioguanine, cytarabine, and daunorubicin (TAD) and high-dose cytarabine and mitoxantrone (HAM) for induction, TAD for consolidation, and either prolonged maintenance by reduced monthly TAD or TAD-HAM-TAD and one course of intensive consolidation by sequential HAM in adult patients at all ages with de novo acute myeloid leukemia (AML): a randomized trial of the German AML Cooperative Group.

PubMed

Büchner, Thomas; Hiddemann, Wolfgang; Berdel, Wolfgang E; Wörmann, Bernhard; Schoch, Claudia; Fonatsch, Christa; Löffler, Helmut; Haferlach, Torsten; Ludwig, Wolf-Dieter; Maschmeyer, Georg; Staib, Peter; Aul, Carlo; Gruneisen, Andreas; Lengfelder, Eva; Frickhofen, Norbert; Kern, Wolfgang; Serve, Hubert L; Mesters, Rolf M; Sauerland, Maria Cristina; Heinecke, Achim

2003-12-15

To examine the efficacy of prolonged maintenance chemotherapy versus intensified consolidation therapy for patients with acute myeloid leukemia (AML). Eight hundred thirty-two patients (median age, 54 years; range, 16 to 82 years) with de novo AML were randomly assigned to receive 6-thioguanine, cytarabine, and daunorubicin (TAD) plus cytarabine and mitoxantrone (HAM; cytarabine 3 g/m2 [age < 60 years] or 1 g/m2 [age > or = 60 years] x 6) induction, TAD consolidation, and monthly modified TAD maintenance for 3 years, or TAD-HAM-TAD and one course of intensive consolidation with sequential HAM (S-HAM) with cytarabine 1 g/m2 (age < 60 years) or 0.5 g/m2 (age > or = 60 years) x 8 instead of maintenance. A total of 69.2% patients went into complete remission (CR). Median relapse-free survival (RFS) was 19 months for patients on the maintenance arm, with 31.4% of patients relapse-free at 5 years, versus 12 months for patients on the S-HAM arm, with 24.7% of patients relapse-free at 5 years (P =.0118). RFS from maintenance was superior in patients with poor risk by unfavorable karyotype, age > or = 60 years, lactate dehydrogenase level greater than 700 U/L, or day 16 bone marrow blasts greater than 40% (P =.0061) but not in patients with good risk by complete absence of any poor risk factors. Although a survival benefit in the CR patients is not significant (P =.085), more surviving patients in the maintenance than in the S-HAM arm remain in first CR (P =.026). We conclude that TAD-HAM-TAD-maintenance first-line treatment has a higher curative potential than TAD-HAM-TAD-S-HAM and improves prognosis even among patients with poor prognosis.

An Improved Theoretical Aerodynamic Derivatives Computer Program for Sounding Rockets

NASA Technical Reports Server (NTRS)

Barrowman, J. S.; Fan, D. N.; Obosu, C. B.; Vira, N. R.; Yang, R. J.

1979-01-01

The paper outlines a Theoretical Aerodynamic Derivatives (TAD) computer program for computing the aerodynamics of sounding rockets. TAD outputs include normal force, pitching moment and rolling moment coefficient derivatives as well as center-of-pressure locations as a function of the flight Mach number. TAD is applicable to slender finned axisymmetric vehicles at small angles of attack in subsonic and supersonic flows. TAD improvement efforts include extending Mach number regions of applicability, improving accuracy, and replacement of some numerical integration algorithms with closed-form integrations. Key equations used in TAD are summarized and typical TAD outputs are illustrated for a second-stage Tomahawk configuration.

TADS: A CFD-based turbomachinery and analysis design system with GUI. Volume 1: Method and results

NASA Technical Reports Server (NTRS)

Topp, D. A.; Myers, R. A.; Delaney, R. A.

1995-01-01

The primary objective of this study was the development of a CFD (Computational Fluid Dynamics) based turbomachinery airfoil analysis and design system, controlled by a GUI (Graphical User Interface). The computer codes resulting from this effort are referred to as TADS (Turbomachinery Analysis and Design System). This document is the Final Report describing the theoretical basis and analytical results from the TADS system, developed under Task 18 of NASA Contract NAS3-25950, ADPAC System Coupling to Blade Analysis & Design System GUI. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) in an interactive package. Throughflow analysis capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of the various programs was done in such a way that alternative solvers or grid generators could be easily incorporated into the TADS framework. Results of aerodynamic calculations using the TADS system are presented for a highly loaded fan, a compressor stator, a low speed turbine blade and a transonic turbine vane.

Enhanced reduction of excess sludge and nutrient removal in a pilot-scale A2O-MBR-TAD system.

PubMed

Ventura, J S; Seo, S; Chung, I; Yeom, I; Kim, H; Oh, Y; Jahng, D

2011-01-01

In this study, a pilot scale anaerobic-anoxic-oxic (A2O) process with submerged membrane (MBR) in the oxic tank was coupled with thermophilic aerobic digestion (TAD) reactor and was operated for longer than 600 days to treat real domestic wastewater. Regardless of the varying conditions of the system, the A2O-MBR-TAD process removed MLSS, TCOD, BOD, TN, TP, and E. coli about 99%, 96%, 96%, 70%, 83%, and 99%, respectively. The additional TP removal of the system was due to the precipitating agent directly added in the oxic reactor, without which TP removal was about 56%. In the TAD reactor, receiving MLSS from the oxic tank (MBR), about 25% of TSS and VSS were solubilized during 2 days of retention. The effluent of the TAD reactor was recycled into the anoxic tank of A2O-MBR to provide organic carbon for denitrification and cryptic growth. By controlling the flowrate of wasting stream from the MBR, sludge production decreased to almost zero. From these results, it was concluded that the A2O-MBR-TAD process could be a reliable option for excellent effluent quality and near zero-sludge production.

Organization and PprB-dependent control of the Pseudomonas aeruginosa tad Locus, involved in Flp pilus biology.

PubMed

Bernard, Christophe S; Bordi, Christophe; Termine, Elise; Filloux, Alain; de Bentzmann, Sophie

2009-03-01

Bacterial attachment to the substratum involves several cell surface organelles, including various types of pili. The Pseudomonas aeruginosa Tad machine assembles type IVb pili, which are required for adhesion to abiotic surfaces and to eukaryotic cells. Type IVb pili consist of a major subunit, the Flp pilin, processed by the FppA prepilin peptidase. In this study, we investigated the regulatory mechanism of the tad locus. We showed that the flp gene is expressed late in the stationary growth phase in aerobic conditions. We also showed that the tad locus was composed of five independent transcriptional units. We used transcriptional fusions to show that tad gene expression was positively controlled by the PprB response regulator. We subsequently showed that PprB bound to the promoter regions, directly controlling the expression of these genes. We then evaluated the contribution of two genes, tadF and rcpC, to type IVb pilus assembly. The deletion of these two genes had no effect on Flp production, pilus assembly, or Flp-mediated adhesion to abiotic surfaces in our conditions. However, our results suggest that the putative RcpC protein modifies the Flp pilin, thereby promoting Flp-dependent adhesion to eukaryotic cells.

The connection between BRG1, CTCF and topoisomerases at TAD boundaries.

PubMed

Barutcu, A Rasim; Lian, Jane B; Stein, Janet L; Stein, Gary S; Imbalzano, Anthony N

2017-03-04

The eukaryotic genome is partitioned into topologically associating domains (TADs). Despite recent advances characterizing TADs and TAD boundaries, the organization of these structures is an important dimension of genome architecture and function that is not well understood. Recently, we demonstrated that knockdown of BRG1, an ATPase driving the chromatin remodeling activity of mammalian SWI/SNF enzymes, globally alters long-range genomic interactions and results in a reduction of TAD boundary strength. We provided evidence suggesting that this effect may be due to BRG1 affecting nucleosome occupancy around CTCF sites present at TAD boundaries. In this review, we elaborate on our findings and speculate that BRG1 may contribute to the regulation of the structural and functional properties of chromatin at TAD boundaries by affecting the function or the recruitment of CTCF and DNA topoisomerase complexes.

The Complement C3a-C3aR Axis Promotes Development of Thoracic Aortic Dissection via Regulation of MMP2 Expression.

PubMed

Ren, Weihong; Liu, Yan; Wang, Xuerui; Piao, Chunmei; Ma, Youcai; Qiu, Shulan; Jia, Lixin; Chen, Boya; Wang, Yuan; Jiang, Wenjian; Zheng, Shuai; Liu, Chang; Dai, Nan; Lan, Feng; Zhang, Hongjia; Song, Wen-Chao; Du, Jie

2018-03-01

Thoracic aortic dissection (TAD), once ruptured, is devastating to patients, and no effective pharmaceutical therapy is available. Anaphylatoxins released by complement activation are involved in a variety of diseases. However, the role of the complement system in TAD is unknown. We found that plasma levels of C3a, C4a, and C5a were significantly increased in patients with TAD. Elevated circulating C3a levels were also detected in the developmental process of mouse TAD, which was induced by β-aminopropionitrile monofumarate (BAPN) treatment, with enhanced expression of C1q and properdin in mouse dissected aortas. These findings indicated activation of classical and alternative complement pathways. Further, expression of C3aR was obviously increased in smooth muscle cells of human and mouse dissected aortas, and knockout of C3aR notably inhibited BAPN-induced formation and rupture of TAD in mice. C3aR antagonist administered pre- and post-BAPN treatment attenuated the development of TAD. We found that C3aR knockout decreased matrix metalloproteinase 2 (MMP2) expression in BAPN-treated mice. Additionally, recombinant C3a stimulation enhanced MMP2 expression and activation in smooth muscle cells that were subjected to mechanical stretch. Finally, we generated MMP2-knockdown mice by in vivo MMP2 short hairpin RNA delivery using recombinant adeno-associated virus and found that MMP2 deficiency significantly reduced the formation of TAD. Therefore, our study suggests that the C3a - C3aR axis contributes to the development of TAD via regulation of MMP2 expression. Targeting the C3a-C3aR axis may represent a strategy for inhibiting the formation of TAD. Copyright © 2018 by The American Association of Immunologists, Inc.

Treatment manuals and the advancement of psychoanalytic knowledge: The Treatment Manual of the Tavistock Adult Depression Study.

PubMed

Taylor, David

2015-06-01

This paper has two aims: first, it seeks to understand the absence of treatment manuals in psychoanalysis. Secondly, it summarizes the treatment manual of the Tavistock Adult Depression Study, which describes the form of psychoanalytic psychotherapy whose effectiveness has been evaluated both in the Tavistock Adult Depression Study (TADS); and in the German Die Langzeittherapie bei chronischen Depressionen (LAC) Studie. Throughout the history of psychoanalysis, opinions about treatment manuals, empirical research and their antecedents have been deeply divided. After tracing the often polarized unfolding of these matters, the paper proposes that emotional and cognitive difficulties as well as scientific ones underpin their persistence. It is suggested that greater familiarity with them may lead to better combinations of outcome research and psychoanalysis: for example, the Tavistock manual seeks to match one account of the objects, aims, values, spirit and methods of psychoanalysis (as well as of connected forms of psychoanalytic psychotherapy); and also to meet what is required of treatment manuals by random allocation controlled trials. It has been a crucial element in the above studies of the outcome of long-term psychoanalytic psychotherapies with chronically depressed patients. After describing the Tavistock Manual, the paper concludes suggesting that, if appropriately constructed, treatment manuals can make a contribution to the advancement of specifically psychoanalytic knowledge. Copyright © 2015 Institute of Psychoanalysis.

CAPERalpha is a novel Rel-TAD-interacting factor that inhibits lymphocyte transformation by the potent Rel/NF-kappaB oncoprotein v-Rel.

PubMed

Dutta, Jui; Fan, Gaofeng; Gélinas, Céline

2008-11-01

The Rel/NF-kappaB transcription factors are constitutively activated in many human cancers. The Rel proteins in this family are implicated in leukemia/lymphomagenesis, but the mechanism is not completely understood. Previous studies showed that the transcription activation domains (TADs) of the viral oncoprotein v-Rel and its cellular Rel/NF-kappaB homologues c-Rel and RelA are key determinants of their different transforming activities in primary lymphocytes. Substitution of a Rel TAD for that of RelA conferred a strong transforming phenotype upon RelA, which otherwise failed to transform cells. To gain insights into protein interactions that influence cell transformation by the Rel TADs, we identified factors that interact with the TAD of v-Rel, the most oncogenic member of the Rel/NF-kappaB family. We report that the coactivator for transcription factors AP-1 and estrogen receptors, CAPERalpha, interacts with the v-Rel TAD and potently synergizes v-Rel-mediated transactivation. Importantly, coexpression of CAPERalpha markedly reduced and delayed v-Rel's transforming activity in primary lymphocytes, whereas a dominant-negative mutant enhanced the kinetics of v-Rel-mediated transformation. Furthermore, small interfering RNA-mediated knockdown of CAPERalpha in v-Rel-transformed lymphocytes significantly enhanced colony formation in soft agar. Since the potency of Rel-mediated transactivation is an important determinant of lymphocyte transformation, as is Rel's ability to induce transcriptional repression, these data suggest that CAPERalpha's interaction with the Rel TAD could modulate Rel/NF-kappaB's transforming activity by facilitating expression or dampening repression of specific gene subsets important for oncogenesis. Overall, this study identifies CAPERalpha as a new transcriptional coregulator for v-Rel and reveals an important role in modulating Rel's oncogenic activity.

The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

PubMed Central

Rodríguez-Carballo, Eddie; Lopez-Delisle, Lucille; Zhan, Ye; Fabre, Pierre J.; Beccari, Leonardo; El-Idrissi, Imane; Huynh, Thi Hanh Nguyen; Ozadam, Hakan; Dekker, Job; Duboule, Denis

2017-01-01

The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole HoxD cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context. PMID:29273679

The novel dopant for hole-transporting material opens a new processing route to efficiently reduce hysteresis and improve stability of planar perovskite solar cells

NASA Astrophysics Data System (ADS)

Luo, Junsheng; Jia, Chunyang; Wan, Zhongquan; Han, Fei; Zhao, Bowen; Wang, Ruilin

2017-02-01

Perovskite solar cells (PSCs) emerging as the most promising next-generation photovoltaic devices have been received great attention. In the PSC device, admittedly, Spiro-OMeTAD is the most widely used hole-transporting material (HTM). However, the pristine Spiro-OMeTAD suffers from low hole mobility and conductivity, which requires chemical dopants (Li-TFSI and tBP) to increase conductivity thereby improving power conversion efficiency (PCE). Discouragingly, hygroscopic Li-TFSI can gravely degrade the perovskite film and diminish the stability of PSC. Meanwhile, tBP also gives rise to the degradation of perovskite film by forming a [PbI2·tBP] coordinated complex or iodopyridinate complex. In this study, F4-TCNQ is introduced into Spiro-OMeTAD as an alternative dopant to replace the commonly used Li-TFSI and tBP. By optimizing the doping concentration of F4-TCNQ, the PSC based on 1.5 mol% F4-TCNQ doped Spiro-OMeTAD exhibits the best PCE as high as 12.93%, which is comparable to that of 14.32% for reference device with Li-TFSI and tBP doped Spiro-OMeTAD. Moreover, the PSC based on F4-TCNQ doped Spiro-OMeTAD shows lower hysteresis and better stability. This work not only offers a promising dopant for Spiro-OMeTAD, but also provides a viable approach to address the challenges of hysteresis and instability.

Aeration control of thermophilic aerobic digestion using fluorescence monitoring.

PubMed

Kim, Young-Kee; Oh, Byung-Keun

2009-01-01

The thermophilic aerobic digestion (TAD) process is recognized as an effective method for rapid waste activated sludge (WAS) degradation and the deactivation of pathogenic microorganisms. Yet, high energy costs due to heating and aeration have limited the commercialization of economical TAD processes. Previous research on autothermal thermophilic aerobic digestion (ATAD) has already reduced the heating cost. However, only a few studies have focused on reducing the aeration cost. Therefore, this study applied a two-step aeration control strategy to a fill-and-draw mode semicontinuous TAD process. The NADH-dependent fluorescence was monitored throughout the TAD experiment, and the aeration rate shifted according to the fluorescence intensity. As a result, the simple two-step aeration control operation achieved a 20.3% reduction in the total aeration, while maintaining an effective and stable operation. It is also expected that more savings can be achieved with a further reduction of the lower aeration rate or multisegmentation of the aeration rate.

Late postoperative analysis of the tip-apex distance (TAD) in pertrochanteric fractures: is there an accommodation of the implant within the bone?

PubMed

Aihara, Leandro Jun; Nanni, Rafael Augusto; Carvalho, Marina Sousa; Zamboni, Caio; Durigan, Jorge R; Hungria Neto, José S; Mercadante, Marcelo T; Christian, Ralph W; Hungria, José O S

2017-10-01

This study measured the tip-apex distance (TAD) values in the immediate postoperative period and following weight-bearing and fracture impaction in patients undergoing osteosynthesis with dynamic hip screw and cephalomedullary nail. To correlate the Baumgaertner index in the immediate postoperative period with values obtained after impaction of the fracture with the accommodation of the cephalic implant in the femoral head. Radiographic TAD measurements were taken with AGFA-VIEW ® of 82 patients with a mean age of 72 years with pertrochanteric fractures who were operated on and the fracture fixed with DHS- Synthes ® , TFN-Synthes ® , or Gamma Nail III-Stryker ® in the immediate postoperative period, and following weight-bearing and fracture impaction (mean 3-8 weeks after surgery). The overall average TAD decreased from 20.3mm to 18.2mm. Regardless of the instability of the fracture, the age of the patient or the implant used, TAD decreased between the immediate postoperative period and following fracture impaction. The osteosynthesis of pertrochanteric fractures was associated with important accommodation of the cephalic implant in the femoral head with decreased TAD values after weight-bearing. © 2017 Elsevier Ltd. All rights reserved.

A Case Study of Technical Assistance to Demonstration Programs for Young Handicapped Children. Part I.

ERIC Educational Resources Information Center

Behr, Shirley K.; And Others

The interim report presents an evaluation of TADS (Technical Assistance Development System) through case studies of TADS technical assistance to the staffs of two demonstration programs for preschool handicapped children and their families. Purposes of the study included obtaining indepth descriptions of the technical assistance process to…

Spatial organization of chromatin domains and compartments in single chromosomes

NASA Astrophysics Data System (ADS)

Wang, Siyuan; Su, Jun-Han; Beliveau, Brian; Bintu, Bogdan; Moffitt, Jeffrey; Wu, Chao-Ting; Zhuang, Xiaowei

The spatial organization of chromatin critically affects genome function. Recent chromosome-conformation-capture studies have revealed topologically associating domains (TADs) as a conserved feature of chromatin organization, but how TADs are spatially organized in individual chromosomes remains unknown. Here, we developed an imaging method for mapping the spatial positions of numerous genomic regions along individual chromosomes and traced the positions of TADs in human interphase autosomes and X chromosomes. We observed that chromosome folding deviates from the ideal fractal-globule model at large length scales and that TADs are largely organized into two compartments spatially arranged in a polarized manner in individual chromosomes. Active and inactive X chromosomes adopt different folding and compartmentalization configurations. These results suggest that the spatial organization of chromatin domains can change in response to regulation.

TADS and Technical Assistance.

ERIC Educational Resources Information Center

Trohanis, Pascal L.

1983-01-01

Accomplishments of the Technical Assistance Development System (TADS) are cited, current challenges (including program development, and communication and coordination) are noted, and the mission mandated for TADS is outlined. (CL)

The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes.

PubMed

Rodríguez-Carballo, Eddie; Lopez-Delisle, Lucille; Zhan, Ye; Fabre, Pierre J; Beccari, Leonardo; El-Idrissi, Imane; Huynh, Thi Hanh Nguyen; Ozadam, Hakan; Dekker, Job; Duboule, Denis

2017-11-15

The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos , we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole HoxD cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context. © 2017 Rodríguez-Carballo et al.; Published by Cold Spring Harbor Laboratory Press.

Combined mesophilic anaerobic and thermophilic aerobic digestion process: effect on sludge degradation and variation of sludge property.

PubMed

Cheng, Jiehong; Ji, Yuehong; Kong, Feng; Chen, Xian

2013-12-01

One-stage autothermal thermophilic aerobic digestion (ATAD) is effective for the reduction of volatile solids (VSs) and pathogen in sewage sludges. A novel process of combining mesophilic (<35 °C) anaerobic digestion with a thermophilic (55 °C) aerobic digestion process (AN/TAD) occurred in a one-stage digester, which was designed for aeration energy savings. The efficiency of sludge degradation and variation of sludge properties by batch experiments were evaluated for the AN/TAD digester with an effective volume of 23 L for 30 days compared with conventional thermophilic aerobic digestion (TAD). The AN/TAD system can efficiently achieve sludge stabilization on the 16th day with a VS removal rate of 38.1 %. The AN/TAD system was operated at lower ORP values in a digestion period with higher contents of total organic compounds, volatile fatty acids, protein, and polysaccharide in the soluble phase than those of the TAD system, which can rapidly decreased and had low values in the late period of digestion for the AN/TAD system. In the AN/TAD system, intracellular substances had lysis because of initial hydrolytic acidification.

Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics

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

Zamora, Richard James; Voter, Arthur F.; Perez, Danny

Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling time scales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The Temperature Accelerated Dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiplemore » states. Here we utilize a discrete event-based application simulator to introduce and explore a new Speculatively Parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Finally, following this method, we discover that a nontrivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications.« less

Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics

DOE PAGES

Zamora, Richard James; Voter, Arthur F.; Perez, Danny; ...

2016-12-01

Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling time scales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The Temperature Accelerated Dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiplemore » states. Here we utilize a discrete event-based application simulator to introduce and explore a new Speculatively Parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Finally, following this method, we discover that a nontrivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications.« less

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

PubMed Central

Giorgetti, Luca; Galupa, Rafael; Nora, Elphège P.; Piolot, Tristan; Lam, France; Dekker, Job; Tiana, Guido; Heard, Edith

2015-01-01

Summary A new level of chromosome organization, Topologically Associating Domains (TADs), was recently uncovered by chromosome-confirmation-capture (3C) techniques. To explore TAD structure and function, we developed a polymer model that can extract the full repertoire of chromatin conformations within TADs from population-based 3C data. This model predicts actual physical distances and to what extent chromosomal contacts vary between cells. It also identifies interactions within single TADs that stabilize boundaries between TADs and allows us to identify and genetically validate key structural elements within TADs. Combining the model’s predictions with high-resolution DNA FISH and quantitative RNA FISH for TADs within the X-inactivation center (Xic), we dissect the relationship between transcription and spatial proximity to cis-regulatory elements. We demonstrate that contacts between potential regulatory elements occur in the context of fluctuating structures rather than stable loops and propose that such fluctuations may contribute to asymmetric expression in the Xic during X inactivation. PMID:24813616

Cr(VI) removal from aqueous solution by thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1 in the presence of single and multiple heavy metals.

PubMed

Li, Han; Huang, Shaobin; Zhang, Yongqing

2016-09-01

Cr(VI) pollution is increasing continuously as a result of ongoing industrialization. In this study, we investigated the thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1, isolated from the biofilm of a biotrickling filter used in nitrogen oxides (NOX) removal, with respect to its ability to remove Cr(VI) from an aqueous solution. TAD1 was capable of reducing Cr(VI) from an initial concentration of 10 mg/L to non-detectable levels over a pH range of 7-9 and at a temperature range of 30-50°C. TAD1 simultaneously removed both Cr(VI) and NO3 (-)-N at 50°C, when the pH was 7 and the initial Cr(VI) concentration was 15 mg/L. The reduction of Cr(VI) to Cr(III) correlated with the growth metabolic activity of TAD1. The presence of other heavy metals (Cu, Zn, and Ni) inhibited the ability of TAD1 to remove Cr(VI). The metals each individually inhibited Cr(VI) removal, and the extent of inhibition increased in a cooperative manner in the presence of a combination of the metals. The addition of biodegradable cellulose acetate microspheres (an adsorption material) weakened the toxicity of the heavy metals; in their presence, the Cr(VI) removal efficiency returned to a high level. The feasibility and applicability of simultaneous nitrate removal and Cr(VI) reduction by strain TAD1 is promising, and may be an effective biological method for the clean-up of wastewater.

The tad locus: postcards from the widespread colonization island.

PubMed

Tomich, Mladen; Planet, Paul J; Figurski, David H

2007-05-01

The Tad (tight adherence) macromolecular transport system, which is present in many bacterial and archaeal species, represents an ancient and major new subtype of type II secretion. The tad genes are present on a genomic island named the widespread colonization island (WCI), and encode the machinery that is required for the assembly of adhesive Flp (fimbrial low-molecular-weight protein) pili. The tad genes are essential for biofilm formation, colonization and pathogenesis in the genera Aggregatibacter (Actinobacillus), Haemophilus, Pasteurella, Pseudomonas, Yersinia, Caulobacter and perhaps others. Here we review the structure, function and evolution of the Tad secretion system.

Biparietal/transverse abdominal diameter ratio ≤ 1: potential marker for open spina bifida at 11-13-week scan.

PubMed

Simon, E G; Arthuis, C J; Haddad, G; Bertrand, P; Perrotin, F

2015-03-01

In the first trimester of pregnancy, a biparietal diameter (BPD) below the 5(th) percentile is a simple marker that enables the prenatal detection of half of all cases of open spina bifida. We hypothesized that relating the BPD measurement to the transverse abdominal diameter (TAD) might be another simple and effective screening method. In this study we assessed the performance of using the BPD/TAD ratio during the first trimester of pregnancy in screening for open spina bifida. A total of 20,551 first-trimester ultrasound scans (11-13 weeks' gestation), performed between 2000 and 2013, were analyzed retrospectively; there were 26 cases of open spina bifida and 17,665 unaffected pregnancies with a crown-rump length of 45-84 mm and a record of both BPD and TAD measurements. The mean (± SD) BPD/TAD ratio was 1.00 ± 0.06 for fetuses with spina bifida and 1.13 ± 0.06 for those without (P < 0.0001). A BPD ≤ 5(th) percentile enabled the prenatal detection of 46.2% of spina bifida cases, while a BPD/TAD ratio of ≤ 1.00 detected 69.2%. If we considered cases in which either BPD was ≤ 5(th) percentile or BPD/TAD ratio was ≤ 1, we identified 76.9% of cases. In the latter case, the false-positive rate was 5.1%, while that for using a combination of both BPD ≤ 5th percentile and BPD/TAD ratio ≤ 1 was 0.6%, with a sensitivity of 38.5%. The positive predictive value of using a combination of BPD ≤ 5th percentile and BPD/TAD ratio ≤ 1 for detecting spina bifida was 8.5%. Between 11 and 13 weeks' gestation, relating BPD to TAD improves considerably the diagnostic performance of using BPD measurement alone in screening for open spina bifida. Screening using this marker is simple and applicable to a large population. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.

Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics

NASA Astrophysics Data System (ADS)

Junghans, Christoph; Mniszewski, Susan; Voter, Arthur; Perez, Danny; Eidenbenz, Stephan

2014-03-01

We present an example of a new class of tools that we call application simulators, parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation (PDES). We demonstrate our approach with a TADSim application simulator that models the Temperature Accelerated Dynamics (TAD) method, which is an algorithmically complex member of the Accelerated Molecular Dynamics (AMD) family. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We further extend TADSim to model algorithm extensions to standard TAD, such as speculative spawning of the compute-bound stages of the algorithm, and predict performance improvements without having to implement such a method. Focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights into the TAD algorithm behavior and suggested extensions to the TAD method.

A mathematical simulation of the tip-apex distance and the calcar-referenced tip-apex distance for intertrochanteric fractures reduced with lag screws.

PubMed

Li, Shuang; Chang, Shi-Min; Jin, Yan-Min; Zhang, Ying-Qi; Niu, Wen-Xin; Du, Shou-Chao; Zhang, Li-Zhi; Ma, Hui

2016-06-01

As a predictor of the risk of lag screw cutout, it was recommended that keeping tip-apex distance (TAD)<25mm and placing the screw centrally or inferiorly, but positioning the lag screw too inferiorly in the head would produce TAD>25mm. We aim to simulate various positions of the lag screw in the femoral head and identify whether 25mm is a suitable cut-off value that favours all sizes of femoral heads with intertrochanteric fractures of the hip. Using a general mathematical software, the positions of the screw tip points were simulated. The virtual anterior-posterior and lateral views were then visualised, and the locus of the screw tips was projected into a Cartesian coordinate system according to the TAD and calcar-referenced tip-apex distance (CalTAD) formulas. Each original virtual anterior-posterior and lateral image was zoomed and compiled to match a calculated average image. The screw tip points were recorded, traced and compiled into volumes which could be used to visualise the screw's movements and positioning within the femoral head. The extracted volumes were calculated when 10mm

Ascending aortic elongation and the risk of dissection.

PubMed

Krüger, Tobias; Forkavets, Oksana; Veseli, Kujtim; Lausberg, Henning; Vöhringer, Luise; Schneider, Wilke; Bamberg, Fabian; Schlensak, Christian

2016-08-01

Unlike aneurysm formation, the role of ascending aortic elongation in the pathogenesis of Type A aortic dissection (TAD) is largely unclear. We investigated the morphology of healthy, dissected and predissection aortas with a focus on ascending aortic length. We retrospectively compared clinical and computer tomography angiography (CTA) data from TAD patients (n = 130), patients who developed a TAD in the further clinical course (preTAD, n = 16) and healthy control patients who received a CTA for non-aortic emergencies (n = 165). The length of the ascending aorta was defined as the distance between the sinotubular junction (STJ) and the brachiocephalic trunk (BCT) at the central line, the outer and inner curvature as well as the direct distance in the frontal and sagittal planes. Additionally, the aortic diameters were analysed. In the healthy controls, we found a positive correlation of age with the aortic diameter (r = 0.57) and aortic length (r = 0.42). The correlation of the respective parameters with the body size was negligible (r < 0.2). The median ascending aortic diameter at the height of the pulmonary artery in TAD (50 mm) was significantly (P < 0.001) larger compared with the respective diameter of the healthy aortas (34 mm). The diameter of the preTAD aortas (40 mm) was also significantly larger compared with the healthy controls. These proportions were similar in all the aortic diameters. The midline length of the healthy ascending aortas was 71 mm. In the preTAD and TAD aortas, the same values were 81 mm and 92 mm, respectively (both P < 0.001). We evaluated the linear distance between the STJ and the BCT in the frontal plane as an easy-to-measure parameter of aortic length. In the TAD aortas (108 mm) and preTAD aortas (97 mm), this distance was significantly longer compared with the healthy aortas (84 mm). Aortic diameter might not be an optimal parameter to predict dissection. Most aortas dissect at diameters below 55 mm. Both the TAD and preTAD aortas were elongated compared with the healthy controls. Thus, aortic elongation may play a role in the pathogenesis of and may be a risk factor for TAD. © The Author 2016. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Interleukin-6 downregulated vascular smooth muscle cell contractile proteins via ATG4B-mediated autophagy in thoracic aortic dissection.

PubMed

An, Zhao; Qiao, Fan; Lu, Qijue; Ma, Ye; Liu, Yang; Lu, Fanglin; Xu, Zhiyun

2017-12-01

Interleukin-6 (IL-6) overexpression played an important role in the pathogenesis of thoracic aortic dissection (TAD). Our previous study found enhanced autophagy accompanying with contractile proteins α smooth muscle actin (α-SMA) and smooth muscle 22α (SM22α) degradation in TAD aortic vascular smooth muscle cells (VSMCs). Autophagy is an important way for intracellular proteins degradation, while IL-6 has been found as a contributing factor of autophagy in some cancers. These indicated IL-6 might contribute to the occurrence of TAD by promoting autophagy-induced contractile proteins degradation, which has not been investigated. The aim of the present study is to verify this hypothesis and investigate the mechanism of it. We collected 10 TAD and 10 control aortic specimens from patients underwent TAD surgical repair and coronary artery bypass grafting, respectively. Quantitative real-time polymerase chain reaction was used to detect mRNA expression. Protein expression level was assessed by enzyme-linked immunosorbent assay, western blot, and immunohistochemistry. Microtubule-associated protein 1 light chain 3 beta overexpression adenovirus with green and red fluorescent protein tags and transmission electron microscopy were used to detect autophagy level in VSMCs. 3-Methyladenine (3-MA) and chloroquine were used to block autophagy in human VSMCs. Experiment results showed that the expression of IL-6 was significantly increased accompanying with up-regulated autophagy in TAD aortic wall compared with controls. In vitro results showed that IL-6 stimulation decreased the expression of VSMCs contractile proteins α-SMA and SM22α accompanying with up-regulated autophagy. Blocking autophagy with 3-MA or chloroquine inhibited IL-6 induced α-SMA and SM22α degradation. Further investigation showed that autophagy-related 4B cysteine peptidase (ATG4B) was significantly overexpressed in TAD aortic wall and played important role in IL-6 induced autophagy up-regulation. ATG4B knockdown blocked IL-6-induced autophagy and α-SMA and SM22α degradation, while ATG4B overexpression partly replaced the function of IL-6 in human VSMCs. In conclusion, our study demonstrated that IL-6 downregulated expression of VSMCs contractile proteins α-SMA and SM22α via enhancing ATG4B-mediated autophagy in TAD.

Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains.

PubMed

Ea, Vuthy; Sexton, Tom; Gostan, Thierry; Herviou, Laurie; Baudement, Marie-Odile; Zhang, Yunzhe; Berlivet, Soizik; Le Lay-Taha, Marie-Noëlle; Cathala, Guy; Lesne, Annick; Victor, Jean-Marc; Fan, Yuhong; Cavalli, Giacomo; Forné, Thierry

2015-08-15

In higher eukaryotes, the genome is partitioned into large "Topologically Associating Domains" (TADs) in which the chromatin displays favoured long-range contacts. While a crumpled/fractal globule organization has received experimental supports at higher-order levels, the organization principles that govern chromatin dynamics within these TADs remain unclear. Using simple polymer models, we previously showed that, in mouse liver cells, gene-rich domains tend to adopt a statistical helix shape when no significant locus-specific interaction takes place. Here, we use data from diverse 3C-derived methods to explore chromatin dynamics within mouse and Drosophila TADs. In mouse Embryonic Stem Cells (mESC), that possess large TADs (median size of 840 kb), we show that the statistical helix model, but not globule models, is relevant not only in gene-rich TADs, but also in gene-poor and gene-desert TADs. Interestingly, this statistical helix organization is considerably relaxed in mESC compared to liver cells, indicating that the impact of the constraints responsible for this organization is weaker in pluripotent cells. Finally, depletion of histone H1 in mESC alters local chromatin flexibility but not the statistical helix organization. In Drosophila, which possesses TADs of smaller sizes (median size of 70 kb), we show that, while chromatin compaction and flexibility are finely tuned according to the epigenetic landscape, chromatin dynamics within TADs is generally compatible with an unconstrained polymer configuration. Models issued from polymer physics can accurately describe the organization principles governing chromatin dynamics in both mouse and Drosophila TADs. However, constraints applied on this dynamics within mammalian TADs have a peculiar impact resulting in a statistical helix organization.

Gene panel sequencing in heritable thoracic aortic disorders and related entities - results of comprehensive testing in a cohort of 264 patients.

PubMed

Campens, Laurence; Callewaert, Bert; Muiño Mosquera, Laura; Renard, Marjolijn; Symoens, Sofie; De Paepe, Anne; Coucke, Paul; De Backer, Julie

2015-02-03

Heritable Thoracic Aortic Disorders (H-TAD) may present clinically as part of a syndromic entity or as an isolated (nonsyndromic) manifestation. About one dozen genes are now available for clinical molecular testing. Targeted single gene testing is hampered by significant clinical overlap between syndromic H-TAD entities and the absence of discriminating features in isolated cases. Therefore panel testing of multiple genes has now emerged as the preferred approach. So far, no data on mutation detection rate with this technique have been reported. We performed Next Generation Sequencing (NGS) based screening of the seven currently most prevalent H-TAD-associated genes (FBN1, TGFBR1/2, TGFB2, SMAD3, ACTA2 and COL3A1) on 264 samples from unrelated probands referred for H-TAD and related entities. Patients fulfilling the criteria for Marfan syndrome (MFS) were only included if targeted FBN1 sequencing and MLPA analysis were negative. A mutation was identified in 34 patients (13%): 12 FBN1, one TGFBR1, two TGFBR2, three TGFB2, nine SMAD3, four ACTA2 and three COL3A1 mutations. We found mutations in FBN1 (N = 3), TGFBR2 (N = 1) and COL3A1 (N = 2) in patients without characteristic clinical features of syndromal H-TAD. Six TAD patients harboring a mutation in SMAD3 and one TAD patient with a TGFB2 mutation fulfilled the diagnostic criteria for MFS. NGS based H-TAD panel testing efficiently reveals a mutation in 13% of patients. Our observations emphasize the clinical overlap between patients harboring mutations in syndromic and nonsyndromic H-TAD related genes as well as within syndromic H-TAD entities, justifying a widespread application of this technique.

Transactivation domain of p53 regulates DNA repair and integrity in human iPS cells.

PubMed

Kannappan, Ramaswamy; Mattapally, Saidulu; Wagle, Pooja A; Zhang, Jianyi

2018-05-18

The role of p53 transactivation domain (p53-TAD), a multifunctional and dynamic domain, on DNA repair and retaining DNA integrity in human iPS cells has never been studied. p53-TAD was knocked out in iPS cells using CRISPR/Cas9 and was confirmed by DNA sequencing. p53-TAD KO cells were characterized by: accelerated proliferation, decreased population doubling time, and unaltered Bcl2, BBC3, IGF1R, Bax and altered Mdm2, p21, and PIDD transcripts expression. In p53-TAD KO cells p53 regulated DNA repair proteins XPA, DNA polH and DDB2 expression were found to be reduced compared to p53-WT cells. Exposure to low dose of doxorubicin (Doxo) induced similar DNA damage and DNA damage response (DDR) measured by RAD50 and MRE11 expression, Checkpoint kinase 2 activation and γH2A.X recruitment at DNA strand breaks in both the cell groups indicating silencing p53-TAD do not affect DDR mechanism upstream of p53. Following removal of Doxo p53-WT hiPS cells underwent DNA repair, corrected their damaged DNA and restored DNA integrity. Conversely, p53-TAD KO hiPS cells did not undergo complete DNA repair and failed to restore DNA integrity. More importantly continuous culture of p53-TAD KO hiPS cells underwent G2/M cell cycle arrest and expressed cellular senescent marker p16 INK4a . Our data clearly shows that silencing transactivation domain of p53 did not affect DDR but affected the DNA repair process implying the crucial role of p53 transactivation domain in maintaining DNA integrity. Therefore, activating p53-TAD domain using small molecules may promote DNA repair and integrity of cells and prevent senescence.

NASA Langley Atmospheric Science Data Center Toolsets for Airborne Data (TAD): Common Variable Naming Schema

NASA Astrophysics Data System (ADS)

Chen, G.; Early, A. B.; Peeters, M. C.

2014-12-01

NASA has conducted airborne tropospheric chemistry studies for about three decades. These field campaigns have generated a great wealth of observations, which are characterized by a wide range of trace gases and aerosol properties. The airborne observational data have often been used in assessment and validation of models and satellite instruments. One particular issue is a lack of consistent variable naming across field campaigns, which makes cross-mission data discovery difficult. The ASDC Toolset for Airborne Data (TAD) is being designed to meet the user community needs for manipulating aircraft data for scientific research on climate change and air quality relevant issues. As part of this effort, a common naming system was developed to provide a link between variables from different aircraft field studies. This system covers all current and past airborne in-situ measurements housed at the ASDC, as well as select NOAA missions. The TAD common variable naming system consists of 6 categories and 3 sub-levels. The top-level category is primarily defined by the physical characteristics of the measurement: e.g., aerosol, cloud, trace gases. The sub-levels were designed to organize the variables according to nature of measurement (e.g., aerosol microphysical and optical properties) or chemical structures (e.g., carbon compound). The development of the TAD common variable naming system was in consultation with staff from the Global Change Master Directory (GCMD) and referenced/expanded the existing Climate and Forecast (CF) variable naming conventions. The detailed structure of the TAD common variable naming convention and its application in TAD development will be presented.

Benzoyl Peroxide as an Efficient Dopant for Spiro-OMeTAD in Perovskite Solar Cells.

PubMed

Liu, Qiuju; Fan, Lisheng; Zhang, Qin'e; Zhou, An'an; Wang, Baozeng; Bai, Hua; Tian, Qingyong; Fan, Bin; Zhang, Tongyi

2017-08-10

Although organic small molecule spiro-OMeTAD is widely used as a hole-transport material in perovskite solar cells, its limited electric conductivity poses a bottleneck in the efficiency improvement of perovskite solar cells. Here, a low-cost and easy-fabrication technique is developed to enhance the conductivity and hole-extraction ability of spiro-OMeTAD by doping it with commercially available benzoyl peroxide (BPO). The experimental results show that the conductivity increases several orders of magnitude, from 6.2×10 -6  S cm -1 for the pristine spiro-OMeTAD to 1.1×10 -3  S cm -1 at 5 % BPO doping and to 2.4×10 -2  S cm -1 at 15 % BPO doping, which considerably outperform the conductivity of 4.62×10 -4  S cm -1 for the currently used oxygen-doped spiro-OMeTAD. The fluorescence spectra suggest that the BPO-doped spiro-OMeTAD-OMeTAD layer is able to efficiently extract holes from CH 3 NH 3 PbI 3 and thus greatly enhances the charge transfer. The BPO-doped spiro-OMeTAD is used in the fabrication of perovskite solar cells, which exhibit enhancement in the power conversion efficiency. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A concise approach for building the s-T diagram for Mn-Fe-P-Si hysteretic magnetocaloric material

NASA Astrophysics Data System (ADS)

Christiaanse, T. V.; Campbell, O.; Trevizoli, P. V.; Misra, S.; van Asten, D.; Zhang, L.; Govindappa, P.; Niknia, I.; Teyber, R.; Rowe, A.

2017-09-01

The use of first order magnetocaloric materials (FOM’s) in magnetic cycles is of interest for the development of efficient magnetic heat pumps. FOM’s present promising magnetocaloric properties; however, hysteresis reduces the reversible adiabatic temperature change (Δ Tad ) of these materials, and consequently, impacts performance. The present paper evaluates the reversible Δ Tad in a FOM. Six samples of the Mn-Fe-P-Si material with different transition temperatures are examined. The samples are measured for heat capacity, magnetization, and adiabatic temperature change using heating and cooling protocols to characterize hysteresis. After correcting demagnetizing fields, the entropy-temperature (s-T ) diagrams are constructed and used to calculate adiabatic temperature change using four different thermal paths. The post-calculated Δ Tad is compared with experimental data from direct Δ Tad measurements. Most of the samples of Mn-Fe-P-Si show that post-calculated Δ Tad resulting from the heating zero field and cooling in-field entropy curves align best with the Δ Tad measurements. The impact of the demagnetizing field is shown in terms of absolute variation to the post-calculated Δ Tad . A functional representation is used to explain observed data sensitivities in the post-calculated Δ Tad .

TADS: A CFD-Based Turbomachinery Analysis and Design System with GUI: Methods and Results. 2.0

NASA Technical Reports Server (NTRS)

Koiro, M. J.; Myers, R. A.; Delaney, R. A.

1999-01-01

The primary objective of this study was the development of a Computational Fluid Dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a Graphical User Interface (GUI). The computer codes resulting from this effort are referred to as TADS (Turbomachinery Analysis and Design System). This document is the Final Report describing the theoretical basis and analytical results from the TADS system developed under Task 10 of NASA Contract NAS3-27394, ADPAC System Coupling to Blade Analysis & Design System GUI, Phase II-Loss, Design and. Multi-stage Analysis. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) or a 3-D solver with slip condition on the end walls (B2BADPAC) in an interactive package. Throughflow analysis and design capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of the various programs was done in such a way that alternative solvers or grid generators could be easily incorporated into the TADS framework. Results of aerodynamic calculations using the TADS system are presented for a multistage compressor, a multistage turbine, two highly loaded fans, and several single stage compressor and turbine example cases.

TADS--A CFD-Based Turbomachinery Analysis and Design System with GUI: User's Manual. 2.0

NASA Technical Reports Server (NTRS)

Koiro, M. J.; Myers, R. A.; Delaney, R. A.

1999-01-01

The primary objective of this study was the development of a Computational Fluid Dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a Graphical User Interface (GUI). The computer codes resulting from this effort are referred to as TADS (Turbomachinery Analysis and Design System). This document is intended to serve as a User's Manual for the computer programs which comprise the TADS system, developed under Task 18 of NASA Contract NAS3-27350, ADPAC System Coupling to Blade Analysis & Design System GUI and Task 10 of NASA Contract NAS3-27394, ADPAC System Coupling to Blade Analysis & Design System GUI, Phase II-Loss, Design and, Multi-stage Analysis. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) in an interactive package. Throughflow analysis and design capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of the various programs was done in such a way that alternative solvers or grid generators could be easily incorporated into the TADS framework. Results of aerodynamic calculations using the TADS system are presented for a highly loaded fan, a compressor stator, a low speed turbine blade and a transonic turbine vane.

The tight-adhesion proteins TadGEF of Bradyrhizobium diazoefficiens USDA 110 are involved in cell adhesion and infectivity on soybean roots.

PubMed

Mongiardini, Elías J; Parisi, Gustavo D; Quelas, Juan I; Lodeiro, Aníbal R

2016-01-01

Adhesion of symbiotic bacteria to host plants is an essential early step of the infection process that leads to the beneficial interaction. In the Bradyrhizobium diazoefficiens-soybean symbiosis few molecular determinants of adhesion are known. Here we identified the tight-adhesion gene products TadGEF in the open-reading frames blr3941-blr3943 of the B. diazoefficiens USDA 110 complete genomic sequence. Predicted structure of TadG indicates a transmembrane domain and two extracytosolic domains, from which the C-terminal has an integrin fold. TadE and TadF are also predicted as bearing transmembrane segments. Mutants in tadG or the small cluster tadGEF were impaired in adhesion to soybean roots, and the root infection was delayed. However, nodule histology was not compromised by the mutations, indicating that these effects were restricted to the earliest contact of the B. diazoefficiens and root surfaces. Knowledge of preinfection determinants is important for development of inoculants that are applied to soybean crops worldwide. Copyright © 2015 Elsevier GmbH. All rights reserved.

Screening of cardiovascular risk factors in patients with schizophrenia and patients treated with antipsychotic drugs: are we equally exhaustive as with the general population?

PubMed

Castillo-Sánchez, Miguel; Fàbregas-Escurriola, Mireia; Bergè-Baquero, Daniel; Fernández-SanMartín, MªIsabel; Goday-Arno, Albert

2017-01-01

Many studies have previously shown increased cardiovascular risk factors related to schizophrenia independently from the use of antipsychotic drugs. However, a poorer effort in clinical detection and management of cardiovascular risk in patients with severe mental illness could also explain these results. To test this hypothesis, we analyzed the differences in screening and incidence of cardiovascular risk factors between schizophrenia, non-schizophrenic patients on treatment with antipsychotic drugs (NS-TAD) and the general population. Data from adult subjects assessed by high-quality register general practitioners from 2006 to 2011 were extracted from the Catalonian SIDIAP database. The schizophrenia, NS-TAD, and control groups were compared in terms of measurements and incidence of diabetes, dyslipidemia, obesity, hypertension, and smoking. A total of 4911 patients in the schizophrenia group, 4157 in NS-TAD group, and 98644 in the control group were included. Schizophrenia patients were screened for dyslipidemia and diabetes more frequently than the control group, while for obesity or hypertension, they were screened equal to controls. Also, as compared to the control group, the NS-TAD group was more frequently screened for obesity with no differences in dyslipidemia and diabetes and less frequently for hypertension. Smoking was less frequently screened in both study groups. The incidence of all risk factors studied in both study groups was higher than or equal to the control group, except for hypertension, which had lower incidence. The lack of screening of risk factors does not appear decisive in the increased cardiovascular risk of patients diagnosed with schizophrenia seen in primary care. Studies evaluating the possible under diagnosis of the risk factors are required. Schizophrenia (SZ); Treatment with antipsychotic drugs (TAD); Cardiovascular risk factor/s (CVRF); Without schizophrenia but on therapy with antipsychotic drugs (NS-TAD); Defined Daily Dose (DDD).

Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor

PubMed Central

O'Connell Motherway, Mary; Zomer, Aldert; Leahy, Sinead C.; Reunanen, Justus; Bottacini, Francesca; Claesson, Marcus J.; O'Brien, Frances; Flynn, Kiera; Casey, Patrick G.; Moreno Munoz, Jose Antonio; Kearney, Breda; Houston, Aileen M.; O'Mahony, Caitlin; Higgins, Des G.; Shanahan, Fergus; Palva, Airi; de Vos, Willem M.; Fitzgerald, Gerald F.; Ventura, Marco; O'Toole, Paul W.; van Sinderen, Douwe

2011-01-01

Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis of Bifidobacterium colonization and persistence remains poorly understood. Transcriptome analysis of the Bifidobacterium breve UCC2003 2.42-Mb genome in a murine colonization model revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene cluster designated “tad2003.” Mutational analysis demonstrated that the tad2003 gene cluster is essential for efficient in vivo murine gut colonization, and immunogold transmission electron microscopy confirmed the presence of Tad pili at the poles of B. breve UCC2003 cells. Conservation of the Tad pilus-encoding locus among other B. breve strains and among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host colonization and persistence mechanism for bifidobacteria. PMID:21690406

Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.

PubMed

O'Connell Motherway, Mary; Zomer, Aldert; Leahy, Sinead C; Reunanen, Justus; Bottacini, Francesca; Claesson, Marcus J; O'Brien, Frances; Flynn, Kiera; Casey, Patrick G; Munoz, Jose Antonio Moreno; Kearney, Breda; Houston, Aileen M; O'Mahony, Caitlin; Higgins, Des G; Shanahan, Fergus; Palva, Airi; de Vos, Willem M; Fitzgerald, Gerald F; Ventura, Marco; O'Toole, Paul W; van Sinderen, Douwe

2011-07-05

Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis of Bifidobacterium colonization and persistence remains poorly understood. Transcriptome analysis of the Bifidobacterium breve UCC2003 2.42-Mb genome in a murine colonization model revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene cluster designated "tad(2003)." Mutational analysis demonstrated that the tad(2003) gene cluster is essential for efficient in vivo murine gut colonization, and immunogold transmission electron microscopy confirmed the presence of Tad pili at the poles of B. breve UCC2003 cells. Conservation of the Tad pilus-encoding locus among other B. breve strains and among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host colonization and persistence mechanism for bifidobacteria.

Differential response of wheat cultivars to Pseudomonas brassicacearum and take-all decline soil.

PubMed

Yang, Mingming; Mavrodi, Dmitri; Thomashow, Linda S; Weller, David M

2018-06-15

2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. in the P. fluorescens complex are primarily responsible for a natural suppression of take-all of wheat known as take-all decline (TAD) in many fields in the USA. P. brassicacearum, the most common DAPG producer found in TAD soils in the Pacific Northwest (PNW) of the USA, has biocontrol, growth promoting and phytotoxic activities. In this study, we explored how the wheat cultivar affects the level of take-all suppression when grown in a TAD soil, and how cultivars respond to colonization by P. brassicacearum. Three cvs. Tara, Finley and Buchanan supported similar rhizosphere population sizes of P. brassicacearum when grown in a TAD soil, however they developed significantly different amounts of take-all. Cultivars Tara and Buchanan developed the least and most take-all, respectively, and Finley showed an intermediate amount of disease. However, when grown in TAD soil that was pasteurized to eliminate both DAPG producers and take-all suppression, all three cultivars were equally susceptible to take-all. The three cultivars also responded differently to the colonization and phytotoxicity of P. brassicacearum strains Q8r1-96 and L5.1-96, which are characteristic of DAPG producers in PNW TAD soils. As compared to cv. Tara, cv. Buchanan showed significantly reduced seedling emergence and root growth when colonized by P. brassicacearum, and the response of Finley was intermediate. However, all cultivars emerged equally when treated with a DAPG-deficient mutant of Q8r1-96. Our results indicate that wheat cultivars grown in a TAD soil modulate both the robustness of take-all suppression and the potential phytotoxicity of the antibiotic DAPG.

Traveling Atmospheric Disturbances (TADs) in the thermosphere inferred from accelerometer data at three altitudes

NASA Astrophysics Data System (ADS)

Bruinsma, Sean; Forbes, Jeffrey

2010-05-01

Densities derived from accelerometer measurements on the GRACE, CHAMP and Air Force/SETA satellites near 490, 390, and 220 km, respectively, are used to elucidate global-scale characteristics of traveling atmospheric disturbances. The accelerometers on the CHAMP and GRACE satellites have made it possible to accumulate near-continuous records of thermosphere density between about 320 and 490 km since May 2001, and July 2002, respectively. They have recorded the response to virtually every significant geomagnetic storm during this period. CHAMP and GRACE are in (near) polar and quasi-circular orbits, sampling 24 hr local time approximately every 4 and 5 months, respectively. These capabilities offer unique opportunities to study the temporal and latitudinal responses of the thermosphere to geomagnetic disturbances. The Air Force/SETA accelerometer data have also been processed, but the analysis is more complicated due to data gaps. Significant and unambiguous TAD activity in the observed response of the thermosphere was detected for about 25 events with CHAMP and GRACE, and less than 10 with SETA. The atmospheric variability is evaluated by de-trending the data, allowing the extraction of specific ranges in horizontal scale, and analyzing density "residuals". The scale of the perturbation is decisive for its lifetime and relative amplitude. Sometimes the disturbances represent wave-like structures propagating far from the source, and these so-called ‘TADs' were detected and described for the May 2003 storm for the first time. Some TADs traveled over the pole into the opposite hemisphere; this was found in both CHAMP and GRACE data. Most TADs propagate equatorward, but poleward propagating TADs have on occasion been detected too. The estimated speeds and amplitudes of the observed TADs, and their dependence on altitude and solar and geomagnetic activity in particular, will be presented in this poster.

How to address patients' defences: a pilot study of the accuracy of defence interpretations and alliance.

PubMed

Junod, Olivier; de Roten, Yves; Martinez, Elena; Drapeau, Martin; Despland, Jean-Nicolas

2005-12-01

This pilot study examined the accuracy of therapist defence interpretations (TAD) in high-alliance patients (N = 7) and low-alliance patients (N = 8). TAD accuracy was assessed in the two subgroups by comparing for each case the patient's most frequent defensive level with the most frequent defensive level addressed by the therapist when making defence interpretations. Results show that in high-alliance patient-therapist dyads, the therapists tend to address accurate or higher (more mature) defensive level than patients most frequent level. On the other hand, the therapists address lower (more immature) defensive level in low-alliance dyads. These results are discussed along with possible ways to better assess TAD accuracy.

The modern temperature-accelerated dynamics approach

DOE PAGES

Zamora, Richard J.; Uberuaga, Blas P.; Perez, Danny; ...

2016-06-01

Accelerated molecular dynamics (AMD) is a class of MD-based methods used to simulate atomistic systems in which the metastable state-to-state evolution is slow compared with thermal vibrations. Temperature-accelerated dynamics (TAD) is a particularly efficient AMD procedure in which the predicted evolution is hastened by elevating the temperature of the system and then recovering the correct state-to-state dynamics at the temperature of interest. TAD has been used to study various materials applications, often revealing surprising behavior beyond the reach of direct MD. This success has inspired several algorithmic performance enhancements, as well as the analysis of its mathematical framework. Recently, thesemore » enhancements have leveraged parallel programming techniques to enhance both the spatial and temporal scaling of the traditional approach. Here, we review the ongoing evolution of the modern TAD method and introduce the latest development: speculatively parallel TAD.« less

Generation of Traveling Atmospheric Disturbances During a Pulsating Geomagnetic Storm

NASA Astrophysics Data System (ADS)

Gardner, L. C.; Schunk, R. W.

2009-12-01

Traveling Atmospheric Disturbances (TAD’s) are studied with a 3-D high-resolution (1°x3°) global thermosphere/ionosphere model to determine the importance of the high-latitude production mechanisms contained in the model. The possible production mechanisms are the oval size, the precipitating electron characteristic energy and energy flux, and the cross polar cap potential. The production mechanisms are pulsed at a one-hour period, as was observed in a recent long-duration geomagnetic storm. With auroral pulsation a TAD is generated that propagates equatorward away from the high-latitude auroral oval, depositing energy and transporting mass and momentum into the mid- and low-latitude thermosphere system. Depending on the amount of energy input into the high-latitude auroral zone, the TAD may travel to mid-latitudes, low-latitudes, or if sufficient energy is deposited, the TAD may even propagate across the opposite pole. These and other aspects of TAD generation will be shown.

On-the-fly transition search and applications to temperature-accelerated dynamics

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Amar, Jacques

2015-03-01

Temperature-accelerated dynamics (TAD) is a powerful method to study non-equilibrium processes and has been providing surprising insights for a variety of systems. While serial TAD simulations have been limited by the roughly N3 increase in the computational cost as a function of the number of atoms N in the system, recently we have shown that by carrying out parallel TAD simulations which combine spatial decomposition with our semi-rigorous synchronous sublattice algorithm, significantly improved scaling is possible. However, in this approach the size of activated events is limited by the processor size while the dynamics is not exact. Here we discuss progress in improving the scaling of serial TAD by combining the use of on-the-fly transition searching with our previously developed localized saddle-point method. We demonstrate improved performance for the cases of Ag/Ag(100) annealing and Cu/Cu(100) growth. Supported by NSF DMR-1410840.

Health impact assessment of air pollution in Valladolid, Spain

PubMed Central

Cárdaba Arranz, Mario; Muñoz Moreno, María Fe; Armentia Medina, Alicia; Alonso Capitán, Margarita; Carreras Vaquer, Fernando; Almaraz Gómez, Ana

2014-01-01

Objective To estimate the attributable and targeted avoidable deaths (ADs; TADs) of outdoor air pollution by ambient particulate matter (PM10), PM2.5 and O3 according to specific WHO methodology. Design Health impact assessment. Setting City of Valladolid, Spain (around 300 000 residents). Data sources Demographics; mortality; pollutant concentrations collected 1999–2008. Main outcome measures Attributable fractions; ADs and TADs per year for 1999–2008. Results Higher TADs estimates (shown here) were obtained when assuming as ‘target’ concentrations WHO Air Quality Guidelines instead of Directive 2008/50/EC. ADs are considered relative to pollutant background levels. All-cause mortality associated to PM10 (all ages): 52 ADs (95% CI 39 to 64); 31 TADs (95% CI 24 to 39).All-cause mortality associated to PM10 (<5 years): 0 ADs (95% CI 0 to 1); 0 TADs (95% CI 0 to 1). All-cause mortality associated to PM2.5 (>30 years): 326 ADs (95% CI 217 to 422); 231 TADs (95% CI 153 to 301). Cardiopulmonary and lung cancer mortality associated to PM2.5 (>30 years): ▸ Cardiopulmonary: 186 ADs (95% CI 74 to 280); 94 TADs (95% CI 36 to 148). ▸ Lung cancer : 51 ADs (95% CI 21 to 73); 27 TADs (95% CI 10 to 41).All-cause, respiratory and cardiovascular mortality associated to O3 (all ages): ▸ All-cause: 52ADs (95% CI 25 to 77) ; 31 TADs (95% CI 15 to 45). ▸ Respiratory: 5ADs (95% CI −2 to 13) ; 3 TADs (95% CI −1 to 8). ▸ Cardiovascular: 30 ADs (95% CI 8 to 51) ; 17 TADs (95% CI 5 to 30). Negative estimates which should be read as zero were obtained when pollutant concentrations were below counterfactuals or assumed risk coefficients were below one. Conclusions Our estimates suggest a not negligible negative impact on mortality of outdoor air pollution. The implementation of WHO methodology provides critical information to distinguish an improvement range in air pollution control. PMID:25326212

Understanding the Photovoltaic Performance of Perovskite-Spirobifluorene Solar Cells.

PubMed

Song, Zhen; Liu, Jiang; Wang, Gang; Zuo, Wentao; Liao, Cheng; Mei, Jun

2017-11-03

Lead halide perovskite solar cells with remarkable power conversion efficiency have attracted much attention in recent years. However, there still exist many problems with their use that are not completely understood, and further studies are needed. Herein, the hole-transport layer dependence of the photovoltaic performance of perovskite solar cells is investigated in detail. It is found that devices freshly prepared using pristine 2,2',7,7'-tetrakis-(N,N-di-p-methoxyphenylamine)-9,9'-spirobifluorene (spiro-OMeTAD) and Li-doped spiro-OMeTAD as hole-transport layers exhibit S-shaped current density-voltage curves with poor fill factors. The devices show progressively improved fill factors and efficiencies upon exposure to air, which is attributed to air-induced conductivity improvement in the spiro-OMeTAD layer. After introducing a cobalt salt dopant (FK209) into the spiro-OMeTAD layer, the corresponding devices show remarkable performance without the need of air exposure. These results confirm that the dopant not only increases the conductivity of spiro-OMeTAD layer, but also tunes the surface potential, which helps to improve charge transport and reduce the recombination loss. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chronic treatment with tadalafil improves endothelial function in men with increased cardiovascular risk.

PubMed

Rosano, Giuseppe M C; Aversa, Antonio; Vitale, Cristiana; Fabbri, Andrea; Fini, Massimo; Spera, Giovanni

2005-02-01

Erectile dysfunction (ED) is often associated with a cluster of risk factors for coronary artery disease and reduced endothelial function. Acute and chronic administration of oral sildenafil, a phosphodiesterase type 5 (PDE5) inhibitor, improves endothelial function in patients with ED. Tadalafil (TAD) is a new PDE5 inhibitor with a long half life that allows alternate day administration. Aim of the study was to evaluate whether chronic therapy (4 weeks) with TAD improves endothelial function in patients with increased cardiovascular risk and whether this effect is sustained after discontinuation of therapy. We randomized 32 patients with increased cardiovascular risk to receive either TAD 20 mg on alternate days or matching placebo (PLB) for 4 weeks. Patients underwent evaluation of brachial artery flow-mediated dilation (FMD), nitrite/nitrate and endothelin-1 plasma levels at baseline, at the end of treatment period and after two-weeks follow-up. At 4 weeks, FMD was significantly improved by TAD (from 4.2+/-3.2 to 9.3+/-3.7%, p<0.01 vs. baseline), but was not modified by PLB (from 4.1+/-2.8 to 4.0+/-3.4%, p=NS). At 6 weeks the benefit in FMD was sustained in patients that received TAD (9.1+/-3.9% vs. 4.2+/-3.2%, p=0.01 vs. baseline; 9.1+/-3.9% vs. 9.3+/-3.7%, vs. 4 weeks, p=NS) while no changes in FMD were observed in patients randomized to PLB. Also, compared to baseline, a net increase in nitrite/nitrate levels (38.2+/-12.3 vs. 52.6+/-11.7 and 51.1+/-3.1, p<0.05) and a decrease in endothelin-1 levels (3.3+/-0.9 vs. 2.9.+/-0.7 and 2.9+/-0.9, p<0.05) was found both at four and six-weeks after TAD; these changes were inversely correlated as shown by regression analysis (adjusted R2=0.81, p<0.0001). Chronic therapy with TAD improves endothelial function in patients with increased cardiovascular risk regardless their degree of ED. The benefit of this therapy is sustained for at least two weeks after the discontinuation of therapy. Larger studies are needed in order to assess the possible clinical implications of chronic therapy with TAD.

A Case Study of Technical Assistance to Demonstration Programs for Young Handicapped Children. Part III.

ERIC Educational Resources Information Center

Behr, Shirley K.; And Others

The report describes the third and final year of a 3-year case study of the technical assistance process as implemented by the Technical Assistance Development System (TADS) for the staffs of two demonstration programs for preschool handicapped children and their families. Following a review of TADS and the two demonstration programs, the…

Webinar: Airborne Data Discovery and Analysis with Toolsets for Airborne Data (TAD)

Atmospheric Science Data Center

2016-10-18

Webinar: Airborne Data Discovery and Analysis with Toolsets for Airborne Data (TAD) Wednesday, October 26, 2016 Join us on ... and flight data ranges are available. Registration is now open.  Access the full announcement   For TAD Information, ...

TADS Needs Assessment Procedures Manual, Summer 1980.

ERIC Educational Resources Information Center

Black, Talbot; And Others

The TADS (Technical Assistance Development System) Needs Assessment Manual is designed to guide the comprehensive review of Handicapped Children's Early Education Program (HCEEP) demonstration projects in identifying technical assistance needs. An introduction reviews the TADS technical assistance model which includes program planning, needs…

TAD- THEORETICAL AERODYNAMICS PROGRAM

NASA Technical Reports Server (NTRS)

Barrowman, J.

1994-01-01

This theoretical aerodynamics program, TAD, was developed to predict the aerodynamic characteristics of vehicles with sounding rocket configurations. These slender, axisymmetric finned vehicle configurations have a wide range of aeronautical applications from rockets to high speed armament. Over a given range of Mach numbers, TAD will compute the normal force coefficient derivative, the center-of-pressure, the roll forcing moment coefficient derivative, the roll damping moment coefficient derivative, and the pitch damping moment coefficient derivative of a sounding rocket configured vehicle. The vehicle may consist of a sharp pointed nose of cone or tangent ogive shape, up to nine other body divisions of conical shoulder, conical boattail, or circular cylinder shape, and fins of trapezoid planform shape with constant cross section and either three or four fins per fin set. The characteristics computed by TAD have been shown to be accurate to within ten percent of experimental data in the supersonic region. The TAD program calculates the characteristics of separate portions of the vehicle, calculates the interference between separate portions of the vehicle, and then combines the results to form a total vehicle solution. Also, TAD can be used to calculate the characteristics of the body or fins separately as an aid in the design process. Input to the TAD program consists of simple descriptions of the body and fin geometries and the Mach range of interest. Output includes the aerodynamic characteristics of the total vehicle, or user-selected portions, at specified points over the mach range. The TAD program is written in FORTRAN IV for batch execution and has been implemented on an IBM 360 computer with a central memory requirement of approximately 123K of 8 bit bytes. The TAD program was originally developed in 1967 and last updated in 1972.

TADtool: visual parameter identification for TAD-calling algorithms.

PubMed

Kruse, Kai; Hug, Clemens B; Hernández-Rodríguez, Benjamín; Vaquerizas, Juan M

2016-10-15

Eukaryotic genomes are hierarchically organized into topologically associating domains (TADs). The computational identification of these domains and their associated properties critically depends on the choice of suitable parameters of TAD-calling algorithms. To reduce the element of trial-and-error in parameter selection, we have developed TADtool: an interactive plot to find robust TAD-calling parameters with immediate visual feedback. TADtool allows the direct export of TADs called with a chosen set of parameters for two of the most common TAD calling algorithms: directionality and insulation index. It can be used as an intuitive, standalone application or as a Python package for maximum flexibility. TADtool is available as a Python package from GitHub (https://github.com/vaquerizaslab/tadtool) or can be installed directly via PyPI, the Python package index (tadtool). kai.kruse@mpi-muenster.mpg.de, jmv@mpi-muenster.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Fear of dental pain in Italian children: child personality traits and parental dental fear.

PubMed

D'Alessandro, Giovanni; Alkhamis, Nadia; Mattarozzi, Katia; Mazzetti, Michela; Piana, Gabriela

2016-06-01

Dental anxiety could impede dental treatment in children. Evidence shows that parents' fear of dentists contributes to children's anxiety towards dentists. The aim of the present study was to determine whether and to what extent: a) parents' anxiety and depression personality traits, b) parent's dental fear, and c) child personality traits can predict children's dental anxiety in an Italian population. One hundred and four children (5-14 years old) and one of their parents participated in the study. Well-known and validated questionnaires were administered to children (MCDASf, CFSS-DS, TAD) and parents (FDPQ, STAI Y1, Y2, and BDI-II). Dental anxiety is significantly associated with the anxiety personality trait and depression of the child and with parental fear of dental pain. A hierarchical regression analysis showed that, regardless of age and gender, the best predictor of child dental anxiety is parent's fear of dental pain, rather than relatively stable temperaments of the child. In line with the literature concerning adults, these findings highlight the children dental anxiety as a complex phenomena consisting of different components, including the child's personality traits (anxiety trait and depression) and parents' dental fear. Clinical implications of this evidence are discussed. © 2015 American Association of Public Health Dentistry.

Pronounced impairment of everyday skills and self-care in posterior cortical atrophy.

PubMed

Shakespeare, Timothy J; Yong, Keir X X; Foxe, David; Hodges, John; Crutch, Sebastian J

2015-01-01

Posterior cortical atrophy (PCA) is a neurodegenerative syndrome characterized by progressive visual dysfunction and parietal, occipital, and occipitotemporal atrophy. The aim of this study was to compare the impact of PCA and typical Alzheimer's disease (tAD) on everyday functional abilities and neuropsychiatric status. The Cambridge Behavioural Inventory-Revised was given to carers of 32 PCA and 71 tAD patients. PCA patients showed significantly greater impairment in everyday skills and self-care while the tAD group showed greater impairment in aspects of memory and orientation, and motivation. We suggest that PCA poses specific challenges for those caring for people affected by the condition.

A TAD better for myeloma therapy?

PubMed

Giralt, Sergio

2010-02-11

In this issue of Blood, Lokhorst and colleagues report on the results of HOVON-50, a phase 3 randomized trial designed to evaluate the effects of thalidomide during induction treatment and as maintenance in patients with multiple myeloma. There were 556 patients randomly assigned either to 3 cycles of VAD or to TAD. All patients were to receive high-dose melphalan with autologous stem cell support followed by maintenance with interferon for the VAD arm or thalidomide for the TAD arm.(1) This study together with other randomized and nonrandomized trials establish a definitive role for thalidomide as induction therapy in conjunction with dexamethasone, anthracyclines, and alkylating agents.

A Tad pilus promotes the establishment and resistance of Vibrio vulnificus biofilms to mechanical clearance.

PubMed

Pu, Meng; Rowe-Magnus, Dean Allistair

2018-01-01

Vibrio vulnificus is autochthonous to estuaries and warm coastal waters. Infection occurs via open wounds or ingestion, where its asymptomatic colonization of seafood, most infamously oysters, provides a gateway into the human food chain. Colonization begins with initial surface contact, which is often mediated by bacterial surface appendages called pili. Type IV Tad pili are widely distributed in the Vibrionaceae, but evidence for a physiological role for these structures is scant. The V. vulnificus genome codes for three distinct tad loci. Recently, a positive correlation was demonstrated between the expression of tad-3 and the phenotypes of a V. vulnificus descendent (NT) that exhibited increased biofilm formation, auto-aggregation, and oyster colonization relative to its parent. However, the mechanism by which tad pilus expression promoted these phenotypes was not determined. Here, we show that deletion of the tad pilin gene ( flp ) altered the near-surface motility profile of NT cells from high curvature, orbital retracing patterns characteristic of cells actively probing the surface to low curvature traces indicative of wandering and diminished bacteria-surface interactions. The NT flp pilin mutant also exhibited decreased initial surface attachment, attenuated auto-aggregation and formed fragile biofilms that disintegrated under hydrodynamic flow. Thus, the tad-3 locus, designated iam , promoted i nitial surface attachment, a uto-aggregation and resistance to m echanical clearance of V. vulnificus biofilms. The prevalence of tad loci in the Vibrionaceae suggests that they may play equally important roles in other family members.

Effectiveness of 3 methods of anchorage reinforcement for maximum anchorage in adolescents: A 3-arm multicenter randomized clinical trial.

PubMed

Sandler, Jonathan; Murray, Alison; Thiruvenkatachari, Badri; Gutierrez, Rodrigo; Speight, Paul; O'Brien, Kevin

2014-07-01

The objective of this 3-arm parallel randomized clinical trial was to compare the effectiveness of temporary anchorage devices (TADs), Nance button palatal arches, and headgear for anchorage supplementation in the treatment of patients with malocclusions that required maximum anchorage. This trial was conducted between August 2008 and February 2013 in 2 orthodontic departments in the United Kingdom. The study included 78 patients (ages, 12-18 years; mean age, 14.2 years) who needed maximum anchorage. Eligibility criteria included no active caries, exemplary oral hygiene, and maximum anchorage required. The primary outcome was mesial molar movement during the period in which anchorage supplementation was required. The secondary outcomes were duration of anchorage reinforcement, number of treatment visits, number of casual and failed appointments, total treatment time, dento-occlusal change, and patients' perceptions of the method of anchorage supplementation. Treatment allocation was implemented by contacting via the Internet the randomization center at the University of Nottingham, Clinical Trials Unit. The randomization was based on a computer-generated pseudo-random code with random permuted blocks of randomly varying size. A research assistant who was blinded to the group allocation recorded all data. The patients were randomly allocated to receive anchorage supplementation with TADs, a Nance button on a palatal arch, or headgear. They were all treated with maxillary and mandibular preadjusted edgewise fixed appliances with 0.022-in slot prescription brackets. They were followed until orthodontic treatment was complete. Seventy-eight patients were randomized in a 1:1:1 ratio among the 3 groups. The baseline characteristics were similar in the groups, and they were treated for an average of 27.4 months (SD, 7.1 months); 71 completed orthodontic treatment. The data were analyzed on a per-protocol basis and showed no differences in the effectiveness of anchorage supplementation between TADs, Nance button palatal arches, and headgear. Compared with headgear, the average mesial movements of the maxillary right molar were 0.62 mm (-0.32 to 1.55 mm) with the Nance and -0.58 mm (-1.53 to 0.36 mm) with TADs; the maxillary left molar was moved -0.09 mm (-1.00 to 0.83 mm) with the Nance and -0.96 mm (-1.89 to -0.04 mm) with the TADs. Peer assessment rating scores were significantly better with the TADs than in the headgear and Nance groups. The patient questionnaires showed that comfort levels on placement of the TADs and the Nance were similar. Headgear was more troublesome and less popular with the patients. There was no difference in the effectiveness between the 3 groups in terms of anchorage support. There were more problems with the headgear and Nance buttons than with the TADs. The quality of treatment was better with TADs. As a result, TADS might be the preferred method for reinforcing orthodontic anchorage in patients who need maximum anchorage. ClinicalTrials.gov Identifier: NCT00995436. The protocol was published on the above site before the trial commencement. The British Orthodontic Society Foundation funded the study and American Orthodontics provided all the TADs and associated equipment. Copyright © 2014 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Effect of TADs on the F-region of Low midlatitude ionosphere during intense geomagnetic storm.

NASA Astrophysics Data System (ADS)

Upadhayaya, Arun Kumar; Joshi, Shivani; Singh Dabas, Raj; Das, Rupesh M.; Yadav, Sneha

Effect of TAD's on the F region ionosphere of low-mid latitude ionosphere during three intense storms of20 th Nov,2003(-422nT),30 th Oct 2003(-383nT),07Nov,2004(-373nT)respectively are studued using ionosonde data of Delhi(28ø N 77øE).It has been seen that the electon density profile in the F1 region are greatly influenced by the TAD's presence. Further the pre-existing F1 cusp become better devloped during the passage of TAD's.

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

Shim, Yunsic; Amar, Jacques G.

While temperature-accelerated dynamics (TAD) is a powerful method for carrying out non-equilibrium simulations of systems over extended time scales, the computational cost of serial TAD increases approximately as N{sup 3} where N is the number of atoms. In addition, although a parallel TAD method based on domain decomposition [Y. Shim et al., Phys. Rev. B 76, 205439 (2007)] has been shown to provide significantly improved scaling, the dynamics in such an approach is only approximate while the size of activated events is limited by the spatial decomposition size. Accordingly, it is of interest to develop methods to improve the scalingmore » of serial TAD. As a first step in understanding the factors which determine the scaling behavior, we first present results for the overall scaling of serial TAD and its components, which were obtained from simulations of Ag/Ag(100) growth and Ag/Ag(100) annealing, and compare with theoretical predictions. We then discuss two methods based on localization which may be used to address two of the primary “bottlenecks” to the scaling of serial TAD with system size. By implementing both of these methods, we find that for intermediate system-sizes, the scaling is improved by almost a factor of N{sup 1/2}. Some additional possible methods to improve the scaling of TAD are also discussed.« less

Improved scaling of temperature-accelerated dynamics using localization

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Amar, Jacques G.

2016-07-01

While temperature-accelerated dynamics (TAD) is a powerful method for carrying out non-equilibrium simulations of systems over extended time scales, the computational cost of serial TAD increases approximately as N3 where N is the number of atoms. In addition, although a parallel TAD method based on domain decomposition [Y. Shim et al., Phys. Rev. B 76, 205439 (2007)] has been shown to provide significantly improved scaling, the dynamics in such an approach is only approximate while the size of activated events is limited by the spatial decomposition size. Accordingly, it is of interest to develop methods to improve the scaling of serial TAD. As a first step in understanding the factors which determine the scaling behavior, we first present results for the overall scaling of serial TAD and its components, which were obtained from simulations of Ag/Ag(100) growth and Ag/Ag(100) annealing, and compare with theoretical predictions. We then discuss two methods based on localization which may be used to address two of the primary "bottlenecks" to the scaling of serial TAD with system size. By implementing both of these methods, we find that for intermediate system-sizes, the scaling is improved by almost a factor of N1/2. Some additional possible methods to improve the scaling of TAD are also discussed.

Large scale genomic reorganization of topological domains at the HoxD locus.

PubMed

Fabre, Pierre J; Leleu, Marion; Mormann, Benjamin H; Lopez-Delisle, Lucille; Noordermeer, Daan; Beccari, Leonardo; Duboule, Denis

2017-08-07

The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts. To assess the structure-function relationships underlying such interactions, we measured compaction levels and TAD discreteness using a combination of chromosome conformation capture (4C-seq) and DNA FISH. We assessed the robustness of the TAD architecture by using a series of genomic deletions and inversions that impact the integrity of this chromatin domain and that remodel long-range contacts. We report multi-partite associations between HoxD genes and up to three enhancers. We find that the loss of native chromatin topology leads to the remodeling of TAD structure following distinct parameters. Our results reveal that the recomposition of TAD architectures after large genomic re-arrangements is dependent on a boundary-selection mechanism in which CTCF mediates the gating of long-range contacts in combination with genomic distance and sequence specificity. Accordingly, the building of a recomposed TAD at this locus depends on distinct functional and constitutive parameters.

Dual Strategy With Oral Phosphodiesterase Type 5 Inhibition and Intracavernosal Implantation of Mesenchymal Stem Cells Is Superior to Individual Approaches in the Recovery of Erectile and Cavernosal Functions After Cavernous Nerve Injury in Rats.

PubMed

Martínez-Salamanca, Juan I; Zurita, Mercedes; Costa, Carla; Martínez-Salamanca, Eduardo; Fernández, Argentina; Castela, Angela; Vaquero, Jesús; Carballido, Joaquín; Angulo, Javier

2016-01-01

Novel effective therapeutic strategies are necessary for treating erectile dysfunction secondary to cavernous nerve injury (CNI). To functionally evaluate the benefits of long-term oral treatment with a phosphodiesterase type 5 inhibitor on the potential capacity of intracavernosal cell therapy to recover erectile function after CNI. Bilateral crush CNI (BCNI) was produced in anesthetized male rats. After BCNI, rats were treated with the phosphodiesterase type 5 inhibitor tadalafil (TAD; 5 mg/kg/d orally; BCNI + TAD), a single intracavernosal injection of bone marrow-derived mesenchymal stem cells (BMSCs; BCNI + BMSC), or dual therapy (BCNI + BMSC + TAD). Ex vivo function of the corpus cavernosum (CC) and in vivo intracavernosal pressure responses to CN electrical stimulation were evaluated 4 weeks after BCNI. Trichrome staining and terminal 2'-deoxyuridine-5'-triphosphate nick-end labeling assay were used for fibrosis and apoptosis determination, respectively, in the CC. In vivo erectile responses in anesthetized rats, ex vivo evaluation of endothelium-dependent relaxation, neurogenic relaxation and neurogenic contraction in CC strips, and histologic evaluation of fibrosis and apoptosis in cavernosal tissue. BCNI resulted in a marked decrease of erectile responses that were partly recovered in the BCNI + TAD and BCNI + BMSC groups. Complete recovery of erectile function was achieved only in the BCNI + BMSC + TAD group. Endothelium-dependent and nitric oxide donor-induced relaxations of the CC were not altered by BCNI or the treatments. BCNI resulted in enhanced neurogenic adrenergic contractions and impaired nitrergic relaxations of the CC. The BCNI + TAD group displayed diminished neurogenic contractions, whereas the BCNI + TAD and BCNI + BMSC groups showed partly recovered nitrergic responses. In the BCNI + BMSC + TAD group, neurogenic contractions were decreased and nitrergic relaxations were normalized. Cavernosal apoptosis and fibrosis were similarly prevented in the BCNI + TAD, BCNI + BMSC, and BCNI + BMSC + TAD groups. A dual strategy combining the intracavernosal injection of BMSCs and oral administration of TAD was superior to individual approaches in normalizing neurogenic control of cavernosal tone and preserving erectile function after CNI, suggesting the potential of this dual strategy in the future management of erectile dysfunction after radical prostatectomy. Copyright © 2016 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

Wide-line NMR and DSC studies on intrinsically disordered p53 transactivation domain and its helically pre-structured segment

PubMed Central

Tompa, Peter; Han, Kyou-Hoon; Bokor, Mónika; Kamasa, Pawel; Tantos, Ágnes; Fritz, Beáta; Kim, Do-Hyoung; Lee, Chewook; Verebélyi, Tamás; Tompa, Kálmán

2016-01-01

Wide-line 1H NMR intensity and differential scanning calorimetry measurements were carried out on the intrinsically disordered 73-residue full transactivation domain (TAD) of the p53 tumor suppressor protein and two peptides: one a wild type p53 TAD peptide with a helix pre-structuring property, and a mutant peptide with a disabled helix-forming propensity. Measurements were carried out in order to characterize their water and ion binding characteristics. By quantifying the number of hydrate water molecules, we provide a microscopic description for the interactions of water with a wild-type p53 TAD and two p53 TAD peptides. The results provide direct evidence that intrinsically disordered proteins (IDPs) and a less structured peptide not only have a higher hydration capacity than globular proteins, but are also able to bind a larger amount of charged solute ions. [BMB Reports 2016; 49(9): 497-501] PMID:27418282

Two independent modes of chromatin organization revealed by cohesin removal.

PubMed

Schwarzer, Wibke; Abdennur, Nezar; Goloborodko, Anton; Pekowska, Aleksandra; Fudenberg, Geoffrey; Loe-Mie, Yann; Fonseca, Nuno A; Huber, Wolfgang; H Haering, Christian; Mirny, Leonid; Spitz, Francois

2017-11-02

Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes.

Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments

PubMed Central

de las Heras, Jose I.; Czapiewski, Rafal; Sivakumar, Aishwarya; Kerr, Alastair R.W.; Schirmer, Eric C.

2017-01-01

The 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. Studies have focused either on lamina-associated domains (LADs) or on topologically associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs sharing functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1–DamID during Jurkat T-cell activation, finding significant genome reorganization at the nuclear periphery dominated by release of loci frequently important for T-cell function. To assess how these changes at the nuclear periphery influence wider genome organization, our DamID data sets were contrasted with TADs and compartments. Features of specific repositioning events were then tested by fluorescence in situ hybridization during T-cell activation. First, considerable overlap between TADs and LADs was observed with the TAD repositioning as a unit. Second, A1 and A2 subcompartments are segregated in 3D space through differences in proximity to LADs along chromosomes. Third, genes and a putative enhancer in LADs that were released from the periphery during T-cell activation became preferentially associated with A2 subcompartments and were constrained to the relative proximity of the lamina. Thus, lamina associations influence internal nuclear organization, and changes in LADs during T-cell activation may provide an important additional mode of gene regulation. PMID:28424353

Locally adaptive parallel temperature accelerated dynamics method

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Amar, Jacques G.

2010-03-01

The recently-developed temperature-accelerated dynamics (TAD) method [M. Sørensen and A.F. Voter, J. Chem. Phys. 112, 9599 (2000)] along with the more recently developed parallel TAD (parTAD) method [Y. Shim et al, Phys. Rev. B 76, 205439 (2007)] allow one to carry out non-equilibrium simulations over extended time and length scales. The basic idea behind TAD is to speed up transitions by carrying out a high-temperature MD simulation and then use the resulting information to obtain event times at the desired low temperature. In a typical implementation, a fixed high temperature Thigh is used. However, in general one expects that for each configuration there exists an optimal value of Thigh which depends on the particular transition pathways and activation energies for that configuration. Here we present a locally adaptive high-temperature TAD method in which instead of using a fixed Thigh the high temperature is dynamically adjusted in order to maximize simulation efficiency. Preliminary results of the performance obtained from parTAD simulations of Cu/Cu(100) growth using the locally adaptive Thigh method will also be presented.

Copper nanocluster growth at experimental conditions using temperature accelerated dynamics

NASA Astrophysics Data System (ADS)

Dias, C. S.; Cadilhe, A. C.; Voter, A. F.

2009-03-01

We study the dynamics of vapor phase cluster growth near experimental conditions of pressure at temperatures below 200K. To this end, we carried out temperature accelerated dynamics (TAD) simulations at different vapor pressures to characterize the morphology of the resulting nanoparticles, which leads to a range of values of the flux of impinging atoms at fixed vapor temperature. At typical experimental pressures of 10-3-10-4 bar TAD provides substantial boost over regular Molecular Dynamics (MD). TAD is also advantageous over MD, regarding the sampling of the network of visited states, which provides a deeper understanding of the evolution of the system. We characterize the growth of such clusters at different vapor pressures.

PDE5 Inhibitor Tadalafil and Hydroxychloroquine Cotreatment Provides Synergistic Protection against Type 2 Diabetes and Myocardial Infarction in Mice

PubMed Central

Wang, Rui; Xi, Lei

2017-01-01

Diabetes is associated with a high risk for ischemic heart disease. We have previously shown that phosphodiesterase 5 inhibitor tadalafil (TAD) induces cardioprotection against ischemia/ reperfusion (I/R) injury in diabetic mice. Hydroxychloroquine (HCQ) is a widely used antimalarial and anti-inflammatory drug that has been reported to reduce hyperglycemia in diabetic patients. Therefore, we hypothesized that a combination of TAD and HCQ may induce synergistic cardioprotection in diabetes. We also investigated the role of insulin-Akt-mammalian target of rapamycin (mTOR) signaling, which regulates protein synthesis and cell survival. Adult male db/db mice were randomized to receive vehicle, TAD (6 mg/kg), HCQ (50 mg/kg), or TAD + HCQ daily by gastric gavage for 7 days. Hearts were isolated and subjected to 30-minute global ischemia, followed by 1-hour reperfusion in Langendorff mode. Cardiac function and myocardial infarct size were determined. Plasma glucose, insulin and lipid levels, and relevant pancreatic and cardiac protein markers were measured. Treatment with TAD + HCQ reduced myocardial infarct size (17.4% ± 4.3% vs. 37.8% ± 4.9% in control group, P < 0.05) and enhanced the production of ATP. The TAD + HCQ combination treatment also reduced fasting blood glucose, plasma free fatty acids, and triglyceride levels. Furthermore, TAD + HCQ increased plasma insulin levels (513 ± 73 vs. 232 ± 30 mU/liter, P < 0.05) with improved insulin sensitivity, larger pancreatic β-cell area, and pancreas mass. Insulin-like growth factor-1 (IGF-1) levels were also elevated by TAD + HCQ (343 ± 14 vs. 262 ± 22 ng/ml, P < 0.05). The increased insulin/IGF-1 resulted in activation of downstream Akt/mTOR cellular survival pathway. These results suggest that combination treatment with TAD and HCQ could be a novel and readily translational pharmacotherapy for reducing cardiovascular risk factors and protecting against myocardial I/R injury in type 2 diabetes. PMID:28123046

Quantitative analysis of the guest-concentration dependence of the mobility in a disordered fluorene-arylamine host-guest system in the guest-to-guest regime

NASA Astrophysics Data System (ADS)

Nicolai, H. T.; Hof, A. J.; Lu, M.; Blom, P. W. M.; de Vries, R. J.; Coehoorn, R.

2011-11-01

The charge transport in a polyspirobifluorene derivative with copolymerized N,N,N',N'-tetraaryldiamino biphenyl (TAD) hole transport units is investigated as a function of the TAD content. For TAD concentrations larger than 5%, guest-to-guest transport is observed. It is demonstrated that in this regime the charge carrier density dependent mobility can be described consistently with the extended Gaussian disorder model, with a density of hopping sites which is proportional to the TAD concentration and comparable to the molecular density.

British Orthodontic Society national audit of temporary anchorage devices (TADs): report of the first thousand TADs placed.

PubMed

Bearn, David R; Alharbi, Fahad

2015-09-01

To provide data from the British Orthodontic Society (BOS) national clinical audit on temporary anchorage device (TAD) use following the recommendations of the National Institute for Health and Clinical Excellence (NIHCE) Design and setting: The Audit commenced on 1 January 2008 and is still ongoing. This article reports the data for TADs placed from 1 January 2008 to 1 November 2013. Audit data was collected from participants using a system of both on-line data entry and hard copy forms. The criteria and standards for the audit were set following the NIHCE report in conjunction with the Development and Standards Committee of the BOS. Virtually all participants used the on-line data entry available on the BOS website. The data submitted was checked and entered manually into an Excel spreadsheet, and transferred to SPSS for analysis. Written information and documented discussion of risks were provided in over 90% of TADs placed, but 17.4% were placed without a specific signed consent form. Temporary anchorage device failure rate was 24.2% overall. Among failed TADs, 93.1% were lost or removed due to excess mobility. Infection or inflammation resulting in loss or removal was reported in 6% of TADs. The only audit standard that was met was failures due to infection of inflammation. The rest of the audit standards were not met. Recommendations are made to address these issues.

Diversity of thermophilic populations during thermophilic aerobic digestion of potato peel slurry.

PubMed

Ugwuanyi, J O; Harvey, L M; McNeil, B

2008-01-01

To study the diversity of thermophiles during thermophilic aerobic digestion (TAD) of agro-food waste slurries under conditions similar to full-scale processes. Population diversity and development in TAD were studied by standard microbiological techniques and the processes monitored by standard fermentation procedures. Facultative thermophiles were identified as Bacillus coagulans and B. licheniformis, while obligate thermophiles were identified as B. stearothermophilus. They developed rapidly to peaks of 10(7) to 10(8) in

Improvement of Insulin Sensitivity by Isoenergy High Carbohydrate Traditional Asian Diet: A Randomized Controlled Pilot Feasibility Study

PubMed Central

Hsu, William C.; Lau, Ka Hei Karen; Matsumoto, Motonobu; Moghazy, Dalia; Keenan, Hillary; King, George L.

2014-01-01

The prevalence of diabetes is rising dramatically among Asians, with increased consumption of the typical Western diet as one possible cause. We explored the metabolic responses in East Asian Americans (AA) and Caucasian Americans (CA) when transitioning from a traditional Asian diet (TAD) to a typical Western diet (TWD), which has not been reported before. This 16-week randomized control pilot feasibility study, included 28AA and 22CA who were at risk of developing type 2 diabetes. Eight weeks of TAD were provided to all participants, followed by 8 weeks of isoenergy TWD (intervention) or TAD (control). Anthropometric measures, lipid profile, insulin resistance and inflammatory markers were assessed. While on TAD, both AA and CA improved in insulin AUC (−960.2 µU/mL×h, P = 0.001) and reduced in weight (−1.6 kg; P<0.001), body fat (−1.7%, P<0.001) and trunk fat (−2.2%, P<0.001). Comparing changes from TAD to TWD, AA had a smaller weight gain (−1.8 to 0.3 kg, P<0.001) than CA (−1.4 to 0.9 kg, P = 0.001), but a greater increase in insulin AUC (AA: −1402.4 to 606.2 µU/mL×h, P = 0.015 vs CA: −466.0 to 223.5 µU/mL×h, P = 0.034) and homeostatic static model assessment-insulin resistance (HOMA-IR) (AA: −0.3 to 0.2, P = 0.042 vs CA: −0.1 to 0.0, P = 0.221). Despite efforts to maintain isoenergy state and consumption of similar energy, TAD induced weight loss and improved insulin sensitivity in both groups, while TWD worsened the metabolic profile. Trial Registration: ClinicalTrials.gov NCT00379548 PMID:25226279

Vertebrate-like CRYPTOCHROME 2 from monarch regulates circadian transcription via independent repression of CLOCK and BMAL1 activity

PubMed Central

Zhang, Ying; Markert, Matthew J.; Groves, Shayna C.; Hardin, Paul E.; Merlin, Christine

2017-01-01

Circadian repression of CLOCK-BMAL1 by PERIOD and CRYPTOCHROME (CRY) in mammals lies at the core of the circadian timekeeping mechanism. CRY repression of CLOCK-BMAL1 and regulation of circadian period are proposed to rely primarily on competition for binding with coactivators on an α-helix located within the transactivation domain (TAD) of the BMAL1 C terminus. This model has, however, not been tested in vivo. Here, we applied CRISPR/Cas9-mediated mutagenesis in the monarch butterfly (Danaus plexippus), which possesses a vertebrate-like CRY (dpCRY2) and an ortholog of BMAL1, to show that insect CRY2 regulates circadian repression through TAD α-helix–dependent and –independent mechanisms. Monarch mutants lacking the BMAL1 C terminus including the TAD exhibited arrhythmic eclosion behavior. In contrast, mutants lacking the TAD α-helix but retaining the most distal C-terminal residues exhibited robust rhythms during the first day of constant darkness (DD1), albeit with a delayed peak of eclosion. Phase delay in this mutant on DD1 was exacerbated in the presence of a single functional allele of dpCry2, and rhythmicity was abolished in the absence of dpCRY2. Reporter assays in Drosophila S2 cells further revealed that dpCRY2 represses through two distinct mechanisms: a TAD-dependent mechanism that involves the dpBMAL1 TAD α-helix and dpCLK W328 and a TAD-independent mechanism involving dpCLK E333. Together, our results provide evidence for independent mechanisms of vertebrate-like CRY circadian regulation on the BMAL1 C terminus and the CLK PAS-B domain and demonstrate the importance of a BMAL1 TAD-independent mechanism for generating circadian rhythms in vivo. PMID:28831003

Vertebrate-like CRYPTOCHROME 2 from monarch regulates circadian transcription via independent repression of CLOCK and BMAL1 activity.

PubMed

Zhang, Ying; Markert, Matthew J; Groves, Shayna C; Hardin, Paul E; Merlin, Christine

2017-09-05

Circadian repression of CLOCK-BMAL1 by PERIOD and CRYPTOCHROME (CRY) in mammals lies at the core of the circadian timekeeping mechanism. CRY repression of CLOCK-BMAL1 and regulation of circadian period are proposed to rely primarily on competition for binding with coactivators on an α-helix located within the transactivation domain (TAD) of the BMAL1 C terminus. This model has, however, not been tested in vivo. Here, we applied CRISPR/Cas9-mediated mutagenesis in the monarch butterfly ( Danaus plexippus ), which possesses a vertebrate-like CRY (dpCRY2) and an ortholog of BMAL1, to show that insect CRY2 regulates circadian repression through TAD α-helix-dependent and -independent mechanisms. Monarch mutants lacking the BMAL1 C terminus including the TAD exhibited arrhythmic eclosion behavior. In contrast, mutants lacking the TAD α-helix but retaining the most distal C-terminal residues exhibited robust rhythms during the first day of constant darkness (DD1), albeit with a delayed peak of eclosion. Phase delay in this mutant on DD1 was exacerbated in the presence of a single functional allele of dpCry2 , and rhythmicity was abolished in the absence of dpCRY2. Reporter assays in Drosophila S2 cells further revealed that dpCRY2 represses through two distinct mechanisms: a TAD-dependent mechanism that involves the dpBMAL1 TAD α-helix and dpCLK W328 and a TAD-independent mechanism involving dpCLK E333. Together, our results provide evidence for independent mechanisms of vertebrate-like CRY circadian regulation on the BMAL1 C terminus and the CLK PAS-B domain and demonstrate the importance of a BMAL1 TAD-independent mechanism for generating circadian rhythms in vivo.

Tadalafil modulates aromatase activity and androgen receptor expression in a human osteoblastic cell in vitro model.

PubMed

Aversa, A; Fittipaldi, S; Bimonte, V M; Wannenes, F; Papa, V; Francomano, D; Greco, E A; Lenzi, A; Migliaccio, S

2016-02-01

Phosphodiesterase type-5 inhibitor (PDE5i) tadalafil administration in men with erectile dysfunction is associated with increased testosterone/estradiol ratio, leading to hypothesize a potential increased effect of androgen action on target tissues. We aimed to characterize, in a cellular model system in vitro, the potential modulation of aromatase and sex steroid hormone receptors upon exposure to tadalafil (TAD). Human osteoblast-like cells SAOS-2 were chosen as an in vitro model system since osteoblasts are target of steroid hormones. Cells were tested for viability upon TAD exposure, which increased cell proliferation. Then, cells were treated with/without TAD for several times to evaluate potential modulation in PDE5, aromatase (ARO), androgen (AR) and estrogen (ER) receptor expression. Osteoblasts express significant levels of both PDE5 mRNA and protein. Exposure of cells to increasing concentrations of TAD (10(-8)-10(-7) M) decreased PDE5 mRNA and protein expression. Also, TAD inhibited ARO mRNA and protein expression leading to an increase in testosterone levels in the supernatants. Interestingly, TAD increased total AR mRNA and protein expression and decreased ERα, with an increased ratio of AR/ER, suggesting preferential androgenic vs estrogenic pathway activation. Our results demonstrate for the first time that TAD decreases ARO expression and increases AR protein expression in human SAOS-2, strongly suggesting a new control of steroid hormones pathway by PDE5i. These findings might represent the first evidence of translational actions of PDE5i on AR, which leads to hypothesize a growing relevance of this molecule in men with prostate cancer long-term treated with TAD for sexual rehabilitation.

The motion of throw away detectors relative to the space shuttle

NASA Technical Reports Server (NTRS)

Mullins, L. D.

1975-01-01

The motions of throw away detectors (TAD's) are analyzed using the linearized relative motion equations. The TAD's are to be used in the amps program as diagnostic instruments for making various measurements near the shuttle. The TAD's are ejected from the shuttle in arbitrary directions with small relative velocities (0.1 to 1.0 m/s) their subsequent trajectories relative to the shuttle are analyzed. Initial conditions that are likely to result in recontact between the TAD and the shuttle are identified. The sensitivity of the motion to variations in the initial conditions, possibly resulting from inaccuracy in the ejection mechanism, are analyzed as are effects of atmospheric drag. A targeting method, a method of giving the TAD correct initial conditions such that it will pass through a given point relative to the shuttle at a given time, is developed. The results of many specific cases are presented in graphical form.

Effect of arylamine hole-transport units on the performance of blue polyspirobifulorene light-emitting diodes

NASA Astrophysics Data System (ADS)

Abbaszadeh, Davood; Nicolai, Herman T.; Crǎciun, N. Irina; Blom, Paul W. M.

2014-11-01

The operation of blue light-emitting diodes based on polyspirobifluorene with a varying number of N ,N ,N',N' tetraaryldiamino biphenyl (TAD) hole-transport units (HTUs) is investigated. Assuming that the electron transport is not affected by the incorporation of TAD units, model calculations predict that a concentration of 5% HTU leads to an optimal efficiency for this blue-emitting polymer. However, experimentally an optimum performance is achieved for 10% TAD HTUs. Analysis of the transport and recombination shows that polymer light-emitting diodes with 5%, 7.5%, and 12.5% TAD units follow the predicted behavior. The enhanced performance of the polymer with 10% TAD originates from a decrease in the number of electron traps, which is typically a factor of three lower than the universal value found in many polymers. This reduced number of traps leads to a reduction of nonradiative recombination and exciton quenching at the cathode.

Combined mesophilic anaerobic and thermophilic aerobic digestion process for high-strength food wastewater to increase removal efficiency and reduce sludge discharge.

PubMed

Jang, H M; Park, S K; Ha, J H; Park, J M

2014-01-01

In this study, a process that combines the mesophilic anaerobic digestion (MAD) process with thermophilic aerobic digestion (TAD) for high-strength food wastewater (FWW) treatment was developed to examine the removal of organic matter and methane production. All effluent discharged from the MAD process was separated into solid and liquid portions. The liquid part was discarded and the sludge part was passed to the TAD process for further degradation. Then, the digested sludge from the TAD process was recycled back to the MAD unit to achieve low sludge discharge from the combined process. The reactor combination was operated in two phases: during Phase I, 40 d of total hydraulic retention time (HRT) was applied; during Phase II, 20 d was applied. HRT of the TAD process was fixed at 5 d. For a comparison, a control process (single-stage MAD) was operated with the same HRTs of the combined process. Our results indicated that the combined process showed over 90% total solids, volatile solids and chemical oxygen demand removal efficiencies. In addition, the combined process showed a significantly higher methane production rate than that of the control process. Consequently, the experimental data demonstrated that the combined MAD-TAD process was successfully employed for high-strength FWW treatment with highly efficient organic matter reduction and methane production.

Residual life assessment of the SSME/ATD HPOTP turnaround duct (TAD)

NASA Technical Reports Server (NTRS)

Gross, R. Steven

1996-01-01

This paper is concerned with the prediction of the low cycle thermal fatigue behavior of a component in a developmental (ATD) high pressure liquid oxygen turbopump (HPOTP) for the Space Shuttle Main Engine (SSME). This component is called the Turnaround Duct (TAD). The TAD is a complex single piece casting of MAR-M-247 material. Its function is to turn the hot turbine exhaust gas (1200 F hydrogen rich gas steam) such that it can exhaust radially out of the turbopump. In very simple terms, the TAD consists of two rings connected axially by 22 hollow airfoil shaped struts with the turning vanes placed at the top, middle, and bottom of each strut. The TAD is attached to the other components of the pump via bolts passing through 14 of the 22 struts. Of the remaining 8 struts, four are equally spaced (90 deg interval) and containing a cooling tube through which liquid hydrogen passes on its way to cool the shaft bearing assemblies. The remaining 4 struts are empty. One of the pump units in the certification test series was destructively examined after 22 test firings. Substantial axial cracking was found in two of the struts which contain cooling tubes. None of the other 20 struts showed any sign of internal cracking. This unusual low cycle thermal fatigue behavior within the two cooling tube struts is the focus of this study.

Femoral neck-shaft angle in extra-capsular proximal femoral fracture fixation; does it make a TAD of difference?

PubMed

Walton, N P; Wynn-Jones, H; Ward, M S; Wimhurst, J A

2005-11-01

The effect of femoral neck-shaft angle and implant type on the accuracy of lag screw placement in extra-capsular proximal femoral fracture fixation was investigated. Radiographs of all extra-capsular proximal femoral fractures seen in one unit over 18 months were reviewed. Of 399 cases, 307 (237 female, 70 male) were included in the study as they had no contra-lateral proximal femoral metal work. Femoral neck-shaft angle (NSA) of the uninjured hip and magnification adjusted tip-apex distance (TAD) of femoral head lag screw were measured. Type of fixation implant was 135 degrees classic hip screw (CHS) (n=144) or 130 degrees intra-medullary hip screw (IMHS) (n=163). Mean contra-lateral NSA was 130.2 degrees (112.9--148 degrees ) and 64 patients (58 female, 6 male) had a NSA <125 degrees . Mean adjusted TAD was 18.7 mm (5.8--43.8mm) and 88.9% of cases had a TAD of less than 25 mm. TAD values were significantly greater using an IMHS if NSA was <125 degrees than if NSA was >125 degrees (p=0.028). This was not the case with the CHS. The use of the 130 degrees -IMHS in patients with a NSA <125 degrees leads to poorer lag screw placement than if NSA >125 degrees and caution is advocated when using this device in such cases.

Toolsets for Airborne Data (TAD): Improving Machine Readability for ICARTT Data Files

NASA Astrophysics Data System (ADS)

Northup, E. A.; Early, A. B.; Beach, A. L., III; Kusterer, J.; Quam, B.; Wang, D.; Chen, G.

2015-12-01

NASA has conducted airborne tropospheric chemistry studies for about three decades. These field campaigns have generated a great wealth of observations, including a wide range of the trace gases and aerosol properties. The ASDC Toolsets for Airborne Data (TAD) is designed to meet the user community needs for manipulating aircraft data for scientific research on climate change and air quality relevant issues. TAD makes use of aircraft data stored in the International Consortium for Atmospheric Research on Transport and Transformation (ICARTT) file format. ICARTT has been the NASA standard since 2010, and is widely used by NOAA, NSF, and international partners (DLR, FAAM). Its level of acceptance is due in part to it being generally self-describing for researchers, i.e., it provides necessary data descriptions for proper research use. Despite this, there are a number of issues with the current ICARTT format, especially concerning the machine readability. In order to overcome these issues, the TAD team has developed an "idealized" file format. This format is ASCII and is sufficiently machine readable to sustain the TAD system, however, it is not fully compatible with the current ICARTT format. The process of mapping ICARTT metadata to the idealized format, the format specifics, and the actual conversion process will be discussed. The goal of this presentation is to demonstrate an example of how to improve the machine readability of ASCII data format protocols.

A Compositional Translation of Timed Automata with Deadlines to Uppaal Timed Automata

NASA Astrophysics Data System (ADS)

Gómez, Rodolfo

Timed Automata with Deadlines (TAD) are a form of timed automata that admit a more natural representation of urgent actions, with the additional advantage of avoiding the most common form of timelocks. We offer a compositional translation of a practically useful subset of TAD to timed safety automata (the well-known variant of timed automata where time progress conditions are expressed by invariants). More precisely, we translate networks of TAD to the modeling language of Uppaal, a state-of-the-art verification tool for timed automata. We also describe an implementation of this translation, which allows Uppaal to aid the design and analysis of TAD models.

Identification of a tetrameric assembly domain in the C terminus of heat-activated TRPV1 channels.

PubMed

Zhang, Feng; Liu, Shuang; Yang, Fan; Zheng, Jie; Wang, KeWei

2011-04-29

Transient receptor potential (TRP) channels as cellular sensors are thought to function as tetramers. Yet, the molecular determinants governing channel multimerization remain largely elusive. Here we report the identification of a segment comprising 21 amino acids (residues 752-772 of mouse TRPV1) after the known TRP-like domain in the channel C terminus that functions as a tetrameric assembly domain (TAD). Purified recombinant C-terminal proteins of TRPV1-4, but not the N terminus, mediated the protein-protein interaction in an in vitro pulldown assay. Western blot analysis combined with electrophysiology and calcium imaging demonstrated that TAD exerted a robust dominant-negative effect on wild-type TRPV1. When fused with the membrane-tethered peptide Gap43, the TAD blocked the formation of stable homomultimers. Calcium imaging and current recordings showed that deletion of the TAD in a poreless TRPV1 mutant subunit suppressed its dominant-negative phenotype, confirming the involvement of the TAD in assembly of functional channels. Our findings suggest that the C-terminal TAD in TRPV1 channels functions as a domain that is conserved among TRPV1-4 and mediates a direct subunit-subunit interaction for tetrameric assembly.

Different Spectrophotometric Methods for Simultaneous Determination of Trelagliptin and Its Acid Degradation Product

PubMed Central

Hassan, Mostafa A.; Zaghary, Wafaa A.

2018-01-01

New spectrophotometric and chemometric methods were carried out for the simultaneous assay of trelagliptin (TRG) and its acid degradation product (TAD) and applied successfully as a stability indicating assay to recently approved Zafatek® tablets. TAD was monitored using TLC to ensure complete degradation. Furthermore, HPLC was used to confirm dealing with one major acid degradation product. The proposed methods were developed by manipulating zero-order, first-derivative, and ratio spectra of TRG and TAD using simultaneous equation, first-derivative, and mean-centering methods, respectively. Using Spectra Manager II and Minitab v.14 software, the absorbance at 274 nm–260.4 nm, amplitudes at 260.4 nm–274.0 nm, and mean-centered values at 287.6 nm–257.2 nm were measured against methanol as a blank for TRG and TAD, respectively. Linearity and the other validation parameters were acceptable at concentration ranges of 5–50 μg/mL and 2.5–25 μg/mL for TRG and TAD, respectively. Using one-way analysis of variance (ANOVA), the optimized methods were compared and proved to be accurate for the simultaneous assay of TRG and TAD. PMID:29629213

Different Spectrophotometric Methods for Simultaneous Determination of Trelagliptin and Its Acid Degradation Product.

PubMed

Mowaka, Shereen; Ayoub, Bassam M; Hassan, Mostafa A; Zaghary, Wafaa A

2018-01-01

New spectrophotometric and chemometric methods were carried out for the simultaneous assay of trelagliptin (TRG) and its acid degradation product (TAD) and applied successfully as a stability indicating assay to recently approved Zafatek® tablets. TAD was monitored using TLC to ensure complete degradation. Furthermore, HPLC was used to confirm dealing with one major acid degradation product. The proposed methods were developed by manipulating zero-order, first-derivative, and ratio spectra of TRG and TAD using simultaneous equation, first-derivative, and mean-centering methods, respectively. Using Spectra Manager II and Minitab v.14 software, the absorbance at 274 nm-260.4 nm, amplitudes at 260.4 nm-274.0 nm, and mean-centered values at 287.6 nm-257.2 nm were measured against methanol as a blank for TRG and TAD, respectively. Linearity and the other validation parameters were acceptable at concentration ranges of 5-50  μ g/mL and 2.5-25  μ g/mL for TRG and TAD, respectively. Using one-way analysis of variance (ANOVA), the optimized methods were compared and proved to be accurate for the simultaneous assay of TRG and TAD.

Accumulation of subcutaneous fat, but not visceral fat, is a predictor of adiponectin levels in preterm infants at term-equivalent age.

PubMed

Nakano, Yuya; Itabashi, Kazuo; Sakurai, Motoichiro; Aizawa, Madoka; Dobashi, Kazushige; Mizuno, Katsumi

2014-05-01

Preterm infants have altered fat tissue development, including a higher percentage of fat mass and increased volume of visceral fat. They also have altered adiponectin levels, including a lower ratio of high-molecular-weight adiponectin (HMW-Ad) to total adiponectin (T-Ad) at term-equivalent age, compared with term infants. The objective of this study was to investigate the association between adiponectin levels and fat tissue accumulation or distribution in preterm infants at term-equivalent age. Cross-sectional clinical study. Study subjects were 53 preterm infants born at ≤34weeks gestation with a mean birth weight of 1592g. Serum levels of T-Ad and HMW-Ad were measured and a computed tomography (CT) scan was performed at the level of the umbilicus at term-equivalent age to analyze how fat tissue accumulation or distribution was correlated with adiponectin levels. T-Ad (r=0.315, p=0.022) and HMW-Ad levels (r=0.338, p=0.013) were positively associated with subcutaneous fat area evaluated by performing CT scan at term-equivalent age, but were not associated with visceral fat area in simple regression analyses. In addition, T-Ad (β=0.487, p=0.003) and HMW-Ad levels (β=0.602, p<0.001) were positively associated with subcutaneous fat tissue area, but they were not associated with visceral fat area also in multiple regression analyses. Subcutaneous fat accumulation contributes to increased levels of T-Ad and HMW-Ad, while visceral fat accumulation does not influence adiponectin levels in preterm infants at term-equivalent age. Copyright © 2014 Elsevier Ltd. All rights reserved.

Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments.

PubMed

Robson, Michael I; de Las Heras, Jose I; Czapiewski, Rafal; Sivakumar, Aishwarya; Kerr, Alastair R W; Schirmer, Eric C

2017-07-01

The 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. Studies have focused either on lamina-associated domains (LADs) or on topologically associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs sharing functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1-DamID during Jurkat T-cell activation, finding significant genome reorganization at the nuclear periphery dominated by release of loci frequently important for T-cell function. To assess how these changes at the nuclear periphery influence wider genome organization, our DamID data sets were contrasted with TADs and compartments. Features of specific repositioning events were then tested by fluorescence in situ hybridization during T-cell activation. First, considerable overlap between TADs and LADs was observed with the TAD repositioning as a unit. Second, A1 and A2 subcompartments are segregated in 3D space through differences in proximity to LADs along chromosomes. Third, genes and a putative enhancer in LADs that were released from the periphery during T-cell activation became preferentially associated with A2 subcompartments and were constrained to the relative proximity of the lamina. Thus, lamina associations influence internal nuclear organization, and changes in LADs during T-cell activation may provide an important additional mode of gene regulation. © 2017 Robson et al.; Published by Cold Spring Harbor Laboratory Press.

Enhancement of proteolytic enzyme activity excreted from Bacillus stearothermophilus for a thermophilic aerobic digestion process.

PubMed

Kim, Young-Kee; Bae, Jin-Hye; Oh, Byung-Keun; Lee, Won Hong; Choi, Jeong-Woo

2002-04-01

Proteolysis is one of the main enzymatic reactions involved in waste activated sludge (WAS) digestion. In this study, proteases excreted from Bacillus stearothermophilus (ATCC 31197) were classified, and an enhancement of protease activity was achieved using economical chemical additives for WAS digestion. Proteases excreted from B. stearothermophilus were classified into two families: serine and metallo-proteases. Various metal ions were investigated as additives which could potentially enhance protease activity. It was observed that Ca2+ and Fe2+ could markedly activate these enzymes. These results were applied to thermophilic aerobic digestion (TAD) of industrial WAS using B. stearothermophilus. The addition of these divalent ions enhanced the degradation performance of the TAD process in terms of reducing the total suspended solids (TSSs), the dissolved organic carbon (DOC) content, and the intracellular and extracellular protein concentrations. The best result, with respect to protein reduction in a digestion experiment, was obtained by the addition of 2 mM Ca2+. Therefore, a proposed TAD process activated by calcium addition can be successfully used for industrial and municipal WAS digestion to the upgrading of TAD process performance.

PDE5 Inhibitor Tadalafil and Hydroxychloroquine Cotreatment Provides Synergistic Protection against Type 2 Diabetes and Myocardial Infarction in Mice.

PubMed

Wang, Rui; Xi, Lei; Kukreja, Rakesh C

2017-04-01

Diabetes is associated with a high risk for ischemic heart disease. We have previously shown that phosphodiesterase 5 inhibitor tadalafil (TAD) induces cardioprotection against ischemia/ reperfusion (I/R) injury in diabetic mice. Hydroxychloroquine (HCQ) is a widely used antimalarial and anti-inflammatory drug that has been reported to reduce hyperglycemia in diabetic patients. Therefore, we hypothesized that a combination of TAD and HCQ may induce synergistic cardioprotection in diabetes. We also investigated the role of insulin-Akt-mammalian target of rapamycin (mTOR) signaling, which regulates protein synthesis and cell survival. Adult male db/db mice were randomized to receive vehicle, TAD (6 mg/kg), HCQ (50 mg/kg), or TAD + HCQ daily by gastric gavage for 7 days. Hearts were isolated and subjected to 30-minute global ischemia, followed by 1-hour reperfusion in Langendorff mode. Cardiac function and myocardial infarct size were determined. Plasma glucose, insulin and lipid levels, and relevant pancreatic and cardiac protein markers were measured. Treatment with TAD + HCQ reduced myocardial infarct size (17.4% ± 4.3% vs. 37.8% ± 4.9% in control group, P < 0.05) and enhanced the production of ATP. The TAD + HCQ combination treatment also reduced fasting blood glucose, plasma free fatty acids, and triglyceride levels. Furthermore, TAD + HCQ increased plasma insulin levels (513 ± 73 vs. 232 ± 30 mU/liter, P < 0.05) with improved insulin sensitivity, larger pancreatic β -cell area, and pancreas mass. Insulin-like growth factor-1 (IGF-1) levels were also elevated by TAD + HCQ (343 ± 14 vs. 262 ± 22 ng/ml, P < 0.05). The increased insulin/IGF-1 resulted in activation of downstream Akt/mTOR cellular survival pathway. These results suggest that combination treatment with TAD and HCQ could be a novel and readily translational pharmacotherapy for reducing cardiovascular risk factors and protecting against myocardial I/R injury in type 2 diabetes. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Three-D Flow Analysis of the Alternate SSME HPOT TAD

NASA Technical Reports Server (NTRS)

Kubinski, Cheryl A.

1993-01-01

This paper describes the results of numerical flow analyses performed in support of design development of the Space Shuttle Main Engine Alternate High Pressure Oxidizer Turbine Turn-around duct (TAD). The flow domain has been modeled using a 3D, Navier-Stokes, general purpose flow solver. The goal of this effort is to achieve an alternate TAD exit flow distribution which closely matches that of the baseline configuration. 3D Navier Stokes CFD analyses were employed to evaluate numerous candidate geometry modifications to the TAD flowpath in order to achieve this goal. The design iterations are summarized, as well as a description of the computational model, numerical results and the conclusions based on these calculations.

Speculation and replication in temperature accelerated dynamics

DOE PAGES

Zamora, Richard J.; Perez, Danny; Voter, Arthur F.

2018-02-12

Accelerated Molecular Dynamics (AMD) is a class of MD-based algorithms for the long-time scale simulation of atomistic systems that are characterized by rare-event transitions. Temperature-Accelerated Dynamics (TAD), a traditional AMD approach, hastens state-to-state transitions by performing MD at an elevated temperature. Recently, Speculatively-Parallel TAD (SpecTAD) was introduced, allowing the TAD procedure to exploit parallel computing systems by concurrently executing in a dynamically generated list of speculative future states. Although speculation can be very powerful, it is not always the most efficient use of parallel resources. In this paper, we compare the performance of speculative parallelism with a replica-based technique, similarmore » to the Parallel Replica Dynamics method. A hybrid SpecTAD approach is also presented, in which each speculation process is further accelerated by a local set of replicas. Finally and overall, this work motivates the use of hybrid parallelism whenever possible, as some combination of speculation and replication is typically most efficient.« less

Speculation and replication in temperature accelerated dynamics

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

Zamora, Richard J.; Perez, Danny; Voter, Arthur F.

Accelerated Molecular Dynamics (AMD) is a class of MD-based algorithms for the long-time scale simulation of atomistic systems that are characterized by rare-event transitions. Temperature-Accelerated Dynamics (TAD), a traditional AMD approach, hastens state-to-state transitions by performing MD at an elevated temperature. Recently, Speculatively-Parallel TAD (SpecTAD) was introduced, allowing the TAD procedure to exploit parallel computing systems by concurrently executing in a dynamically generated list of speculative future states. Although speculation can be very powerful, it is not always the most efficient use of parallel resources. In this paper, we compare the performance of speculative parallelism with a replica-based technique, similarmore » to the Parallel Replica Dynamics method. A hybrid SpecTAD approach is also presented, in which each speculation process is further accelerated by a local set of replicas. Finally and overall, this work motivates the use of hybrid parallelism whenever possible, as some combination of speculation and replication is typically most efficient.« less

Application To Bilayer System With Water-Soluble Contrast Enhancing Material

NASA Astrophysics Data System (ADS)

Yabuta, Mitsuo; Ito, Naoki; Yamazaki, Hiroyuki; Nakayama, Toshimasa

1987-09-01

We have developed ,a water-soluble contrast enhancing material, TAD-436 ( Tokyo Ohka. Anti-Defocus Material ) which is consisted of a water-soluble diazonium salt as bleaching compounds and a water-soluble anion type polymer as binder polymers. Needless to say that water is used as solvent in TAD; therefore, it can be spincoated directly on a positive photoresist layer of a quinonediazide-novolak resin type without causing intermixing and furtheremore the bilayer can be developed without stripping TAD immediately after exposure. TAD shows a satisfactory bleaching characteristics on g-line, increases r-value of underlying photoresist and reduces the thickness loss of photoresist layer in unexposed area. Application to bilayer system with TAD will raise the resolution of underlying photoresist and when the focus depth is changed it will make the change in the resist profile small. As the result of it, the notches in the resist patterns on steps is reduced, making the difference in the linewidth between the top and the bottom of steps small.

Incidence of Branching Patterns Variations of the Arch in Aortic Dissection in Chinese Patients

PubMed Central

Tapia, G. Pullas; Zhu, Xiaohua; Xu, Jing; Liang, Pan; Su, Gang; Liu, Hai; Liu, Yang; Shu, Liliang; Liu, Shuiqi; Huang, Chen

2015-01-01

Abstract Several authors have described anatomic variations of the aortic arch in 13% to 20% of the patients who do not have aortic disease. However, few studies have evaluated these patterns in the thoracic aortic dissection (TAD). In the authors’ knowledge, this is the first survey that specifically investigates the frequency of these variations in a broad, nonselected group of Chinese patients with aortic dissection. Furthermore, it compares this group with a group of patients without aortic disease. The objective of this study was to define the variation frequency of the aortic arch branches pattern using the tomographic studies of 525 Chinese patients with a diagnosis of TAD. The Stanford classification was used to set the site of the initial tear of the dissection. In addition, we performed an epidemiological analysis of the aortic arch anatomic variations in TAD, and its possible implications for surgical or endovascular treatment. The general hypothesis proposal asserted that Chinese patients with dissection of the aorta have a similar incidence of variations of the aortic arch to the patients without aortic disease. A retrospective study of cases and controls was carried out using the tomographic studies (CT) of all patients admitted to the First Affiliated Hospital of Zhengzhou University, located at Henan-China, with a confirmed diagnosis of aortic dissection from January 2012 until December 2014. The group of cases consisted of 525 patients: 374 men and 151 women, with a mean age of 52.27 years (range, 20–89). The average age of the patients with Stanford A and B aortic dissection was 49.46 and 53.67, respectively. The control group consisted of 525 unselected patients without TAD who underwent a CT scan of the chest due to other indications. This group consisted of 286 men and 239 women, with a mean age of 53.60 years (range, 18–89). All the patients with aneurysm or dissection were excluded from the control group. We performed a statistical analysis of demographic data. The study found 7 different patterns of the aortic arch on both groups of cases and controls. Within the 525 patients with TAD were observed 85 (16.19%) anatomical variations, while the control group showed 112 variations (21.33%); P = 0.033. The most common anatomical variant was the bovine arch, found in 62 (11.80%) cases of TAD compared with 77 (14.66%) in the control group; P = 0.172. Anatomical variations were observed in 14.32% of the patients with Stanford A dissection and 17.09% of the patients with Stanford B dissection; P = 0.425. Patients with Stanford A dissection showed the pattern of bovine arch in 23 (13.21%) of 174 cases. In contrast, the patients with Stanford B dissection showed it in 39 (11.11%) of 351 cases; P = 0.481. The anatomical variant defined as vertebral artery of direct origin of the aortic arch was more frequent in the patients with Stanford B dissection (5.12%). The patients with Stanford A dissection presented this pattern in 1.14% of the cases; P = 0.025. This study observed an increased frequency of aortic dissection in the subgroup from 41 to 60 years old. In the subgroup from 41 to 60 years old without TAD, a greater frequency of anatomical variations were found than in the patients with TAD (20.81% vs 14.23%; P = 0.050). The same fashion was seen in patients older than 80 years (27.27% vs 0%; P = 0.030). The anatomical variations of the aortic arch with TAD occurred in 14.97% of the male patients and 19.20% of the female patients compared to 21.67% to 20.92% in the control group; P = 0.026 and P = 0.681, respectively. The aortic arch variations were found less frequently in the TAD group than in the control group in the present Chinese series. The bovine arch was considered the variant pattern of the major frequency in the patients with TAD and the control group. The anatomical variant of 4 branches, defined as vertebral artery of direct origin of the aortic arch, was more frequent in patients with Stanford B aortic dissection than in the patients with Stanford A. This finding might show an association between the geometry of the aortic arch and the site of onset of first intimal tear of dissection. PMID:25929931

Incidence of branching patterns variations of the arch in aortic dissection in Chinese patients.

PubMed

Tapia, G Pullas; Zhu, Xiaohua; Xu, Jing; Liang, Pan; Su, Gang; Liu, Hai; Liu, Yang; Shu, Liliang; Liu, Shuiqi; Huang, Chen

2015-05-01

Several authors have described anatomic variations of the aortic arch in 13% to 20% of the patients who do not have aortic disease. However, few studies have evaluated these patterns in the thoracic aortic dissection (TAD). In the authors' knowledge, this is the first survey that specifically investigates the frequency of these variations in a broad, nonselected group of Chinese patients with aortic dissection. Furthermore, it compares this group with a group of patients without aortic disease.The objective of this study was to define the variation frequency of the aortic arch branches pattern using the tomographic studies of 525 Chinese patients with a diagnosis of TAD. The Stanford classification was used to set the site of the initial tear of the dissection. In addition, we performed an epidemiological analysis of the aortic arch anatomic variations in TAD, and its possible implications for surgical or endovascular treatment. The general hypothesis proposal asserted that Chinese patients with dissection of the aorta have a similar incidence of variations of the aortic arch to the patients without aortic disease.A retrospective study of cases and controls was carried out using the tomographic studies (CT) of all patients admitted to the First Affiliated Hospital of Zhengzhou University, located at Henan-China, with a confirmed diagnosis of aortic dissection from January 2012 until December 2014. The group of cases consisted of 525 patients: 374 men and 151 women, with a mean age of 52.27 years (range, 20-89). The average age of the patients with Stanford A and B aortic dissection was 49.46 and 53.67, respectively. The control group consisted of 525 unselected patients without TAD who underwent a CT scan of the chest due to other indications. This group consisted of 286 men and 239 women, with a mean age of 53.60 years (range, 18-89). All the patients with aneurysm or dissection were excluded from the control group. We performed a statistical analysis of demographic data.The study found 7 different patterns of the aortic arch on both groups of cases and controls. Within the 525 patients with TAD were observed 85 (16.19%) anatomical variations, while the control group showed 112 variations (21.33%); P = 0.033. The most common anatomical variant was the bovine arch, found in 62 (11.80%) cases of TAD compared with 77 (14.66%) in the control group; P = 0.172. Anatomical variations were observed in 14.32% of the patients with Stanford A dissection and 17.09% of the patients with Stanford B dissection; P = 0.425. Patients with Stanford A dissection showed the pattern of bovine arch in 23 (13.21%) of 174 cases. In contrast, the patients with Stanford B dissection showed it in 39 (11.11%) of 351 cases; P = 0.481. The anatomical variant defined as vertebral artery of direct origin of the aortic arch was more frequent in the patients with Stanford B dissection (5.12%). The patients with Stanford A dissection presented this pattern in 1.14% of the cases; P = 0.025. This study observed an increased frequency of aortic dissection in the subgroup from 41 to 60 years old. In the subgroup from 41 to 60 years old without TAD, a greater frequency of anatomical variations were found than in the patients with TAD (20.81% vs 14.23%; P = 0.050). The same fashion was seen in patients older than 80 years (27.27% vs 0%; P = 0.030). The anatomical variations of the aortic arch with TAD occurred in 14.97% of the male patients and 19.20% of the female patients compared to 21.67% to 20.92% in the control group; P = 0.026 and P = 0.681, respectively.The aortic arch variations were found less frequently in the TAD group than in the control group in the present Chinese series. The bovine arch was considered the variant pattern of the major frequency in the patients with TAD and the control group. The anatomical variant of 4 branches, defined as vertebral artery of direct origin of the aortic arch, was more frequent in patients with Stanford B aortic dissection than in the patients with Stanford A.This finding might show an association between the geometry of the aortic arch and the site of onset of first intimal tear of dissection.

Targeted Analyte Detection by Standard Addition Improves Detection Limits in MALDI Mass Spectrometry

PubMed Central

Eshghi, Shadi Toghi; Li, Xingde; Zhang, Hui

2014-01-01

Matrix-assisted laser desorption/ionization has proven an effective tool for fast and accurate determination of many molecules. However, the detector sensitivity and chemical noise compromise the detection of many invaluable low-abundance molecules from biological and clinical samples. To challenge this limitation, we developed a targeted analyte detection (TAD) technique. In TAD, the target analyte is selectively elevated by spiking a known amount of that analyte into the sample, thereby raising its concentration above the noise level, where we take advantage of the improved sensitivity to detect the presence of the endogenous analyte in the sample. We assessed TAD on three peptides in simple and complex background solutions with various exogenous analyte concentrations in two MALDI matrices. TAD successfully improved the limit of detection (LOD) of target analytes when the target peptides were added to the sample in a concentration close to optimum concentration. The optimum exogenous concentration was estimated through a quantitative method to be approximately equal to the original LOD for each target. Also, we showed that TAD could achieve LOD improvements on an average of 3-fold in a simple and 2-fold in a complex sample. TAD provides a straightforward assay to improve the LOD of generic target analytes without the need for costly hardware modifications. PMID:22877355

Targeted analyte detection by standard addition improves detection limits in matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Toghi Eshghi, Shadi; Li, Xingde; Zhang, Hui

2012-09-18

Matrix-assisted laser desorption/ionization (MALDI) has proven an effective tool for fast and accurate determination of many molecules. However, the detector sensitivity and chemical noise compromise the detection of many invaluable low-abundance molecules from biological and clinical samples. To challenge this limitation, we developed a targeted analyte detection (TAD) technique. In TAD, the target analyte is selectively elevated by spiking a known amount of that analyte into the sample, thereby raising its concentration above the noise level, where we take advantage of the improved sensitivity to detect the presence of the endogenous analyte in the sample. We assessed TAD on three peptides in simple and complex background solutions with various exogenous analyte concentrations in two MALDI matrices. TAD successfully improved the limit of detection (LOD) of target analytes when the target peptides were added to the sample in a concentration close to optimum concentration. The optimum exogenous concentration was estimated through a quantitative method to be approximately equal to the original LOD for each target. Also, we showed that TAD could achieve LOD improvements on an average of 3-fold in a simple and 2-fold in a complex sample. TAD provides a straightforward assay to improve the LOD of generic target analytes without the need for costly hardware modifications.

TAD-free analysis of architectural proteins and insulators.

PubMed

Mourad, Raphaël; Cuvier, Olivier

2018-03-16

The three-dimensional (3D) organization of the genome is intimately related to numerous key biological functions including gene expression and DNA replication regulations. The mechanisms by which molecular drivers functionally organize the 3D genome, such as topologically associating domains (TADs), remain to be explored. Current approaches consist in assessing the enrichments or influences of proteins at TAD borders. Here, we propose a TAD-free model to directly estimate the blocking effects of architectural proteins, insulators and DNA motifs on long-range contacts, making the model intuitive and biologically meaningful. In addition, the model allows analyzing the whole Hi-C information content (2D information) instead of only focusing on TAD borders (1D information). The model outperforms multiple logistic regression at TAD borders in terms of parameter estimation accuracy and is validated by enhancer-blocking assays. In Drosophila, the results support the insulating role of simple sequence repeats and suggest that the blocking effects depend on the number of repeats. Motif analysis uncovered the roles of the transcriptional factors pannier and tramtrack in blocking long-range contacts. In human, the results suggest that the blocking effects of the well-known architectural proteins CTCF, cohesin and ZNF143 depend on the distance between loci, where each protein may participate at different scales of the 3D chromatin organization.

Multiple Taf subunits of TFIID interact with Ino2 activation domains and contribute to expression of genes required for yeast phospholipid biosynthesis.

PubMed

Hintze, Stefan; Engelhardt, Maike; van Diepen, Laura; Witt, Eric; Schüller, Hans-Joachim

2017-12-01

Expression of phospholipid biosynthetic genes in yeast requires activator protein Ino2 which can bind to the UAS element inositol/choline-responsive element (ICRE) and trigger activation of target genes, using two separate transcriptional activation domains, TAD1 and TAD2. However, it is still unknown which cofactors mediate activation by TADs of Ino2. Here, we show that multiple subunits of basal transcription factor TFIID (TBP-associated factors Taf1, Taf4, Taf6, Taf10 and Taf12) are able to interact in vitro with activation domains of Ino2. Interaction was no longer observed with activation-defective variants of TAD1. We were able to identify two nonoverlapping regions in the N-terminus of Taf1 (aa 1-100 and aa 182-250) each of which could interact with TAD1 of Ino2 as well as with TAD4 of activator Adr1. Specific missense mutations within Taf1 domain aa 182-250 affecting basic and hydrophobic residues prevented interaction with wild-type TAD1 and caused reduced expression of INO1. Using chromatin immunoprecipitation we demonstrated Ino2-dependent recruitment of Taf1 and Taf6 to ICRE-containing promoters INO1 and CHO2. Transcriptional derepression of INO1 was no longer possible with temperature-sensitive taf1 and taf6 mutants cultivated under nonpermissive conditions. This result supports the hypothesis of Taf-dependent expression of structural genes activated by Ino2. © 2017 John Wiley & Sons Ltd.

Transcriptional activation of the tad type IVb pilus operon by PypB in Yersinia enterocolitica.

PubMed

Schilling, Jennifer; Wagner, Karin; Seekircher, Stephanie; Greune, Lilo; Humberg, Verena; Schmidt, M Alexander; Heusipp, Gerhard

2010-07-01

Type IV pili are virulence factors in various bacteria and mediate, among other functions, the colonization of diverse surfaces. Various subclasses of type IV pili have been identified, but information on pilus expression, biogenesis, and the associated phenotypes is sparse for the genus Yersinia. We recently described the identification of PypB as a transcriptional regulator in Yersinia enterocolitica. Here we show that the pypB gene is associated with the tad locus, a genomic island that is widespread among bacterial and archaeal species. The genetic linkage of pypB with the tad locus is conserved throughout the yersiniae but is not found among other bacteria carrying the tad locus. We show that the genes of the tad locus form an operon in Y. enterocolitica that is controlled by PypB and that pypB is part of this operon. The tad genes encode functions necessary for the biogenesis of the Flp subfamily of type IVb pili initially described for Aggregatibacter actinomycetemcomitans to mediate a tight-adherence phenotype. In Y. enterocolitica, the Flp pilin protein shows some peculiarities in its amino acid sequence that imply similarities as well as differences compared to typical motifs found in the Flp subtype of type IVb pili. Flp is expressed and processed after PypB overproduction, resulting in microcolony formation but not in increased adherence to biotic or abiotic surfaces. Our data describe the transcriptional regulation of the tad type IVb pilus operon by PypB in Y. enterocolitica but fail to show most previously described phenotypes associated with this type of pilus in other bacteria.

Nonspecific Adherence by Actinobacillus actinomycetemcomitans Requires Genes Widespread in Bacteria and Archaea

PubMed Central

Kachlany, Scott C.; Planet, Paul J.; Bhattacharjee, Mrinal K.; Kollia, Evyenia; DeSalle, Rob; Fine, Daniel H.; Figurski, David H.

2000-01-01

The gram-negative coccobacillus, Actinobacillus actinomycetemcomitans, is the putative agent for localized juvenile periodontitis, a particularly destructive form of periodontal disease in adolescents. This bacterium has also been isolated from a variety of other infections, notably endocarditis. Fresh clinical isolates of A. actinomycetemcomitans form tenacious biofilms, a property likely to be critical for colonization of teeth and other surfaces. Here we report the identification of a locus of seven genes required for nonspecific adherence of A. actinomycetemcomitans to surfaces. The recently developed transposon IS903φkan was used to isolate mutants of the rough clinical isolate CU1000 that are defective in tight adherence to surfaces (Tad−). Unlike wild-type cells, Tad− mutant cells adhere poorly to surfaces, fail to form large autoaggregates, and lack long, bundled fibrils. Nucleotide sequencing and genetic complementation analysis revealed a 6.7-kb region of the genome with seven adjacent genes (tadABCDEFG) required for tight adherence. The predicted TadA polypeptide is similar to VirB11, an ATPase involved in macromolecular transport. The predicted amino acid sequences of the other Tad polypeptides indicate membrane localization but no obvious functions. We suggest that the tad genes are involved in secretion of factors required for tight adherence of A. actinomycetemcomitans. Remarkably, complete and highly conserved tad gene clusters are present in the genomes of the bubonic plague bacillus Yersinia pestis and the human and animal pathogen Pasteurella multocida. Partial tad loci also occur in strikingly diverse Bacteria and Archaea. Our results show that the tad genes are required for tight adherence of A. actinomycetemcomitans to surfaces and are therefore likely to be essential for colonization and pathogenesis. The occurrence of similar genes in a wide array of microorganisms indicates that they have important functions. We propose that tad-like genes have a significant role in microbial colonization. PMID:11029439

An in silico approach to investigate the source of the controversial interpretations about the phenotypic results of the human AhR-gene G1661A polymorphism.

PubMed

Aftabi, Younes; Colagar, Abasalt Hosseinzadeh; Mehrnejad, Faramarz

2016-03-21

Aryl hydrocarbon receptor (AhR) acts as an enhancer binding ligand-activated intracellular receptor. Chromatin remodeling components and general transcription factors such as TATA-binding protein (TBP) are evoked on AhR-target genes by interaction with its flexible transactivation domain (TAD). AhR-G1661A single nucleotide polymorphism (SNP: rs2066853) causes an arginine to lysine substitution in the acidic sub-domain of TAD at position 554 (R554K). Although, numerous studies associate the SNP with some abnormalities such as cancer, other reliable investigations refuse the associations. Consequently, the interpretation of the phenotypic results of G1661A-transition has been controversial. In this study, an in silico analysis were performed to investigate the possible effects of the transition on AhR-mRNA, protein structure, interaction properties and modifications. The analysis revealed that the R554K substitution affects secondary structure and solvent accessibility of adjacent residues. Also, it causes to decreasing of the AhR stability; altering the hydropathy features of the local sequence and changing the pattern of the residues at the binding site of the TAD-acidic sub-domain. Generating of new sites for ubiquitination and acetylation for AhR-K554 variant respectively at positions 544 and 560 was predicted. Our findings intensify the idea that the AhR-G1661A transition may affects AhR-TAD interactions, especially with the TBP, which influence AhR-target genes expression. However, the previously reported flexibility of the modular TAD could act as an intervening factor, moderate the SNP effects and causes distinct outcomes in different individuals and tissues. Copyright © 2016 Elsevier Ltd. All rights reserved.

Eradication of Transboundary Animal Diseases: Can the Rinderpest Success Story be Repeated?

PubMed

Thomson, G R; Penrith, M-L

2017-04-01

A matrix system was developed to aid in the evaluation of the technical amenability to eradication, through mass vaccination, of transboundary animal diseases (TADs). The system involved evaluation of three basic criteria - disease management efficiency, surveillance and epidemiological factors - each in turn comprised of a number of elements (17 in all). On that basis, 25 TADs that have occurred or do occur in southern Africa and for which vaccines are available, in addition to rinderpest (incorporated as a yardstick because it has been eradicated worldwide), were ranked. Cluster analysis was also applied using the same criteria to the 26 diseases, creating division into three groups. One cluster contained only diseases transmitted by arthropods (e.g. African horse sickness and Rift Valley fever) and considered difficult to eradicate because technologies for managing parasitic arthropods on a large scale are unavailable, while a second cluster contained diseases that have been widely considered to be eradicable [rinderpest, canine rabies, the Eurasian serotypes of foot and mouth disease virus (O, A, C & Asia 1) and peste des petits ruminants] as well classical swine fever, Newcastle disease and lumpy skin disease. The third cluster contained all the other TADs evaluated with the implication that these constitute TADs that would be more difficult to eradicate. However, it is acknowledged that the scores assigned in the course of this study may be biased. The point is that the system proposed offers an objective method for assessment of the technical eradicability of TADs; the rankings and groupings derived during this study are less important than the provision of a systematic approach for further development and evaluation. © 2015 Blackwell Verlag GmbH.

Acid additives enhancing the conductivity of spiro-OMeTAD toward high-efficiency and hysteresis-less planar perovskite solar cells

DOE PAGES

Li, Zhen; Tinkham, Jonathan; Schulz, Philip; ...

2016-10-28

A general doping strategy, using a wide range of acids with different p K a values as additive, is demonstrated to enhance the conductivity of spiro-OMeTAD, the dominant hole transport material in perovskite solar cells (PSCs). Here, hysteresis-less planar PSCs with ≈19% efficiency and better open-circuit voltage and fill factor is achieved with acid doped spiro-OMeTAD.

LncRNA Expression Profile of Human Thoracic Aortic Dissection by High-Throughput Sequencing.

PubMed

Sun, Jie; Chen, Guojun; Jing, Yuanwen; He, Xiang; Dong, Jianting; Zheng, Junmeng; Zou, Meisheng; Li, Hairui; Wang, Shifei; Sun, Yili; Liao, Wangjun; Liao, Yulin; Feng, Li; Bin, Jianping

2018-01-01

In this study, the long non-coding RNA (lncRNA) expression profile in human thoracic aortic dissection (TAD), a highly lethal cardiovascular disease, was investigated. Human TAD (n=3) and normal aortic tissues (NA) (n=3) were examined by high-throughput sequencing. Bioinformatics analyses were performed to predict the roles of aberrantly expressed lncRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to validate the results. A total of 269 lncRNAs (159 up-regulated and 110 down-regulated) and 2, 255 mRNAs (1 294 up-regulated and 961 down-regulated) were aberrantly expressed in human TAD (fold-change> 1.5, P< 0.05). QRT-PCR results of five dysregulated genes were consistent with HTS data. A lncRNA-mRNA coexpression analysis showed positive correlations between the up-regulated lncRNA (ENSG00000269936) and its adjacent up-regulated mRNA (MAP2K6, R=0.940, P< 0.01), and between the down-regulated lncRNA_1421 and its down-regulated mRNAs (FBLN5, R=0.950, P< 0.01; ACTA2, R=0.96, P< 0.01; TIMP3, R=0.96, P< 0.05). The lncRNA-miRNA-mRNA network indicated that the up-regulated lncRNA XIST and p21 had similar sequences targeted by has-miR-17-5p. The results of luciferase assay and fluorescence immuno-cytochemistry were consistent with that. And qRT-PCR results showed that lncRNA XIST and p21 were expressed at a higher level and has-miR-17-5p was expressed at a lower level in TAD than in NA. The predicted binding motifs of three up-regulated lncRNAs (ENSG00000248508, ENSG00000226530, and EG00000259719) were correlated with up-regulated RUNX1 (R=0.982, P< 0.001; R=0.967, P< 0.01; R=0.960, P< 0.01, respectively). Our study revealed a set of dysregulated lncRNAs and predicted their multiple potential functions in human TAD. These findings suggest that lncRNAs are novel potential therapeutic targets for human TAD. © 2018 The Author(s). Published by S. Karger AG, Basel.

Large-scale traveling atmospheric disturbances (LSTADs) in the thermosphere inferred from CHAMP, GRACE, and SETA accelerometer data

NASA Astrophysics Data System (ADS)

Bruinsma, Sean L.; Forbes, Jeffrey M.

2010-08-01

Densities derived from accelerometer measurements on the GRACE, CHAMP, and Air Force/SETA satellites near 490, 390, and 220 km, respectively, are used to elucidate global-scale characteristics of traveling atmospheric disturbances (TADs). Several characteristics elucidated in numerical simulations are confirmed in this study, namely: (1) propagation speeds increase from the lower thermosphere to the upper thermosphere; (2) propagation to the equator and even into the opposite hemisphere can occur; (3) greater attenuation of TADs occurs during daytime and at higher levels of solar activity (i.e., more wave activity during nighttime and solar minimum), presumably due to the greater influence of ion drag. In addition, we find that the occurrence of significant TAD activity emanating from the auroral regions does not reflect a clear relation with the level of planetary magnetic activity as measured by Kp. There is also evidence of waves originating in the tropics, presumably due to convective sources; to some extent this may contribute to the Kp and solar flux relationships noted above. Further elucidation of local time, season, and altitude dependences of TAD propagation characteristics may be forthcoming from density measurements from the GOCE and Swarm missions.

Mortality impact of thoracic aortic disease in São Paulo state from 1998 to 2007

PubMed Central

Dias, Ricardo Ribeiro; Mejia, Omar Asdrubal Vilca; Fernandes, Fábio; Ramires, Félix José Alvarez; Mady, Charles; Stolf, Noedir Antonio Groppo; Jatene, Fabio Biscegli

2013-01-01

Background The epidemiological characteristics of thoracic aortic diseases (TAD) in the State of São Paulo and in Brazil, as well as their impact on the survival of these patients have yet to be analyzed. Objectives To evaluate the mortality impact of TAD and characterize it epidemiologically. Methods Retrospective analysis of data from the public health system for the TAD registry codes of hospitalizations, procedures and deaths, from the International Code of Diseases (ICD-10), registered at the Ministry of Health of São Paulo State from January 1998 to December 2007. Results They were 9.465 TAD deaths, 5.500 men (58.1%) and 3.965 women (41.9%); 6.721 dissections (71%) and 2.744. aneurysms. In 86.3% of cases the diagnosis was attained during autopsy. There were 6.109 hospitalizations, of which 67.9% were males; 21.2% of them died (69% men), with similar proportions of dissection and aneurysm between sexes, respectively 54% and 46%, but with different mortality. Men with TAD die more often than women (OR = 1.5). The age distribution for deaths and hospitalizations was similar with predominance in the 6th decade. They were 3.572 surgeries (58% of hospitalizations) with 20.3% mortality (patients kept in clinical treatment showed 22.6% mortality; p = 0.047). The number of hospitalizations, surgeries, deaths of in-patients and general deaths by TAD were progressively greater than the increase in population over time. Conclusions Specific actions for the early identification of these patients, as well as the viability of their care should be implemented to reduce the apparent progressive mortality from TAD seen among our population. PMID:24100695

Regulatory variants of FOXG1 in the context of its topological domain organisation.

PubMed

Mehrjouy, Mana M; Fonseca, Ana Carolina S; Ehmke, Nadja; Paskulin, Giorgio; Novelli, Antonio; Benedicenti, Francesco; Mencarelli, Maria Antonietta; Renieri, Alessandra; Busa, Tiffany; Missirian, Chantal; Hansen, Claus; Abe, Kikue Terada; Speck-Martins, Carlos Eduardo; Vianna-Morgante, Angela M; Bak, Mads; Tommerup, Niels

2018-02-01

FOXG1 syndrome is caused by FOXG1 intragenic point mutations, or by long-range position effects (LRPE) of intergenic structural variants. However, the size of the FOXG1 regulatory landscape is uncertain, because the associated topologically associating domain (TAD) in fibroblasts is split into two domains in embryonic stem cells (hESC). Indeed, it has been suggested that the pathogenetic mechanism of deletions that remove the stem-cell-specific TAD boundary may be enhancer adoption due to ectopic activity of enhancer(s) located in the distal hESC-TAD. Herein we map three de novo translocation breakpoints to the proximal regulatory domain of FOXG1. The classical FOXG1 syndrome in these and in other translocation patients, and in a patient with an intergenic deletion that removes the hESC-specific TAD boundary, do not support the hypothesised enhancer adoption as a main contributor to the FOXG1 syndrome. Also, virtual 4 C and HiC-interaction data suggest that the hESC-specific TAD boundary may not be critical for FOXG1 regulation in a majority of human cells and tissues, including brain tissues and a neuronal progenitor cell line. Our data support the importance of a critical regulatory region (SRO) proximal to the hESC-specific TAD boundary. We further narrow this critical region by a deletion distal to the hESC-specific boundary, associated with a milder clinical phenotype. The distance from FOXG1 to the SRO ( > 500 kb) highlight a limitation of ENCODE DNase hypersensitivity data for functional prediction of LRPE. Moreover, the SRO has little overlap with a cluster of frequently associating regions (FIREs) located in the proximal hESC-TAD.

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

Tranter, P.

Tender-assisted drilling (TAD) involves the use of tender support vessel (TSV) during the drilling phase of platform development to provide drilling utilities to the platform-mounted drilling package. The TSV provides facilities such as mud mixing, storage, pumping, bulk storage, hotel accommodations, and power. Thus, the platform topsides and jacket weight and size can be smaller and less expensive. The paper discusses the advantages and disadvantages of TAD, then describes the TAD vessel, semisubmersible, platform cost savings, accommodations, drilling and workovers, and field experience.

Definition of Throw-Away Detectors (TADs) and VLF antenna for the AMPS laboratory

NASA Technical Reports Server (NTRS)

Koons, H. C.; Fennell, J. F.

1975-01-01

A Throw Away Detector (TAD)/subsatellite to be used as an experiment platform for the test flights to map the EMI from the shuttle and during the AMPS science flights is defined. A range of instrument platforms of varying capabilities is examined with emphasis on the EMI test vehicle. The operational support requirements of TAD/subsatellites are determined. The throw away detector is envisioned as a simple instrument package for supporting specific experiments.

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits.

PubMed

Wang, Min; Hancock, Timothy P; Chamberlain, Amanda J; Vander Jagt, Christy J; Pryce, Jennie E; Cocks, Benjamin G; Goddard, Mike E; Hayes, Benjamin J

2018-05-24

Topological association domains (TADs) are chromosomal domains characterised by frequent internal DNA-DNA interactions. The transcription factor CTCF binds to conserved DNA sequence patterns called CTCF binding motifs to either prohibit or facilitate chromosomal interactions. TADs and CTCF binding motifs control gene expression, but they are not yet well defined in the bovine genome. In this paper, we sought to improve the annotation of bovine TADs and CTCF binding motifs, and assess whether the new annotation can reduce the search space for cis-regulatory variants. We used genomic synteny to map TADs and CTCF binding motifs from humans, mice, dogs and macaques to the bovine genome. We found that our mapped TADs exhibited the same hallmark properties of those sourced from experimental data, such as housekeeping genes, transfer RNA genes, CTCF binding motifs, short interspersed elements, H3K4me3 and H3K27ac. We showed that runs of genes with the same pattern of allele-specific expression (ASE) (either favouring paternal or maternal allele) were often located in the same TAD or between the same conserved CTCF binding motifs. Analyses of variance showed that when averaged across all bovine tissues tested, TADs explained 14% of ASE variation (standard deviation, SD: 0.056), while CTCF explained 27% (SD: 0.078). Furthermore, we showed that the quantitative trait loci (QTLs) associated with gene expression variation (eQTLs) or ASE variation (aseQTLs), which were identified from mRNA transcripts from 141 lactating cows' white blood and milk cells, were highly enriched at putative bovine CTCF binding motifs. The linearly-furthermost, and most-significant aseQTL and eQTL for each genic target were located within the same TAD as the gene more often than expected (Chi-Squared test P-value < 0.001). Our results suggest that genomic synteny can be used to functionally annotate conserved transcriptional components, and provides a tool to reduce the search space for causative regulatory variants in the bovine genome.

Concomitant Phosphodiesterase 5 Inhibition Enhances Myocardial Protection by Inhaled Nitric Oxide in Ischemia-Reperfusion Injury.

PubMed

Lux, Arpad; Pokreisz, Peter; Swinnen, Melissa; Caluwe, Ellen; Gillijns, Hilde; Szelid, Zsolt; Merkely, Bela; Janssens, Stefan P

2016-02-01

Enhanced cyclic guanosine monophosphate (cGMP) signaling may attenuate myocardial ischemia-reperfusion injury (I/R) and improve left ventricular (LV) functional recovery after myocardial infarction (MI). We investigated the cardioprotection afforded by inhaled NO (iNO), the phosphodiesterase 5 (PDE5)-specific inhibitor tadalafil (TAD), or their combination (iNO+TAD) in C57Bl6J mice subjected to 6-minute left anterior descending artery ligation followed by reperfusion. We measured plasma and cardiac concentrations of cGMP during early reperfusion, quantified myocardial necrosis and inflammation by serial troponin-I (TnI) and myeloperoxidase-positive cell infiltration at day 3, and evaluated LV function and remodeling after 4 weeks using echocardiography and pressure-conductance catheterization. Administration of iNO, TAD, or both during I/R was safe and hemodynamically well tolerated. Compared with untreated mice (CON), only iNO+TAD increased plasma and cardiac-cGMP levels during early reperfusion (80 ± 12 versus 36 ± 6 pmol/ml and 0.15 ± 0.02 versus 0.05 ± 0.01 pmol/mg protein, P < 0.05 for both). Moreover, iNO+TAD reduced TnI at 4 hours to a greater extent (P < 0.001 versus CON) than either alone (P < 0.05 versus CON) and was associated with significantly less myocardial inflammatory cell infiltration at day 3. After 4 weeks and compared with CON, iNO+TAD was associated with increased fractional shortening (43 ± 1 versus 33 ± 2%, P < 0.01), larger stroke volumes (14.9 ± 1.2 versus 10.2 ± 0.9 μl, P < 0.05), enhanced septal and posterior wall thickening (P < 0.05 and P < 0.001, respectively), and attenuated LV dilatation (P < 0.001), whereas iNO or TAD alone conferred less benefit. Thus, iNO+TAD has superior efficacy to limit early reperfusion injury and attenuate adverse LV remodeling. Combination of inhaled NO with a long-acting PDE5 inhibitor may represent a promising strategy to reduce ischemic damage following reperfusion and better preserve LV function. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

Comparison of protocols for measuring and calculating postmortem submersion intervals for human analogs in fresh water.

PubMed

Humphreys, Michael K; Panacek, Edward; Green, William; Albers, Elizabeth

2013-03-01

Protocols for determining postmortem submersion interval (PMSI) have long been problematic for forensic investigators due to the wide variety of factors affecting the rate of decomposition of submerged carrion. Likewise, it has been equally problematic for researchers to develop standardized experimental protocols to monitor underwater decomposition without artificially affecting the decomposition rate. This study compares two experimental protocols: (i) underwater in situ evaluation with photographic documentation utilizing the Heaton et al. total aquatic decomposition (TAD) score and (ii) weighing the carrion before and after submersion. Complete forensic necropsies were performed as a control. Perinatal piglets were used as human analogs. The results of this study indicate that in order to objectively measure decomposition over time, the human analog should be examined at depth using the TAD scoring system rather than utilizing a carrion weight evaluation. The acquired TAD score can be used to calculate an approximate PMSI. © 2012 American Academy of Forensic Sciences.

More than a Tad: spatiotemporal control of Caulobacter pili.

PubMed

Mignolet, Johann; Panis, Gaël; Viollier, Patrick H

2018-04-01

The Type IV pilus (T4P) is a powerful and sophisticated bacterial nanomachine involved in numerous cellular processes, including adhesion, DNA uptake and motility. Aside from the well-described subtype T4aP of the Gram-negative genera, including Myxococcus, Pseudomonas and Neisseria, the Tad (tight adherence) pilus secretion system re-shuffles homologous parts from other secretion systems along with uncharacterized components into a new type of protein translocation apparatus. A representative of the Tad apparatus, the Caulobacter crescentus pilus assembly (Cpa) machine is built exclusively at the newborn cell pole once per cell cycle. Recent comprehensive genetic analyses unearthed a myriad of spatiotemporal determinants acting on the Tad/Cpa system, many of which are conserved in other α-proteobacteria, including obligate intracellular pathogens and symbionts. Copyright © 2017 Elsevier Ltd. All rights reserved.

Adjustments of the TaD electron density reconstruction model with GNSS-TEC parameters for operational application purposes

NASA Astrophysics Data System (ADS)

Kutiev, Ivan; Marinov, Pencho; Fidanova, Stefka; Belehaki, Anna; Tsagouri, Ioanna

2012-12-01

Validation results on the latest version of TaD model (TaDv2) show realistic reconstruction of the electron density profiles (EDPs) with an average error of 3 TECU, similar to the error obtained from GNSS-TEC calculated paremeters. The work presented here has the aim to further improve the accuracy of the TaD topside reconstruction, adjusting the TEC parameter calculated from TaD model with the TEC parameter calculated by GNSS transmitting RINEX files provided by receivers co-located with the Digisondes. The performance of the new version is tested during a storm period demonstrating further improvements in respect to the previous version. Statistical comparison of modeled and observed TEC confirms the validity of the proposed adjustment. A significant benefit of the proposed upgrade is that it facilitates the real-time implementation of TaD. The model needs a reliable measure of the scale height at the peak height, which is supposed to be provided by Digisondes. Oftenly, the automatic scaling software fails to correctly calculate the scale height at the peak, Hm, due to interferences in the receiving signal. Consequently the model estimated topside scale height is wrongly calculated leading to unrealistic results for the modeled EDP. The proposed TEC adjustment forces the model to correctly reproduce the topside scale height, despite the inaccurate values of Hm. This adjustment is very important for the application of TaD in an operational environment.

Expression, fermentation and purification of a predicted intrinsically disordered region of the transcription factor, NFAT5.

PubMed

DuMond, Jenna F; He, Yi; Burg, Maurice B; Ferraris, Joan D

2015-11-01

Hypertonicity stimulates Nuclear Factor of Activated T-cells 5 (NFAT5) nuclear localization and transactivating activity. Many transcription factors are known to contain intrinsically disordered regions (IDRs) which become more structured with local environmental changes such as osmolality, temperature and tonicity. The transactivating domain of NFAT5 is predicted to be intrinsically disordered under normal tonicity, and under high NaCl, the activity of this domain is increased. To study the binding of co-regulatory proteins at IDRs a cDNA construct expressing the NFAT5 TAD was created and transformed into Escherichia coli cells. Transformed E. coli cells were mass produced by fermentation and extracted by cell lysis to release the NFAT5 TAD. The NFAT5 TAD was subsequently purified using a His-tag column, cation exchange chromatography as well as hydrophobic interaction chromatography and then characterized by mass spectrometry (MS). Published by Elsevier Inc.

Nitrogen removal characteristics analyzed with gas and microbial community in thermophilic aerobic digestion for piggery waste treatment.

PubMed

Lee, J W; Lee, H W; Kim, S W; Lee, S Y; Park, Y K; Han, J H; Choi, S I; Yi, Y S; Yun, Z

2004-01-01

In order to characterize the nitrogen conversion characteristics in a thermophilic aerobic digestion (TAD) system, a laboratory study has been conducted with the analysis of effluent gas and microbial community in the sludge samples. The lab TAD system was operated with HRT of 3 days and 60 degrees C. Based on the nitrogen mass balance, it has been found that about 2/3 of the daily load of nitrogen was converted to the gaseous form of nitrogen whereas cellular transformation and unmetabolized nitrogen accounted for about 1/3. Among the gaseous nitrogen transformation, significant amount of influent nitrogen had been converted to N2 gas (29% of influent N) and N2O (9% of influent N). Ammonia conversion was only 28% of influent N. The detection of N2O gas is a clear indication of the biological nitrogen reduction process in the thermophilic aerobic digester. No conclusive evidence for the existence of aerobic deammonification has been found. The microbial community analysis showed that thermophilic bacteria such as Bacillus thermocloacae, Bacillus sp. and Clostridial groups dominated in this TAD reactor. The diverse microbial community in TAD sludge may play an important role in removing both strong organics and nitrogen from piggery waste.

Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains.

PubMed

Tiana, Guido; Amitai, Assaf; Pollex, Tim; Piolot, Tristan; Holcman, David; Heard, Edith; Giorgetti, Luca

2016-03-29

Experiments based on chromosome conformation capture have shown that mammalian genomes are partitioned into topologically associating domains (TADs), within which the chromatin fiber preferentially interacts. TADs may provide three-dimensional scaffolds allowing genes to contact their appropriate distal regulatory DNA sequences (e.g., enhancers) and thus to be properly regulated. Understanding the cell-to-cell and temporal variability of the chromatin fiber within TADs, and what determines them, is thus of great importance to better understand transcriptional regulation. We recently described an equilibrium polymer model that can accurately predict cell-to-cell variation of chromosome conformation within single TADs, from chromosome conformation capture-based data. Here we further analyze the conformational and energetic properties of our model. We show that the chromatin fiber within TADs can easily fluctuate between several conformational states, which are hierarchically organized and are not separated by important free energy barriers, and that this is facilitated by the fact that the chromatin fiber within TADs is close to the onset of the coil-globule transition. We further show that in this dynamic state the properties of the chromatin fiber, and its contact probabilities in particular, are determined in a nontrivial manner not only by site-specific interactions between strongly interacting loci along the fiber, but also by nonlocal correlations between pairs of contacts. Finally, we use live-cell experiments to measure the dynamics of the chromatin fiber in mouse embryonic stem cells, in combination with dynamical simulations, and predict that conformational changes within one TAD are likely to occur on timescales that are much shorter than the duration of one cell cycle. This suggests that genes and their regulatory elements may come together and disassociate several times during a cell cycle. These results have important implications for transcriptional regulation as they support the concept of highly dynamic interactions driven by a complex interplay between site-specific interactions and the intrinsic biophysical properties of the chromatin fiber. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Understanding the synthesis, performance, and passivation of metal oxide photocathodes

NASA Astrophysics Data System (ADS)

Flynn, Cory James

Metal oxides are ubiquitous in semiconductor technologies for their ease of synthesis, chemical stability, and tunable optical/electronic properties. These properties are especially important to fabricating efficient photoelectrodes for solar-energy applications. To counter inherent problems in these materials, new strategies were developed and successfully implemented on the widely-utilized p-type semiconductor, NiO. As the size of semiconductor materials shrink, the surface-to-volume ratio increases and surface defects dominate the performance of the materials. Surface defects can alter the optical and electronic characteristics of materials by changing the Fermi level, charge-carrier mobility, and surface reactivity. We first present a strategy to increase the electrical mobility of mesoporous metal oxide electrode materials by optimizing shape morphology. Transitioning from nanospheres to hexagonal nanoplatelets increased the charge-carrier mobility by one order of magnitude. We then employed this improved material with a new vapor-phase deposition method termed targeted atomic deposition (TAD) to selectively passivate defect sites in semiconductor nanomaterials. We demonstrated the capabilities of this passivation method by applying a TAD of aluminum onto NiO. By exploiting a temperature-dependent deposition process, we selectively passivated the highly reactive sites in NiO: oxygen dangling bonds associated with Ni vacancies. The TAD treatment completely passivated all measurable surface defects, optically bleached the material, and significantly improved all photovoltaic performance metrics in dye-sensitized solar cells. The technique was proven to be generic to numerous forms of NiO. While the implementation of TAD of Al was successful, the process involved pulsing two precursors to passivate the material. Ideally, the TAD process should require only a single precursor and continuous exposure. We utilized a continuous flow of diborane to perform a TAD of B onto NiO. The TAD process was successfully implemented in a simplified manner. The treatment moderately increased DSSC performance and proved viability with a different vapor-phase precursor.

A Randomized Controlled Trial Comparing the Letter Project Advance Directive to Traditional Advance Directive.

PubMed

Periyakoil, Vyjeyanthi S; Neri, Eric; Kraemer, Helena

2017-09-01

Simpler alternatives to traditional advance directives that are easy to understand and available in multiple formats and can be initiated by patients and families will help facilitate advance care planning. The goal of this study was to compare the acceptability of the letter advance directive (LAD) to the traditional advance directive (TAD) of the state of California. A web-based, randomized controlled trial was conducted, in which the participants were randomized to one of two types of advance directives (ADs): the LAD (intervention) or the TAD (control). Primary outcomes were participant ratings of the ease, value, and their level of comfort in the AD document they completed. A total of 400 participants completed the study, with 216 randomized to the LAD and 184 to the TAD by a computerized algorithm. Overall, participants preferred the LAD to the TAD (success rate difference [SRD] = 0.46, 95th percentile confidence interval [CI]: 0.36-0.56, p < 0.001). The participants felt that, compared to the TAD, the LAD was easier to read and understand (SRD = 0.56, CI: 0.47-0.65, p < 0.001); better reflected what matters most to them (SRD = 0.39, CI: 0.29-0.48, p < 0.001); helped stimulate their thinking about the types of treatments they wanted at the end of life (SRD = 0.32, CI: 0.23-0.42, p < 0.001); allowed them to describe how they made medical decisions in their family (SRD = 0.31, CI: 0.21-0.40, p < 0.001); and could help their doctor(s) (SRD = 0.24, CI: 0.13-0.34, p < 0.001) and their families (SRD = 0.19, CI: 0.08-0.28, p < 0.001) understand their end-of-life treatment preferences. Patients reported the letter advance directive to be a better alternative to the traditional advance directive form.

77 FR 2716 - Questar Pipeline Company; Notice of Application

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-19

[email protected] , or to Tad M. Taylor, Division Counsel, Questar Pipeline Company, 180 East 100 South, P.O. Box 45360, Salt Lake City, Utah 84145-0360, or by calling (801) 324-5531 (telephone) tad.taylor...

Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods?

PubMed

Nora, Elphège P; Dekker, Job; Heard, Edith

2013-09-01

We discuss here a series of testable hypotheses concerning the role of chromosome folding into topologically associating domains (TADs). Several lines of evidence suggest that segmental packaging of chromosomal neighborhoods may underlie features of chromatin that span large domains, such as heterochromatin blocks, association with the nuclear lamina and replication timing. By defining which DNA elements preferentially contact each other, the segmentation of chromosomes into TADs may also underlie many properties of long-range transcriptional regulation. Several observations suggest that TADs can indeed provide a structural basis to regulatory landscapes, by controlling enhancer sharing and allocation. We also discuss how TADs may shape the evolution of chromosomes, by causing maintenance of synteny over large chromosomal segments. Finally we suggest a series of experiments to challenge these ideas and provide concrete examples illustrating how they could be practically applied. © 2013 The Authors. Bioessays published by WILEY Periodicals, Inc.

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

PubMed Central

Nora, Elphège P; Dekker, Job; Heard, Edith

2013-01-01

We discuss here a series of testable hypotheses concerning the role of chromosome folding into topologically associating domains (TADs). Several lines of evidence suggest that segmental packaging of chromosomal neighborhoods may underlie features of chromatin that span large domains, such as heterochromatin blocks, association with the nuclear lamina and replication timing. By defining which DNA elements preferentially contact each other, the segmentation of chromosomes into TADs may also underlie many properties of long-range transcriptional regulation. Several observations suggest that TADs can indeed provide a structural basis to regulatory landscapes, by controlling enhancer sharing and allocation. We also discuss how TADs may shape the evolution of chromosomes, by causing maintenance of synteny over large chromosomal segments. Finally we suggest a series of experiments to challenge these ideas and provide concrete examples illustrating how they could be practically applied. PMID:23832846

Reversible TAD Chemistry as a Convenient Tool for the Design of (Re)processable PCL-Based Shape-Memory Materials.

PubMed

Defize, Thomas; Riva, Raphaël; Thomassin, Jean-Michel; Alexandre, Michaël; Herck, Niels Van; Prez, Filip Du; Jérôme, Christine

2017-01-01

A chemically cross-linked but remarkably (re)processable shape-memory polymer (SMP) is designed by cross-linking poly(ε-caprolactone) (PCL) stars via the efficient triazolinedione click chemistry, based on the very fast and reversible Alder-ene reaction of 1,2,4-triazoline-3,5-dione (TAD) with indole compounds. Typically, a six-arm star-shaped PCL functionalized by indole moieties at the chain ends is melt-blended with a bisfunctional TAD, directly resulting in a cross-linked PCL-based SMP without the need of post-curing treatment. As demonstrated by the stress relaxation measurement, the labile character of the TAD-indole adducts under stress allows for the solid-state plasticity reprocessing of the permanent shape at will by compression molding of the raw cross-linked material, while keeping excellent shape-memory properties. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cryptochrome 1 regulates the circadian clock through dynamic interactions with the BMAL1 C-terminus

PubMed Central

Sammons, Patrick J.; Khan, Sanjoy K.; Parsley, Nicole C.; Ramanathan, Chidambaram; Lee, Hsiau-Wei; Liu, Andrew C.; Partch, Carrie L.

2015-01-01

The molecular circadian clock in mammals is generated from transcriptional activation by the bHLH-PAS transcription factor CLOCK–BMAL1 and subsequent repression by PERIOD and CRYPTOCHROME (CRY). The mechanism by which CRYs repress CLOCK–BMAL1 to close the negative feedback loop and generate 24-hour timing is not known. Here we show that CRY1 competes for binding with coactivators to the intrinsically unstructured C-terminal transactivation domain (TAD) of BMAL1 to establish a functional switch between activation and repression of CLOCK–BMAL1. Mutations within the TAD that alter affinities for coregulators change the balance of repression and activation to consequently change intrinsic circadian period or eliminate cycling altogether. Our results suggest that CRY1 fulfills its role as an essential circadian repressor by sequestering the TAD from coactivators and highlight regulation of the BMAL1 TAD as a critical mechanism for establishing circadian timing. PMID:25961797

Cavernous neurotomy in the rat is associated with the onset of an overt condition of hypogonadism.

PubMed

Vignozzi, Linda; Filippi, Sandra; Morelli, Annamaria; Marini, Mirca; Chavalmane, Aravinda; Fibbi, Benedetta; Silvestrini, Enrico; Mancina, Rosa; Carini, Marco; Vannelli, G Barbara; Forti, Gianni; Maggi, Mario

2009-05-01

Most men following radical retropubic prostatectomy (RRP) are afflicted by erectile dysfunction (ED). RRP-related ED occurs as a result of surgically elicited neuropraxia, leading to histological changes in the penis, including collagenization of smooth muscle and endothelial damage. To verify whether hypogonadism could contribute to the pathogenesis of RRP-ED. Effects of testosterone (T), alone or in association with long-term tadalafil (Tad) treatment in a rat model of bilateral cavernous neurotomy (BCN). Penile tissues from rats were harvested for vasoreactivity studies 3 months post-BCN. Penile oxygenation was evaluated by hypoxyprobe immunostaining. Phosphodiesterase type 5 (PDE5), endothelial nitric oxide synthase (eNOS), and neuronal nitric oxide synthase (nNOS) mRNA expression were quantified by Real Time quantitative reverse transcription polymerase chain reaction (qRT-PCR). In BCN rats, we observed the onset of an overt condition of hypogonadism, characterized by reduced T plasma level, reduced ventral prostate weight, reduced testis function (including testis weight and number of Leydig cells), with an inadequate compensatory increase of luteinizing hormone. BCN induced massive penile hypoxia, decreased muscle/fiber ratio, nNOS, eNOS, PDE5 expression, increased sensitivity to the nitric oxide donor, sodium nitroprusside (SNP), and reduced the relaxant response to acetylcholine (Ach), as well as unresponsiveness to acute Tad dosing. In BCN rats, chronic Tad-administration normalizes penile oxygenation, smooth muscle loss, PDE5 expression, SNP sensitivity, and the responsiveness to the acute Tad administration. Chronic Tad treatment was ineffective in counteracting the reduction of nNOS and eNOS expression, along with Ach responsiveness. T supplementation, in combination with Tad, reverted some of the aforementioned alterations, restoring smooth muscle content, eNOS expression, as well as the relaxant response of penile strips to Ach, but not nNOS expression. BCN was associated with hypogonadism, probably of central origin. T supplementation in hypogonadal BCN rats ameliorates some aspects of BCN-induced ED, including collagenization of penile smooth muscle and endothelial dysfunction, except surgically induced altered nNOS expression.

Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.

PubMed

Glinsky, Gennadi V

2018-03-01

Transposable elements have made major evolutionary impacts on creation of primate-specific and human-specific genomic regulatory loci and species-specific genomic regulatory networks (GRNs). Molecular and genetic definitions of human-specific changes to GRNs contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically associating domains (TADs) that are significantly enriched for HSGRL and designated rapidly evolving in human TADs. Here, the analysis of HSGRL, hESC-enriched enhancers, super-enhancers (SEs), and specific sub-TAD structures termed super-enhancer domains (SEDs) has been performed. In the hESC genome, 331 of 504 (66%) of SED-harboring TADs contain HSGRL and 68% of SEDs co-localize with HSGRL, suggesting that emergence of HSGRL may have rewired SED-associated GRNs within specific TADs by inserting novel and/or erasing existing non-coding regulatory sequences. Consequently, markedly distinct features of the principal regulatory structures of interphase chromatin evolved in the hESC genome compared to mouse: the SED quantity is 3-fold higher and the median SED size is significantly larger. Concomitantly, the overall TAD quantity is increased by 42% while the median TAD size is significantly decreased (p = 9.11E-37) in the hESC genome. Present analyses illustrate a putative global role for transposable elements and HSGRL in shaping the human-specific features of the interphase chromatin organization and functions, which are facilitated by accelerated creation of novel transcription factor binding sites and new enhancers driven by targeted placement of HSGRL at defined genomic coordinates. A trend toward the convergence of TAD and SED architectures of interphase chromatin in the hESC genome may reflect changes of 3D-folding patterns of linear chromatin fibers designed to enhance both regulatory complexity and functional precision of GRNs by creating predominantly a single gene (or a set of functionally linked genes) per regulatory domain structures. Collectively, present analyses reveal critical evolutionary contributions of transposable elements and distal enhancers to creation of thousands primate- and human-specific elements of a chromatin folding code, which defines the 3D context of interphase chromatin both restricting and facilitating biological functions of GRNs.

Increased levels of interleukin-22 in thoracic aorta and plasma from patients with acute thoracic aortic dissection.

PubMed

Ye, Jing; Wang, Menglong; Jiang, Huimin; Ji, Qingwei; Huang, Ying; Liu, Jianfang; Zeng, Tao; Xu, Yao; Wang, Zhen; Lin, Yingzhong; Wan, Jun

2017-11-03

Interleukin (IL)-22 plays important roles in the development of arterial disease, including atherosclerosis and hypertension. However, the relationship between IL-22 and acute thoracic aortic dissection (TAD) remains unknown. Blood samples were collected from patients with chest pain who underwent computed tomography angiography of the thoracic aorta but had no known preoperative diagnosis of coronary artery disease, peripheral artery disease, arthritis, and/or membranous nephropathy. Patients were divided into non-AD (NAD) and TAD groups, and the plasma concentrations of IL-22, IL-6 and tumor necrosis factor (TNF)-α were measured. In addition, aortic tissue samples from acute TAD patients and normal donors were collected, and the expression levels of IL-22 and IL-22 receptor 1 (IL-22R1) were measured. IL-22, IL-6 and TNF-α levels were significantly higher in acute TAD patients than in NAD patients (IL-22, NAD group: 27.0 (19.1, 38.6) pg/ml vs. TAD group: 32.9 (20.6, 58.3) pg/ml, p<0.0001). The correlation analysis showed that IL-22 levels were positively correlated with levels of IL-6, TNF-α, fasting glucose, blood pressure, white blood cells, C-reactive proteins and D-dimers. Binary logistic regression analyses showed that IL-22 was independently associated with the presence of acute TAD (OR 1.169, 95% CI 1.069 to 1.277; p=0.001). In addition, compared with aortic tissue of normal controls, TAD aortas showed increased expression of IL-22 and IL-22R1, especially in the torn section (IL-22, non-torn section: 2.8±0.5/HPF vs. torn section 2.8±0.5/HPF, p<0.001). Additionally, macrophage but not T lymphocyte infiltration was significantly increased in the torn section (Macrophage, non-torn section: 2.2±0.6/HPF vs. torn section 5.7±1.2/HPF, p<0.001; T lymphocyte, non-torn section: 2.7±0.9/HPF vs. torn section 2.4±0.5/HPF, p=0.28), as evidenced by increased positive staining for the macrophage marker CD68, as opposed to the T cell marker CD3. IL-22 levels may correlate with the presence of acute TAD. Copyright © 2017 Elsevier B.V. All rights reserved.

Canadian Cardiovascular Society position statement on the management of thoracic aortic disease.

PubMed

Boodhwani, Munir; Andelfinger, Gregor; Leipsic, Jonathon; Lindsay, Thomas; McMurtry, M Sean; Therrien, Judith; Siu, Samuel C

2014-06-01

This Canadian Cardiovascular Society position statement aims to provide succinct perspectives on key issues in the management of thoracic aortic disease (TAD). This document is not a comprehensive overview of TAD and important elements of the epidemiology, presentation, diagnosis, and management of acute aortic syndromes are deliberately not discussed; readers are referred to the 2010 guidelines published by the American Heart Association, American College of Cardiology, American Association for Thoracic Surgery, and other stakeholders. Rather, this document is a practical guide for clinicians managing adult patients with TAD. Topics covered include size thresholds for surgical intervention, emerging therapies, imaging modalities, medical and lifestyle management, and genetics of TAD. The primary panel consisted of experts from a variety of disciplines that are essential for comprehensive management of TAD patients. The methodology involved a focused literature review with an emphasis on updates since 2010 and the use of Grading of Recommendations Assessment, Development, and Evaluation methodology to arrive at specific recommendations. The final document then underwent review by a secondary panel. This document aims to provide recommendations for most patients and situations. However, the ultimate judgement regarding the management of any individual patients should be made by their health care team. Copyright © 2014 Canadian Cardiovascular Society. Published by Elsevier Inc. All rights reserved.

Use of miniplates as a method for orthodontic anchorage: a case report.

PubMed

Peres, Fernando Gianzanti; Padovan, Luis Eduardo Marques; Kluppel, Leandro Eduardo; Albuquerque, Gustavo Calvalcanti; Souza, Paulo Cesar Ulson de; Claudino, Marcela

2016-01-01

Temporary anchorage devices (TADs) have been developed to be used as direct adjuncts in orthodontic treatment and have facilitated treatment of more complex orthodontic cases, including patients with dental impaction. This clinical case reports the applicability of TADs in the orthodontic treatment of a patient with impacted mandibular second molars. Surgical and orthodontic procedures related to the use of miniplates were also discussed in this study. The use of temporary anchorage devices, such as miniplates, can be suggested as an alternative to treat patients with impacted mandibular second molars.

Treatment for Adolescents With Depression Study (TADS): Safety Results

PubMed Central

Emslie, Graham; Kratochvil, Christopher; Vitiello, Benedetto; Silva, Susan; Mayes, Taryn; McNulty, Steven; Weller, Elizabeth; Waslick, Bruce; Casat, Charles; Walkup, John; Pathak, Sanjeev; Rohde, Paul; Posner, Kelly; March, John

2012-01-01

Objective To compare the rates of physical, psychiatric, and suicide-related events in adolescents with MDD treated with fluoxetine alone (FLX), cognitive-behavioral therapy (CBT), combination treatment (COMB), or placebo (PBO). Method Safety assessments included adverse events (AEs) collected by spontaneous report, as well as systematic measures for specific physical and psychiatric symptoms. Suicidal ideation and suicidal behavior were systematically assessed by self- and clinician reports. Suicidal events were also reanalyzed by the Columbia Group and expert raters using the Columbia-Classification Algorithm for Suicidal Assessment used in the U.S. Food and Drug Administration reclassification effort. Results Depressed adolescents reported high rates of physical symptoms at baseline, which improved as depression improved. Sedation, insomnia, vomiting, and upper abdominal pain occurred in at least 2% of those treated with FLX and/or COMB and at twice the rate of placebo. The rate of psychiatric AEs was 11% in FLX, 5.6% in COMB, 4.5% in PBO, and 0.9% in CBT. Suicidal ideation improved overall, with greatest improvement in COMB. Twenty-four suicide-related events occurred during the 12-week period: 5 patients (4.7%) in COMB, 10 (9.2%) in FLX, 5 (4.5%) in CBT, and 3 (2.7%) in placebo. Statistically, only FLX had more suicide-related events than PBO (p = .0402, odds ratio [OR] = 3.7, 95% CI 1.00–13.7). Only five actual attempts occurred (2 COMB, 2 FLX, 1 CBT, 0 PBO). There were no suicide completions. Conclusions Different methods for eliciting AEs produce different results. In general, as depression improves, physical complaints and suicidal ideation decrease in proportion to treatment benefit. In this study, psychiatric AEs and suicide-related events are more common in FLX-treated patients. COMB treatment may offer a more favorable safety profile than medication alone in adolescent depression. PMID:17135989

Analysis of dystonic tremor in musicians using empirical mode decomposition.

PubMed

Lee, A; Schoonderwaldt, E; Chadde, M; Altenmüller, E

2015-01-01

Test the hypotheses that tremor amplitude in musicians with task-specific dystonia is higher at the affected finger (dystonic tremor, DT) or the adjacent finger (tremor associated with dystonia, TAD) than (1) in matched fingers of healthy musicians and non-musicians and (2) within patients in the unaffected and non-adjacent fingers of the affected side within patients. We measured 21 patients, 21 healthy musicians and 24 non-musicians. Participants exerted a flexion-extension movement. Instantaneous frequency and amplitude values were obtained with empirical mode decomposition and a Hilbert-transform, allowing to compare tremor amplitudes throughout the movement at various frequency ranges. We did not find a significant difference in tremor amplitude between patients and controls for either DT or TAD. Neither differed tremor amplitude in the within-patient comparisons. Both hypotheses were rejected and apparently neither DT nor TAD occur in musician's dystonia of the fingers. This is the first study assessing DT and TAD in musician's dystonia. Our finding suggests that even though MD is an excellent model for malplasticity due to excessive practice, it does not seem to provide a good model for DT. Rather it seems that musician's dystonia may manifest itself either as dystonic cramping without tremor or as task-specific tremor without overt dystonic cramping. Copyright © 2014 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Design of a thermally controlled sequence of triazolinedione-based click and transclick reactions† †Electronic supplementary information (ESI) available: Additional figures, experimental details, synthesis and analysis of all the model compounds and polymers, computational methods and relevant theoretical data. See DOI: 10.1039/c7sc00119c Click here for additional data file.

PubMed Central

Houck, Hannes A.; De Bruycker, Kevin; Billiet, Stijn; Dhanis, Bastiaan; Goossens, Hannelore; Catak, Saron; Van Speybroeck, Veronique

2017-01-01

The reaction of triazolinediones (TADs) and indoles is of particular interest for polymer chemistry applications, as it is a very fast and irreversible additive-free process at room temperature, but can be turned into a dynamic covalent bond forming process at elevated temperatures, giving a reliable bond exchange or ‘transclick’ reaction. In this paper, we report an in-depth study aimed at controlling the TAD–indole reversible click reactions through rational design of modified indole reaction partners. This has resulted in the identification of a novel class of easily accessible indole derivatives that give dynamic TAD-adduct formation at significantly lower temperatures. We further demonstrate that these new substrates can be used to design a directed cascade of click reactions of a functionalized TAD moiety from an initial indole reaction partner to a second indole, and finally to an irreversible reaction partner. This controlled sequence of click and transclick reactions of a single TAD reagent between three different substrates has been demonstrated both on small molecule and macromolecular level, and the factors that control the reversibility profiles have been rationalized and guided by mechanistic considerations supported by theoretical calculations. PMID:28507685

Adaptive temperature-accelerated dynamics

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Amar, Jacques G.

2011-02-01

We present three adaptive methods for optimizing the high temperature Thigh on-the-fly in temperature-accelerated dynamics (TAD) simulations. In all three methods, the high temperature is adjusted periodically in order to maximize the performance. While in the first two methods the adjustment depends on the number of observed events, the third method depends on the minimum activation barrier observed so far and requires an a priori knowledge of the optimal high temperature T^{opt}_{high}(E_a) as a function of the activation barrier Ea for each accepted event. In order to determine the functional form of T^{opt}_{high}(E_a), we have carried out extensive simulations of submonolayer annealing on the (100) surface for a variety of metals (Ag, Cu, Ni, Pd, and Au). While the results for all five metals are different, when they are scaled with the melting temperature Tm, we find that they all lie on a single scaling curve. Similar results have also been obtained for (111) surfaces although in this case the scaling function is slightly different. In order to test the performance of all three methods, we have also carried out adaptive TAD simulations of Ag/Ag(100) annealing and growth at T = 80 K and compared with fixed high-temperature TAD simulations for different values of Thigh. We find that the performance of all three adaptive methods is typically as good as or better than that obtained in fixed high-temperature TAD simulations carried out using the effective optimal fixed high temperature. In addition, we find that the final high temperatures obtained in our adaptive TAD simulations are very close to our results for T^{opt}_{high}(E_a). The applicability of the adaptive methods to a variety of TAD simulations is also briefly discussed.

Evolutionary dynamics of 3D genome architecture following polyploidization in cotton.

PubMed

Wang, Maojun; Wang, Pengcheng; Lin, Min; Ye, Zhengxiu; Li, Guoliang; Tu, Lili; Shen, Chao; Li, Jianying; Yang, Qingyong; Zhang, Xianlong

2018-02-01

The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor. Here, we characterize 3D genome architectures for diploid and tetraploid cotton, and find the existence of A/B compartments and topologically associated domains (TADs). By comparing each subgenome in tetraploids with its extant diploid progenitor, we find that genome allopolyploidization has contributed to the switching of A/B compartments and the reorganization of TADs in both subgenomes. We also show that the formation of TAD boundaries during polyploidization preferentially occurs in open chromatin, coinciding with the deposition of active chromatin modification. Furthermore, analysis of inter-subgenomic chromatin interactions has revealed the spatial proximity of homoeologous genes, possibly associated with their coordinated expression. This study advances our understanding of chromatin organization in plants and sheds new light on the relationship between 3D genome evolution and transcriptional regulation.

Microbial community structure in a thermophilic aerobic digester used as a sludge pretreatment process for the mesophilic anaerobic digestion and the enhancement of methane production.

PubMed

Jang, Hyun Min; Park, Sang Kyu; Ha, Jeong Hyub; Park, Jong Moon

2013-10-01

An effective two-stage sewage sludge digestion process, consisting of thermophilic aerobic digestion (TAD) followed by mesophilic anaerobic digestion (MAD), was developed for efficient sludge reduction and methane production. Using TAD as a biological pretreatment, the total volatile suspended solid reduction (VSSR) and methane production rate (MPR) in the MAD reactor were significantly improved. According to denaturing gradient gel electrophoresis (DGGE) analysis, the results indicated that the dominant bacteria species such as Ureibacillus thermophiles and Bacterium thermus in TAD were major routes for enhancing soluble organic matter. TAD pretreatment using a relatively short SRT of 1 day showed highly increased soluble organic products and positively affected an increment of bacteria populations which performed interrelated microbial metabolisms with methanogenic species in the MAD; consequently, a quantitative real-time PCR indicated greatly increased Methanosarcinales (acetate-utilizing methanogens) in the MAD, resulting in enhanced methane production. Copyright © 2013 Elsevier Ltd. All rights reserved.

Lateral cis-1,3,5,7-tetraazadecalin podands and their complexes: synthesis, structure, and strong binding with Pb(II) and other heavy metal ions.

PubMed

Reany, Ofer; Fuchs, Benzion

2013-02-18

The chemistry and complexation behavior of diaminal podands based on cis-1,3,5,7-tetraazadecalin (cis-TAD) were elaborated, reassessed, and extended. The synthesis of 2,6-bis(hydroxymethylene)-cis-TAD (9) and 2,6-bis(α,α'-dimethyl-β- hydroxyethyl)-cis-TAD (10) as well as of suitably substituted 2,6-diaryl-cis-TAD podands is laid out. For the latter, the effect of electron donating or withdrawing substituents on the benzaldehyde reagents was examined while 9 and 10 were probed and showed considerable propensity for heavy metal-ion chelation. The [Cd(II)·(9)] and [Pb(II)·(9)] complexes stood out indeed, and their structure and properties show a particularly interesting 5-amino-1,3-diazane chelation type and strong ligand-ion binding mode, with intramolecular donor exchange in solution, all strongly influenced by the anomeric effect in the ligand.

Exploring Tyrosine-Triazolinedione (TAD) Reactions for the Selective Conjugation and Cross-Linking of N-Carboxyanhydride (NCA) Derived Synthetic Copolypeptides.

PubMed

Hanay, Saltuk B; Ritzen, Bas; Brougham, Dermot; Dias, Aylvin A; Heise, Andreas

2017-07-01

Highly efficient functionalization and cross-linking of polypeptides is achieved via tyrosine-triazolinedione (TAD) conjugation chemistry. The feasibility of the reaction is demonstrated by the reaction of 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD) with tyrosine containing block copolymer poly(ethylene glycol)-Tyr 4 as well as a statistical copolymer of tyrosine and lysine (poly(Lys 40 -st-Tyr 10 )) prepared form N-carboxyanhydride polymerization. Selective reaction of PTAD with the tyrosine units is obtained and verified by size exclusion chromatography and NMR spectroscopy. Moreover, two monofunctional and two difunctional TAD molecules are synthesized. It is found that their stability in the aqueous reaction media significantly varied. Under optimized reaction conditions selective functionalization and cross-linking, yielding polypeptide hydrogels, can be achieved. TAD-mediated conjugation can offer an interesting addition in the toolbox of selective (click-like) polypeptide conjugation methodologies as it does not require functional non-natural amino acids. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens

PubMed Central

Glinsky, Gennadi V.

2016-01-01

Abstract Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8–10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P < 0.0001 in all instances). Present analysis supports the idea that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: (i) recombination-associated exaptation of the highly conserved ancestral regulatory DNA segments; (ii) human-specific insertions of transposable elements. PMID:27503290

Comparison of Barley Succession and Take-All Disease as Environmental Factors Shaping the Rhizobacterial Community during Take-All Decline▿

PubMed Central

Schreiner, Karin; Hagn, Alexandra; Kyselková, Martina; Moënne-Loccoz, Yvan; Welzl, Gerhard; Munch, Jean Charles; Schloter, Michael

2010-01-01

The root disease take-all, caused by Gaeumannomyces graminis var. tritici, can be managed by monoculture-induced take-all decline (TAD). This natural biocontrol mechanism typically occurs after a take-all outbreak and is believed to arise from an enrichment of antagonistic populations in the rhizosphere. However, it is not known whether these changes are induced by the monoculture or by ecological rhizosphere conditions due to a disease outbreak and subsequent attenuation. This question was addressed by comparing the rhizosphere microflora of barley, either inoculated with the pathogen or noninoculated, in a microcosm experiment in five consecutive vegetation cycles. TAD occurred in soil inoculated with the pathogen but not in noninoculated soil. Bacterial community analysis using terminal restriction fragment length polymorphism of 16S rRNA showed pronounced population shifts in the successive vegetation cycles, but pathogen inoculation had little effect. To elucidate rhizobacterial dynamics during TAD development, a 16S rRNA-based taxonomic microarray was used. Actinobacteria were the prevailing indicators in the first vegetation cycle, whereas the third cycle—affected most severely by take-all—was characterized by Proteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and Acidobacteria. Indicator taxa for the last cycle (TAD) belonged exclusively to Proteobacteria, including several genera with known biocontrol traits. Our results suggest that TAD involves monoculture-induced enrichment of plant-beneficial taxa. PMID:20525871

Toolsets for Airborne Data Beta Release

Atmospheric Science Data Center

2014-09-17

... create merge files based on a user’s choice of time base. In addition, the TAD merge feature allows users to generate standard deviation ... to the TAD database. We are currently focused on the in situ measurements and we want to hear from you about the need for other data ...

Making National Headlines: The Media Magic of Tad Foote.

ERIC Educational Resources Information Center

Dudley, Christopher

1988-01-01

On becoming president of the University of Miami, Tad Foote began a long-term campaign of media access, making a point of being both honest and available. His experience as a former journalist helps him both understand the needs of news editors and write articles himself. (MSE)

Consultation and the TADS Experience. Occasional Paper Number 1.

ERIC Educational Resources Information Center

Trohanis, Pascal L.; And Others

During the past 10 years, the Technical Assistance Development System's (TADS) staff and advisory board members along with 500 other people have provided consultation services to model demonstration programs and state education agencies that help young handicapped children and their families. Consultants are usually located through a sponsor or…

TADS Final Evaluation Report, 1980-81. Appendix S.

ERIC Educational Resources Information Center

Suarez, Tanya M.; And Others

The document contains the final report of the Technical Assistance Development System (TADS), a program which provided technical assistance (TA) services to 53 Handicapped Children's Early Education Program (HCEEP) demonstration projects and 13 State Implementation Grants (SIGs). The evaluation report is divided into five sections. Section 1…

Aerodynamics of Sounding-Rocket Geometries

NASA Technical Reports Server (NTRS)

Barrowman, J.

1982-01-01

Theoretical aerodynamics program TAD predicts aerodynamic characteristics of vehicles with sounding-rocket configurations. These slender, Axisymmetric finned vehicles have a wide range of aeronautical applications from rockets to high-speed armament. TAD calculates characteristics of separate portions of vehicle, calculates interference between portions, and combines results to form total vehicle solution.

TADS: Technical Assistance Development System.

ERIC Educational Resources Information Center

Epting, Rosemary, Ed.

Described is the Technical Assistance Development System (TADS), a component of the Frank Porter Graham Child Development Center of the University of North Carolina at Chapel Hill which offers support services to preschool demonstration centers for handicapped children in the First Chance Network. Discussed are the four types of services offered:…

Evaluation: The TADS Experience. Occasional Paper Number 4.

ERIC Educational Resources Information Center

Suarez, Tanya M.; Vandiviere, Patricia

The paper considers the issues, decisions, and practices involved in evaluating the Technical Assistance Development System (TADS), a project to provide assistance to demonstration projects and start education agency grantees in the Handicapped Children's Early Education Program. Section 1 considers the focus for the evaluation in terms of its…

Toward Affective Development: A Program to Stimulate Psychological and Affective Development.

ERIC Educational Resources Information Center

Pearl, Linda F.

1987-01-01

Toward Affective Development (TAD), a 191-lesson program designed to stimulate psychological and affective development for third- through sixth-graders, can be used in special education, resource rooms, and remedial settings. TAD's five sections encompass: openness to experience, effects of emotions, group dynamics, individuality, and conflict…

Electron Echo 6 - a Study by Particle Detectors of Electrons Artificially Injected Into the Magnetosphere.

NASA Astrophysics Data System (ADS)

Malcolm, Perry Robert

The ECHO-6 sounding rocket was launched from the Poker Flat Research Range, Alaska on 30 March 1983. A Terrier-Black Brant launch vehicle carried the payload on a northward trajectory over an auroral arc and to an apogee of 216 kilometers. The primary objective of the ECHO-6 experiment was to evaluate electric fields, magnetic fields, and plasma processes in the distant magnetosphere by injecting electron beams in the ionosphere and observing conjugate echoes. The experiment succeeded in injecting 10-36 KeV beams during the existence of a moderate growth phase aurora, an easterly electrojet system, and a pre -midnight inflation condition of the magnetosphere. The ECHO-6 payload system consisted of an accelerator MAIN payload, a free-flying Plasma Diagnostics Package (PDP), and four rocket propelled Throw Away Detectors (TADs). The PDP was ejected from the MAIN payload to analyze electric fields, plasma particles, energetic electrons, and photometric effects produced by beam injections. The TADs were ejected from the MAIN payload in a pattern to detect echoes in the conjugate echo region south of the beam emitting MAIN payload. The TADs reached distances exceeding 3 kilometers from the MAIN payload and made measurements of the ambient electrons by means of solid state detectors and electrostatic analyzers. In spite of the perfect operation of the TAD system and a rigorous analysis of the particle data, no conjugate echoes have been identified. Through the use of a new dynamic magnetic field model (Olson and Pfitzer, 1982) and satellite magnetometer measurements, it has been determined that the echoing electrons returned out of range of the TADs as a result of their bounce times and curvature-gradient drifts being increased beyond the expected limits for an inflated magnetic field. This dynamic model was then applied to the study of echoes seen during the ECHO-4 flight resulting in a significant increase in the calculated energy of the echo electrons and better agreement between the locally measured and bounce integrated electric field.

Use of miniplates as a method for orthodontic anchorage: a case report

PubMed Central

Peres, Fernando Gianzanti; Padovan, Luis Eduardo Marques; Kluppel, Leandro Eduardo; Albuquerque, Gustavo Calvalcanti; de Souza, Paulo Cesar Ulson; Claudino, Marcela

2016-01-01

ABSTRACT Introduction: Temporary anchorage devices (TADs) have been developed to be used as direct adjuncts in orthodontic treatment and have facilitated treatment of more complex orthodontic cases, including patients with dental impaction. Objectives: This clinical case reports the applicability of TADs in the orthodontic treatment of a patient with impacted mandibular second molars. Surgical and orthodontic procedures related to the use of miniplates were also discussed in this study. Conclusions: The use of temporary anchorage devices, such as miniplates, can be suggested as an alternative to treat patients with impacted mandibular second molars. PMID:27901235

Complete genome sequence of the aerobically denitrifying thermophilic bacterium Chelatococcus daeguensis TAD1.

PubMed

Yang, Yunlong; Lin, Ershu; Huang, Shaobin

Chelatococcus daeguensis TAD1 is a themophilic bacterium isolated from a biotrickling filter used to treat NOx in Ruiming Power Plant, located in Guangzhou, China, which shows an excellent aerobic denitrification activity at high temperature. The complete genome sequence of this strain was reported in the present study. Genes related to the aerobic denitrification were identified through whole genome analysis. This work will facilitate the mechanism of aerobic denitrification and provide evidence for its potential application in the nitrogen removal. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Influence of thermophilic aerobic digestion as a sludge pre-treatment and solids retention time of mesophilic anaerobic digestion on the methane production, sludge digestion and microbial communities in a sequential digestion process.

PubMed

Jang, Hyun Min; Cho, Hyun Uk; Park, Sang Kyu; Ha, Jeong Hyub; Park, Jong Moon

2014-01-01

In this study, the changes in sludge reduction, methane production and microbial community structures in a process involving two-stage thermophilic aerobic digestion (TAD) and mesophilic anaerobic digestion (MAD) under different solid retention times (SRTs) between 10 and 40 days were investigated. The TAD reactor (RTAD) was operated with a 1-day SRT and the MAD reactor (RMAD) was operated at three different SRTs: 39, 19 and 9 days. For a comparison, control MAD (RCONTROL) was operated at three different SRTs of 40, 20 and 10 days. Our results reveal that the sequential TAD-MAD process has about 42% higher methane production rate (MPR) and 15% higher TCOD removal than those of RCONTROL when the SRT decreased from 40 to 20 days. Denaturing gradient gel electrophoresis (DGGE) and real-time PCR results indicate that RMAD maintained a more diverse bacteria and archaea population compared to RCONTROL, due to the application of the biological TAD pre-treatment process. In RTAD, Ureibacillus thermophiles and Bacterium thermus were the major contributors to the increase in soluble organic matter. In contrast, Methanosaeta concilii, a strictly aceticlastic methanogen, showed the highest population during the operation of overall SRTs in RMAD. Interestingly, as the SRT decreased to 20 days, syntrophic VFA oxidizing bacteria, Clostridium ultunense sp., and a hydrogenotrophic methanogen, Methanobacterium beijingense were detected in RMAD and RCONTROL. Meanwhile, the proportion of archaea to total microbe in RMAD and RCONTROL shows highest values of 10.5 and 6.5% at 20-d SRT operation, respectively. Collectively, these results demonstrate that the increased COD removal and methane production at different SRTs in RMAD might be attributed to the increased synergism among microbial species by improving the hydrolysis of the rate limiting step in sludge with the help of the biological TAD pre-treatment. Copyright © 2013 Elsevier Ltd. All rights reserved.

Systemic Delivery of Oncolytic Adenoviruses Targeting Transforming Growth Factor-β Inhibits Established Bone Metastasis in a Prostate Cancer Mouse Model

PubMed Central

Hu, Zebin; Gupta, Janhavi; Zhang, Zhenwei; Gerseny, Helen; Berg, Arthur; Chen, Yun Ju; Zhang, Zhiling; Du, Hongyan; Brendler, Charles B.; Xiao, Xianghui; Pienta, Kenneth J.; Guise, Theresa; Lee, Chung; Stern, Paula H.; Stock, Stuart

2012-01-01

Abstract We have examined whether Ad.sTβRFc and TAd.sTβRFc, two oncolytic viruses expressing soluble transforming growth factor-β receptor II fused with human Fc (sTGFβRIIFc), can be developed to treat bone metastasis of prostate cancer. Incubation of PC-3 and DU-145 prostate tumor cells with Ad.sTβRFc and TAd.sTβRFc produced sTGFβRIIFc and viral replication; sTGFβRIIFc caused inhibition of TGF-β-mediated SMAD2 and SMAD3 phosphorylation. Ad(E1-).sTβRFc, an E1– adenovirus, produced sTGFβRIIFc but failed to replicate in tumor cells. To examine the antitumor response of adenoviral vectors, PC-3-luc cells were injected into the left heart ventricle of nude mice. On day 9, mice were subjected to whole-body bioluminescence imaging (BLI). Mice bearing hind-limb tumors were administered viral vectors via the tail vein on days 10, 13, and 17 (2.5×1010 viral particles per injection per mouse, each injection in a 0.1-ml volume), and subjected to BLI and X-ray radiography weekly until day 53. Ad.sTβRFc, TAd.sTβRFc, and Ad(E1-).sTβRFc caused significant inhibition of tumor growth; however, Ad.sTβRFc was the most effective among all the vectors. Only Ad.sTβRFc and TAd.sTβRFc inhibited tumor-induced hypercalcemia. Histomorphometric and synchrotron micro-computed tomographic analysis of isolated bones indicated that Ad.sTβRFc induced significant reduction in tumor burden, osteoclast number, and trabecular and cortical bone destruction. These studies suggest that Ad.sTβRFc and TAd.sTβRFc can be developed as potential new therapies for prostate cancer bone metastasis. PMID:22551458

[Response and prognosis of patients with multiple myeloma induced by PAD/TAD].

PubMed

Zeng, Tianmei; He, Haiyan; Shi, Haotian; Xi, Hao; Du, Juan; Zhang, Chunyang; Jiang, Hua; Fu, Weijun; Zhou, Fan; Hou, Jian

2015-03-17

To evaluate the impact of cytogenetic grouping and autologous stem cell transplantation on the prognosis of patients with multiple myeloma (MM) induced by PAD (velcade+epirubicin+dexamethasone) and TAD (thalidomide+epirubicin+dexamethasone). A total of 191 patients with a definite diagnosis of MM were enrolled from May 2008 to December 2013 into this prospective study. They were non-randomly induced by PAD (n = 132) or TAD (n = 59) plus autologous stem cell transplantation or chemotherapy. Response and survival rates were also analyzed between two groups. The overall response rates of PAD and TAD groups were 84.4% (108/128) and 69.5% (41/59) (P = 0.011) respectively. The very good partial remission (VGPR) rates were 70.3% (90/128) and 32.2% (19/59) (P < 0.001) and near complete remission/complete remission (nCR/CR) rates 68.0% (87/128) and 25.4% (15/59) respectively (P < 0.001). Both progression-free survival (PFS) and overall survival (OS) showed no significant inter-group difference (P = 0.223, 0.989). The survival analysis of PAD group showed that FISH high-risk group had shorter PFS and OS than FISH low-risk group (15.2 vs 19.1 months for PFS, P = 0.098; 41.2 months vs non-attaining for OS, P = 0.017). In FISH high-risk group, patients consolidated with autologous stem cell transplantation showed longer PFS than those with chemotherapy (17.8 vs 14.6 months, P = 0.029) while the OS showed no difference (P = 0.840). In FISH low-risk group, no difference were observed in PFS and OS between patients with consolidation therapies alone (P = 0.131, 0.294). The response rates are higher in patients induced by PAD than by TAD. After PAD induction, cytogenetic grouping may further distinguish the prognosis of MM patients. For FISH high-risk patients, their PFS is prolonged by autologous stem cell transplantation.

Comparison of temporary anchorage devices and transpalatal arch-mediated anchorage reinforcement during canine retraction

PubMed Central

Kecik, Defne

2016-01-01

Objective: The purpose of this study was to compare the dental and skeletal effects of canine retraction using conventional anchorage reinforcement systems and comparing them with the usage of TADs. Materials and Methods: The sample consisted of 50 patients having Class I malocclusions with bimaxillary protrusion indicated for first premolar extraction, and allocated into two groups. The first group consisted of 25 patients with a mean age of 18,7 years (min:14, max:22 years, 16 girls and 9 boys) that TADs were applied as an anchorage mechanic between attached gingiva of upper second premolar and first molar teeth. The second group consisted of 25 patients with a mean age of 19,4 years (min:15, max:23 years, 14 girls and 11 boys) that conventional molar anchorage with Transpalatal arch (TPA) was applied for the anchorage mechanics against canine retraction. Results: The results showed that mean mesial movement and the tipping of the first molars in TAD group between T0 - T1 were insignificant (P > 0,05), however in the TPA group were significant (P<0,01). Vertical movement of the molars were not significant when two groups were compared (P>0,05). Conclusion: Although TPA is a useful appliance, it doesn't provide an effective anchorage control on anteroposterior movement maxillary first molar teeth concerning first premolar extraction treatment. TADs are more convenient to provide absolute anchorage during maxillary canine retraction in contrast to transpalatal arch. PMID:28042267

Comparison of temporary anchorage devices and transpalatal arch-mediated anchorage reinforcement during canine retraction.

PubMed

Kecik, Defne

2016-01-01

The purpose of this study was to compare the dental and skeletal effects of canine retraction using conventional anchorage reinforcement systems and comparing them with the usage of TADs. The sample consisted of 50 patients having Class I malocclusions with bimaxillary protrusion indicated for first premolar extraction, and allocated into two groups. The first group consisted of 25 patients with a mean age of 18,7 years (min:14, max:22 years, 16 girls and 9 boys) that TADs were applied as an anchorage mechanic between attached gingiva of upper second premolar and first molar teeth. The second group consisted of 25 patients with a mean age of 19,4 years (min:15, max:23 years, 14 girls and 11 boys) that conventional molar anchorage with Transpalatal arch (TPA) was applied for the anchorage mechanics against canine retraction. The results showed that mean mesial movement and the tipping of the first molars in TAD group between T0 - T1 were insignificant ( P > 0,05), however in the TPA group were significant ( P <0,01). Vertical movement of the molars were not significant when two groups were compared ( P >0,05). Although TPA is a useful appliance, it doesn't provide an effective anchorage control on anteroposterior movement maxillary first molar teeth concerning first premolar extraction treatment. TADs are more convenient to provide absolute anchorage during maxillary canine retraction in contrast to transpalatal arch.

Microbial Insight into a Pilot-Scale Enhanced Two-Stage High-Solid Anaerobic Digestion System Treating Waste Activated Sludge.

PubMed

Wu, Jing; Cao, Zhiping; Hu, Yuying; Wang, Xiaolu; Wang, Guangqi; Zuo, Jiane; Wang, Kaijun; Qian, Yi

2017-11-30

High solid anaerobic digestion (HSAD) is a rapidly developed anaerobic digestion technique for treating municipal sludge, and has been widely used in Europe and Asia. Recently, the enhanced HSAD process with thermal treatment showed its advantages in both methane production and VS reduction. However, the understanding of the microbial community is still poor. This study investigated microbial communities in a pilot enhanced two-stage HSAD system that degraded waste activated sludge at 9% solid content. The system employed process "thermal pre-treatment (TPT) at 70 °C, thermophilic anaerobic digestion (TAD), and mesophilic anaerobic digestion (MAD)". Hydrogenotrophic methanogens Methanothermobacter spp. dominated the system with relative abundance up to about 100% in both TAD and MAD. Syntrophic acetate oxidation (SAO) bacteria were discovered in TAD, and they converted acetate into H₂ and CO₂ to support hydrogenotrophic methanogenesis. The microbial composition and conversion route of this system are derived from the high solid content and protein content in raw sludge, as well as the operational conditions. This study could facilitate the understanding of the enhanced HSAD process, and is of academic and industrial importance.

Microbial Insight into a Pilot-Scale Enhanced Two-Stage High-Solid Anaerobic Digestion System Treating Waste Activated Sludge

PubMed Central

Wu, Jing; Cao, Zhiping; Hu, Yuying; Wang, Xiaolu; Wang, Guangqi; Zuo, Jiane; Wang, Kaijun; Qian, Yi

2017-01-01

High solid anaerobic digestion (HSAD) is a rapidly developed anaerobic digestion technique for treating municipal sludge, and has been widely used in Europe and Asia. Recently, the enhanced HSAD process with thermal treatment showed its advantages in both methane production and VS reduction. However, the understanding of the microbial community is still poor. This study investigated microbial communities in a pilot enhanced two-stage HSAD system that degraded waste activated sludge at 9% solid content. The system employed process “thermal pre-treatment (TPT) at 70 °C, thermophilic anaerobic digestion (TAD), and mesophilic anaerobic digestion (MAD)”. Hydrogenotrophic methanogens Methanothermobacter spp. dominated the system with relative abundance up to about 100% in both TAD and MAD. Syntrophic acetate oxidation (SAO) bacteria were discovered in TAD, and they converted acetate into H2 and CO2 to support hydrogenotrophic methanogenesis. The microbial composition and conversion route of this system are derived from the high solid content and protein content in raw sludge, as well as the operational conditions. This study could facilitate the understanding of the enhanced HSAD process, and is of academic and industrial importance. PMID:29189754

Combustion synthesis of ceramic and metal-matrix composites

NASA Technical Reports Server (NTRS)

Moore, John J.; Feng, Heng J.; Hunter, Kevin J.; Wirth, David G.

1993-01-01

Combustion synthesis or self-propagating high temperature synthesis (SHS) is effected by heating a reactant mixture, to above the ignition temperature (Tig) whereupon an exothermic reaction is initiated which produces a maximum or combustion temperature, Tc. These SHS reactions are being used to produce ceramics, intermetallics, and composite materials. One of the major limitations of this process is that relatively high levels of porosity, e.g., 50 percent, remain in the product. Conducting these SHS reactions under adiabatic conditions, the maximum temperature is the adiabatic temperature, Tad, and delta H (Tad) = 0, Tad = Tc. If the reactants or products go through a phase change, the latent heat of transformation needs to be taken into account.

76 FR 27164 - Extension of Accreditation Agreement With Colorado Department of Human Services Under the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-10

... applications by the TAD by expending its own funds and other resources for materials development, staff... application deadline'' (TAD) and ``deadline for initial accreditation or approval'' (DIAA) shall have the... 96.97, use its best efforts to evaluate and decide by the DIAA all applications for accreditation...

TADS and Technical Assistance: Readings on System Design, Needs Assessment, Consultation, and Evaluation.

ERIC Educational Resources Information Center

Trohanis, Pascal L., Ed.

The document reviews the technical assistance process used by TADS (Technical Assistance Development System), a project to provide support to HCEEP (Handicapped Children's Early Education Program) demonstration projects serving young handicapped children and their families. Chapter 1, by P. Trohanis, focuses on a number of questions that people…

Relationships between self-reported childhood traumatic experiences, attachment style, neuroticism and features of borderline personality disorders in patients with mood disorders.

PubMed

Baryshnikov, Ilya; Joffe, Grigori; Koivisto, Maaria; Melartin, Tarja; Aaltonen, Kari; Suominen, Kirsi; Rosenström, Tom; Näätänen, Petri; Karpov, Boris; Heikkinen, Martti; Isometsä, Erkki

2017-03-01

Co-occurring borderline personality disorder (BPD) features have a marked impact on treatment of patients with mood disorders. Overall, high neuroticism, childhood traumatic experiences (TEs) and insecure attachment are plausible aetiological factors for BPD. However, their relationship with BPD features specifically among patients with mood disorders remains unclear. We investigated these relationships among unipolar and bipolar mood disorder patients. As part of the Helsinki University Psychiatric Consortium study, the McLean Screening Instrument (MSI), the Experiences in Close Relationships-Revised (ECR-R), the Short Five (S5) and the Trauma and Distress Scale (TADS) were filled in by patients with mood disorders (n=282) in psychiatric care. Correlation coefficients between total scores of scales and their dimensions were estimated, and multivariate regression (MRA) and mediation analyses were conducted. Spearman's correlations were strong (rho=0.58; p<0.001) between total scores of MSI and S5 Neuroticism and moderate (rho=0.42; p<0.001) between MSI and TADS as well as between MSI and ECR-R Attachment Anxiety. In MRA, young age, S5 Neuroticism and TADS predicted scores of MSI (p<0.001). ECR-R Attachment Anxiety mediated 33% (CI=17-53%) of the relationships between TADS and MSI. Cross-sectional questionnaire study. We found moderately strong correlations between self-reported BPD features and concurrent high neuroticism, reported childhood traumatic experiences and Attachment Anxiety also among patients with mood disorders. Independent predictors for BPD features include young age, frequency of childhood traumatic experiences and high neuroticism. Insecure attachment may partially mediate the relationship between childhood traumatic experiences and borderline features among mood disorder patients. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of tip apex distance and cut-out complications between helical blades and lag screws in intertrochanteric fractures among the elderly: a meta-analysis.

PubMed

Li, Shuang; Chang, Shi-Min; Niu, Wen-Xin; Ma, Hui

2015-11-01

To investigate whether helical blade implant systems have advantages in terms of tip apex distance (TAD) and cut-out rate in comparison to conventional lag screws for intertrochanteric fractures in a geriatric population. Methods: Relevant articles were sourced from the MEDLINE, Embase, Ovid and Cochrane Library databases from inception through March 2015. All randomized controlled trials (RCTs) comparing outcomes between helical blade and lag screw implant systems were selected. Mean TAD values and reported cut-out complications were noted. Each author independently assessed the relevance of the enrolled studies and the quality of the extracted data. Data were analyzed using R software. Ten studies including 1831 patients were eligible for this review, seven of which were included in a combined analysis of dichotomous outcomes and five in a combined analysis of continuous outcomes. The results revealed that, compared with lag screw implantations, the use of helical blades led to a lower rate of cut-out complications (95 % CI: 0.28–0.96, P = 0.036). Patients who experienced cut-out complications had a significantly greater tip apex distance (95 % CI: 0.68–1.34, P < 0.001). However, the actual tip apex distances were similar between the screw group and blade group (95 % CI: −0.44–0.79, P = 0.58). No difference in TAD values was found between blades and screws. In addition, the cut-out risk in the blade-design group was lower than that of the screw group. Therefore, TAD is not an accurate predictor of cut-out risk.

Topologically associating domains are stable units of replication-timing regulation.

PubMed

Pope, Benjamin D; Ryba, Tyrone; Dileep, Vishnu; Yue, Feng; Wu, Weisheng; Denas, Olgert; Vera, Daniel L; Wang, Yanli; Hansen, R Scott; Canfield, Theresa K; Thurman, Robert E; Cheng, Yong; Gülsoy, Günhan; Dennis, Jonathan H; Snyder, Michael P; Stamatoyannopoulos, John A; Taylor, James; Hardison, Ross C; Kahveci, Tamer; Ren, Bing; Gilbert, David M

2014-11-20

Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.

Condensin-driven remodelling of X chromosome topology during dosage compensation

NASA Astrophysics Data System (ADS)

Crane, Emily; Bian, Qian; McCord, Rachel Patton; Lajoie, Bryan R.; Wheeler, Bayly S.; Ralston, Edward J.; Uzawa, Satoru; Dekker, Job; Meyer, Barbara J.

2015-07-01

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure. Here we perform genome-wide chromosome conformation capture analysis, fluorescent in situ hybridization (FISH), and RNA-seq to obtain comprehensive three-dimensional (3D) maps of the Caenorhabditis elegans genome and to dissect X chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian topologically associating domains (TADs). TADs on X chromosomes have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X chromosomes coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X chromosomes by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X chromosomes while regulating gene expression chromosome-wide.

Topologically-associating domains are stable units of replication-timing regulation

PubMed Central

Pope, Benjamin D.; Ryba, Tyrone; Dileep, Vishnu; Yue, Feng; Wu, Weisheng; Denas, Olgert; Vera, Daniel L.; Wang, Yanli; Hansen, R. Scott; Canfield, Theresa K.; Thurman, Robert E.; Cheng, Yong; Gülsoy, Günhan; Dennis, Jonathan H.; Snyder, Michael P.; Stamatoyannopoulos, John A.; Taylor, James; Hardison, Ross C.; Kahveci, Tamer; Ren, Bing; Gilbert, David M.

2014-01-01

Summary Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program1. During mammalian development, at least half the genome changes replication timing, primarily in units of 400–800 kb (“replication domains”; RDs), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements2–7. Early and late replication correlate strongly with open and closed chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, lamina-associated domains (LADs)4,5,8,9. Recent Hi-C mapping has unveiled a substructure of topologically-associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to RDs8,10. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale11,12. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure8,9,13. Here, we localize boundaries of RDs to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, RD boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure RD boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell type specific sub-nuclear compartmentalization with developmentally stable chromosome domains and offer a unified model for large-scale chromosome structure and function. PMID:25409831

Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation

PubMed Central

Crane, Emily; Bian, Qian; McCord, Rachel Patton; Lajoie, Bryan R.; Wheeler, Bayly S.; Ralston, Edward J.; Uzawa, Satoru; Dekker, Job; Meyer, Barbara J.

2015-01-01

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure1,2. Here we perform genome-wide chromosome conformation capture analysis, FISH, and RNA-seq to obtain comprehensive 3D maps of the Caenorhabditis elegans genome and to dissect X-chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half3–7. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes5,6. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian Topologically Associating Domains (TADs)8,9. TADs on X have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X while regulating gene expression chromosome wide. PMID:26030525

A PROP1-binding factor, AES cloned by yeast two-hybrid assay represses PROP1-induced Pit-1 gene expression.

PubMed

Sugiyama, Yuka; Ikeshita, Nobuko; Shibahara, Hiromi; Yamamoto, Daisuke; Kawagishi, Mayuko; Iguchi, Genzo; Iida, Keiji; Takahashi, Yutaka; Kaji, Hidesuke; Chihara, Kazuo; Okimura, Yasuhiko

2013-08-25

PROP1 mutation causes combined pituitary hormone deficiency (CPHD). Several mutations are located in a transactivation domain (TAD) of Prop1, and the loss of TAD binding to cofactors is likely the cause of CPHD. PROP1 cofactors have not yet been identified. In the present study, we aimed to identify the PROP1-interacting proteins from the human brain cDNA library. Using a yeast two-hybrid assay, we cloned nine candidate proteins that may bind to PROP1. Of those nine candidates, amino-terminal enhancer of split (AES) was the most abundant, and we analyzed the AES function. AES dose-dependently decreased the PROP1-induced Pit-1 reporter gene expression. An immunoprecipitation assay revealed the relationship between AES and PROP1. In a mammalian two-hybrid assay, a leucine zipper-like motif of the AES Q domain was identified as a region that interacted with TAD. These results indicated that AES was a corepressor of PROP1. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens.

PubMed

Glinsky, Gennadi V

2016-09-19

Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8-10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P < 0.0001 in all instances). Present analysis supports the idea that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: (i) recombination-associated exaptation of the highly conserved ancestral regulatory DNA segments; (ii) human-specific insertions of transposable elements. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Functional Characterization of the Serine-Rich Tract of Varicella-Zoster Virus IE62.

PubMed

Kim, Seong K; Shakya, Akhalesh K; Kim, Seongman; O'Callaghan, Dennis J

2016-01-15

The immediate early 62 protein (IE62) of varicella-zoster virus (VZV), a major viral trans-activator, initiates the virus life cycle and is a key component of pathogenesis. The IE62 possesses several domains essential for trans-activation, including an acidic trans-activation domain (TAD), a serine-rich tract (SRT), and binding domains for USF, TFIIB, and TATA box binding protein (TBP). Transient-transfection assays showed that the VZV IE62 lacking the SRT trans-activated the early VZV ORF61 promoter at only 16% of the level of the full-length IE62. When the SRT of IE62 was replaced with the SRT of equine herpesvirus 1 (EHV-1) IEP, its trans-activation activity was completely restored. Herpes simplex virus 1 (HSV-1) ICP4 that lacks a TAD very weakly (1.5-fold) trans-activated the ORF61 promoter. An IE62 TAD-ICP4 chimeric protein exhibited trans-activation ability (10.2-fold), indicating that the IE62 TAD functions with the SRT of HSV-1 ICP4 to trans-activate viral promoters. When the serine and acidic residues of the SRT were replaced with Ala, Leu, and Gly, trans-activation activities of the modified IE62 proteins IE62-SRTΔSe and IE62-SRTΔAc were reduced to 46% and 29% of wild-type activity, respectively. Bimolecular complementation assays showed that the TAD of IE62, EHV-1 IEP, and HSV-1 VP16 interacted with Mediator 25 in human melanoma MeWo cells. The SRT of IE62 interacted with the nucleolar-ribosomal protein EAP, which resulted in the formation of globular structures within the nucleus. These results suggest that the SRT plays an important role in VZV viral gene expression and replication. The immediate early 62 protein (IE62) of varicella-zoster virus (VZV) is a major viral trans-activator and is essential for viral growth. Our data show that the serine-rich tract (SRT) of VZV IE62, which is well conserved within the alphaherpesviruses, is needed for trans-activation mediated by the acidic trans-activation domain (TAD). The TADs of IE62, EHV-1 IEP, and HSV-1 VP16 interacted with cellular Mediator 25 in bimolecular complementation assays. The interaction of the IE62 SRT with nucleolar-ribosomal protein EAP resulted in the formation of globular structures within the nucleus. Understanding the mechanisms by which the TAD and SRT of IE62 contribute to the function of this essential regulatory protein is important in understanding the gene program of this human pathogen. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Functional Characterization of the Serine-Rich Tract of Varicella-Zoster Virus IE62

PubMed Central

Shakya, Akhalesh K.; Kim, Seongman; O'Callaghan, Dennis J.

2015-01-01

ABSTRACT The immediate early 62 protein (IE62) of varicella-zoster virus (VZV), a major viral trans-activator, initiates the virus life cycle and is a key component of pathogenesis. The IE62 possesses several domains essential for trans-activation, including an acidic trans-activation domain (TAD), a serine-rich tract (SRT), and binding domains for USF, TFIIB, and TATA box binding protein (TBP). Transient-transfection assays showed that the VZV IE62 lacking the SRT trans-activated the early VZV ORF61 promoter at only 16% of the level of the full-length IE62. When the SRT of IE62 was replaced with the SRT of equine herpesvirus 1 (EHV-1) IEP, its trans-activation activity was completely restored. Herpes simplex virus 1 (HSV-1) ICP4 that lacks a TAD very weakly (1.5-fold) trans-activated the ORF61 promoter. An IE62 TAD-ICP4 chimeric protein exhibited trans-activation ability (10.2-fold), indicating that the IE62 TAD functions with the SRT of HSV-1 ICP4 to trans-activate viral promoters. When the serine and acidic residues of the SRT were replaced with Ala, Leu, and Gly, trans-activation activities of the modified IE62 proteins IE62-SRTΔSe and IE62-SRTΔAc were reduced to 46% and 29% of wild-type activity, respectively. Bimolecular complementation assays showed that the TAD of IE62, EHV-1 IEP, and HSV-1 VP16 interacted with Mediator 25 in human melanoma MeWo cells. The SRT of IE62 interacted with the nucleolar-ribosomal protein EAP, which resulted in the formation of globular structures within the nucleus. These results suggest that the SRT plays an important role in VZV viral gene expression and replication. IMPORTANCE The immediate early 62 protein (IE62) of varicella-zoster virus (VZV) is a major viral trans-activator and is essential for viral growth. Our data show that the serine-rich tract (SRT) of VZV IE62, which is well conserved within the alphaherpesviruses, is needed for trans-activation mediated by the acidic trans-activation domain (TAD). The TADs of IE62, EHV-1 IEP, and HSV-1 VP16 interacted with cellular Mediator 25 in bimolecular complementation assays. The interaction of the IE62 SRT with nucleolar-ribosomal protein EAP resulted in the formation of globular structures within the nucleus. Understanding the mechanisms by which the TAD and SRT of IE62 contribute to the function of this essential regulatory protein is important in understanding the gene program of this human pathogen. PMID:26537679

Planar Perovskite Solar Cells with High Open-Circuit Voltage Containing a Supramolecular Iron Complex as Hole Transport Material Dopant.

PubMed

Saygili, Yasemin; Turren-Cruz, Silver-Hamill; Olthof, Selina; Saes, Bartholomeus Wilhelmus Henricus; Pehlivan, Ilknur Bayrak; Saliba, Michael; Meerholz, Klaus; Edvinsson, Tomas; Zakeeruddin, Shaik M; Grätzel, Michael; Correa-Baena, Juan-Pablo; Hagfeldt, Anders; Freitag, Marina; Tress, Wolfgang

2018-04-26

In perovskite solar cells (PSCs), the most commonly used hole transport material (HTM) is spiro-OMeTAD, which is typically doped by metalorganic complexes, for example, based on Co, to improve charge transport properties and thereby enhance the photovoltaic performance of the device. In this study, we report a new hemicage-structured iron complex, 1,3,5-tris(5'-methyl-2,2'-bipyridin-5-yl)ethylbenzene Fe(III)-tris(bis(trifluoromethylsulfonyl)imide), as a p-type dopant for spiro-OMeTAD. The formal redox potential of this compound was measured as 1.29 V vs. the standard hydrogen electrode, which is slightly (20 mV) more positive than that of the commercial cobalt dopant FK209. Photoelectron spectroscopy measurements confirm that the iron complex acts as an efficient p-dopant, as evidenced in an increase of the spiro-OMeTAD work function. When fabricating planar PSCs with the HTM spiro-OMeTAD doped by 5 mol % of the iron complex, a power conversion efficiency of 19.5 % (AM 1.5G, 100 mW cm -2 ) is achieved, compared to 19.3 % for reference devices with FK209. Open circuit voltages exceeding 1.2 V at 1 sun and reaching 1.27 V at 3 suns indicate that recombination at the perovskite/HTM interface is low when employing this iron complex. This work contributes to recent endeavors to reduce recombination losses in perovskite solar cells. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Volunteer Rehabilitation Technology: International Perspectives and Possibilities. Report of a Symposium Sponsored by the RESNA (ICAART) Conference (Montreal, Canada, June 27, 1988). Monograph Number Forty-Two.

ERIC Educational Resources Information Center

Tobias, Jim, Ed.; Woods, Diane E., Ed.

Symposium papers describe programs which use volunteers to provide rehabilitation technology services. George Winston describes Australia's Technical Aid to the Disabled (TAD), focusing on volunteer recruitment and selection, legal liability, volunteer insurance, advantages and limitations of the volunteer approach, and the TAD organization,…

Form and function of topologically associating genomic domains in budding yeast.

PubMed

Eser, Umut; Chandler-Brown, Devon; Ay, Ferhat; Straight, Aaron F; Duan, Zhijun; Noble, William Stafford; Skotheim, Jan M

2017-04-11

The genome of metazoan cells is organized into topologically associating domains (TADs) that have similar histone modifications, transcription level, and DNA replication timing. Although similar structures appear to be conserved in fission yeast, computational modeling and analysis of high-throughput chromosome conformation capture (Hi-C) data have been used to argue that the small, highly constrained budding yeast chromosomes could not have these structures. In contrast, herein we analyze Hi-C data for budding yeast and identify 200-kb scale TADs, whose boundaries are enriched for transcriptional activity. Furthermore, these boundaries separate regions of similarly timed replication origins connecting the long-known effect of genomic context on replication timing to genome architecture. To investigate the molecular basis of TAD formation, we performed Hi-C experiments on cells depleted for the Forkhead transcription factors, Fkh1 and Fkh2, previously associated with replication timing. Forkhead factors do not regulate TAD formation, but do promote longer-range genomic interactions and control interactions between origins near the centromere. Thus, our work defines spatial organization within the budding yeast nucleus, demonstrates the conserved role of genome architecture in regulating DNA replication, and identifies a molecular mechanism specifically regulating interactions between pericentric origins.

A semi-supervised classification algorithm using the TAD-derived background as training data

NASA Astrophysics Data System (ADS)

Fan, Lei; Ambeau, Brittany; Messinger, David W.

2013-05-01

In general, spectral image classification algorithms fall into one of two categories: supervised and unsupervised. In unsupervised approaches, the algorithm automatically identifies clusters in the data without a priori information about those clusters (except perhaps the expected number of them). Supervised approaches require an analyst to identify training data to learn the characteristics of the clusters such that they can then classify all other pixels into one of the pre-defined groups. The classification algorithm presented here is a semi-supervised approach based on the Topological Anomaly Detection (TAD) algorithm. The TAD algorithm defines background components based on a mutual k-Nearest Neighbor graph model of the data, along with a spectral connected components analysis. Here, the largest components produced by TAD are used as regions of interest (ROI's),or training data for a supervised classification scheme. By combining those ROI's with a Gaussian Maximum Likelihood (GML) or a Minimum Distance to the Mean (MDM) algorithm, we are able to achieve a semi supervised classification method. We test this classification algorithm against data collected by the HyMAP sensor over the Cooke City, MT area and University of Pavia scene.

Reaching extended length-scales with temperature-accelerated dynamics

NASA Astrophysics Data System (ADS)

Amar, Jacques G.; Shim, Yunsic

2013-03-01

In temperature-accelerated dynamics (TAD) a high-temperature molecular dynamics (MD) simulation is used to accelerate the search for the next low-temperature activated event. While TAD has been quite successful in extending the time-scales of simulations of non-equilibrium processes, due to the fact that the computational work scales approximately as the cube of the number of atoms, until recently only simulations of relatively small systems have been carried out. Recently, we have shown that by combining spatial decomposition with our synchronous sublattice algorithm, significantly improved scaling is possible. However, in this approach the size of activated events is limited by the processor size while the dynamics is not exact. Here we discuss progress in developing an alternate approach in which high-temperature parallel MD along with localized saddle-point (LSAD) calculations, are used to carry out TAD simulations without restricting the size of activated events while keeping the dynamics ``exact'' within the context of harmonic transition-state theory. In tests of our LSAD method applied to Ag/Ag(100) annealing and Cu/Cu(100) growth simulations we find significantly improved scaling of TAD, while maintaining a negligibly small error in the energy barriers. Supported by NSF DMR-0907399.

Protective effects of total alkaloids from Dendrobium crepidatum against LPS-induced acute lung injury in mice and its chemical components.

PubMed

Hu, Yang; Ren, Jie; Wang, Lei; Zhao, Xin; Zhang, Mian; Shimizu, Kuniyoshi; Zhang, Chaofeng

2018-05-01

Dendrobium crepidatum was one of the sources of Herba Dendrobii, a famous and precious traditional Chinese medicine. Indolizine-type alkaloids are the main characteristic ingredients of D. crepidatum, which possesses a variety of changeable skeletons. In the present study, we found that the total alkaloids of D. crepidatum (TAD) can inhibit the production of nitric oxide (NO) in lipopolysaccharide (LPS)-activated macrophages and showed protective effects against LPS-induced acute lung injury (ALI) in mice through downregulating the TLR4-mediated MyD88/MAPK signaling pathway. Further phytochemical study showed that six previously undescribed indolizine-type compounds, including a racemic mixture (dendrocrepidine A-E) were isolated from TAD. Meanwhile, dendrocrepidine F was separated into a pair of enantiomers by a chiral chromatography, and their absolute configurations were assigned by single-crystal X-ray diffraction analysis. The isomer (-)-dendrocrepidine F showed higher anti-inflammatory effects by inhibiting NO production in LPS-treated macrophages with an IC 50 value of 13.3 μM. Taken together, indolizine-type alkaloids are the active components of D. crepidatum through downregulating the TLR4-mediated pathway, indicating some kind of therapy of TAD for ALI treatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Acoustic cryocooler

DOEpatents

Swift, Gregory W.; Martin, Richard A.; Radenbaugh, Ray

1990-01-01

An acoustic cryocooler with no moving parts is formed from a thermoacoustic driver (TAD) driving a pulse tube refrigerator (PTR) through a standing wave tube. Thermoacoustic elements in the TAD are spaced apart a distance effective to accommodate the increased thermal penetration length arising from the relatively low TAD operating frequency in the range of 15-60 Hz. At these low operating frequencies, a long tube is required to support the standing wave. The tube may be coiled to reduce the overall length of the cryocooler. One or two PTR's are located on the standing wave tube adjacent antinodes in the standing wave to be driven by the standing wave pressure oscillations. It is predicted that a heat input of 1000 W at 1000 K will maintian a cooling load of 5 W at 80 K.

Solvent control of the morphology of the hole transport layer for high-performance perovskite solar cells

NASA Astrophysics Data System (ADS)

Xie, Xiaoyin; Liu, Guanchen; Chen, Li; Li, Shuangcui; Liu, Zhihai

2017-11-01

We investigated the effect of the morphology of 2,2‧,7,7‧-tetrakis-(N,N-di-p-methoxyphenylamine)-9,9‧-spirobifluorene (spiro-OMeTAD) prepared using chlorobenzene (CB) and 1,2-dichlorobenzene (DCB) on the performance of perovskite solar cells (PSCs). We find that a more uniform and smoother spiro-OMeTAD layer was obtained using DCB than CB. The PSCs prepared using DCB exhibited a higher power conversion efficiency (PCE = 16.2%) than those obtained using CB (PCE = 14.5%). The hysteresis was reduced from 4.8% to 0.6%, with improved stability. The highest PCE of PSCs prepared using DCB was 16.6%, indicating that the use of DCB for spiro-OMeTAD processing enables the fabrication of high-performance PSCs.

Implicit measurement of the latent heat in a magnetocaloric NiMnIn Heusler alloy

NASA Astrophysics Data System (ADS)

Ghahremani, Mohammadreza; ElBidweihy, Hatem; Bennett, Lawrence H.; Della Torre, Edward; Zou, Min; Johnson, Francis

2013-05-01

The latent heat linked with the first-order transformation of a NiMnIn Heusler alloy has been studied through direct measurements of the adiabatic temperature change, ΔTad, during magnetization process. The experimental procedure used guarantees independent data points and negates any contribution of hysteretic losses to the magnetocaloric effect. Thus, the differences between the magnitudes of ΔTad measurements during the magnetization with the initial temperature change directions from low-to-high and high-to-low are solely attributed to the latent heat exchange, which accompanies the irreversible structural first-order transformation. An estimate of the latent heat inducing such differences is about 0.292 J/g.

Impedance spectroscopy study of 2, 2, 7, 7' -tetra kis-(N,N-di-4-methoxy phenyl amino)-9,9'-spirobifluorene thin films

NASA Astrophysics Data System (ADS)

Rana, Omwati; Agrawal, Kalpana; Rajput, S. S.; Zulfequar, M.; Husain, M.; Kamalasanan, M. N.; Srivastava, Ritu

2016-05-01

The electrical properties of thermally evaporated film of 2,2,7,7'-tetrakis-(N,N-di-4-methoxyphenylamino)-9,9'-spirobifluorene (Spiro MeO TAD) have been investigated for hole only devices as a function of temperatures at frequency range from 1Hz to 1 MHz using Impedance spectroscopy. Cole-Cole plots, at each temperature, show semicircles that can be modeled with a contact resistance and parallel resistance -capacitor(R-C) circuits. Bulk resistance decreases and electrical conductivity increases with increasing temperature which indicate negative temperature coefficient of resistance nature and short range translational type hopping mechanism in Spiro MeO TAD thin films.

Developing Toolsets for AirBorne Data (TAD): Overview of Design Concept

NASA Astrophysics Data System (ADS)

Parker, L.; Perez, J.; Chen, G.; Benson, A.; Peeters, M. C.

2013-12-01

NASA has conducted airborne tropospheric chemistry studies for about three decades. These field campaigns have generated a great wealth of observations, including a wide range of the trace gases and aerosol properties. Even though the spatial and temporal coverage is limited, the aircraft data offer high resolution and comprehensive simultaneous coverage of many variables, e.g. ozone precursors, intermediate photochemical species, and photochemical products. The recent NASA Earth Venture Program has generated an unprecedented amount of aircraft observations in terms of the sheer number of measurements and data volume. The ASDC Toolset for Airborne Data (TAD) is being designed to meet the user community needs for aircraft data for scientific research on climate change and air quality relevant issues, particularly: 1) Provide timely access to a broad user community, 2) Provide an intuitive user interface to facilitate quick discovery of the variables and data, 3) Provide data products and tools to facilitate model assessment activities, e.g., merge files and data subsetting capabilities, 4) Provide simple utility 'calculators', e.g., unit conversion and aerosol size distribution processing, and 5) Provide Web Coverage Service capable tools to enhance the data usability. The general strategy and design of TAD will be presented.

Success rates and factors associated with failure of temporary anchorage devices: A prospective clinical trial.

PubMed

Aly, Shehab A; Alyan, Doha; Fayed, Mona S; Alhammadi, Maged S; Mostafa, Yehya A

2018-03-06

The objective of the present study was to investigate success rates and associated factors affecting temporary anchorage device (TAD) failure in different biomechanical applications. A total of 180 TADs were used as a part of 82 patients' treatment plan (24 males and 58 females); their mean age was 21.41 years. Three types of TADs were used: 50 (3M ESPE, Neuss, Germany), 56 (Bone screw; Jeil Medical, Seoul, Korea), and 74 (Morelli, Sorocaba, Brazil). Eight maxillary and four mandibular sites were selected for insertion. Three different lengths (6, 8, and 10 mm) and three different diameters (1.5, 1.6, and 1.8 mm) were used. The force levels were set at 50, 100, 150, 200, and 250 g. Patient-, implant-, and operator-dependent factors were evaluated throughout the 266 days of function. Qualitative variables were described by proportions and percentages and analyzed using χ 2 test. The overall success rate was 82.2%. The higher age group showed a significantly higher success rate. Oral hygiene showed a statistically-significant (P ˂ .05) difference between both success and failure groups. All other patient-related factors showed no significant differences. Regarding force levels used, the highest success rate was in 250 g and the lowest was in 100 g. There were no significant differences between both groups regarding other implant- and operator-related factors. Temporary anchorage devices have a good success rate and are beneficial to be integrated in orthodontic treatment planning. Patient age, oral hygiene, and force level are the most significant factors affecting TAD success. © 2018 John Wiley & Sons Australia, Ltd.

Global ionospheric and thermospheric response to the 5 April 2010 geomagnetic storm: An integrated data-model investigation

NASA Astrophysics Data System (ADS)

Lu, G.; Hagan, M. E.; Häusler, K.; Doornbos, E.; Bruinsma, S.; Anderson, B. J.; Korth, H.

2014-12-01

We present a case study of the 5 April 2010 geomagnetic storm using observations and numerical simulations. The event was driven by a fast-moving coronal mass ejection and despite being a moderate storm with a minimum Dst near -50 nT, the event exhibited elevated thermospheric density and surges of traveling atmospheric disturbances (TADs) more typically seen during major storms. The Thermosphere-Ionosphere-Mesosphere-Electrodynamics General Circulation Model (TIMEGCM) was used to assess how these features were generated and developed during the storm. The model simulations gave rise to TADs that were highly nonuniform with strong latitude and longitude/local time dependence. The TAD phase speeds ranged from 640 m/s to 780 m/s at 400 km and were ~5% lower at 300 km and approximately 10-15% lower at 200 km. In the lower thermosphere around 100 km, the TAD signatures were nearly unrecognizable due to much stronger influence of upward propagating atmospheric tides. The thermosphere simulation results were compared to observations available from the Gravity Field and Steady-State Ocean Circulation Explorer (GOCE), CHAllenging Minisatellite Payload (CHAMP) and Gravity Recovery and Climate Experiment (GRACE) satellites. Comparison with GOCE data shows that the TIMEGCM reproduced the cross-track winds over the polar region very well. The model-data comparison also revealed some differences, specifically, the simulations underestimated neutral mass density in the upper thermosphere above ~300 km and overestimated the storm recovery tome by 6 h. These discrepancies indicate that some heating or circulation dynamics and potentially cooling processes are not fully represented in the simulations, and also that updates to some parameterization schemes in the TIMEGCM are warranted.

Anomaly clustering in hyperspectral images

NASA Astrophysics Data System (ADS)

Doster, Timothy J.; Ross, David S.; Messinger, David W.; Basener, William F.

2009-05-01

The topological anomaly detection algorithm (TAD) differs from other anomaly detection algorithms in that it uses a topological/graph-theoretic model for the image background instead of modeling the image with a Gaussian normal distribution. In the construction of the model, TAD produces a hard threshold separating anomalous pixels from background in the image. We build on this feature of TAD by extending the algorithm so that it gives a measure of the number of anomalous objects, rather than the number of anomalous pixels, in a hyperspectral image. This is done by identifying, and integrating, clusters of anomalous pixels via a graph theoretical method combining spatial and spectral information. The method is applied to a cluttered HyMap image and combines small groups of pixels containing like materials, such as those corresponding to rooftops and cars, into individual clusters. This improves visualization and interpretation of objects.

Prevalence of Flp Pili-Encoding Plasmids in Cutibacterium acnes Isolates Obtained from Prostatic Tissue

PubMed Central

Davidsson, Sabina; Carlsson, Jessica; Mölling, Paula; Gashi, Natyra; Andrén, Ove; Andersson, Swen-Olof; Brzuszkiewicz, Elzbieta; Poehlein, Anja; Al-Zeer, Munir A.; Brinkmann, Volker; Scavenius, Carsten; Nazipi, Seven; Söderquist, Bo; Brüggemann, Holger

2017-01-01

Inflammation is one of the hallmarks of prostate cancer. The origin of inflammation is unknown, but microbial infections are suspected to play a role. In previous studies, the Gram-positive, low virulent bacterium Cutibacterium (formerly Propionibacterium) acnes was frequently isolated from prostatic tissue. It is unclear if the presence of the bacterium represents a true infection or a contamination. Here we investigated Cutibacterium acnes type II, also called subspecies defendens, which is the most prevalent type among prostatic C. acnes isolates. Genome sequencing of type II isolates identified large plasmids in several genomes. The plasmids are highly similar to previously identified linear plasmids of type I C. acnes strains associated with acne vulgaris. A PCR-based analysis revealed that 28.4% (21 out of 74) of all type II strains isolated from cancerous prostates carry a plasmid. The plasmid shows signatures for conjugative transfer. In addition, it contains a gene locus for tight adherence (tad) that is predicted to encode adhesive Flp (fimbrial low-molecular weight protein) pili. In subsequent experiments a tad locus-encoded putative pilin subunit was identified in the surface-exposed protein fraction of plasmid-positive C. acnes type II strains by mass spectrometry, indicating that the tad locus is functional. Additional plasmid-encoded proteins were detected in the secreted protein fraction, including two signal peptide-harboring proteins; the corresponding genes are specific for type II C. acnes, thus lacking from plasmid-positive type I C. acnes strains. Further support for the presence of Flp pili in C. acnes type II was provided by electron microscopy, revealing cell appendages in tad locus-positive strains. Our study provides new insight in the most prevalent prostatic subspecies of C. acnes, subsp. defendens, and indicates the existence of Flp pili in plasmid-positive strains. Such pili may support colonization and persistent infection of human prostates by C. acnes. PMID:29201018

Predicting chromatin architecture from models of polymer physics.

PubMed

Bianco, Simona; Chiariello, Andrea M; Annunziatella, Carlo; Esposito, Andrea; Nicodemi, Mario

2017-03-01

We review the picture of chromatin large-scale 3D organization emerging from the analysis of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a complex higher-order organization, extending from the sub-Mb to chromosomal scales, hierarchically folded in a structure of domains-within-domains (metaTADs). The domain folding hierarchy is partially conserved throughout differentiation, and deeply correlated to epigenomic features. Rearrangements in the metaTAD topology relate to gene expression modifications: in particular, in neuronal differentiation models, topologically associated domains (TADs) tend to have coherent expression changes within architecturally conserved metaTAD niches. To identify the nature of architectural domains and their molecular determinants within a principled approach, we discuss models based on polymer physics. We show that basic concepts of interacting polymer physics explain chromatin spatial organization across chromosomal scales and cell types. The 3D structure of genomic loci can be derived with high accuracy and its molecular determinants identified by crossing information with epigenomic databases. In particular, we illustrate the case of the Sox9 locus, linked to human congenital disorders. The model in-silico predictions on the effects of genomic rearrangements are confirmed by available 5C data. That can help establishing new diagnostic tools for diseases linked to chromatin mis-folding, such as congenital disorders and cancer.

A conserved tad pilus promotes Vibrio vulnificus oyster colonization.

PubMed

Pu, Meng; Duriez, Patrick; Arazi, Mattan; Rowe-Magnus, Dean A

2018-02-01

Vibrio vulnificus has the highest death rate (>35%) and per-case economic burden ($3.3 million) of any foodborne pathogen in the United States. Infections occur via open wounds or following ingestion of contaminated seafood, most infamously oysters. We isolated a 1000th generation descendant, designated NT that exhibited increased biofilm and aggregate formation relative to its parent. We identified two significant causal changes underlying these phenotypes. First, the entire 24-kb capsular polysaccharide biosynthesis locus, which is essential for virulence but inhibits biofilm formation, had been purged from the genome. However, NT formed more extensive biofilms and aggregates than a defined cps mutant, suggesting that additional factor(s) contributed to its phenotypes. Second, the expression of a tight adherence (tad) pilus locus was elevated in NT. Deletion of the associated pilin (flp) decreased NT biofilm and aggregate formation. Furthermore, NTΔflp strains were deficient relative to NT in an oyster colonization model, demonstrating a positive correlation between the biofilm and aggregation phenotypes associated with Tad pilus production and efficient bacterial retention by feeding oysters. Despite being widely distributed in the Vibrionaceae, this is the first demonstration of a bona fide physiological role for a Tad pilus in this bacterial family. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Assessing the impact of background spectral graph construction techniques on the topological anomaly detection algorithm

NASA Astrophysics Data System (ADS)

Ziemann, Amanda K.; Messinger, David W.; Albano, James A.; Basener, William F.

2012-06-01

Anomaly detection algorithms have historically been applied to hyperspectral imagery in order to identify pixels whose material content is incongruous with the background material in the scene. Typically, the application involves extracting man-made objects from natural and agricultural surroundings. A large challenge in designing these algorithms is determining which pixels initially constitute the background material within an image. The topological anomaly detection (TAD) algorithm constructs a graph theory-based, fully non-parametric topological model of the background in the image scene, and uses codensity to measure deviation from this background. In TAD, the initial graph theory structure of the image data is created by connecting an edge between any two pixel vertices x and y if the Euclidean distance between them is less than some resolution r. While this type of proximity graph is among the most well-known approaches to building a geometric graph based on a given set of data, there is a wide variety of dierent geometrically-based techniques. In this paper, we present a comparative test of the performance of TAD across four dierent constructs of the initial graph: mutual k-nearest neighbor graph, sigma-local graph for two different values of σ > 1, and the proximity graph originally implemented in TAD.

Stable chromosome condensation revealed by chromosome conformation capture

PubMed Central

Eagen, Kyle P.; Hartl, Tom A.; Kornberg, Roger D.

2015-01-01

SUMMARY Chemical cross-linking and DNA sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes. PMID:26544940

Comparison of anchorage reinforcement with temporary anchorage devices or a Herbst appliance during lingual orthodontic protraction of mandibular molars without maxillary counterbalance extraction.

PubMed

Metzner, Rebecca; Schwestka-Polly, Rainer; Helms, Hans-Joachim; Wiechmann, Dirk

2015-06-20

Orthodontic protraction of mandibular molars without maxillary counterbalance extraction in cases of aplasia or extraction requires stable anchorage. Reinforcement may be achieved by using either temporary anchorage devices (TAD) or a fixed, functional appliance. The objective was to compare the clinical effectiveness of both methods by testing the null-hypothesis of no significant difference in velocity of space closure (in mm/month) between them. In addition, we set out to describe the quality of posterior space management and treatment-related factors, such as loss of anchorage (assessed in terms of proportions of gap closure by posterior protraction or anterior retraction), frequencies of incomplete space closure, and potential improvement in the sagittal canine relationship. Twenty-seven subjects (15 male/12 female) with a total of 36 sites treated with a lingual multi-bracket appliance were available for retrospective evaluation of the effects of anchorage reinforcement achieved with either a Herbst appliance (n(subjects) = 15; 7 both-sided/8 single-sided Herbst appliances; n(sites) = 22) or TADs (n(subjects )= 12; 2 both-sided; 10 single-sided; n(sites) = 14). Descriptive analysis was based on measurements using intra-oral photographs which were individually scaled to corresponding plaster casts and taken on insertion of anchorage mechanics (T1), following removal of anchorage mechanics (T2), and at the end of multi-bracket treatment (T3). The null-hypothesis was rejected: The rate of mean molar protraction was significantly faster in the Herbst-reinforced group (0.51 mm/month) than in the TAD group (0.35). While complete space closure by sheer protraction of posterior teeth was achieved in all Herbst-treated cases, space closure in the TAD group was achieved in 76.9% of subjects by sheer protraction of molars, and it was incomplete in 50% of cases (mean gap residues: 1 mm). Whilst there was a deterioration in the canine relationship towards Angle-Class II malocclusion in 57.14% of space closure sites in TAD-treated subjects (indicating a loss of anchorage), an improvement in canine occlusion was observed in 90.9% of Herbst-treated cases. Subjects requiring rapid space closure by molar protraction in combination with a correction of distal occlusion may benefit from using Herbst appliances for anterior segment anchorage reinforcement rather than TAD anchorage.

Toolsets for Airborne Data (TAD): Enhanced Airborne Data Merging Functionality through Spatial and Temporal Subsetting

NASA Astrophysics Data System (ADS)

Early, A. B.; Chen, G.; Beach, A. L., III; Northup, E. A.

2016-12-01

NASA has conducted airborne tropospheric chemistry studies for over three decades. These field campaigns have generated a great wealth of observations, including a wide range of the trace gases and aerosol properties. The Atmospheric Science Data Center (ASDC) at NASA Langley Research Center in Hampton Virginia originally developed the Toolsets for Airborne Data (TAD) web application in September 2013 to meet the user community needs for manipulating aircraft data for scientific research on climate change and air quality relevant issues. The analysis of airborne data typically requires data subsetting, which can be challenging and resource intensive for end users. In an effort to streamline this process, the TAD toolset enhancements will include new data subsetting features and updates to the current database model. These will include two subsetters: temporal and spatial, and vertical profile. The temporal and spatial subsetter will allow users to both focus on data from a specific location and/or time period. The vertical profile subsetter will retrieve data collected during an individual aircraft ascent or descent spiral. This effort will allow for the automation of the typically labor-intensive manual data subsetting process, which will provide users with data tailored to their specific research interests. The development of these enhancements will be discussed in this presentation.

Comparative analysis of zonal systems for macro-level crash modeling.

PubMed

Cai, Qing; Abdel-Aty, Mohamed; Lee, Jaeyoung; Eluru, Naveen

2017-06-01

Macro-level traffic safety analysis has been undertaken at different spatial configurations. However, clear guidelines for the appropriate zonal system selection for safety analysis are unavailable. In this study, a comparative analysis was conducted to determine the optimal zonal system for macroscopic crash modeling considering census tracts (CTs), state-wide traffic analysis zones (STAZs), and a newly developed traffic-related zone system labeled traffic analysis districts (TADs). Poisson lognormal models for three crash types (i.e., total, severe, and non-motorized mode crashes) are developed based on the three zonal systems without and with consideration of spatial autocorrelation. The study proposes a method to compare the modeling performance of the three types of geographic units at different spatial configurations through a grid based framework. Specifically, the study region is partitioned to grids of various sizes and the model prediction accuracy of the various macro models is considered within these grids of various sizes. These model comparison results for all crash types indicated that the models based on TADs consistently offer a better performance compared to the others. Besides, the models considering spatial autocorrelation outperform the ones that do not consider it. Based on the modeling results and motivation for developing the different zonal systems, it is recommended using CTs for socio-demographic data collection, employing TAZs for transportation demand forecasting, and adopting TADs for transportation safety planning. The findings from this study can help practitioners select appropriate zonal systems for traffic crash modeling, which leads to develop more efficient policies to enhance transportation safety. Copyright © 2017 Elsevier Ltd and National Safety Council. All rights reserved.

Dynamics, Conformational Entropy, and Frustration in Protein-Protein Interactions Involving an Intrinsically Disordered Protein Domain.

PubMed

Lindström, Ida; Dogan, Jakob

2018-05-18

Intrinsically disordered proteins (IDPs) are abundant in the eukaryotic proteome. However, little is known about the role of subnanosecond dynamics and the conformational entropy that it represents in protein-protein interactions involving IDPs. Using nuclear magnetic resonance side chain and backbone relaxation, stopped-flow kinetics, isothermal titration calorimetry, and computational studies, we have characterized the interaction between the globular TAZ1 domain of the CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2). We show that the TAZ1/TAD-STAT2 complex retains considerable subnanosecond motions, with TAD-STAT2 undergoing only a partial disorder-to-order transition. We report here the first experimental determination of the conformational entropy change for both binding partners in an IDP binding interaction and find that the total change even exceeds in magnitude the binding enthalpy and is comparable to the contribution from the hydrophobic effect, demonstrating its importance in the binding energetics. Furthermore, we show that the conformational entropy change for TAZ1 is also instrumental in maintaining a biologically meaningful binding affinity. Strikingly, a spatial clustering of very high amplitude motions and a cluster of more rigid sites in the complex exist, which through computational studies we found to overlap with regions that experience energetic frustration and are less frustrated, respectively. Thus, the residual dynamics in the bound state could be necessary for faster dissociation, which is important for proteins that interact with multiple binding partners.

Longitudinal study of the ionospheric response to the geomagnetic storm of 15 May 2005 and manifestation of TADs

NASA Astrophysics Data System (ADS)

Sharma, S.; Galav, P.; Dashora, N.; Pandey, R.

2011-06-01

Response of low latitude ionosphere to the geomagnetic storm of 15 May 2005 has been studied using total electron content (TEC) data, obtained from three GPS stations namely, Yibal, Udaipur and Kunming situated near the northern crest of equatorial ionization anomaly at different longitudes. Solar wind parameters, north-south component of the interplanetary magnetic field (IMF Bz) and AE index data have been used to infer the strength of the geomagnetic storm. A large value of eastward interplanetary electric field at 06:15 UT, during the time of maximum southward IMF Bz has been used to infer the transmission of an eastward prompt penetration electric field (PPEF) which resulted in a peak in TEC at 07:45 UT due to the local uplift of plasma in the low latitudes near the anomaly crest over a wide range of longitudes. Wave-like modulations superposed over the second enhancement in TEC between 09:15 UT to 10:30 UT have been observed at all the three stations. The second enhancement in TEC along with the modulations of up to 5 TECU have been attributed to the combined effect of super plasma fountain and traveling atmospheric disturbances (TAD). Observed large enhancements in TEC are a cause of concern for satellite based navigation and ground positioning. Increased [O/N2] ratio between 09:15 UT to 10:15 UT when modulations in TEC have been also observed, confirms the presence of TADs over a wide range of longitudes.

NASA Langley Atmospheric Science Data Center Toolsets for Airborne Data (TAD): User Interface Design and Development

NASA Astrophysics Data System (ADS)

Beach, A. L., III; Early, A. B.; Chen, G.; Parker, L.

2014-12-01

NASA has conducted airborne tropospheric chemistry studies for about three decades. These field campaigns have generated a great wealth of observations, which are characterized by a wide range of trace gases and aerosol properties. The airborne observational data have often been used in assessment and validation of models and satellite instruments. The ASDC Toolset for Airborne Data (TAD) is being designed to meet the user community needs for manipulating aircraft data for scientific research on climate change and air quality relevant issues. Given the sheer volume of data variables across field campaigns and instruments reporting data on different time scales, this data is often difficult and time-intensive for researchers to analyze. The TAD web application is designed to provide an intuitive user interface (UI) to facilitate quick and efficient discovery from a vast number of airborne variables and data. Users are given the option to search based on high-level parameter groups, individual common names, mission and platform, as well as date ranges. Experienced users can immediately filter by keyword using the global search option. Once the user has chosen their required variables, they are given the option to either request PI data files based on their search criteria or create merged data, i.e. geo-located data from one or more measurement PIs. The purpose of the merged data feature is to allow users to compare data from one flight, as not all data from each flight is taken on the same time scale. Time bases can be continuous or based on the time base from one of the measurement time scales and intervals. After an order is submitted and processed, an ASDC email is sent to the user with a link for data download. The TAD user interface design, application architecture, and proposed future enhancements will be presented.

Tunnel Vision in Population Research: A Case in Point.

ERIC Educational Resources Information Center

Serron, Luis A.

This paper takes a critical look at a demographic study of Mexico, namely, Tad Fisher's "Mexico: The Problem of People". Fisher's study relies heavily on population growth as a poverty generating factor. The paper states that Fisher's study exhibited perceptual narrowness by not considering the Marxist interpretation that capitalist…

Producing methane, methanol and electricity from organic waste of fermentation reaction using novel microbes.

PubMed

Dhiman, Saurabh Sudha; Shrestha, Namita; David, Aditi; Basotra, Neha; Johnson, Glenn R; Chadha, Bhupinder S; Gadhamshetty, Venkataramana; Sani, Rajesh K

2018-06-01

Residual solid and liquid streams from the one-pot CRUDE (Conversion of Raw and Untreated Disposal into Ethanol) process were treated with two separate biochemical routes for renewable energy transformation. The solid residual stream was subjected to thermophilic anaerobic digestion (TAD), which produced 95 ± 7 L methane kg -1 volatile solid with an overall energy efficiency of 12.9 ± 1.7%. A methanotroph, Methyloferula sp., was deployed for oxidation of mixed TAD biogas into methanol. The residual liquid stream from CRUDE process was used in a Microbial Fuel Cell (MFC) to produce electricity. Material balance calculations confirmed the integration of biochemical routes (i.e. CRUDE, TAD, and MFC) for developing a sustainable approach of energy regeneration. The current work demonstrates the utilization of different residual streams originated after food waste processing to release minimal organic load to the environment. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.

PubMed

Gustafson, Chelsea L; Parsley, Nicole C; Asimgil, Hande; Lee, Hsiau-Wei; Ahlbach, Christopher; Michael, Alicia K; Xu, Haiyan; Williams, Owen L; Davis, Tara L; Liu, Andrew C; Partch, Carrie L

2017-05-18

The C-terminal transactivation domain (TAD) of BMAL1 (brain and muscle ARNT-like 1) is a regulatory hub for transcriptional coactivators and repressors that compete for binding and, consequently, contributes to period determination of the mammalian circadian clock. Here, we report the discovery of two distinct conformational states that slowly exchange within the dynamic TAD to control timing. This binary switch results from cis/trans isomerization about a highly conserved Trp-Pro imide bond in a region of the TAD that is required for normal circadian timekeeping. Both cis and trans isomers interact with transcriptional regulators, suggesting that isomerization could serve a role in assembling regulatory complexes in vivo. Toward this end, we show that locking the switch into the trans isomer leads to shortened circadian periods. Furthermore, isomerization is regulated by the cyclophilin family of peptidyl-prolyl isomerases, highlighting the potential for regulation of BMAL1 protein dynamics in period determination. Copyright © 2017 Elsevier Inc. All rights reserved.

Enhanced Versus Conventional Sludge Anaerobic Processes: Performances and Techno-Economic Assessment.

PubMed

Gianico, Andrea; Bertanza, Giorgio; Braguglia, Camilla M; Canato, Matteo; Gallipoli, Agata; Laera, Giuseppe; Levantesi, Caterina; Mininni, Giuseppe

2016-05-01

Sewage sludge processing is a key issue in water resource recovery facilities due to the inefficacy of conventional treatments to produce high quality biosolids to be safely used in agriculture. Under this framework, the performances of several enhanced stabilization processes, namely ultrasound-pretreated Mesophilic Anaerobic Digestion (US+MAD), thermophilic anaerobic digestion (TAD), thermal-pretreated TAD (TH+TAD) and ultrasound-pretreated inverse Temperature Phased Anaerobic Digestion (US+iTPAD) have been investigated. Such enhanced processes resulted in higher biogas yields and higher destruction of pathogens with respect to conventional MAD process, thus suggesting their feasibility in full-scale implementation perspectives. A procedure for technical-economic comparison of new sludge processing lines against conventional ones (benchmarking) was developed, based on the definition of technical issues (e.g. reliability, complexity, etc.) which are rated for each situation. Moreover, capital and operating costs were estimated. The enhanced processes analyzed in this work showed some potentially critical items, mainly related to energy balance and reagent consumption.

Crystallization and preliminary X-ray crystallographic analysis of the tRNA-specific adenosine deaminase from Streptococcus pyogenes

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

Ku, Min-Je; Lee, Won-Ho; Biotechnology and Genetic Engineering, Korea University, Seoul 136-701

2005-04-01

The tRNA-specific adenosine deaminase from the pathogenic bacteria S. pyogenes has been overexpressed and crystallized. The tRNA-specific adenosine deaminase from the pathogenic bacteria Streptococcus pyogenes (spTAD) has been overexpressed in Escherichia coli and crystallized in the presence of Zn{sup 2+} ion at 295 K using ammonium sulfate as a precipitant. Flash-cooled crystals of spTAD diffracted to 2.0 Å using 30%(v/v) glycerol as a cryoprotectant. X-ray diffraction data have been collected to 2.0 Å using synchrotron radiation. The crystal belongs to the tetragonal space group P4{sub 2}2{sub 1}2, with unit-cell parameters a = b = 81.042, c = 81.270 Å. Themore » asymmetric unit contains one subunit of spTAD, with a corresponding crystal volume per protein weight (V{sub M}) of 3.3 Å{sup 3} Da{sup −1} and a solvent content of 62.7%.« less

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

PubMed

Nora, Elphège P; Goloborodko, Anton; Valton, Anne-Laure; Gibcus, Johan H; Uebersohn, Alec; Abdennur, Nezar; Dekker, Job; Mirny, Leonid A; Bruneau, Benoit G

2017-05-18

The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Furthermore, our data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization. Copyright © 2017 Elsevier Inc. All rights reserved.

Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization

PubMed Central

Nora, Elphège P.; Goloborodko, Anton; Valton, Anne-Laure; Gibcus, Johan H.; Uebersohn, Alec; Abdennur, Nezar; Dekker, Job; Mirny, Leonid A.; Bruneau, Benoit G.

2017-01-01

Summary The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Further, our data support that CTCF mediates transcriptional insulator function through enhancer-blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding these results provide new fundamental insights into the rules governing mammalian genome organization. PMID:28525758

Spiro-OMeTAD single crystals: Remarkably enhanced charge-carrier transport via mesoscale ordering

PubMed Central

Shi, Dong; Qin, Xiang; Li, Yuan; He, Yao; Zhong, Cheng; Pan, Jun; Dong, Huanli; Xu, Wei; Li, Tao; Hu, Wenping; Brédas, Jean-Luc; Bakr, Osman M.

2016-01-01

We report the crystal structure and hole-transport mechanism in spiro-OMeTAD [2,2′,7,7′-tetrakis(N,N-di-p-methoxyphenyl-amine)9,9′-spirobifluorene], the dominant hole-transporting material in perovskite and solid-state dye-sensitized solar cells. Despite spiro-OMeTAD’s paramount role in such devices, its crystal structure was unknown because of highly disordered solution-processed films; the hole-transport pathways remained ill-defined and the charge carrier mobilities were low, posing a major bottleneck for advancing cell efficiencies. We devised an antisolvent crystallization strategy to grow single crystals of spiro-OMeTAD, which allowed us to experimentally elucidate its molecular packing and transport properties. Electronic structure calculations enabled us to map spiro-OMeTAD’s intermolecular charge-hopping pathways. Promisingly, single-crystal mobilities were found to exceed their thin-film counterparts by three orders of magnitude. Our findings underscore mesoscale ordering as a key strategy to achieving breakthroughs in hole-transport material engineering of solar cells. PMID:27152342

Can protein-fortified pasta serve as a meat substitute?

PubMed

Bingham, C J; Tsay, R; Babayan, V K; Blackburn, G L

1982-01-01

A seventeen-day metabolic balance study was conducted with 13 healthy adult subjects to test the protein utilization of a meat-based diet and a protein-fortified pasta diet in an isonitrogenous, isocaloric inpatient study (averaging 112 gm of protein, and 2,500 cal). Intakes of calories, protein, fat, and carbohydrates, as well as ratios of meat protein or protein-fortified pasta protein (PEP), were controlled throughout the diets. The study was comprised of three experimental periods: a seven-day meat-protein control period, representing the typical american diet (TAD), averaging 18% protein, 40% fat, and 42% carbohydrate, a seven-day protein-enriched pasta control period (PEP), averaging 18% protein, 29% fat, and 53% carbohydrates, and a three-day PEP period composed of varied recipes, averaging 18% protein, 29% fat, and 53% carbohydrates. The subjects who consumed both the TAD and PEP diets achieved nitrogen balance (2.5 gN +/- 0.7 on the TAD, 2 gN +/- 0 on PEP with the PEP diet resulting in a decrease in plasma cholesterol (32 mg/dl, P less than .005), and a decrease in systolic (5.25 mm/Hg P less than .025) and diastolic blood pressure (5 mm/Hg, P less than .05), which was associated with an increase in urinary sodium excretion (19 +/- 17 mEq/day, P less than .025). In this study, it was determined that protein-fortified pasta may serve as a meat alternative. The PEP diet, which includes a beneficial change in fat/carbohydrate ratio, can alter lipid profiles, blood pressure, and sodium excretion, thus leading to improved health status and a decrease in cardiac risk factors.

How does transportation affordability vary among TODs, TADs, and other areas?

DOT National Transportation Integrated Search

2017-08-01

Transit-oriented development (TOD) has gained popularity worldwide as a sustainable form of urbanism; it concentrates development near a transit station so as to reduce auto-dependency and increase ridership. Existing travel behavior studies in the c...

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.

PubMed

Wolff, Joachim; Bhardwaj, Vivek; Nothjunge, Stephan; Richard, Gautier; Renschler, Gina; Gilsbach, Ralf; Manke, Thomas; Backofen, Rolf; Ramírez, Fidel; Grüning, Björn A

2018-06-13

Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization. With the Galaxy HiCExplorer web server, users with little bioinformatic background can perform every step of the analysis in one workflow: mapping of the raw sequence data, creation of Hi-C contact matrices, quality assessment, correction of contact matrices and identification of topological associated domains (TADs) and A/B compartments. Users can create publication ready plots of the contact matrix, A/B compartments, and TADs on a selected genomic locus, along with additional information like gene tracks or ChIP-seq signals. Galaxy HiCExplorer is freely usable at: https://hicexplorer.usegalaxy.eu and is available as a Docker container: https://github.com/deeptools/docker-galaxy-hicexplorer.

Assessing Meritorious Teacher Performance: A Differential Validity Study.

ERIC Educational Resources Information Center

Ellett, Chad D; Capie, William

The Teacher Assessment and Development System (TADS) - Meritorious Teacher Program (MTP) FORM instrument is used in the Dade County Public Schools, Miami, Florida, to evaluate teachers. Its validity for decisions concerning merit pay for master teachers was examined in this study. Specifically, its ability to discriminate between high performing…

SSME 3-D Turnaround Duct flow analysis - CFD predictions

NASA Technical Reports Server (NTRS)

Brankovic, Andreja; Stowers, Steven T.; Mcconnaughey, Paul

1988-01-01

CFD analysis is presently employed to obtain an improved flowfield for an individual flowpath in the case of the Space Shuttle Main Engine's High Pressure Fuel Turbopump Turn-Around Duct (TAD), which conducts the flow exiting from the gas turbines into the fuel bowl. It is demonstrated that the application of CFD to TAD flow analysis, giving attention to the duct's configuration and to the number, shape, and alignment of the diffuser struts, can enhance understanding of flow physics and result in improved duct design and performance.

Titan Aerial Daughtercraft (TAD) for Surface Studies from a Lander or Balloon

NASA Astrophysics Data System (ADS)

Matthies, L.; Tokumaru, P.; Sherrit, S.; Beauchamp, P.

2014-06-01

Recent rapid progress on autonomous navigation of micro air vehicles for terrestrial applications opens new possibilities for a small aerial vehicle that could deploy from a Titan lander or balloon to acquire samples for analysis on the mothership.

Exploring the electrochemical properties of hole transport materials with spiro-cores for efficient perovskite solar cells from first-principles.

PubMed

Chi, Wei-Jie; Li, Quan-Song; Li, Ze-Sheng

2016-03-21

Perovskite solar cells (PSCs) with organic small molecules as hole transport materials (HTMs) have attracted considerable attention due to their power conversion efficiencies as high as 20%. In the present work, three new spiro-type hole transport materials with spiro-cores, i.e. Spiro-F1, Spiro-F2 and Spiro-F3, are investigated by using density functional theory combined with the Marcus theory and Einstein relation. Based on the calculated and experimental highest occupied molecular orbital (HOMO) levels of 30 reference molecules, an empirical equation, which can predict the HOMO levels of hole transport materials accurately, is proposed. Moreover, a simplified method, in which the hole transport pathways are simplified to be one-dimensional, is presented and adopted to qualitatively compare the molecular hole mobilities. The calculated results show that the perovskite solar cells with the new hole transport materials can have higher open-circuit voltages due to the lower HOMO levels of Spiro-F1 (-5.31 eV), Spiro-F2 (-5.42 eV) and Spiro-F3 (-5.10 eV) compared with that of Spiro-OMeTAD (-5.09 eV). Furthermore, the hole mobilities of Spiro-F1 (1.75 × 10(-2) cm(2) V(-1) s(-1)) and Spiro-F3 (7.59 × 10(-3) cm(2) V(-1) s(-1)) are 3.1 and 1.4 times that of Spiro-OMeTAD (5.65 × 10(-3) cm(2) V(-1) s(-1)) respectively, due to small reorganization energies and large transfer integrals. Interestingly, the stability properties of Spiro-F1 and Spiro-F2 are shown to be comparable to that of Spiro-OMeTAD, and the dimers of Spiro-F2 and Spiro-F3 possess better stability than that of Spiro-OMeTAD. Taking into consideration the appropriate HOMO level, improved hole mobility and enhanced stability, Spiro-F1 and Spiro-F3 may become the most promising alternatives to Spiro-OMeTAD. The present work offers a new design strategy and reliable calculation methods towards the development of excellent organic small molecules as HTMs for highly efficient and stable PSCs.

Regional and international approaches on prevention and control of animal transboundary and emerging diseases.

PubMed

Domenech, J; Lubroth, J; Eddi, C; Martin, V; Roger, F

2006-10-01

Transboundary animal diseases pose a serious risk to the world animal agriculture and food security and jeopardize international trade. The world has been facing devastating economic losses from major outbreaks of transboundary animal diseases (TADs) such as foot-and-mouth disease, classical swine fever, rinderpest, peste des petits ruminants (PPR), and Rift Valley fever. Lately the highly pathogenic avian influenza (HPAI) due to H5N1 virus, has become an international crisis as all regions around the world can be considered at risk. In the past decades, public health authorities within industrialized countries have been faced with an increasing number of food safety issues. The situation is equally serious in developing countries. The globalization of food (and feed) trade, facilitated by the liberalization of world trade, while offering many benefits and opportunities, also represents new risks. The GF-TADs Global Secretariat has carried out several regional consultations for the identification of priority diseases and best ways for their administration, prevention and control. In the questionnaires carried out and through the consultative process, it was noted that globally, FMD was ranked as the first and foremost priority. Rift Valley fever, and today highly pathogenic avian influenza, are defined as major animal diseases which also affect human health. PPR and CBPP, a disease which is particularly serious in Africa and finally, African swine fever (ASF) and classical swine fever (CSF) are also regionally recognised as top priorities on which the Framework is determined to work. The FAO philosophy--shared by the OIE--embraces the need to prevent and control TADs and emerging diseases at their source, which is most of the time in developing countries. Regional and international approaches have to be followed, and the FAO and OIE GF-TADs initiative provides the appropriate concepts and objectives as well as an organizational framework to link international and regional organizations at the service of their countries to better prevent and control the risks on animal and human health and the economic impact of TADs and emerging animal diseases.

The mechanism of ΔT variation in coupled heat transfer and phase transformation for elastocaloric materials and its application in materials characterization

NASA Astrophysics Data System (ADS)

Qian, Suxin; Yuan, Lifen; Yu, Jianlin; Yan, Gang

2017-11-01

Elastocaloric cooling serves as a promising environmental friendly candidate with substantial energy saving potential as the next generation cooling technology for air-conditioning, refrigeration, and electronic cooling applications. The temperature change (ΔT) of elastocaloric materials is a direct measure of their elastocaloric effect, which scales proportionally with the device cooling performance based on this phenomenon. Here, the underlying physics between the measured ΔT and the adiabatic temperature span ΔTad is revealed by theoretical investigation of the simplified energy equation describing the coupled simultaneous heat transfer and phase transformation processes. The revealed relation of ΔT depends on a simple and symmetric non-linear function, which requires the introduction of an important dimensionless number Φ, defined as the ratio between convective heat transfer energy and variation of internal energy of the material. The theory was supported by more than 100 data points from the open literature for four different material compositions. Based on the theory, a data sampling and reduction technique was proposed to assist future material characterization studies. Instead of approaching ΔTad by applying an ultrafast strain rate in the old way, the proposed prediction of ΔTad is based on the non-linear least squares fitting method with the measured ΔT dataset at different strain rates within the moderate range. Numerical case studies indicated that the uncertainty associated with the proposed method is within ±1 K if the sampled data satisfied two conditions. In addition, the heat transfer coefficient can be estimated as a by-product of the least squares fitting method proposed in this study.

Understanding the Structural Ensembles of a Highly Extended Disordered Protein†

PubMed Central

Daughdrill, Gary W.; Kashtanov, Stepan; Stancik, Amber; Hill, Shannon E.; Helms, Gregory; Muschol, Martin

2013-01-01

Developing a comprehensive description of the equilibrium structural ensembles for intrinsically disordered proteins (IDPs) is essential to understanding their function. The p53 transactivation domain (p53TAD) is an IDP that interacts with multiple protein partners and contains numerous phosphorylation sites. Multiple techniques were used to investigate the equilibrium structural ensemble of p53TAD in its native and chemically unfolded states. The results from these experiments show that the native state of p53TAD has dimensions similar to a classical random coil while the chemically unfolded state is more extended. To investigate the molecular properties responsible for this behavior, a novel algorithm that generates diverse and unbiased structural ensembles of IDPs was developed. This algorithm was used to generate a large pool of plausible p53TAD structures that were reweighted to identify a subset of structures with the best fit to small angle X-ray scattering data. High weight structures in the native state ensemble show features that are localized to protein binding sites and regions with high proline content. The features localized to the protein binding sites are mostly eliminated in the chemically unfolded ensemble; while, the regions with high proline content remain relatively unaffected. Data from NMR experiments support these results, showing that residues from the protein binding sites experience larger environmental changes upon unfolding by urea than regions with high proline content. This behavior is consistent with the urea-induced exposure of nonpolar and aromatic side-chains in the protein binding sites that are partially excluded from solvent in the native state ensemble. PMID:21979461

Effectiveness of TAD-anchored maxillary protraction in late mixed dentition.

PubMed

Feng, Xiaoxia; Li, Jianhua; Li, Yu; Zhao, Zhihe; Zhao, Sen; Wang, Jue

2012-11-01

To evaluate the effectiveness of temporary anchorage device (TAD)-anchored maxillary protraction (MP) in terms of the skeletal and dentoalveolar changes and to compare it with traditional tooth-anchored MP. A computerized literature search for relative randomized controlled trials and prospective controlled trials was performed in PubMed, MEDLINE, Cochrane Central Register of Controlled Trials, Embase, CNKI, and Google Scholar, complemented with manual search. Data extraction and quality assessment were carried out by two reviewers independently. Meta-analysis was followed when possible; otherwise, description was done. Forty articles were found, among which four trials were qualified for meta-analysis. The results showed that there was significant difference between TAD-anchored MP and untreated control in terms of maxillary advancement (weighted mean differences (WMD) 3.08 mm; 95% CI: 1.61 to approximately 4.56; P < .0001), but there were no consistent points in terms of mandibular rotation. Also, there were significant differences between both treatment patterns regarding maxillary advancement (WMD 1.41 mm; 95% CI: 0.47 to approximately 2.35; P  =  .003), mandibular rotation (WMD -1.39°, 95% CI: -2.47 to approximately -0.31; P  =  .01), proclination of maxillary incisors (WMD -2.29°; 95% CI: -4.41 to approximately -0.17; P  =  .03), and extrusion of maxillary molars (WMD -1.68 mm; 95% CI: -2.51 to approximately -0.85; P < .0001). According to the present results, TAD-anchored MP might have a greater maxillary advancement effect and might reduce skeletal and dental side effects, compared with tooth-anchored MP.

Adiabatic magnetocaloric effect in Ni50Mn35In15 ribbons

NASA Astrophysics Data System (ADS)

Álvarez-Alonso, P.; Aguilar-Ortiz, C. O.; Camarillo, J. P.; Salazar, D.; Flores-Zúñiga, H.; Chernenko, V. A.

2016-11-01

Heusler-type Ni-Mn-based metamagnetic shape memory alloys (MetaMSMAs) are promising candidates for magnetic refrigeration. To increase heat exchange rate and efficiency of cooling, the material should have a high surface/volume ratio. In this work, the typical Ni50Mn35In15 MetaMSMA was selected to fabricate thin ribbons by melt-spinning. The characteristic transformations of the ribbons were determined by calorimetry, X-ray diffraction, scanning electron microscopy and thermomagnetization measurements. The inverse and conventional magnetocaloric effects (MCEs) associated with the martensitic transformation (MT) and the ferromagnetic transition of the austenite (TCA), respectively, were measured directly by the adiabatic method (ΔTad) and indirectly by estimating the magnetic entropy change from magnetization measurements. It is found that the ribbons exhibit large values of ΔTad = -1.1 K at μ0ΔH = 1.9 T, in the vicinity of the MT temperature of 300 K for inverse MCE, and ΔTad = 2.3 K for conventional MCE at TCA = 309 K. This result strongly motivates further development of different MetaMSMA refrigerants shaped as ribbons.

An innovative intermittent-vacuum assisted thermophilic anaerobic digestion process for effective animal manure utilization and treatment.

PubMed

Zhang, Renchuan; Anderson, Erik; Addy, Min; Deng, Xiangyuan; Kabir, Fayal; Lu, Qian; Ma, Yiwei; Cheng, Yanling; Liu, Yuhuan; Chen, Paul; Ruan, Roger

2017-11-01

Intermittent-vacuum stripping (IVS) was developed as a pretreatment for thermophilic anaerobic digestion (TAD) to improve methanogenesis and hydrolysis activity through preventing free ammonia and hydrogen sulfide (H 2 S) inhibition from liquid swine manure (LSM). Over 98% of ammonia and 38% organic nitrogen were removed in 60min from 55°C to 85°C with vacuum pressure (from 100.63±3.79mmHg to 360.91±7.39mmHg) at initial pH 10.0 by IVS. Thermophilic methanogenesis and hydrolysis activity of pretreated LSM increased 52.25% (from 11.56±1.75% to 17.60±0.49%) in 25days and 40% (from 10days to 6days) in bio-methane potential assay. Over 80% H 2 S and total nitrogen were removed by IVS assistance, while around 70% nitrogen was recycled as ammonium sulfate. Therefore, IVS-TAD combination could be an effective strategy to improve TAD efficiency, whose elution is more easily utilized in algae cultivation and/or hydroponic system. Copyright © 2017 Elsevier Ltd. All rights reserved.

Separation of tricyclic antidepressants by capillary zone electrophoresis with N,N,N',N'-tetramethyl-1,3-butanediamine (TMBD) as an effective electrolyte additive.

PubMed

Dell'Aquila, Caterina

2002-09-05

Five tricyclic antidepressants (TADs), desipramyne, nortriptyline, imipramine, doxepin and amitriptyline, were separated by using the N,N,N',N'-tetramethyl-1,3-butanediamine (TMBD) as additive in the background electrolyte solution. Because the tricyclic antidepressants are similar in structure, mass and pka values, their separation, by capillary zone electrophoresis, requires the careful manipulation of parameters, such as the pH and the composition of the electrolyte solution. As basic drugs, the TADs interact with the silanol groups on the capillary wall giving rise to peak broadening and asymmetry, non reproducible migration times and failing in selectivity. Different concentrations of TMBD (40, 60, 100 and 150 mM) were used at pH 9.5, but only a 100 mM TMBD allowed a good separation and a high efficiency for all the TADs. At this pH the separation was not possible without additive. This result is due to the reduced electroosmotic flow whose mobility is at a value of 10(-9) m(2) V(-1) s(-1).

Cobalt dopant with deep redox potential for organometal halide hybrid solar cells.

PubMed

Koh, Teck Ming; Dharani, Sabba; Li, Hairong; Prabhakar, Rajiv Ramanujam; Mathews, Nripan; Grimsdale, Andrew C; Mhaisalkar, Subodh G

2014-07-01

In this work, we report a new cobalt(III) complex, tris[2-(1H-pyrazol-1-yl)pyrimidine]cobalt(III) tris[bis(trifluoromethylsulfonyl)imide] (MY11), with deep redox potential (1.27 V vs NHE) as dopant for 2,2',7,7'-tetrakis-(N,N-di-p-methoxyphenylamine)-9,9'-spirobifluorene (spiro-OMeTAD). This dopant possesses, to the best of our knowledge, the deepest redox potential among all cobalt-based dopants used in solar cell applications, allowing it to dope a wide range of hole-conductors. We demonstrate the tuning of redox potential of the Co dopant by incorporating pyrimidine moiety in the ligand. We characterize the optical and electrochemical properties of the newly synthesized dopant and show impressive spiro-to-spiro(+) conversion. Lastly, we fabricate high efficiency perovskite-based solar cells using MY11 as dopant for molecular hole-conductor, spiro-OMeTAD, to reveal the impact of this dopant in photovoltaic performance. An overall power conversion efficiency of 12% is achieved using MY11 as p-type dopant to spiro-OMeTAD. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transit-oriented development: an examination of America's transit precincts in 2000 & 2010.

DOT National Transportation Integrated Search

2013-06-01

This study creates a typology of all fixed transit precincts across the United States to categorize all stations as either a Transit Oriented Development (TOD), Transit Adjacent Development (TAD) or hybrid. This typology is based on an index that acc...

Fate of antibiotic resistance genes and metal resistance genes during thermophilic aerobic digestion of sewage sludge.

PubMed

Jang, Hyun Min; Lee, Jangwoo; Kim, Young Beom; Jeon, Jong Hun; Shin, Jingyeong; Park, Mee-Rye; Kim, Young Mo

2018-02-01

This study examines the fate of twenty-three representative antibiotic resistance genes (ARGs) encoding tetracyclines, sulfonamides, quinolones, β-lactam antibiotics, macrolides, florfenicol and multidrug resistance during thermophilic aerobic digestion (TAD) of sewage sludge. The bacterial community, class 1 integrons (intI1) and four metal resistance genes (MRGs) were also quantified to determine the key drivers of changes in ARGs during TAD. At the end of digestion, significant decreases in the quantities of ARGs, MRGs and intI1 as well as 16S rRNA genes were observed. Partial redundancy analysis (RDA) showed that shifts in temperature were the key factors affecting a decrease in ARGs. Shifts in temperature led to decreased amounts of ARGs by reducing resistome and bacterial diversity, rather than by lowering horizontal transfer potential via intI1 or co-resistance via MRGs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Measurement of magnetocaloric effect in pulsed magnetic fields with the help of infrared fiber optical temperature sensor

NASA Astrophysics Data System (ADS)

Kamantsev, Alexander P.; Koledov, Victor V.; Mashirov, Alexey V.; Shavrov, Vladimir G.; Yen, N. H.; Thanh, P. T.; Quang, V. M.; Dan, N. H.; Los, Anton S.; Gilewski, Andrzej; Tereshina, Irina S.; Butvina, Leonid N.

2017-10-01

We present a new technique for experimental study of kinetics of phase transitions (PTs) and direct measurement of the magnetocaloric effect (MCE) in pulsed magnetic fields by using the fast response temperature probe with infrared fiber optical (IRFO) sensor. As demonstration of the new technique, the results are presented of MCE measurements for Gd near Curie point: ΔTad = 21.3 K under pulsed magnetic field μ0H = 12.7 T; and inverse MCE for Fe48Rh52 sample at initial temperature 305.1 K: ΔTad = -4.5 K under pulsed magnetic field μ0H = 8.5 T. Also, the energy losses on magnetization near the 1st order PT were calculated from the results of direct measurements of magnetization versus time for Fe48Rh52 sample: W = 45 J/kg.

Potential application of CuSbS2 as the hole transport material in perovskite solar cell: A simulation study

NASA Astrophysics Data System (ADS)

Teimouri, R.; Mohammadpour, R.

2018-06-01

CH3 NH3 PbI3 (MAPbI3) thin film solar cells, which are reported at laboratory efficiency scale of nearly 22%, are the subject of much attention by energy researchers due to their low cost buildup, acceptable efficiency, high absorption coefficient and diffusion length. The main purpose of this research is to simulate the structure of thin film perovskite solar cells through numerical simulation of SCAPS based on the empirical data for different hole transport layers. After simulating the initial structure of FTO/TiO2/CH3NH3PbI3/Spiro-OMeTAD solar cell, the hole transport layer Spiro-OMeTAD thickness was optimized on a small scale using modeling. The researchers also sought to reduce the amount of this material and the cost of construction. Ultimately, an optimum thickness of 140 nm was obtained for this cell with efficiency of 22.88%. The effect of employing alternative inorganic hole transport layer was investigated as a substitute for Spiro-OMeTAD; Copper antimony sulphide (CuSbS2) was selected due to abundant and available material and high open circuit voltage of about 988 mV. Thickness variations were also performed on a MAPbI3/CuSbS2 solar cell. Finally, It has obtained that perovskite solar cell with 120 nm-thick of CuSbS2 has 23.14% conversion efficiency with acceptable VOC and JSC values.

Yield and protein quality of thermophilic Bacillus spp. biomass related to thermophilic aerobic digestion of agricultural wastes for animal feed supplementation.

PubMed

Ugwuanyi, J Obeta

2008-05-01

Bacillus spp. responsible for thermophilic aerobic digestion (TAD) of agricultural wastes were studied for their growth rate, yield and protein quality (amino acid profile) under conditions that approximate full-scale waste digestion as pointers to the capacity of TAD to achieve protein enrichment of wastes for reuse in animal feeding. Specific growth rates of the thermophiles varied with temperature and aeration rates. For Bacillus coagulans, the highest specific growth rate was 1.98 muh(-1); for Bacillus licheniformis 2.56 muh(-1) and for Bacillus stearothermophilus 2.63 muh(-1). Molar yield of B. stearothermophilus on glucose increased with temperature to a peak of 0.404 g g(-1) at 50 degrees C before declining. Peak concentration of overflow metabolite (acetate) increased from 10 mmol at 45 degrees C to 34 mmol at 65 degrees C before declining. Accumulation of biomass in all three isolates decreased with increase in temperature while protein content of biomass increased. Highest biomass protein (79%) was obtained in B. stearothermophilus at 70 degrees C. Content of most essential amino acids of the biomass improved with temperature. Amino acid profile of the biomass was comparable to or superior to the FAO standard for SCP intended for use in animal feeding. Culture condition (waste digestion condition) may be manipulated to optimize protein yield and quality of waste digested by TAD for recycling in animal feed.

The role of the Department of Homeland Security, Science and Technology Directorate in the development of vaccines and diagnostics for Transboundary Animal Diseases.

PubMed

Colby, M; Coats, M; Brake, D; Fine, J

2013-01-01

The development of countermeasures to support an effective response to Transboundary Animal Diseases (TAD) poses a challenge on a global scale and necessitates the coordinated involvement of scientists from government, industry and academia, as well as regulatory entities. The Agricultural Defense Branch under the Chemical and Biological Defense Division (CBD) of the Department of Homeland Security (DHS), Science and Technology Directorate (S&T) supports this important mission within the United States. This article provides an overview of the Agricultural Defense Branch's vaccine and diagnostic TAD project.

The investigation of fast neutron Threshold Activation Detectors (TAD)

NASA Astrophysics Data System (ADS)

Gozani, T.; King, M. J.; Stevenson, J.

2012-02-01

The detection of fast neutrons is usually done by liquid hydrogenous organic scintillators, where the separation between the ever present gamma rays and neutrons is achieved by the pulse shape discrimination (PSD). In many practical situation the detection of fast neutrons has to be carried out while the intense source (be it neutrons, gamma rays or x-rays) that creates these neutrons, for example by the fission process, is present. This source, or ``flash'', usually blinds the neutron detectors and temporarily incapacitates them. By the time the detectors recover the prompt neutron signature does not exist. Thus to overcome the blinding background, one needs to search for processes whereby the desired signature, such as fission neutrons could in some way be measured long after the fission occurred and when the neutron detector is fully recovered from the overload. A new approach was proposed and demonstrated a good sensitivity for the detection of fast neutrons in adverse overload situations where normally it could not be done. A temporal separation of the fission event from the prompt neutrons detection is achieved via the activation process. The main idea, called Threshold Activation Detection (or detector)-TAD, is to find appropriate substances that can be selectively activated by the fission neutrons and not by the source radiation, and then measure the radioactively decaying activation products (typically beta and γ-rays) well after the source pulse has ended. The activation material should possess certain properties: a suitable half-life; an energy threshold below which the numerous source neutrons will not activate it (e.g. about 3 MeV); easily detectable activation products and has a usable cross section for the selected reaction. Ideally the substance would be part of the scintillator. There are several good candidates for TAD. The first one we have selected is based on fluorine. One of the major advantages of this element is the fact that it is a major constituent of available scintillators (e.g., BaF2, CaF2, hydrogen free liquid fluorocarbon). Thus the activation products of the fast prompt neutrons, in particular, the beta particles, can be measured with a very high efficiency in the detector. Other detectors and substances were investigated, such as 6Li and even common detectors such as NaI. The principles and experimental results obtained with F, NaI and 6Li based TAD are shown. The various contributing activation products are identified. The insensitivity of the fluorine based TAD to (d,D) neutrons is demonstrated. Ways and means to reduce or subtract the various neutron induced activations of NaI detector are elucidated along with its fast neutron detection capabilities. 6Li could also be a useful TAD.

Advances in the Synthesis of Small Molecules as Hole Transport Materials for Lead Halide Perovskite Solar Cells.

PubMed

Rodríguez-Seco, Cristina; Cabau, Lydia; Vidal-Ferran, Anton; Palomares, Emilio

2018-04-17

Over hundreds of new organic semiconductor molecules have been synthesized as hole transport materials (HTMs) for perovskite solar cells. However, to date, the well-known N 2 , N 2 , N 2' , N 2' , N 7 , N 7 , N 7' , octakis-(4-methoxyphenyl)-9,9-spirobi-[9,9'-spirobi[9 H-fluorene]-2,2',7,7'-tetramine (spiro-OMeTAD) is still the best choice for the best perovskite device performance. Nevertheless, there is a consensus that spiro-OMeTAD by itself is not stable enough for long-term stable devices, and its market price makes its use in large-scale production costly. Novel synthetic routes for new HTMs have to be sought that can be carried out in fewer synthetic steps and can be easily scaled up for commercial purposes. On the one hand, synthetic chemists have taken, as a first approach, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels of the spiro-OMeTAD molecule as a reference to synthesize molecules with similar energy levels, although these HOMO and LUMO energy levels often have been measured indirectly in solution using cyclic voltammetry. On the other hand, the "spiro" chemical core has also been studied as a structural motif for novel HTMs. However, only a few molecules incorporated as HTMs in complete functional perovskite solar cells have been capable of matching the performance of the best-performing perovskite solar cells made using spiro-OMeTAD. In this Account, we describe the advances in the synthesis of HTMs that have been tested in perovskite solar cells. The comparison of solar cell efficiencies is of course very challenging because the solar cell preparation conditions may differ from laboratory to laboratory. To extract valuable information about the HTM molecular structure-device function relationship, we describe those examples that always have used spiro-OMeTAD as a control device and have always used identical experimental conditions (e.g., the use of the same chemical dopant for the HTM or the lack of it). The pioneering work was focused on well-understood organic semiconductor moieties such as arylamine, carbazole, and thiophene. Those chemical structures have been largely employed and studied as HTMs, for instance, in organic light-emitting devices. Interestingly, most research groups have reported the hole mobility values for their novel HTMs. However, only a few examples have been found that have measured the HOMO and LUMO energy levels using advanced spectroscopic techniques to determine these reference energy values directly. Moreover, it has been shown that those molecules, upon interacting with the perovskite layer, often have different HOMO and LUMO energies than the values estimated indirectly using solution-based electrochemical methods. Last but not least, porphyrins and phthalocyanines have also been synthesized as potential HTMs for perovskite solar cells. Their optical and physical properties, such as high absorption and good energy transfer capabilities, open new possibilities for HTMs in perovskite solar cells.

Improved productivity of poly (3-hydroxybutyrate) (PHB) in thermophilic Chelatococcus daeguensis TAD1 using glycerol as the growth substrate in a fed-batch culture.

PubMed

Cui, Bin; Huang, Shaobin; Xu, Fuqian; Zhang, Ruijian; Zhang, Yongqing

2015-07-01

A particularly successful polyhydroxyalkanoate (PHA) in industrial applications is poly (3-hydroxybutyrate) (PHB). However, one of the major obstacles for wider application of PHB is the cost of its production and purification. Therefore, it is desirable to discover a method for producing PHB in large quantities at a competitive price. Glycerol is a cheap and widely used carbon source that can be applied in PHB production process. There are numerous advantages to operating fermentation at elevated temperatures; only several thermophilic bacteria are able to accumulate PHB when glycerol is the growth substrate. Here, we report on the possibility of increasing PHB production at low cost using thermophilic Chelatococcus daeguensis TAD1 when glycerol is the growth substrate in a fed-batch culture. We found that (1) excess glycerol inhibited PHB accumulation and (2) organic nitrogen sources, such as tryptone and yeast extract, promoted the growth of C. daeguensis TAD1. In the batch fermentation experiments, we found that using glycerol at low concentrations as the sole carbon source, along with the addition of mixed nitrate (NH4Cl, tryptone, and yeast extract), stimulated PHB accumulation in C. daeguensis TAD1. The results showed that the PHB productivity decreased in the following order: two-stage fed-batch fermentation > fed-batch fermentation > batch fermentation. In optimized culture conditions, a PHB amount of 17.4 g l(-1) was obtained using a two-stage feeding regimen, leading to a productivity rate of 0.434 g l(-1) h(-1), which is the highest productivity rate reported for PHB to date. This high PHB biosynthetic productivity could decrease the total production cost, allowing for further development of industrial applications of PHB.

Mediator Tail Module Is Required for Tac1-Activated CDR1 Expression and Azole Resistance in Candida albicans.

PubMed

Liu, Zhongle; Myers, Lawrence C

2017-11-01

The human fungal pathogen Candida albicans develops drug resistance after long-term exposure to azole drugs in the treatment of chronic candidiasis. Gain-of-function (GOF) mutations in the transcription factor Tac1 and the consequent expression of its targets, drug efflux pumps Cdr1 and Cdr2, are a common mechanism by which C. albicans acquires fluconazole resistance. The mechanism by which GOF mutations hyperactivate Tac1 is currently unknown. Here, we define a transcriptional activation domain (TAD) at the C terminus of Tac1. GOF mutations within the Tac1 TAD, outside the context of full-length Tac1, generally do not enhance its absolute potential as a transcriptional activator. Negative regulation of the Tac1 TAD by the Tac1 middle region is necessary for the activating effect of GOF mutations or fluphenazine to be realized. We have found that full-length Tac1, when hyperactivated by xenobiotics or GOF mutations, facilitates the recruitment of the Mediator coactivator complex to the CDR1 promoter. Azole resistance and the activation of Tac1 target genes, such as CDR1 , are dependent on the Tac1 TAD and subunits of the Mediator tail module. The dependence of different Tac1 target promoters on the Mediator tail module, however, varies widely. Lastly, we show that hyperactivation of Tac1 is correlated with its Mediator-dependent phosphorylation, a potentially useful biomarker for Tac1 hyperactivation. The role of Mediator in events downstream of Tac1 hyperactivation in fluconazole-resistant clinical isolates is complex and provides opportunities and challenges for therapeutic intervention. Copyright © 2017 American Society for Microbiology.

Quantitative Analysis of NF-κB Transactivation Specificity Using a Yeast-Based Functional Assay

PubMed Central

Sharma, Vasundhara; Jordan, Jennifer J.; Ciribilli, Yari; Resnick, Michael A.; Bisio, Alessandra; Inga, Alberto

2015-01-01

The NF-κB transcription factor family plays a central role in innate immunity and inflammation processes and is frequently dysregulated in cancer. We developed an NF-κB functional assay in yeast to investigate the following issues: transactivation specificity of NF-κB proteins acting as homodimers or heterodimers; correlation between transactivation capacity and in vitro DNA binding measurements; impact of co-expressed interacting proteins or of small molecule inhibitors on NF-κB-dependent transactivation. Full-length p65 and p50 cDNAs were cloned into centromeric expression vectors under inducible GAL1 promoter in order to vary their expression levels. Since p50 lacks a transactivation domain (TAD), a chimeric construct containing the TAD derived from p65 was also generated (p50TAD) to address its binding and transactivation potential. The p50TAD and p65 had distinct transactivation specificities towards seventeen different κB response elements (κB-REs) where single nucleotide changes could greatly impact transactivation. For four κB-REs, results in yeast were predictive of transactivation potential measured in the human MCF7 cell lines treated with the NF-κB activator TNFα. Transactivation results in yeast correlated only partially with in vitro measured DNA binding affinities, suggesting that features other than strength of interaction with naked DNA affect transactivation, although factors such as chromatin context are kept constant in our isogenic yeast assay. The small molecules BAY11-7082 and ethyl-pyruvate as well as expressed IkBα protein acted as NF-κB inhibitors in yeast, more strongly towards p65. Thus, the yeast-based system can recapitulate NF-κB features found in human cells, thereby providing opportunities to address various NF-κB functions, interactions and chemical modulators. PMID:26147604

Effect of aeration rate and waste load on evolution of volatile fatty acids and waste stabilization during thermophilic aerobic digestion of a model high strength agricultural waste.

PubMed

Ugwuanyi, J Obeta; Harvey, L M; McNeil, B

2005-04-01

Thermophilic aerobic digestion (TAD) is a relatively new, dynamic and versatile low technology for the economic processing of high strength waste slurries. Waste so treated may be safely disposed of or reused. In this work a model high strength agricultural waste, potato peel, was subjected to TAD to study the effects of oxygen supply at 0.1, 0.25, 0.5 and 1.0 vvm (volume air per volume slurry per minute) under batch conditions at 55 degrees C for 156 h on the process. Process pH was controlled at 7.0 or left unregulated. Effects of waste load, as soluble chemical oxygen demand (COD), on TAD were studied at 4.0, 8.0, 12.0 and 16.0 gl(-1) (soluble COD) at pH 7.0, 0.5 vvm and 55 degrees C. Efficiency of treatment, as degradation of total solids, total suspended solids and soluble solid, as well as soluble COD significantly increased with aeration rate, while acetate production increased as the aeration rate decreased or waste load increased, signifying deterioration in treatment. Negligible acetate, and no other acids were produced at 1.0 vvm. Production of propionate and other acids increased after acetate concentration had started to decrease and, during unregulated reactions coincided with the drop in the pH of the slurry. Acetate production was more closely associated with periods of oxygen limitation than were other acids. Reduction in oxygen availability led to deterioration in treatment efficiency as did increase in waste load. These variables may be manipulated to control treated waste quality.

Subsetting Tools for Enabling Easy Access to International Airborne Chemistry Data

NASA Astrophysics Data System (ADS)

Northup, E. A.; Chen, G.; Quam, B. M.; Beach, A. L., III; Silverman, M. L.; Early, A. B.

2017-12-01

In response to the Research Opportunities in Earth and Space Science (ROSES) 2015 release announcement for Advancing Collaborative Connections for Earth System Science (ACCESS), researchers at NASA Langley Research Center (LaRC) proposed to extend the capabilities of the existing Toolsets for Airborne Data (TAD) to include subsetting functionality to allow for easier access to international airborne field campaign data. Airborne field studies are commonly used to gain a detailed understanding of atmospheric processes for scientific research on international climate change and air quality issues. To accommodate the rigorous process for manipulating airborne field study chemistry data, and to lessen barriers for researchers, TAD was created with the ability to geolocate data from various sources measured on different time scales from a single flight. The analysis of airborne chemistry data typically requires data subsetting, which can be challenging and resource-intensive for end users. In an effort to streamline this process, new data subsetting features and updates to the current database model will be added to the TAD toolset. These will include two subsetters: temporal and spatial, and vertical profile. The temporal and spatial subsetter will allow users to both focus on data from a specific location and/or time period. The vertical profile subsetter will retrieve data collected during an individual aircraft ascent or descent spiral. These new web-based tools will allow for automation of the typically labor-intensive manual data subsetting process, which will provide users with data tailored to their specific research interests. The system has been designed to allow for new in-situ airborne missions to be added as they become available, with only minor pre-processing required. The development of these enhancements will be discussed in this presentation.

Effectiveness of time-related interventions in children with ADHD aged 9-15 years: a randomized controlled study.

PubMed

Wennberg, Birgitta; Janeslätt, Gunnel; Kjellberg, Anette; Gustafsson, Per A

2018-03-01

Specific problems with time and timing that affect daily routines, homework, school work, and social relations have been recognized in children with ADHD. The primary treatments for children with ADHD do not specifically focus on time-related difficulties. The aim of this randomized controlled study (RCT) was to investigate how multimodal interventions, consisting of training in time-processing ability (TPA) and compensation with time-assistive devices (TAD), affect TPA and daily time management (DTM) in children with ADHD and time difficulties, compared with only educational intervention. Thirty-eight children on stable medication for ADHD in the 9-15-year age range were randomly allocated to an intervention or a control group. The children's TPA was measured with a structured assessment (KaTid), and the children's DTM was rated by a parent questionnaire (Time-Parent scale) and by children's self-reporting (Time-Self-rating). The intervention consisted of time-skill training and compensation with TAD. Data were analysed for differences in TPA and in DTM between the control and intervention groups in the 24-week follow-up. Children in the intervention group increased their TPA significantly (p = 0.019) more compared to the control group. The largest increase was in orientation to time. In addition, the parents in the intervention group rated their children's DTM as significantly (p = 0.01) improved compared with the parents in the control group. According to the children, their DTM was not significantly changed. In conclusion, a multimodal intervention consisting of time-skill training and TAD improved TPA and DTM in children with ADHD aged 9-15 years.

Ene reaction of singlet oxygen, triazolinedione, and nitrosoarene with chiral deuterium-labeled allylic alcohols: the interdependence of diastereoselectivity and regioselectivity discloses mechanistic insights into the hydroxy-group directivity.

PubMed

Adam, Waldemar; Bottke, Nils; Krebs, Oliver; Lykakis, Ioannis; Orfanopoulos, Michael; Stratakis, Manolis

2002-12-04

The ene reaction of singlet oxygen ((1)O(2)), triazolinedione (TAD), and nitrosoarene, specifically 4-nitronitrosobenzene (ArNO), with the tetrasubstituted 1,3-allylically strained, chiral allylic alcohol 3,4-dimethylpent-3-en-2-ol (2) leads to the threo-configured ene products in high diastereoselectivity, a consequence of the hydroxy-group directivity. Hydrogen bonding favors formation of the threo-configured encounter complex threo-EC in the early stage of ene reaction. For the analogous twix deuterium-labeled allylic alcohol Z-2-d(3), a hitherto unrecognized dichotomy between (1)O(2) and the ArNO and TAD enophiles is disclosed in the regioselectivity of the tetrasubstituted alcohol: Whereas for ArNO and TAD, hydrogen bonding with the allylic hydroxy group dictates the regioselectivity (twix selectivity), for (1)O(2), the cis effect dominates (twin/trix selectivity). From the interdependence between the twix/twin regioselectivity and the threo/erythro diastereoselectivity, it has been recognized that the enophile also attacks the allylic alcohol from the erythro pi face without assistance by hydrogen bonding with the allylic hydroxy functionality.

Argonaute2 and LaminB modulate gene expression by controlling chromatin topology

PubMed Central

Nazer, Ezequiel; Dale, Ryan K.; Chinen, Madoka; Radmanesh, Behram

2018-01-01

Drosophila Argonaute2 (AGO2) has been shown to regulate expression of certain loci in an RNA interference (RNAi)-independent manner, but its genome-wide function on chromatin remains unknown. Here, we identified the nuclear scaffolding protein LaminB as a novel interactor of AGO2. When either AGO2 or LaminB are depleted in Kc cells, similar transcription changes are observed genome-wide. In particular, changes in expression occur mainly in active or potentially active chromatin, both inside and outside LaminB-associated domains (LADs). Furthermore, we identified a somatic target of AGO2 transcriptional repression, no hitter (nht), which is immersed in a LAD located within a repressive topologically-associated domain (TAD). Null mutation but not catalytic inactivation of AGO2 leads to ectopic expression of nht and downstream spermatogenesis genes. Depletion of either AGO2 or LaminB results in reduced looping interactions within the nht TAD as well as ectopic inter-TAD interactions, as detected by 4C-seq analysis. Overall, our findings reveal coordination of AGO2 and LaminB function to dictate genome architecture and thereby regulate gene expression. PMID:29529026

Optimization process planning using hybrid genetic algorithm and intelligent search for job shop machining.

PubMed

Salehi, Mojtaba; Bahreininejad, Ardeshir

2011-08-01

Optimization of process planning is considered as the key technology for computer-aided process planning which is a rather complex and difficult procedure. A good process plan of a part is built up based on two elements: (1) the optimized sequence of the operations of the part; and (2) the optimized selection of the machine, cutting tool and Tool Access Direction (TAD) for each operation. In the present work, the process planning is divided into preliminary planning, and secondary/detailed planning. In the preliminary stage, based on the analysis of order and clustering constraints as a compulsive constraint aggregation in operation sequencing and using an intelligent searching strategy, the feasible sequences are generated. Then, in the detailed planning stage, using the genetic algorithm which prunes the initial feasible sequences, the optimized operation sequence and the optimized selection of the machine, cutting tool and TAD for each operation based on optimization constraints as an additive constraint aggregation are obtained. The main contribution of this work is the optimization of sequence of the operations of the part, and optimization of machine selection, cutting tool and TAD for each operation using the intelligent search and genetic algorithm simultaneously.

Optimization process planning using hybrid genetic algorithm and intelligent search for job shop machining

PubMed Central

Salehi, Mojtaba

2010-01-01

Optimization of process planning is considered as the key technology for computer-aided process planning which is a rather complex and difficult procedure. A good process plan of a part is built up based on two elements: (1) the optimized sequence of the operations of the part; and (2) the optimized selection of the machine, cutting tool and Tool Access Direction (TAD) for each operation. In the present work, the process planning is divided into preliminary planning, and secondary/detailed planning. In the preliminary stage, based on the analysis of order and clustering constraints as a compulsive constraint aggregation in operation sequencing and using an intelligent searching strategy, the feasible sequences are generated. Then, in the detailed planning stage, using the genetic algorithm which prunes the initial feasible sequences, the optimized operation sequence and the optimized selection of the machine, cutting tool and TAD for each operation based on optimization constraints as an additive constraint aggregation are obtained. The main contribution of this work is the optimization of sequence of the operations of the part, and optimization of machine selection, cutting tool and TAD for each operation using the intelligent search and genetic algorithm simultaneously. PMID:21845020

International Schools for Young Astronomers Teaching for Astronomy Development: two programmes of the International Astronomical Union

NASA Astrophysics Data System (ADS)

Gerbaldi, Michèle; DeGreve, Jean-Pierre; Guinan, Edward

2011-06-01

This text outlines the main features of two educational programmes of the International Astronomical Union (IAU): the International Schools for Young Astronomers (ISYA) and the Teaching for Astronomy Development programme (TAD), developed since 1967. The main goal of the International Schools for Young Astronomers (ISYA) is to support astronomy (education and research) in developing countries in organizing a 3-week School for students with typically M.Sc. degrees. The context in which the ISYA were developed changed drastically during the last decade. From a time when access to large telescopes was difficult and mainly organized on a nation-basis, nowadays the archives of astronomical data have accumulated at the same time that many major telescope become accessible, and they are accessible from everywhere, the concept of virtual observatory reinforcing this access. A second programme of the IAU, Teaching for Astronomy Development (TAD), partially based on a School, but also of shorter duration (typically one week) has a complementary objective. It is dedicated to assist countries that have little or no astronomical activity, but that wish to enhance their astronomy education. The fast development of the TAD programme over the past years is emphasized.

Synthesis, conformational analysis, and biological activity of new analogues of thiazole-4-carboxamide adenine dinucleotide (TAD) as IMP dehydrogenase inhibitors.

PubMed

Franchetti, Palmarisa; Cappellacci, Loredana; Pasqualini, Michela; Petrelli, Riccardo; Jayaprakasan, Vetrichelvan; Jayaram, Hiremagalur N; Boyd, Donald B; Jain, Manojkumar D; Grifantini, Mario

2005-03-15

Thiazole-4-carboxamide adenine dinucleotide (TAD) analogues T-2'-MeAD (1) and T-3'-MeAD (2) containing, respectively, a methyl group at the ribose 2'-C-, and 3'-C-position of the adenosine moiety, were prepared as potential selective human inosine monophosphate dehydrogenase (IMPDH) type II inhibitors. The synthesis of heterodinucleotides was carried out by CDI-catalyzed coupling reaction of unprotected 2'-C-methyl- or 3'-C-methyl-adenosine 5'-monophosphate with 2',3'-O-isopropylidene-tiazofurin 5'-monophosphate, and then deisopropylidenation. Biological evaluation of dinucleotides 1 and 2 as inhibitors of recombinant human IMPDH type I and type II resulted in a good activity. Inhibition of both isoenzymes by T-2'-MeAD and T-3'-MeAD was noncompetitive with respect to NAD substrate. Binding of T-3'-MeAD was comparable to that of parent compound TAD, while T-2'-MeAD proved to be a weaker inhibitor. However, no significant difference was found in inhibition of the IMPDH isoenzymes. T-2'-MeAD and T-3'-MeAD were found to inhibit the growth of K562 cells (IC(50) 30.7 and 65.0muM, respectively).

Novel compounds TAD-1822-7-F2 and F5 inhibited HeLa cells growth through the JAK/Stat signaling pathway.

PubMed

Yang, Tianfeng; Shi, Xianpeng; Kang, Yuan; Zhu, Man; Fan, Mengying; Zhang, Dongdong; Zhang, Yanmin

2018-07-01

Cervical carcinoma remains the second most common malignancy with a high mortality rate among women worldwide. TAD-1822-7-F2 (F2) and TAD-1822-7-F5 (F5) are novel compounds synthesized on the chemical structure of taspine derivatives, and show an effective suppression for HeLa cells. Our study aims to confirm the potential targets of F2 and F5, and investigate the underlying mechanism of the inhibitory effect on HeLa cells. In this study, Real Time Cell Analysis and crystal violet staining assay were conducted to investigate the effect of F2 and F5 on HeLa cells proliferation. And the analytical methods of surface plasmon resonance and quartz crystal microbalance were established and employed to study the interaction between F2 and F5 and potential target protein JAK2, suggesting that both compounds have strong interaction with the JAK2 protein. Western blot analysis, immunofluorescence staining study and PCR was conducted to investigate the molecules of JAK/Stat signaling pathway. Interestingly, F2 and F5 showed diverse regulation for signaling molecules because of their different chemical structure. F2 increased the expression of JAK2 and downregulated the level of P-JAK1 and P-JAK2, and decreased P-Stat3 (Ser727). While F5 could increase the expression of JAK2 and naturally decrease the phosphorylation of JAK1 and Tyk2, and decreased the expression of P-Stat6. Moreover, F2 and F5 showed the same downregulation on the P-Stat3 (Tyr705). Therefore, F2 and F5 could target the JAK2 protein and prevent the phosphorylation of JAKs to suppress the phosphorylation of the downstream effector Stats, which suggested that F2 and F5 have great potential to be the inhibitors of the JAK/Stat signaling pathway. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Radiographic Review of Helical Blade Versus Lag Screw Fixation for Cephalomedullary Nailing of Low-Energy Peritrochanteric Femur Fractures: There is a Difference in Cutout.

PubMed

Stern, Lorraine C; Gorczyca, John T; Kates, Stephen; Ketz, John; Soles, Gillian; Humphrey, Catherine A

2017-06-01

To compare the rate of cutout of helical blades and lag screws in low-energy peritrochanteric femur fractures treated with a cephalomedullary nail (CMN). Retrospective review. Academic medical center. Overall, this study included 362 patients with an average age of 83 year old, a majority of whom were women, and had sustained a low-energy peritrochanteric femur fracture treated with a CMN. All patients had at least 3 months of clinical and radiographic follow, with an average follow-up of 11 months and a range of 3-88 months follow-up. Cephalomedullary nailing with the use of a helical blade or single lag screw for proximal fixation. Cutout of the helical blade or lag screw. Twenty-two cutouts occurred, 14 (15.1%) of 93 patients with helical blades and 8 (3.0%) of 269 patients with lag screws. Cutout with the helical blade was significantly more frequent than with the lag screw (P = 0.0001). The average tip-apex distance (TAD) was significantly greater for those patients who experienced cutout both for the helical blades (23.5 vs. 19.7 mm; P = 0.0194) and lag screws (24.5 vs. 20.0 mm; P = 0.0197). An absolute TAD predictive of cutout could not be determined. When the helical blade was used, implant cutout occurred at a significantly higher rate compared with lag screw fixation. There was not a threshold TAD that was predictive of cutout for either implant. Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

Effect of process temperature, pH and suspended solids content upon pasteurization of a model agricultural waste during thermophilic aerobic digestion.

PubMed

Ugwuanyi, J O; Harvey, L M; McNeil, B

1999-09-01

Thermophilic aerobic digestion(TAD), or liquid composting, is a versatile new process for the treatment and stabilization of high strength wastes of liquid or, perhaps more importantly, slurry consistency. The pattern of inactivation of various pathogenic and indicator organisms was studied using batch digestions under conditions that may be expected to be found in full-scale TAD processes. Rapid inactivation of test populations occurred within the first 10 min from the start of digestion. The inactivation rate was slightly lower when digestions were conducted below 60 degrees C. In some instances, a 'tail' was apparent, possibly indicating the survival of relatively resistant sub-populations particularly in the case of Serratia marcescens and Enterococcus faecalis, or of clumping or attachment of cells to particulate materials. The effect of pH on the inactivation of the test populations depended on the temperature of digestion, but varied with the test population. At 55 degrees C Escherichia coli was more sensitive to temperature effects at pH 7 than at pH 8, but was more sensitive at pH 8, 60 degrees C. The reverse was the case at 60 degrees C for Ent. faecalis. An increase in the solid content of the digesting waste caused a progressive increase in the protection of test organisms from thermal inactivation. Challenging a TAD process with test strains allows (via estimation of D-values) a quantification of the cidal effects of such processes, with a view to manipulating process variables to enhance such effects.

TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics

DOE PAGES

Mniszewski, Susan M.; Junghans, Christoph; Voter, Arthur F.; ...

2015-04-16

Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family ofmore » molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Finally, focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.« less

A Case Study of Technical Assistance to Demonstration Programs for Young Handicapped Children. Part II.

ERIC Educational Resources Information Center

Behr, Shirley K.; And Others

A project to provide technical assistance to staffs of two demonstration programs for preschool handicapped children and their families is described. The focus was technical assistance developed and exercised by the Technical Assistance Development System (TADS), which assisted in the development of the Handicapped Children's Early Education…

A multi-stage traveling-wave thermoacoustically-driven refrigeration system operating at liquefied natural gas temperature

NASA Astrophysics Data System (ADS)

Luo, K.; Sun, D. M.; Zhang, J.; Shen, Q.; Zhang, N.

2017-12-01

This study proposes a multi-stage travelling-wave thermoacoustically refrigeration system (TAD-RS) operating at liquefied natural gas temperature, which consists of two thermoacoustic engines (TAE) and one thermoacoustic refrigerator (TAR) in a closed-loop configuration. Three thermoacoustic units connect each other through a resonance tube of small cross-sectional area, achieving “self-matching” for efficient thermoacoustic conversion. Based on the linear thermoacoustic theory, a model of the proposed system has been built by using DeltaEC program to show the acoustic field characteristics and performance. It is shown that with pressurized 5 MPa helium as working gas, the TAEs are able to build a stable and strong acoustic field with a frequency of about 85 Hz. When hot end temperature reaches 923 K, this system can provide about 1410 W cooling power at 110 K with an overall exergy efficiency of 15.5%. This study indicates a great application prospect of TAD-RS in the field of natural gas liquefaction with a large cooling capacity and simple structure.

Cell-cycle dynamics of chromosomal organisation at single-cell resolution

PubMed Central

Nagano, Takashi; Lubling, Yaniv; Várnai, Csilla; Dudley, Carmel; Leung, Wing; Baran, Yael; Mendelson-Cohen, Netta; Wingett, Steven; Fraser, Peter; Tanay, Amos

2017-01-01

Summary Chromosomes in proliferating metazoan cells undergo dramatic structural metamorphoses every cell cycle, alternating between highly condensed mitotic structures facilitating chromosome segregation, and decondensed interphase structures accommodating transcription, gene silencing and DNA replication. Here we use single-cell Hi-C to study chromosome conformations in thousands of individual cells, and discover a continuum of cis-interaction profiles that finely position individual cells along the cell cycle. We show that chromosomal compartments, topological associated domains (TADs), contact insulation and long-range loops, all defined by bulk Hi-C maps, are governed by distinct cell-cycle dynamics. In particular, DNA replication correlates with build-up of compartments and reduction in TAD insulation, while loops are generally stable from G1 through S and G2. Whole-genome 3D structural models reveal a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data thereby allow for re-interpretation of chromosome conformation maps through the prism of the cell cycle. PMID:28682332

Understanding thread properties for red blood cell antigen assays: weak ABO blood typing.

PubMed

Nilghaz, Azadeh; Zhang, Liyuan; Li, Miaosi; Ballerini, David R; Shen, Wei

2014-12-24

"Thread-based microfluidics" research has so far focused on utilizing and manipulating the wicking properties of threads to form controllable microfluidic channels. In this study we aim to understand the separation properties of threads, which are important to their microfluidic detection applications for blood analysis. Confocal microscopy was utilized to investigate the effect of the microscale surface morphologies of fibers on the thread's separation efficiency of red blood cells. We demonstrated the remarkably different separation properties of threads made using silk and cotton fibers. Thread separation properties dominate the clarity of blood typing assays of the ABO groups and some of their weak subgroups (Ax and A3). The microfluidic thread-based analytical devices (μTADs) designed in this work were used to accurately type different blood samples, including 89 normal ABO and 6 weak A subgroups. By selecting thread with the right surface morphology, we were able to build μTADs capable of providing rapid and accurate typing of the weak blood groups with high clarity.

The Genomic Landscape of Balanced Cytogenetic Abnormalities Associated with Human Congenital Anomalies

PubMed Central

Redin, Claire; Brand, Harrison; Collins, Ryan L.; Kammin, Tammy; Mitchell, Elyse; Hodge, Jennelle C.; Hanscom, Carrie; Pillalamarri, Vamsee; Seabra, Catarina M.; Abbott, Mary-Alice; Abdul-Rahman, Omar A.; Aberg, Erika; Adley, Rhett; Alcaraz-Estrada, Sofia L.; Alkuraya, Fowzan S.; An, Yu; Anderson, Mary-Anne; Antolik, Caroline; Anyane-Yeboa, Kwame; Atkin, Joan F.; Bartell, Tina; Bernstein, Jonathan A.; Beyer, Elizabeth; Blumenthal, Ian; Bongers, Ernie M.H.F.; Brilstra, Eva H.; Brown, Chester W.; Brüggenwirth, Hennie T.; Callewaert, Bert; Chiang, Colby; Corning, Ken; Cox, Helen; Cuppen, Edwin; Currall, Benjamin B.; Cushing, Tom; David, Dezso; Deardorff, Matthew A.; Dheedene, Annelies; D’Hooghe, Marc; de Vries, Bert B.A.; Earl, Dawn L.; Ferguson, Heather L.; Fisher, Heather; FitzPatrick, David R.; Gerrol, Pamela; Giachino, Daniela; Glessner, Joseph T.; Gliem, Troy; Grady, Margo; Graham, Brett H.; Griffis, Cristin; Gripp, Karen W.; Gropman, Andrea L.; Hanson-Kahn, Andrea; Harris, David J.; Hayden, Mark A.; Hill, Rosamund; Hochstenbach, Ron; Hoffman, Jodi D.; Hopkin, Robert J.; Hubshman, Monika W.; Innes, A. Micheil; Irons, Mira; Irving, Melita; Jacobsen, Jessie C.; Janssens, Sandra; Jewett, Tamison; Johnson, John P.; Jongmans, Marjolijn C.; Kahler, Stephen G.; Koolen, David A.; Korzelius, Jerome; Kroisel, Peter M.; Lacassie, Yves; Lawless, William; Lemyre, Emmanuelle; Leppig, Kathleen; Levin, Alex V.; Li, Haibo; Li, Hong; Liao, Eric C.; Lim, Cynthia; Lose, Edward J.; Lucente, Diane; Macera, Michael J.; Manavalan, Poornima; Mandrile, Giorgia; Marcelis, Carlo L.; Margolin, Lauren; Mason, Tamara; Masser-Frye, Diane; McClellan, Michael W.; Zepeda Mendoza, Cinthya J.; Menten, Björn; Middelkamp, Sjors; Mikami, Liya R.; Moe, Emily; Mohammed, Shehla; Mononen, Tarja; Mortenson, Megan E.; Moya, Graciela; Nieuwint, Aggie W.; Ordulu, Zehra; Parkash, Sandhya; Pauker, Susan P.; Pereira, Shahrin; Perrin, Danielle; Phelan, Katy; Piña Aguilar, Raul E.; Poddighe, Pino J.; Pregno, Giulia; Raskin, Salmo; Reis, Linda; Rhead, William; Rita, Debra; Renkens, Ivo; Roelens, Filip; Ruliera, Jayla; Rump, Patrick; Schilit, Samantha L.P.; Shaheen, Ranad; Sparkes, Rebecca; Spiegel, Erica; Stevens, Blair; Stone, Matthew R.; Tagoe, Julia; Thakuria, Joseph V.; van Bon, Bregje W.; van de Kamp, Jiddeke; van Der Burgt, Ineke; van Essen, Ton; van Ravenswaaij-Arts, Conny M.; van Roosmalen, Markus J.; Vergult, Sarah; Volker-Touw, Catharina M.L.; Warburton, Dorothy P.; Waterman, Matthew J.; Wiley, Susan; Wilson, Anna; Yerena-de Vega, Maria de la Concepcion A.; Zori, Roberto T.; Levy, Brynn; Brunner, Han G.; de Leeuw, Nicole; Kloosterman, Wigard P.; Thorland, Erik C.; Morton, Cynthia C.; Gusella, James F.; Talkowski, Michael E.

2017-01-01

Despite their clinical significance, characterization of balanced chromosomal abnormalities (BCAs) has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and revealed complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. This study proposes that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements, and provides insight into novel pathogenic mechanisms such as altered regulation due to changes in chromosome topology. PMID:27841880

Identifying the charge generation dynamics in Cs+-based triple cation mixed perovskite solar cells.

PubMed

Salado, Manuel; Kokal, Ramesh K; Calio, Laura; Kazim, Samrana; Deepa, Melepurath; Ahmad, Shahzada

2017-08-30

Triple cation based perovskite solar cells offer enhanced moisture tolerance and stability compared to mixed perovskites. Slight substitution of methyl ammonium or formamidinium cation by cesium (Cs + ), was also reported to eliminate halide segregation due to its smaller size. To elucidate the device kinetics and understand the role of the Cs, we undertook different modes of scanning probe microscopy and electrochemical impedance spectroscopy (EIS) experiments. Kelvin probe force microscopy revealed that the incorporation of the Cs cation increases the contact potential difference (CPD), this CPD further increases when Spiro-OMeTAD is used as a hole transport material. The current at the nanoscale level shows improvement with Cs inclusion and further enhancement by the Spiro-OMeTAD deposition, studied under light illumination, which supports the high photocurrent density obtained from the cells. EIS demonstrates that in a triple cation environment, reduced carrier recombination at the TiO 2 /perovskite interface was also obtained which in turn allow us to achieve a higher V oc value.

An Aquatic Decomposition Scoring Method to Potentially Predict the Postmortem Submersion Interval of Bodies Recovered from the North Sea.

PubMed

van Daalen, Marjolijn A; de Kat, Dorothée S; Oude Grotebevelsborg, Bernice F L; de Leeuwe, Roosje; Warnaar, Jeroen; Oostra, Roelof Jan; M Duijst-Heesters, Wilma L J

2017-03-01

This study aimed to develop an aquatic decomposition scoring (ADS) method and investigated the predictive value of this method in estimating the postmortem submersion interval (PMSI) of bodies recovered from the North Sea. This method, consisting of an ADS item list and a pictorial reference atlas, showed a high interobserver agreement (Krippendorff's alpha ≥ 0.93) and hence proved to be valid. This scoring method was applied to data, collected from closed cases-cases in which the postmortal submersion interval (PMSI) was known-concerning bodies recovered from the North Sea from 1990 to 2013. Thirty-eight cases met the inclusion criteria and were scored by quantifying the observed total aquatic decomposition score (TADS). Statistical analysis demonstrated that TADS accurately predicts the PMSI (p < 0.001), confirming that the decomposition process in the North Sea is strongly correlated to time. © 2017 American Academy of Forensic Sciences.

A TAD further: exogenous control of gene activation.

PubMed

Mapp, Anna K; Ansari, Aseem Z

2007-01-23

Designer molecules that can be used to impose exogenous control on gene transcription, artificial transcription factors (ATFs), are highly desirable as mechanistic probes of gene regulation, as potential therapeutic agents, and as components of cell-based devices. Recently, several advances have been made in the design of ATFs that activate gene transcription (activator ATFs), including reports of small-molecule-based systems and ATFs that exhibit potent activity. However, the many open mechanistic questions about transcriptional activators, in particular, the structure and function of the transcriptional activation domain (TAD), have hindered rapid development of synthetic ATFs. A compelling need thus exists for chemical tools and insights toward a more detailed portrait of the dynamic process of gene activation.

A six-year retrospective analysis of cut-out risk predictors in cephalomedullary nailing for pertrochanteric fractures: Can the tip-apex distance (TAD) still be considered the best parameter?

PubMed

Caruso, G; Bonomo, M; Valpiani, G; Salvatori, G; Gildone, A; Lorusso, V; Massari, L

2017-08-01

Intramedullary fixation is considered the most stable treatment for pertrochanteric fractures of the proximal femur and cut-out is one of the most frequent mechanical complications. In order to determine the role of clinical variables and radiological parameters in predicting the risk of this complication, we analysed the data pertaining to a group of patients recruited over the course of six years. A total of 571 patients were included in this study, which analysed the incidence of cut-out in relation to several clinical variables: age; gender; the AO Foundation and Orthopaedic Trauma Association classification system (AO/OTA); type of nail; cervical-diaphyseal angle; surgical wait times; anti-osteoporotic medication; complete post-operative weight bearing; and radiological parameters (namely the lag-screw position with respect to the femoral head, the Cleveland system, the tip-apex distance (TAD), and the calcar-referenced tip-apex distance (CalTAD)). The incidence of cut-out across the sample was 5.6%, with a higher incidence in female patients. A significantly higher risk of this complication was correlated with lag-screw tip positioning in the upper part of the femoral head in the anteroposterior radiological view, posterior in the latero-lateral radiological view, and in the Cleveland peripheral zones. The tip-apex distance and the calcar-referenced tip-apex distance were found to be highly significant predictors of the risk of cut-out at cut-offs of 30.7 mm and 37.3 mm, respectively, but the former appeared more reliable than the latter in predicting the occurrence of this complication. The tip-apex distance remains the most accurate predictor of cut-out, which is significantly greater above a cut-off of 30.7 mm. Cite this article: G. Caruso, M. Bonomo, G. Valpiani, G. Salvatori, A. Gildone, V. Lorusso, L. Massari. A six-year retrospective analysis of cut-out risk predictors in cephalomedullary nailing for pertrochanteric fractures: Can the tip-apex distance (TAD) still be considered the best parameter?. Bone Joint Res 2017;6:481-488. DOI: 10.1302/2046-3758.68.BJR-2016-0299.R1. © 2017 Caruso et al.

A two-layer structured PbI2 thin film for efficient planar perovskite solar cells.

PubMed

Ying, Chao; Shi, Chengwu; Wu, Ni; Zhang, Jincheng; Wang, Mao

2015-07-28

In this paper, a two-layer structured PbI2 thin film was constructed by the spin-coating procedure using a 0.80 M PbI2 solution in DMF and subsequent close-spaced vacuum thermal evaporation using PbI2 powder as a source. The bottom PbI2 thin film was compact with a sheet-like appearance, parallel to the FTO substrate, and can be easily converted to a compact perovskite thin film to suppress the charge recombination of the electrons of the TiO2 conduction band and the holes of the spiro-OMeTAD valence band. The top PbI2 thin film was porous with nano-sheet arrays, perpendicular to the FTO substrate, and can be easily converted to a porous perovskite thin film to improve the hole migration from the perovskite to spiro-OMeTAD and the charge separation at the perovskite/spiro-OMeTAD interface. The planar perovskite solar cells based on the two-layer structured PbI2 thin film exhibited a photoelectric conversion efficiency of 11.64%, along with an open-circuit voltage of 0.90 V, a short-circuit photocurrent density of 19.29 mA cm(-2) and a fill factor of 0.67.

COMMUNICATION: Stochastic resonance and the evolution of Daphnia foraging strategy

NASA Astrophysics Data System (ADS)

Dees, Nathan D.; Bahar, Sonya; Moss, Frank

2008-12-01

Search strategies are currently of great interest, with reports on foraging ranging from albatrosses and spider monkeys to microzooplankton. Here, we investigate the role of noise in optimizing search strategies. We focus on the zooplankton Daphnia, which move in successive sequences consisting of a hop, a pause and a turn through an angle. Recent experiments have shown that their turning angle distributions (TADs) and underlying noise intensities are similar across species and age groups, suggesting an evolutionary origin of this internal noise. We explore this hypothesis further with a digital simulation (EVO) based solely on the three central Darwinian themes: inheritability, variability and survivability. Separate simulations utilizing stochastic resonance (SR) indicate that foraging success, and hence fitness, is maximized at an optimum TAD noise intensity, which is represented by the distribution's characteristic width, σ. In both the EVO and SR simulations, foraging success is the criterion, and the results are the predicted characteristic widths of the TADs that maximize success. Our results are twofold: (1) the evolving characteristic widths achieve stasis after many generations; (2) as a hop length parameter is changed, variations in the evolved widths generated by EVO parallel those predicted by SR. These findings provide support for the hypotheses that (1) σ is an evolved quantity and that (2) SR plays a role in evolution.

Creating an Awareness of Alternatives to Psycho-Social Situations in Elementary School Children.

ERIC Educational Resources Information Center

LeCapitaine, John E.

This study was designed to determine the effectiveness of 18 selected lessons from Dupont's Toward Affective Development (TAD) program for creating an awareness in students of alternatives to psycho-social situations. Using a sample of 60 subjects randomly selected from 111 sixth-grade students in northwest Wisconsin, two experimental and two…

Currently important animal disease management issues in sub-Saharan Africa.

PubMed

Thomson, G R

2009-03-01

The present international approach to management of transboundary animal diseases (TADs) is based on the assumption that most can be eradicated; consequently, that is the usual objective adopted by international organizations concerned with animal health. However, for sub-Saharan Africa and southern Africa more particularly, eradication of most TADs is impossible for the foreseeable future for a variety of technical, financial and logistical reasons. Compounding this, the present basis for access to international markets for products derived from animals requires that the area of origin (country or zone) is free from trade-influencing TADs. The ongoing development of transfrontier conservation areas (TFCAs), extending across huge areas of southern Africa, therefore presents a development conundrum because it makes creation of geographic areas free from TADs more difficult and brings development based on wildlife conservation on the one hand and that based on livestock production on the other into sharp conflict. Sub-Saharan Africa is consequently confronted by a complex problem that contributes significantly to retarded rural development which, in turn, impedes poverty alleviation. In southern Africa specifically, foot-and-mouth disease (FMD) presents the greatest problem in relation to access to international markets for animal products. However, it is argued that this problem could be overcome by a combination between (1) implementation of a commodity-based approach to trade in products derived from animals and (2) amendment of the international standards for FMD specifically (i.e. the FMD chapter in the Terrestrial Animal Health Code of the World Organisation for Animal Health [OIE]) so that occurrence of SAT serotype viruses in free-living African buffalo need not necessarily mean exclusion of areas where buffalo occur from international markets for animal products. This would overcome a presently intractable constraint to market access for southern African countries and enable conservation and livestock production to be more effectively integrated, to the benefit of both.

Primary sensory neuron-specific interference of TRPV1 signaling by adeno-associated virus-encoded TRPV1 peptide aptamer attenuates neuropathic pain

PubMed Central

Xiang, Hongfei; Liu, Zhen; Wang, Fei; Xu, Hao; Roberts, Christopher; Fischer, Gregory; Stucky, Cheryl L; Dean, Caron; Pan, Bin; Hogan, Quinn H; Yu, Hongwei

2017-01-01

Background TRPV1 (transient receptor potential vanilloid subfamily member 1) is a pain signaling channel highly expressed in primary sensory neurons. Attempts for analgesia by systemic TRPV1 blockade produce undesirable side effects, such as hyperthermia and impaired heat pain sensation. One approach for TRPV1 analgesia is to target TRPV1 along the peripheral sensory pathway. Results For functional blockade of TRPV1 signaling, we constructed an adeno-associated virus (AAV) vector expressing a recombinant TRPV1 interfering peptide aptamer, derived from a 38mer tetrameric assembly domain (TAD), encompassing residues 735 to 772 of rat TRPV1, fused to the C-terminus of enhanced green fluorescent protein (EGFP). AAV-targeted sensory neurons expressing EGFP-TAD after vector injection into the dorsal root ganglia (DRG) revealed decreased inward calcium current and diminished intracellular calcium accumulation in response to capsaicin, compared to neurons of naïve or expressing EGFP alone. To examine the potential for treating neuropathic pain, AAV-EGFP-TAD was injected into fourth and fifth lumbar (L) DRGs of rats subjected to neuropathic pain by tibial nerve injury (TNI). Results showed that AAV-directed selective expression of EGFP-TAD in L4/L5 DRG neuron somata, and their peripheral and central axonal projections can limit TNI-induced neuropathic pain behavior, including hypersensitivity to heat and, to a less extent, mechanical stimulation. Conclusion Selective inhibition of TRPV1 activity in primary sensory neurons by DRG delivery of AAV-encoded analgesic interfering peptide aptamers is efficacious in attenuation of neuropathic pain. With further improvements of vector constructs and in vivo application, this approach might have the potential to develop as an alternative gene therapy strategy to treat chronic pain, especially heat hypersensitivity, without complications due to systemic TRPV1 blockade. PMID:28604222

Are Village Animal Health Workers Able to Assist in Strengthening Transboundary Animal Disease Control in Cambodia?

PubMed

Stratton, J; Toribio, J-A L M L; Suon, S; Young, J R; Cowled, B; Windsor, P A

2017-04-01

A cross-sectional survey of 445 Village Animal Health Workers (VAHWs) from 19 provinces in Cambodia was undertaken. The aim was to establish their levels of training, farm visit frequency, reasons for visits and disease reporting practices, enabling the strengths and weaknesses of the VAHW system in Cambodia to be determined, in providing both a fee-based smallholder livestock clinical service and a government partnership in transboundary animal disease (TAD) surveillance and control. The study used 'guided group interviews' and identified that VAHWs had good contact with farmers with 61.5% making more than one farm visit daily. However, incomes from services remained low, with 45% VAHWs obtaining between 20 and 40% of their household income from VAHW activities. VAHWs recorded relatively high rates of disease reporting, with 72% claiming they report diseases immediately and 74% undertaking monthly reporting to veterinary authorities. Logistic regression analysis revealed VAHW contact frequency with district and/or provincial officers was associated with more VAHW farm visits, and frequency of VAHW visits to smallholder farms was positively associated with average monthly expenditure on animal medication and equipment. This suggests that increased veterinary extension to VAHWs and access to veterinary equipment, vaccines and drugs may further increase VAHW-farmer engagement. VAHWs provide an accessible, market-based, animal health 'treatment and reporting' service linked to livestock smallholders across Cambodia. However, for improved TAD prevention and more efficient control of outbreaks, research that assesses provision of an animal health 'preventive-based' business model is urgently needed to reduce both the costs to farmers and the risks to the economy due to foot-and-mouth disease and other TADs in Cambodia. © 2015 Blackwell Verlag GmbH.

Unsteady Flow Simulations in Support of the SSME HEX Turning Vane Cracking Investigation with the ATD HPOTP

NASA Technical Reports Server (NTRS)

Dougherty, N. S.; Burnette, D. W.; Holt, J. B.; Nesman, T.

1993-01-01

Unsteady flow computations are being performed with the P&W (ATD) and the Rocketdyne baseline configurations of the SSME LO2 turbine turnaround duct (TAD) and heat exchanger (HEX). The work is in support of the HEX inner turning vane cracking investigation. Fatigue cracking has occurred during hot firings with the P&W configuration on the HEX inner vane, and it appears the fix will involve changes to the TAD splitter vane position and to the TAD inner wall curvature to reduce the dynamic loading on the inner vane. Unsteady flow computations on the P&W baseline and fix and on the Rocketdyne baseline reference follow steady-flow screening computations done by MSFC/ED32 on several trial configurations arriving at the fix. The P&W TAD inlet velocity profile has a strong radial velocity component that directs the flow toward the inner wall and raises the local velocity a factor of two and the dynamic pressure a factor, of four. The fix is intended to redistribute the flow more evenly across the HEX inner and outer vanes like the Rocketdyne baseline reference. Vane buffeting at frequencies around 4,000 Hz is the leading suspected cause of the problem. Our simulations (work in progress) are being done with the USA 2D axisymmetric code approximating the flow as axisymmetric u+v 2D (axial, u, and radial, v, components only). The HEX coils are included in the model to make sure the fix does not adversely affect the HEX environment. Turbulent kinetic energy, k, levels where k = 1/2 v' rms2 are locally as high as 10,000 ft2/sec2 for the P&W baseline at the engine interface (between the TAD and HEX) at the HEX inner vane location. However, k is less than 8,000 on the HEX outer vane and only about 4,500 on the HEX inner vane for the Rocketdyne baseline. Unsteady turbulence intensity, v'rms/v, and pressure, p', are being computed in the present computations to compare with steady-flow Reynolds-averaged computations where p'rms = const (pk) for overall rms random turbulence from 0.1 to 12,000 Hz frequency. Random overall static, p'rms fluctuations as large as 1.7 psi are estimated from k on the HEX inner vane for the P&W baseline configuration but only about 0.7 psi for the Rocketdyne configuration.

Understanding Motivations to Adopt Once-a-Day Milking amongst New Zealand Dairy Farmers

ERIC Educational Resources Information Center

Bewsell, D.; Clark, D. A.; Dalley, D. E.

2008-01-01

This paper reports the results of a study to understand why some New Zealand dairy farmers are changing from twice-a-day (TAD) to once-a-day (OAD) milking. Increasing herd size, unavailability of suitable labour and changing lifestyle expectations from farmers and their staff have led some to explore OAD milking as a means of alleviating these…

Influence of Nonfused Cores on the Photovoltaic Performance of Linear Triphenylamine-Based Hole-Transporting Materials for Perovskite Solar Cells.

PubMed

Wu, Yungen; Wang, Zhihui; Liang, Mao; Cheng, Hua; Li, Mengyuan; Liu, Liyuan; Wang, Baiyue; Wu, Jinhua; Prasad Ghimire, Raju; Wang, Xuda; Sun, Zhe; Xue, Song; Qiao, Qiquan

2018-05-30

The core plays a crucial role in achieving high performance of linear hole transport materials (HTMs) toward the perovskite solar cells (PSCs). Most studies focused on the development of fused heterocycles as cores for HTMs. Nevertheless, nonfused heterocycles deserve to be studied since they can be easily synthesized. In this work, we reported a series of low-cost triphenylamine HTMs (M101-M106) with different nonfused cores. Results concluded that the introduced core has a significant influence on conductivity, hole mobility, energy level, and solubility of linear HTMs. M103 and M104 with nonfused oligothiophene cores are superior to other HTMs in terms of conductivity, hole mobility, and surface morphology. PSCs based on M104 exhibited the highest power conversion efficiency of 16.50% under AM 1.5 sun, which is comparable to that of spiro-OMeTAD (16.67%) under the same conditions. Importantly, the employment of M104 is highly economical in terms of the cost of synthesis as compared to that of spiro-OMeTAD. This work demonstrated that nonfused heterocycles, such as oligothiophene, are promising cores for high performance of linear HTMs toward PSCs.

Comparative Efficacy of 2 Topical Anesthetics for the Placement of Orthodontic Temporary Anchorage Devices

PubMed Central

Reznik, Derek S; Jeske, Arthur H; Chen, Jung-Wei; English, Jeryl

2009-01-01

This study compared the effectiveness of topical benzocaine 20% versus a combination of lidocaine, tetracaine, and phenylephrine in providing sufficient analgesia for the placement of orthodontic temporary anchorage devices (TADs). The 2 topical anesthetics were tested against each other bilaterally using a randomized, double-blind, crossover design. The agents were left in place for the amount of time prescribed by the manufacturer. The TAD was then placed, and each subject rated the degree of pain on a Heft-Parker visual analogue scale. A pulse oximeter was used to record the preoperative and postoperative pulse rates. Statistically significant differences in perceived pain (P < .05) and success rate (P < .01) between drugs were seen, but no significant difference in pulse rate change between the topical anesthetics was observed (P > .05). It was concluded that when the efficacy of topical benzocaine and of a combination product was compared as the sole anesthetic to facilitate acceptable pain control for placement of orthodontic temporary anchorage devices, the combination product was considerably more efficacious. PMID:19769421

Impacts of zero valent iron, natural zeolite and Dnase on the fate of antibiotic resistance genes during thermophilic and mesophilic anaerobic digestion of swine manure.

PubMed

Zhang, Junya; Sui, Qianwen; Zhong, Hui; Meng, Xiaoshan; Wang, Ziyue; Wang, Yawei; Wei, Yuansong

2018-06-01

This study investigated the fate of antibiotic resistance genes (ARGs) during mesophilic (mAD) and thermophilic digestion (tAD) of swine manure through zero valent iron (ZVI), natural zeolite and Dnase addition. Changes of microbial community, intI1, heavy metal resistance genes (MRGs) and virulence factors (VFs) were followed to clarify the influencing factors to ARGs reduction. Results showed that AD could realize ARGs reduction with tAD superior to mAD, and ZVI and natural zeolite could further enhance the reduction, especially for natural zeolite addition at mAD. The reduction efficiency of the relative abundance of ARGs was increased by 33.3% and 138.5% after ZVI and natural zeolite addition, respectively, but Dnase deteriorated ARGs reduction at mAD. Most of ARGs could be reduced effectively except sulII and tetM. Network analysis and partial redundancy analysis indicated that co-occurrence of MRGs followed by microbial community contributed the most to the variation of ARGs fate among treatments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Protein enrichment of corn cob heteroxylan waste slurry by thermophilic aerobic digestion using Bacillus stearothermophilus.

PubMed

Ugwuanyi, J Obeta; Harvey, Linda M; McNeil, Brian

2008-10-01

Thermophilic aerobic digestion (TAD) of heteroxylan waste was implemented at waste load of 30gL(-1) with mineral nitrogen supplementation to study effect of the process on waste degradation, protein accretion and quality. Digestions were carried out at 45 50, 55, 60 and 65 degrees C using Bacillusstearothermophilus in a CSTR under batch conditions at 1.0vvm aeration rate, pH 7.0 for a maximum of 120h. Amylase and xylanase activities appeared rapidly in the digest, while basal protease activity appeared early in the digestion and increased towards end of the processes. Highest degradation of volatile suspended solid, hemicellulose and fibre occurred at 55 degrees C while highest degradation of total suspended solid occurred at 60 degrees C. Highest protein accretion (258.8%) and assimilation of mineral nitrogen and soluble protein occurred at 55 degrees C. The % content of amino acids of digest crude protein increased relative to raw waste and with digestion temperature. Quality of digest protein was comparable to the FAO standard for feed use. TAD has potentials for use in the protein enrichment of waste.

Large low-field magnetocaloric effect in directionally solidified Ni55Mn18+xGa27-x (x = 0, 1, 2) alloys

NASA Astrophysics Data System (ADS)

Li, Zhenzhuang; Li, Zongbin; Yang, Bo; Yang, Yiqiao; Zhang, Yudong; Esling, Claude; Zhao, Xiang; Zuo, Liang

2018-01-01

The magnetostructural transformation and magnetocaloric effect of directionally solidified polycrystalline Ni55Mn18+xGa27-x (x = 0, 1, 2) alloys were studied. It is shown the directionally solidified alloys form coarse columnar-shaped grains with strong 〈0 0 1〉A (the subscript A refers to austenite) preferred orientation along the solidification direction. Through Mn substitution for Ga, a coupled magnetostructural transformation was realized in Ni55Mn19Ga26 and Ni55Mn20Ga25 alloys. Large adiabatic temperature variation (ΔTad) of 1.47 K and 1.57 K under the low field change of 1.5 T were achieved in these two alloys, respectively. Such ΔTad values are obviously higher than that obtained from a single martensitic transformation and magnetic transition. The present results demonstrate that proper composition tuning to achieve magnetostructural transformation as well as increasing the grain size and preferential orientation degree through directional solidification could be an economical processing route to optimize magnetocaloric properties in polycrystalline Ni-Mn-Ga based alloys.

Toolsets for Airborne Data (TAD): Customized Data Merging Function

NASA Astrophysics Data System (ADS)

Benson, A.; Peeters, M. C.; Perez, J.; Parker, L.; Chen, G.

2013-12-01

NASA has conducted airborne tropospheric chemistry studies for about three decades. These field campaigns have generated a great wealth of observations, including a wide range of the trace gases and aerosol properties. The ASDC Toolset for Airborne Data (TAD) is being designed to meet the user community needs for manipulating aircraft data for scientific research on climate change and air quality relevant issues. Prior to the actual toolset development, a comprehensive metadata database was created to compensate for the absence of standardization of the ICARTT data format in which the data is stored. This database tracks the Principal Investigator-provided metadata, and links the measurement variables to a common naming system that was developed as a part of this project. This database is used by the data merging module. Most aircraft data reported during a single flight is not on a consistent time base and is difficult to intercompare. This module provides the user with the ability to merge original data measurements from multiple data providers into a specified time interval or common time base. The database development, common naming scheme and data merge module development will be presented.

Effects of stabilization and sludge properties in a combined process of anaerobic digestion and thermophilic aerobic digestion.

PubMed

Cheng, Jiehong; Kong, Feng; Zhu, Jun; Wu, Xiao

2015-01-01

A novel process of combining mesophilic (<35°C) anaerobic digestion with the thermophilic (55°C) aerobic digestion process (AN-TAD) was designed to stabilize sludge and economize aeration energy. Effects of stabilization and sludge properties for AN-TAD process were evaluated by batch experiments during a 25 d digestion period. The sludges digested by AN-TAD process achieved the requirements for Class-A sludge standard. The sludge at total solid (TS) 5.4% had the highest value of decay coefficient K(d(55)) at 0.1851 d(-1) among the three TS contents according to the first-order kinetics equation. Oxidation reduction potential at below 0 mV remained for sludges at TSs of 6.5%, 5.4%, and 4.6% for at least 15 d because of initial hydrolytic-acidification. Concentrations of nitrogen and phosphorus in sludges at TSs of 6.5%, 5.4%, and 4.6% gradually increased up to the highest values in the supernatant during the initial 13 d, causing low utilized value in land application as a fertilizer. Prolonging the retention time for more than 15 d was considered because soluble phosphorus precipitated in the solid phase. High content of soluble organic matters of the soluble chemical oxygen demand, protein, and polysaccharide in the supernatant caused deterioration in sludge dewaterability rates.

Enhanced detection and visualization of anomalies in spectral imagery

NASA Astrophysics Data System (ADS)

Basener, William F.; Messinger, David W.

2009-05-01

Anomaly detection algorithms applied to hyperspectral imagery are able to reliably identify man-made objects from a natural environment based on statistical/geometric likelyhood. The process is more robust than target identification, which requires precise prior knowledge of the object of interest, but has an inherently higher false alarm rate. Standard anomaly detection algorithms measure deviation of pixel spectra from a parametric model (either statistical or linear mixing) estimating the image background. The topological anomaly detector (TAD) creates a fully non-parametric, graph theory-based, topological model of the image background and measures deviation from this background using codensity. In this paper we present a large-scale comparative test of TAD against 80+ targets in four full HYDICE images using the entire canonical target set for generation of ROC curves. TAD will be compared against several statistics-based detectors including local RX and subspace RX. Even a perfect anomaly detection algorithm would have a high practical false alarm rate in most scenes simply because the user/analyst is not interested in every anomalous object. To assist the analyst in identifying and sorting objects of interest, we investigate coloring of the anomalies with principle components projections using statistics computed from the anomalies. This gives a very useful colorization of anomalies in which objects of similar material tend to have the same color, enabling an analyst to quickly sort and identify anomalies of highest interest.

Target detection using the background model from the topological anomaly detection algorithm

NASA Astrophysics Data System (ADS)

Dorado Munoz, Leidy P.; Messinger, David W.; Ziemann, Amanda K.

2013-05-01

The Topological Anomaly Detection (TAD) algorithm has been used as an anomaly detector in hyperspectral and multispectral images. TAD is an algorithm based on graph theory that constructs a topological model of the background in a scene, and computes an anomalousness ranking for all of the pixels in the image with respect to the background in order to identify pixels with uncommon or strange spectral signatures. The pixels that are modeled as background are clustered into groups or connected components, which could be representative of spectral signatures of materials present in the background. Therefore, the idea of using the background components given by TAD in target detection is explored in this paper. In this way, these connected components are characterized in three different approaches, where the mean signature and endmembers for each component are calculated and used as background basis vectors in Orthogonal Subspace Projection (OSP) and Adaptive Subspace Detector (ASD). Likewise, the covariance matrix of those connected components is estimated and used in detectors: Constrained Energy Minimization (CEM) and Adaptive Coherence Estimator (ACE). The performance of these approaches and the different detectors is compared with a global approach, where the background characterization is derived directly from the image. Experiments and results using self-test data set provided as part of the RIT blind test target detection project are shown.

Molar distalization with the assistance of Temporary Anchorage Devices.

PubMed

Palencar, Adrian J

2015-01-01

This article describes efficient techniques for distalization of maxillary and mandibular molars with the assistance of Temporary Anchorage Devices (TADs). There are numerous occasions where the distalization of molars is required in lieu of the odontectomy of bicuspids. In the past, extra-oral force has been used, (i.e. Cervical or Combination Head Gear, or intra-oral force, i.e. Posterior Sagittal Appliance, Modified Greenfield Appliance, Williams DMJ 20001, CD Distalizer, Magill Sagittal, Pendulum Appliance, etc.). All the intra-oral appliances have a common denominator the orthodontic clinician has to deal with, the undesirable expression of the Third Law of Newton. The utilization of TADs allows us to circumvent this shortcoming, establishing an absolute anchorage, and thus completely negate the expression of the Third Law of Newton.

Renewable and Sustainable Study of Groundwater Flow System based on Numerical Simulation in Qaidam Basin, China

NASA Astrophysics Data System (ADS)

Cui, Y.

2015-12-01

In order to study surface water and groundwater exchange and renewal capacity of groundwater system of Qaidam Basin, inland northwest China, TOUGH2 (Transport of Unsaturated Groundwater and Heat 2) simulation software was used to establish a two-dimensional variable saturated numerical model of a typical cross-section from the Nuomuhong river to the Amunike mountain. According to previous results, evaporation is a function of soil saturation given as an upper boundary to characterize water transport near surface through iterative calculation. Parameters were calibrated with 52 groundwater observation data by trial-and-error method. Particle tracking and isotopic dating results were combined to simulate groundwater age and calibrate models. The results showed that the typical profile of Qaidam basin can be divided into three lumped groundwater flow systems: (1) The circulation depth (CD) of local groundwater flow system is about 200m, where discharge in this lumped system accounts for 74.4% of the total amount of discharge (TAD), of which spring overflow constitutes large fraction. Groundwater age is generally less than 500 years and renewal rate is 1.13% a-1; (2) The CD of middle flow system can reach 800m, where it takes up 18.5% of TAD, evaporation and river overflows is the main outlet of discharge. Groundwater age is generally less than 10ka and renewal rate is 0.094% a-1; (3) The CD of regional flow system is from 1000 to 1500m. It accounts for 7.1% of TAD, of which evaporation is the largest component. Groundwater age is from 10ka to 50ka and renewal rate of which is 0.0074% a-1. Sulingguole river is the discharge area of regional groundwater system, the age of which is greater than 30ka. The method used here can obtain the renewal capacity of groundwater system and better reflect regional circulation characteristics, which have certain significance for the urgent study of regional groundwater circulation and flow systems in areas with limited available data.

First Chance Network and Technical Assistance

ERIC Educational Resources Information Center

Trohanis, Pascal L.

1973-01-01

Article seeks to cover the following topics: an overview of First Chance; a description of TADS (Technical Assistance Development System); and a discussion of the organization's Media and Information division. (Author)

Structural organization of the inactive X chromosome in the mouse

PubMed Central

Giorgetti, Luca; Lajoie, Bryan R.; Carter, Ava C.; Attia, Mikael; Zhan, Ye; Xu, Jin; Chen, Chong Jian; Kaplan, Noam; Chang, Howard Y.; Heard, Edith; Dekker, Job

2017-01-01

X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region1,2, although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts3. A role for Xist in organizing the inactive X (Xi) chromosome has been proposed4–6. Recent chromosome conformation capture approaches have revealed global loss of local structure on the Xi chromosome and formation of large mega-domains, separated by a region containing the DXZ4 macrosatellite7–10. However, the molecular architecture of the Xi chromosome, in both the silent and expressed regions, remains unclear. Here we investigate the structure, chromatin accessibility and expression status of the mouse Xi chromosome in highly polymorphic clonal neural progenitors (NPCs) and embryonic stem cells. We demonstrate a crucial role for Xist and the DXZ4-containing boundary in shaping Xi chromosome structure using allele-specific genome-wide chromosome conformation capture (Hi-C) analysis, an assay for transposase-accessible chromatin with high throughput sequencing (ATAC–seq) and RNA sequencing. Deletion of the boundary disrupts mega-domain formation, and induction of Xist RNA initiates formation of the boundary and the loss of DNA accessibility. We also show that in NPCs, the Xi chromosome lacks active/inactive compartments and topologically associating domains (TADs), except around genes that escape XCI. Escapee gene clusters display TAD-like structures and retain DNA accessibility at promoter-proximal and CTCF-binding sites. Furthermore, altered patterns of facultative escape genes in different neural progenitor clones are associated with the presence of different TAD-like structures after XCI. These findings suggest a key role for transcription and CTCF in the formation of TADs in the context of the Xi chromosome in neural progenitors. PMID:27437574

Astronomy for a Better World: IAU OAD Task Force-1 Programs for Advancing Astronomy Education and Research in Universities in Developing Countries

NASA Astrophysics Data System (ADS)

Guinan, Edward; Kolenberg, Katrien

2015-03-01

We discuss the IAU Commission 46 and Office for Astronomy Development (OAD) programs that support advancing Astronomy education and research primarily in universities in developing countries. The bulk of these operational activities will be coordinated through the OAD's newly installed Task Force 1. We outline current (and future) IAU/OAD Task Force-1 programs that promote the development of University-level Astronomy at both undergraduate and graduate levels. Among current programs discussed are the past and future expanded activities of the International School for Young Astronomers (ISYA) and the Teaching Astronomy for Development (TAD) programs. The primary role of the ISYA program is the organization of a three week School for students for typically M.Sc. and Ph.D students. The ISYA is a very successful program that will now be offered more frequently through the generous support of the Kavli Foundation. The IAU/TAD program provides aid and resources for the development of teaching, education and research in Astronomy. The TAD program is dedicated to assist countries that have little or no astronomical activity, but that wish to develop or enhance Astronomy education. Over the last ten years, the ISYA and TAD programs have supported programs in Africa, Asia, Central America and the Caribbean, the Middle East, South East and West Asia, and South America. Several examples are given. Several new programs being considered by OAD Task Force-1 are also discussed. Other possible programs being considered are the introduction of modular Astronomy courses into the university curricula (or improve present courses) as well as providing access to ``remote learning`` courses and Virtual Astronomy labs in developing countries. Another possible new program would support visits of astronomers from technically advanced countries to spend their sabbatical leaves teaching and advising University Astronomy programs in developing countries. Suggestions for new Task Force -1 programs are also welcomed. Useful information about the participation of IAU members and volunteers in these programs will be discussed and practical information will be provided.

Recording of Terahertz Pulses of Microsecond Duration Using the Thermoacoustic Effect

NASA Astrophysics Data System (ADS)

Andreev, V. G.; Vdovin, V. A.; Kalynov, Yu. K.

2014-01-01

We consider the possibility of using a thermoacoustic detector (TAD) for recording of high-power pulse radiation at frequencies of 0.55, 0.68, and 0.87 THz. Electromagnetic wave is transformed into an acoustic wave in a structure consisting of a 10-nm thick chromium film deposited on a quartz substrate and a layer of the immersion liquid that is in contact with the film. It is shown that for the pulse of microsecond duration (3-10 μs) the waveform detected by the thermoacoustic detector is matched with high accuracy to the derivative of the terahertz pulse profile. For recording of electromagnetic radiation in the 0.5-0.9 THz frequency range it is possible to employ the simplified design of TAD, in which a transparent quartz substrate is in contact with a layer of water or ethanol.

Rational Design of Molecular Hole-Transporting Materials for Perovskite Solar Cells: Direct versus Inverted Device Configurations.

PubMed

Grisorio, Roberto; Iacobellis, Rosabianca; Listorti, Andrea; De Marco, Luisa; Cipolla, Maria Pia; Manca, Michele; Rizzo, Aurora; Abate, Antonio; Gigli, Giuseppe; Suranna, Gian Paolo

2017-07-26

Due to a still limited understanding of the reasons making 2,2',7,7'-tetrakis(N,N-di-p-methoxyphenylamine)-9,9'-spirobifluorene (Spiro-OMeTAD) the state-of-the-art hole-transporting material (HTM) for emerging photovoltaic applications, the molecular tailoring of organic components for perovskite solar cells (PSCs) lacks in solid design criteria. Charge delocalization in radical cationic states can undoubtedly be considered as one of the essential prerequisites for an HTM, but this aspect has been investigated to a relatively minor extent. In marked contrast with the 3-D structure of Spiro-OMeTAD, truxene-based HTMs Trux1 and Trux2 have been employed for the first time in PSCs fabricated with a direct (n-i-p) or inverted (p-i-n) architecture, exhibiting a peculiar behavior with respect to the referential HTM. Notwithstanding the efficient hole extraction from the perovskite layer exhibited by Trux1 and Trux2 in direct configuration devices, their photovoltaic performances were detrimentally affected by their poor hole transport. Conversely, an outstanding improvement of the photovoltaic performances in dopant-free inverted configuration devices compared to Spiro-OMeTAD was recorded, ascribable to the use of thinner HTM layers. The rationalization of the photovoltaic performances exhibited by different configuration devices discussed in this paper can provide new and unexpected prospects for engineering the interface between the active layer of perovskite-based solar cells and the hole transporters.

Regional Seismology in Argentina

DTIC Science & Technology

1981-05-11

Ingenierfa y Cioncias Exactas, Fisicas y Naturales , San Juan. Volponi, F.S., 1974. La Sismicidad del Territorie Argentino en Rela- cidn con las Nuevas Ideas...and J., Rendiguren, 1963. El "Ruidem del Suelo (Ground *Noise*). Acts, Ciayana do Izigenieria, YU.’ No.6. Facial- tad de Ingenierfa y Ciencias ...Exactas, Fificas y Naturales , San Juan. lossl, 1.3., 1979. Retudie do le. Actividad Sfmuioa do Is. Provincia ?ucuusn (Study of Seismic Activity for

Induction regimens for transplant-eligible patients with newly diagnosed multiple myeloma: a network meta-analysis of randomized controlled trials

PubMed Central

Zeng, Zi-Hang; Chen, Jia-Feng; Li, Yi-Xuan; Zhang, Ran; Xiao, Ling-Fei; Meng, Xiang-Yu

2017-01-01

Objective The aim of this study was to compare the early efficacy and survivals of induction regimens for transplant-eligible patients with untreated multiple myeloma. Materials and methods A comprehensive literature search in electronic databases was conducted for relevant randomized controlled trials (RCTs). Eligible studies were selected according to the predefined selection criteria, before they were evaluated for methodological quality. Basic characteristics and data for network meta-analysis (NMA) were extracted from included trials and pooled in our meta-analysis. The end points were the overall response rate (ORR), progression-free survival (PFS), and overall survival (OS). Results A total of 14 RCTs that included 4,763 patients were analyzed. The post-induction ORR was higher with bortezomib plus thalidomide plus dexamethasone (VTD) regimens, and VTD was better than the majority of other regimens. For OS, VTD plus cyclophosphamide (VTDC) regimens showed potential superiority over other regimens, but the difference was not statistically significant. The PFS was longer with thalidomide plus doxorubicin plus dexamethasone (TAD) regimens for transplant-eligible patients with newly diagnosed multiple myeloma (NDMM). Conclusion The NMA demonstrated that the VTD, VTDC, and TAD regimens are most beneficial in terms of ORR, OS, and PFS for transplant-eligible patients with NDMM, respectively. PMID:28744159

Temporary anchorage devices (TADs) in orthodontics: review of the factors that influence the clinical success rate of the mini-implants.

PubMed

Leo, M; Cerroni, L; Pasquantonio, G; Condò, S G; Condò, R

2016-01-01

The mini-implant, temporary anchorage devices (TADS), are now a common method of treatment in Orthodontics with versatility, minimal invasiveness and the relationship between costs and benefits that they offer even today. Skeletal anchorage has, to a large degree, replaced conventional anchorage in situations where anchorage is considered either critical, insufficient, or likely to result in undesirable side effects such as vertical displacements generated by inter-maxillary force systems. The objective of this study is to carry out a review about the factors that seem affect the success or failure rate of orthodontic mini-implants. A computerized literature review was performed by searching the MEDLINE database (Entrez PubMed, www.ncbi.nlm.nih.gov), Google Scholar, Scopus, Cochrane Central Register of Controlled Trials, Isi Web of Knowledge until March 2016 . The main subject heading "orthodontics" was combined with these keywords mini-implant, mini-screw, micro-implants, mini-implant success rate, mini-implant failure rate, skeletal anchorage, temporary anchorage device (TADS). In the selection process, abstracts were initially read independently by two researchers to identify potentially eligible full text papers which were then retrieved and assessed in order to decide on the final inclusion. The clinical success of orthodontic anchorage by mini-implants depends on the stability of the miniscrews used for fixation. For good stability, the application site must provide bone of good quantity and quality. We can reasonably assume that the stability of the anchorage of the mini-implants could be optimized by selecting a position with particular characteristics of quality and quantity of bone, in relation to cortical and total mandibular and jaw bone thickness. These expected informations are important because they indicates that the bone quality and quantity are significant when considering an implant placement site, but also that there are other confounding factors influencing the success rate.

Managing Large Datasets for Atmospheric Research

NASA Technical Reports Server (NTRS)

Chen, Gao

2015-01-01

Since the mid-1980s, airborne and ground measurements have been widely used to provide comprehensive characterization of atmospheric composition and processes. Field campaigns have generated a wealth of insitu data and have grown considerably over the years in terms of both the number of measured parameters and the data volume. This can largely be attributed to the rapid advances in instrument development and computing power. The users of field data may face a number of challenges spanning data access, understanding, and proper use in scientific analysis. This tutorial is designed to provide an introduction to using data sets, with a focus on airborne measurements, for atmospheric research. The first part of the tutorial provides an overview of airborne measurements and data discovery. This will be followed by a discussion on the understanding of airborne data files. An actual data file will be used to illustrate how data are reported, including the use of data flags to indicate missing data and limits of detection. Retrieving information from the file header will be discussed, which is essential to properly interpreting the data. Field measurements are typically reported as a function of sampling time, but different instruments often have different sampling intervals. To create a combined data set, the data merge process (interpolation of all data to a common time base) will be discussed in terms of the algorithm, data merge products available from airborne studies, and their application in research. Statistical treatment of missing data and data flagged for limit of detection will also be covered in this section. These basic data processing techniques are applicable to both airborne and ground-based observational data sets. Finally, the recently developed Toolsets for Airborne Data (TAD) will be introduced. TAD (tad.larc.nasa.gov) is an airborne data portal offering tools to create user defined merged data products with the capability to provide descriptive statistics and the option to treat measurement uncertainty.

(Con)text-specific effects of visual dysfunction on reading in posterior cortical atrophy.

PubMed

Yong, Keir X X; Shakespeare, Timothy J; Cash, Dave; Henley, Susie M D; Warren, Jason D; Crutch, Sebastian J

2014-08-01

Reading deficits are a common early feature of the degenerative syndrome posterior cortical atrophy (PCA) but are poorly understood even at the single word level. The current study evaluated the reading accuracy and speed of 26 PCA patients, 17 typical Alzheimer's disease (tAD) patients and 14 healthy controls on a corpus of 192 single words in which the following perceptual properties were manipulated systematically: inter-letter spacing, font size, length, font type, case and confusability. PCA reading was significantly less accurate and slower than tAD patients and controls, with performance significantly adversely affected by increased letter spacing, size, length and font (cursive < non-cursive), and characterised by visual errors (69% of all error responses). By contrast, tAD and control accuracy rates were at or near ceiling, letter spacing was the only perceptual factor to influence reading speed in the same direction as controls, and, in contrast to PCA patients, control reading was faster for larger font sizes. The inverse size effect in PCA (less accurate reading of large than small font size print) was associated with lower grey matter volume in the right superior parietal lobule. Reading accuracy was associated with impairments of early visual (especially crowding), visuoperceptual and visuospatial processes. However, these deficits were not causally related to a universal impairment of reading as some patients showed preserved reading for small, unspaced words despite grave visual deficits. Rather, the impact of specific types of visual dysfunction on reading was found to be (con)text specific, being particularly evident for large, spaced, lengthy words. These findings improve the characterisation of dyslexia in PCA, shed light on the causative and associative factors, and provide clear direction for the development of reading aids and strategies to maximise and sustain reading ability in the early stages of disease. Copyright © 2014. Published by Elsevier Ltd.

(Con)text-specific effects of visual dysfunction on reading in posterior cortical atrophy

PubMed Central

Yong, Keir X.X.; Shakespeare, Timothy J.; Cash, Dave; Henley, Susie M.D.; Warren, Jason D.; Crutch, Sebastian J.

2014-01-01

Reading deficits are a common early feature of the degenerative syndrome posterior cortical atrophy (PCA) but are poorly understood even at the single word level. The current study evaluated the reading accuracy and speed of 26 PCA patients, 17 typical Alzheimer's disease (tAD) patients and 14 healthy controls on a corpus of 192 single words in which the following perceptual properties were manipulated systematically: inter-letter spacing, font size, length, font type, case and confusability. PCA reading was significantly less accurate and slower than tAD patients and controls, with performance significantly adversely affected by increased letter spacing, size, length and font (cursive < non-cursive), and characterised by visual errors (69% of all error responses). By contrast, tAD and control accuracy rates were at or near ceiling, letter spacing was the only perceptual factor to influence reading speed in the same direction as controls, and, in contrast to PCA patients, control reading was faster for larger font sizes. The inverse size effect in PCA (less accurate reading of large than small font size print) was associated with lower grey matter volume in the right superior parietal lobule. Reading accuracy was associated with impairments of early visual (especially crowding), visuoperceptual and visuospatial processes. However, these deficits were not causally related to a universal impairment of reading as some patients showed preserved reading for small, unspaced words despite grave visual deficits. Rather, the impact of specific types of visual dysfunction on reading was found to be (con)text specific, being particularly evident for large, spaced, lengthy words. These findings improve the characterisation of dyslexia in PCA, shed light on the causative and associative factors, and provide clear direction for the development of reading aids and strategies to maximise and sustain reading ability in the early stages of disease. PMID:24841985

Identification of type IV collagen exposure as a molecular imaging target for early detection of thoracic aortic dissection

PubMed Central

Xu, Ke; Xu, Chen; Zhang, Yanzhenzi; Qi, Feiran; Yu, Bingran; Li, Ping; Jia, Lixin; Li, Yulin; Xu, Fu-jian; Du, Jie

2018-01-01

Thoracic aortic dissection (TAD) is an aggressive and life-threatening vascular disease and there is no effective means of early diagnosis of dissection. Type IV collagen (Col-IV) is a major component of the sub-endothelial basement membrane, which is initially exposed followed by endothelial injury as early-stage event of TAD. So, we want to build a noninvasive diagnostic method to detect early dissection by identifying the exposed Col-IV via MRI. Methods: Col-IV-targeted magnetic resonance/ fluorescence dual probe (Col-IV-DOTA-Gd-rhodamine B; CDR) was synthesized by amide reaction and coordination reaction. Flow cytometry analysis was used to evaluate the cell viability of SMC treated with CDR and fluorescence assays were used to assess the Col-IV targeting ability of CDR in vitro. We then examined the sensitivity and specificity of CDR at different stages of TAD via MRI and bioluminescence imaging in vivo. Results: The localization of Col-IV (under the intima) was observed by histology images. CDR bound specifically to Col-IV-expressing vascular smooth muscle cells and BAPN-induced dissected aorta. The CDR signal was co-detected by magnetic resonance imaging (MRI) and bioluminescence imaging as early as 2 weeks after BAPN administration (pre-dissection stage). The ability to detect rupture of dissected aorta was indicated by a strong normalized signal enhancement (NSE) in vivo. Moreover, NSE was negatively correlated with the time of dissection rupture after BAPN administration (r2 = 0.8482). Conclusion: As confirmed by in vivo studies, the CDR can identify the exposed Col-IV in degenerated aorta to monitor the progress of aortic dissection from the early stage to the rupture via MRI. Thus, CDR-enhanced MRI proposes a potential method for dissection screening, and for monitoring disease progression and therapeutic response. PMID:29290819

ECS Maintenance Wed. 12/28

Atmospheric Science Data Center

2016-12-27

Date(s):  Wednesday, December 28, 2016 Time:  12 am - 12 pm EDT Event Impact:  The Data Pool, MISR order and browse tools, TAD, TES and MOPITT Search and Subset Applications, and Reverb will be unavailable...

Reorganization of chromosome architecture in replicative cellular senescence.

PubMed

Criscione, Steven W; De Cecco, Marco; Siranosian, Benjamin; Zhang, Yue; Kreiling, Jill A; Sedivy, John M; Neretti, Nicola

2016-02-01

Replicative cellular senescence is a fundamental biological process characterized by an irreversible arrest of proliferation. Senescent cells accumulate a variety of epigenetic changes, but the three-dimensional (3D) organization of their chromatin is not known. We applied a combination of whole-genome chromosome conformation capture (Hi-C), fluorescence in situ hybridization, and in silico modeling methods to characterize the 3D architecture of interphase chromosomes in proliferating, quiescent, and senescent cells. Although the overall organization of the chromatin into active (A) and repressive (B) compartments and topologically associated domains (TADs) is conserved between the three conditions, a subset of TADs switches between compartments. On a global level, the Hi-C interaction matrices of senescent cells are characterized by a relative loss of long-range and gain of short-range interactions within chromosomes. Direct measurements of distances between genetic loci, chromosome volumes, and chromatin accessibility suggest that the Hi-C interaction changes are caused by a significant reduction of the volumes occupied by individual chromosome arms. In contrast, centromeres oppose this overall compaction trend and increase in volume. The structural model arising from our study provides a unique high-resolution view of the complex chromosomal architecture in senescent cells.

Test and Evaluation of the Man-Machine Interface between the Apache Longbow and an Unmanned Aerial Vehicle

DTIC Science & Technology

2000-04-01

two week test was a part of an The Boeing Company is studying a concept that on- going Boeing internal research and development involves teaming a...study and effectiveness of attack/reconnaissance teams. A assessment of employment modes and their major concern is the level of crew interaction...Based on the UAV control mode, these controls will Test subjects received training concerning the operate either the TADS sensors (control mode mne

Functional and topological characteristics of mammalian regulatory domains

PubMed Central

Symmons, Orsolya; Uslu, Veli Vural; Tsujimura, Taro; Ruf, Sandra; Nassari, Sonya; Schwarzer, Wibke; Ettwiller, Laurence; Spitz, François

2014-01-01

Long-range regulatory interactions play an important role in shaping gene-expression programs. However, the genomic features that organize these activities are still poorly characterized. We conducted a large operational analysis to chart the distribution of gene regulatory activities along the mouse genome, using hundreds of insertions of a regulatory sensor. We found that enhancers distribute their activities along broad regions and not in a gene-centric manner, defining large regulatory domains. Remarkably, these domains correlate strongly with the recently described TADs, which partition the genome into distinct self-interacting blocks. Different features, including specific repeats and CTCF-binding sites, correlate with the transition zones separating regulatory domains, and may help to further organize promiscuously distributed regulatory influences within large domains. These findings support a model of genomic organization where TADs confine regulatory activities to specific but large regulatory domains, contributing to the establishment of specific gene expression profiles. PMID:24398455

Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and Evolution.

PubMed

Galupa, Rafael; Heard, Edith

2018-04-23

The packaging of genetic material into chromatin and chromosomes has been recognized for more than a century, thanks to microscopy and biochemical approaches. This was followed by the progressive realization that chromatin organization is critical for genome functions such as transcription and DNA replication and repair. The recent discovery that chromosomes are partitioned at the submegabase scale into topologically associating domains (TADs) has implications for our understanding of gene regulation during developmental processes such as X-chromosome inactivation, as well as for evolution and for the search for disease-associated loci. Here we discuss our current knowledge about this recently recognized level of mammalian chromosome organization, with a special emphasis on the potential role of TADs as a structural basis for the function and evolution of mammalian regulatory landscapes. © 2017 Galupa and Heard; Published by Cold Spring Harbor Laboratory Press.

Detection and identification of glycoyessotoxin A in a culture of the dinoflagellate Protoceratium reticulatum.

PubMed

Paz, Beatriz; Riobó, Pilar; Souto, María L; Gil, Laura V; Norte, Manuel; Fernández, José J; Franco, José M

2006-11-01

The toxin composition of a culture of the dinoflagellate Protoceratium reticulatum was investigated using LC-FLD, after derivatization with DMEQ-TAD (4-(2-(6,7-dimethoxy-4-methyl-3-oxo-3,4-dihydroquinoxalimylethyl)-1,2,4-triazoline-3,5-dione)). Besides yessotoxin (YTX), the new YTX analogue, glycoyessotoxin A (G-YTXA) was detected in culture medium as well as in cells. The conditions for extraction were optimized and the production profile established. Retention time of the resulting fluorescent G-YTXA adduct was identified by comparison of the appropriate standard. Additionally, both G-YTXA and the DMEQ-TAD-G-YTXA adduct were confirmed by LC-MS showing ion peaks at m/z 1273 [M-2Na+H](-) and m/z 1618 [M-2Na+H](-), respectively. The LC-MS(n) displayed a fragmentation pattern similar to that of the YTX series.

Interpretation FTIR spectrum of seawater and sediment in the Ambon Bay (TAD)

NASA Astrophysics Data System (ADS)

Patty, Diana Julaidy; Loupatty, Grace; Sopalauw, Fitria

2017-01-01

Research has done to interpretated FTIR spectrum of seawaters and sediment of the Ambon Bay (TAD). Analysis of samples of sediment and seawater using FTIR spectroscopy. The results showed the sand sediment samples identified Stretch bond OH group (3600-3500 cm-1), N-H Stretch (3400-3300 cm-1), C≡N (2250 cm-1), and NH bending (1640 to 1550 cm-1). And for seawater samples identified bonding group that is N-H Stretch (3400-3350 cm-1), N-H bending (1640 to 1550 cm-1) and C=O (1670-1640 cm-1). The existence of functional groups, carbonyl (C=O), alcohol (OH), carboxyl (COOH) can cause the complexation of metal cations. And the results showed analysis group N-O bond-containing compounds Nitro indicate heavy metal content of Lead (Pb) and group N-H bond-containing compound Amina indicate heavy metal content of Cadmium (Cd).

Shape transitions in strained islands: kinetics versus energetics

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Kryukov, Yevgen; Amar, Jacques

2011-03-01

Recently, it has been argued that the shape transition from compact to ramified islands observed experimentally in submonolayer Cu/Ni(100) growth is not due to kinetics but can be understood in terms of energetic arguments. In order to determine the responsible mechanisms we have carried out temperature-accelerated dynamics (TAD) simulations as well as energetics calculations. Surprisingly, our results indicate that the strain-energy contribution to the dependence of island-energy on shape is relatively weak. In contrast, our TAD simulations indicate that unexpected concerted motions occurring at step edges may be responsible. The energy barriers for these concerted motions are significantly lower than for Cu/Cu(100) and Ni/Ni(100), decrease with increasing island size, and appear to saturate for islands larger than 300 - 400 atoms. These results suggest that the shape transition is of kinetic origin but is strongly mediated by strain. Supported by NSF-DMR 0907399.

Localized saddle-point search and application to temperature-accelerated dynamics

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Callahan, Nathan B.; Amar, Jacques G.

2013-03-01

We present a method for speeding up temperature-accelerated dynamics (TAD) simulations by carrying out a localized saddle-point (LSAD) search. In this method, instead of using the entire system to determine the energy barriers of activated processes, the calculation is localized by only including a small chunk of atoms around the atoms directly involved in the transition. Using this method, we have obtained N-independent scaling for the computational cost of the saddle-point search as a function of system size N. The error arising from localization is analyzed using a variety of model systems, including a variety of activated processes on Ag(100) and Cu(100) surfaces, as well as multiatom moves in Cu radiation damage and metal heteroepitaxial growth. Our results show significantly improved performance of TAD with the LSAD method, for the case of Ag/Ag(100) annealing and Cu/Cu(100) growth, while maintaining a negligibly small error in energy barriers.

Sb2S3/Spiro-OMeTAD Inorganic-Organic Hybrid p-n Junction Diode for High Performance Self-Powered Photodetector.

PubMed

Bera, Ashok; Das Mahapatra, Ayon; Mondal, Sulakshana; Basak, Durga

2016-12-21

Organic-inorganic hybrid diodes are very promising for solution processing, low cost, high performance optoelectronic devices. Here, we report a high quality p-n heterojunction diode composed of n-type inorganic Sb 2 S 3 and p-type organic 2,2',7,7'-tetrakis-(N,N-di-p-methoxyphenylamine)-9,9'-spirobifluorene (spiro-OMeTAD) with a rectification ratio of ∼10 2 at an applied bias of 1 V. On illumination with visible light (470 nm, 1.82 mW/cm 2 ), the current value in our device becomes 8 × 10 2 times that of its dark value even at a zero bias condition. The estimated responsivity value at zero bias is 0.087 A/W which is so far the highest reported for any organic-inorganic hybrid photodiode, to the best of our knowledge. It also exhibits a fast photoresponse time of <25 ms (instrumental limit). More importantly, our device can also detect visible light with power density as low as 8 μW/cm 2 with a photocurrent density of 1.2 μA/cm 2 and a photocurrent to dark current ratio of more than 8. We also demonstrate that the values of responsivity, short circuit current, and open circuit voltage of the photodetector can be improved significantly using a thin layer of TiO 2 hole-blocking layer. These findings suggest Sb 2 S 3 /spiro-OMeTAD heterojuncton as a promising candidate for efficient self-powered low visible light photodetector.

Should Tricuspid Annuloplasty be Performed With Pulmonary Valve Replacement for Pulmonary Regurgitation in Repaired Tetralogy of Fallot?

PubMed

Kurkluoglu, Mustafa; John, Anitha S; Cross, Russell; Chung, David; Yerebakan, Can; Zurakowski, David; Jonas, Richard A; Sinha, Pranava

2015-01-01

Indications for prophylactic tricuspid annuloplasty in patients with pulmonary regurgitation (PR) after tetralogy of Fallot (TOF) repair are unclear and often extrapolated from acquired functional tricuspid regurgitation (TR) data in adults, where despite correction of primary left heart pathology, progressive tricuspid annular dilation is noted beyond a threshold diameter >4 cm (21 mm/m(2)). We hypothesized that unlike in adult functional TR, in pure volume-overload conditions such as patients with PR after TOF, the tricuspid valve size is likely to regress after pulmonary valve replacement (PVR). A total of 43 consecutive patients who underwent PVR from 2005 until 2012 at a single institution were retrospectively reviewed. Absolute and indexed tricuspid annulus diameters (TADs), tricuspid annulus Z-scores, grade of TR along with right ventricular size, and function indices were recorded before and after PVR. Preoperative and postoperative echocardiographic data were available in all patients. A higher tricuspid valve Z-score correlated with greater TR both preoperatively (P = 0.005) and postoperatively (P = 0.02). Overall reductions in the absolute and indexed TAD and tricuspid valve Z-scores were seen postoperatively, with greater absolute as well as percentage reduction seen with larger preoperative TAD index (P = 0.007) and higher tricuspid annulus Z-scores (P = 0.06). In pure volume-overload conditions such as patients with PR after TOF, reduction in the tricuspid valve size is seen after PVR. Concomitant tricuspid annuloplasty should not be considered based on tricuspid annular dilation alone. Copyright © 2015 Elsevier Inc. All rights reserved.

Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement.

PubMed

Lindström, Ida; Dogan, Jakob

2017-08-15

A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein-protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein-protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation-condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs.

Should the tip-apex distance (TAD) rule be modified for the proximal femoral nail antirotation (PFNA)? A retrospective study.

PubMed

Nikoloski, Andrej N; Osbrough, Anthony L; Yates, Piers J

2013-10-17

Unstable proximal femoral fractures are common and challenging for the orthopaedic surgeon. Often, these are treated with intramedullary nails. The most common mode of failure of any device to treat these fractures is cut-out. The Synthes proximal femoral nail antirotation (PFNA) is unique because it is the only proximal femoral intramedullary nail which employs a helical blade in lieu of a lag screw. The optimal tip-apex distance is 25 mm or less for a dynamic hip screw. The optimal blade tip placement is not known for the PFNA. The aim of this study is to determine if the traditional tip-apex distance rule (<25 mm) applies to the PFNA. A retrospective study of all proximal femoral fractures treated with the PFNA in Western Australian public teaching hospitals between August 2006 and October 2007 was performed. Cases were identified from company and theatre implant use records. Patient demographic data was obtained from hospital records. Fractures were classified according to Arbeitsgemeinschaft für Osteosynthesefragen/Association for the Study of Internal Fixation. Fracture reduction, distal locking type and blade position within the head (tip-apex distance and Cleveland zone) were recorded from the intraoperative and immediate postoperative radiographs. Postoperative radiographs obtained in the routine treatment of patients were studied for review looking primarily for cut-out. Clinical outcomes were measured with the Oxford hip score. One hundred eighty-eight PFNAs were implanted during the study period, with 178 cases included in this study. Ninety-seven patients could be followed up clinically. There were 18 surgical implant-related failures (19%). The single most common mode of failure was cut-out in six cases (6.2%). Three cut-outs (two medial perforation and one varus collapse) occurred with tip-apex distance (TAD) less than 20 mm. There was no cut-out in cases where the TAD was from 20-30 mm. There were three implant-related failures (nail fracture, missed nail and loose locking screw), four implant-related femoral fractures, two non-unions, two delayed unions and one loss of reduction. The PFNA is a suitable fixation device for the treatment of unstable proximal femoral fractures. There were still a relatively large number of cut-outs, and the tip-apex distance in the failures showed a bimodal distribution, not like previously demonstrated with dynamic hip screw. We propose that the helical blade behaves differently to a screw, and placement too close to the subchondral bone may lead to penetration through the head.

78 FR 46860 - Proposed Waiver and Extension of the Project Period for the Technical Assistance Coordination Center

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-02

... funded centers, professional organizations, and other stakeholders to collaborate, solve problems...; (b) maintaining a Web site that houses tools that TA&D Network projects have developed or can use in...

ASDC Tools Temporarily Unavailable

Atmospheric Science Data Center

2015-12-21

... The ASDC will be conducting maintenance due to an unexpected power outage. The Data Pool, MISR order and browse tools, TAD, TES and ... may be unavailable during maintenance. Data processing and distribution may be impacted and systems are expected to return to normal ...

Principles and Procedures in Technical Assistance: An Approach to Educational Change

ERIC Educational Resources Information Center

Lillie, David L.; Black, Talbot

1976-01-01

The Technical Assistance Development System (TADS) has developed through the years a system for technical assistance and has identified some important principles that should be followed in the operation of organizational support systems. (Author/ER)

α1A-Adrenergic Receptor Antagonism Improves Erectile and Cavernosal Responses in Rats With Cavernous Nerve Injury and Enhances Neurogenic Responses in Human Corpus Cavernosum From Patients With Erectile Dysfunction Secondary to Radical Prostatectomy.

PubMed

Martínez-Salamanca, Juan I; La Fuente, José M; Martínez-Salamanca, Eduardo; Fernández, Argentina; Pepe-Cardoso, Augusto J; Louro, Nuno; Carballido, Joaquín; Angulo, Javier

2016-12-01

Cavernous nerve injury (CNI) in rats and radical prostatectomy (RP) in men result in loss of nitrergic function and increased adrenergic-neurogenic contractions of cavernosal tissue. To evaluate the modulation of the α-adrenergic system as a strategy to relieve erectile dysfunction (ED) and functional cavernosal alterations induced by CNI. A non-selective α-blocker (phentolamine 1 mg/kg daily), a selective α 1A -blocker (silodosin [SILOD] 0.1 mg/kg daily), or vehicle was orally administered for 4 weeks after bilateral crush CNI (BCNI). Erectile and neurogenic responses of the corpus cavernosum (CC) were evaluated. The acute effects of SILOD also were evaluated in vivo (0.03 mg/kg intravenously) and ex vivo (10 nmol/L). The effects of SILOD and tadalafil (TAD) on nitrergic relaxations were determined in human CC from patients with ED with a vascular etiology or ED secondary to RP. Erectile responses in vivo in rats and neurogenic contractions and relaxations of rat and human CC. Long-term treatment with SILOD significantly improved erectile responses and allowed for the potentiation of erectile responses by acute treatment with TAD (0.3 mg/kg intravenously) in rats with BCNI. SILOD partly recovered nitrergic relaxations and normalized neurogenic contractions in CC from rats with BCNI. Long-term treatment with SILOD partly prevented BCNI-induced decreases in neuronal nitric oxide synthase expression. Acute administration of SILOD (0.03 mg/kg intravenously) improved erectile responses in vivo and potentiated nitrergic relaxation and decreased neurogenic contractions ex vivo in CC from rats with BCNI. In human CC from patients with ED with a vascular etiology, TAD (30 nmol/L), SILOD (10 nmol/L), or their combination increased nitrergic relaxations. Potentiation by TAD was lost in human CC from patients with ED after RP but was recovered after co-treatment with SILOD. α-Adrenergic modulation, especially selective α 1A -blockade, improves erectile and cavernosal functions after BCNI. Modulation of the adrenergic system, mainly in combination strategies, could have a role in the management of ED after RP. Copyright © 2016 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

Travel assistant device (TAD) to aid transit riders with special needs.

DOT National Transportation Integrated Search

2008-08-01

The goal of the Americans with Disabilities (ADA) Act is to provide equal opportunity, full participation, and independence to persons with disabilities. The inability to travel, or the lack of knowledge in accessing the available transportation opti...

Division XII / Commission 46 / Program Group Teaching for Astronomy Development

NASA Astrophysics Data System (ADS)

Guinan, Edward F.; Marschall, Laurence A.

Annual reports of the IAU Commission 46 Program Group Teaching for Astronomy Development (TAD) for the years 2006 and 2007 have been published in IAU Information Bulletin 100, 47; and 101, 40. Here the 2008 report is presented.

The Effect of Sub-Auroral Polarization Streams (SAPS) on Ionosphere and Thermosphere during 2015 St. Patrick's Day storm: Global Ionosphere-Thermosphere Model (GITM) Simulations

NASA Astrophysics Data System (ADS)

Guo, J.; Deng, Y.; Zhang, D.; Lu, Y.; Sheng, C.

2017-12-01

Sub-Auroral Polarization Streams (SAPS) are incorporated into the non-hydrostatic Global Ionosphere-Thermosphere Model (GITM), revealing the complex effects on neutral dynamics and ion-neutral coupling processes. The intense westward ion stream could enhance the neutral zonal wind within the SAPS channel. Through neutral dynamics the neutrals then divide into two streams, one turns poleward and the other turns equatorward, forming a two-cell pattern in the SAPS-changed wind. The significant Joule heating induced by SAPS also leads to traveling atmospheric disturbances (TAD) accompanied by traveling ionospheric disturbances (TID), increasing the total electron content (TEC) by 2-8 TECu in the mid-latitude ionosphere. We investigate the potential causes of the reported poleward wind surge during the St. Patrick's Day storm in 2015. It is confirmed that Coriolis force on the westward zonal wind can contribute the poleward wind during post-SAPS interval. In addition, the simulations imply that the sudden decrease of heating rate within auroral oval could result in a TAD propagating equatorward, which could also be responsible for the sudden poleward wind surge. This study highlights the complicated effects of SAPS on ion-neutral coupling and neutral dynamics.

Extrinsic ion migration in perovskite solar cells

DOE PAGES

Li, Zhen; Xiao, Chuanxiao; Yang, Ye; ...

2017-04-10

In this study, the migration of intrinsic ions (e.g., MA +, Pb 2+, I –) in organic–inorganic hybrid perovskites has received significant attention with respect to the critical roles of these ions in the hysteresis and degradation in perovskite solar cells (PSCs). Here, we demonstrate that extrinsic ions (e.g., Li +, H +, Na +), when used in the contact layers in PSCs, can migrate across the perovskite layer and strongly impact PSC operation. In a TiO 2/perovskite/spiro-OMeTAD-based PSC, Li +-ion migration from spiro-OMeTAD to the perovskite and TiO 2 layer is illustrated by time-of-flight secondary-ion mass spectrometry. The movementmore » of Li + ions in PSCs plays an important role in modulating the solar cell performance, tuning TiO 2 carrier-extraction properties, and affecting hysteresis in PSCs. The influence of Li +-ion migration was investigated using time-resolved photoluminescence, Kelvin probe force microscopy, and external quantum efficiency spectra. Other extrinsic ions such as H + and Na + also show a clear impact on the performance and hysteresis in PSCs. Understanding the impacts of extrinsic ions in perovskite-based devices could lead to new material and device designs to further advance perovskite technology for various applications.« less

Enhancing agricultural productivity and rural incomes through sustainable use of natural resources in the semi arid tropics.

PubMed

Wani, Suhas P; Dixin, Yin; Li, Zhong; Dar, William D; Chander, Girish

2012-03-30

A participatory watershed management approach is one of the tested, sustainable and eco-friendly options to upgrade rain-fed agriculture to meet growing food demand along with additional multiple benefits in terms of improving livelihoods, addressing equity issues and biodiversity concerns. Watershed interventions at study sites in Thailand (Tad Fa and Wang Chai) and India (Kothapally) effectively reduced runoff and the associated soil loss. Such interventions at Xiaoxincun (China) and Wang Chai improved groundwater recharging and availability. Enhanced productive transpiration increased rainwater use efficiency for crop production by 13-29% at Xiaoxincun; 13-160% at Lucheba (China), 32-37% at Tad Fa and 23-46% at Wang Chai and by two to five times at Kothapally. Watershed interventions increased significantly the additional net returns from crop production as compared with the pre-watershed intervention period. Increased water availability opened up options for crop diversification with high-value crops, including increased forage production and boosted livestock-based livelihoods. In dryland tropics, integrated watershed management approach enabled farmers to diversify the systems along with increasing agricultural productivity through increased water availability, while conserving the natural resource base. Household incomes increased substantially, leading to improved living and building the resilience of the community and natural resources. Copyright © 2011 Society of Chemical Industry.

Meso-Scale Wetting of Paper Towels

NASA Astrophysics Data System (ADS)

Abedsoltan, Hossein

In this study, a new experimental approach is proposed to investigate the absorption properties of some selected retail paper towels. The samples were selected from two important manufacturing processes, conventional wet pressing (CWP) considered value products, and through air drying (TAD) considered as high or premium products. The tested liquids were water, decane, dodecane, and tetradecane with the total volumes in micro-liter range. The method involves the point source injection of liquid with different volumetric flowrates, in the nano-liter per second range. The local site for injection was chosen arbitrarily on the sample surface. The absorption process was monitored and recorded as the liquid advances, with two distinct imaging system methods, infrared imaging and optical imaging. The microscopic images were analyzed to calculate the wetted regions during the absorption test, and the absorption diagrams were generated. These absorption diagrams were dissected to illustrate the absorption phenomenon, and the absorption properties of the samples. The local (regional) absorption rates were computed for Mardi Gras and Bounty Basic as the representative samples for CWP and TAD, respectively in order to be compared with the absorption capacity property of these two samples. Then, the absorption capacity property was chosen as an index factor to compare the absorption properties of all the tested paper towels.

Maintenance Downtime October 17 - 23, 2014

Atmospheric Science Data Center

2014-10-23

... Impact:  The ASDC will be conducting extended system maintenance Fri 10/17@4pm - Thu 10/23@4pm  EDT Please expect: ... and Customization Tool -  AMAPS, CALIPSO, CERES, MOPITT, TES and TAD Search and Subset Tools   All systems will be ...

Regions of very low H3K27me3 partition the Drosophila genome into topological domains

PubMed Central

Flower, Rosalyn; Choo, Siew Woh

2017-01-01

It is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood. We have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing moderate-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4/Putzig. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the transcription start sites of housekeeping genes than with the H3K27me3 domain boundaries. While we have not demonstrated causality, we suggest that the D domain chromatin state, characterised by very low or absent H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome. PMID:28282436

History of the Army Ground Forces. Study Number 24. History of the Mountain Training Center

DTIC Science & Technology

1948-01-01

yaws, pius the knowledge of mevoral experienced mountaineers and skiers in the Office of the Quartermster General. On 20 May 1943 the Mountain and... skier ? Or will a mini- of knowledge and proficiency be sufficient? These are the questions that tad to be answered before the large-scale trainiag of...the prerogatives of Army co-nand were subordinated to the superior knowledge and skills of the mountaineering experts who had come into the Army7

STAT3 or USF2 Contributes to HIF Target Gene Specificity

PubMed Central

Pawlus, Matthew R.; Wang, Liyi; Murakami, Aya; Dai, Guanhai; Hu, Cheng-Jun

2013-01-01

The HIF1- and HIF2-mediated transcriptional responses play critical roles in solid tumor progression. Despite significant similarities, including their binding to promoters of both HIF1 and HIF2 target genes, HIF1 and HIF2 proteins activate unique subsets of target genes under hypoxia. The mechanism for HIF target gene specificity has remained unclear. Using siRNA or inhibitor, we previously reported that STAT3 or USF2 is specifically required for activation of endogenous HIF1 or HIF2 target genes. In this study, using reporter gene assays and chromatin immuno-precipitation, we find that STAT3 or USF2 exhibits specific binding to the promoters of HIF1 or HIF2 target genes respectively even when over-expressed. Functionally, HIF1α interacts with STAT3 to activate HIF1 target gene promoters in a HIF1α HLH/PAS and N-TAD dependent manner while HIF2α interacts with USF2 to activate HIF2 target gene promoters in a HIF2α N-TAD dependent manner. Physically, HIF1α HLH and PAS domains are required for its interaction with STAT3 while both N- and C-TADs of HIF2α are involved in physical interaction with USF2. Importantly, addition of functional USF2 binding sites into a HIF1 target gene promoter increases the basal activity of the promoter as well as its response to HIF2+USF2 activation while replacing HIF binding site with HBS from a HIF2 target gene does not change the specificity of the reporter gene. Importantly, RNA Pol II on HIF1 or HIF2 target genes is primarily associated with HIF1α or HIF2α in a STAT3 or USF2 dependent manner. Thus, we demonstrate here for the first time that HIF target gene specificity is achieved by HIF transcription partners that are required for HIF target gene activation, exhibit specific binding to the promoters of HIF1 or HIF2 target genes and selectively interact with HIF1α or HIF2α protein. PMID:23991099

Augmented reality fluoroscopy simulation of the guide-wire insertion in DHS surgery: A proof of concept study.

PubMed

van Duren, B H; Sugand, K; Wescott, R; Carrington, R; Hart, A

2018-05-01

Hip fractures contribute to a significant clinical burden globally with over 1.6 million cases per annum and up to 30% mortality rate within the first year. Insertion of a dynamic hip screw (DHS) is a frequently performed procedure to treat extracapsular neck of femur fractures. Poorly performed DHS fixation of extracapsular neck of femur fractures can result in poor mobilisation, chronic pain, and increased cut-out rate requiring revision surgery. A realistic, affordable, and portable fluoroscopic simulation system can improve performance metrics in trainees, including the tip-apex distance (the only clinically validated outcome), and improve outcomes. We developed a digital fluoroscopic imaging simulator using orthogonal cameras to track coloured markers attached to the guide-wire which created a virtual overlay on fluoroscopic images of the hip. To test the accuracy with which the augmented reality system could track a guide-wire, a standard workshop femur was used to calibrate the system with a positional marker fixed to indicate the apex; this allowed for comparison between guide-wire tip-apex distance (TAD) calculated by the system to be compared to that physically measured. Tests were undertaken to determine: (1) how well the apex could be targeted; (2) the accuracy of the calculated TAD. (3) The number of iterations through the algorithm giving the optimal accuracy-time relationship. The calculated TAD was found to have an average root mean square error of 4.2 mm. The accuracy of the algorithm was shown to increase with the number of iterations up to 20 beyond which the error asymptotically converged to an error of 2 mm. This work demonstrates a novel augmented reality simulation of guide-wire insertion in DHS surgery. To our knowledge this has not been previously achieved. In contrast to virtual reality, augmented reality is able to simulate fluoroscopy while allowing the trainee to interact with real instrumentation and performing the procedure on workshop bone models. Copyright © 2018 IPEM. Published by Elsevier Ltd. All rights reserved.

June 2017 Atmospheric Science Forum Newsletter

Atmospheric Science Data Center

2017-07-05

June 2017 Atmospheric Science Forum Newsletter Friday, June 30, 2017 ... DISCOVER-AQ campaign available on Toolsets for Airborne Data (TAD), release of the CERES EBAF TOA and SURFACE Edition 4.0 data products, and the MOPITT V7 product upgrade. Access the full article at: ...

Extended Maintenance Downtime 12/14 - 12/18

Atmospheric Science Data Center

2015-12-07

... am - 12/18 @ 5 pm EST Event Impact:  File System Maintenance will be performed on a number of the large file systems ... and Customization Tool -  AMAPS, CALIPSO, CERES, MOPITT, TES and TAD Search and Subset Tools   While some sites and tools may ...

Extended Maintenance Downtime 02/29 - 03/04

Atmospheric Science Data Center

2016-02-22

... @ 8am - 03/04 @ 4pm EST Event Impact:  System Maintenance will be performed at the ASDC the week of February 29th ... and Customization Tool -  AMAPS, CALIPSO, CERES, MOPITT, TES and TAD Search and Subset Tools   While some sites and tools may ...

Distalization of maxillary arch and correction of Class II with mini-implants: A report of two cases

PubMed Central

Tekale, Pawankumar Dnyandeo; Vakil, Ketan K.; Vakil, Jeegar K.; Gore, Ketan A.

2015-01-01

This article reports the successful use of mini-screws in the maxilla to treat two patients of age 21-year and 17-year-old girls. Both the patients had a skeletal Class II malocclusion with protrusive maxillary teeth and angels Class II mal-occlusion. Temporary anchorage devices (TADs) in the posterior dental region between maxillary second premolar and maxillary first molar teeth on both sides were used as anchorage for the retraction and intrusion of her maxillary anterior teeth. Those appliances, combined with a compensatory curved maxillary archwire, eliminated spacing, deep bite, forwardly placed and proclined upper front teeth and the protrusive profile, corrected the molar relationship from Class II to Class I. With no extra TADs in the anterior region for intrusion, the treatment was workable and simple. The patient received a satisfactory occlusion and an attractive smile. This technique requires minimal compliance and is particularly useful for correcting Class II patients with protrusive maxillary front teeth and dental deep bite. PMID:26097360

Effects of organic loading rates on reactor performance and microbial community changes during thermophilic aerobic digestion process of high-strength food wastewater.

PubMed

Jang, Hyun Min; Lee, Jae Won; Ha, Jeong Hyub; Park, Jong Moon

2013-11-01

To evaluate the applicability of single-stage thermophilic aerobic digestion (TAD) process treating high-strength food wastewater (FWW), TAD process was operated at four organic loading rates (OLRs) from 9.2 to 37.2 kg COD/m(3)d. The effects of OLRs on microbial community changes were also examined. The highest volumetric removal rate (13.3 kg COD/m(3)d) and the highest thermo-stable protease activity (0.95 unit/mL) were detected at OLR=18.6 kg COD/m(3)d. Denaturing gradient gel electrophoresis (DGGE) profiles and quantitative PCR (qPCR) results showed significant microbial community shifts in response to changes in OLR. In particular, DGGE and phylogenetic analysis demonstrate that the presence of Bacillus sp. (phylum of Firmicutes) was strongly correlated with efficient removal of organic particulates from high-strength food wastewater. Copyright © 2013 Elsevier Ltd. All rights reserved.

D-A-D-Typed Hole Transport Materials for Efficient Perovskite Solar Cells: Tuning Photovoltaic Properties via the Acceptor Group.

PubMed

Xu, Peng; Liu, Peng; Li, Yuanyuan; Xu, Bo; Kloo, Lars; Sun, Licheng; Hua, Yong

2018-06-13

Two D-A-D-structured hole-transport materials (YN1 and YN2) have been synthesized and used in perovskite solar cells. The two HTMs have low-lying HOMO levels and impressive mobility. Perovskite-based solar cells (PSCs) fabricated with YN2 showed a power conversion efficiency (PCE) value of 19.27% in ambient air, which is significantly higher than that of Spiro-OMeTAD (17.80%). PSCs based on YN1 showed an inferior PCE of 16.03%. We found that the incorporation of the stronger electron-withdrawing group in the HTM YN2 improves the PCE of PSCs. Furthermore, the YN2-based PSCs exhibit good long-term stability retaining 91.3% of its initial efficiency, whereas PSCs based on Spiro-OMeTAD retained only 42.2% after 1000 h lifetime (dark conditions). These promising results can provide a new strategy for the design of D-A-D HTMs for PSC applications in future.

[Hypertension in Mexican adults: prevalence, diagnosis and type of treatment. Ensanut MC 2016.

PubMed

Campos-Nonato, Ismael; Hernández-Barrera, Lucía; Pedroza-Tobías, Andrea; Medina, Catalina; Barquera, Simón

2018-01-01

To describe the prevalence, awareness and proportion of adults with an adequate control of hypertension. Blood pressure was measured at 8 352 adults who participated in the Ensanut MC 2016. The adults who reported having diagnosis of hypertension or had systolic blood pressure values (TAS) ≥140mmHg or diastolic blood pressure (TAD) ≥90mmHg were classified as hypertensive. Hypertension was considered controlled when blood pressure was TAS <140mmHg and TAD <90mmHg. The prevalence of hypertension was 25.5%. Of these, 40.0% were unaware of having high blood pressure. Of the hypertensive adults who had previous diagnosis of hypertension and receiving drug treatment (79.3%), 45.6% had blood pressure under control. A high percentage of adults are unaware of having hypertension and nearly half have inadequate control. The relevance of current programmes for diagnosing hypertension should be assessed, as well as the effectiveness of their control strategies.

Amorphous Hole-Transporting Material based on 2,2'-Bis-substituted 1,1'-Biphenyl Scaffold for Application in Perovskite Solar Cells.

PubMed

Magomedov, Artiom; Sakai, Nobuya; Kamarauskas, Egidijus; Jokubauskaitė, Gabrielė; Franckevičius, Marius; Jankauskas, Vygintas; Snaith, Henry J; Getautis, Vytautas

2017-05-04

Perovskite solar cells are considered a promising technology for solar-energy conversion, with power conversion efficiencies currently exceeding 20 %. In most of the reported devices, Spiro-OMeTAD is used for positive-charge extraction and transport layer. Although a number of alternative hole-transporting materials with different aromatic or heteroaromatic fragments have already been synthesized, a cheap and well-performing hole-transporting material is still in high demand. In this work, a two-step synthesis of a carbazole-based hole-transporting material is presented. Synthesized compounds exhibited amorphous nature, good solubility and thermal stability. The perovskite solar cells employing the newly synthesized material generated a power conversion efficiency of 16.5 % which is slightly lower than that obtained with Spiro-OMeTAD (17.5 %). The low-cost synthesis and high performance makes our hole-transport material promising for applications in perovskite-based optoelectronic devices. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chromosomal Organization by an Interplay of Loop Extrusion and Compartment Interaction

NASA Astrophysics Data System (ADS)

Nuebler, Johannes; Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid

The chromatin fiber in eukaryotic nuclei is far from being simply a confined but otherwise randomly arranged polymer. Rather, it shows a high degree of spatial organization on all length scales, from individual nucleosomes up to well-segregated chromosome territories. On intermediate scales, chromosome conformation capture techniques have revealed two ubiquitous modes of organization: an alternating structure of A/B compartments, where each type preferentially associates with other base pairs of its type, and, typically on a smaller scale, the formation of topologically associating domains (TADs) with increased association within each domain but not across boundaries. The mechanisms behind this organization are only beginning to emerge. We review how the model of active loop extrusion can explain in a unified way such diverse phenomena as TAD formation and mitotic compaction and segregation, and we address in particular to what extent the interplay of active loop extrusion and compartment structure is compatible with recent experiments that interfere with the loading of the proposed loop extrusion factor cohesin. 4D Nucleome.

Benefits of Mobile Phone Technology for Personal Environmental Monitoring

PubMed Central

Carrasco-Turigas, Glòria; Seto, Edmund; Jerrett, Michael; Nieuwenhuijsen, Mark J

2016-01-01

Background Tracking individuals in environmental epidemiological studies using novel mobile phone technologies can provide valuable information on geolocation and physical activity, which will improve our understanding of environmental exposures. Objective The objective of this study was to assess the performance of one of the least expensive mobile phones on the market to track people's travel-activity pattern. Methods Adults living and working in Barcelona (72/162 bicycle commuters) carried simultaneously a mobile phone and a Global Positioning System (GPS) tracker and filled in a travel-activity diary (TAD) for 1 week (N=162). The CalFit app for mobile phones was used to log participants’ geographical location and physical activity. The geographical location data were assigned to different microenvironments (home, work or school, in transit, others) with a newly developed spatiotemporal map-matching algorithm. The tracking performance of the mobile phones was compared with that of the GPS trackers using chi-square test and Kruskal-Wallis rank sum test. The minute agreement across all microenvironments between the TAD and the algorithm was compared using the Gwet agreement coefficient (AC1). Results The mobile phone acquired locations for 905 (29.2%) more trips reported in travel diaries than the GPS tracker (P<.001) and had a median accuracy of 25 m. Subjects spent on average 57.9%, 19.9%, 9.0%, and 13.2% of time at home, work, in transit, and other places, respectively, according to the TAD and 57.5%, 18.8%, 11.6%, and 12.1%, respectively, according to the map-matching algorithm. The overall minute agreement between both methods was high (AC1 .811, 95% CI .810-.812). Conclusions The use of mobile phones running the CalFit app provides better information on which microenvironments people spend their time in than previous approaches based only on GPS trackers. The improvements of mobile phone technology in microenvironment determination are because the mobile phones are faster at identifying first locations and capable of getting location in challenging environments thanks to the combination of assisted-GPS technology and network positioning systems. Moreover, collecting location information from mobile phones, which are already carried by individuals, allows monitoring more people with a cheaper and less burdensome method than deploying GPS trackers. PMID:27833069

76 FR 45235 - Notice of Submission for OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-28

... interested in comments which: (1) Evaluate whether the proposed collection of information is necessary for... practical utility; (2) Evaluate the accuracy of the agency's estimate of the burden of the proposed... detailed descriptive information of TA&D Program grantees' activities concerning the topic areas addressed...

Toolsets for Airborne Data - URS and New Documentation

Atmospheric Science Data Center

2015-03-23

... geolocated) files based on a user’s choice of time base. In addition, the TAD merge feature allows users to generate standard deviations ... NASA airborne missions. We are currently focused on in situ measurements and we would like to hear from you about the need for other ...

Diversity, virulence and 2,4-diacetylphloroglucinol sensitivity of Gaeumannomyces graminis var. tritici isolates from Washington State.

USDA-ARS?s Scientific Manuscript database

Populations of 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas fluorescens buildup in soils that have undergone continuous wheat or barley monoculture, resulting in take-all decline (TAD). We tested whether Gaeumannomyces graminis var. tritici (Ggt) isolates (causal agent of take-all) in mon...

A modified reverse one-hybrid screen identifies transcriptional activation in Phyochrome-Interacting Factor 3

USDA-ARS?s Scientific Manuscript database

Transcriptional activation domains (TAD) are difficult to predict and identify, since they are not conserved and have little consensus. Here, we describe a yeast-based screening method that is able to identify individual amino acid residues involved in transcriptional activation in a high throughput...

Training Parents to Teach; Four Models. First Chance for Children, Vol. 3.

ERIC Educational Resources Information Center

Grim, Janet, Ed.

Described in a monograph published by the Technical Assistance Delivery System (TADS) are the rationale, intake and screening procedures, service delivery, liaison and follow through, and evaluation of parent training models from four preschool demonstration centers for handicapped children. An overview discusses the purposes and dimensions of…

The Development of a Needs Assessment Process. Occasional Paper Number 3.

ERIC Educational Resources Information Center

Black, Talbot; And Others

The paper considers the concept of needs assessment in terms of the activities of TADS (Technical Assistance Development System), a project to provide support services to model demonstration projects and state education agency grantees of the Handicapped Children's Early Education Program. Section 1 defines needs assessment, describes approaches…

Mainstreaming Handicapped Preschoolers. Proceedings of a Topical Workshop. TADscripts '82.

ERIC Educational Resources Information Center

Anderson, Joan; Black, Talbot

The document offers proceedings from a Technical Assistance Development System (TADS) topical workshop designed to explore the implications of mainstreaming for early childhood education. The first section contains an adaptation of the keynote address by A. Turnbull titled "Integration of Handicapped Children in Home, School, and…

An Input Evaluation of Three Technical Assistance Needs Assessment Strategies.

ERIC Educational Resources Information Center

Suarez, Tanya M.; Cox, James O.

The Technical Assistance Development System--TADS (a project to provide technical assistance to personnel implementing programs for preschool handicapped children and their families) conducted an evaluation of three technical assistance needs assessment strategies during 1979-80. The three strategies were: (1) on-site--conducted by a trained needs…

National Evaluation of the IDEA Technical Assistance & Dissemination Program. NCEE 2014-4000

ERIC Educational Resources Information Center

Daley,Tamara C.; Fiore, Thomas A.; Bollmer, Julie; Nimkoff, Tamara; Lysy, Chris

2013-01-01

Under the Individuals with Disabilities Education Act (IDEA), the Technical Assistance and Dissemination (TA&D) Program is the U.S. Department of Education's (ED) primary vehicle for providing technical assistance (TA) to individuals and organizations responsible for serving children with disabilities and their families. The evaluation is part…

Misunderstood Superheroes: Batman and Performance Based Logistics

DTIC Science & Technology

2009-02-01

the mass community. How do the Batman myth , ethos, and psychology pertain to PBL? PBL—born on the dark side in the 1990s, perhaps with a tad of...without PBL. Now, that’s about as scary as Batman’s psychotic nemesis, the Joker! Business Case Analysis The most debated characteristic of Batman is why

75 FR 55785 - Office of Special Education Programs, Office of Special Education and Rehabilitative Services...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-14

... appropriate assessments of students with disabilities, as well as emerging issues related to the inclusion of... assistance to States regarding the inclusion of students with disabilities as they develop new academic... Improve Services and Results for Children with Disabilities program (TA&D), authorized under section 663...

Nonmonotonic dose response curves (NMDRCs) are common after Estrogen or Androgen signaling pathway disruption. Fact or Falderal?##

EPA Science Inventory

Nonmonotonic dose response curves (NMDRCs) are common after Estrogen or Androgen signaling pathway disruption. Fact or Falderal? Leon Earl Gray Jr, USEPA, ORD, NHEERL, TAD, RTB. RTP, NC, USA The shape of the dose response curve in the low dose region has been debated since th...

Responses of Boys and Girls to a Behaviorally Focused School Attitude Questionnaire

ERIC Educational Resources Information Center

Whaley-Klahn, Mary Anne; And Others

1976-01-01

In response to the Teacher Approval-Disapproval Scale (TADS), elementary school boys report receiving more personal disapproval and less personal approval from their teachers than do elementary school girls, but boys and girls do not differ in reporting how frequently their teachers distribute approvals and disapprovals to the whole class. (Author)

District-Level Perspective on Innovative Approaches in Performance Appraisal: Integration and Refinement.

ERIC Educational Resources Information Center

Gray, Patrick

The Dade County (Florida) Public School System is replacing its Teacher Assessment and Development System (TADS), initiated in 1982, with systems that draw on recent research, link teaching skills to school improvement, and recognize and reward advanced pedagogy. The comprehensive approach will integrate subordinate and peer assessment through a…

Seafarers, Great Circles, and a Tad of Rhumb: Understanding the Mercator Misconception

ERIC Educational Resources Information Center

DiSpezio, Michael A.

2010-01-01

Being flat, Mercator maps inherently misrepresent some aspects of Earth's geography. That's because there is absolutely no way to simultaneously conserve all of the elements of three-dimensional space in a two-dimensional model. To dispel misconceptions, check out the Activity Worksheet and the website resources included in this article. Along…

A Reply to John W. Friesen and Tad Guzie.

ERIC Educational Resources Information Center

De Ruyter, Doret

1999-01-01

Replies to two authors who commented on an article about Christian schools in a pluralistic society. The paper focuses on four questions and comments from both of the commentaries related to spirituality and religious education. It also discusses the issue of educating for critical thinking and defends the original article's central ideas and…

A TAD closer to ATM.

PubMed

Aymard, Francois; Legube, Gaëlle

2016-05-01

Ataxia telangiectasia mutated (ATM) has been known for decades as the main kinase mediating the DNA double-strand break response. Our recent findings suggest that its major role at the sites of breaks likely resides in its ability to modify both the local chromatin landscape and the global chromosome organization in order to promote repair accuracy.

Dynamic interplay and function of multiple noncoding genes governing X chromosome inactivation

PubMed Central

Yue, Minghui; Richard, John Lalith Charles

2015-01-01

There is increasing evidence for the emergence of long noncoding RNAs (IncRNAs) as important components, especially in the regulation of gene expression. In the event of X chromosome inactivation, robust epigenetic marks are established in a long noncoding Xist RNA-dependent manner, giving rise to a distinct epigenetic landscape on the inactive X chromosome (Xi). The X inactivation center (Xic is essential for induction of X chromosome inactivation and harbors two topologically associated domains (TADs) to regulate monoallelic Xist expression: one at the noncoding Xist gene and its upstream region, and the other at the antisense Tsix and its upstream region. The monoallelic expression of Xist is tightly regulated by these two functionally distinct TADs as well as their constituting IncRNAs and proteins. In this review, we summarize recent updates in our knowledge of IncRNAs found at the Xic and discuss their overall mechanisms of action. We also discuss our current understanding of the molecular mechanism behind Xist RNA-mediated induction of the repressive epigenetic landscape at the Xi. PMID:26260844

Linamarase activities in Bacillus spp. responsible for thermophilic aerobic digestion of agricultural wastes for animal nutrition.

PubMed

Ugwuanyi, J Obeta; Harvey, L M; McNeil, B

2007-01-01

Thermophilic Bacillus spp. isolated from thermophilic aerobic digestion (TAD) of model agricultural slurry were screened for ability to secret linamarase activity and degrade linamarin, a cyanogenic glycoside toxin abundant in cassava. Screening was performed by both linamarin - picrate assay and by p-nitrophenyl beta-D-glucoside (PNPG) degradation, and results of both assays were related. Linamarase positive isolates were identified as Bacillus coagulans, Bacillus licheniformis and Bacillus stearothermophilus. Enzyme production was growth related and peak production was reached in 48 h in B. coagulans and 36 h in B. stearothermophilus. B. coagulans produced over 40 times greater activity than B. stearothermophilus. Enzyme productivity in shake flask was not strictly related to screening assay result. Crude enzyme of B. coagulans was optimally active at 75 degrees C while that of B. stearothermophilus was optimally active at 80 degrees C and both had optimum activity at pH 8.0. The thermophilic and neutrophilic- to marginally alkaline activity of the crude enzymes could be very useful in the detoxification and reprocessing of cyanogens containing cassava wastes by TAD for use in animal nutrition.

The membrane-topogenic vectorial behaviour of Nrf1 controls its post-translational modification and transactivation activity.

PubMed

Zhang, Yiguo; Hayes, John D

2013-01-01

The integral membrane-bound Nrf1 transcription factor fulfils important functions in maintaining cellular homeostasis and organ integrity, but how it is controlled vectorially is unknown. Herein, creative use of Gal4-based reporter assays with protease protection assays (GRAPPA), and double fluorescence protease protection (dFPP), reveals that the membrane-topogenic vectorial behaviour of Nrf1 dictates its post-translational modification and transactivation activity. Nrf1 is integrated within endoplasmic reticulum (ER) membranes through its NHB1-associated TM1 in cooperation with other semihydrophobic amphipathic regions. The transactivation domains (TADs) of Nrf1, including its Asn/Ser/Thr-rich (NST) glycodomain, are transiently translocated into the ER lumen, where it is glycosylated in the presence of glucose to become a 120-kDa isoform. Thereafter, the NST-adjoining TADs are partially repartitioned out of membranes into the cyto/nucleoplasmic side, where Nrf1 is subject to deglycosylation and/or proteolysis to generate 95-kDa and 85-kDa isoforms. Therefore, the vectorial process of Nrf1 controls its target gene expression.

2D black phosphorous nanosheets as a hole transporting material in perovskite solar cells

NASA Astrophysics Data System (ADS)

Muduli, Subas Kumar; Varrla, Eswaraiah; Kulkarni, Sneha Avinash; Han, Guifang; Thirumal, Krishnamoorthy; Lev, Ovadia; Mhaisalkar, Subodh; Mathews, Nripan

2017-12-01

We demonstrate for the first-time liquid exfoliated few layers of 2D Black phosphorus (BP) nanosheets as a hole transporting material (HTM) for perovskite based solar cells. The photoelectron spectroscopy in air (PESA) measurements confirm the low laying valence band level of BP nanosheets (-5.2 eV) favourable for hole injection from CH3NH3PbI3 (MAPbI3). Our results show that ∼25% improvement in power conversion efficiency (PCE) of η = 16.4% for BP nanosheets + Spiro-OMeTAD as an HTM as compared to spiro-OMeTAD (η = 13.1%). When BP nanosheets are exclusively utilised as an HTM, a PCE of η = 7.88% is noted, an improvement over the 4% PCE values observed for HTM free devices. Photoluminescence (PL) quenching of MAPbI3 and impedance measurements further confirm the charge extraction ability of BP nanosheets. The structural and optical characterization of liquid exfoliated BP nanosheets is discussed in detail with the aid of transmission electron microscopy, Raman spectroscopy, absorption spectroscopy and photo-electron spectroscopy.

The basic helix-loop-helix differentiation factor Nex1/MATH-2 functions as a key activator of the GAP-43 gene

PubMed Central

Uittenbogaard, Martine; Martinka, Debra L.; Chiaramello, Anne

2006-01-01

Nex1/MATH-2 is a neurogenic basic Helix-Loop-Helix (bHLH) transcription factor that belongs to the NeuroD subfamily. Its expression parallels that of the GAP-43 gene and peaks during brain development, when neurite outgrowth and synaptogenesis are highly active. We previously observed a direct correlation between the levels of expression of Nex1 and GAP-43 proteins, which resulted in extensive neurite outgrowth and neuronal differentiation of PC12 cells in the absence of nerve growth factor. Since the GAP-43 gene is a target for bHLH regulation, we investigated whether Nex1 could regulate the activity of the GAP-43 promoter. We found that among the members of the NeuroD subfamily, Nex1 promoted maximal activity of the GAP-43 promoter. The Nex1-mediated activity is restricted to the conserved E1–E2 cluster located near the major transcription start sites. By electrophoretic mobility shift assay and site-directed mutagenesis, we showed that Nex1 binds as homodimers and that the E1 E-box is a high affinity binding site. We further found that Nex1 released the ME1 E-protein-mediated repression in a concentration dependent manner. Thus, the E1–E2 cluster has a dual function: it can mediate activation or repression depending on the interacting bHLH proteins. Finally, a series of N-terminal and C-terminal deletions revealed that Nex1 transcriptional activity is linked to two distinct transactivation domains, TAD1 and TAD2, with TAD1 being unique to Nex1. Together, our results suggest that Nex1 may engage in selective interactions with components of the core transcriptional machinery whose assembly is dictated by the architecture of the GAP-43 promoter and cellular environment. PMID:12562512

Productive, economic and risk assessment of grazing dairy systems with supplemented cows milked once a day.

PubMed

Lazzarini, B; Lopez-Villalobos, N; Lyons, N; Hendrikse, L; Baudracco, J

2018-05-01

Milking cows once a day (OAD) is a herd management practice that may help to reduce working effort and labour demand in dairy farms. However, a decrease in milk yield per cow occurs in OAD systems compared with twice a day (TAD) systems and this may affect profitability of dairy systems. The objective of this study was to assess productive and economic impact and risk of reducing milking frequency from TAD to OAD for grazing dairy systems, using a whole-farm model. Five scenarios were evaluated by deterministic and stochastic simulations: one scenario under TAD milking (TADAR) and four scenarios under OAD milking. The OAD scenarios assumed that milk yield per cow decreased by 30% (OAD30), 24% (OAD24), 19% (OAD19) and 10% (OAD10), compared with TADAR scenario, based on experimental and commercial farms data. Stocking rate (SR) was increased in all OAD scenarios compared to TADAR and two levels of reduction in labour cost were tested, namely 15% and 30%. Milk and concentrate feeds prices, and pasture and crop yields, were allowed to behave stochastically to account for market and climate variations, respectively, to perform risk analyses. Scenario OAD10 showed similar milk yield per ha compared with TADAR, as the increased SR compensated for the reduction in milk yield per cow. For scenarios OAD30, OAD24 and OAD19 the greater number of cows per ha partially compensated for the reduction of milk yield per cow and milk yield per ha decreased 21%, 15% and 10%, respectively, compared with TADAR. Farm operating profit per ha per year also decreased in all OAD scenarios compared with TADAR, and were US$684, US$161, US$ 303, US$424 and US$598 for TADAR, OAD30, OAD24, OAD19, OAD10, respectively, when labour cost was reduced 15% in OAD scenarios. When labour cost was reduced 30% in OAD scenarios, only OAD10 showed higher profit (US$706) than TADAR. Stochastic simulations showed that exposure to risk would be higher in OAD scenarios compared with TADAR. Results showed that OAD milking systems might be an attractive alternative for farmers who can either afford a reduction in profit to gain better and more flexible working conditions or can minimise milk yield loss and greatly reduce labour cost.

The Theory of Adaptive Dispersion and Acoustic-phonetic Properties of Cross-language Lexical-tone Systems

NASA Astrophysics Data System (ADS)

Alexander, Jennifer Alexandra

Lexical-tone languages use fundamental frequency (F0/pitch) to convey word meaning. About 41.8% of the world's languages use lexical tone (Maddieson, 2008), yet those systems are under-studied. I aim to increase our understanding of speech-sound inventory organization by extending to tone-systems a model of vowel-system organization, the Theory of Adaptive Dispersion (TAD) (Liljencrants and Lindblom, 1972). This is a cross-language investigation of whether and how the size of a tonal inventory affects (A) acoustic tone-space size and (B) dispersion of tone categories within the tone-space. I compared five languages with very different tone inventories: Cantonese (3 contour, 3 level tones); Mandarin (3 contour, 1 level tone); Thai (2 contour, 3 level tones); Yoruba (3 level tones only); and Igbo (2 level tones only). Six native speakers (3 female) of each language produced 18 CV syllables in isolation, with each of his/her language's tones, six times. I measured tonal F0 across the vowel at onset, midpoint, and offglide. Tone-space size was the F0 difference in semitones (ST) between each language's highest and lowest tones. Tone dispersion was the F0 distance (ST) between two tones shared by multiple languages. Following the TAD, I predicted that languages with larger tone inventories would have larger tone-spaces. Against expectations, tone-space size was fixed across level-tone languages at midpoint and offglide, and across contour-tone languages (except Thai) at offglide. However, within each language type (level-tone vs. contour-tone), languages with smaller tone inventories had larger tone spaces at onset. Tone-dispersion results were also unexpected. The Cantonese mid-level tone was further dispersed from a tonal baseline than the Yoruba mid-level tone; Cantonese mid-level tone dispersion was therefore greater than theoretically necessary. The Cantonese high-level tone was also further dispersed from baseline than the Mandarin high-level tone -- at midpoint and offglide only. The TAD cannot account for these results. A follow-up analysis indicates that tone-space size differs as a function of tone-language type: level-tone and contour-tone systems may not be comparable. Another analysis plots tones in an onset F0 x offglide F0 space (following Barry and Blamey, 2004). Preliminary results indicate that the languages' tones are well-separated in this space.

Benefits of Mobile Phone Technology for Personal Environmental Monitoring.

PubMed

Donaire-Gonzalez, David; Valentín, Antònia; de Nazelle, Audrey; Ambros, Albert; Carrasco-Turigas, Glòria; Seto, Edmund; Jerrett, Michael; Nieuwenhuijsen, Mark J

2016-11-10

Tracking individuals in environmental epidemiological studies using novel mobile phone technologies can provide valuable information on geolocation and physical activity, which will improve our understanding of environmental exposures. The objective of this study was to assess the performance of one of the least expensive mobile phones on the market to track people's travel-activity pattern. Adults living and working in Barcelona (72/162 bicycle commuters) carried simultaneously a mobile phone and a Global Positioning System (GPS) tracker and filled in a travel-activity diary (TAD) for 1 week (N=162). The CalFit app for mobile phones was used to log participants' geographical location and physical activity. The geographical location data were assigned to different microenvironments (home, work or school, in transit, others) with a newly developed spatiotemporal map-matching algorithm. The tracking performance of the mobile phones was compared with that of the GPS trackers using chi-square test and Kruskal-Wallis rank sum test. The minute agreement across all microenvironments between the TAD and the algorithm was compared using the Gwet agreement coefficient (AC1). The mobile phone acquired locations for 905 (29.2%) more trips reported in travel diaries than the GPS tracker (P<.001) and had a median accuracy of 25 m. Subjects spent on average 57.9%, 19.9%, 9.0%, and 13.2% of time at home, work, in transit, and other places, respectively, according to the TAD and 57.5%, 18.8%, 11.6%, and 12.1%, respectively, according to the map-matching algorithm. The overall minute agreement between both methods was high (AC1 .811, 95% CI .810-.812). The use of mobile phones running the CalFit app provides better information on which microenvironments people spend their time in than previous approaches based only on GPS trackers. The improvements of mobile phone technology in microenvironment determination are because the mobile phones are faster at identifying first locations and capable of getting location in challenging environments thanks to the combination of assisted-GPS technology and network positioning systems. Moreover, collecting location information from mobile phones, which are already carried by individuals, allows monitoring more people with a cheaper and less burdensome method than deploying GPS trackers. ©David Donaire-Gonzalez, Antònia Valentín, Audrey de Nazelle, Albert Ambros, Glòria Carrasco-Turigas, Edmund Seto, Michael Jerrett, Mark J Nieuwenhuijsen. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 10.11.2016.

Computational Fluid Dynamics Analysis of Thoracic Aortic Dissection

NASA Astrophysics Data System (ADS)

Tang, Yik; Fan, Yi; Cheng, Stephen; Chow, Kwok

2011-11-01

Thoracic Aortic Dissection (TAD) is a cardiovascular disease with high mortality. An aortic dissection is formed when blood infiltrates the layers of the vascular wall, and a new artificial channel, the false lumen, is created. The expansion of the blood vessel due to the weakened wall enhances the risk of rupture. Computational fluid dynamics analysis is performed to study the hemodynamics of this pathological condition. Both idealized geometry and realistic patient configurations from computed tomography (CT) images are investigated. Physiological boundary conditions from in vivo measurements are employed. Flow configuration and biomechanical forces are studied. Quantitative analysis allows clinicians to assess the risk of rupture in making decision regarding surgical intervention.

Enhancer-Derived lncRNAs Regulate Genome Architecture: Fact or Fiction?

PubMed

Fanucchi, Stephanie; Mhlanga, Musa M

2017-06-01

How does the non-coding portion of the genome contribute to the regulation of genome architecture? A recent paper by Tan et al. focuses on the relationship between cis-acting complex-trait-associated lincRNAs and the formation of chromosomal contacts in topologically associating domains (TADs). Copyright © 2017 Elsevier Ltd. All rights reserved.

At-a-Glance B3 Resource Guide for Supporting Academic Achievement for Students with Disabilities

ERIC Educational Resources Information Center

Regional Resource Center Program, 2011

2011-01-01

This results improvement resource guide includes a listing of TA&D programs and centers that provide technical assistance related to academic achievement results improvement for students with disabilities. The website URL, target audience(s), and purpose are provided for each center/program. In addition, a brief example describing the…

Low Density Real Gas Flows About Hypersonic Vehicles.

DTIC Science & Technology

1991-11-01

equations with fully-coupled finite rate air chemistry. The development of the HYLDA code was motivated by the difficulty of current wind tunnel...2ps,,.,, - psj = , (3-30) PN. 2pNwa - pNead u Uadj v Vadj w T Wadj bc 2TLMau - TadJ where PS4 -- PSj if noncatalytic wall = calculated if catalytic wall

A TAD Closer to Understanding Dosage Compensation.

PubMed

Wood, Andrew J; Bickmore, Wendy A

2015-06-08

Eukaryotic chromosomes are organized into topological domains, but how these are established and maintained is poorly understood. Writing in Nature, Crane et al. (2015) show that a specialized condensin complex enforces the domain boundaries along the C. elegans X chromosome to equalize transcription from the X between males and hermaphrodites. Copyright © 2015 Elsevier Inc. All rights reserved.

Emphasis. Volume 3, Number 3, Spring 1980 through Volume 5, Number 2, Winter 1982 (Seven Issues).

ERIC Educational Resources Information Center

Assael, Daniel, Ed.; And Others

1982-01-01

Seven issues of the newsletter/journal from the Technical Assistance Development System (TADS) address a vareity of topics related to special education for young handicapped children. Among articles included are a description of a rural workshop sponsored by an affiliate of the Handicapped Children's Early Education Program (HCEEP), electronics…

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

PubMed Central

Barutcu, A. Rasim; Lajoie, Bryan R.; Fritz, Andrew J.; McCord, Rachel P.; Nickerson, Jeffrey A.; van Wijnen, Andre J.; Lian, Jane B.; Stein, Janet L.; Dekker, Job; Stein, Gary S.; Imbalzano, Anthony N.

2016-01-01

The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma-related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucleosomes at target regions. Although the transcriptional role of SMARCA4 at gene promoters is well-studied, less is known about its role in higher-order genome organization. SMARCA4 knockdown in human mammary epithelial MCF-10A cells resulted in 176 up-regulated genes, including many related to lipid and calcium metabolism, and 1292 down-regulated genes, some of which encode extracellular matrix (ECM) components that can exert mechanical forces and affect nuclear structure. ChIP-seq analysis of SMARCA4 localization and SMARCA4-bound super-enhancers demonstrated extensive binding at intergenic regions. Furthermore, Hi-C analysis showed extensive SMARCA4-mediated alterations in higher-order genome organization at multiple resolutions. First, SMARCA4 knockdown resulted in clustering of intra- and inter-subtelomeric regions, demonstrating a novel role for SMARCA4 in telomere organization. SMARCA4 binding was enriched at topologically associating domain (TAD) boundaries, and SMARCA4 knockdown resulted in weakening of TAD boundary strength. Taken together, these findings provide a dynamic view of SMARCA4-dependent changes in higher-order chromatin organization and gene expression, identifying SMARCA4 as a novel component of chromatin organization. PMID:27435934

Anomaly detection in hyperspectral imagery: statistics vs. graph-based algorithms

NASA Astrophysics Data System (ADS)

Berkson, Emily E.; Messinger, David W.

2016-05-01

Anomaly detection (AD) algorithms are frequently applied to hyperspectral imagery, but different algorithms produce different outlier results depending on the image scene content and the assumed background model. This work provides the first comparison of anomaly score distributions between common statistics-based anomaly detection algorithms (RX and subspace-RX) and the graph-based Topological Anomaly Detector (TAD). Anomaly scores in statistical AD algorithms should theoretically approximate a chi-squared distribution; however, this is rarely the case with real hyperspectral imagery. The expected distribution of scores found with graph-based methods remains unclear. We also look for general trends in algorithm performance with varied scene content. Three separate scenes were extracted from the hyperspectral MegaScene image taken over downtown Rochester, NY with the VIS-NIR-SWIR ProSpecTIR instrument. In order of most to least cluttered, we study an urban, suburban, and rural scene. The three AD algorithms were applied to each scene, and the distributions of the most anomalous 5% of pixels were compared. We find that subspace-RX performs better than RX, because the data becomes more normal when the highest variance principal components are removed. We also see that compared to statistical detectors, anomalies detected by TAD are easier to separate from the background. Due to their different underlying assumptions, the statistical and graph-based algorithms highlighted different anomalies within the urban scene. These results will lead to a deeper understanding of these algorithms and their applicability across different types of imagery.

Division XII / Commission 46 / Program Group Exchnage of Astronomers

NASA Astrophysics Data System (ADS)

Percy, John R.; Leung, Kam-Ching; Tolbert, Charles R.

The Commission 46 Program Group Exchange of Astronomers (PG-EA) provides travel grants to astronomers and advanced students for research or study trips of at least three months duration. Highest priority is given to applicants from developing countries whose visits will benefit them, their institution and country, and the institution visited. This program, if used strategically, has the potential to support other Commission 46 programs such as Teaching for Astronomical Development (PG-TAD) and World Wide Development of Astronomy (PG-WWDA). Complete information about the program, and the application procedure, can be found at .

Non-extraction treatment of a Class III skeletal case.

PubMed

Gonzalez, Bulmario

2009-01-01

Adult Class III Skeletal treatment options have generally included some form of surgery (Maxillary advancement in midface deficient cases and/or Mandibular set-back). This article discusses non-surgical treatment of an adult patient using the combined concepts of mandibular molar distalization enhanced with TADs and non-extraction camouflage dental correction through maxillary incisor protraction and mandibular incisor lingualization.

Thermally Activated Driver

NASA Technical Reports Server (NTRS)

Kinard, William H.; Murray, Robert C.; Walsh, Robert F.

1987-01-01

Space-qualified, precise, large-force, thermally activated driver (TAD) developed for use in space on astro-physics experiment to measure abundance of rare actinide-group elements in cosmic rays. Actinide cosmic rays detected using thermally activated driver as heart of event-thermometer (ET) system. Thermal expansion and contraction of silicone oil activates driver. Potential applications in fluid-control systems where precise valve controls are needed.

Giant field-induced adiabatic temperature changes in Ni-Mn-In-based Heusler alloys

NASA Astrophysics Data System (ADS)

Pandey, Sudip; Quetz, Abdiel; Aryal, Anil; Dubenko, Igor; Mazumdar, Dipanjan; Blinov, Mikhail; Prudnikov, Valerii; Rodionov, Igor; Granovsky, Alexander; Stadler, Shane; Ali, Naushad

Direct measurements of the adiabatic temperature change (ΔTAD) of Ni50Mn35In14.5B0.5 have been done using an adiabatic magnetocalorimeter in a temperature range of 250-350 K, and with magnetic field changes up to ΔH =1.8 T. The initial susceptibility in the low magnetic field region drastically increases with temperature starting at about 300 K. Magnetocaloric effects (MCE) parameters were found to be a linear function of H2 / 3 in the vicinity of the second order transitions (SOT), whereas the first order transitions (FOT) do not obey the H2 / 3 law due to the discontinuity of the transition. The relative cooling power (RCP) based on the adiabatic temperature change for a magnetic field change of 1.8 T has been estimated. Maximum values of ΔTAD = -2.6 K and 1.7 K were observed at FOT and SOT for ΔH =1.8 T, respectively. Acknowledgement: This work was supported by the Office of Basic Energy Sciences, Material Science Division of the U.S. Department of Energy, DOE Grant No. DE-FG02-06ER46291 (SIU) and DE-FG02-13ER46946 (LSU).

Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex

PubMed Central

Tsurumura, Toshiharu; Tsumori, Yayoi; Qiu, Hao; Oda, Masataka; Sakurai, Jun; Nagahama, Masahiro; Tsuge, Hideaki

2013-01-01

Clostridium perfringens iota-toxin (Ia) mono-ADP ribosylates Arg177 of actin, leading to cytoskeletal disorganization and cell death. To fully understand the reaction mechanism of arginine-specific mono-ADP ribosyl transferase, the structure of the toxin-substrate protein complex must be characterized. Recently, we solved the crystal structure of Ia in complex with actin and the nonhydrolyzable NAD+ analog βTAD (thiazole-4-carboxamide adenine dinucleotide); however, the structures of the NAD+-bound form (NAD+-Ia-actin) and the ADP ribosylated form [Ia-ADP ribosylated (ADPR)-actin] remain unclear. Accidentally, we found that ethylene glycol as cryo-protectant inhibits ADP ribosylation and crystallized the NAD+-Ia-actin complex. Here we report high-resolution structures of NAD+-Ia-actin and Ia-ADPR-actin obtained by soaking apo-Ia-actin crystal with NAD+ under different conditions. The structures of NAD+-Ia-actin and Ia-ADPR-actin represent the pre- and postreaction states, respectively. By assigning the βTAD-Ia-actin structure to the transition state, the strain-alleviation model of ADP ribosylation, which we proposed previously, is experimentally confirmed and improved. Moreover, this reaction mechanism appears to be applicable not only to Ia but also to other ADP ribosyltransferases. PMID:23382240

Solution-Processed Cu(In, Ga)(S, Se)2 Nanocrystal as Inorganic Hole-Transporting Material for Efficient and Stable Perovskite Solar Cells.

PubMed

Xu, Lu; Deng, Lin-Long; Cao, Jing; Wang, Xin; Chen, Wei-Yi; Jiang, Zhiyuan

2017-12-01

Perovskite solar cells are emerging as one of the most promising candidates for solar energy harvesting. To date, most of the high-performance perovskite solar cells have exclusively employed organic hole-transporting materials (HTMs) such as 2,2',7,7'-tetrakis-(N,N-di-p-methoxyphenylamine)-9,9'-spirobifluorene (spiro-OMeTAD) or polytriarylamine (PTAA) which are often expensive and have low hole mobility. Almost all these HTMs reported needed lithium salt, e.g., lithium bis(trifluoromethylsulfonyl)imide (Li-TFSI) doping, to improve hole mobility and performance. However, the use of Li-TFSI should be avoided because the hygroscopic nature of Li-TFSI could cause decomposition of perovskite and reduce device stability. Herein, we employed solution-processed CuIn 0.1 Ga 0.9 (S 0.9 Se 0.1 ) 2 (CIGSSe) nanocrystals as a novel inorganic HTM in perovskite solar cells. A power conversion efficiency of 9.15% was obtained for CIGSSe-based devices with improved stability, compared to devices using spiro-OMeTAD as HTM. This work offers a promising candidate of Cu-based inorganic HTM for efficient and stable perovskite solar cells.

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design.

PubMed

Kim, Ji Hun; Titus, Katelyn R; Gong, Wanfeng; Beagan, Jonathan A; Cao, Zhendong; Phillips-Cremins, Jennifer E

2018-05-14

Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library. Here, we describe 5C-ID, a new version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ Chromosome-Conformation-Capture (3C)) and ligation-mediated amplification performed with a double alternating primer design. We demonstrate that 5C-ID produces higher-resolution 3D genome folding maps with reduced spatial noise using markedly lower cell numbers than canonical 5C. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C. Copyright © 2018 Elsevier Inc. All rights reserved.

Magnetic and magnetocaloric properties of HoCr0.75Fe0.25O3 compound

NASA Astrophysics Data System (ADS)

Kotnana, Ganesh; Babu, P. D.; Jammalamadaka, S. Narayana

2018-05-01

We report on the magnetic and magnetocaloric properties of HoCr0.75Fe0.25O3 compound around the Néel temperature (TN), which is due to Cr3+ ordering. Susceptibility (χ) vs. temperature (T) graph of HoCr0.75Fe0.25O3 compound infer two transitions due to the ordering of Cr3+ moments (TN ˜ 155 K) and Ho3+ moments (TNHo ˜ 8 K). Magnetic entropy (-ΔSM) value of 1.14 J kg-1 K-1 around 157.5 K with a magnetic field (H) of 90 kOe is attributed to antiferromagnetic (AFM) ordering of Cr3+ moments. A maximum value of adiabatic temperature (ΔTad) ˜ 0.41 K around TN is obtained and is found to increases with applied magnetic field. Negative slope for H/M vs. M2 graph is evident for HoCr0.75Fe0.25O3 compound below TN, which indicates the first order phase transition. Quantified values of -ΔSM and ΔTad open the way to explore rare earth orthochromites for the MCE properties and refrigeration applications.

Hydrophobic Polystyrene Passivation Layer for Simultaneously Improved Efficiency and Stability in Perovskite Solar Cells.

PubMed

Li, Minghua; Yan, Xiaoqin; Kang, Zhuo; Huan, Yahuan; Li, Yong; Zhang, Ruxiao; Zhang, Yue

2018-06-06

The major restraint for the commercialization of the high-performance hybrid metal halide perovskite solar cells is the long-term stability, especially at the infirm interface between the perovskite film and organic charge-transfer layer. Recently, engineering the interface between the perovskite and spiro-OMeTAD becomes an effective strategy to simultaneously improve the efficiency and stability in the perovskite solar cells. In this work, we demonstrated that introducing an interfacial polystyrene layer between the perovskite film and spiro-OMeTAD layer can effectively improve the perovskite solar cells photovoltaic performance. The inserted polystyrene layer can passivate the interface traps and defects effectively and decrease the nonradiative recombination, leading to enhanced photoluminescence intensity and carrier lifetime, without compromising the carrier extraction and transfer. Under the optimized condition, the perovskite solar cells with the polystyrene layer achieve an enhanced average power efficiency of about 19.61% (20.46% of the best efficiency) from about 17.63% with negligible current density-voltage hysteresis. Moreover, the optimized perovskite solar cells with the hydrophobic polystyrene layer can maintain about 85% initial efficiency after 2 months storage in open air conditions without encapsulation.

Detection and tracking of a moving target using SAR images with the particle filter-based track-before-detect algorithm.

PubMed

Gao, Han; Li, Jingwen

2014-06-19

A novel approach to detecting and tracking a moving target using synthetic aperture radar (SAR) images is proposed in this paper. Achieved with the particle filter (PF) based track-before-detect (TBD) algorithm, the approach is capable of detecting and tracking the low signal-to-noise ratio (SNR) moving target with SAR systems, which the traditional track-after-detect (TAD) approach is inadequate for. By incorporating the signal model of the SAR moving target into the algorithm, the ambiguity in target azimuth position and radial velocity is resolved while tracking, which leads directly to the true estimation. With the sub-area substituted for the whole area to calculate the likelihood ratio and a pertinent choice of the number of particles, the computational efficiency is improved with little loss in the detection and tracking performance. The feasibility of the approach is validated and the performance is evaluated with Monte Carlo trials. It is demonstrated that the proposed approach is capable to detect and track a moving target with SNR as low as 7 dB, and outperforms the traditional TAD approach when the SNR is below 14 dB.

Detection and Tracking of a Moving Target Using SAR Images with the Particle Filter-Based Track-Before-Detect Algorithm

PubMed Central

Gao, Han; Li, Jingwen

2014-01-01

A novel approach to detecting and tracking a moving target using synthetic aperture radar (SAR) images is proposed in this paper. Achieved with the particle filter (PF) based track-before-detect (TBD) algorithm, the approach is capable of detecting and tracking the low signal-to-noise ratio (SNR) moving target with SAR systems, which the traditional track-after-detect (TAD) approach is inadequate for. By incorporating the signal model of the SAR moving target into the algorithm, the ambiguity in target azimuth position and radial velocity is resolved while tracking, which leads directly to the true estimation. With the sub-area substituted for the whole area to calculate the likelihood ratio and a pertinent choice of the number of particles, the computational efficiency is improved with little loss in the detection and tracking performance. The feasibility of the approach is validated and the performance is evaluated with Monte Carlo trials. It is demonstrated that the proposed approach is capable to detect and track a moving target with SNR as low as 7 dB, and outperforms the traditional TAD approach when the SNR is below 14 dB. PMID:24949640

Reaching extended length-scales with accelerated dynamics

NASA Astrophysics Data System (ADS)

Hubartt, Bradley; Shim, Yunsic; Amar, Jacques

2012-02-01

While temperature-accelerated dynamics (TAD) has been quite successful in extending the time-scales for non-equilibrium simulations of small systems, the computational time increases rapidly with system size. One possible solution to this problem, which we refer to as parTAD^1 is to use spatial decomposition combined with our previously developed semi-rigorous synchronous sublattice algorithm^2. However, while such an approach leads to significantly better scaling as a function of system-size, it also artificially limits the size of activated events and is not completely rigorous. Here we discuss progress we have made in developing an alternative approach in which localized saddle-point searches are combined with parallel GPU-based molecular dynamics in order to improve the scaling behavior. By using this method, along with the use of an adaptive method to determine the optimal high-temperature^3, we have been able to significantly increase the range of time- and length-scales over which accelerated dynamics simulations may be carried out. [1] Y. Shim et al, Phys. Rev. B 76, 205439 (2007); ibid, Phys. Rev. Lett. 101, 116101 (2008). [2] Y. Shim and J.G. Amar, Phys. Rev. B 71, 125432 (2005). [3] Y. Shim and J.G. Amar, J. Chem. Phys. 134, 054127 (2011).

Shape transitions in strained Cu islands on Ni(100): kinetics versus energetics

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Amar, Jacques

2012-02-01

We examine the shape transition from compact to ramified islands observed in submonolayer Cu/Ni(100) growth. Recently, it has been argued that this transition is not due to a growth instability but can be understood in terms of energetic arguments. In order to determine the responsible mechanisms we have carried out energetics calculations as well as temperature-accelerated dynamics (TAD) and kinetic Monte Carlo (KMC) simulations. Our results indicate that the shape transition cannot be explained by equilibrium arguments, but is instead due to kinetic effects which are mediated by strain. In particular, by calculating the relevant line-tension and strain energies, we find that the equilibrium critical island-width is at least four orders of magnitude larger than the experimentally observed arm-width. In contrast, our TAD simulations indicate that unexpected concerted motions occurring at step edges are responsible. The energy barriers for these concerted motions decrease with increasing island size and appear to saturate for islands larger than 300 - 400 atoms. By including these strain-induced kinetic processes in our KMC simulations of island-growth, we have been able to explain both the temperature- and coverage-dependence of the island morphology.

Bright Visible-Infrared Light Emitting Diodes Based on Hybrid Halide Perovskite with Spiro-OMeTAD as a Hole-Injecting Layer.

PubMed

Jaramillo-Quintero, Oscar A; Sanchez, Rafael S; Rincon, Marina; Mora-Sero, Ivan

2015-05-21

Hybrid halide perovskites that are currently intensively studied for photovoltaic applications, also present outstanding properties for light emission. Here, we report on the preparation of bright solid state light emitting diodes (LEDs) based on a solution-processed hybrid lead halide perovskite (Pe). In particular, we have utilized the perovskite generally described with the formula CH3NH3PbI(3-x)Cl(x) and exploited a configuration without electron or hole blocking layer in addition to the injecting layers. Compact TiO2 and Spiro-OMeTAD were used as electron and hole injecting layers, respectively. We have demonstrated a bright combined visible-infrared radiance of 7.1 W·sr(-1)·m(-2) at a current density of 232 mA·cm(-2), and a maximum external quantum efficiency (EQE) of 0.48%. The devices prepared surpass the EQE values achieved in previous reports, considering devices with just an injecting layer without any additional blocking layer. Significantly, the maximum EQE value of our devices is obtained at applied voltages as low as 2 V, with a turn-on voltage as low as the Pe band gap (V(turn-on) = 1.45 ± 0.06 V). This outstanding performance, despite the simplicity of the approach, highlights the enormous potentiality of Pe-LEDs. In addition, we present a stability study of unsealed Pe-LEDs, which demonstrates a dramatic influence of the measurement atmosphere on the performance of the devices. The decrease of the electroluminescence (EL) under continuous operation can be attributed to an increase of the non-radiative recombination pathways, rather than a degradation of the perovskite material itself.

Highly Sensitive Determination of the Polaron-Induced Optical Absorption of Organic Charge-Transport Materials

NASA Astrophysics Data System (ADS)

Rabe, T.; Görrn, P.; Lehnhardt, M.; Tilgner, M.; Riedl, T.; Kowalsky, W.

2009-04-01

We examine polaron-induced absorption in organic transport materials using a highly sensitive measurement technique. A hole only device is embedded into a low-loss TE2 waveguide structure, and the current induced change of the waveguide absorption is measured. The exemplary study of 2,2',7,7'-tetrakis(N,N-diphenylamine)-9,9'-spiro-bifluorene (S-TAD) reveals a very low polaron absorption cross section of σp≤2.6×10-18cm2 for 560 nm ≤λ≤660nm. The accuracy of this data is unsurpassed by other techniques used for the unambiguous study of polaronic species in organic thin films.

Neutron threshold activation detectors (TAD) for the detection of fissions

NASA Astrophysics Data System (ADS)

Gozani, Tsahi; Stevenson, John; King, Michael J.

2011-10-01

Prompt fission neutrons are one of the strongest signatures of the fission process. Depending on the fission inducing radiation, their average number ranges from 2.5 to 4 neutrons per fission. They are more energetic and abundant, by about 2 orders of magnitude, than the delayed neutrons (≈3 vs. ≈0.01) that are commonly used as indicators for the presence of fissionable materials. The detection of fission prompt neutrons, however, has to be done in the presence of extremely intense probing radiation that stimulated them. During irradiation, the fission stimulation radiation, X-rays or neutrons, overwhelms the neutron detectors and temporarily incapacitate them. Consequently, by the time the detectors recover from the source radiation, fission prompt neutrons are no longer emitted. In order to measure the prompt fission signatures under these circumstances, special measures are usually taken with the detectors such as heavy shielding with collimation, use of inefficient geometries, high pulse height bias and gamma-neutron separation via pulse-shape discrimination with an appropriate organic scintillator. These attempts to shield the detector from the flash of radiation result in a major loss of sensitivity. It can lead to a complete inability to detect the fission prompt neutrons. In order to overcome the blinding induced background from the source radiation, the detection of prompt fission neutrons needs to occur long after the fission event and after the detector has fully recovered from the source overload. A new approach to achieve this is to detect the delayed activation induced by the fission neutrons. The approach demonstrates a good sensitivity in adverse overload situations (gamma and neutron "flash") where fission prompt neutrons could normally not be detected. The new approach achieves the required temporal separation between the detection of prompt neutrons and the detector overload by the neutron activation of the detector material. The technique, called Threshold Activation Detection (TAD), is to utilize appropriate substances that can be selectively activated by the fission neutrons and not by the source radiation and then measure the radioactively decaying activation products (typically beta and gamma rays) well after the source pulse. The activation material should possess certain properties: a suitable half-life of the order of seconds; an energy threshold below which the numerous source neutrons will not activate it (e.g., 3 MeV); easily detectable activation products (typically >1 MeV beta and gamma rays) and have a usable cross-section for the selected reaction. Ideally the substance would be a part of the scintillator. There are several good material candidates for the TAD, including fluorine, which is a major constituent of available scintillators such as BaF 2, CaF 2 and hydrogen free liquid fluorocarbon. Thus the fluorine activation products, in particular the beta particles, can be measured with a very high efficiency in the detector. The principles, applications and experimental results obtained with the fluorine based TAD are discussed.

Hybrid alkali-hydrodynamic disintegration of waste-activated sludge before two-stage anaerobic digestion process.

PubMed

Grübel, Klaudiusz; Suschka, Jan

2015-05-01

The first step of anaerobic digestion, the hydrolysis, is regarded as the rate-limiting step in the degradation of complex organic compounds, such as waste-activated sludge (WAS). The aim of lab-scale experiments was to pre-hydrolyze the sludge by means of low intensive alkaline sludge conditioning before applying hydrodynamic disintegration, as the pre-treatment procedure. Application of both processes as a hybrid disintegration sludge technology resulted in a higher organic matter release (soluble chemical oxygen demand (SCOD)) to the liquid sludge phase compared with the effects of processes conducted separately. The total SCOD after alkalization at 9 pH (pH in the range of 8.96-9.10, SCOD = 600 mg O2/L) and after hydrodynamic (SCOD = 1450 mg O2/L) disintegration equaled to 2050 mg/L. However, due to the synergistic effect, the obtained SCOD value amounted to 2800 mg/L, which constitutes an additional chemical oxygen demand (COD) dissolution of about 35 %. Similarly, the synergistic effect after alkalization at 10 pH was also obtained. The applied hybrid pre-hydrolysis technology resulted in a disintegration degree of 28-35%. The experiments aimed at selection of the most appropriate procedures in terms of optimal sludge digestion results, including high organic matter degradation (removal) and high biogas production. The analyzed soft hybrid technology influenced the effectiveness of mesophilic/thermophilic anaerobic digestion in a positive way and ensured the sludge minimization. The adopted pre-treatment technology (alkalization + hydrodynamic cavitation) resulted in 22-27% higher biogas production and 13-28% higher biogas yield. After two stages of anaerobic digestion (mesophilic conditions (MAD) + thermophilic anaerobic digestion (TAD)), the highest total solids (TS) reduction amounted to 45.6% and was received for the following sample at 7 days MAD + 17 days TAD. About 7% higher TS reduction was noticed compared with the sample after 9 days MAD + 15 days TAD. Similar results were obtained for volatile solids (VS) reduction after two-stage anaerobic digestion. The highest decrease of VS was obtained when the first stage, the mesophilic digestion which lasted 7 days, was followed by thermophilic digestion for 17 days.

Expression of the Flp proteins by Haemophilus ducreyi is necessary for virulence in human volunteers.

PubMed

Janowicz, Diane M; Cooney, Sean A; Walsh, Jessica; Baker, Beth; Katz, Barry P; Fortney, Kate R; Zwickl, Beth W; Ellinger, Sheila; Munson, Robert S

2011-09-22

Haemophilus ducreyi, the causative agent of the sexually transmitted disease chancroid, contains a flp (fimbria like protein) operon that encodes proteins predicted to contribute to adherence and pathogenesis. H. ducreyi mutants that lack expression of Flp1 and Flp2 or TadA, which has homology to NTPases of type IV secretion systems, have decreased abilities to attach to and form microcolonies on human foreskin fibroblasts (HFF). A tadA mutant is attenuated in its ability to cause disease in human volunteers and in the temperature dependent rabbit model, but a flp1flp2 mutant is virulent in rabbits. Whether a flp deletion mutant would cause disease in humans is not clear. We constructed 35000HPΔflp1-3, a deletion mutant that lacks expression of all three Flp proteins but has an intact tad secretion system. 35000HPΔflp1-3 was impaired in its ability to form microcolonies and to attach to HFF in vitro when compared to its parent (35000HP). Complementation of the mutant with flp1-3 in trans restored the parental phenotype. To test whether expression of Flp1-3 was necessary for virulence in humans, ten healthy adult volunteers were experimentally infected with a fixed dose of 35000HP (ranging from 54 to 67 CFU) on one arm and three doses of 35000HPΔflp1-3 (ranging from 63 to 961 CFU) on the other arm. The overall papule formation rate for the parent was 80% (95% confidence interval, CI, 55.2%-99.9%) and for the mutant was 70.0% (95% CI, 50.5%-89.5%) (P = 0.52). Mutant papules were significantly smaller (mean, 11.2 mm2) than were parent papules (21.8 mm2) 24 h after inoculation (P = 0.018). The overall pustule formation rates were 46.7% (95% CI 23.7-69.7%) at 30 parent sites and 6.7% (95% CI, 0.1-19.1%) at 30 mutant sites (P = 0.001). These data suggest that production and secretion of the Flp proteins contributes to microcolony formation and attachment to HFF cells in vitro. Expression of flp1-3 is also necessary for H. ducreyi to initiate disease and progress to pustule formation in humans. Future studies will focus on how Flp proteins contribute to microcolony formation and attachment in vivo. © 2011 Janowicz et al; licensee BioMed Central Ltd.

Comparative treatment of dye-rich wastewater in engineered wetland systems (EWSs) vegetated with different plants.

PubMed

Mbuligwe, Stephen E

2005-01-01

In Dar es Salaam City there are more than a thousand tie-and-dye (TAD) small-scale industries (SSIs) that discharge dye-rich wastewater indiscriminately with resultant water pollution. Due to the decentralised nature of the TAD SSIs, coupled with financial constraints facing their operators, control of their pollution needs a simple cost-effective waste treatment technology. Engineered wetland systems (EWSs) constitute such a technology. A pilot scale EWS was evaluated with respect to its effectiveness in treating dye-rich wastewater. The role of wetland plants was assessed through comparing treatment performance efficiencies between an unplanted and vegetated EWS beds. On the whole, it has been demonstrated that the EWS has the potential to effectively treat dye-rich wastewater. Colour, which is the most apparent problem issue with textile wastewater, was reduced by 72-77%. COD was reduced by 68-73%, while sulphate was reduced by 53-59%. The proportionately high COD removal suggests the reduction in colour was accompanied by almost complete degradation of dyes and daughter products. The overall treatment efficiency of the vegetated units was more than twice as high as that of the unplanted bed. On average, the bed vegetated with coco yam plants performed better (7.6%) than the one planted with cattail plants.

The chemistry of nicotinamide adenine dinucleotide (NAD) analogues containing C-nucleosides related to nicotinamide riboside.

PubMed

Pankiewicz, Krzysztof W; Watanabe, Kyoichi A; Lesiak-Watanabe, Krystyna; Goldstein, Barry M; Jayaram, Hiremagalur N

2002-04-01

Oncolytic C-nucleosides, tiazofurin (2-beta-D-ribofuranosylthiazole-4-carboxamide) and benzamide riboside (3-beta-D-ribofuranosylbenzamide) are converted in cell into active metabolites thiazole-4-carboxamide- and benzamide adenine dinucleotide, TAD and BAD, respectively. TAD and BAD as NAD analogues were found to bind at the nicotinamide adenine dinucleotide (cofactor NAD) site of inosine monophosphate dehydrogenase (IMPDH), an important target in cancer treatment. The synthesis and evaluation of anticancer activity of a number of C-nucleosides related to tiazofurin and nicotinamide riboside then followed and are reviewed herein. Interestingly, pyridine C-nucleosides (such as C-nicotinamide riboside) are not metabolized into the corresponding NAD analogues in cell. Their conversion by chemical methods is described. As dinucleotides these compounds show inhibition of IMPDH in low micromolar level. Also, the synthesis of BAD in metabolically stable bis(phosphonate) form is discussed indicating the usefulness of such preformed inhibitors in drug development. Among tiazofurin analogues, Franchetti and Grifantini found, that the replacement of the sulfur by oxygen (as in oxazafurin) but not the removal of nitrogen (tiophenfurin) of the thiazole ring resulted in inactive compounds. The anti cancer activity of their synthetic dinucleotide analogues indicate that inactive compounds are not only poorly metabolized in cell but also are weak inhibitors of IMPDH as dinucleotides.

Global Atmosphere Watch Workshop on Measurement-Model ...

EPA Pesticide Factsheets

The World Meteorological Organization’s (WMO) Global Atmosphere Watch (GAW) Programme coordinates high-quality observations of atmospheric composition from global to local scales with the aim to drive high-quality and high-impact science while co-producing a new generation of products and services. In line with this vision, GAW’s Scientific Advisory Group for Total Atmospheric Deposition (SAG-TAD) has a mandate to produce global maps of wet, dry and total atmospheric deposition for important atmospheric chemicals to enable research into biogeochemical cycles and assessments of ecosystem and human health effects. The most suitable scientific approach for this activity is the emerging technique of measurement-model fusion for total atmospheric deposition. This technique requires global-scale measurements of atmospheric trace gases, particles, precipitation composition and precipitation depth, as well as predictions of the same from global/regional chemical transport models. The fusion of measurement and model results requires data assimilation and mapping techniques. The objective of the GAW Workshop on Measurement-Model Fusion for Global Total Atmospheric Deposition (MMF-GTAD), an initiative of the SAG-TAD, was to review the state-of-the-science and explore the feasibility and methodology of producing, on a routine retrospective basis, global maps of atmospheric gas and aerosol concentrations as well as wet, dry and total deposition via measurement-model

Viscous flow computations for elliptical two-duct version of the SSME hot gas manifold

NASA Technical Reports Server (NTRS)

Roger, R. P.

1986-01-01

The objective of the effort was to numerically simulate viscous subsonic flow in a proposed elliptical two-duct version of the fuel side Hot Gas Manifold (HGM) for the Space Shuttle Main Engine (SSME). The numerical results were to complement both water flow and air flow experiments in the two-duct geometry performed at NASA-MSFC and Rocketdyne. The three-dimensional character of the HGM consists of two essentially different geometries. The first part of the construction is a concentric shell duct structure which channels the gases from a turbine exit into the second part comprised of two cylindrically shaped transfer ducts. The initial concentric shell portion can be further subdivided into a turnaround section and a bowl section. The turnaround duct (TAD) changes the direction of the mean flow by 180 degress from a smaller radius to a larger radius duct which discharges into the bowl. The cylindrical transfer ducts are attached to the bowl on one side thus providing a plane of symmetry midway between the two. Centerline flow distance from the TAD inlet to the transfer duct exit is approximately two feet. Details of the approach used to numerically simulate laminar or turbulent flow in the HGM geometry are presented. Computational results are presented and discussed.

Insights into the mechanism of human papillomavirus E2-induced procaspase-8 activation and cell death

NASA Astrophysics Data System (ADS)

Singh, Nitu; Senapati, Sanjib; Bose, Kakoli

2016-02-01

High-risk human papillomavirus (HR-HPV) E2 protein, the master regulator of viral life cycle, induces apoptosis of host cell that is independent of its virus-associated regulatory functions. E2 protein of HR-HPV18 has been found to be involved in novel FADD-independent activation of caspase-8, however, the molecular basis of this unique non-death-fold E2-mediated apoptosis is poorly understood. Here, with an interdisciplinary approach that involves in silico, mutational, biochemical and biophysical probes, we dissected and characterized the E2-procasapse-8 binding interface. Our data demonstrate direct non-homotypic interaction of HPV18 E2 transactivation domain (TAD) with α2/α5 helices of procaspase-8 death effector domain-B (DED-B). The observed interaction mimics the homotypic DED-DED complexes, wherein the conserved hydrophobic motif of procaspase-8 DED-B (F122/L123) occupies a groove between α2/α3 helices of E2 TAD. This interaction possibly drives DED oligomerization leading to caspase-8 activation and subsequent cell death. Furthermore, our data establish a model for E2-induced apoptosis in HR-HPV types and provide important clues for designing E2 analogs that might modulate procaspase-8 activation and hence apoptosis.

Verification of threshold activation detection (TAD) technique in prompt fission neutron detection using scintillators containing 19F

NASA Astrophysics Data System (ADS)

Sibczynski, P.; Kownacki, J.; Moszyński, M.; Iwanowska-Hanke, J.; Syntfeld-Każuch, A.; Gójska, A.; Gierlik, M.; Kaźmierczak, Ł.; Jakubowska, E.; Kędzierski, G.; Kujawiński, Ł.; Wojnarowicz, J.; Carrel, F.; Ledieu, M.; Lainé, F.

2015-09-01

In the present study ⌀ 5''× 3'' and ⌀ 2''× 2'' EJ-313 liquid fluorocarbon as well as ⌀ 2'' × 3'' BaF2 scintillators were exposed to neutrons from a 252Cf neutron source and a Sodern Genie 16GT deuterium-tritium (D+T) neutron generator. The scintillators responses to β- particles with maximum endpoint energy of 10.4 MeV from the n+19F reactions were studied. Response of a ⌀ 5'' × 3'' BC-408 plastic scintillator was also studied as a reference. The β- particles are the products of interaction of fast neutrons with 19F which is a component of the EJ-313 and BaF2 scintillators. The method of fast neutron detection via fluorine activation is already known as Threshold Activation Detection (TAD) and was proposed for photofission prompt neutron detection from fissionable and Special Nuclear Materials (SNM) in the field of Homeland Security and Border Monitoring. Measurements of the number of counts between 6.0 and 10.5 MeV with a 252Cf source showed that the relative neutron detection efficiency ratio, defined as epsilonBaF2 / epsilonEJ-313-5'', is 32.0% ± 2.3% and 44.6% ± 3.4% for front-on and side-on orientation of the BaF2, respectively. Moreover, the ⌀ 5'' EJ-313 and side-on oriented BaF2 were also exposed to neutrons from the D+T neutron generator, and the relative efficiency epsilonBaF2 / epsilonEJ-313-5'' was estimated to be 39.3%. Measurements of prompt photofission neutrons with the BaF2 detector by means of data acquisition after irradiation (out-of-beam) of nuclear material and between the beam pulses (beam-off) techniques were also conducted on the 9 MeV LINAC of the SAPHIR facility.

The electron Echo 6 mechanical deployment systems

NASA Technical Reports Server (NTRS)

Meyers, S. C.; Steffen, J. E.; Malcolm, P. R.; Winckler, J. R.

1984-01-01

The Echo 6 sounding rocket payload was flown on a Terrier boosted Black Brant vehicle on March 30, 1983. The experiment requirements resulted in the new design of a rocket propelled Throw Away Detector System (TADS) with onboard Doppler radar, a free-flyer forward experiment designated the Plasma Diagnostic Package (PDP), and numerous other basic systems. The design, developmental testing, and flight preparations of the payload and the mechanical deployment systems are described.

The SXT conjugative element and linear prophage N15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the Paracoccus aminophilus plasmid pAMI2.

PubMed

Dziewit, Lukasz; Jazurek, Magdalena; Drewniak, Lukasz; Baj, Jadwiga; Bartosik, Dariusz

2007-03-01

A group of proteic toxin-antitoxin (TA) cassettes whose representatives are widely distributed among bacterial genomes has been identified. These cassettes occur in chromosomes, plasmids, bacteriophages, and noncomposite transposons, as well as in the SXT conjugative element of Vibrio cholerae. The following four homologous loci were subjected to detailed comparative studies: (i) tad-ata from plasmid pAMI2 of Paracoccus aminophilus (the prototype of this group), (ii) gp49-gp48 from the linear bacteriophage N15 of Escherichia coli, (iii) s045-s044 from SXT, and (iv) Z3230-Z3231 from the genomic island of enterohemorrhagic Escherichia coli O157:H7 strain EDL933. Functional analysis revealed that all but one of these loci (Z3230-Z3231) are able to stabilize heterologous replicons, although the host ranges varied. The TA cassettes analyzed have the following common features: (i) the toxins are encoded by the first gene of each operon; (ii) the antitoxins contain a predicted helix-turn-helix motif of the XRE family; and (iii) the cassettes have two promoters that are different strengths, one which is located upstream of the toxin gene and one which is located upstream of the antitoxin gene. All four toxins tested are functional in E. coli; overexpression of the toxins (in the absence of antitoxin) results in a bacteriostatic effect manifested by elongation of bacterial cells and growth arrest. The toxins have various effects on cell viability, which suggests that they may recognize different intracellular targets. Preliminary data suggest that different cellular proteases are involved in degradation of antitoxins encoded by the loci analyzed.

Verification Tests of the US Electricar Corp. Lectric Leopard.

DTIC Science & Technology

1980-10-01

Recharge control. The vehicle shall have a recharge control which is adequate to mieet the requirements of energy, life , and safety as such... life . (1) Time vehicle shall he capable of at least 75 percent of the range specified in 475.10 (e) after 12 imonths or 15.000 kin of norrmal use...Copies Addressee No. Coies Addrese I Department of Transportation 1 Conell Uiversity Library, FOB 10A, TAD494.6 Joe Roman, Associate Director 800

Response to copper of Acidithiobacillus ferrooxidans ATCC 23270 grown in elemental sulfur.

PubMed

Almárcegui, Rodrigo J; Navarro, Claudio A; Paradela, Alberto; Albar, Juan Pablo; von Bernath, Diego; Jerez, Carlos A

2014-11-01

The response of Acidithiobacillus ferrooxidans ATCC 23270 to copper was analyzed in sulfur-grown cells by using quantitative proteomics. Forty-seven proteins showed altered levels in cells grown in the presence of 50 mM copper sulfate. Of these proteins, 24 were up-regulated and 23 down-regulated. As seen before in ferrous iron-grown cells, there was a notorious up-regulation of RND-type Cus systems and different RND-type efflux pumps, indicating that these proteins are very important in copper resistance. Copper also triggered the down-regulation of the major outer membrane porin of A. ferrooxidans in sulfur-grown bacteria, suggesting they respond to the metal by decreasing the influx of cations into the cell. On the contrary, copper in sulfur-grown cells caused an overexpression of putative TadA and TadB proteins known to be essential for biofilm formation in bacteria. Surprisingly, sulfur-grown microorganisms showed increased levels of proteins related with energy generation (rus and petII operons) in the presence of copper. Although rus operon is overexpressed mainly in cells grown in ferrous iron, the up-regulation of rusticyanin in sulfur indicates a possible role for this protein in copper resistance as well. Finally, copper response in A. ferrooxidans appears to be influenced by the substrate being oxidized by the microorganism. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

NIAC Phase 1 Final Study Report on Titan Aerial Daughtercraft

NASA Technical Reports Server (NTRS)

Matthies, Larry

2017-01-01

Saturns giant moon Titan has become one of the most fascinating bodies in the Solar System. Even though it is a billion miles from Earth, data from the Cassini mission reveals that Titan has a very diverse, Earth-like surface, with mountains, fluvial channels, lakes, evaporite basins, plains, dunes, and seas [Lopes 2010] (Figure 1). But unlike Earth, Titans surface likely is composed of organic chemistry products derived from complex atmospheric photochemistry [Lorenz 2008]. In addition, Titan has an active meteorological system with observed storms and precipitation-induced surface darkening suggesting a hydrocarbon cycle analogous to Earths water cycle [Turtle 2011].Titan is the richest laboratory in the solar system for studying prebiotic chemistry, which makes studying its chemistry from the surface and in the atmosphere one of the most important objectives in planetary science [Decadal 2011]. The diversity of surface features on Titan related to organic solids and liquids makes long-range mobility with surface access important [Decadal 2011]. This has not been possible to date, because mission concepts have had either no mobility (landers), no surface access (balloons and airplanes), or low maturity, high risk, and/or high development costs for this environment (e,g. large, self-sufficient, long-duration helicopters). Enabling in situ mobility could revolutionize Titan exploration, similarly to the way rovers revolutionized Mars exploration. Recent progress on several fronts has suggested that small-scale rotorcraft deployed as daughtercraft from a lander or balloon mothercraft may be an effective, affordable approach to expanding Titan surface access. This includes rapid progress on autonomous navigation capabilities of such aircraft for terrestrial applications and on miniaturization, driven by the consumer mobile electronics market, of high performance of sensors, processors, and other avionics components needed for such aircraft. Chemical analysis, for example with a mass spectrometer, will be important to any Titan surface mission. Anticipating that it may be more practical to host chemical analysis instruments on a mothership than a daughtercraft, we defined system and mission concepts that deploy a small rotorcraft, termed a Titan Aerial Daughtercraft (TAD), from a lander or balloon to perform high-resolution imaging and mapping, potentially land to acquire microscopic images or other in situ measurements, and acquire samples to return to analytical instruments on the mothership. In principle, the ability to recharge batteries in TAD from a radioisotope or other long-lived power source on the mothership could enable multiple sorties. For a lander-based mission, a variety of landing sites is conceivable, including near lake margins, in dry lake beds, or in regions of plains, dunes, or putative cryovolanic or impact melt features. Such missions may require landing with greater precision than in previous missions (Huygens) and mission studies; this could also enhance the ability of TAD to reach interesting terrain from the landing site. Precision descent may also benefit balloon missions, with or without a daughtercraft, by increasing the probability that the balloon will drift over desired terrain early in its mission. Given these potential benefits, the overall concept studied here includes brief consideration of precision descent for landing or balloon deployment, followed by one or more sorties by a rotorcraft deployed from the mothership, with the ability to return to the mothership.

Problems with the Small Business Administration’s Merit Appraisal and Compensation System.

DTIC Science & Technology

1981-09-21

TAD-AI07 181 GENERAL ACCOUNTING OFFICE WASHINGTON DC FEDERAL PERS-ETC F/6 5/9 PROBLEMS WITH THE SMALL BUSINESS ADMINISTRATION’S MERIT APPRAIS--ETC(U...Adninistrator, Small Business Administration Dear Mr. Car D Subjec::/ Problems with the Small Business Administra- tjon’s Merit Appraisal and Compensation...System, (rLP68 8i 71). We reviewed the Small Business Administration’s (SBA’s) performance appraisal/merit pay program as part of our review of

Air Land Sea Bulletin. Issue No. 2010-2, May 2010

DTIC Science & Technology

2010-05-01

progresses, flight leads should reference each J3.5 via bullseye and/or TN (i.e., TN 12345 would be passed as “ JACKAL 12345”) to convey the picture to...call to reference data link display; may be followed by amplifying info JACKAL Surveillance NPG of Link 16/TADIL J Reference surveillance track...numbers with the term “ JACKAL <TN>” Normally used in reference to land track (3.5). COPY Directive call to input a hooked symbol on the TAD into the

Production and release of yessotoxins by the dinoflagellates Protoceratium reticulatum and Lingulodinium polyedrum in culture.

PubMed

Paz, Beatriz; Riobó, Pilar; Fernández, M Luisa; Fraga, Santiago; Franco, José M

2004-09-01

The presence of YTX was confirmed in Protoceratium reticulatum cultures and detected for the first time in Lingulodinium polyedrum cultures, mainly in the cells but also, to a lesser extent, dissolved in the culture medium. The production of yessotoxins (YTXs) by cultures of different strains of P. reticulatum and L. polyedrum was studied with liquid chromatography coupled to fluorometric detection using the dienophile reagent DMEQ-TAD and liquid chromatography-mass spectrometry. When comparing toxin production at different stages of culture growth, larger amounts of toxins were observed in the cellular fraction and in the culture medium at the last stage of the culture (day 21) in both species. Although YTX was detected in culture medium, with this study it was not possible to explain which is the release mechanism of the toxin in the medium.

SU-F-I-77: Radiation Dose in Cardiac Catheterization Procedures: Impact of a Systematic Reduction in Pulsed Fluoroscopy Frame Rate

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

Schultz, C; Dixon, S

Purpose: To evaluate whether one small systematic reduction in fluoroscopy frame rate has a significant effect on the total air kerma and/or dose area product for diagnostic and interventional cardiac catheterization procedures. Methods: The default fluoroscopy frame rate (FFR) was lowered from 15 to 10 fps in 5 Siemens™ Axiom Artis cardiac catheterization labs (CCL) on July 1, 2013. A total of 7212 consecutive diagnostic and interventional CCL procedures were divided into two study groups: 3602 procedures from 10/1/12 –6/30/13 with FFR of 15 fps; and 3610 procedures 7/1/13 – 3/31/14 at 10 fps. For each procedure, total air kermamore » (TAK), fluoroscopy skin dose (FSD), total/fluoroscopy dose area products (TAD, FAD), and total fluoroscopy time (FT) were recorded. Patient specific data collected for each procedure included: BSA, sex, height, weight, interventional versus diagnostic; and elective versus emergent. Results: For pre to post change in FFR, each categorical variable was compared using Pearson’s Chi-square test, Odds ratios and 95% confidence intervals. No statistically significant difference in BSA, height, weight, number of interventional versus diagnostic, elective versus emergent procedures was found between the two study groups. Decreasing the default FFR from 15 fps to 10 fps in the two study groups significantly reduced TAK from 1305 to 1061 mGy (p<0.0001), FSD from 627 to 454 mGy (p<0.0001), TAD from 8681 to 6991 uGy × m{sup 2}(p<0.0001), and FAD from 4493 to 3297 uGy × m{sup 2}(p<0.0001). No statistically significant difference in FT was noted. Clinical image quality was not analyzed, and reports of noticeable effects were minimal. From July 1, 2013 to date, the default FFR has remained 10 fps. Conclusion: Reducing the FFR from 15 to 10 fps significantly reduced total air kerma and dose area product which may decrease risk for potential radiation-induced skin injuries and improve patient outcomes.« less

Algorithm for cellular reprogramming.

PubMed

Ronquist, Scott; Patterson, Geoff; Muir, Lindsey A; Lindsly, Stephen; Chen, Haiming; Brown, Markus; Wicha, Max S; Bloch, Anthony; Brockett, Roger; Rajapakse, Indika

2017-11-07

The day we understand the time evolution of subcellular events at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology. With data-guided frameworks we can develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. Here we describe an approach for optimizing the use of transcription factors (TFs) in cellular reprogramming, based on a device commonly used in optimal control. We construct an approximate model for the natural evolution of a cell-cycle-synchronized population of human fibroblasts, based on data obtained by sampling the expression of 22,083 genes at several time points during the cell cycle. To arrive at a model of moderate complexity, we cluster gene expression based on division of the genome into topologically associating domains (TADs) and then model the dynamics of TAD expression levels. Based on this dynamical model and additional data, such as known TF binding sites and activity, we develop a methodology for identifying the top TF candidates for a specific cellular reprogramming task. Our data-guided methodology identifies a number of TFs previously validated for reprogramming and/or natural differentiation and predicts some potentially useful combinations of TFs. Our findings highlight the immense potential of dynamical models, mathematics, and data-guided methodologies for improving strategies for control over biological processes. Copyright © 2017 the Author(s). Published by PNAS.

Charge Transport in Spiro-OMeTAD Investigated through Space-Charge-Limited Current Measurements

NASA Astrophysics Data System (ADS)

Röhr, Jason A.; Shi, Xingyuan; Haque, Saif A.; Kirchartz, Thomas; Nelson, Jenny

2018-04-01

Extracting charge-carrier mobilities for organic semiconductors from space-charge-limited conduction measurements is complicated in practice by nonideal factors such as trapping in defects and injection barriers. Here, we show that by allowing the bandlike charge-carrier mobility, trap characteristics, injection barrier heights, and the shunt resistance to vary in a multiple-trapping drift-diffusion model, a numerical fit can be obtained to the entire current density-voltage curve from experimental space-charge-limited current measurements on both symmetric and asymmetric 2 ,2',7 ,7' -tetrakis(N ,N -di-4-methoxyphenylamine)-9 ,9' -spirobifluorene (spiro-OMeTAD) single-carrier devices. This approach yields a bandlike mobility that is more than an order of magnitude higher than the effective mobility obtained using analytical approximations, such as the Mott-Gurney law and the moving-electrode equation. It is also shown that where these analytical approximations require a temperature-dependent effective mobility to achieve fits, the numerical model can yield a temperature-, electric-field-, and charge-carrier-density-independent mobility. Finally, we present an analytical model describing trap-limited current flow through a semiconductor in a symmetric single-carrier device. We compare the obtained charge-carrier mobility and trap characteristics from this analytical model to the results from the numerical model, showing excellent agreement. This work shows the importance of accounting for traps and injection barriers explicitly when analyzing current density-voltage curves from space-charge-limited current measurements.

Pinning, thermally activated depinning and their importance for tuning the nanoprecipitate size and density in high J c YBa 2Cu 3O 7-x films

NASA Astrophysics Data System (ADS)

Chen, Zhijun; Kametani, Fumitake; Gurevich, Alex; Larbalestier, David

2009-12-01

YBa 2Cu 3O 7-x (Y123) films with quantitatively controlled artificial nanoprecipitate pinning centers were grown by pulsed laser deposition (PLD) and characterized by transport over wide temperature ( T) and magnetic field ( H) ranges and by transmission electron microscopy (TEM). The critical current density J c was found to be determined by the interplay of strong vortex pinning and thermally activated depinning (TAD), which together produced a non-monotonic dependence of J c on c-axis pin spacing d c. At low T and H, J c increased with decreasing d c, reaching the very high J c ∼ 48 MA/cm 2 ∼20% of the depairing current density J d at 10 K, self-field and d c ∼ 10 nm, but at higher T and H when TAD effects become significant, J c was optimized at larger d c because longer vortex segments confined between nanoprecipitates are less prone to thermal fluctuations. We conclude that precipitates should extend at least several coherence lengths along vortices in order to produce irreversibility fields H irr(77 K) greater than 7 T and maximum bulk pinning forces F p,max(77 K) greater than 7-8 GN/m 3 (values appropriate for H parallel to the c-axis). Our results show that there is no universal pin array that optimizes J c at all T and H.

Mapping the Shh long-range regulatory domain

PubMed Central

Anderson, Eve; Devenney, Paul S.; Hill, Robert E.; Lettice, Laura A.

2014-01-01

Coordinated gene expression controlled by long-distance enhancers is orchestrated by DNA regulatory sequences involving transcription factors and layers of control mechanisms. The Shh gene and well-established regulators are an example of genomic composition in which enhancers reside in a large desert extending into neighbouring genes to control the spatiotemporal pattern of expression. Exploiting the local hopping activity of the Sleeping Beauty transposon, the lacZ reporter gene was dispersed throughout the Shh region to systematically map the genomic features responsible for expression activity. We found that enhancer activities are retained inside a genomic region that corresponds to the topological associated domain (TAD) defined by Hi-C. This domain of approximately 900 kb is in an open conformation over its length and is generally susceptible to all Shh enhancers. Similar to the distal enhancers, an enhancer residing within the Shh second intron activates the reporter gene located at distances of hundreds of kilobases away, suggesting that both proximal and distal enhancers have the capacity to survey the Shh topological domain to recognise potential promoters. The widely expressed Rnf32 gene lying within the Shh domain evades enhancer activities by a process that may be common among other housekeeping genes that reside in large regulatory domains. Finally, the boundaries of the Shh TAD do not represent the absolute expression limits of enhancer activity, as expression activity is lost stepwise at a number of genomic positions at the verges of these domains. PMID:25252942

Comparison of algorithms for blood stain detection applied to forensic hyperspectral imagery

NASA Astrophysics Data System (ADS)

Yang, Jie; Messinger, David W.; Mathew, Jobin J.; Dube, Roger R.

2016-05-01

Blood stains are among the most important types of evidence for forensic investigation. They contain valuable DNA information, and the pattern of the stains can suggest specifics about the nature of the violence that transpired at the scene. Early detection of blood stains is particularly important since the blood reacts physically and chemically with air and materials over time. Accurate identification of blood remnants, including regions that might have been intentionally cleaned, is an important aspect of forensic investigation. Hyperspectral imaging might be a potential method to detect blood stains because it is non-contact and provides substantial spectral information that can be used to identify regions in a scene with trace amounts of blood. The potential complexity of scenes in which such vast violence occurs can be high when the range of scene material types and conditions containing blood stains at a crime scene are considered. Some stains are hard to detect by the unaided eye, especially if a conscious effort to clean the scene has occurred (we refer to these as "latent" blood stains). In this paper we present the initial results of a study of the use of hyperspectral imaging algorithms for blood detection in complex scenes. We describe a hyperspectral imaging system which generates images covering 400 nm - 700 nm visible range with a spectral resolution of 10 nm. Three image sets of 31 wavelength bands were generated using this camera for a simulated indoor crime scene in which blood stains were placed on a T-shirt and walls. To detect blood stains in the scene, Principal Component Analysis (PCA), Subspace Reed Xiaoli Detection (SRXD), and Topological Anomaly Detection (TAD) algorithms were used. Comparison of the three hyperspectral image analysis techniques shows that TAD is most suitable for detecting blood stains and discovering latent blood stains.