C-Terminal End-Directed Protein Elimination by CRL2 Ubiquitin Ligases.

PubMed

Lin, Hsiu-Chuan; Yeh, Chi-Wei; Chen, Yen-Fu; Lee, Ting-Ting; Hsieh, Pei-Yun; Rusnac, Domnita V; Lin, Sung-Ya; Elledge, Stephen J; Zheng, Ning; Yen, Hsueh-Chi S

2018-05-17

The proteolysis-assisted protein quality control system guards the proteome from potentially detrimental aberrant proteins. How miscellaneous defective proteins are specifically eliminated and which molecular characteristics direct them for removal are fundamental questions. We reveal a mechanism, DesCEND (destruction via C-end degrons), by which CRL2 ubiquitin ligase uses interchangeable substrate receptors to recognize the unusual C termini of abnormal proteins (i.e., C-end degrons). C-end degrons are mostly less than ten residues in length and comprise a few indispensable residues along with some rather degenerate ones. The C-terminal end position is essential for C-end degron function. Truncated selenoproteins generated by translation errors and the USP1 N-terminal fragment from post-translational cleavage are eliminated by DesCEND. DesCEND also targets full-length proteins with naturally occurring C-end degrons. The C-end degron in DesCEND echoes the N-end degron in the N-end rule pathway, highlighting the dominance of protein "ends" as indicators for protein elimination. Copyright © 2018 Elsevier Inc. All rights reserved.

Renewable Fuel Pathways II Final Rule to Identify Additional Fuel Pathways under Renewable Fuel Standard Program

EPA Pesticide Factsheets

This final rule describes EPA’s evaluation of biofuels derived from biogas fuel pathways under the RFS program and other minor amendments related to survey requirements associated with ULSD program and misfueling mitigation regulations for E15.

[New italian law about end of life: self-determination and shared care pathway.

PubMed

Ciliberti, Rosagemma; Gulino, Matteo; Gorini, Ilaria

2018-05-01

The Italian Parliament has recently approved the Law n. 219/2017 concerning "Rules on informed consent and advance directives". The manuscript points out the main key points of the new law, in order to clarify the role of the advance directives and to provide clear operational guidelines for healthcare personnel. Taking into consideration the Italian deontological and juridical context, along with the main jurisprudential judgements, the law has been analysed. The Authors discussed the new rules and the bioethical issues also in relation to the provisions stated by the Convention on Human Rights and Biomedicine (Convention of Oviedo). The new law deals with relevant issues that were confined to jurisprudential rulings so far, such as the informed consent, the withdrawal/withholding of medical treatment (including artificial nutrition and hydration), the content of medical information, including the modalities, the medical responsibility and, finally, the value of advance directives. In the Authors' opinion this law provides essential rules to expressly strengthen the patients' autonomy, eliminating the juridical uncertainty on many central issues (such us, for example, the refusal of life-sustainment treatments) that have been the subject of contradictory judgments ruled by the Italian Courts. Nevertheless, advance directives should be regarded as a dynamic tools of relationship between physicians and assisted person and, thus, as an essential integrant part of the advance care planning. The education of health professionals and citizens about end of life issues is the basis for the successful implementation of this legislation.

12 CFR 1026.57 - Reporting and marketing rules for college student open-end credit.

Code of Federal Regulations, 2012 CFR

2012-01-01

... TRUTH IN LENDING (REGULATION Z) Special Rules Applicable to Credit Card Accounts and Open-End Credit.... (a) Definitions—(1) College student credit card. The term “college student credit card” as used in this section means a credit card issued under a credit card account under an open-end (not home-secured...

12 CFR 226.57 - Reporting and marketing rules for college student open-end credit.

Code of Federal Regulations, 2012 CFR

2012-01-01

... to Credit Card Accounts and Open-End Credit Offered to College Students § 226.57 Reporting and marketing rules for college student open-end credit. (a) Definitions: (1) College student credit card. The term “college student credit card” as used in this section means a credit card issued under a credit...

12 CFR 1026.57 - Reporting and marketing rules for college student open-end credit.

Code of Federal Regulations, 2014 CFR

2014-01-01

... TRUTH IN LENDING (REGULATION Z) Special Rules Applicable to Credit Card Accounts and Open-End Credit.... (a) Definitions—(1) College student credit card. The term “college student credit card” as used in this section means a credit card issued under a credit card account under an open-end (not home-secured...

12 CFR 1026.57 - Reporting and marketing rules for college student open-end credit.

Code of Federal Regulations, 2013 CFR

2013-01-01

... TRUTH IN LENDING (REGULATION Z) Special Rules Applicable to Credit Card Accounts and Open-End Credit.... (a) Definitions. (1) College student credit card. The term “college student credit card” as used in this section means a credit card issued under a credit card account under an open-end (not home-secured...

12 CFR 226.57 - Reporting and marketing rules for college student open-end credit.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Applicable to Credit Card Accounts and Open-End Credit Offered to College Students § 226.57 Reporting and marketing rules for college student open-end credit. (a) Definitions: (1) College student credit card. The term “college student credit card” as used in this section means a credit card issued under a credit...

12 CFR 226.57 - Reporting and marketing rules for college student open-end credit.

Code of Federal Regulations, 2011 CFR

2011-01-01

... to Credit Card Accounts and Open-End Credit Offered to College Students § 226.57 Reporting and marketing rules for college student open-end credit. (a) Definitions: (1) College student credit card. The term “college student credit card” as used in this section means a credit card issued under a credit...

12 CFR 226.57 - Reporting and marketing rules for college student open-end credit.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Applicable to Credit Card Accounts and Open-End Credit Offered to College Students § 226.57 Reporting and marketing rules for college student open-end credit. (a) Definitions: (1) College student credit card. The term “college student credit card” as used in this section means a credit card issued under a credit...

WellnessRules: A Web 3.0 Case Study in RuleML-Based Prolog-N3 Profile Interoperation

NASA Astrophysics Data System (ADS)

Boley, Harold; Osmun, Taylor Michael; Craig, Benjamin Larry

An interoperation study, WellnessRules, is described, where rules about wellness opportunities are created by participants in rule languages such as Prolog and N3, and translated within a wellness community using RuleML/XML. The wellness rules are centered around participants, as profiles, encoding knowledge about their activities conditional on the season, the time-of-day, the weather, etc. This distributed knowledge base extends FOAF profiles with a vocabulary and rules about wellness group networking. The communication between participants is organized through Rule Responder, permitting wellness-profile translation and distributed querying across engines. WellnessRules interoperates between rules and queries in the relational (Datalog) paradigm of the pure-Prolog subset of POSL and in the frame (F-logic) paradigm of N3. An evaluation of Rule Responder instantiated for WellnessRules revealed acceptable Web response times.

The VTAC Committee: developing guidance for an alternative regulatory pathway to the anadromous salmonid protection rules

Treesearch

Michael Liquori; Peter Cafferata; Kevin Boston; Richard Gienger; David Hope

2012-01-01

In recent decades, riparian protection standards have been guided by generalized prescriptive rules. With the passage of the Anadromous Salmonid Protection rules in 2009, the Board of Forestry and Fire Protection (Board) established a regulatory pathway that provides an alternative approach for riparian protection based on site-specific criteria (14 CCR § 916....

Ethics and end of life care: the Liverpool Care Pathway and the Neuberger Review.

PubMed

Wrigley, Anthony

2015-08-01

The Liverpool Care Pathway for the Dying has recently been the topic of substantial media interest and also been subject to the independent Neuberger Review. This review has identified clear failings in some areas of care and recommended the Liverpool Care Pathway be phased out. I argue that while the evidence gathered of poor incidences of practice by the Review is of genuine concern for end of life care, the inferences drawn from this evidence are inconsistent with the causes for the concern. Seeking to end an approach that is widely seen as best practice and which can genuinely deliver high quality care because of negative impressions that have been formed from failing to implement it properly is not a good basis for radically overhauling our approach to end of life care. I conclude that improvements in training, communication and ethical decision-making, without the added demand to end the Liverpool Care Pathway, would have resulted in a genuine advance in end of life care. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

The implementation of an end-of-life integrated care pathway in a Chinese population.

PubMed

Lo, S-H; Chan, C-Y; Chan, C-H; Sze, W-k; Yuen, K-K; Wong, C-S; Ng, T-Y; Tung, Y

2009-08-01

The integrated care pathway is used in end-of-life care to improve quality of care; the Liverpool Care Pathway (LCP) has been used in Europe and North America. Tuen Mun Hospital is a regional hospital in Hong Kong, China. The End-of-life Care Pathway (ECP) based on the concepts used in the Liverpool Care Pathway, was developed, with modification to suit the local condition. Criteria for entry onto the ECP were that the multidisciplinary team agreed the patient was dying, and was at least two of the following: bedbound; semi-comatose; only able to take sips of fluid; no longer able to take tablets. The ECP template replaced all other inpatient documents. The ECP was implemented in the palliative care unit for terminal cancer patients. An audit was performed to review the result. Fifty-one Chinese patients were included in the audit with mean age 64. The median duration of ECP use was 24 hours. All patients had current medication assessed and non-essential drugs were discontinued. The audit result suggested integrated care pathway in end-of-life care could be implemented successfully in an Oriental culture. The acceptance of using the ECP as a standard clinical practice takes time and education. Appropriate template design and supervision are the keys to success.

Ubiquitin-protein ligases in muscle wasting: multiple parallel pathways?

NASA Technical Reports Server (NTRS)

Lecker, Stewart H.; Goldberg, A. L. (Principal Investigator)

2003-01-01

PURPOSE OF REVIEW: Studies in a wide variety of animal models of muscle wasting have led to the concept that increased protein breakdown via the ubiquitin-proteasome pathway is responsible for the loss of muscle mass seen as muscle atrophy. The complexity of the ubiquitination apparatus has hampered our understanding of how this pathway is activated in atrophying muscles and which ubiquitin-conjugating enzymes in muscle are responsible. RECENT FINDINGS: Recent experiments have shown that two newly identified ubiquitin-protein ligases (E3s), atrogin-1/MAFbx and MURF-1, are critical in the development of muscle atrophy. Other in-vitro studies also implicated E2(14k) and E3alpha, of the N-end rule pathway, as playing an important role in the process. SUMMARY: It seems likely that multiple pathways of ubiquitin conjugation are activated in parallel in atrophying muscle, perhaps to target for degradation specific classes of muscle proteins. The emerging challenge will be to define the protein targets for, as well as inhibitors of, these E3s.

The Mechanism of Double-Strand DNA Break Repair by the Nonhomologous DNA End Joining Pathway

PubMed Central

Lieber, Michael R.

2011-01-01

Double-strand DNA breaks are common events in eukaryotic cells, and there are two major pathways for repairing them: homologous recombination and nonhomologous DNA end joining (NHEJ). The diverse causes of DSBs result in a diverse chemistry of DNA ends that must be repaired. Across NHEJ evolution, the enzymes of the NHEJ pathway exhibit a remarkable degree of structural tolerance in the range of DNA end substrate configurations upon which they can act. In vertebrate cells, the nuclease, polymerases and ligase of NHEJ are the most mechanistically flexible and multifunctional enzymes in each of their classes. Unlike repair pathways for more defined lesions, NHEJ repair enzymes act iteratively, act in any order, and can function independently of one another at each of the two DNA ends being joined. NHEJ is critical not only for the repair of pathologic DSBs as in chromosomal translocations, but also for the repair of physiologic DSBs created during V(D)J recombination and class switch recombination. Therefore, patients lacking normal NHEJ are not only sensitive to ionizing radiation, but also severely immunodeficient. PMID:20192759

Evaluating multiepisode events: boundary conditions for the peak-end rule.

PubMed

Miron-Shatz, Talya

2009-04-01

This study advances our understanding of how people arrive at retrospective evaluations of multiepisode experiences. Large samples from the United States, France, and Denmark (810, 820, and 805 participants, respectively) reported their feelings during each episode of the previous day using the Day Reconstruction Method. The duration-weighted average of these feelings represented the normative approach to evaluation, and, contrary to the predictions of the peak-end rule, the average was the best predictor of retrospective evaluations of the day. To capture participants' heuristic evaluation, they also reported having a wonderful (peak) and/or awful (low) moment during the previous day. The results indicate that retrospective evaluations of multiepisode events rely on the averaged ratings of emotions, ignore ends, and also consider the presence of lows, and occasionally peaks, as subjectively defined by those experiencing them. Peaks and lows contribute more to comparative, rather than absolute evaluations. Future research should examine whether these findings extend to other multiepisode events that, unlike days, form cohesive units in terms of their content, goal, and emotionality. (c) 2009 APA, all rights reserved.

29 CFR 825.602 - Special rules for school employees, limitations on leave near the end of an academic term.

Code of Federal Regulations, 2014 CFR

2014-07-01

... near the end of an academic term. 825.602 Section 825.602 Labor Regulations Relating to Labor... on leave near the end of an academic term. (a) There are also different rules for instructional... days. (b) For purposes of these provisions, academic term means the school semester, which typically...

29 CFR 825.602 - Special rules for school employees, limitations on leave near the end of an academic term.

Code of Federal Regulations, 2013 CFR

2013-07-01

... near the end of an academic term. 825.602 Section 825.602 Labor Regulations Relating to Labor... on leave near the end of an academic term. (a) There are also different rules for instructional... days. (b) For purposes of these provisions, academic term means the school semester, which typically...

29 CFR 825.602 - Special rules for school employees, limitations on leave near the end of an academic term.

Code of Federal Regulations, 2010 CFR

2010-07-01

... near the end of an academic term. 825.602 Section 825.602 Labor Regulations Relating to Labor... on leave near the end of an academic term. (a) There are also different rules for instructional... days. (b) For purposes of these provisions, “academic term” means the school semester, which typically...

29 CFR 825.602 - Special rules for school employees, limitations on leave near the end of an academic term.

Code of Federal Regulations, 2011 CFR

2011-07-01

... near the end of an academic term. 825.602 Section 825.602 Labor Regulations Relating to Labor... on leave near the end of an academic term. (a) There are also different rules for instructional... days. (b) For purposes of these provisions, “academic term” means the school semester, which typically...

29 CFR 825.602 - Special rules for school employees, limitations on leave near the end of an academic term.

Code of Federal Regulations, 2012 CFR

2012-07-01

... near the end of an academic term. 825.602 Section 825.602 Labor Regulations Relating to Labor... on leave near the end of an academic term. (a) There are also different rules for instructional... days. (b) For purposes of these provisions, “academic term” means the school semester, which typically...

Diagnostic Accuracy of a New High-Sensitivity Troponin I Assay and Five Accelerated Diagnostic Pathways for Ruling Out Acute Myocardial Infarction and Acute Coronary Syndrome.

PubMed

Greenslade, Jaimi H; Carlton, Edward W; Van Hise, Christopher; Cho, Elizabeth; Hawkins, Tracey; Parsonage, William A; Tate, Jillian; Ungerer, Jacobus; Cullen, Louise

2018-04-01

This diagnostic accuracy study describes the performance of 5 accelerated chest pain pathways, calculated with the new Beckman's Access high-sensitivity troponin I assay. High-sensitivity troponin I was measured with presentation and 2-hour blood samples in 1,811 patients who presented to an emergency department (ED) in Australia. Patients were classified as being at low risk according to 5 rules: modified accelerated diagnostic protocol to assess patients with chest pain symptoms using troponin as the only biomarker (m-ADAPT), the Emergency Department Assessment of Chest Pain Score (EDACS) pathway, the History, ECG, Age, Risk Factors, and Troponin (HEART) pathway, the No Objective Testing Rule, and the new Vancouver Chest Pain Rule. Endpoints were 30-day acute myocardial infarction and acute coronary syndrome. Measures of diagnostic accuracy for each rule were calculated. Data included 96 patients (5.3%) with acute myocardial infarction and 139 (7.7%) with acute coronary syndrome. The new Vancouver Chest Pain Rule and No Objective Testing Rule had high sensitivity for acute myocardial infarction (100%; 95% confidence interval [CI] 96.2% to 100% for both) and acute coronary syndrome (98.6% [95% CI 94.9% to 99.8%] and 99.3% [95% CI 96.1% to 100%]). The m-ADAPT, EDACS, and HEART pathways also yielded high sensitivity for acute myocardial infarction (96.9% [95% CI 91.1% to 99.4%] for m-ADAPT and 97.9% [95% CI 92.7% to 99.7%] for EDACS and HEART), but lower sensitivity for acute coronary syndrome (≤95.0% for all). The m-ADAPT, EDACS, and HEART rules classified more patients as being at low risk (64.3%, 62.5%, and 49.8%, respectively) than the new Vancouver Chest Pain Rule and No Objective Testing Rule (28.2% and 34.5%, respectively). In this cohort with a low prevalence of acute myocardial infarction and acute coronary syndrome, using the Beckman's Access high-sensitivity troponin I assay with the new Vancouver Chest Pain Rule or No Objective Testing Rule enabled

Exploring the combinatorial space of complete pathways to chemicals.

PubMed

Wang, Lin; Ng, Chiam Yu; Dash, Satyakam; Maranas, Costas D

2018-04-06

Computational pathway design tools often face the challenges of balancing the stoichiometry of co-metabolites and cofactors, and dealing with reaction rule utilization in a single workflow. To this end, we provide an overview of two complementary stoichiometry-based pathway design tools optStoic and novoStoic developed in our group to tackle these challenges. optStoic is designed to determine the stoichiometry of overall conversion first which optimizes a performance criterion (e.g. high carbon/energy efficiency) and ensures a comprehensive search of co-metabolites and cofactors. The procedure then identifies the minimum number of intervening reactions to connect the source and sink metabolites. We also further the pathway design procedure by expanding the search space to include both known and hypothetical reactions, represented by reaction rules, in a new tool termed novoStoic. Reaction rules are derived based on a mixed-integer linear programming (MILP) compatible reaction operator, which allow us to explore natural promiscuous enzymes, engineer candidate enzymes that are not already promiscuous as well as design de novo enzymes. The identified biochemical reaction rules then guide novoStoic to design routes that expand the currently known biotransformation space using a single MILP modeling procedure. We demonstrate the use of the two computational tools in pathway elucidation by designing novel synthetic routes for isobutanol. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Surveying N2O-producing pathways in bacteria.

PubMed

Stein, Lisa Y

2011-01-01

Nitrous oxide (N(2)O) is produced by bacteria as an intermediate of both dissimilatory and detoxification pathways under a range of oxygen levels, although the majority of N(2)O is released in suboxic to anoxic environments. N(2)O production under physiologically relevant conditions appears to require the reduction of nitric oxide (NO) produced from the oxidation of hydroxylamine (nitrification), reduction of nitrite (denitrification), or by host cells of pathogenic bacteria. In a single bacterial isolate, N(2)O-producing pathways can be complex, overlapping, involve multiple enzymes with the same function, and require multiple layers of regulatory machinery. This overview discusses how to identify known N(2)O-producing inventory and regulatory sequences within bacterial genome sequences and basic physiological approaches for investigating the function of that inventory. A multitude of review articles have been published on individual enzymes, pathways, regulation, and environmental significance of N(2)O-production encompassing a large diversity of bacterial isolates. The combination of next-generation deep sequencing platforms, emerging proteomics technologies, and basic microbial physiology can be used to expand what is known about N(2)O-producing pathways in individual bacterial species to discover novel inventory and unifying features of pathways. A combination of approaches is required to understand and generalize the function and control of N(2)O production across a range of temporal and spatial scales within natural and host environments. Copyright © 2011 Elsevier Inc. All rights reserved.

Extending double modulation: combinatorial rules for identifying the modulations necessary for determining elasticities in metabolic pathways.

PubMed

Giersch, C; Cornish-Bowden, A

1996-10-07

The double modulation method for determining the elasticities of pathway enzymes, originally devised by Kacser & Burns (Biochem. Soc. Trans. 7, 1149-1160, 1979), is extended to pathways of complex topological structure, including branching and feedback loops. An explicit system of linear equations for the unknown elasticities is derived. The constraints imposed on this linear system imply that modulations of more than one enzyme are not necessarily independent. Simple combinatorial rules are described for identifying without using any algebra the set of independent modulations that allow the determination of the elasticities of any enzyme. By repeated application, the minimum numbers of modulations required to determine the elasticities of all enzymes of a given pathway can be determined. The procedure is illustrated with numerous examples.

Developmental Pathways from Childhood Aggression-Disruptiveness, Chronic Peer Rejection and Deviant Friendships to Early-Adolescent Rule Breaking

PubMed Central

Ettekal, Idean; Ladd, Gary W.

2015-01-01

Childhood aggression-disruptiveness, chronic peer rejection, and deviant friendships were examined as predictors of early-adolescent rule breaking behaviors. Using a sample of 383 children (193 girls and 190 boys) who were followed from ages 6 to 14, peer rejection trajectories were identified and incorporated into a series of alternative models to assess how chronic peer rejection and deviant friendships mediate the association between stable childhood aggression-disruptiveness and early-adolescent rule breaking. There were multiple mediated pathways to rule breaking that included both behavioral and relational risk factors and findings were consistent for boys and girls. Results have implications for better understanding the influence of multiple social processes in the continuity of antisocial behaviors from middle childhood to early adolescence. PMID:25403544

Jahn-Teller effect versus Hund's rule coupling in C60N-

NASA Astrophysics Data System (ADS)

Wehrli, S.; Sigrist, M.

2007-09-01

We propose variational states for the ground state and the low-energy collective rotator excitations in negatively charged C60N- ions (N=1,…,5) . The approach includes the linear electron-phonon coupling and the Coulomb interaction on the same level. The electron-phonon coupling is treated within the effective mode approximation which yields the linear t1u⊗Hg Jahn-Teller problem whereas the Coulomb interaction gives rise to Hund’s rule coupling for N=2,3,4 . The Hamiltonian has accidental SO(3) symmetry which allows an elegant formulation in terms of angular momenta. Trial states are constructed from coherent states and using projection operators onto angular momentum subspaces which results in good variational states for the complete parameter range. The evaluation of the corresponding energies is to a large extent analytical. We use the approach for a detailed analysis of the competition between Jahn-Teller effect and Hund’s rule coupling, which determines the spin state for N=2,3,4 . We calculate the low-spin-high-spin gap for N=2,3,4 as a function of the Hund’s rule coupling constant J . We find that the experimentally measured gaps suggest a coupling constant in the range J=60-80meV . Using a finite value for J , we recalculate the ground state energies of the C60N- ions and find that the Jahn-Teller energy gain is partly counterbalanced by the Hund’s rule coupling. In particular, the ground state energies for N=2,3,4 are almost equal.

Medicare Program; End-Stage Renal Disease Prospective Payment System, Payment for Renal Dialysis Services Furnished to Individuals With Acute Kidney Injury, and End-Stage Renal Disease Quality Incentive Program. Final rule.

PubMed

2017-11-01

This rule updates and makes revisions to the end-stage renal disease (ESRD) prospective payment system (PPS) for calendar year (CY) 2018. It also updates the payment rate for renal dialysis services furnished by an ESRD facility to individuals with acute kidney injury (AKI). This rule also sets forth requirements for the ESRD Quality Incentive Program (QIP), including for payment years (PYs) 2019 through 2021.

The role of the non-homologous end-joining pathway in lymphocyte development.

PubMed

Rooney, Sean; Chaudhuri, Jayanta; Alt, Frederick W

2004-08-01

One of the most toxic insults a cell can incur is a disruption of its linear DNA in the form of a double-strand break (DSB). Left unrepaired, or repaired improperly, these lesions can result in cell death or neoplastic transformation. Despite these dangers, lymphoid cells purposely introduce DSBs into their genome to maximize the diversity and effector functions of their antigen receptor genes. While the generation of breaks requires distinct lymphoid-specific factors, their resolution requires various ubiquitously expressed DNA-repair proteins, known collectively as the non-homologous end-joining pathway. In this review, we discuss the factors that constitute this pathway as well as the evidence of their involvement in two lymphoid-specific DNA recombination events.

After the Liverpool Care Pathway--development of heuristics to guide end of life care for people with dementia: protocol of the ALCP study.

PubMed

Davies, N; Manthorpe, J; Sampson, E L; Iliffe, S

2015-09-02

End of life care guidance for people with dementia is lacking and this has been made more problematic in England with the removal of one of the main end of life care guidelines which offered some structure, the Liverpool Care Pathway. This guidance gap may be eased with the development of heuristics (rules of thumb) which offer a fast and frugal form of decision-making. To develop a toolkit of heuristics (rules of thumb) for practitioners to use when caring for people with dementia at the end of life. A mixed-method study using a co-design approach to develop heuristics in three phases. In phase 1, we will conduct at least six focus groups with family carers, health and social care practitioners from both hospital and community care services, using the 'think-aloud' method to understand decision-making processes and to develop a set of heuristics. The focus group topic guide will be developed from the findings of a previous study of 46 interviews of family carers about quality end-of-life care for people with dementia and a review of the literature. A multidisciplinary development team of health and social care practitioners will synthesise the findings from the focus groups to devise and refine a toolkit of heuristics. Phase 2 will test the use of heuristics in practice in five sites: one general practice, one community nursing team, one hospital ward and two palliative care teams working in the community. Phase 3 will evaluate and further refine the toolkit of heuristics through group interviews, online questionnaires and semistructured interviews. This study has received ethical approval from a local NHS research ethics committee (Rec ref: 15/LO/0156). The findings of this study will be presented in peer-reviewed publications and national and international conferences. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

On determining firing delay time of transitions for Petri net based signaling pathways by introducing stochastic decision rules.

PubMed

Miwa, Yoshimasa; Li, Chen; Ge, Qi-Wei; Matsuno, Hiroshi; Miyano, Satoru

2010-01-01

Parameter determination is important in modeling and simulating biological pathways including signaling pathways. Parameters are determined according to biological facts obtained from biological experiments and scientific publications. However, such reliable data describing detailed reactions are not reported in most cases. This prompted us to develop a general methodology of determining the parameters of a model in the case of that no information of the underlying biological facts is provided. In this study, we use the Petri net approach for modeling signaling pathways, and propose a method to determine firing delay times of transitions for Petri net models of signaling pathways by introducing stochastic decision rules. Petri net technology provides a powerful approach to modeling and simulating various concurrent systems, and recently have been widely accepted as a description method for biological pathways. Our method enables to determine the range of firing delay time which realizes smooth token flows in the Petri net model of a signaling pathway. The availability of this method has been confirmed by the results of an application to the interleukin-1 induced signaling pathway.

On determining firing delay time of transitions for petri net based signaling pathways by introducing stochastic decision rules.

PubMed

Miwa, Yoshimasa; Li, Chen; Ge, Qi-Wei; Matsuno, Hiroshi; Miyano, Satoru

2011-01-01

Parameter determination is important in modeling and simulating biological pathways including signaling pathways. Parameters are determined according to biological facts obtained from biological experiments and scientific publications. However, such reliable data describing detailed reactions are not reported in most cases. This prompted us to develop a general methodology of determining the parameters of a model in the case of that no information of the underlying biological facts is provided. In this study, we use the Petri net approach for modeling signaling pathways, and propose a method to determine firing delay times of transitions for Petri net models of signaling pathways by introducing stochastic decision rules. Petri net technology provides a powerful approach to modeling and simulating various concurrent systems, and recently have been widely accepted as a description method for biological pathways. Our method enables to determine the range of firing delay time which realizes smooth token flows in the Petri net model of a signaling pathway. The availability of this method has been confirmed by the results of an application to the interleukin-1 induced signaling pathway.

Spectral sum rules for confining large-N theories

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

Cherman, Aleksey; McGady, David A.; Yamazaki, Masahito

2016-06-17

We consider asymptotically-free four-dimensional large-$N$ gauge theories with massive fermionic and bosonic adjoint matter fields, compactified on squashed three-spheres, and examine their regularized large-$N$ confined-phase spectral sums. The analysis is done in the limit of vanishing ’t Hooft coupling, which is justified by taking the size of the compactification manifold to be small compared to the inverse strong scale Λ ₋1. We find our results motivate us to conjecture some universal spectral sum rules for these large $N$ gauge theories.

What do we really know about the ubiquitin-proteasome pathway in muscle atrophy?

PubMed

Jagoe, R T; Goldberg, A L

2001-05-01

Studies of many different rodent models of muscle wasting have indicated that accelerated proteolysis via the ubiquitin-proteasome pathway is the principal cause of muscle atrophy induced by fasting, cancer cachexia, metabolic acidosis, denervation, disuse, diabetes, sepsis, burns, hyperthyroidism and excess glucocorticoids. However, our understanding about how muscle proteins are degraded, and how the ubiquitin-proteasome pathway is activated in muscle under these conditions, is still very limited. The identities of the important ubiquitin-protein ligases in skeletal muscle, and the ways in which they recognize substrates are still largely unknown. Recent in-vitro studies have suggested that one set of ubquitination enzymes, E2(14K) and E3(alpha), which are responsible for the 'N-end rule' system of ubiquitination, plays an important role in muscle, especially in catabolic states. However, their functional significance in degrading different muscle proteins is still unclear. This review focuses on the many gaps in our understanding of the functioning of the ubiquitin-proteasome pathway in muscle atrophy, and highlights the strengths and limitations of the different experimental approaches used in such studies.

What do we really know about the ubiquitin-proteasome pathway in muscle atrophy?

NASA Technical Reports Server (NTRS)

Jagoe, R. T.; Goldberg, A. L.

2001-01-01

Studies of many different rodent models of muscle wasting have indicated that accelerated proteolysis via the ubiquitin-proteasome pathway is the principal cause of muscle atrophy induced by fasting, cancer cachexia, metabolic acidosis, denervation, disuse, diabetes, sepsis, burns, hyperthyroidism and excess glucocorticoids. However, our understanding about how muscle proteins are degraded, and how the ubiquitin-proteasome pathway is activated in muscle under these conditions, is still very limited. The identities of the important ubiquitin-protein ligases in skeletal muscle, and the ways in which they recognize substrates are still largely unknown. Recent in-vitro studies have suggested that one set of ubquitination enzymes, E2(14K) and E3(alpha), which are responsible for the 'N-end rule' system of ubiquitination, plays an important role in muscle, especially in catabolic states. However, their functional significance in degrading different muscle proteins is still unclear. This review focuses on the many gaps in our understanding of the functioning of the ubiquitin-proteasome pathway in muscle atrophy, and highlights the strengths and limitations of the different experimental approaches used in such studies.

A path planning method for robot end effector motion using the curvature theory of the ruled surfaces

NASA Astrophysics Data System (ADS)

Güler, Fatma; Kasap, Emin

Using the curvature theory for the ruled surfaces a technique for robot trajectory planning is presented. This technique ensures the calculation of robot’s next path. The positional variation of the Tool Center Point (TCP), linear velocity, angular velocity are required in the work area of the robot. In some circumstances, it may not be physically achievable and a re-computation of the robot trajectory might be necessary. This technique is suitable for re-computation of the robot trajectory. We obtain different robot trajectories which change depending on the darboux angle function and define trajectory ruled surface family with a common trajectory curve with the rotation trihedron. Also, the motion of robot end effector is illustrated with examples.

26 CFR 301.6501(n)-1 - Special rules for chapter 42 and similar taxes.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 18 2011-04-01 2011-04-01 false Special rules for chapter 42 and similar taxes. 301.6501(n)-1 Section 301.6501(n)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE... Assessment and Collection § 301.6501(n)-1 Special rules for chapter 42 and similar taxes. (a) Return filed by...

26 CFR 301.6501(n)-1 - Special rules for chapter 42 and similar taxes.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 18 2010-04-01 2010-04-01 false Special rules for chapter 42 and similar taxes. 301.6501(n)-1 Section 301.6501(n)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE... Assessment and Collection § 301.6501(n)-1 Special rules for chapter 42 and similar taxes. (a) Return filed by...

Alternative end-joining repair pathways are the ultimate backup for abrogated classical non-homologous end-joining and homologous recombination repair: Implications for the formation of chromosome translocations.

PubMed

Iliakis, George; Murmann, Tamara; Soni, Aashish

2015-11-01

DNA double strand breaks (DSB) are the most deleterious lesions for the integrity of the genome, as their misrepair can lead to the formation of chromosome translocations. Cells have evolved two main repair pathways to suppress the formation of these genotoxic lesions: homology-dependent, error-free homologous recombination repair (HRR), and potentially error-prone, classical, DNA-PK-dependent non-homologous end-joining (c-NHEJ). The most salient feature of c-NHEJ, speed, will largely suppress chromosome translocation formation, while sequence alterations at the junction remain possible. It is now widely accepted that when c-NHEJ is inactivated, globally or locally, an alternative form of end-joining (alt-EJ) removes DSBs. Alt-EJ operates with speed and fidelity markedly lower than c-NHEJ, causing thus with higher probability chromosome translocations, and generating more extensive sequence alterations at the junction. Our working hypothesis is that alt-EJ operates as a backup to c-NHEJ. Recent results show that alt-EJ can also backup abrogated HRR in G2 phase cells, again at the cost of elevated formation of chromosome translocations. These observations raise alt-EJ to a global rescuing mechanism operating on ends that have lost their chromatin context in ways that compromise processing by HRR or c-NHEJ. While responsible for eliminating from the genome highly cytotoxic DNA ends, alt-EJ provides this function at the price of increased translocation formation. Here, we analyze recent literature on the mechanisms of chromosome translocation formation and propose a functional hierarchy among DSB processing pathways that makes alt-EJ the global backup pathway. We discuss possible ramifications of this model in cellular DSB management and pathway choice, and analyze its implications in radiation carcinogenesis and the design of novel therapeutic approaches. Copyright © 2015 Elsevier B.V. All rights reserved.

Characterization of Clostridium thermocellum strains with disrupted fermentation end product pathways

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

Van Der Veen, Douwe; Lo, Jonathan; Brown, Steven D

2013-01-01

Clostridium thermocellum is a thermophilic, cellulolytic anaerobe that is a candidate microorganism for industrial biofuels production. Strains with mutations in genes associated with production of Llactate ( ldh) and/or acetate ( pta) were characterized to gain insight into the intracellular processes that convert cellobiose to ethanol and other fermentation end products. Cellobiose-grown cultures of the ldh strain had identical biomass accumulation, fermentation end products, transcription profile and intracellular metabolite concentrations compared to its parent strain (DSM1313 hpt spo0A). The pta-deficient strain grew slower and had 30% lower final biomass concentration compared to the parent strain, yet produced 75% more ethanol.more » A ldh pta double mutant strain evolved for faster growth had growth rate and ethanol yield comparable to the parent strain, whereas its biomass accumulation was comparable to pta. Free amino acids were secreted by all examined strains, with both pta strains secreting higher amounts of alanine, valine, isoleucine, proline, glutamine, and threonine. Valine concentration for ldh pta reached 5 mM by the end of growth, or 2.7% of the substrate carbon utilized. These secreted amino acid concentrations correlate with increased intracellular pyruvate concentrations, up to 6-fold in the pta and 16-fold in the ldh pta strain. We hypothesize that the deletions in fermentation end product pathways result in an intracellular redox imbalance, which the organism attempts to relieve, in part by recycling NADP+ through increased production of amino acids.« less

Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways

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

Van Der Veen, Douwe; Lo, Jonathan; Brown, Steven D

2013-01-01

Clostridium thermocellum is a thermophilic, cellulolytic anaerobe that is a candidate microorganism for industrial biofuels production. Strains with mutations in genes associated with production of L-lactate (Dldh) and/or acetate (Dpta) were characterized to gain insight into the intracellular processes that convert cellobiose to ethanol and other fermentation end-products. Cellobiose-grown cultures of the Dldh strain had identical biomass accumulation, fermentation end-products, transcription profile, and intracellular metabolite concentrations compared to its parent strain (DSM1313 Dhpt Dspo0A). The Dpta-deficient strain grew slower and had 30 % lower final biomass concentration compared to the parent strain, yet produced 75% more ethanol. A Dldh Dptamore » double-mutant strain evolved for faster growth had a growth rate and ethanol yield comparable to the parent strain, whereas its biomass accumulation was comparable to Dpta. Free amino acids were secreted by all examined strains, with both Dpta strains secreting higher amounts of alanine, valine, isoleucine, proline, glutamine, and threonine. Valine concentration for Dldh Dpta reached 5 mM by the end of growth, or 2.7 % of the substrate carbon utilized. These secreted amino acid concentrations correlate with increased intracellular pyruvate concentrations, up to sixfold in the Dpta and 16-fold in the Dldh Dpta strain. We hypothesize that the deletions in fermentation end-product pathways result in an intracellular redox imbalance, which the organism attempts to relieve, in part by recycling NADP* through increased production of amino acids.« less

N-cadherin expression in palisade nerve endings of rat vellus hairs.

PubMed

Kaidoh, Toshiyuki; Inoué, Takao

2008-02-01

Palisade nerve endings (PNs) are mechanoreceptors around vellus hairs of mammals. Each lanceolate nerve ending (LN) of the PN is characterized by a sensory nerve ending symmetrically sandwiched by two processes of type II terminal Schwann cells (tSCIIs). However, the molecular mechanisms underlying the structural organization of the PN are poorly understood. Electron microscopy showed that adherens junctions appeared to adhere to the sensory nerve ending and tSCII processes, so we examined the location of the N-cadherin adhesion system in PNs of rat vellus hairs by using immunoelectron microscopy. N-cadherin localized near both ends of the cell boundary between sensory nerve ending and tSCII processes, which corresponded to the sites of adherens junctions. We further found cadherin-associated proteins, alpha- and beta-catenins, at the linings of adherens junctions. Three-dimensional reconstruction of immunoelectron microscopic serial thin sections showed four linear arrays of N-cadherin arranged longitudinally along the LN beneath the four longitudinal borders of two tSCII processes. In contrast, sensory nerve fibers just proximal to the LNs formed common unmyelinated nerve fibers, in which N-cadherin was located mainly at the mesaxon of type I terminal Schwann cells (tSCIs). These results suggest that the four linear arrays of N-cadherin-mediated junctions adhere the sensory nerve ending and tSCII processes side by side to form the characteristic structure of the LN, and the structural differences between the LNs and the proximal unmyelinated nerve fibers possibly are due to the difference in the pattern of N-cadherin expression between sensory nerve endings and tSCII or tSCI processes. (c) 2007 Wiley-Liss, Inc.

Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery.

PubMed

Bosl, William J

2007-02-15

Expert knowledge in journal articles is an important source of data for reconstructing biological pathways and creating new hypotheses. An important need for medical research is to integrate this data with high throughput sources to build useful models that span several scales. Researchers traditionally use mental models of pathways to integrate information and development new hypotheses. Unfortunately, the amount of information is often overwhelming and these are inadequate for predicting the dynamic response of complex pathways. Hierarchical computational models that allow exploration of semi-quantitative dynamics are useful systems biology tools for theoreticians, experimentalists and clinicians and may provide a means for cross-communication. A novel approach for biological pathway modeling based on hybrid intelligent systems or soft computing technologies is presented here. Intelligent hybrid systems, which refers to several related computing methods such as fuzzy logic, neural nets, genetic algorithms, and statistical analysis, has become ubiquitous in engineering applications for complex control system modeling and design. Biological pathways may be considered to be complex control systems, which medicine tries to manipulate to achieve desired results. Thus, hybrid intelligent systems may provide a useful tool for modeling biological system dynamics and computational exploration of new drug targets. A new modeling approach based on these methods is presented in the context of hedgehog regulation of the cell cycle in granule cells. Code and input files can be found at the Bionet website: www.chip.ord/~wbosl/Software/Bionet. This paper presents the algorithmic methods needed for modeling complicated biochemical dynamics using rule-based models to represent expert knowledge in the context of cell cycle regulation and tumor growth. A notable feature of this modeling approach is that it allows biologists to build complex models from their knowledge base without

DNA Ligase C1 Mediates the LigD-Independent Nonhomologous End-Joining Pathway of Mycobacterium smegmatis

PubMed Central

Bhattarai, Hitesh; Gupta, Richa

2014-01-01

Nonhomologous end joining (NHEJ) is a recently described bacterial DNA double-strand break (DSB) repair pathway that has been best characterized for mycobacteria. NHEJ can religate transformed linear plasmids, repair ionizing radiation (IR)-induced DSBs in nonreplicating cells, and seal I-SceI-induced chromosomal DSBs. The core components of the mycobacterial NHEJ machinery are the DNA end binding protein Ku and the polyfunctional DNA ligase LigD. LigD has three autonomous enzymatic modules: ATP-dependent DNA ligase (LIG), DNA/RNA polymerase (POL), and 3′ phosphoesterase (PE). Although genetic ablation of ku or ligD abolishes NHEJ and sensitizes nonreplicating cells to ionizing radiation, selective ablation of the ligase activity of LigD in vivo only mildly impairs NHEJ of linearized plasmids, indicating that an additional DNA ligase can support NHEJ. Additionally, the in vivo role of the POL and PE domains in NHEJ is unclear. Here we define a LigD ligase-independent NHEJ pathway in Mycobacterium smegmatis that requires the ATP-dependent DNA ligase LigC1 and the POL domain of LigD. Mycobacterium tuberculosis LigC can also support this backup NHEJ pathway. We also demonstrate that, although dispensable for efficient plasmid NHEJ, the activities of the POL and PE domains are required for repair of IR-induced DSBs in nonreplicating cells. These findings define the genetic requirements for a LigD-independent NHEJ pathway in mycobacteria and demonstrate that all enzymatic functions of the LigD protein participate in NHEJ in vivo. PMID:24957619

Exploration of SWRL Rule Bases through Visualization, Paraphrasing, and Categorization of Rules

NASA Astrophysics Data System (ADS)

Hassanpour, Saeed; O'Connor, Martin J.; Das, Amar K.

Rule bases are increasingly being used as repositories of knowledge content on the Semantic Web. As the size and complexity of these rule bases increases, developers and end users need methods of rule abstraction to facilitate rule management. In this paper, we describe a rule abstraction method for Semantic Web Rule Language (SWRL) rules that is based on lexical analysis and a set of heuristics. Our method results in a tree data structure that we exploit in creating techniques to visualize, paraphrase, and categorize SWRL rules. We evaluate our approach by applying it to several biomedical ontologies that contain SWRL rules, and show how the results reveal rule patterns within the rule base. We have implemented our method as a plug-in tool for Protégé-OWL, the most widely used ontology modeling software for the Semantic Web. Our tool can allow users to rapidly explore content and patterns in SWRL rule bases, enabling their acquisition and management.

N400 elicited by incongruent ending words of Chinese idioms in healthy adults.

PubMed

Chen, Xing-shi; Tang, Yun-xiang; Xiao, Ze-ping; Wang, Ji-jun; Zhang, Ming-dao; Zhang, Zai-fu; Hu, Zhen-yu; Lou, Fei-ying; Chen, Chong; Zhang, Tian-hong

2010-03-20

Prior research about N400 has been mainly based on English stimuli, while the cognitive processing of Chinese characters is still unclear. The aim of the present study was to further investigate the semantic processing of Chinese idioms. Event related potentials (ERP) component N400 was elicited by 38 pairs of matching (congruent) and mismatching (incongruent) ended Chinese idioms: ending words with same phoneme but different shape and meaning (sPdSdM), with similar shape but different phoneme and meaning (sSdPdM), with same meaning but different phoneme and shape (sMdPdS), and words with different phoneme, shape and meaning (dPdSdM) and recorded by Guangzhou Runjie WJ-1 ERP instruments. In 62 right-handed healthy adults (age 19 - 50 years), N400 amplitudes and latencies were compared between matching and mismatching conditions at Fz, Cz and Pz. N400 showed a midline distribution and could be elicited in electrodes Fz, Cz and Pz. The mean values of N400 latencies and amplitudes were obtained for matching and mismatching ending words in healthy adults. Significant differences were found in N400 latencies and amplitudes in matching and mismatching ending-words idioms in healthy adults (P < 0.05). Compared with matching ending-words idioms, N400 latencies were prolonged and the amplitudes were increased in mismatching ones. N400s elicited by different types of stimuli showed different latencies and amplitudes, and longest N400 latency and largest N400 amplitude were elicited by ending-words with dPdSdM. No gender difference was found of N400 latency and amplitude in this study (P > 0.05). Compared with English stimuli, Chinese ideographic words could provide more flexible stimuli for N400 research in that the words have 3-dimension changes - phoneme, shape and meaning. Features of N400 elicited by matching and mismatching ending words in Chinese idioms are mainly determined by the meaning of the word. Some issues of N400 elicited by Chinese characters deserve further

Medicare program; End-Stage Renal Disease prospective payment system, quality incentive program, and Durable Medical Equipment, Prosthetics, Orthotics, and Supplies. Final rule.

PubMed

2014-11-06

This final rule will update and make revisions to the End-Stage Renal Disease (ESRD) prospective payment system (PPS) for calendar year (CY) 2015. This rule also finalizes requirements for the ESRD quality incentive program (QIP), including for payment years (PYs) 2017 and 2018. This rule will also make a technical correction to remove outdated terms and definitions. In addition, this final rule sets forth the methodology for adjusting Durable Medical Equipment, Prosthetics, Orthotics, and Supplies (DMEPOS) fee schedule payment amounts using information from the Medicare DMEPOS Competitive Bidding Program (CBP); makes alternative payment rules for certain DME under the Medicare DMEPOS CBP; clarifies the statutory Medicare hearing aid coverage exclusion and specifies devices not subject to the hearing aid exclusion; will not update the definition of minimal self-adjustment; clarifies the Change of Ownership (CHOW) and provides for an exception to the current requirements; revises the appeal provisions for termination of a CBP contract, including the beneficiary notification requirement under the Medicare DMEPOS CBP, and makes a technical change to the regulation related to the conditions for awarding contracts for furnishing infusion drugs under the Medicare DMEPOS CBP.

Aspartate Carbamyltransferase : Site of End-Product Inhibition of the Orotate Pathway in Intact Cells of Cucurbita pepo.

PubMed

Lovatt, C J; Cheng, A H

1984-07-01

Lovatt et al. (1979 Plant Physiol 64: 562-569) have previously demonstrated that end-product inhibition functions as a mechanism regulating the activity of the orotic acid pathway in intact cells of roots excised from 2-day-old squash plants (Cucurbita pepo L. cv Early Prolific Straightneck). Uridine (0.5 millimolar final concentration) or one of its metabolites inhibited the incorporation of NaH(14)CO(3), but not [(14)C]carbamylaspartate or [(14)C]orotic acid, into uridine nucleotides (SigmaUMP). Thus, regulation of de novo pyrimidine biosynthesis was demonstrated to occur at one or both of the first two reactions of the orotic acid pathway, those catalyzed by carbamylphosphate synthetase (CPSase) and aspartate carbamyltransferase (ACTase). The results of the present study provide evidence that ACTase alone is the site of feedback control by added uridine or one of its metabolites. Evidence demonstrating regulation of the orotic acid pathway by end-product inhibition at ACTase, but not at CPSase, includes the following observations: (a) addition of uridine (0.5 millimolar final concentration) inhibited the incorporation of NaH(14)CO(3) into SigmaUMP by 80% but did not inhibit the incorporation of NaH(14)CO(3) into arginine; (b) inhibition of the orotate pathway by added uridine was not reversed by supplying exogenous ornithine (5 millimolar final concentration), while the incorporation of NaH(14)CO(3) into arginine was stimulated more than 15-fold when both uridine and ornithine were added; (c) incorporation of NaH(14)CO(3) into arginine increased, with or without added ornithine when the de novo pyrimidine pathway was inhibited by added uridine; and (d) in assays employing cell-free extracts prepared from 2-day-old squash roots, the activity of ACTase, but not CPSase, was inhibited by added pyrimidine nucleotides.

The End of the HIPAA Privacy Rule? Currents in Contemporary Bioethics.

PubMed

Rothstein, Mark A

2016-06-01

The HIPAA Privacy Rule is notoriously weak because of its incomplete coverage, numerous exclusions and exemptions, and limited rights for individuals. The three areas in which it provides the most protection are fundraising, marketing, and research. Provisions of the 21st Century Cures Act, pending in Congress, and the Notice of Proposed Rulemaking to amend the federal research regulations (Common Rule), awaiting final regulatory action, would weaken the privacy protections for research. If these measures are adopted, the HIPAA Privacy Rule would have so little value that it might not be worth the aggravation and burden. © 2016 American Society of Law, Medicine & Ethics.

Automated visualization of rule-based models

PubMed Central

Tapia, Jose-Juan; Faeder, James R.

2017-01-01

Frameworks such as BioNetGen, Kappa and Simmune use “reaction rules” to specify biochemical interactions compactly, where each rule specifies a mechanism such as binding or phosphorylation and its structural requirements. Current rule-based models of signaling pathways have tens to hundreds of rules, and these numbers are expected to increase as more molecule types and pathways are added. Visual representations are critical for conveying rule-based models, but current approaches to show rules and interactions between rules scale poorly with model size. Also, inferring design motifs that emerge from biochemical interactions is an open problem, so current approaches to visualize model architecture rely on manual interpretation of the model. Here, we present three new visualization tools that constitute an automated visualization framework for rule-based models: (i) a compact rule visualization that efficiently displays each rule, (ii) the atom-rule graph that conveys regulatory interactions in the model as a bipartite network, and (iii) a tunable compression pipeline that incorporates expert knowledge and produces compact diagrams of model architecture when applied to the atom-rule graph. The compressed graphs convey network motifs and architectural features useful for understanding both small and large rule-based models, as we show by application to specific examples. Our tools also produce more readable diagrams than current approaches, as we show by comparing visualizations of 27 published models using standard graph metrics. We provide an implementation in the open source and freely available BioNetGen framework, but the underlying methods are general and can be applied to rule-based models from the Kappa and Simmune frameworks also. We expect that these tools will promote communication and analysis of rule-based models and their eventual integration into comprehensive whole-cell models. PMID:29131816

Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival

PubMed Central

Piegorsch, Walter W.; Lussier, Yves A.

2015-01-01

Motivation: The conventional approach to personalized medicine relies on molecular data analytics across multiple patients. The path to precision medicine lies with molecular data analytics that can discover interpretable single-subject signals (N-of-1). We developed a global framework, N-of-1-pathways, for a mechanistic-anchored approach to single-subject gene expression data analysis. We previously employed a metric that could prioritize the statistical significance of a deregulated pathway in single subjects, however, it lacked in quantitative interpretability (e.g. the equivalent to a gene expression fold-change). Results: In this study, we extend our previous approach with the application of statistical Mahalanobis distance (MD) to quantify personal pathway-level deregulation. We demonstrate that this approach, N-of-1-pathways Paired Samples MD (N-OF-1-PATHWAYS-MD), detects deregulated pathways (empirical simulations), while not inflating false-positive rate using a study with biological replicates. Finally, we establish that N-OF-1-PATHWAYS-MD scores are, biologically significant, clinically relevant and are predictive of breast cancer survival (P < 0.05, n = 80 invasive carcinoma; TCGA RNA-sequences). Conclusion: N-of-1-pathways MD provides a practical approach towards precision medicine. The method generates the magnitude and the biological significance of personal deregulated pathways results derived solely from the patient’s transcriptome. These pathways offer the opportunities for deriving clinically actionable decisions that have the potential to complement the clinical interpretability of personal polymorphisms obtained from DNA acquired or inherited polymorphisms and mutations. In addition, it offers an opportunity for applicability to diseases in which DNA changes may not be relevant, and thus expand the ‘interpretable ‘omics’ of single subjects (e.g. personalome). Availability and implementation: http://www.lussierlab.net/publications/N-of-1

17 CFR 239.14 - Form N-2 for closed end management investment companies registered on Form N-8A.

Code of Federal Regulations, 2010 CFR

2010-04-01

... management investment companies registered on Form N-8A. 239.14 Section 239.14 Commodity and Securities... Registration Statements § 239.14 Form N-2 for closed end management investment companies registered on Form N... closed end management investment companies registered under the Investment Company Act of 1940 on form N...

Activation of the CXCL16/CXCR6 Pathway by Inflammation Contributes to Atherosclerosis in Patients with End-stage Renal Disease.

PubMed

Hu, Ze Bo; Chen, Yan; Gong, Yu Xiang; Gao, Min; Zhang, Yang; Wang, Gui Hua; Tang, Ri Ning; Liu, Hong; Liu, Bi Cheng; Ma, Kun Ling

2016-01-01

Background: Chronic inflammation plays a critical role in the progression of atherosclerosis (AS). This study aimed to determine the effects of the CXC chemokine ligand 16 (CXCL16)/CXC chemokine receptor 6 (CXCR6) pathway on cholesterol accumulation in the radial arteries of end-stage renal disease (ESRD) patients with concomitant microinflammation and to further investigate the potential effects of the purinergic receptor P2X ligand-gated ion channel 7 (P2X7R). Methods: Forty-three ESRD patients were divided into the control group (n=17) and the inflamed group (n=26) based on plasma C-reactive protein (CRP) levels. Biochemical indexes and lipid profiles of the patients were determined. Surgically removed tissues from the radial arteries of patients receiving arteriovenostomy were used for preliminary evaluation of AS. Haematoxylin-eosin (HE) and Filipin staining were performed to assess foam cell formation. CXCL16/CXCR6 pathway-related protein expression, P2X7R protein expression and the expression of monocyte chemotactic protein-1 (MCP-1), tumour necrosis factor-α (TNF-α), and CD68 were detected by immunohistochemical and immunofluorescence staining. Results: Inflammation increased both MCP-1 and TNF-α expression and macrophage infiltration in radial arteries. Additionally, foam cell formation significantly increased in the radial arteries of the inflamed group compared to that of the controls. Further analysis showed that protein expression of CXCL16, CXCR6, disintegrin and metalloproteinase-10 (ADAM10) in the radial arteries of the inflamed group was significantly increased. Furthermore, CXCL16 expression was positively correlated with P2X7R expression in the radial arteries of ESRD patients. Conclusions: Inflammation contributed to foam cell formation in the radial arteries of ESRD patients via activation of the CXCL16/CXCR6 pathway, which may be regulated by P2X7R.

The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends

PubMed Central

Aniukwu, Jideofor; Glickman, Michael S.; Shuman, Stewart

2008-01-01

Mycobacteria can repair DNA double-strand breaks (DSBs) via a nonhomologous end-joining (NHEJ) system that includes a dedicated DNA ligase (LigD) and the DNA end-binding protein Ku. Here we exploit an improved plasmid-based NHEJ assay and a collection of Mycobacterium smegmatis strains bearing deletions or mutations in Ku or the DNA ligases to interrogate the contributions of LigD’s three catalytic activities (polymerase, ligase, and 3′ phosphoesterase) and structural domains (POL, LIG, and PE) to the efficiency and molecular outcomes of NHEJ in vivo. By analyzing in parallel the repair of blunt, 5′ overhang, and 3′ overhang DSBs, we discovered a novel end-joining pathway specific to breaks with 3′ overhangs that is Ku- and LigD-independent and perfectly faithful. This 3′ overhang NHEJ pathway is independent of ligases B and C; we surmise that it relies on NAD+-dependent LigA, the essential replicative ligase. We find that efficient repair of blunt and 5′ overhang DSBs depends stringently on Ku and the LigD POL domain, but not on the LigD polymerase activity, which mainly serves to promote NHEJ infidelity. The lack of an effect of PE-inactivating LigD mutations on NHEJ outcomes, especially the balance between deletions and insertions at blunt or 5′ overhang breaks, argues against LigD being the catalyst of deletion formation. Ligase-inactivating LigD mutations (or deletion of the LIG domain) have a modest impact on the efficiency of blunt and 5′ overhang DSB repair, because the strand sealing activity can be provided in trans by one of the other resident ATP-dependent ligases (likely LigC). Reliance on the backup ligase is accompanied by a drastic loss of fidelity during blunt end and 5′ overhang DSB repair. We conclude that the mechanisms of mycobacterial NHEJ are many and the outcomes depend on the initial structures of the DSBs and the available ensemble of end-processing and end-sealing components, which are not limited to Ku and LigD. PMID

17 CFR 239.15 - Form N-1 for open-end management investment companies registered on Form N-8A.

Code of Federal Regulations, 2010 CFR

2010-04-01

... management investment companies registered on Form N-8A. 239.15 Section 239.15 Commodity and Securities... Registration Statements § 239.15 Form N-1 for open-end management investment companies registered on Form N-8A...-end management investment companies that are separate accounts of insurance companies as defined by...

Structural Insights Into DNA Repair by RNase T—An Exonuclease Processing 3′ End of Structured DNA in Repair Pathways

PubMed Central

Hsiao, Yu-Yuan; Fang, Woei-Horng; Lee, Chia-Chia; Chen, Yi-Ping; Yuan, Hanna S.

2014-01-01

DNA repair mechanisms are essential for preservation of genome integrity. However, it is not clear how DNA are selected and processed at broken ends by exonucleases during repair pathways. Here we show that the DnaQ-like exonuclease RNase T is critical for Escherichia coli resistance to various DNA-damaging agents and UV radiation. RNase T specifically trims the 3′ end of structured DNA, including bulge, bubble, and Y-structured DNA, and it can work with Endonuclease V to restore the deaminated base in an inosine-containing heteroduplex DNA. Crystal structure analyses further reveal how RNase T recognizes the bulge DNA by inserting a phenylalanine into the bulge, and as a result the 3′ end of blunt-end bulge DNA can be digested by RNase T. In contrast, the homodimeric RNase T interacts with the Y-structured DNA by a different binding mode via a single protomer so that the 3′ overhang of the Y-structured DNA can be trimmed closely to the duplex region. Our data suggest that RNase T likely processes bulge and bubble DNA in the Endonuclease V–dependent DNA repair, whereas it processes Y-structured DNA in UV-induced and various other DNA repair pathways. This study thus provides mechanistic insights for RNase T and thousands of DnaQ-like exonucleases in DNA 3′-end processing. PMID:24594808

First vaccine approval under the FDA Animal Rule

PubMed Central

Beasley, David W C; Brasel, Trevor L; Comer, Jason E

2016-01-01

The US Food and Drug Administration’s Animal Rule was established to facilitate licensure of new products for life-threatening conditions when traditional efficacy trials in humans are unethical or impractical. In November, 2015 BioThrax became the first vaccine to receive approval for a new indication via this pathway. The basis for this approval and use of Animal Rule or other non-traditional approval pathways for licensure of vaccines for serious conditions are discussed. PMID:29263855

The Pathway Coexpression Network: Revealing pathway relationships

PubMed Central

Tanzi, Rudolph E.

2018-01-01

A goal of genomics is to understand the relationships between biological processes. Pathways contribute to functional interplay within biological processes through complex but poorly understood interactions. However, limited functional references for global pathway relationships exist. Pathways from databases such as KEGG and Reactome provide discrete annotations of biological processes. Their relationships are currently either inferred from gene set enrichment within specific experiments, or by simple overlap, linking pathway annotations that have genes in common. Here, we provide a unifying interpretation of functional interaction between pathways by systematically quantifying coexpression between 1,330 canonical pathways from the Molecular Signatures Database (MSigDB) to establish the Pathway Coexpression Network (PCxN). We estimated the correlation between canonical pathways valid in a broad context using a curated collection of 3,207 microarrays from 72 normal human tissues. PCxN accounts for shared genes between annotations to estimate significant correlations between pathways with related functions rather than with similar annotations. We demonstrate that PCxN provides novel insight into mechanisms of complex diseases using an Alzheimer’s Disease (AD) case study. PCxN retrieved pathways significantly correlated with an expert curated AD gene list. These pathways have known associations with AD and were significantly enriched for genes independently associated with AD. As a further step, we show how PCxN complements the results of gene set enrichment methods by revealing relationships between enriched pathways, and by identifying additional highly correlated pathways. PCxN revealed that correlated pathways from an AD expression profiling study include functional clusters involved in cell adhesion and oxidative stress. PCxN provides expanded connections to pathways from the extracellular matrix. PCxN provides a powerful new framework for interrogation of

Induction and repair of DNA double strand breaks: the increasing spectrum of non-homologous end joining pathways.

PubMed

Mladenov, Emil; Iliakis, George

2011-06-03

A defining characteristic of damage induced in the DNA by ionizing radiation (IR) is its clustered character that leads to the formation of complex lesions challenging the cellular repair mechanisms. The most widely investigated such complex lesion is the DNA double strand break (DSB). DSBs undermine chromatin stability and challenge the repair machinery because an intact template strand is lacking to assist restoration of integrity and sequence in the DNA molecule. Therefore, cells have evolved a sophisticated machinery to detect DSBs and coordinate a response on the basis of inputs from various sources. A central function of cellular responses to DSBs is the coordination of DSB repair. Two conceptually different mechanisms can in principle remove DSBs from the genome of cells of higher eukaryotes. Homologous recombination repair (HRR) uses as template a homologous DNA molecule and is therefore error-free; it functions preferentially in the S and G2 phases. Non-homologous end joining (NHEJ), on the other hand, simply restores DNA integrity by joining the two ends, is error prone as sequence is only fortuitously preserved and active throughout the cell cycle. The basis of DSB repair pathway choice remains unknown, but cells of higher eukaryotes appear programmed to utilize preferentially NHEJ. Recent work suggests that when the canonical DNA-PK dependent pathway of NHEJ (D-NHEJ), becomes compromised an alternative NHEJ pathway and not HRR substitutes in a quasi-backup function (B-NHEJ). Here, we outline aspects of DSB induction by IR and review the mechanisms of their processing in cells of higher eukaryotes. We place particular emphasis on backup pathways of NHEJ and summarize their increasing significance in various cellular processes, as well as their potential contribution to carcinogenesis. 2011 Elsevier B.V. All rights reserved.

Lego bricks and the octet rule: Molecular models for biochemical pathways with plastic, interlocking toy bricks.

PubMed

Lin, Henry J; Lehoang, Jennifer; Kwan, Isabel; Baghaee, Anita; Prasad, Priya; Ha-Chen, Stephanie J; Moss, Tanesha; Woods, Jeremy D

2018-01-01

The 8 studs on a 2 × 4 Lego brick conveniently represent the outer shell of electrons for carbon, nitrogen, and oxygen atoms. We used Lego bricks to model these atoms, which are then joined together to form molecules by following the Lewis octet rule. A variety of small biological molecules can be modeled in this way, such as most amino acids, fatty acids, glucose, and various intermediate metabolites. Model building with these familiar toys can be a helpful, hands-on exercise for learning-or re-learning-biochemical pathways. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):54-57, 2018. © 2017 The International Union of Biochemistry and Molecular Biology.

Thaw; New Rules to End the Cable TV Freeze.

ERIC Educational Resources Information Center

National Cable Television Association, Inc., Washington, DC.

The report summarizes the Federal Communications Commission's (FCC) rulemaking of February 3, 1972 for cable television (CATV) concerning what channels must be carried in certain categories of broadcast markets, use of non-broadcast channels, technical standards, and federal/state/local regulatory relationships. The report highlights the rule that…

Homologous recombination and non-homologous end-joining repair pathways in bovine embryos with different developmental competence

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

Henrique Barreta, Marcos; Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS; Garziera Gasperin, Bernardo

2012-10-01

This study investigated the expression of genes controlling homologous recombination (HR), and non-homologous end-joining (NHEJ) DNA-repair pathways in bovine embryos of different developmental potential. It also evaluated whether bovine embryos can respond to DNA double-strand breaks (DSBs) induced with ultraviolet irradiation by regulating expression of genes involved in HR and NHEJ repair pathways. Embryos with high, intermediate or low developmental competence were selected based on the cleavage time after in vitro insemination and were removed from in vitro culture before (36 h), during (72 h) and after (96 h) the expected period of embryonic genome activation. All studied genes weremore » expressed before, during and after the genome activation period regardless the developmental competence of the embryos. Higher mRNA expression of 53BP1 and RAD52 was found before genome activation in embryos with low developmental competence. Expression of 53BP1, RAD51 and KU70 was downregulated at 72 h and upregulated at 168 h post-insemination in response to DSBs induced by ultraviolet irradiation. In conclusion, important genes controlling HR and NHEJ DNA-repair pathways are expressed in bovine embryos, however genes participating in these pathways are only regulated after the period of embryo genome activation in response to ultraviolet-induced DSBs.« less

Implementation of artificial intelligence rules in a data base management system

NASA Technical Reports Server (NTRS)

Feyock, S.

1986-01-01

The intelligent front end prototype was transformed into a RIM-integrated system. A RIM-based expert system was written which demonstrated the developed capability. The use of rules to produce extensibility of the intelligent front end, including the concept of demons and rule manipulation rules were investigated. Innovative approaches such as syntax programming were to be considered.

[Role of Ski/SnoN protein in the regulation of TGF-beta signal pathway].

PubMed

Lu, Zhao-hui; Chen, Jie

2003-04-01

TGF-beta signal pathway plays an important role in the cell growth, differentiation, formation of extracellular matrix, embryo development and carcinogenesis, etc. However, the regulation of TGF-beta pathway is not totally understood. In 1999, three independent research groups found that Ski/SnoN protein could inhibit the TGF-beta mediated transcription by recruiting N-CoR, a transcription co-repressor. Later studies suggested that TGF-beta and SMADs degraded the Ski/SnoN protein by mediating ubiquitin linkage, showing negative feedback regulation. The important findings in Ski/SnoN laid the theoretical foundation for demonstrating the function of TGF-beta signal pathway.

Conformance Testing: Measurement Decision Rules

NASA Technical Reports Server (NTRS)

Mimbs, Scott M.

2010-01-01

The goal of a Quality Management System (QMS) as specified in ISO 9001 and AS9100 is to provide assurance to the customer that end products meet specifications. Measuring devices, often called measuring and test equipment (MTE), are used to provide the evidence of product conformity to specified requirements. Unfortunately, processes that employ MTE can become a weak link to the overall QMS if proper attention is not given to the measurement process design, capability, and implementation. Documented "decision rules" establish the requirements to ensure measurement processes provide the measurement data that supports the needs of the QMS. Measurement data are used to make the decisions that impact all areas of technology. Whether measurements support research, design, production, or maintenance, ensuring the data supports the decision is crucial. Measurement data quality can be critical to the resulting consequences of measurement-based decisions. Historically, most industries required simplistic, one-size-fits-all decision rules for measurements. One-size-fits-all rules in some cases are not rigorous enough to provide adequate measurement results, while in other cases are overly conservative and too costly to implement. Ideally, decision rules should be rigorous enough to match the criticality of the parameter being measured, while being flexible enough to be cost effective. The goal of a decision rule is to ensure that measurement processes provide data with a sufficient level of quality to support the decisions being made - no more, no less. This paper discusses the basic concepts of providing measurement-based evidence that end products meet specifications. Although relevant to all measurement-based conformance tests, the target audience is the MTE end-user, which is anyone using MTE other than calibration service providers. Topics include measurement fundamentals, the associated decision risks, verifying conformance to specifications, and basic measurement

Efficient photocatalytic degradation of gaseous N,N-dimethylformamide in tannery waste gas using doubly open-ended Ag/TiO2 nanotube array membranes

NASA Astrophysics Data System (ADS)

Zhao, Yang; Ma, Lin; Chang, Wenkai; Huang, Zhiding; Feng, Xugen; Qi, Xiaoxia; Li, Zenghe

2018-06-01

Gaseous N,N-dimethylformamide (DMF), typical volatile organic compound exhausted from manufacturing factories, may damage the health of workers under long-term exposure even at low levels. The defined geometry, porous surface and highly ordered channels make the free-standing anodic TiO2 nanotube (TiNT) arrays particularly suitable for applications of practical air purification by flow-through photocatalysis. In the present work, crystallized doubly open-ended Ag/TiNT array membranes were designed and prepared by employing a lift-off process based on an anodization-annealing-anodization-etching sequence, followed by uniform Ag nanoparticles decoration. For the photocatalytic degradation of gaseous DMF at low concentration levels close to that found in realistic pollutant air, an analytical methodology for the monitoring and determination of degradation process was developed based on the coupling of headspace sampling with gas chromatography mass spectrometry (HS-GC-MS). The doubly open-ended Ag/TiNT arrays exhibited higher removal efficiency of gaseous DMF from air compared with conventional bottom-closed Ag/TiNT arrays and pure bottomless TiNT arrays. These results indicated that the photocatalytic properties of TiNT arrays were improved with the open-bottom morphology and the Ag nanoparticles decoration. Based on the analysis with GC-MS and high performance ion chromatography (HPIC), it was found that demethylation is the main pathway of DMF degradation in photocatalytic reactions. Furthermore, decontamination of actual polluted tannery waste gas collected in leather factory proved that the photocatalysis on doubly open-ended Ag/TiNT array membrane is an efficient way and a promising application to treat air contaminated by DMF despite the complexity of various volatile organic compounds.

Limit of validity of Ostwald's rule of stages in a statistical mechanical model of crystallization.

PubMed

Hedges, Lester O; Whitelam, Stephen

2011-10-28

We have only rules of thumb with which to predict how a material will crystallize, chief among which is Ostwald's rule of stages. It states that the first phase to appear upon transformation of a parent phase is the one closest to it in free energy. Although sometimes upheld, the rule is without theoretical foundation and is not universally obeyed, highlighting the need for microscopic understanding of crystallization controls. Here we study in detail the crystallization pathways of a prototypical model of patchy particles. The range of crystallization pathways it exhibits is richer than can be predicted by Ostwald's rule, but a combination of simulation and analytic theory reveals clearly how these pathways are selected by microscopic parameters. Our results suggest strategies for controlling self-assembly pathways in simulation and experiment.

Developmental pathways of change in fitness and motor competence are related to overweight and obesity status at the end of primary school.

PubMed

Rodrigues, Luis P; Stodden, David F; Lopes, Vítor P

2016-01-01

To test how different developmental pathways of health-related physical fitness and motor competence tests relate to weight status (overweight and obesity) at the end of primary school. Longitudinal study on growth, health-related physical fitness, and motor competence of 472 primary school children assessed yearly throughout 1st to 4th grade, with an average age of 6.3±0.7 years of age at 1st grade. Children's pathways of change on each of the fitness and motor competence tests were determined along the four years of the study. Participants were divided into three groups according to their rate of change in each test over time: Low Rate of Change, Average Rate of Change, and High Rate of Change. A logistic regression was used to predict the odds ratio of becoming overweight or obese, depending on the developmental pathway of change in fitness and motor competence across childhood. Children with a low or average rate of change in their developmental pathways of fitness and motor competence were several times more prone to become overweight or obese at the end of primary school (OR 2.0 to 6.3), independent of sex and body mass index at baseline. Specifically, a negative developmental pathway (Low Rate of Change) in cardiorespiratory fitness demonstrated over a six-fold elevated risk of being overweight or obese, compared to peers with a positive pathway. Not all children improve their motor competence and fitness levels over time and many actually regress over time. Developing positive fitness and motor competence pathways during childhood protects from obesity and overweight. Copyright © 2015 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

The Overtime Rule in the National Football League: Fair or Unfair?

ERIC Educational Resources Information Center

Gorgievski, Nicholas; DeFranco, Thomas C.; Swaminatha, Hariharan; Sofronas, Kimberly S.

2010-01-01

In 1974, the National Football League (NFL) initiated a sudden death overtime rule for games ending in a tie score at the end of regulation time. The rule states that the sudden death system of determining the winner shall prevail when the score is tied at the end of the regulation playing time of all NFL games. The team scoring first during…

N. River Street, east side of street at Sound End ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

N. River Street, east side of street at Sound End - River Street Historic District, Bounded by West Saint James Street, West Santa Clara Street, Pleasant Street, & Guadalupe River, San Jose, Santa Clara County, CA

Increased integrity of white matter pathways after dual n-back training.

PubMed

Salminen, Tiina; Mårtensson, Johan; Schubert, Torsten; Kühn, Simone

2016-06-01

Dual n-back WM training has been shown to produce broad transfer effects to different untrained cognitive functions. The task is demanding to the cognitive system because it includes a bi-modal (auditory and visual) dual-task component. A previous WM training study showed increased white matter integrity in the parietal lobe as well as the anterior part of the corpus callosum after visual n-back training. We investigated dual n-back training-related changes in white matter pathways. We anticipated dual n-back training to increase white matter integrity in pathways that connect brain regions related to WM processes. Additionally, we hypothesized that dual n-back training would produce more brain-wide white matter changes than single n-back training because of the involvement of two modalities and the additional dual-task coordination component of the task. The dual n-back training group showed increased white matter integrity (reflected as increased fractional anisotropy, FA) after training. The effects were mostly left lateralized as compared with changes from pretest to posttest in the passive and active control groups. Additionally, significant effects were observed in the anterior part of the corpus callosum, when the training group was compared with the passive control group. There were no changes in pretest to posttest FA changes between the passive and active control groups. The results therefore show that dual n-back training produces increased integrity in white matter pathways connecting different brain regions. The results are discussed in reference to the bi-modal dual-task component of the training task. Copyright © 2016 Elsevier Inc. All rights reserved.

SOUTHERN END OF ASSEMBLY PLANT, LOOKING N ON SECOND FLOOR, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

SOUTHERN END OF ASSEMBLY PLANT, LOOKING N ON SECOND FLOOR, WHICH DID NOT EXIST ON DURING SHIP BUILDING DAYS. NOTE VEHICLE ELEVATOR. ABOVE AND TO THE LEFT IS SHIP BUILDING BALCONY. - B Building, 3001 Miller Road, Dearborn, MI

Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation

PubMed Central

2014-01-01

Introduction Discrimination of rheumatoid arthritis (RA) patients from patients with other inflammatory or degenerative joint diseases or healthy individuals purely on the basis of genes differentially expressed in high-throughput data has proven very difficult. Thus, the present study sought to achieve such discrimination by employing a novel unbiased approach using rule-based classifiers. Methods Three multi-center genome-wide transcriptomic data sets (Affymetrix HG-U133 A/B) from a total of 79 individuals, including 20 healthy controls (control group - CG), as well as 26 osteoarthritis (OA) and 33 RA patients, were used to infer rule-based classifiers to discriminate the disease groups. The rules were ranked with respect to Kiendl’s statistical relevance index, and the resulting rule set was optimized by pruning. The rule sets were inferred separately from data of one of three centers and applied to the two remaining centers for validation. All rules from the optimized rule sets of all centers were used to analyze their biological relevance applying the software Pathway Studio. Results The optimized rule sets for the three centers contained a total of 29, 20, and 8 rules (including 10, 8, and 4 rules for ‘RA’), respectively. The mean sensitivity for the prediction of RA based on six center-to-center tests was 96% (range 90% to 100%), that for OA 86% (range 40% to 100%). The mean specificity for RA prediction was 94% (range 80% to 100%), that for OA 96% (range 83.3% to 100%). The average overall accuracy of the three different rule-based classifiers was 91% (range 80% to 100%). Unbiased analyses by Pathway Studio of the gene sets obtained by discrimination of RA from OA and CG with rule-based classifiers resulted in the identification of the pathogenetically and/or therapeutically relevant interferon-gamma and GM-CSF pathways. Conclusion First-time application of rule-based classifiers for the discrimination of RA resulted in high performance, with means

DNA Damage Response Factors from Diverse Pathways, Including DNA Crosslink Repair, Mediate Alternative End Joining

PubMed Central

Howard, Sean M.; Yanez, Diana A.; Stark, Jeremy M.

2015-01-01

Alternative end joining (Alt-EJ) chromosomal break repair involves bypassing classical non-homologous end joining (c-NHEJ), and such repair causes mutations often with microhomology at the repair junction. Since the mediators of Alt-EJ are not well understood, we have sought to identify DNA damage response (DDR) factors important for this repair event. Using chromosomal break reporter assays, we surveyed an RNAi library targeting known DDR factors for siRNAs that cause a specific decrease in Alt-EJ, relative to an EJ event that is a composite of Alt-EJ and c-NHEJ (Distal-EJ between two tandem breaks). From this analysis, we identified several DDR factors that are specifically important for Alt-EJ relative to Distal-EJ. While these factors are from diverse pathways, we also found that most of them also promote homologous recombination (HR), including factors important for DNA crosslink repair, such as the Fanconi Anemia factor, FANCA. Since bypass of c-NHEJ is likely important for both Alt-EJ and HR, we disrupted the c-NHEJ factor Ku70 in Fanca-deficient mouse cells and found that Ku70 loss significantly diminishes the influence of Fanca on Alt-EJ. In contrast, an inhibitor of poly ADP-ribose polymerase (PARP) causes a decrease in Alt-EJ that is enhanced by Ku70 loss. Additionally, the helicase/nuclease DNA2 appears to have distinct effects from FANCA and PARP on both Alt-EJ, as well as end resection. Finally, we found that the proteasome inhibitor Bortezomib, a cancer therapeutic that has been shown to disrupt FANC signaling, causes a significant reduction in both Alt-EJ and HR, relative to Distal-EJ, as well as a substantial loss of end resection. We suggest that several distinct DDR functions are important for Alt-EJ, which include promoting bypass of c-NHEJ and end resection. PMID:25629353

Rule breaking mediates the developmental association between GABRA2 and adolescent substance abuse.

PubMed

Trucco, Elisa M; Villafuerte, Sandra; Heitzeg, Mary M; Burmeister, Margit; Zucker, Robert A

2014-12-01

This study's primary aim was to examine age-specific associations between GABRA2, rule breaking, problematic alcohol use, and substance abuse symptomatology. The secondary aim was to examine the extent to which rule breaking mediates the GABRA2-substance abuse relationship. A sample (n = 518) of primarily male (70.9%) and White (88.8%) adolescents from the Michigan Longitudinal Study was assessed from ages 11-18. Age-specific effects of GABRA2 on rule breaking, problematic alcohol use, and substance abuse symptomatology were examined using nested path models. The role of rule breaking as a mediator in the association between GABRA2 and substance abuse outcomes was tested using prospective cross-lagged path models. GABRA2 is significantly (p < 0.05) associated with rule breaking in mid- to late-adolescence, but not substance abuse symptomatology across adolescence. GABRA2 effects on problematic alcohol use and substance abuse symptomatology operate largely (45.3% and 71.1%, respectively, p < 0.05) via rule breaking in midadolescence. GABRA2 represents an early risk factor for an externalizing pathway to the development of problematic alcohol and drug use. © 2014 The Authors. Journal of Child Psychology and Psychiatry. © 2014 Association for Child and Adolescent Mental Health.

20 CFR 218.38 - When a spouse annuity ends.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false When a spouse annuity ends. 218.38 Section... ANNUITY BEGINNING AND ENDING DATES When an Annuity Ends § 218.38 When a spouse annuity ends. (a) General rules. A spouse annuity ends with the earliest of— (1) The last day of the month before the month in...

End-to-end modeling as part of an integrated research program in the Bering Sea

NASA Astrophysics Data System (ADS)

Punt, André E.; Ortiz, Ivonne; Aydin, Kerim Y.; Hunt, George L.; Wiese, Francis K.

2016-12-01

Traditionally, the advice provided to fishery managers has focused on the trade-offs between short- and long-term yields, and between future resource size and expected future catches. The harvest control rules that are used to provide management advice consequently relate catches to stock biomass levels expressed relative to reference biomass levels. There are, however, additional trade-offs. Ecosystem-based fisheries management (EBFM) aims to consider fish and fisheries in their ecological context, taking into account physical, biological, economic, and social factors. However, making EBFM operational remains challenging. It is generally recognized that end-to-end modeling should be a key part of implementing EBFM, along with harvest control rules that use information in addition to estimates of stock biomass to provide recommendations for management actions. Here we outline the process for selecting among alternative management strategies in an ecosystem context and summarize a Field-integrated End-To-End modeling program, or FETE, intended to implement this process as part of the Bering Sea Project. A key aspect of this project was that, from the start, the FETE included a management strategy evaluation component to compare management strategies. Effective use of end-to-end modeling requires that the models developed for a system are indeed integrated across climate drivers, lower trophic levels, fish population dynamics, and fisheries and their management. We summarize the steps taken by the program managers to promote integration of modeling efforts by multiple investigators and highlight the lessons learned during the project that can be used to guide future use and design of end-to-end models.

Heparanase induced by advanced glycation end products (AGEs) promotes macrophage migration involving RAGE and PI3K/AKT pathway

PubMed Central

2013-01-01

Background Advanced glycation end products (AGEs), inflammatory-associated macrophage migration and accumulation are crucial for initiation and progression of diabetic vascular complication. Enzymatic activity of heparanase (HPA) is implicated strongly in dissemination of metastatic tumor cells and cells of the immune system. In addition, HPA enhances the phosphorylation of selected signaling molecules including AKT pathway independent of enzymatic activity. However, virtually nothing is presently known the role of HPA during macrophage migration exposed to AGEs involving signal pathway. Methods These studies were carried out in Ana-1 macrophages. Macrophage viability was measured by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assays. HPA and AKT protein expression in macrophages are analysed by Western blotting and HPA mRNA expression by real time quantitative RT-PCR. Release of HPA was determined by ELISA. Macrophage migration was assessed by Transwell assays. Results HPA protein and mRNA were found to be increased significantly in AGEs-treated macrophages. Pretreatment with anti-HPA antibody which recognizes the nonenzymatic terminal of HPA prevented AGEs-induced AKT phosphorylation and macrophage migration. LY294002 (PI3k/AKT inhibitor) inhibited AGEs-induced macrophage migration. Furthermore, pretreatment with anti-receptor for advanced glycation end products (RAGE) antibody attenuated AGEs-induced HPA expression, AKT phosphorylation and macrophage migration. Conclusions These data indicate that AGEs-induced macrophage migration is dependent on HPA involving RAGE-HPA-PI3K/AKT pathway. The nonenzymatic activity of HPA may play a key role in AGEs-induced macrophage migration associated with inflammation in diabetic vascular complication. PMID:23442498

Effects of collagen membranes enriched with in vitro-differentiated N1E-115 cells on rat sciatic nerve regeneration after end-to-end repair.

PubMed

Amado, Sandra; Rodrigues, Jorge M; Luís, Ana L; Armada-da-Silva, Paulo A S; Vieira, Márcia; Gartner, Andrea; Simões, Maria J; Veloso, António P; Fornaro, Michele; Raimondo, Stefania; Varejão, Artur S P; Geuna, Stefano; Maurício, Ana C

2010-02-11

Peripheral nerves possess the capacity of self-regeneration after traumatic injury but the extent of regeneration is often poor and may benefit from exogenous factors that enhance growth. The use of cellular systems is a rational approach for delivering neurotrophic factors at the nerve lesion site, and in the present study we investigated the effects of enwrapping the site of end-to-end rat sciatic nerve repair with an equine type III collagen membrane enriched or not with N1E-115 pre-differentiated neural cells. After neurotmesis, the sciatic nerve was repaired by end-to-end suture (End-to-End group), end-to-end suture enwrapped with an equine collagen type III membrane (End-to-EndMemb group); and end-to-end suture enwrapped with an equine collagen type III membrane previously covered with neural cells pre-differentiated in vitro from N1E-115 cells (End-to-EndMembCell group). Along the postoperative, motor and sensory functional recovery was evaluated using extensor postural thrust (EPT), withdrawal reflex latency (WRL) and ankle kinematics. After 20 weeks animals were sacrificed and the repaired sciatic nerves were processed for histological and stereological analysis. Results showed that enwrapment of the rapair site with a collagen membrane, with or without neural cell enrichment, did not lead to any significant improvement in most of functional and stereological predictors of nerve regeneration that we have assessed, with the exception of EPT which recovered significantly better after neural cell enriched membrane employment. It can thus be concluded that this particular type of nerve tissue engineering approach has very limited effects on nerve regeneration after sciatic end-to-end nerve reconstruction in the rat.

Integrands for QCD rational terms and {N} = {4} SYM from massive CSW rules

NASA Astrophysics Data System (ADS)

Elvang, Henriette; Freedman, Daniel Z.; Kiermaier, Michael

2012-06-01

We use massive CSW rules to derive explicit compact expressions for integrands of rational terms in QCD with any number of external legs. Specifically, we present all- n integrands for the one-loop all-plus and one-minus gluon amplitudes in QCD. We extract the finite part of spurious external-bubble contributions systematically; this is crucial for the application of integrand-level CSW rules in theories without supersymmetry. Our approach yields integrands that are independent of the choice of CSW reference spinor even before integration. Furthermore, we present a recursive derivation of the recently proposed massive CSW-style vertex expansion for massive tree amplitudes and loop integrands on the Coulomb-branch of {N} = {4} SYM. The derivation requires a careful study of boundary terms in all-line shift recursion relations, and provides a rigorous (albeit indirect) proof of the recently proposed construction of massive amplitudes from soft-limits of massless on-shell amplitudes. We show that the massive vertex expansion manifestly preserves all holomorphic and half of the anti-holomorphic supercharges, diagram-by-diagram, even off-shell.

Schedules of controlled substances: placement of 5-methoxy-N,N-dimethyltryptamine into Schedule I of the Controlled Substances Act. Final rule.

PubMed

2010-12-20

With the issuance of this final rule, the Deputy Administrator of the Drug Enforcement Administration (DEA) places the substance 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT), including its salts, isomers and salts of isomers whenever the existence of such salts, isomers, and salts of isomers is possible, into schedule I of the Controlled Substances Act (CSA). This action by the DEA Deputy Administrator is based on a scheduling recommendation from the Assistant Secretary for Health of the Department of Health and Human Services (DHHS) and a DEA review indicating that 5-MeO-DMT meets the criteria for placement in schedule I of the CSA. This final rule will impose the criminal sanctions and regulatory controls of schedule I substances under the CSA on the manufacture, distribution, dispensing, importation, exportation, and possession of 5-MeO-DMT.

Auxin Biosynthesis in Pea: Characterization of the Tryptamine Pathway1[W][OA

PubMed Central

Quittenden, Laura J.; Davies, Noel W.; Smith, Jason A.; Molesworth, Peter P.; Tivendale, Nathan D.; Ross, John J.

2009-01-01

One pathway leading to the bioactive auxin, indole-3-acetic acid (IAA), is known as the tryptamine pathway, which is suggested to proceed in the sequence: tryptophan (Trp), tryptamine, N-hydroxytryptamine, indole-3-acetaldoxime, indole-3-acetaldehyde (IAAld), IAA. Recently, this pathway has been characterized by the YUCCA genes in Arabidopsis (Arabidopsis thaliana) and their homologs in other species. YUCCA is thought to be responsible for the conversion of tryptamine to N-hydroxytryptamine. Here we complement the genetic findings with a compound-based approach in pea (Pisum sativum), detecting potential precursors by gas chromatography/tandem-mass spectrometry. In addition, we have synthesized deuterated forms of many of the intermediates involved, and have used them to quantify the endogenous compounds, and to investigate their metabolic fates. Trp, tryptamine, IAAld, indole-3-ethanol, and IAA were detected as endogenous constituents, whereas indole-3-acetaldoxime and one of its products, indole-3-acetonitrile, were not detected. Metabolism experiments indicated that the tryptamine pathway to IAA in pea roots proceeds in the sequence: Trp, tryptamine, IAAld, IAA, with indole-3-ethanol as a side-branch product of IAAld. N-hydroxytryptamine was not detected, but we cannot exclude that it is an intermediate between tryptamine and IAAld, nor can we rule out the possibility of a Trp-independent pathway operating in pea roots. PMID:19710233

Diversity in the protein N-glycosylation pathways among campylobacter species

USDA-ARS?s Scientific Manuscript database

The foodborne bacterial pathogen, Campylobacter jejuni, possesses an N-linked protein glycosylation (pgl) pathway involved in adding conserved heptasaccharides to asparaginecontaining motifs of >60 proteins, and releasing the same glycan into its periplasm as free oligosaccharides. In this study, co...

Feynman-like rules for calculating n-point correlators of the primordial curvature perturbation

NASA Astrophysics Data System (ADS)

Valenzuela-Toledo, César A.; Rodríguez, Yeinzon; Beltrán Almeida, Juan P.

2011-10-01

A diagrammatic approach to calculate n-point correlators of the primordial curvature perturbation ζ was developed a few years ago following the spirit of the Feynman rules in Quantum Field Theory. The methodology is very useful and time-saving, as it is for the case of the Feynman rules in the particle physics context, but, unfortunately, is not very well known by the cosmology community. In the present work, we extend such an approach in order to include not only scalar field perturbations as the generators of ζ, but also vector field perturbations. The purpose is twofold: first, we would like the diagrammatic approach (which we would call the Feynman-like rules) to become widespread among the cosmology community; second, we intend to give an easy tool to formulate any correlator of ζ for those cases that involve vector field perturbations and that, therefore, may generate prolonged stages of anisotropic expansion and/or important levels of statistical anisotropy. Indeed, the usual way of formulating such correlators, using the Wick's theorem, may become very clutter and time-consuming.

Optical Selection Rule of Excitons in Gapped Chiral Fermion Systems

NASA Astrophysics Data System (ADS)

Zhang, Xiaoou; Shan, Wen-Yu; Xiao, Di

2018-02-01

We show that the exciton optical selection rule in gapped chiral fermion systems is governed by their winding number w , a topological quantity of the Bloch bands. Specifically, in a CN-invariant chiral fermion system, the angular momentum of bright exciton states is given by w ±1 +n N with n being an integer. We demonstrate our theory by proposing two chiral fermion systems capable of hosting dark s -like excitons: gapped surface states of a topological crystalline insulator with C4 rotational symmetry and biased 3 R -stacked MoS2 bilayers. In the latter case, we show that gating can be used to tune the s -like excitons from bright to dark by changing the winding number. Our theory thus provides a pathway to electrical control of optical transitions in two-dimensional material.

Algebraic Approaches for Scalable End-to-End Monitoring and Diagnosis

NASA Astrophysics Data System (ADS)

Zhao, Yao; Chen, Yan

The rigidity of the Internet architecture led to flourish in the research of end-to-end based systems. In this chapter, we describe a linear algebra-based end-to-end monitoring and diagnosis system. We first propose a tomography-based overlay monitoring system (TOM). Given n end hosts, TOM selectively monitors a basis set of O(nlogn) paths out of all n(n - 1) end-to-end paths. Any end-to-end path can be written as a unique linear combination of paths in the basis set. Consequently, by monitoring loss rates for the paths in the basis set, TOM infers loss rates for all end-to-end paths. Furthermore, leveraging on the scalable measurements from the TOM system, we propose the Least-biased End-to-End Network Diagnosis (in short, LEND) system. We define a minimal identifiable link sequence (MILS) as a link sequence of minimal length whose properties can be uniquely identified from end-to-end measurements. LEND applies an algebraic approach to find out the MILSes and infers the properties of the MILSes efficiently. This also means LEND system achieves the finest diagnosis granularity under the least biased statistical assumptions.

Evaluation of the Dignity Care Pathway for community nurses caring for people at the end of life.

PubMed

Johnston, Bridget; Östlund, Ulrika; Brown, Hilary

2012-10-01

People nearing the end of life fear loss of dignity, and a central tenet of palliative care is to help people die with dignity. The Dignity Care Pathway (DCP) is an intervention based on the Chochinov theoretical model of dignity care. It has four sections: a manual, a Patient Dignity Inventory, reflective questions, and care actions. The feasibility and acceptability of the DCP were evaluated using a qualitative design with a purposive sample of community nurses. Data was collected from April to October 2010 using in-depth interviews, reflective diaries, and case studies and then analysed using framework analysis. The DCP was acceptable to the community nurses, helped them identify when patients were at the end of life, identified patients' key concerns, and aided nurses in providing holistic end-of-life care. It requires the nurse to have excellent communication skills. Some of the nurses found it hard to initiate a conversation on dignity-conserving care. The DCP helps nurses to deliver individualised care and psychological care, which has previously been identified as a difficult area for community nurses. All of the nurses wished to continue to use the DCP and would recommend it to others.

Effects of collagen membranes enriched with in vitro-differentiated N1E-115 cells on rat sciatic nerve regeneration after end-to-end repair

PubMed Central

2010-01-01

Peripheral nerves possess the capacity of self-regeneration after traumatic injury but the extent of regeneration is often poor and may benefit from exogenous factors that enhance growth. The use of cellular systems is a rational approach for delivering neurotrophic factors at the nerve lesion site, and in the present study we investigated the effects of enwrapping the site of end-to-end rat sciatic nerve repair with an equine type III collagen membrane enriched or not with N1E-115 pre-differentiated neural cells. After neurotmesis, the sciatic nerve was repaired by end-to-end suture (End-to-End group), end-to-end suture enwrapped with an equine collagen type III membrane (End-to-EndMemb group); and end-to-end suture enwrapped with an equine collagen type III membrane previously covered with neural cells pre-differentiated in vitro from N1E-115 cells (End-to-EndMembCell group). Along the postoperative, motor and sensory functional recovery was evaluated using extensor postural thrust (EPT), withdrawal reflex latency (WRL) and ankle kinematics. After 20 weeks animals were sacrificed and the repaired sciatic nerves were processed for histological and stereological analysis. Results showed that enwrapment of the rapair site with a collagen membrane, with or without neural cell enrichment, did not lead to any significant improvement in most of functional and stereological predictors of nerve regeneration that we have assessed, with the exception of EPT which recovered significantly better after neural cell enriched membrane employment. It can thus be concluded that this particular type of nerve tissue engineering approach has very limited effects on nerve regeneration after sciatic end-to-end nerve reconstruction in the rat. PMID:20149260

Modeling of a C-end rule peptide adsorbed onto gold nanoparticles.

PubMed

Triguero, Jordi; Flores-Ortega, Alejandra; Zanuy, David; Alemán, Carlos

2018-01-01

The RPAR peptide, a prototype C-end Rule (CendR) sequence that binds to neuropilin-1 (NRP-1), has potential therapeutic uses as internalization trigger in anticancer nanodevices. Recently, the functionalization of gold nanoparticles with CendR peptides has been proved to be a successful strategy to target the NRP-1 receptor in prostate cancer cells. In this work, we investigate the influence of two gold surface facets, (100) and (111), on the conformational preferences of RPAR using molecular dynamics simulations. Both clustering and conformational analyses revealed that the peptide backbone becomes very rigid upon adsorption onto gold, which is a very fast and favored process, the only flexibility being attributed to the side chains of the two Arg residues. Thus, the different components of RPAR tend to adopt an elongated shape, which is characterized by the pseudo-extended conformation of both the backbone and the Arg side chains. This conformation is very different from the already known bioactive conformation, indicating that RPAR is drastically affected by the substrate. Interestingly, the preferred conformations of the peptide adsorbed onto gold facets are not stabilized by salt bridges and/or specific intramolecular hydrogen bonds, which represent an important difference with respect to the conformations found in other environments (e.g. the peptide in solution and interacting with NRP-1 receptor). However, the conformational changes induced by the substrate are not detrimental for the use of gold nanoparticles as appropriate vehicles for the transport and targeted delivery of the RPAR. Thus, once their high affinity for the NRP-1 receptor induces the targeted delivery of the elongated peptide molecules from the gold nanoparticles, the lack of intramolecular interactions facilitates their evolution towards the bioactive conformation, increasing the therapeutic efficacy of the peptide. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Widespread neural oscillations in the delta band dissociate rule convergence from rule divergence during creative idea generation.

PubMed

Boot, Nathalie; Baas, Matthijs; Mühlfeld, Elisabeth; de Dreu, Carsten K W; van Gaal, Simon

2017-09-01

Critical to creative cognition and performance is both the generation of multiple alternative solutions in response to open-ended problems (divergent thinking) and a series of cognitive operations that converges on the correct or best possible answer (convergent thinking). Although the neural underpinnings of divergent and convergent thinking are still poorly understood, several electroencephalography (EEG) studies point to differences in alpha-band oscillations between these thinking modes. We reason that, because most previous studies employed typical block designs, these pioneering findings may mainly reflect the more sustained aspects of creative processes that extend over longer time periods, and that still much is unknown about the faster-acting neural mechanisms that dissociate divergent from convergent thinking during idea generation. To this end, we developed a new event-related paradigm, in which we measured participants' tendency to implicitly follow a rule set by examples, versus breaking that rule, during the generation of novel names for specific categories (e.g., pasta, planets). This approach allowed us to compare the oscillatory dynamics of rule convergent and rule divergent idea generation and at the same time enabled us to measure spontaneous switching between these thinking modes on a trial-to-trial basis. We found that, relative to more systematic, rule convergent thinking, rule divergent thinking was associated with widespread decreases in delta band activity. Therefore, this study contributes to advancing our understanding of the neural underpinnings of creativity by addressing some methodological challenges that neuroscientific creativity research faces. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rules based process window OPC

NASA Astrophysics Data System (ADS)

O'Brien, Sean; Soper, Robert; Best, Shane; Mason, Mark

2008-03-01

As a preliminary step towards Model-Based Process Window OPC we have analyzed the impact of correcting post-OPC layouts using rules based methods. Image processing on the Brion Tachyon was used to identify sites where the OPC model/recipe failed to generate an acceptable solution. A set of rules for 65nm active and poly were generated by classifying these failure sites. The rules were based upon segment runlengths, figure spaces, and adjacent figure widths. 2.1 million sites for active were corrected in a small chip (comparing the pre and post rules based operations), and 59 million were found at poly. Tachyon analysis of the final reticle layout found weak margin sites distinct from those sites repaired by rules-based corrections. For the active layer more than 75% of the sites corrected by rules would have printed without a defect indicating that most rulesbased cleanups degrade the lithographic pattern. Some sites were missed by the rules based cleanups due to either bugs in the DRC software or gaps in the rules table. In the end dramatic changes to the reticle prevented catastrophic lithography errors, but this method is far too blunt. A more subtle model-based procedure is needed changing only those sites which have unsatisfactory lithographic margin.

Multiple programmed cell death pathways are involved in N-methyl-N-nitrosourea-induced photoreceptor degeneration.

PubMed

Reisenhofer, Miriam; Balmer, Jasmin; Zulliger, Rahel; Enzmann, Volker

2015-05-01

To identify programmed cell death (PCD) pathways involved in N-methyl-N-nitrosourea (MNU)-induced photoreceptor (PR) degeneration. Adult C57BL/6 mice received a single MNU i.p. injection (60 mg/kg bodyweight), and were observed over a period of 7 days. Degeneration was visualized by H&E overview staining and electron microscopy. PR cell death was measured by quantifying TUNEL-positive cells in the outer nuclear layer (ONL). Activity measurements of key PCD enzymes (calpain, caspases) were used to identify the involved cell death pathways. Furthermore, the expression level of C/EBP homologous protein (CHOP) and glucose-regulated protein 78 (GRP78), key players in endoplasmic reticulum (ER) stress-induced apoptosis, was analyzed using quantitative real-time PCR. A decrease in ONL thickness and the appearance of apoptotic PR nuclei could be detected beginning 3 days post-injection (PI). This was accompanied by an increase of TUNEL-positive cells. Significant upregulation of activated caspases (3, 9, 12) was found at different time periods after MNU injection. Additionally, several other players of nonconventional PCD pathways were also upregulated. Consequently, calpain activity increased in the ONL, with a maximum on day 7 PI and an upregulation of CHOP and GRP78 expression beginning on day 1 PI was found. The data indicate that regular apoptosis is the major cause of MNU-induced PR cell death. However, alternative PCD pathways, including ER stress and calpain activation, are also involved. Knowledge about the mechanisms involved in this mouse model of PR degeneration could facilitate the design of putative combinatory therapeutic approaches.

43 CFR 4.100 - General rules and guidelines.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false General rules and guidelines. 4.100... rules and guidelines. (a) Effective date and applicability—(1) Effective date and general applicability..., in which event the period shall run to the end of the next business day. (e) General guidelines—(1...

Exploring the pathways leading from disadvantage to end-stage renal disease for indigenous Australians.

PubMed

Cass, Alan; Cunningham, Joan; Snelling, Paul; Wang, Zhiqiang; Hoy, Wendy

2004-02-01

Indigenous Australians are disadvantaged, relative to other Australians, over a range of socio-economic and health measures. The age- and sex-adjusted incidence of end-stage renal disease (ESRD)--the irreversible preterminal phase of chronic renal failure--is almost nine times higher amongst Indigenous than it is amongst non-indigenous Australians. A striking gradient exists from urban to remote regions, where the standardised ESRD incidence is from 20 to more than 30 times the national incidence. We discuss the profound impact of renal disease on Indigenous Australians and their communities. We explore the linkages between disadvantage, often accompanied by geographic isolation, and both the initiation of renal disease, and its progression to ESRD. Purported explanations for the excess burden of renal disease in indigenous populations can be categorised as: primary renal disease explanations;genetic explanations;early development explanations; and socio-economic explanations. We discuss the strengths and weaknesses of these explanations and suggest a new hypothesis which integrates the existing evidence. We use this hypothesis to illuminate the pathways between disadvantage and the human biological processes which culminate in ESRD, and to propose prevention strategies across the life-course of Indigenous Australians to reduce their ESRD risk. Our hypothesis is likely to be relevant to an understanding of patterns of renal disease in other high-risk populations, particularly indigenous people in the developed world and people in developing countries. Furthermore, analogous pathways might be relevant to other chronic diseases, such as diabetes and cardiovascular disease. If we are able to confirm the various pathways from disadvantage to human biology, we will be better placed to advocate evidence-based interventions, both within and beyond the scope of the health-care system, to address the excess burden of renal and other chronic diseases among affected

Modifying an Insect Cell N-Glycan Processing Pathway Using CRISPR-Cas Technology.

PubMed

Mabashi-Asazuma, Hideaki; Kuo, Chu-Wei; Khoo, Kay-Hooi; Jarvis, Donald L

2015-10-16

Fused lobes (FDL) is an enzyme that simultaneously catalyzes a key trimming reaction and antagonizes elongation reactions in the insect N-glycan processing pathway. Accordingly, FDL function accounts, at least in part, for major differences in the N-glycosylation patterns of glycoproteins produced by insect and mammalian cells. In this study, we used the CRISPR-Cas9 system to edit the fdl gene in Drosophila melanogaster S2 cells. CRISPR-Cas9 editing produced a high frequency of site-specific nucleotide insertions and deletions, reduced the production of insect-type, paucimannosidic products (Man3GlcNAc2), and led to the production of partially elongated, mammalian-type complex N-glycans (GlcNAc2Man3GlcNAc2) in S2 cells. As CRISPR-Cas9 has not been widely used to analyze or modify protein glycosylation pathways or edit insect cell genes, these results underscore its broad utility as a tool for these purposes. Our results also confirm the key role of FDL at the major branch point distinguishing insect and mammalian N-glycan processing pathways. Finally, the new FDL-deficient S2 cell derivative produced in this study will enable future bottom-up glycoengineering efforts designed to isolate insect cell lines that can efficiently produce recombinant glycoproteins with chemically predefined oligosaccharide side-chain structures.

Diagnostic Pathway with Multiparametric Magnetic Resonance Imaging Versus Standard Pathway: Results from a Randomized Prospective Study in Biopsy-naïve Patients with Suspected Prostate Cancer.

PubMed

Porpiglia, Francesco; Manfredi, Matteo; Mele, Fabrizio; Cossu, Marco; Bollito, Enrico; Veltri, Andrea; Cirillo, Stefano; Regge, Daniele; Faletti, Riccardo; Passera, Roberto; Fiori, Cristian; De Luca, Stefano

2017-08-01

An approach based on multiparametric magnetic resonance imaging (mpMRI) might increase the detection rate (DR) of clinically significant prostate cancer (csPCa). To compare an mpMRI-based pathway with the standard approach for the detection of prostate cancer (PCa) and csPCa. Between November 2014 and April 2016, 212 biopsy-naïve patients with suspected PCa (prostate specific antigen level ≤15 ng/ml and negative digital rectal examination results) were included in this randomized clinical trial. Patients were randomized into a prebiopsy mpMRI group (arm A, n=107) or a standard biopsy (SB) group (arm B, n=105). In arm A, patients with mpMRI evidence of lesions suspected for PCa underwent mpMRI/transrectal ultrasound fusion software-guided targeted biopsy (TB) (n=81). The remaining patients in arm A (n=26) with negative mpMRI results and patients in arm B underwent 12-core SB. The primary end point was comparison of the DR of PCa and csPCa between the two arms of the study; the secondary end point was comparison of the DR between TB and SB. The overall DRs were higher in arm A versus arm B for PCa (50.5% vs 29.5%, respectively; p=0.002) and csPCa (43.9% vs 18.1%, respectively; p<0.001). Concerning the biopsy approach, that is, TB in arm A, SB in arm A, and SB in arm B, the overall DRs were significantly different for PCa (60.5% vs 19.2% vs 29.5%, respectively; p<0.001) and for csPCa (56.8% vs 3.8% vs 18.1%, respectively; p<0.001). The reproducibility of the study could have been affected by the single-center nature. A diagnostic pathway based on mpMRI had a higher DR than the standard pathway in both PCa and csPCa. In this randomized trial, a pathway for the diagnosis of prostate cancer based on multiparametric magnetic resonance imaging (mpMRI) was compared with the standard pathway based on random biopsy. The mpMRI-based pathway had better performance than the standard pathway. Copyright © 2016 European Association of Urology. Published by Elsevier B.V. All

Possible involvement of the JAK/STAT signaling pathway in N-acetylcysteine-mediated antidepressant-like effects.

PubMed

Al-Samhari, Marwa M; Al-Rasheed, Nouf M; Al-Rejaie, Salim; Al-Rasheed, Nawal M; Hasan, Iman H; Mahmoud, Ayman M; Dzimiri, Nduna

2016-03-01

Advances in depression research have targeted inflammation and oxidative stress to develop novel types of treatment. The JAK/STAT signaling pathway plays pivotal roles in immune and inflammatory responses. The present study was designed to investigate the effects of N-acetylcysteine, a putative precursor of the antioxidant glutathione, in an animal model of depression, with an emphasis on the JAK/STAT signaling pathway. Fluoxetine, a classical antidepressant drug was also under investigation. Male Wistar rats were subjected to forced swimming test and given N-acetylcysteine and fluoxetine immediately after the pre-test session, 5 h later and 1 h before the test session of the forced swimming test. N-acetylcysteine decreased immobility time (P < 0.05), serum corticosterone (P < 0.001), and hydrogen peroxide (P < 0.001), while restored glutathione concentration. Treatment of the rats with N-acetylcysteine produced significant (P < 0.001) down-regulation of STAT3 mRNA expression and protein phosphorylation. On the other hand, N-acetylcysteine significantly (P < 0.001) increased SOCS3 gene expression; however, SOCS3 protein was not changed. In conclusion, our study suggests that modulation of the JAK/STAT pathway might mediate the antidepressant-like effects of N-acetylcysteine. Therefore, depression research may target the JAK/STAT signaling pathway to provide a novel effective therapy. © 2015 by the Society for Experimental Biology and Medicine.

Possible involvement of the JAK/STAT signaling pathway in N-acetylcysteine-mediated antidepressant-like effects

PubMed Central

Al-Samhari, Marwa M; Al-Rasheed, Nouf M; Al-Rejaie, Salim; Al-Rasheed, Nawal M; Hasan, Iman H; Dzimiri, Nduna

2015-01-01

Advances in depression research have targeted inflammation and oxidative stress to develop novel types of treatment. The JAK/STAT signaling pathway plays pivotal roles in immune and inflammatory responses. The present study was designed to investigate the effects of N-acetylcysteine, a putative precursor of the antioxidant glutathione, in an animal model of depression, with an emphasis on the JAK/STAT signaling pathway. Fluoxetine, a classical antidepressant drug was also under investigation. Male Wistar rats were subjected to forced swimming test and given N-acetylcysteine and fluoxetine immediately after the pre-test session, 5 h later and 1 h before the test session of the forced swimming test. N-acetylcysteine decreased immobility time (P < 0.05), serum corticosterone (P < 0.001), and hydrogen peroxide (P < 0.001), while restored glutathione concentration. Treatment of the rats with N-acetylcysteine produced significant (P < 0.001) down-regulation of STAT3 mRNA expression and protein phosphorylation. On the other hand, N-acetylcysteine significantly (P < 0.001) increased SOCS3 gene expression; however, SOCS3 protein was not changed. In conclusion, our study suggests that modulation of the JAK/STAT pathway might mediate the antidepressant-like effects of N-acetylcysteine. Therefore, depression research may target the JAK/STAT signaling pathway to provide a novel effective therapy. PMID:26643864

Influences of growth parameters on the reaction pathway during GaN synthesis

NASA Astrophysics Data System (ADS)

Zhang, Zhi; Liu, Zhongyi; Fang, Haisheng

2018-01-01

Gallium nitride (GaN) film growth is a complicated physical and chemical process including fluid flow, heat transfer, species transport and chemical reaction. Study of the reaction mechanism, i.e., the reaction pathway, is important for optimizing the growth process in the actual manufacture. In the paper, the growth pathway of GaN in a closed-coupled showerhead metal-organic chemical vapor deposition (CCS-MOCVD) reactor is investigated in detail using computational fluid dynamics (CFD). Influences of the process parameters, such as the chamber pressure, the inlet temperature, the susceptor temperature and the pre-exponential factor, on the reaction pathway are examined. The results show that increases of the chamber pressure or the inlet temperature, as well as reductions of the susceptor temperature or the pre-exponential factor lead to the adduct route dominating the growth. The deposition rate contributed by the decomposition route, however, can be enhanced dramatically by increasing the inlet temperature, the susceptor temperature and the pre-exponential factor.

N-methyl-N'-nitro-N-nitrosoguanidine interferes with the epidermal growth factor receptor-mediated signaling pathway.

PubMed

Gao, Zhihua; Yang, Jun; Huang, Yun; Yu, Yingnian

2005-03-01

Many environmental factors, such as ultraviolet (UV) and arsenic, can induce the clustering of cell surface receptors, including epidermal growth factor receptor (EGFR). This is accompanied by the phosphorylation of the receptors and the activation of ensuing cellular signal transduction pathways, which are implicated in the various cellular responses caused by the exposure to these factors. In this study, we have shown that N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), an alkylating agent, also induced the clustering of EGFR in human amnion FL cells, which was similar in morphology to that of epidermal growth factor treatment. However, MNNG treatment did not activate Ras, the downstream mediator in EGFR signaling pathway, as compared to EGF treatment. The autophosphorylation of tyrosine residues Y1068 and Y1173 at the intracellular domain of EGFR, which is related to Ras activation under EGF treatment, was also not observed by MNNG exposure. Interestingly, although MNNG did not affect the binding of EGF to EGFR, MNNG can interfere with EGF function. For instance, pre-incubating FL cells with MNNG inhibited the autophosphorylation of EGFR by EGF treatment, as well as the activation of Ras. In addition, the phosphorylation of Y845 on EGFR by EGF, which is mediated through c-Src or related kinases but not autophosphorylation, was also affected by MNNG. Therefore, MNNG may influence the tyrosine kinase activity as well as the phosphorylation of EGFR through its interaction with EGFR.

Differences Between Tg2576 and Wild Type Mice in the NMDA Receptor-Nitric Oxide Pathway After Prolonged Application of a Diet High in Advanced Glycation End Products.

PubMed

Kristofikova, Zdena; Ricny, Jan; Sirova, Jana; Ripova, Daniela; Lubitz, Irit; Schnaider-Beeri, Michal

2015-08-01

It has been suggested that advanced glycation end (AGE) products, via cognate receptor activation, are implicated in several diseases, including Alzheimer's disease. The NMDA receptor-nitric oxide pathway appears to be influenced by AGE products and involved in the pathogenesis of this type of dementia. In this study, C57BL/6J (WT) and transgenic (Tg2576) mice expressing human mutant amyloid precursor protein were kept on prolonged (8 months) diets containing regular or high amounts of AGE products. After the decapitation of 11-months old mice, brain tissue analyses were performed [expressions of the NR1, NR2A and NR2B subunits of NMDA receptors, activities of neuronal, endothelial and inducible nitric oxide synthase (nNOS, eNOS and iNOS)]. Moreover, levels of malondialdehyde and of human amyloid β 1-42 were estimated. We found increased activity of nNOS in WT mice maintained on a high compared to regular AGE diet; however, no similar differences were found in Tg2576 mice. In addition, we observed an increase in NR1 expression in Tg2576 compared to WT mice, both kept on a diet high in AGE products. Correlation analyses performed on mice kept on the regular AGE diet supported close links between particular subunits (NR2A-NR2B, in WT as well as in Tg2576 mice), between subunits and synthase (NR2A/NR2B-nNOS, only in WT mice) or between particular synthases (nNOS-iNOS, only in WT). Correlation analysis also revealed differences between WT mice kept on both diets (changed correlations between NR2A/NR2B-nNOS, between nNOS-eNOS and between eNOS-iNOS). Malondialdehyde levels were increased in both Tg2576 groups when compared to the corresponding WT mice, but no effects of the diets were observed. Analogously, no significant effects of diets were found in the levels of soluble or insoluble amyloid β 1-42 in Tg2576 mice. Our results demonstrate that prolonged ingestion of AGE products can influence the NMDA receptor-nitric oxide pathway in the brain and that only WT mice

[Non-nitrification pathway for NH4+ -N removal in pilot-scale drinking water biological processes].

PubMed

Yu, Xin; Ye, Lin; Li, Xu-dong; Zhang, Xiao-jian; Shi, Xu; Liu, Bo; Li, Rui-hua

2008-04-01

The non-nitrification pathway for NH4+ -N removal in pilot-scale drinking water biological treatment processes and its possible mechanism were investigated through calculating N and DO stoichiometric balance. With more than 2 mg/L NH4+ -N in the influent, for the fluidized bed bioreactor (FBBR), the total of NH4+ -N, NO2(-) -N, NO3(-) -N in the influent was 0.91 mg/L higher than that in the effluent, and for the biofilter, its DO consumption was 2.90 mg/L less than the stoichiometric amount. The results suggested that nitrogen loss occurred in both reactors and a part of NH4+ -N was removed through non-nitrification pathway. Because the utilization of phosphorus and organic matters was independent of nitrogen loss, the assimilation and denitrification could be excluded from the possible mechanisms. Because the very low C/N in the influent and the accumulation of NO2(-) -N in the reactors were similar with the wastewater biological processes, the "autotrophic removal of nitrogen" was regarded as the most probable non-nitrification pathway. In this mechanism, the couple of short-cut nitrification and ANAMMOX (or OLAND) leading to the transformation of NH4+ -N and NO2(-) -N into gaseous N2 was responsible for the nitrogen loss in drinking water biological processes.

Investigation of pathways of advanced glycation end-products accumulation in macrophages.

PubMed

Nagai, Ryoji; Fujiwara, Yukio; Mera, Katsumi; Otagiri, Masaki

2007-04-01

Advanced glycation end-products (AGE) play a role in the pathogenesis of several diseases, including diabetic complications and atherosclerosis. In atherosclerotic lesions of human aortas, AGE are localized in the extracellular matrix and intracellularly in foam cells. Two interpretations are possible for AGE accumulation inside macrophages, one is endocytic uptake of extracellular AGE-proteins by scavenger receptors; the other is intracellular AGE formation inside the macrophages. In the present study, we determined the pathways involved in AGE accumulation inside macrophages. RAW 264.7 cells, a murine macrophage cell line, incubated with BSA and 1600 mM glucose for 40 weeks, recognized heavily modified AGE- BSA. In contrast, the cells showed no ligand activity for mildly modified AGE-BSA, prepared by incubating BSA with 50 mM glucose for 24 weeks. Nepsilon-(carboxymethyl)lysine (CML)-modified proteins of about 65 kDa were detected in human monocyte-derived macrophages incubated for 7 days with 30 mM glucose and phorbol myristate acetate. Furthermore, CML was generated when glycated protein was incubated with hypochloric acid. Taken together, our results indicate that AGE detected inside foam cells in atherosclerotic lesions are generated intracellularly rather than representing endocytic uptake of extracellular AGE-proteins by scavenger receptors.

The ClpS-like N-domain is essential for the functioning of Ubr11, an N-recognin in Schizosaccharomyces pombe.

PubMed

Kitamura, Kenji

2014-01-01

Several Ubr ubiquitin ligases recognize the N-terminal amino acid of substrate proteins and promote their degradation via the Arg/N-end rule pathway. The primary destabilizing N-terminal amino acids in yeast are classified into type 1 (Arg, Lys, and His) and type 2 (Phe, Trp, Tyr, Leu, Ile, and Met-Ф) residues. The type 1 and type 2 residues bind to the UBR box and the ClpS/N-domain, respectively, in canonical Ubr ubiquitin ligases that act as N-recognins. In this study, the requirement for type 1 and type 2 amino acid recognition by Schizosaccharomyces pombe Ubr11 was examined in vivo. Consistent with the results of previous studies, the ubr11∆ null mutant was found to be defective in oligopeptide uptake and resistant to ergosterol synthesis inhibitors. Furthermore, the ubr11∆ mutant was also less sensitive to some protein synthesis inhibitors. A ubr11 ClpS/N-domain mutant, which retained ubiquitin ligase activity but could not recognize type 2 amino acids, phenocopied all known defects of the ubr11∆ mutant. However, the recognition of type 1 residues by Ubr11 was not required for its functioning, and no severe physiological abnormalities were observed in a ubr11 mutant defective in the recognition of type 1 residues. These results reinforce the fundamental importance of the ClpS/N-domain for the functioning of the N-recognin, Ubr11.

Timescale analysis of rule-based biochemical reaction networks

PubMed Central

Klinke, David J.; Finley, Stacey D.

2012-01-01

The flow of information within a cell is governed by a series of protein-protein interactions that can be described as a reaction network. Mathematical models of biochemical reaction networks can be constructed by repetitively applying specific rules that define how reactants interact and what new species are formed upon reaction. To aid in understanding the underlying biochemistry, timescale analysis is one method developed to prune the size of the reaction network. In this work, we extend the methods associated with timescale analysis to reaction rules instead of the species contained within the network. To illustrate this approach, we applied timescale analysis to a simple receptor-ligand binding model and a rule-based model of Interleukin-12 (IL-12) signaling in näive CD4+ T cells. The IL-12 signaling pathway includes multiple protein-protein interactions that collectively transmit information; however, the level of mechanistic detail sufficient to capture the observed dynamics has not been justified based upon the available data. The analysis correctly predicted that reactions associated with JAK2 and TYK2 binding to their corresponding receptor exist at a pseudo-equilibrium. In contrast, reactions associated with ligand binding and receptor turnover regulate cellular response to IL-12. An empirical Bayesian approach was used to estimate the uncertainty in the timescales. This approach complements existing rank- and flux-based methods that can be used to interrogate complex reaction networks. Ultimately, timescale analysis of rule-based models is a computational tool that can be used to reveal the biochemical steps that regulate signaling dynamics. PMID:21954150

End-Functionalized Palladium SCS Pincer Polymers via Controlled Radical Polymerizations.

PubMed

Lye, Diane S; Cohen, Aaron E; Wong, Madeleine Z; Weck, Marcus

2017-07-01

A direct and facile route toward semitelechelic polymers, end-functionalized with palladated sulfur-carbon-sulfur pincer (Pd II -pincer) complexes is reported that avoids any post-polymerization step. Key to our methodology is the combination of reversible addition-fragmentation chain-transfer (RAFT) polymerization with functionalized chain-transfer agents. This strategy yields Pd end-group-functionalized materials with monomodal molar mass dispersities (Đ) of 1.18-1.44. The RAFT polymerization is investigated using a Pd II -pincer chain-transfer agent for three classes of monomers: styrene, tert-butyl acrylate, and N-isopropylacrylamide. The ensuing Pd II -pincer end-functionalized polymers are analyzed using 1 H NMR spectroscopy, gel-permeation chromatography, and elemental analysis. The RAFT polymerization methodology provides a direct pathway for the fabrication of Pd II -pincer functionalized polymers with complete end-group functionalization. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Portable design rules for bulk CMOS

NASA Technical Reports Server (NTRS)

Griswold, T. W.

1982-01-01

It is pointed out that for the past several years, one school of IC designers has used a simplified set of nMOS geometric design rules (GDR) which is 'portable', in that it can be used by many different nMOS manufacturers. The present investigation is concerned with a preliminary set of design rules for bulk CMOS which has been verified for simple test structures. The GDR are defined in terms of Caltech Intermediate Form (CIF), which is a geometry-description language that defines simple geometrical objects in layers. The layers are abstractions of physical mask layers. The design rules do not presume the existence of any particular design methodology. Attention is given to p-well and n-well CMOS processes, bulk CMOS and CMOS-SOS, CMOS geometric rules, and a description of the advantages of CMOS technology.

Federal Employees Health Benefits Program and Federal Employees Dental and Vision Insurance Program: eligibility for Pathway Programs participants. Interim final rule with request for comments.

PubMed

2014-01-06

The U.S. Office of Personnel Management (OPM) is issuing an interim final regulation to update the Federal Employees Health Benefits Program (FEHBP) and the Federal Employees Dental and Vision Insurance Program (FEDVIP) regulations to reflect updated election opportunities for participants in the Pathways Programs. The Pathways Programs were created by Executive Order (E.O.) 13562, signed by the President on December 27, 2010, and are designed to enable the Federal Government to compete effectively for students and recent graduates by improving its recruitment efforts through internships and similar programs with Federal agencies. This interim final rule furthers these recruitment and retention efforts by providing health insurance, as well as dental and vision benefits, to eligible program participants and their families.

DNA Packaging Specificity of Bacteriophage N15 with an Excursion into the Genetics of a Cohesive End Mismatch

PubMed Central

Feiss, Michael; Young Min, Jea; Sultana, Sawsan; Patel, Priyal; Sippy, Jean

2015-01-01

During DNA replication by the λ-like bacteriophages, immature concatemeric DNA is produced by rolling circle replication. The concatemers are processed into mature chromosomes with cohesive ends, and packaged into prohead shells, during virion assembly. Cohesive ends are generated by the viral enzyme terminase, which introduces staggered nicks at cos, an approx. 200 bp-long sequence containing subsites cosQ, cosN and cosB. Interactions of cos subsites of immature concatemeric DNA with terminase orchestrate DNA processing and packaging. To initiate DNA packaging, terminase interacts with cosB and nicks cosN. The cohesive ends of N15 DNA differ from those of λ at 2/12 positions. Genetic experiments show that phages with chromosomes containing mismatched cohesive ends are functional. In at least some infections, the cohesive end mismatch persists through cyclization and replication, so that progeny phages of both allelic types are produced in the infected cell. N15 possesses an asymmetric packaging specificity: N15 DNA is not packaged by phages λ or 21, but surprisingly, N15-specific terminase packages λ DNA. Implications for genetic interactions among λ-like bacteriophages are discussed. PMID:26633301

Advanced glycation end product-induced astrocytic differentiation of cultured neurospheres through inhibition of Notch-Hes1 pathway-mediated neurogenesis.

PubMed

Guo, Yijing; Wang, Pin; Sun, Haixia; Cai, Rongrong; Xia, Wenqing; Wang, Shaohua

2013-12-23

This study aims to investigate the roles of the Notch-Hes1 pathway in the advanced glycation end product (AGE)-mediated differentiation of neural stem cells (NSCs). We prepared pLentiLox3.7 lentiviral vectors that express short hairpin RNA (shRNA) against Notch1 and transfected it into NSCs. Cell differentiation was analyzed under confocal laser-scanning microscopy. The percentage of neurons and astrocytes was quantified by normalizing the total number of TUJ1+ (Neuron-specific class III β-tubulin) and GFAP+ (Glial fibrillary acidic protein) cells to the total number of Hoechst 33342-labeled cell nuclei. The protein and gene expression of Notch-Hes1 pathway components was examined via western blot analysis and real-time PCR. After 1 week of incubation, we found that AGE-bovine serum albumin (BSA) (400 μg/mL) induced the astrocytic differentiation of cultured neurospheres and inhibited neuronal formation. The expression of Notch-Hes1 pathway components was upregulated in the cells in the AGE-BSA culture medium. Immunoblot analysis indicated that shRNA silencing of Notch1 expression in NSCs significantly increases neurogenesis and suppresses astrocytic differentiation in NSCs incubated with AGE-BSA. AGEs promote the astrocytic differentiation of cultured neurospheres by inhibiting neurogenesis through the Notch-Hes1 pathway, providing a potential therapeutic target for hyperglycemia-related cognitive deficits.

12 CFR 202.7 - Rules concerning extensions of credit.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 2 2010-01-01 2010-01-01 false Rules concerning extensions of credit. 202.7... EQUAL CREDIT OPPORTUNITY ACT (REGULATION B) § 202.7 Rules concerning extensions of credit. (a.... (c) Action concerning existing open-end accounts—(1) Limitations. In the absence of evidence of the...

C-Jun N-terminal kinase signalling pathway in response to cisplatin.

PubMed

Yan, Dong; An, GuangYu; Kuo, Macus Tien

2016-11-01

Cisplatin (cis diamminedichloroplatinum II, cDDP) is one of the most effective cancer chemotherapeutic agents and is used in the treatment of many types of human malignancies. However, inherent tumour resistance is a major barrier to effective cisplatin therapy. So far, the mechanism of cDDP resistance has not been well defined. In general, cisplatin is considered to be a cytotoxic drug, for damaging DNA and inhibiting DNA synthesis, resulting in apoptosis via the mitochondrial death pathway or plasma membrane disruption. cDDP-induced DNA damage triggers signalling pathways that will eventually decide between cell life and death. As a member of the mitogen-activated protein kinases family, c-Jun N-terminal kinase (JNK) is a signalling pathway in response to extracellular stimuli, especially drug treatment, to modify the activity of numerous proteins locating in the mitochondria or the nucleus. Recent studies suggest that JNK signalling pathway plays a major role in deciding the fate of the cell and inducing resistance to cDDP-induced apoptosis in human tumours. c-Jun N-terminal kinase regulates several important cellular functions including cell proliferation, differentiation, survival and apoptosis while activating and inhibiting substrates for phosphorylation transcription factors (c-Jun, ATF2: Activating transcription factor 2, p53 and so on), which subsequently induce pro-apoptosis and pro-survival factors expression. Therefore, it is suggested that JNK signal pathway is a double-edged sword in cDDP treatment, simultaneously being a significant pro-apoptosis factor but also being associated with increased resistance to cisplatin-based chemotherapy. This review focuses on current knowledge concerning the role of JNK in cell response to cDDP, as well as their role in cisplatin resistance. © 2016 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

43 CFR 4.801 - Suspension of rules.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Special Procedural Rules Applicable to Practice and Procedure for Hearings, Decisions, and Administrative... determination that no party will be unduly prejudiced and the ends of justice will thereby be served. ...

43 CFR 4.801 - Suspension of rules.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Special Procedural Rules Applicable to Practice and Procedure for Hearings, Decisions, and Administrative... determination that no party will be unduly prejudiced and the ends of justice will thereby be served. ...

43 CFR 4.801 - Suspension of rules.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Special Procedural Rules Applicable to Practice and Procedure for Hearings, Decisions, and Administrative... determination that no party will be unduly prejudiced and the ends of justice will thereby be served. ...

43 CFR 4.801 - Suspension of rules.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Special Procedural Rules Applicable to Practice and Procedure for Hearings, Decisions, and Administrative... determination that no party will be unduly prejudiced and the ends of justice will thereby be served. ...

Dynamics Sampling in Transition Pathway Space.

PubMed

Zhou, Hongyu; Tao, Peng

2018-01-09

The minimum energy pathway contains important information describing the transition between two states on a potential energy surface (PES). Chain-of-states methods were developed to efficiently calculate minimum energy pathways connecting two stable states. In the chain-of-states framework, a series of structures are generated and optimized to represent the minimum energy pathway connecting two states. However, multiple pathways may exist connecting two existing states and should be identified to obtain a full view of the transitions. Therefore, we developed an enhanced sampling method, named as the direct pathway dynamics sampling (DPDS) method, to facilitate exploration of a PES for multiple pathways connecting two stable states as well as addition minima and their associated transition pathways. In the DPDS method, molecular dynamics simulations are carried out on the targeting PES within a chain-of-states framework to directly sample the transition pathway space. The simulations of DPDS could be regulated by two parameters controlling distance among states along the pathway and smoothness of the pathway. One advantage of the chain-of-states framework is that no specific reaction coordinates are necessary to generate the reaction pathway, because such information is implicitly represented by the structures along the pathway. The chain-of-states setup in a DPDS method greatly enhances the sufficient sampling in high-energy space between two end states, such as transition states. By removing the constraint on the end states of the pathway, DPDS will also sample pathways connecting minima on a PES in addition to the end points of the starting pathway. This feature makes DPDS an ideal method to directly explore transition pathway space. Three examples demonstrate the efficiency of DPDS methods in sampling the high-energy area important for reactions on the PES.

Bridging of double-stranded breaks by the nonhomologous end-joining ligation complex is modulated by DNA end chemistry.

PubMed

Reid, Dylan A; Conlin, Michael P; Yin, Yandong; Chang, Howard H; Watanabe, Go; Lieber, Michael R; Ramsden, Dale A; Rothenberg, Eli

2017-02-28

The nonhomologous end-joining (NHEJ) pathway is the primary repair pathway for DNA double strand breaks (DSBs) in humans. Repair is mediated by a core complex of NHEJ factors that includes a ligase (DNA Ligase IV; L4) that relies on juxtaposition of 3΄ hydroxyl and 5΄ phosphate termini of the strand breaks for catalysis. However, chromosome breaks arising from biological sources often have different end chemistries, and how these different end chemistries impact the way in which the core complex directs the necessary transitions from end pairing to ligation is not known. Here, using single-molecule FRET (smFRET), we show that prior to ligation, differences in end chemistry strongly modulate the bridging of broken ends by the NHEJ core complex. In particular, the 5΄ phosphate group is a recognition element for L4 and is critical for the ability of NHEJ factors to promote stable pairing of ends. Moreover, other chemical incompatibilities, including products of aborted ligation, are sufficient to disrupt end pairing. Based on these observations, we propose a mechanism for iterative repair of DSBs by NHEJ. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Yap-Hippo pathway regulates cerebral hypoxia-reoxygenation injury in neuroblastoma N2a cells via inhibiting ROCK1/F-actin/mitochondrial fission pathways.

PubMed

Geng, Chizi; Wei, Jianchao; Wu, Chengsi

2018-05-23

Yes-associated protein (Yap), a regulator of cellular apoptosis, has been demonstrated to be involved in cerebral ischemia-reperfusion (IR) injury through poorly defined mechanisms. The present study aimed to explore the role of Yap in regulating cerebral IR injury in vitro, with a focus on mitochondrial fission and ROCK1/F-actin pathways. Our data demonstrated that Yap was actually downregulated in N2a cells after cerebral hypoxia-reoxygenation (HR) injury, and that lower expression of Yap was closely associated with increased cell death. However, the reintroduction of Yap was able to suppress the HR-mediated N2a cells death via blocking the mitochondria-related apoptotic signal. At the molecular levels, Yap overexpression sustained mitochondrial potential, normalized the mitochondrial respiratory function, reduced ROS overproduction, limited HtrA2/Omi release from mitochondria into the nucleus, and suppressed pro-apoptotic proteins activation. Subsequently, functional studies have further illustrated that HR-mediated mitochondrial apoptosis was highly regulated by mitochondrial fission, whereas Yap overexpression was able to attenuate HR-mediated mitochondrial fission and, thus, promote N2a cell survival in the context of HR injury. At last, we demonstrated that Yap handled mitochondrial fission via closing ROCK1/F-actin signaling pathways. Activation of ROCK1/F-actin pathways abrogated the protective role of Yap overexpression on mitochondrial homeostasis and N2a cell survival in the setting of HR injury. Altogether, our data identified Yap as the endogenous defender to relieve HR-mediated nerve damage via antagonizing ROCK1/F-actin/mitochondrial fission pathways.

Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses.

PubMed

Chen, Haifen; Zhou, Xinrui; Zheng, Jie; Kwoh, Chee-Keong

2016-12-05

The human influenza viruses undergo rapid evolution (especially in hemagglutinin (HA), a glycoprotein on the surface of the virus), which enables the virus population to constantly evade the human immune system. Therefore, the vaccine has to be updated every year to stay effective. There is a need to characterize the evolution of influenza viruses for better selection of vaccine candidates and the prediction of pandemic strains. Studies have shown that the influenza hemagglutinin evolution is driven by the simultaneous mutations at antigenic sites. Here, we analyze simultaneous or co-occurring mutations in the HA protein of human influenza A/H3N2, A/H1N1 and B viruses to predict potential mutations, characterizing the antigenic evolution. We obtain the rules of mutation co-occurrence using association rule mining after extracting HA1 sequences and detect co-mutation sites under strong selective pressure. Then we predict the potential drifts with specific mutations of the viruses based on the rules and compare the results with the "observed" mutations in different years. The sites under frequent mutations are in antigenic regions (epitopes) or receptor binding sites. Our study demonstrates the co-occurring site mutations obtained by rule mining can capture the evolution of influenza viruses, and confirms that cooperative interactions among sites of HA1 protein drive the influenza antigenic evolution.

Identification of a Direct Biosynthetic Pathway for UDP-N-Acetylgalactosamine from Glucosamine-6-Phosphate in Thermophilic Crenarchaeon Sulfolobus tokodaii.

PubMed

Dadashipour, Mohammad; Iwamoto, Mariko; Hossain, Mohammad Murad; Akutsu, Jun-Ichi; Zhang, Zilian; Kawarabayasi, Yutaka

2018-05-15

Most organisms, from Bacteria to Eukarya , synthesize UDP- N -acetylglucosamine (UDP-GlcNAc) from fructose-6-phosphate via a four-step reaction, and UDP- N -acetylgalactosamine (UDP-GalNAc) can only be synthesized from UDP-GlcNAc by UDP-GlcNAc 4-epimerase. In Archaea , the bacterial-type UDP-GlcNAc biosynthetic pathway was reported for Methanococcales. However, the complete biosynthetic pathways for UDP-GlcNAc and UDP-GalNAc present in one archaeal species are unidentified. Previous experimental analyses on enzymatic activities of the ST0452 protein, identified from the thermophilic crenarchaeon Sulfolobus tokodaii , predicted the presence of both a bacterial-type UDP-GlcNAc and an independent UDP-GalNAc biosynthetic pathway in this archaeon. In the present work, functional analyses revealed that the recombinant ST2186 protein possessed an glutamine:fructose-6-phosphate amidotransferase activity and that the recombinant ST0242 protein possessed a phosphoglucosamine-mutase activity. Along with the acetyltransferase and uridyltransferase activities of the ST0452 protein, the activities of the ST2186 and ST0242 proteins confirmed the presence of a bacterial-type UDP-GlcNAc biosynthetic pathway in S. tokodaii In contrast, the UDP-GlcNAc 4-epimerase homologue gene was not detected within the genomic data. Thus, it was expected that galactosamine-1-phosphate or galactosamine-6-phosphate (GalN-6-P) was provided by conversion of glucosamine-1-phosphate or glucosamine-6-phosphate (GlcN-6-P). A novel epimerase converting GlcN-6-P to GalN-6-P was detected in a cell extract of S. tokodaii , and the N-terminal sequence of the purified protein indicated that the novel epimerase was encoded by the ST2245 gene. Along with the ST0242 phosphogalactosamine-mutase activity, this observation confirmed the presence of a novel UDP-GalNAc biosynthetic pathway from GlcN-6-P in S. tokodaii Discovery of the novel pathway provides a new insight into the evolution of nucleotide sugar metabolic

Pressure-volume Relationship in the Stress-echocardiography Laboratory: Does (Left Ventricular End-diastolic) Size Matter?

PubMed

Bombardini, Tonino; Mulieri, Louis A; Salvadori, Stefano; Costantino, Marco Fabio; Scali, Maria Chiara; Marzilli, Mario; Picano, Eugenio

2017-02-01

The variation between rest and peak stress end-systolic pressure-volume relation is an afterload-independent index of left ventricular contractility. Whether and to what extent it depends on end-diastolic volume remains unclear. The aim of this study was to assess the dependence of the delta rest-stress end-systolic pressure-volume relation on end-diastolic volume in patients with negative stress echo and all ranges of resting left ventricular function. We analyzed interpretable data obtained in 891 patients (593 men, age 63 ± 12 years) with ejection fraction 47% ± 12%: 338 were normal or near-normal or hypertensive; 229 patients had coronary artery disease; and 324 patients had ischemic or nonischemic dilated cardiomyopathy. They were studied with exercise (n = 172), dipyridamole (n = 482) or dobutamine (n = 237) stress echocardiography. The end-systolic pressure-volume relation was evaluated at rest and peak stress from raw measurement of systolic arterial pressure by cuff sphygmomanometer and end-systolic volume by biplane Simpson rule 2-dimensional echocardiography. Absolute values of delta rest-stress end-systolic pressure-volume relation were higher for exercise and dobutamine than for dipyridamole. In the overall population, an inverse relationship between end-systolic pressure-volume relation and end-diastolic volume was present at rest (r 2 = 0.69, P < .001) and peak stress (r 2 = 0.56, P < .001), but was absent if the delta rest-stress end-systolic pressure-volume relation was considered (r 2 = 0.13). Left ventricular end-diastolic volume does not affect the rest-stress changes in end-systolic pressure-volume relation in either normal or abnormal left ventricles during physical or pharmacological stress. Copyright © 2016 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

Collaboration pathway(s) using new tools for optimizing operational climate monitoring from space

NASA Astrophysics Data System (ADS)

Helmuth, Douglas B.; Selva, Daniel; Dwyer, Morgan M.

2014-10-01

Consistently collecting the earth's climate signatures remains a priority for world governments and international scientific organizations. Architecting a solution requires transforming scientific missions into an optimized robust `operational' constellation that addresses the needs of decision makers, scientific investigators and global users for trusted data. The application of new tools offers pathways for global architecture collaboration. Recent (2014) rulebased decision engine modeling runs that targeted optimizing the intended NPOESS architecture, becomes a surrogate for global operational climate monitoring architecture(s). This rule-based systems tools provide valuable insight for Global climate architectures, through the comparison and evaluation of alternatives considered and the exhaustive range of trade space explored. A representative optimization of Global ECV's (essential climate variables) climate monitoring architecture(s) is explored and described in some detail with thoughts on appropriate rule-based valuations. The optimization tools(s) suggest and support global collaboration pathways and hopefully elicit responses from the audience and climate science shareholders.

The dead donor rule: effect on the virtuous practice of medicine.

PubMed

Chaten, Frank C

2014-07-01

The President's Council on Bioethics in 2008 reaffirmed the necessity of the dead donor rule and the legitimacy of the current criteria for diagnosing both neurological and cardiac death. In spite of this report,many have continued to express concerns about the ethics of donation after circulatory death, the validity of determining death using neurological criteria and the necessity for maintaining the dead donor rule for organ donation. I analysed the dead donor rule for its effect on the virtuous practice of medicine by physicians caring for potential organ donors. The dead donor rule consistently impedes physicians in fulfilling their primary duty to act for the good of their prospective donor patients. This compromises the virtue of fidelity. It also weakens many other virtues necessary for physicians to provide excellent end-of-life care. The dead donor rule, while ethically powerful in theory, loses its force during translation to the bedside. This is so because the rule mandates simultaneous life and death within the same body for organ donation, a biological status that is inherently contradictory. The rule should be rejected as an ethical norm governing vital organ transplantation at the end of life. Its elimination will strengthen the doctor–patient relationship and foster trustworthiness in organ procurement.

Diversity in the protein N-glycosylation pathways within the Campylobacter genus.

PubMed

Nothaft, Harald; Scott, Nichollas E; Vinogradov, Evgeny; Liu, Xin; Hu, Rui; Beadle, Bernadette; Fodor, Christopher; Miller, William G; Li, Jianjun; Cordwell, Stuart J; Szymanski, Christine M

2012-11-01

The foodborne bacterial pathogen, Campylobacter jejuni, possesses an N-linked protein glycosylation (pgl) pathway involved in adding conserved heptasaccharides to asparagine-containing motifs of >60 proteins, and releasing the same glycan into its periplasm as free oligosaccharides. In this study, comparative genomics of all 30 fully sequenced Campylobacter taxa revealed conserved pgl gene clusters in all but one species. Structural, phylogenetic and immunological studies showed that the N-glycosylation systems can be divided into two major groups. Group I includes all thermotolerant taxa, capable of growth at the higher body temperatures of birds, and produce the C. jejuni-like glycans. Within group I, the niche-adapted C. lari subgroup contain the smallest genomes among the epsilonproteobacteria, and are unable to glucosylate their pgl pathway glycans potentially reminiscent of the glucosyltransferase regression observed in the O-glycosylation system of Neisseria species. The nonthermotolerant Campylobacters, which inhabit a variety of hosts and niches, comprise group II and produce an unexpected diversity of N-glycan structures varying in length and composition. This includes the human gut commensal, C. hominis, which produces at least four different N-glycan structures, akin to the surface carbohydrate diversity observed in the well-studied commensal, Bacteroides. Both group I and II glycans are immunogenic and cell surface exposed, making these structures attractive targets for vaccine design and diagnostics.

Advanced Glycation End Products Enhance Macrophages Polarization into M1 Phenotype through Activating RAGE/NF-κB Pathway

PubMed Central

Jin, Xian; Yao, Tongqing; Zhou, Zhong'e; Zhu, Jian; Zhang, Song; Hu, Wei; Shen, Chengxing

2015-01-01

Atherosclerotic lesions are accelerated in patients with diabetes. M1 (classically activated in contrast to M2 alternatively activated) macrophages play key roles in the progression of atherosclerosis. Since advanced glycation end products (AGEs) are major pathogenic factors and active inflammation inducers in diabetes mellitus, this study assessed the effects of AGEs on macrophage polarization. The present study showed that AGEs significantly promoted macrophages to express IL-6 and TNF-α. M1 macrophage markers such as iNOS and surface markers including CD11c and CD86 were significantly upregulated while M2 macrophage markers such as Arg1 and CD206 remained unchanged after AGEs stimulation. AGEs significantly increased RAGE expression in macrophages and activated NF-κB pathway, and the aforementioned effects were partly abolished by administration of anti-RAGE antibody or NF-κB inhibitor PDTC. In conclusion, our results suggest that AGEs enhance macrophage differentiation into proinflammatory M1 phenotype at least partly via RAGE/NF-κB pathway activation. PMID:26114112

A high-level language for rule-based modelling.

PubMed

Pedersen, Michael; Phillips, Andrew; Plotkin, Gordon D

2015-01-01

Rule-based languages such as Kappa excel in their support for handling the combinatorial complexities prevalent in many biological systems, including signalling pathways. But Kappa provides little structure for organising rules, and large models can therefore be hard to read and maintain. This paper introduces a high-level, modular extension of Kappa called LBS-κ. We demonstrate the constructs of the language through examples and three case studies: a chemotaxis switch ring, a MAPK cascade, and an insulin signalling pathway. We then provide a formal definition of LBS-κ through an abstract syntax and a translation to plain Kappa. The translation is implemented in a compiler tool which is available as a web application. We finally demonstrate how to increase the expressivity of LBS-κ through embedded scripts in a general-purpose programming language, a technique which we view as generally applicable to other domain specific languages.

A High-Level Language for Rule-Based Modelling

PubMed Central

Pedersen, Michael; Phillips, Andrew; Plotkin, Gordon D.

2015-01-01

Rule-based languages such as Kappa excel in their support for handling the combinatorial complexities prevalent in many biological systems, including signalling pathways. But Kappa provides little structure for organising rules, and large models can therefore be hard to read and maintain. This paper introduces a high-level, modular extension of Kappa called LBS-κ. We demonstrate the constructs of the language through examples and three case studies: a chemotaxis switch ring, a MAPK cascade, and an insulin signalling pathway. We then provide a formal definition of LBS-κ through an abstract syntax and a translation to plain Kappa. The translation is implemented in a compiler tool which is available as a web application. We finally demonstrate how to increase the expressivity of LBS-κ through embedded scripts in a general-purpose programming language, a technique which we view as generally applicable to other domain specific languages. PMID:26043208

Planning for compliance: OSHA's bloodborne pathogen rule.

PubMed

Bednar, B; Duke, M C

1990-11-01

Overall, the bloodborne pathogen rule constitutes a reasonable response to a significant threat to workplace safety. The risks to dialysis workers from HBV and HIV must be minimized or eliminated and the rule is generally consistent with the consensus approach. Unfortunately for dialysis providers, the rule is not exempt from the law of unintended consequences: government regulation will always have impact beyond its object. Promulgation of the final rule will immediately increase the expenses of dialysis providers. Additionally, the enormity of the HBV and HIV problem coupled with the open-ended nature of the rule's key provisions will almost certainly bring additional costs. So long as dialysis reimbursement remains flat, the unintended consequence of the bloodborne pathogen rule may be to quicken the pace of consolidation in the dialysis service market. The added burden of compliance may be too much for small independent facilities. Only large chains may have the resources to comply and survive. To forestall this effect and to provide employees with maximum protection, all dialysis providers should plan now for compliance.

Termination of String Rewriting Rules that have One Pair of Overlaps

NASA Technical Reports Server (NTRS)

Geser, Alfons; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

This paper presents a partial solution to the long standing open problem of termination of one-rule string rewriting. Overlaps between the two sides of the rule play a central role in existing termination criteria. We characterize termination of all one-rule string rewriting systems that have one such overlap at either end. This both completes a result of Kurth and generalizes a result of Shikishima-Tsuji et al.

DNA Breaks and End Resection Measured Genome-wide by End Sequencing.

PubMed

Canela, Andres; Sridharan, Sriram; Sciascia, Nicholas; Tubbs, Anthony; Meltzer, Paul; Sleckman, Barry P; Nussenzweig, André

2016-09-01

DNA double-strand breaks (DSBs) arise during physiological transcription, DNA replication, and antigen receptor diversification. Mistargeting or misprocessing of DSBs can result in pathological structural variation and mutation. Here we describe a sensitive method (END-seq) to monitor DNA end resection and DSBs genome-wide at base-pair resolution in vivo. We utilized END-seq to determine the frequency and spectrum of restriction-enzyme-, zinc-finger-nuclease-, and RAG-induced DSBs. Beyond sequence preference, chromatin features dictate the repertoire of these genome-modifying enzymes. END-seq can detect at least one DSB per cell among 10,000 cells not harboring DSBs, and we estimate that up to one out of 60 cells contains off-target RAG cleavage. In addition to site-specific cleavage, we detect DSBs distributed over extended regions during immunoglobulin class-switch recombination. Thus, END-seq provides a snapshot of DNA ends genome-wide, which can be utilized for understanding genome-editing specificities and the influence of chromatin on DSB pathway choice. Published by Elsevier Inc.

Biochemical evidence for Ku-independent backup pathways of NHEJ.

PubMed

Wang, Huichen; Perrault, Ange Ronel; Takeda, Yoshihiko; Qin, Wei; Wang, Hongyan; Iliakis, George

2003-09-15

Cells of higher eukaryotes process within minutes double strand breaks (DSBs) in their genome using a non-homologous end joining (NHEJ) apparatus that engages DNA-PKcs, Ku, DNA ligase IV, XRCC4 and other as of yet unidentified factors. Although chemical inhibition, or mutation, in any of these factors delays processing, cells ultimately remove the majority of DNA DSBs using an alternative pathway operating with an order of magnitude slower kinetics. This alternative pathway is active in mutants deficient in genes of the RAD52 epistasis group and frequently joins incorrect ends. We proposed, therefore, that it reflects an alternative form of NHEJ that operates as a backup (B-NHEJ) to the DNA-PK-dependent (D-NHEJ) pathway, rather than homology directed repair of DSBs. The present study investigates the role of Ku in the coordination of these pathways using as a model end joining of restriction endonuclease linearized plasmid DNA in whole cell extracts. Efficient, error-free, end joining observed in such in vitro reactions is strongly inhibited by anti-Ku antibodies. The inhibition requires DNA-PKcs, despite the fact that Ku efficiently binds DNA ends in the presence of antibodies, or in the absence of DNA-PKcs. Strong inhibition of DNA end joining is also mediated by wortmannin, an inhibitor of DNA-PKcs, in the presence but not in the absence of Ku, and this inhibition can be rescued by pre-incubating the reaction with double stranded oligonucleotides. The results are compatible with a role of Ku in directing end joining to a DNA-PK dependent pathway, mediated by efficient end binding and productive interactions with DNA-PKcs. On the other hand, efficient end joining is observed in extracts of cells lacking DNA-PKcs, as well as in Ku-depleted extracts in line with the operation of alternative pathways. Extracts depleted of Ku and DNA-PKcs rejoin blunt ends, as well as homologous ends with 3' or 5' protruding single strands with similar efficiency, but addition of Ku

Biochemical evidence for Ku-independent backup pathways of NHEJ

PubMed Central

Wang, Huichen; Perrault, Ange Ronel; Takeda, Yoshihiko; Qin, Wei; Wang, Hongyan; Iliakis, George

2003-01-01

Cells of higher eukaryotes process within minutes double strand breaks (DSBs) in their genome using a non-homologous end joining (NHEJ) apparatus that engages DNA-PKcs, Ku, DNA ligase IV, XRCC4 and other as of yet unidentified factors. Although chemical inhibition, or mutation, in any of these factors delays processing, cells ultimately remove the majority of DNA DSBs using an alternative pathway operating with an order of magnitude slower kinetics. This alternative pathway is active in mutants deficient in genes of the RAD52 epistasis group and frequently joins incorrect ends. We proposed, therefore, that it reflects an alternative form of NHEJ that operates as a backup (B-NHEJ) to the DNA-PK-dependent (D-NHEJ) pathway, rather than homology directed repair of DSBs. The present study investigates the role of Ku in the coordination of these pathways using as a model end joining of restriction endonuclease linearized plasmid DNA in whole cell extracts. Efficient, error-free, end joining observed in such in vitro reactions is strongly inhibited by anti-Ku antibodies. The inhibition requires DNA-PKcs, despite the fact that Ku efficiently binds DNA ends in the presence of antibodies, or in the absence of DNA-PKcs. Strong inhibition of DNA end joining is also mediated by wortmannin, an inhibitor of DNA-PKcs, in the presence but not in the absence of Ku, and this inhibition can be rescued by pre-incubating the reaction with double stranded oligonucleotides. The results are compatible with a role of Ku in directing end joining to a DNA-PK dependent pathway, mediated by efficient end binding and productive interactions with DNA-PKcs. On the other hand, efficient end joining is observed in extracts of cells lacking DNA-PKcs, as well as in Ku-depleted extracts in line with the operation of alternative pathways. Extracts depleted of Ku and DNA-PKcs rejoin blunt ends, as well as homologous ends with 3′ or 5′ protruding single strands with similar efficiency, but addition of

New force replica exchange method and protein folding pathways probed by force-clamp technique.

PubMed

Kouza, Maksim; Hu, Chin-Kun; Li, Mai Suan

2008-01-28

We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. This new approach was applied to obtain the force-temperature phase diagram and other thermodynamical quantities of the three-domain ubiquitin. Using the C(alpha)-Go model and the Langevin dynamics, we have shown that the refolding pathways of single ubiquitin depend on which terminus is fixed. If the N end is fixed then the folding pathways are different compared to the case when both termini are free, but fixing the C terminal does not change them. Surprisingly, we have found that the anchoring terminal does not affect the pathways of individual secondary structures of three-domain ubiquitin, indicating the important role of the multidomain construction. Therefore, force-clamp experiments, in which one end of a protein is kept fixed, can probe the refolding pathways of a single free-end ubiquitin if one uses either the polyubiquitin or a single domain with the C terminus anchored. However, it is shown that anchoring one end does not affect refolding pathways of the titin domain I27, and the force-clamp spectroscopy is always capable to predict folding sequencing of this protein. We have obtained the reasonable estimate for unfolding barrier of ubiquitin, using the microscopic theory for the dependence of unfolding time on the external force. The linkage between residue Lys48 and the C terminal of ubiquitin is found to have the dramatic effect on the location of the transition state along the end-to-end distance reaction coordinate, but the multidomain construction leaves the transition state almost unchanged. We have found that the maximum force in the force-extension profile from constant velocity force pulling simulations depends on temperature nonlinearly. However, for some narrow temperature interval this dependence becomes

End-of-life decisions and the reinvented Rule of Double Effect: a critical analysis.

PubMed

Lindblad, Anna; Lynöe, Niels; Juth, Niklas

2014-09-01

The Rule of Double Effect (RDE) holds that it may be permissible to harm an individual while acting for the sake of a proportionate good, given that the harm is not an intended means to the good but merely a foreseen side-effect. Although frequently used in medical ethical reasoning, the rule has been repeatedly questioned in the past few decades. However, Daniel Sulmasy, a proponent who has done a lot of work lately defending the RDE, has recently presented a reformulated and more detailed version of the rule. Thanks to its greater precision, this reinvented RDE avoids several problems thought to plague the traditional RDE. Although an improvement compared with the traditional version, we argue that Sulmasy's reinvented RDE will not stand closer scrutiny. Not only has the range of proper applicability narrowed significantly, but, more importantly, Sulmasy fails to establish that there is a morally relevant distinction between intended and foreseen effects. In particular, he fails to establish that there is any distinction that can account for the alleged moral difference between sedation therapy and euthanasia. © 2012 John Wiley & Sons Ltd.

SU-E-T-109: Development of An End-To-End Test for the Varian TrueBeamtm with a Novel Multiple-Dosimetric Modality H and N Phantom

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

Zakjevskii, V; Knill, C; Rakowski, J

2014-06-01

Purpose: To develop a comprehensive end-to-end test for Varian's TrueBeam linear accelerator for head and neck IMRT using a custom phantom designed to utilize multiple dosimetry devices. Methods: The initial end-to-end test and custom H and N phantom were designed to yield maximum information in anatomical regions significant to H and N plans with respect to: i) geometric accuracy, ii) dosimetric accuracy, and iii) treatment reproducibility. The phantom was designed in collaboration with Integrated Medical Technologies. A CT image was taken with a 1mm slice thickness. The CT was imported into Varian's Eclipse treatment planning system, where OARs and themore » PTV were contoured. A clinical template was used to create an eight field static gantry angle IMRT plan. After optimization, dose was calculated using the Analytic Anisotropic Algorithm with inhomogeneity correction. Plans were delivered with a TrueBeam equipped with a high definition MLC. Preliminary end-to-end results were measured using film and ion chambers. Ion chamber dose measurements were compared to the TPS. Films were analyzed with FilmQAPro using composite gamma index. Results: Film analysis for the initial end-to-end plan with a geometrically simple PTV showed average gamma pass rates >99% with a passing criterion of 3% / 3mm. Film analysis of a plan with a more realistic, ie. complex, PTV yielded pass rates >99% in clinically important regions containing the PTV, spinal cord and parotid glands. Ion chamber measurements were on average within 1.21% of calculated dose for both plans. Conclusion: trials have demonstrated that our end-to-end testing methods provide baseline values for the dosimetric and geometric accuracy of Varian's TrueBeam system.« less

The diversity of the N2O reducers matters for the N2O:N2 denitrification end-product ratio across an annual and a perennial cropping system.

PubMed

Domeignoz-Horta, Luiz A; Spor, Aymé; Bru, David; Breuil, Marie-Christine; Bizouard, Florian; Léonard, Joël; Philippot, Laurent

2015-01-01

Agriculture is the main source of terrestrial emissions of N2O, a potent greenhouse gas and the main cause of ozone layer depletion. The reduction of N2O into N2 by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only biological process known to eliminate this greenhouse gas. Recent studies showed that a previously unknown clade of N2O-reducers was related to the capacity of the soil to act as an N2O sink, opening the way for new strategies to mitigate emissions. Here, we investigated whether the agricultural practices could differently influence the two N2O reducer clades with consequences for denitrification end-products. The abundance of N2O-reducers and producers was quantified by real-time PCR, and the diversity of both nosZ clades was determined by 454 pyrosequencing. Potential N2O production and potential denitrification activity were used to calculate the denitrification gaseous end-product ratio. Overall, the results showed limited differences between management practices but there were significant differences between cropping systems in both the abundance and structure of the nosZII community, as well as in the [rN2O/r(N2O+N2)] ratio. More limited differences were observed in the nosZI community, suggesting that the newly identified nosZII clade is more sensitive than nosZI to environmental changes. Potential denitrification activity and potential N2O production were explained mainly by the soil properties while the diversity of the nosZII clade on its own explained 26% of the denitrification end-product ratio, which highlights the importance of understanding the ecology of this newly identified clade of N2O reducers for mitigation strategies.

A Rule-Based Modeling for the Description of Flexible and Self-healing Business Processes

NASA Astrophysics Data System (ADS)

Boukhebouze, Mohamed; Amghar, Youssef; Benharkat, Aïcha-Nabila; Maamar, Zakaria

In this paper we discuss the importance of ensuring that business processes are label robust and agile at the same time robust and agile. To this end, we consider reviewing the way business processes are managed. For instance we consider offering a flexible way to model processes so that changes in regulations are handled through some self-healing mechanisms. These changes may raise exceptions at run-time if not properly reflected on these processes. To this end we propose a new rule based model that adopts the ECA rules and is built upon formal tools. The business logic of a process can be summarized with a set of rules that implement an organization’s policies. Each business rule is formalized using our ECAPE formalism (Event-Condition-Action-Post condition- post Event). This formalism allows translating a process into a graph of rules that is analyzed in terms of reliably and flexibility.

Proteomics and pathway analysis of N-glycosylated mammary gland proteins in response to Escherichia coli mastitis in cattle.

PubMed

Yang, Yongxin; Shen, Weijun; Zhao, Xiaowei; Zhao, Huiling; Huang, Dongwei; Cheng, Guanglong

2014-06-01

The aim of this study was to investigate the N-linked glycosylated protein profile of mammary tissue from healthy cows and cows with mastitis due to Escherichia coli, in order to understand the molecular mechanisms of the host response to mastitis. N-glycopeptides were enriched with a lectin mixture and identified through high-accuracy mass spectrometry. A total of 551 N-glycosylation sites, corresponding to 294 proteins, were identified in the mammary tissues of healthy cows; these glycoproteins were categorised into three functional groups and clustered into 11 specific pathways. A total of 511 N-glycosylation sites, corresponding to 283 glycosylated proteins, were detected in the mammary tissues of cows with E. coli mastitis. There were differences in N-glycosylation sites in 98 proteins in the mammary tissues of healthy cows and cows with mastitis due to E. coli. Most proteins with altered glycosylation were those involved in responses to stress, cell adhesion and the immune response, and were assigned to five specific pathways based on their gene ontology annotation. The results from this study show that the glycosylated protein profile in the mammary tissues of healthy and mastitic cows are different, and altered glycoproteins are associated with several pathways, including the lysosome and O-glycan biosynthesis pathways. Copyright © 2014. Published by Elsevier Ltd.

A radical pathway in catecholase activity with nickel(II) complexes of phenol based "end-off" compartmental ligands.

PubMed

Ghosh, Totan; Adhikary, Jaydeep; Chakraborty, Prateeti; Sukul, Pradip K; Jana, Mahendra Sekhar; Mondal, Tapan Kumar; Zangrando, Ennio; Das, Debasis

2014-01-14

Seven dinuclear and one dinuclear based dicyanamide bridged polymeric Ni(II) complexes of phenol based compartmental ligands (HL(1)-HL(4)) have been synthesized with the aim to investigate their catecholase-like activity and to evaluate the most probable mechanistic pathway involved in this process. The complexes have been characterized by routine physicochemical studies as well as by X-ray single crystal structure analyses namely [Ni2(L(2))(SCN)3(H2O)(CH3OH)] (), [Ni2(L(4))(SCN)3(CH3OH)2] (), [Ni2(L(2))(SCN)2(AcO)(H2O)] (), [Ni2(L(4))(SCN)(AcO)2] (), [Ni2(L(2))(N3)3(H2O)2] (), [Ni2(L(4))(N3)3(H2O)2] (), [Ni2(L(1))(AcO)2(N(CN)2)]n () and [Ni2(L(3))(AcO)2(N(CN)2)] (), [SCN = isothiocyanate, AcO = acetate, N3 = azide, and N(CN)2 = dicyanamide anion; L(1-4) = 2,6-bis(R2-iminomethyl)-4-R1-phenolato, where R1 = methyl and tert-butyl, R2 = N,N-dimethyl ethylene for L(1-2) and R1 = methyl and tert-butyl, R2 = 2-(N-ethyl) pyridine for L(3-4)]. A UV-vis spectrophotometric study using 3,5-di-tert butylcatechol (3,5-DTBC) reveals that all the complexes are highly active in catalyzing the aerobic oxidation of (3,5-DTBC) to 3,5-di-tert-butylbenzoquinone (3,5-DTBQ) in methanol medium with the formation of hydrogen peroxide. An EPR study confirms the generation of radicals during the catalysis. Cyclic voltammetric studies of the complexes in the presence and absence of 3,5-DTBC have been performed. Reduction of Ni(II) to Ni(I) and that of the imine bond of the ligand system have been detected at ∼-1.0 V and ∼-1.5 V, respectively. Coulometric separation of the species at -1.5 V followed by the EPR study at 77 K confirms the species as an organic radical and thus most probably reduced imine species. Spectroelectrochemical analysis at -1.5 V clearly indicates the oxidation of 3,5-DTBC and thus suggests that the radical pathway is supposed to be responsible for the catecholase-like activity exhibited by the nickel complexes. The ligand centred radical generation has further been

Wrapping rules (in) string theory

NASA Astrophysics Data System (ADS)

Bergshoeff, Eric A.; Riccioni, Fabio

2018-01-01

In this paper we show that the number of all 1/2-BPS branes in string theory compactified on a torus can be derived by universal wrapping rules whose formulation we present. These rules even apply to branes in less than ten dimensions whose ten-dimensional origin is an exotic brane. In that case the wrapping rules contain an additional combinatorial factor that is related to the highest dimension in which the ten-dimensional exotic brane, after compactification, can be realized as a standard brane. We show that the wrapping rules also apply to cases with less supersymmetry. As a specific example, we discuss the compactification of IIA/IIB string theory on ( T 4/ ℤ 2) × T n .

Vertical segregation among pathways mediating nitrogen loss (N2 and N2O production) across the oxygen gradient in a coastal upwelling ecosystem

NASA Astrophysics Data System (ADS)

Galán, Alexander; Thamdrup, Bo; Saldías, Gonzalo S.; Farías, Laura

2017-10-01

The upwelling system off central Chile (36.5° S) is seasonally subjected to oxygen (O2)-deficient waters, with a strong vertical gradient in O2 (from oxic to anoxic conditions) that spans a few metres (30-50 m interval) over the shelf. This condition inhibits and/or stimulates processes involved in nitrogen (N) removal (e.g. anammox, denitrification, and nitrification). During austral spring (September 2013) and summer (January 2014), the main pathways involved in N loss and its speciation, in the form of N2 and/or N2O, were studied using 15N-tracer incubations, inhibitor assays, and the natural abundance of nitrate isotopes along with hydrographic information. Incubations were developed using water retrieved from the oxycline (25 m depth) and bottom waters (85 m depth) over the continental shelf off Concepción, Chile. Results of 15N-labelled incubations revealed higher N removal activity during the austral summer, with denitrification as the dominant N2-producing pathway, which occurred together with anammox at all times. Interestingly, in both spring and summer maximum potential N removal rates were observed in the oxycline, where a greater availability of oxygen was observed (maximum O2 fluctuation between 270 and 40 µmol L-1) relative to the hypoxic bottom waters ( < 20 µmol O2 L-1). Different pathways were responsible for N2O produced in the oxycline and bottom waters, with ammonium oxidation and dissimilatory nitrite reduction, respectively, as the main source processes. Ammonium produced by dissimilatory nitrite reduction to ammonium (DNiRA) could sustain both anammox and nitrification rates, including the ammonium utilized for N2O production. The temporal and vertical variability of δ15N-NO3- confirms that multiple N-cycling processes are modulating the isotopic nitrate composition over the shelf off central Chile during spring and summer. N removal processes in this coastal system appear to be related to the availability and distribution of oxygen and

Alcohol Selectivity in a Synthetic Thermophilic n-Butanol Pathway Is Driven by Biocatalytic and Thermostability Characteristics of Constituent Enzymes

PubMed Central

Loder, Andrew J.; Zeldes, Benjamin M.; Garrison, G. Dale; Lipscomb, Gina L.; Adams, Michael W. W.

2015-01-01

n-Butanol is generated as a natural product of metabolism by several microorganisms, but almost all grow at mesophilic temperatures. A synthetic pathway for n-butanol production from acetyl coenzyme A (acetyl-CoA) that functioned at 70°C was assembled in vitro from enzymes recruited from thermophilic bacteria to inform efforts for engineering butanol production into thermophilic hosts. Recombinant versions of eight thermophilic enzymes (β-ketothiolase [Thl], 3-hydroxybutyryl-CoA dehydrogenase [Hbd], and 3-hydroxybutyryl-CoA dehydratase [Crt] from Caldanaerobacter subterraneus subsp. tengcongensis; trans-2-enoyl-CoA reductase [Ter] from Spirochaeta thermophila; bifunctional acetaldehyde dehydrogenase/alcohol dehydrogenase [AdhE] from Clostridium thermocellum; and AdhE, aldehyde dehydrogenase [Bad], and butanol dehydrogenase [Bdh] from Thermoanaerobacter sp. strain X514) were utilized to examine three possible pathways for n-butanol. These pathways differed in the two steps required to convert butyryl-CoA to n-butanol: Thl-Hbd-Crt-Ter-AdhE (C. thermocellum), Thl-Hbd-Crt-Ter-AdhE (Thermoanaerobacter X514), and Thl-Hbd-Crt-Ter-Bad-Bdh. n-Butanol was produced at 70°C, but with different amounts of ethanol as a coproduct, because of the broad substrate specificities of AdhE, Bad, and Bdh. A reaction kinetics model, validated via comparison to in vitro experiments, was used to determine relative enzyme ratios needed to maximize n-butanol production. By using large relative amounts of Thl and Hbd and small amounts of Bad and Bdh, >70% conversion to n-butanol was observed in vitro, but with a 60% decrease in the predicted pathway flux. With more-selective hypothetical versions of Bad and Bdh, >70% conversion to n-butanol is predicted, with a 19% increase in pathway flux. Thus, more-selective thermophilic versions of Bad, Bdh, and AdhE are needed to fully exploit biocatalytic n-butanol production at elevated temperatures. PMID:26253677

Playing by the Rules: Instruction and Acculturation in Role-Playing Games

ERIC Educational Resources Information Center

Neuenschwander, Bryn

2008-01-01

The open-ended, informal, and socially negotiated nature of role-playing games creates a distinct learning challenge for newcomers to the hobby. The explicit rules of the game provide only an incomplete framework for structuring the actions of players, and the expectations and mores of a given group will add other, unspoken rules that discourage…

REVERSALS OF GNEVYSHEV-OHL RULE

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

Tlatov, Andrey G., E-mail: tlatov@mail.ru

2013-08-01

We perform an analysis of the number of sunspot groups in activity cycles from 1610 through the present. Here we use the G{sub n} index, which is defined as the average daily number of sunspot groups in cycle n. There is a high positive correlation between the parameter G{sub n} in the current cycle and an analogous parameter in the following cycle G{sub n{sub +1}} both for pairs of even-odd cycles and odd-even activity cycles. In cycle Nos. 10-21 for pairs of even-odd cycles, the ratio of parameter G{sub n} corresponds to the GO rule G{sub n{sub +1}{sup odd}}/G{sub n}{supmore » even}>1. However, during the period {approx}1745-1850, odd cycles were less than the preceding even cycles G{sub n{sub +1}{sup odd}}/G{sub n}{sup even}<1. The ratio of the parameter G{sub n{sub +1}{sup odd}}/G{sub n}{sup even} has a long-term variation within the range 0.5-1.5 with a period of about 21 activity cycles, and it proves the reversal of the GO rule.« less

Medicare program; standards for quality of water used in dialysis and revised guidelines on reuse of hemodialysis filters for end-stage renal disease (ESRD) patients--HCFA. Final rule.

PubMed

1995-09-18

This final rule revises the Medicare conditions for coverage of suppliers of end-stage renal disease services. The revisions remove general language in the regulations regarding water quality; incorporate by reference standards for monitoring the quality of water used in dialysis as published by the Association for the Advancement of Medical Instrumentation (AAMI) in its document, "Hemodialysis Systems" (second edition); and update existing regulations to incorporate by reference the second edition of AAMI's voluntary guidelines on "Reuse of Hemodialyzers."

Update of ESA EEE parts relifing rules

NASA Astrophysics Data System (ADS)

Le Blanc, P.; Aicardi, C.

2002-12-01

Storage of EEE part represents a key process in space electronics activity. In order to cope with projects time schedule on one hand and with economical procurement constraints on the other hand, parts are often to be stored for quite a long time. Obsolescence issues could make us to build strategic stock in order to be able to still manufacture equipments over time. Up to now several documents ruled the way to de-store (relifed) EEE part in such a way we are able to guaranty their reliability despite their long period of storage. None of these documents backed up their figures and rules with consistent approach and physics. No field return existed or was used to assess these rules. In the frame of a contract from CNES we established an updated rule taking into account field-return and failure mechanisms analysis .We ended up by a new storage and de-storage procedure that is to be included in the ECSS format.

Food-advanced glycation end products aggravate the diabetic vascular complications via modulating the AGEs/RAGE pathway.

PubMed

Lv, Xing; Lv, Gao-Hong; Dai, Guo-Ying; Sun, Hong-Mei; Xu, Hui-Qin

2016-11-01

The aim of this study was to investigate the effects of high-advanced glycation end products (AGEs) diet on diabetic vascular complications. The Streptozocin (STZ)-induced diabetic mice were fed with high-AGEs diet. Diabetic characteristics, indicators of renal and cardiovascular functions, and pathohistology of pancreas, heart and renal were evaluated. AGEs/RAGE/ROS pathway parameters were determined. During the experiments, the diabetic mice exhibited typical characteristics including weight loss, polydipsia, polyphagia, polyuria, high-blood glucose, and low-serum insulin levels. However, high-AGEs diet effectively aggravated these diabetic characteristics. It also increased the 24-h urine protein levels, serum levels of urea nitrogen, creatinine, c-reactive protein (CRP), low density lipoprotein (LDL), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) in the diabetic mice. High-AGEs diet deteriorated the histology of pancreas, heart, and kidneys, and caused structural alterations of endothelial cells, mesangial cells and podocytes in renal cortex. Eventually, high-AGEs diet contributed to the high-AGE levels in serum and kidneys, high-levels of reactive oxygen species (ROS) and low-levels of superoxide dismutase (SOD) in serum, heart, and kidneys. It also upregulated RAGE mRNA and protein expression in heart and kidneys. Our results showed that high-AGEs diet deteriorated vascular complications in the diabetic mice. The activation of AGEs/RAGE/ROS pathway may be involved in the pathogenesis of vascular complications in diabetes. Copyright © 2016 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

Kirchhoff's rule for quantum wires

NASA Astrophysics Data System (ADS)

Kostrykin, V.; Schrader, R.

1999-01-01

We formulate and discuss one-particle quantum scattering theory on an arbitrary finite graph with n open ends and where we define the Hamiltonian to be (minus) the Laplace operator with general boundary conditions at the vertices. This results in a scattering theory with n channels. The corresponding on-shell S-matrix formed by the reflection and transmission amplitudes for incoming plane waves of energy E>0 is given explicitly in terms of the boundary conditions and the lengths of the internal lines. It is shown to be unitary, which may be viewed as the quantum version of Kirchhoff's law. We exhibit covariance and symmetry properties. It is symmetric if the boundary conditions are real. Also there is a duality transformation on the set of boundary conditions and the lengths of the internal lines such that the low-energy behaviour of one theory gives the high-energy behaviour of the transformed theory. Finally, we provide a composition rule by which the on-shell S-matrix of a graph is factorizable in terms of the S-matrices of its subgraphs. All proofs use only known facts from the theory of self-adjoint extensions, standard linear algebra, complex function theory and elementary arguments from the theory of Hermitian symplectic forms.

Modeling Non-homologous End Joining

NASA Technical Reports Server (NTRS)

Li, Yongfeng

2013-01-01

Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several NHEJ proteins such as Ku, DNA-PKcs, XRCC4, Ligase IV and so on. Once DSBs are generated, Ku is first recruited to the DNA end, followed by other NHEJ proteins for DNA end processing and ligation. Because of the direct ligation of break ends without the need for a homologous template, NHEJ turns out to be an error-prone but efficient repair pathway. Some mechanisms have been proposed of how the efficiency of NHEJ repair is affected. The type of DNA damage is an important factor of NHEJ repair. For instance, the length of DNA fragment may determine the recruitment efficiency of NHEJ protein such as Ku [1], or the complexity of the DNA breaks [2] is accounted for the choice of NHEJ proteins and subpathway of NHEJ repair. On the other hand, the chromatin structure also plays a role of the accessibility of NHEJ protein to the DNA damage site. In this talk, some mathematical models of NHEJ, that consist of series of biochemical reactions complying with the laws of chemical reaction (e.g. mass action, etc.), will be introduced. By mathematical and numerical analysis and parameter estimation, the models are able to capture the qualitative biological features and show good agreement with experimental data. As conclusions, from the viewpoint of modeling, how the NHEJ proteins are recruited will be first discussed for connection between the classical sequential model [4] and recently proposed two-phase model [5]. Then how the NHEJ repair pathway is affected, by the length of DNA fragment [6], the complexity of DNA damage [7] and the chromatin structure [8], will be addressed

N Reasons Why Production-Rules are Insufficient Models for Expert System Knowledge Representation Schemes

DTIC Science & Technology

1991-02-01

3 2.2 Hybrid Rule/Fact Schemas .............................................................. 3 3 THE LIMITATIONS OF RULE BASED KNOWLEDGE...or hybrid rule/fact schemas. 2 UNCLASSIFIED .WA UNCLASSIFIED ERL-0520-RR 2.1 Propositional Logic The simplest form of production-rules are based upon...requirements which may lead to poor system performance. 2.2 Hybrid Rule/Fact Schemas Hybrid rule/fact relationships (also known as Predicate Calculus ) have

Nanocrystalline Si pathway induced unipolar resistive switching behavior from annealed Si-rich SiN{sub x}/SiN{sub y} multilayers

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

Jiang, Xiaofan; Ma, Zhongyuan, E-mail: zyma@nju.edu.cn; Yang, Huafeng

2014-09-28

Adding a resistive switching functionality to a silicon microelectronic chip is a new challenge in materials research. Here, we demonstrate that unipolar and electrode-independent resistive switching effects can be realized in the annealed Si-rich SiN{sub x}/SiN{sub y} multilayers with high on/off ratio of 10{sup 9}. High resolution transmission electron microscopy reveals that for the high resistance state broken pathways composed of discrete nanocrystalline silicon (nc-Si) exist in the Si nitride multilayers. While for the low resistance state the discrete nc-Si regions is connected, forming continuous nc-Si pathways. Based on the analysis of the temperature dependent I-V characteristics and HRTEM photos,more » we found that the break-and-bridge evolution of nc-Si pathway is the origin of resistive switching memory behavior. Our findings provide insights into the mechanism of the resistive switching behavior in nc-Si films, opening a way for it to be utilized as a material in Si-based memories.« less

N-terminal acetylation -an Essential Protein Modification Emerges as an Important Regulator of Stress Responses.

PubMed

Linster, Eric; Wirtz, Markus

2018-06-26

N-terminal acetylation (NTA) is a prevalent protein modification in eukaryotes. The majority of proteins is acetylated at their N-terminus in a co-translational manner by ribosome-associated N-terminal acetyltransferases (NAT). However, the recent discovery of Golgi-membrane localized NATs in metazoan, and plastid-localized NATs in plants challenged the dogma of static, co-translational imprinting of the proteome by NTA. Indeed, NTA by the cytosolic NatA is highly dynamic and under hormonal control in plants. Such active control has not been evidenced yet in other eukaryotes and might be an adaptation to the sessile lifestyle of plants forcing them to cope with diverse environmental challenges. The function of NTA for individual proteins is distinct and yet unpredictable. In yeast and humans, NTA has been shown to affect protein-protein interactions, subcellular localization, folding, aggregation, or degradation of a handful of proteins. In particular, the impact of NTA on the protein-turnover is documented by diverse examples in yeast. Consequently, NTA has recently dicovered to be a degradation signal in a distinct branch of the N-end rule pathway ubiquitin-mediated proteolysis. In this review, we summarize the current knowledge on the NAT machinery in higher plants and discuss the potential function of NTA during biotic and abiotic stresses.

12 CFR 226.32 - Requirements for certain closed-end home mortgages.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 12 Banks and Banking 3 2014-01-01 2014-01-01 false Requirements for certain closed-end home... THE FEDERAL RESERVE SYSTEM (CONTINUED) TRUTH IN LENDING (REGULATION Z) Special Rules for Certain Home Mortgage Transactions § 226.32 Requirements for certain closed-end home mortgages. (a) Coverage. (1) Except...

Evolving fuzzy rules for relaxed-criteria negotiation.

PubMed

Sim, Kwang Mong

2008-12-01

In the literature on automated negotiation, very few negotiation agents are designed with the flexibility to slightly relax their negotiation criteria to reach a consensus more rapidly and with more certainty. Furthermore, these relaxed-criteria negotiation agents were not equipped with the ability to enhance their performance by learning and evolving their relaxed-criteria negotiation rules. The impetus of this work is designing market-driven negotiation agents (MDAs) that not only have the flexibility of relaxing bargaining criteria using fuzzy rules, but can also evolve their structures by learning new relaxed-criteria fuzzy rules to improve their negotiation outcomes as they participate in negotiations in more e-markets. To this end, an evolutionary algorithm for adapting and evolving relaxed-criteria fuzzy rules was developed. Implementing the idea in a testbed, two kinds of experiments for evaluating and comparing EvEMDAs (MDAs with relaxed-criteria rules that are evolved using the evolutionary algorithm) and EMDAs (MDAs with relaxed-criteria rules that are manually constructed) were carried out through stochastic simulations. Empirical results show that: 1) EvEMDAs generally outperformed EMDAs in different types of e-markets and 2) the negotiation outcomes of EvEMDAs generally improved as they negotiated in more e-markets.

Phosphatase Complex Pph3/Psy2 Is Involved in Regulation of Efficient Non-Homologous End-Joining Pathway in the Yeast Saccharomyces cerevisiae

PubMed Central

Omidi, Katayoun; Hooshyar, Mohsen; Jessulat, Matthew; Samanfar, Bahram; Sanders, Megan; Burnside, Daniel; Pitre, Sylvain; Schoenrock, Andrew; Xu, Jianhua; Babu, Mohan; Golshani, Ashkan

2014-01-01

One of the main mechanisms for double stranded DNA break (DSB) repair is through the non-homologous end-joining (NHEJ) pathway. Using plasmid and chromosomal repair assays, we showed that deletion mutant strains for interacting proteins Pph3p and Psy2p had reduced efficiencies in NHEJ. We further observed that this activity of Pph3p and Psy2p appeared linked to cell cycle Rad53p and Chk1p checkpoint proteins. Pph3/Psy2 is a phosphatase complex, which regulates recovery from the Rad53p DNA damage checkpoint. Overexpression of Chk1p checkpoint protein in a parallel pathway to Rad53p compensated for the deletion of PPH3 or PSY2 in a chromosomal repair assay. Double mutant strains Δpph3/Δchk1 and Δpsy2/Δchk1 showed additional reductions in the efficiency of plasmid repair, compared to both single deletions which is in agreement with the activity of Pph3p and Psy2p in a parallel pathway to Chk1p. Genetic interaction analyses also supported a role for Pph3p and Psy2p in DNA damage repair, the NHEJ pathway, as well as cell cycle progression. Collectively, we report that the activity of Pph3p and Psy2p further connects NHEJ repair to cell cycle progression. PMID:24498054

Phosphatase complex Pph3/Psy2 is involved in regulation of efficient non-homologous end-joining pathway in the yeast Saccharomyces cerevisiae.

PubMed

Omidi, Katayoun; Hooshyar, Mohsen; Jessulat, Matthew; Samanfar, Bahram; Sanders, Megan; Burnside, Daniel; Pitre, Sylvain; Schoenrock, Andrew; Xu, Jianhua; Babu, Mohan; Golshani, Ashkan

2014-01-01

One of the main mechanisms for double stranded DNA break (DSB) repair is through the non-homologous end-joining (NHEJ) pathway. Using plasmid and chromosomal repair assays, we showed that deletion mutant strains for interacting proteins Pph3p and Psy2p had reduced efficiencies in NHEJ. We further observed that this activity of Pph3p and Psy2p appeared linked to cell cycle Rad53p and Chk1p checkpoint proteins. Pph3/Psy2 is a phosphatase complex, which regulates recovery from the Rad53p DNA damage checkpoint. Overexpression of Chk1p checkpoint protein in a parallel pathway to Rad53p compensated for the deletion of PPH3 or PSY2 in a chromosomal repair assay. Double mutant strains Δpph3/Δchk1 and Δpsy2/Δchk1 showed additional reductions in the efficiency of plasmid repair, compared to both single deletions which is in agreement with the activity of Pph3p and Psy2p in a parallel pathway to Chk1p. Genetic interaction analyses also supported a role for Pph3p and Psy2p in DNA damage repair, the NHEJ pathway, as well as cell cycle progression. Collectively, we report that the activity of Pph3p and Psy2p further connects NHEJ repair to cell cycle progression.

Facet-dependent solar ammonia synthesis of BiOCl nanosheets via a proton-assisted electron transfer pathway

NASA Astrophysics Data System (ADS)

Li, Hao; Shang, Jian; Shi, Jingu; Zhao, Kun; Zhang, Lizhi

2016-01-01

Under the pressure of a fossil fuels shortage and global climate change, solar ammonia synthesis and the need to develop N2 fixation under mild conditions is becoming more urgent need; however, their intrinsic mechanisms still remain unclear. Herein, we demonstrate that the kinetic inertia of N2 can be overcome using oxygen vacancies (OVs) of BiOCl as the catalytic centers to create lower energy molecular steps, which are amendable for the solar light driven N-N triple bond cleavage via a proton-assisted electron transfer pathway. Moreover, the distinct structures of OVs on different BiOCl facets strongly determine the N2 fixation pathways by influencing both the adsorption structure and the activation level of N2. The fixation of terminal end-on bound N2 on the OVs of BiOCl {001} facets follows an asymmetric distal mode by selectively generating NH3, while the reduction of side-on bridging N2 on the OVs of BiOCl {010} facets is more energetically favorable in a symmetric alternating mode to produce N2H4 as the main intermediate.Under the pressure of a fossil fuels shortage and global climate change, solar ammonia synthesis and the need to develop N2 fixation under mild conditions is becoming more urgent need; however, their intrinsic mechanisms still remain unclear. Herein, we demonstrate that the kinetic inertia of N2 can be overcome using oxygen vacancies (OVs) of BiOCl as the catalytic centers to create lower energy molecular steps, which are amendable for the solar light driven N-N triple bond cleavage via a proton-assisted electron transfer pathway. Moreover, the distinct structures of OVs on different BiOCl facets strongly determine the N2 fixation pathways by influencing both the adsorption structure and the activation level of N2. The fixation of terminal end-on bound N2 on the OVs of BiOCl {001} facets follows an asymmetric distal mode by selectively generating NH3, while the reduction of side-on bridging N2 on the OVs of BiOCl {010} facets is more

43 CFR 4.801 - Suspension of rules.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Review Under Part 17 of This Title-Nondiscrimination in Federally Assisted Programs of the Department of... rules. Upon notice to all parties, the responsible Department official or the administrative law judge... determination that no party will be unduly prejudiced and the ends of justice will thereby be served. ...

46 CFR 402.320 - Working rules.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Vincent, N.Y., dated May 1, 1980, amended to March 24, 1999. (2) The Working Rules and Dispatch Procedures... March 30, 1999. (4) The Working Rules for District No. 3, adopted by the Western Great Lakes Pilots Association, LLP, Superior, WI., dated February 24, 2001 amended to February 28, 2007. (b) [Reserved] [USCG...

Differential Modifications of Synaptic Weights During Odor Rule Learning: Dynamics of Interaction Between the Piriform Cortex with Lower and Higher Brain Areas

PubMed Central

Cohen, Yaniv; Wilson, Donald A.; Barkai, Edi

2015-01-01

Learning of a complex olfactory discrimination (OD) task results in acquisition of rule learning after prolonged training. Previously, we demonstrated enhanced synaptic connectivity between the piriform cortex (PC) and its ascending and descending inputs from the olfactory bulb (OB) and orbitofrontal cortex (OFC) following OD rule learning. Here, using recordings of evoked field postsynaptic potentials in behaving animals, we examined the dynamics by which these synaptic pathways are modified during rule acquisition. We show profound differences in synaptic connectivity modulation between the 2 input sources. During rule acquisition, the ascending synaptic connectivity from the OB to the anterior and posterior PC is simultaneously enhanced. Furthermore, post-training stimulation of the OB enhanced learning rate dramatically. In sharp contrast, the synaptic input in the descending pathway from the OFC was significantly reduced until training completion. Once rule learning was established, the strength of synaptic connectivity in the 2 pathways resumed its pretraining values. We suggest that acquisition of olfactory rule learning requires a transient enhancement of ascending inputs to the PC, synchronized with a parallel decrease in the descending inputs. This combined short-lived modulation enables the PC network to reorganize in a manner that enables it to first acquire and then maintain the rule. PMID:23960200

ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis.

PubMed

Mallik, Saurav; Zhao, Zhongming

2017-12-28

For transcriptomic analysis, there are numerous microarray-based genomic data, especially those generated for cancer research. The typical analysis measures the difference between a cancer sample-group and a matched control group for each transcript or gene. Association rule mining is used to discover interesting item sets through rule-based methodology. Thus, it has advantages to find causal effect relationships between the transcripts. In this work, we introduce two new rule-based similarity measures-weighted rank-based Jaccard and Cosine measures-and then propose a novel computational framework to detect condensed gene co-expression modules ( C o n G E M s) through the association rule-based learning system and the weighted similarity scores. In practice, the list of evolved condensed markers that consists of both singular and complex markers in nature depends on the corresponding condensed gene sets in either antecedent or consequent of the rules of the resultant modules. In our evaluation, these markers could be supported by literature evidence, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway and Gene Ontology annotations. Specifically, we preliminarily identified differentially expressed genes using an empirical Bayes test. A recently developed algorithm-RANWAR-was then utilized to determine the association rules from these genes. Based on that, we computed the integrated similarity scores of these rule-based similarity measures between each rule-pair, and the resultant scores were used for clustering to identify the co-expressed rule-modules. We applied our method to a gene expression dataset for lung squamous cell carcinoma and a genome methylation dataset for uterine cervical carcinogenesis. Our proposed module discovery method produced better results than the traditional gene-module discovery measures. In summary, our proposed rule-based method is useful for exploring biomarker modules from transcriptomic data.

12 CFR 1026.32 - Requirements for certain closed-end home mortgages.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 12 Banks and Banking 8 2013-01-01 2013-01-01 false Requirements for certain closed-end home... LENDING (REGULATION Z) Special Rules for Certain Home Mortgage Transactions § 1026.32 Requirements for certain closed-end home mortgages. (a) Coverage. (1) Except as provided in paragraph (a)(2) of this...

12 CFR 226.32 - Requirements for certain closed-end home mortgages.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Requirements for certain closed-end home... THE FEDERAL RESERVE SYSTEM TRUTH IN LENDING (REGULATION Z) Special Rules for Certain Home Mortgage Transactions § 226.32 Requirements for certain closed-end home mortgages. (a) Coverage. (1) Except as provided...

12 CFR 226.32 - Requirements for certain closed-end home mortgages.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 12 Banks and Banking 3 2012-01-01 2012-01-01 false Requirements for certain closed-end home... THE FEDERAL RESERVE SYSTEM TRUTH IN LENDING (REGULATION Z) Special Rules for Certain Home Mortgage Transactions § 226.32 Requirements for certain closed-end home mortgages. (a) Coverage. (1) Except as provided...

12 CFR 1026.32 - Requirements for certain closed-end home mortgages.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 12 Banks and Banking 8 2012-01-01 2012-01-01 false Requirements for certain closed-end home... LENDING (REGULATION Z) Special Rules for Certain Home Mortgage Transactions § 1026.32 Requirements for certain closed-end home mortgages. (a) Coverage. (1) Except as provided in paragraph (a)(2) of this...

Identification of a novel amyloid precursor protein processing pathway that generates secreted N-terminal fragments.

PubMed

Vella, Laura J; Cappai, Roberto

2012-07-01

Alzheimer's disease (AD) is a neurodegenerative disorder of the central nervous system. The proteolytic processing of the amyloid precursor protein (APP) into the β-amyloid (Aβ) peptide is a central event in AD. While the pathway that generates Aβ is well described, many questions remain concerning general APP metabolism and its metabolites. It is becoming clear that the amino-terminal region of APP can be processed to release small N-terminal fragments (NTFs). The purpose of this study was to investigate the occurrence and generation of APP NTFs in vivo and in cell culture (SH-SY5Y) in order to delineate the cellular pathways implicated in their generation. We were able to detect 17- to 28-kDa APP NTFs in human and mouse brain tissue that are distinct from N-APP fragments previously reported. We show that the 17- to 28-kDa APP NTFs were highly expressed in mice from the age of 2 wk to adulthood. SH-SY5Y studies indicate the generation of APP NTFs involves a novel APP processing pathway, regulated by protein kinase C, but independent of α-secretase or β-secretase 1 (BACE) activity. These results identify a novel, developmentally regulated APP processing pathway that may play an important role in the physiological function of APP.

Alcohol Selectivity in a Synthetic Thermophilic n-Butanol Pathway Is Driven by Biocatalytic and Thermostability Characteristics of Constituent Enzymes.

PubMed

Loder, Andrew J; Zeldes, Benjamin M; Garrison, G Dale; Lipscomb, Gina L; Adams, Michael W W; Kelly, Robert M

2015-10-01

n-Butanol is generated as a natural product of metabolism by several microorganisms, but almost all grow at mesophilic temperatures. A synthetic pathway for n-butanol production from acetyl coenzyme A (acetyl-CoA) that functioned at 70°C was assembled in vitro from enzymes recruited from thermophilic bacteria to inform efforts for engineering butanol production into thermophilic hosts. Recombinant versions of eight thermophilic enzymes (β-ketothiolase [Thl], 3-hydroxybutyryl-CoA dehydrogenase [Hbd], and 3-hydroxybutyryl-CoA dehydratase [Crt] from Caldanaerobacter subterraneus subsp. tengcongensis; trans-2-enoyl-CoA reductase [Ter] from Spirochaeta thermophila; bifunctional acetaldehyde dehydrogenase/alcohol dehydrogenase [AdhE] from Clostridium thermocellum; and AdhE, aldehyde dehydrogenase [Bad], and butanol dehydrogenase [Bdh] from Thermoanaerobacter sp. strain X514) were utilized to examine three possible pathways for n-butanol. These pathways differed in the two steps required to convert butyryl-CoA to n-butanol: Thl-Hbd-Crt-Ter-AdhE (C. thermocellum), Thl-Hbd-Crt-Ter-AdhE (Thermoanaerobacter X514), and Thl-Hbd-Crt-Ter-Bad-Bdh. n-Butanol was produced at 70°C, but with different amounts of ethanol as a coproduct, because of the broad substrate specificities of AdhE, Bad, and Bdh. A reaction kinetics model, validated via comparison to in vitro experiments, was used to determine relative enzyme ratios needed to maximize n-butanol production. By using large relative amounts of Thl and Hbd and small amounts of Bad and Bdh, >70% conversion to n-butanol was observed in vitro, but with a 60% decrease in the predicted pathway flux. With more-selective hypothetical versions of Bad and Bdh, >70% conversion to n-butanol is predicted, with a 19% increase in pathway flux. Thus, more-selective thermophilic versions of Bad, Bdh, and AdhE are needed to fully exploit biocatalytic n-butanol production at elevated temperatures. Copyright © 2015, American Society for

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations.

PubMed

Sun, Huiyong; Tian, Sheng; Zhou, Shunye; Li, Youyong; Li, Dan; Xu, Lei; Shen, Mingyun; Pan, Peichen; Hou, Tingjun

2015-02-13

How does a type II inhibitor bind to/unbind from a kinase target is still a confusing question because the small molecule occupies both the ATP pocket and the allosteric pocket of the kinase binding site. Here, by using enhanced sampling simulations (umbrella sampling, US) and two-end-state free energy calculations (MM/GSBA), we systemically studied the dissociation processes of two distinct small molecules escaping from the binding pocket of p38 MAP kinase through the allosteric channel and the ATP channel. The results show that the unbinding pathways along the allosteric channel have much lower PMF depths than those along the ATP channel, suggesting that the allosteric channel is more favorable for the dissociations of the two inhibitors and thereby supporting the general understanding that the largest channel of a target is usually the entry/exit pathway for the binding/dissociation of small molecules. Interestingly, the MM/GBSA approach yielded similar PMF profiles compared with those based on US, a much time consuming approach, indicating that for a general study, such as detecting the important transition state of a ligand binding/unbinding process, MM/GBSA may be a feasible choice.

New accounting rules: asset allocation and portfolio management.

PubMed

Andrew, B K

1997-01-01

New accounting rules went into effect at the end of 1995 that are now starting to affect how medical practices must report income from equity and fixed income investments. This article explores the new accounting rules and considers the other factors that help practices determine investment strategies, including desired investment return, comfort with level of risk, appropriate time horizons, liquidity needs and legal restrictions. The author also presents an example that examines the different considerations that may affect an asset allocation decision, including endowments and operating reserve funds.

17 CFR 239.15A - Form N-1A, registration statement of open-end management investment companies.

Code of Federal Regulations, 2010 CFR

2010-04-01

... statement of open-end management investment companies. 239.15A Section 239.15A Commodity and Securities... Registration Statements § 239.15A Form N-1A, registration statement of open-end management investment companies... management investment companies other than separate accounts of insurance companies registered under the...

Finding pathways to prepare Fe4N thin films at low substrate temperature

NASA Astrophysics Data System (ADS)

Seema, Gupta, Nitiand Mukul

2018-04-01

In Fe-N phase diagram the formation of Fe4N thin films occur in a very narrow region, specially below 573 K. Above this, the range of homogeneity for formation of Fe4N start to increase yielding more favorable conditions for formation of single phase Fe4N. However, when deposited at high substrate temperature (Ts) typically above 650 K, nitrogen (N) tends to diffuse out of the system yielding a N deficient phase. In this work, we attempt to find pathways to deposit Fe4N thin films at low Ts and successfully prepared single phase Fe4N thin films at Ts as low as 423 K. This was achieved by utilizing an underlayer of CrN. We find that such underlayer not only has close lattice matching with Fe4N, it also acts as a diffusion barrier for the film-substrate interface.

Abstinence from cocaine-self-administration activates the nELAV/GAP -43 pathway in the hippocampus: A stress-related effect?

PubMed

Pascale, Alessia; Osera, Cecilia; Moro, Federico; Di Clemente, Angelo; Giannotti, Giuseppe; Caffino, Lucia; Govoni, Stefano; Fumagalli, Fabio; Cervo, Luigi

2016-06-01

We previously demonstrated that nELAV/GAP-43 pathway is pivotal for learning and its hippocampal expression is up-regulated by acute stress following repeated cocaine administration. We therefore hypothesized that abstinence-induced stress may sustain nELAV/GAP-43 pathway during early abstinence following 2 weeks of cocaine self-administration. We found that contingent, but not non-contingent, cocaine exposure selectively increases hippocampal nELAV, but not GAP-43, expression immediately after the last self-administration session, an effect that wanes after 24 h and that comes back 7 days later when nELAV activation becomes associated with increased expression of GAP-43, an effect again observed only in animals self-administering the psychostimulant. Such effect is specific for nELAV since the ubiquitous ELAV/HuR is unchanged. This nELAV profile suggests that its initial transient alteration is perhaps related to the daily administration of cocaine, while the increase in the nELAV/GAP-43 pathway following a week of abstinence may reflect the activation of this cascade as a target of stressful conditions associated with drug-related memories. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The EbpA-RpoN Regulatory Pathway of the Pathogen Leptospira interrogans Is Essential for Survival in the Environment.

PubMed

Hu, Wei-Lin; Pappas, Christopher J; Zhang, Jun-Jie; Yang, You-Yun; Yan, Jie; Picardeau, Mathieu; Yang, X Frank

2017-02-01

Leptospira interrogans is the agent of leptospirosis, a reemerging zoonotic disease. It is transmitted to humans through environmental surface waters contaminated by the urine of mammals chronically infected by pathogenic strains able to survive in water for long periods. Little is known about the regulatory pathways underlying environmental sensing and host adaptation of L. interrogans during its enzootic cycle. This study identifies the EbpA-RpoN regulatory pathway in L. interrogans In this pathway, EbpA, a σ 54 activator and putative prokaryotic enhancer-binding protein (EBP), and the alternative sigma factor RpoN (σ 54 ) control expression of at least three genes, encoding AmtB (an ammonium transport protein) and two proteins of unknown function. Electrophoresis mobility shift assay demonstrated that recombinant RpoN and EbpA bind to the promoter region and upstream of these three identified genes, respectively. Genetic disruption of ebpA in L. interrogans serovar Manilae virtually abolished expression of the three genes, including amtB in two independent ebpA mutants. Complementation of the ebpA mutant restored expression of these genes. Intraperitoneal inoculation of gerbils with the ebpA mutant did not affect mortality. However, the ebpA mutant had decreased cell length in vitro and had a significantly lowered cell density at stationary phase when grown with l-alanine as the sole nitrogen source. Furthermore, the ebpA mutant has dramatically reduced long-term survival ability in water. Together, these studies identify a regulatory pathway, the EbpA-RpoN pathway, that plays an important role in the zoonotic cycle of L. interrogans IMPORTANCE: Leptospirosis is a reemerging disease with global importance. However, our understanding of gene regulation of the spirochetal pathogen Leptospira interrogans is still in its infancy, largely due to the lack of robust tools for genetic manipulation of this spirochete. Little is known about how the pathogen achieves its

The EbpA-RpoN Regulatory Pathway of the Pathogen Leptospira interrogans Is Essential for Survival in the Environment

PubMed Central

Hu, Wei-Lin; Pappas, Christopher J.; Zhang, Jun-Jie; Yang, You-Yun; Yan, Jie

2016-01-01

ABSTRACT Leptospira interrogans is the agent of leptospirosis, a reemerging zoonotic disease. It is transmitted to humans through environmental surface waters contaminated by the urine of mammals chronically infected by pathogenic strains able to survive in water for long periods. Little is known about the regulatory pathways underlying environmental sensing and host adaptation of L. interrogans during its enzootic cycle. This study identifies the EbpA-RpoN regulatory pathway in L. interrogans. In this pathway, EbpA, a σ54 activator and putative prokaryotic enhancer-binding protein (EBP), and the alternative sigma factor RpoN (σ54) control expression of at least three genes, encoding AmtB (an ammonium transport protein) and two proteins of unknown function. Electrophoresis mobility shift assay demonstrated that recombinant RpoN and EbpA bind to the promoter region and upstream of these three identified genes, respectively. Genetic disruption of ebpA in L. interrogans serovar Manilae virtually abolished expression of the three genes, including amtB in two independent ebpA mutants. Complementation of the ebpA mutant restored expression of these genes. Intraperitoneal inoculation of gerbils with the ebpA mutant did not affect mortality. However, the ebpA mutant had decreased cell length in vitro and had a significantly lowered cell density at stationary phase when grown with l-alanine as the sole nitrogen source. Furthermore, the ebpA mutant has dramatically reduced long-term survival ability in water. Together, these studies identify a regulatory pathway, the EbpA-RpoN pathway, that plays an important role in the zoonotic cycle of L. interrogans. IMPORTANCE Leptospirosis is a reemerging disease with global importance. However, our understanding of gene regulation of the spirochetal pathogen Leptospira interrogans is still in its infancy, largely due to the lack of robust tools for genetic manipulation of this spirochete. Little is known about how the pathogen

Effects of Different Ratio of n-6/n-3 Polyunsaturated Fatty Acids on the PI3K/Akt Pathway in Rats with Reflux Esophagitis.

PubMed

Zhuang, Jia-Yuan; Chen, Zhi-Yao; Zhang, Tao; Tang, Du-Peng; Jiang, Xiao-Yin; Zhuang, Ze-Hao

2017-01-30

BACKGROUND We designed this study to investigate the influence of different ratios of n-6/n-3 polyunsaturated fatty acid in the diet of reflux esophagitis (RE) rats' and the effect on the PI3K/Akt pathway. MATERIAL AND METHODS RE rats were randomly divided into a sham group and modeling groups of different concentrations of n-6/n-3 polyunsaturated fatty acid (PUFA): 12:1 group, 10:1 group, 5:1 group, and 1:1 group. RT-PCR and Western-blot were used to detect the expression of PI3K, Akt, p-Akt, NF-κBp50, and NF-κBp65 proteins in esophageal tissue. RESULTS In the n-6/n-3 PUFAs groups the expression of PI3K, Akt, p-Akt, nf-κbp50, and NF-κBp65 mRNA decreased with the decrease in n-6/n-3 ratios in the diet. The lowest expression of each indicator occurred in the 1:1 n-6/n-3 group compared with other n-6/n-3 groups, the difference was statistically significant (p<0.05). CONCLUSIONS The inhibition of n-3 PUFAs in the development of esophageal inflammation in rats with RE was attributed to the function of PI3K/Akt-NF-κB signaling pathway.

76 FR 61282 - Defense Federal Acquisition Regulation Supplement; Definition of “Qualifying Country End Product...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-04

... Federal Acquisition Regulation Supplement; Definition of ``Qualifying Country End Product'' (DFARS Case... Supplement (DFARS) to revise the definition of ``qualifying country end product.'' This final rule eliminates the component test for qualifying country end products that are commercially available off-the-shelf...

QCD Sum Rules and Models for Generalized Parton Distributions

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

Anatoly Radyushkin

2004-10-01

I use QCD sum rule ideas to construct models for generalized parton distributions. To this end, the perturbative parts of QCD sum rules for the pion and nucleon electromagnetic form factors are interpreted in terms of GPDs and two models are discussed. One of them takes the double Borel transform at adjusted value of the Borel parameter as a model for nonforward parton densities, and another is based on the local duality relation. Possible ways of improving these Ansaetze are briefly discussed.

False Position, Double False Position and Cramer's Rule

ERIC Educational Resources Information Center

Boman, Eugene

2009-01-01

We state and prove the methods of False Position (Regula Falsa) and Double False Position (Regula Duorum Falsorum). The history of both is traced from ancient Egypt and China through the work of Fibonacci, ending with a connection between Double False Position and Cramer's Rule.

17 CFR 230.498 - Summary Prospectuses for open-end management investment companies.

Code of Federal Regulations, 2010 CFR

2010-04-01

...-end management investment companies. 230.498 Section 230.498 Commodity and Securities Exchanges... management investment companies. (a) Definitions. For purposes of this section: (1) Class means a class of... reliance on an exemptive rule adopted by the Commission. (3) Fund means an open-end management investment...

Triplet Transport to and Trapping by Acceptor End Groups on Conjugated Polyfluorene Chains

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

Sreearunothai, P.; Miller, J.; Estrada, A.

2011-08-31

Triplet excited states created in polyfluorene (pF) molecules having average lengths up to 170 repeat units were transported to and captured by trap groups at the ends in less {approx}40 ns. Almost all of the triplets attached to the chains reached the trap groups, ruling out the presence of substantial numbers of defects that prevent transport. The transport yields a diffusion coefficient D of at least 3 x 10{sup -4} cm{sup 2} s{sup -1}, which is 30 times typical molecular diffusion and close to a value for triplet transport reported by Keller (J. Am. Chem. Soc.2011, 133, 11289-11298). The tripletmore » states were created in solution by pulse radiolysis; time resolution was limited by the rate of attachment of triplets to the pF chains. Naphthylimide (NI) or anthraquinone (AQ) groups attached to the ends of the chains acted as traps for the triplets, although AQ would not have been expected to serve as a trap on the basis of triplet energies of the separate molecules. The depths of the NI and AQ triplet traps were determined by intermolecular triplet transfer equilibria and temperature dependence. The trap depths are shallow, just a few times thermal energy for both, so a small fraction of the triplets reside in the pF chains in equilibrium with the end-trapped triplets. Trapping by AQ appears to arise from charge transfer interactions between the pF chains and the electron-accepting AQ groups. Absorption bands of the end-trapped triplet states are similar in peak wavelength (760 nm) and shape to the 760 nm bands of triplets in the pF chains but have reduced intensities. When an electron donor, N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD), is added to the solution, it reacts with the end-trapped triplets to remove the 760 nm bands and to make the trapping irreversible. New bands created upon reaction with TMPD may be due to charge transfer states.« less

Final Rule to Identify Additional Fuel Pathways under the Renewable Fuel Standard Program

EPA Pesticide Factsheets

This final rule describes EPA’s evaluation of biofuels produced from camelina oil and energy cane, as well as renewable gasoline and renewable gasoline blendstock made from certain qualifying feedstocks.

Microhomology-mediated End Joining and Homologous Recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells

PubMed Central

Truong, Lan N.; Li, Yongjiang; Shi, Linda Z.; Hwang, Patty Yi-Hwa; He, Jing; Wang, Hailong; Razavian, Niema; Berns, Michael W.; Wu, Xiaohua

2013-01-01

Microhomology-mediated end joining (MMEJ) is a major pathway for Ku-independent alternative nonhomologous end joining, which contributes to chromosomal translocations and telomere fusions, but the underlying mechanism of MMEJ in mammalian cells is not well understood. In this study, we demonstrated that, distinct from Ku-dependent classical nonhomologous end joining, MMEJ—even with very limited end resection—requires cyclin-dependent kinase activities and increases significantly when cells enter S phase. We also showed that MMEJ shares the initial end resection step with homologous recombination (HR) by requiring meiotic recombination 11 homolog A (Mre11) nuclease activity, which is needed for subsequent recruitment of Bloom syndrome protein (BLM) and exonuclease 1 (Exo1) to DNA double-strand breaks (DSBs) to promote extended end resection and HR. MMEJ does not require S139-phosphorylated histone H2AX (γ-H2AX), suggesting that initial end resection likely occurs at DSB ends. Using a MMEJ and HR competition repair substrate, we demonstrated that MMEJ with short end resection is used in mammalian cells at the level of 10–20% of HR when both HR and nonhomologous end joining are available. Furthermore, MMEJ is used to repair DSBs generated at collapsed replication forks. These studies suggest that MMEJ not only is a backup repair pathway in mammalian cells, but also has important physiological roles in repairing DSBs to maintain cell viability, especially under genomic stress. PMID:23610439

RANWAR: rank-based weighted association rule mining from gene expression and methylation data.

PubMed

Mallik, Saurav; Mukhopadhyay, Anirban; Maulik, Ujjwal

2015-01-01

Ranking of association rules is currently an interesting topic in data mining and bioinformatics. The huge number of evolved rules of items (or, genes) by association rule mining (ARM) algorithms makes confusion to the decision maker. In this article, we propose a weighted rule-mining technique (say, RANWAR or rank-based weighted association rule-mining) to rank the rules using two novel rule-interestingness measures, viz., rank-based weighted condensed support (wcs) and weighted condensed confidence (wcc) measures to bypass the problem. These measures are basically depended on the rank of items (genes). Using the rank, we assign weight to each item. RANWAR generates much less number of frequent itemsets than the state-of-the-art association rule mining algorithms. Thus, it saves time of execution of the algorithm. We run RANWAR on gene expression and methylation datasets. The genes of the top rules are biologically validated by Gene Ontologies (GOs) and KEGG pathway analyses. Many top ranked rules extracted from RANWAR that hold poor ranks in traditional Apriori, are highly biologically significant to the related diseases. Finally, the top rules evolved from RANWAR, that are not in Apriori, are reported.

Hund's rule in superatoms with transition metal impurities.

PubMed

Medel, Victor M; Reveles, Jose Ulises; Khanna, Shiv N; Chauhan, Vikas; Sen, Prasenjit; Castleman, A Welford

2011-06-21

The quantum states in metal clusters bunch into supershells with associated orbitals having shapes resembling those in atoms, giving rise to the concept that selected clusters could mimic the characteristics of atoms and be classified as superatoms. Unlike atoms, the superatom orbitals span over multiple atoms and the filling of orbitals does not usually exhibit Hund's rule seen in atoms. Here, we demonstrate the possibility of enhancing exchange splitting in superatom shells via a composite cluster of a central transition metal and surrounding nearly free electron metal atoms. The transition metal d states hybridize with superatom D states and result in enhanced splitting between the majority and minority sets where the moment and the splitting can be controlled by the nature of the central atom. We demonstrate these findings through studies on TMMg(n) clusters where TM is a 3d atom. The clusters exhibit Hund's filling, opening the pathway to superatoms with magnetic shells.

End-group-functionalized poly(N,N-diethylacrylamide) via free-radical chain transfer polymerization: Influence of sulfur oxidation and cyclodextrin on self-organization and cloud points in water

PubMed Central

Reinelt, Sebastian; Steinke, Daniel

2014-01-01

Summary In this work we report the synthesis of thermo-, oxidation- and cyclodextrin- (CD) responsive end-group-functionalized polymers, based on N,N-diethylacrylamide (DEAAm). In a classical free-radical chain transfer polymerization, using thiol-functionalized 4-alkylphenols, namely 3-(4-(1,1-dimethylethan-1-yl)phenoxy)propane-1-thiol and 3-(4-(2,4,4-trimethylpentan-2-yl)phenoxy)propane-1-thiol, poly(N,N-diethylacrylamide) (PDEAAm) with well-defined hydrophobic end-groups is obtained. These end-group-functionalized polymers show different cloud point values, depending on the degree of polymerization and the presence of randomly methylated β-cyclodextrin (RAMEB-CD). Additionally, the influence of the oxidation of the incorporated thioether linkages on the cloud point is investigated. The resulting hydrophilic sulfoxides show higher cloud point values for the lower critical solution temperature (LCST). A high degree of functionalization is supported by 1H NMR-, SEC-, FTIR- and MALDI–TOF measurements. PMID:24778720

Non-lightlike ruled surfaces with constant curvatures in Minkowski 3-space

NASA Astrophysics Data System (ADS)

Ali, Ahmad Tawfik

We study the non-lightlike ruled surfaces in Minkowski 3-space with non-lightlike base curve c(s) =∫(αt + βn + γb)ds, where t, n, b are the tangent, principal normal and binormal vectors of an arbitrary timelike curve Γ(s). Some important results of flat, minimal, II-minimal and II-flat non-lightlike ruled surfaces are studied. Finally, the following interesting theorem is proved: the only non-zero constant mean curvature (CMC) non-lightlike ruled surface is developable timelike ruled surface generated by binormal vector.

Sum Rule for a Schiff-Like Dipole Moment

NASA Astrophysics Data System (ADS)

Raduta, A. A.; Budaca, R.

The energy-weighted sum rule for an electric dipole transition operator of a Schiff type differs from the Thomas-Reiche-Kuhn (TRK) sum rule by several corrective terms which depend on the number of system components, N. For illustration the formalism was applied to the case of Na clusters. One concludes that the random phase approximation (RPA) results for Na clusters obey the modified TRK sum rule.

Non-homologous end joining pathway is the major route of protection against 4β-hydroxywithanolide E-induced DNA damage in MCF-7 cells.

PubMed

You, B-J; Wu, Y-C; Lee, C-L; Lee, H-Z

2014-03-01

4β-Hydroxywithanolide E is a bioactive withanolide extracted from Physalis peruviana. 4β-Hydroxywithanolide E caused reactive oxygen species production and cell apoptosis in human breast cancer MCF-7 cells. We further found that 4β-hydroxywithanolide E induced DNA damage and regulated the DNA damage signaling in MCF-7 cells. The DNA damage sensors and repair proteins act promptly to remove DNA lesions by 4β-hydroxywithanolide E. The ataxia-telangiectasia mutated protein (ATM)-dependent DNA damage signaling pathway is involved in 4β-hydroxywithanolide E-induced apoptosis of MCF-7 cells. Non-homologous end joining pathway, but not homologous recombination, is the major route of protection of MCF-7 cells against 4β-hydroxywithanolide E-induced DNA damage. 4β-Hydroxywithanolide E had no significant impact on the base excision repair pathway. In this study, we examined the 4β-hydroxywithanolide E-induced DNA damage as a research tool in project investigating the DNA repair signaling in breast cancer cells. We also suggest that 4β-hydroxywithanolide E assert its anti-tumor activity in carcinogenic progression and develop into a dietary chemopreventive agent. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mutations in Four Glycosyl Hydrolases Reveal a Highly Coordinated Pathway for Rhodopsin Biosynthesis and N-Glycan Trimming in Drosophila melanogaster

PubMed Central

Rosenbaum, Erica E.; Vasiljevic, Eva; Brehm, Kimberley S.; Colley, Nansi Jo

2014-01-01

As newly synthesized glycoproteins move through the secretory pathway, the asparagine-linked glycan (N-glycan) undergoes extensive modifications involving the sequential removal and addition of sugar residues. These modifications are critical for the proper assembly, quality control and transport of glycoproteins during biosynthesis. The importance of N-glycosylation is illustrated by a growing list of diseases that result from defects in the biosynthesis and processing of N-linked glycans. The major rhodopsin in Drosophila melanogaster photoreceptors, Rh1, is highly unique among glycoproteins, as the N-glycan appears to be completely removed during Rh1 biosynthesis and maturation. However, much of the deglycosylation pathway for Rh1 remains unknown. To elucidate the key steps in Rh1 deglycosylation in vivo, we characterized mutant alleles of four Drosophila glycosyl hydrolases, namely α-mannosidase-II (α-Man-II), α-mannosidase-IIb (α-Man-IIb), a β-N-acetylglucosaminidase called fused lobes (Fdl), and hexosaminidase 1 (Hexo1). We have demonstrated that these four enzymes play essential and unique roles in a highly coordinated pathway for oligosaccharide trimming during Rh1 biosynthesis. Our results reveal that α-Man-II and α-Man-IIb are not isozymes like their mammalian counterparts, but rather function at distinct stages in Rh1 maturation. Also of significance, our results indicate that Hexo1 has a biosynthetic role in N-glycan processing during Rh1 maturation. This is unexpected given that in humans, the hexosaminidases are typically lysosomal enzymes involved in N-glycan catabolism with no known roles in protein biosynthesis. Here, we present a genetic dissection of glycoprotein processing in Drosophila and unveil key steps in N-glycan trimming during Rh1 biosynthesis. Taken together, our results provide fundamental advances towards understanding the complex and highly regulated pathway of N-glycosylation in vivo and reveal novel insights into the

PathNER: a tool for systematic identification of biological pathway mentions in the literature

PubMed Central

2013-01-01

Background Biological pathways are central to many biomedical studies and are frequently discussed in the literature. Several curated databases have been established to collate the knowledge of molecular processes constituting pathways. Yet, there has been little focus on enabling systematic detection of pathway mentions in the literature. Results We developed a tool, named PathNER (Pathway Named Entity Recognition), for the systematic identification of pathway mentions in the literature. PathNER is based on soft dictionary matching and rules, with the dictionary generated from public pathway databases. The rules utilise general pathway-specific keywords, syntactic information and gene/protein mentions. Detection results from both components are merged. On a gold-standard corpus, PathNER achieved an F1-score of 84%. To illustrate its potential, we applied PathNER on a collection of articles related to Alzheimer's disease to identify associated pathways, highlighting cases that can complement an existing manually curated knowledgebase. Conclusions In contrast to existing text-mining efforts that target the automatic reconstruction of pathway details from molecular interactions mentioned in the literature, PathNER focuses on identifying specific named pathway mentions. These mentions can be used to support large-scale curation and pathway-related systems biology applications, as demonstrated in the example of Alzheimer's disease. PathNER is implemented in Java and made freely available online at http://sourceforge.net/projects/pathner/. PMID:24555844

Two Pathways to Stimulus Encoding in Category Learning?

PubMed Central

Davis, Tyler; Love, Bradley C.; Maddox, W. Todd

2008-01-01

Category learning theorists tacitly assume that stimuli are encoded by a single pathway. Motivated by theories of object recognition, we evaluate a dual-pathway account of stimulus encoding. The part-based pathway establishes mappings between sensory input and symbols that encode discrete stimulus features, whereas the image-based pathway applies holistic templates to sensory input. Our experiments use rule-plus-exception structures in which one exception item in each category violates a salient regularity and must be distinguished from other items. In Experiment 1, we find that discrete representations are crucial for recognition of exceptions following brief training. Experiments 2 and 3 involve multi-session training regimens designed to encourage either part or image-based encoding. We find that both pathways are able to support exception encoding, but have unique characteristics. We speculate that one advantage of the part-based pathway is the ability to generalize across domains, whereas the image-based pathway provides faster and more effortless recognition. PMID:19460948

Guiding the folding pathway of DNA origami

NASA Astrophysics Data System (ADS)

Dunn, Katherine E.; Dannenberg, Frits; Ouldridge, Thomas E.; Kwiatkowska, Marta; Turberfield, Andrew J.; Bath, Jonathan

2015-09-01

DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short `staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

Guiding the folding pathway of DNA origami.

PubMed

Dunn, Katherine E; Dannenberg, Frits; Ouldridge, Thomas E; Kwiatkowska, Marta; Turberfield, Andrew J; Bath, Jonathan

2015-09-03

DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

Validity of Vegard’s rule for Al1-xInxN (0.08  <  x  <  0.28) thin films grown on GaN templates

NASA Astrophysics Data System (ADS)

Magalhães, S.; Franco, N.; Watson, I. M.; Martin, R. W.; O'Donnell, K. P.; Schenk, H. P. D.; Tang, F.; Sadler, T. C.; Kappers, M. J.; Oliver, R. A.; Monteiro, T.; Martin, T. L.; Bagot, P. A. J.; Moody, M. P.; Alves, E.; Lorenz, K.

2017-05-01

In this work, comparative x-ray diffraction (XRD) and Rutherford backscattering spectrometry (RBS) measurements allow a comprehensive characterization of Al1-xInxN thin films grown on GaN. Within the limits of experimental accuracy, and in the compositional range 0.08  <  x  <  0.28, the lattice parameters of the alloys generally obey Vegard’s rule, varying linearly with the InN fraction. Results are also consistent with the small deviation from linear behaviour suggested by Darakchieva et al (2008 Appl. Phys. Lett. 93 261908). However, unintentional incorporation of Ga, revealed by atom probe tomography (APT) at levels below the detection limit for RBS, may also affect the lattice parameters. Furthermore, in certain samples the compositions determined by XRD and RBS differ significantly. This fact, which was interpreted in earlier publications as an indication of a deviation from Vegard’s rule, may rather be ascribed to the influence of defects or impurities on the lattice parameters of the alloy. The wide-ranging set of Al1-xInxN films studied allowed furthermore a detailed investigation of the composition leading to lattice-matching of Al1-xInxN/GaN bilayers.

Specific end-to-end attachment of chromosomes in Ornithogalum virens.

PubMed

Ashley, T

1979-08-01

C-banding of nonhomologous chromosomes in haploid generative nuclei of Ornithogalum virens (n = 3) reveals a high degree of specificity with respect to end-to-end connexions. The centromeric end of chromosome 2 preferentially associates with the centromeric end of chromosome 3 and the telomeric end of chromosome 3 associates preferentially with the telomeric end of chromosome 1. This same association of nonhomologous chromosomes persists in prophase nuclei of diploid root tips. In addition, the telomeric ends of the 2 chromosome 2s are connected to one another as are the centromeric ends of the chromosome 1s. This results in a ring of chromosomes in which homologues lie opposite one another. Centromeric ends lie on one side of the nucleus and telomeric ends on the other. It is proposed that this specific association of chromosome ends reflects an order which was probably established at the preceding anaphase or telophase and which persists throughout interphase. The suggestion is made that the proximity of homologous ends and consequently homologous alignment may facilitate initiation of pairing at meiosis.

75 FR 62462 - Additions to the List of Validated End-Users in the People's Republic of China: Hynix...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-12

...In this final rule, the Bureau of Industry and Security amends the Export Administration Regulations (EAR) to add three end-users, Hynix Semiconductor (China) Ltd., Hynix Semiconductor (Wuxi) Ltd. and Lam Research Corporation to the list of validated end-users in the People's Republic of China (PRC). With this rule, exports, reexports and transfers (in-country) of certain items to one facility of Hynix Semiconductor (China) Ltd., one facility of Hynix Semiconductor (Wuxi) Ltd. and nine facilities of Lam Research Corporation in the PRC are now authorized under Authorization Validated End-User (VEU).

Reimagining the learned intermediary rule for the new pharmaceutical marketplace.

PubMed

Hall, Timothy S

2004-01-01

For the past decade, the learned intermediary rule--the rule of tort law that provides that drug manufacturers may satisfy their duty to warn of a drug's dangers by warning the prescribing physician rather than the end user of the drug--has been the subject of vigorous academic debate. That debate has been largely moot, however, as the courts have proven reluctant to make significant inroads on the protection offered by the Rule to drug manufacturers. This Article proposes a new approach to the Rule. Part I discusses the history and overwhelming adoption of the Rule pursuant to the Restatement (Second) of Torts. Part II argues that changes in the health care delivery system have resulted in a legal system that introduces market distortions by effectively immunizing the pharmaceutical industry from the legal and social consequences of its own actions. Part III then sets forth a reconceptualization of the Rule, which preserves the Rule's benefits with respect to the drug industry, the health care system, and the goals of tort law, while also strengthening the protection the tort system offers to individuals injured by prescription drugs.

[The medicine use pathway in paediatrics].

PubMed

Didelot, Nicolas

2016-01-01

The medicine use pathway is a process which is constantly evolving in order to comply with intangible rules. As in other therapeutic fields, the drug regimen in paediatrics must tolerate no error and must be able to detect all warning signs, however minor, in order to optimise this approach. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Can Baird's and Clar's Rules Combined Explain Triplet State Energies of Polycyclic Conjugated Hydrocarbons with Fused 4nπ- and (4n + 2)π-Rings?

PubMed

Ayub, Rabia; Bakouri, Ouissam El; Jorner, Kjell; Solà, Miquel; Ottosson, Henrik

2017-06-16

Compounds that can be labeled as "aromatic chameleons" are π-conjugated compounds that are able to adjust their π-electron distributions so as to comply with the different rules of aromaticity in different electronic states. We used quantum chemical calculations to explore how the fusion of benzene rings onto aromatic chameleonic units represented by biphenylene, dibenzocyclooctatetraene, and dibenzo[a,e]pentalene modifies the first triplet excited states (T 1 ) of the compounds. Decreases in T 1 energies are observed when going from isomers with linear connectivity of the fused benzene rings to those with cis- or trans-bent connectivities. The T 1 energies decreased down to those of the parent (isolated) 4nπ-electron units. Simultaneously, we observe an increased influence of triplet state aromaticity of the central 4n ring as given by Baird's rule and evidenced by geometric, magnetic, and electron density based aromaticity indices (HOMA, NICS-XY, ACID, and FLU). Because of an influence of triplet state aromaticity in the central 4nπ-electron units, the most stabilized compounds retain the triplet excitation in Baird π-quartets or octets, enabling the outer benzene rings to adapt closed-shell singlet Clar π-sextet character. Interestingly, the T 1 energies go down as the total number of aromatic cycles within a molecule in the T 1 state increases.

Defining Alcohol-Specific Rules Among Parents of Older Adolescents: Moving Beyond No Tolerance.

PubMed

Bourdeau, Beth; Miller, Brenda; Vanya, Magdalena; Duke, Michael; Ames, Genevieve

2012-01-01

Parental beliefs and rules regarding their teen's use of alcohol influence teen decisions regarding alcohol use. However, measurement of parental rules regarding adolescent alcohol use has not been thoroughly studied. This study used qualitative interviews with 174 parents of older teens from 100 families. From open-ended questions, themes emerged that describe explicit rules tied to circumscribed use, no tolerance, and "call me." There was some inconsistency in explicit rules with and between parents. Responses also generated themes relating to implicit rules such as expectations and preferences. Parents described their methods of communicating their position via conversational methods, role modeling their own behavior, teaching socially appropriate use of alcohol by offering their teen alcohol, and monitoring their teens' social activities. Findings indicate that alcohol rules are not adequately captured by current assessment measures.

N-n-butyl Haloperidol Iodide Protects against Hypoxia/Reoxygenation Injury in Cardiac Microvascular Endothelial Cells by Regulating the ROS/MAPK/Egr-1 Pathway

PubMed Central

Lu, Shishi; Zhang, Yanmei; Zhong, Shuping; Gao, Fenfei; Chen, Yicun; Li, Weiqiu; Zheng, Fuchun; Shi, Ganggang

2017-01-01

Endothelium dysfunction induced by reactive oxygen species (ROS) is an important initial event at the onset of myocardial ischemia/reperfusion in which the Egr-1 transcription factor often serves as a master switch for various damage pathways following reperfusion injury. We hypothesized that an intracellular ROS/MAPK/Egr-1 signaling pathway is activated in cardiac microvascular endothelial cells (CMECs) following hypoxia/reoxygenation (H/R). ROS generation, by either H/R or the ROS donor xanthine oxidase-hypoxanthine (XO/HX) activated all three MAPKs (ERK1/2, JNK, p38), and induced Egr-1 expression and Egr-1 DNA-binding activity in CMECs, whereas ROS scavengers (EDA and NAC) had the opposite effect following H/R. Inhibitors of all three MAPKs individually inhibited induction of Egr-1 expression by H/R in CMECs. Moreover, N-n-butyl haloperidol (F2), previously shown to protect cardiomyocytes subjected to I/R, dose-dependently downregulated H/R-induced ROS generation, MAPK activation, and Egr-1 expression and activity in CMECs, whereas XO/HX and MAPK activators (EGF, anisomycin) antagonized the effects of F2. Inhibition of the ROS/MAPK/Egr-1 signaling pathway, by either F2, NAC, or inhibition of MAPK, increased CMEC viability and the GSH/GSSG ratio, and decreased Egr-1 nuclear translocation. These results show that the ROS/MAPK/Egr-1 signaling pathway mediates H/R injury in CMECs, and F2 blocks this pathway to protect against H/R injury and further alleviate myocardial I/R injury. PMID:28111550

Exact sum rules for inhomogeneous strings

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

Amore, Paolo, E-mail: paolo.amore@gmail.com

2013-11-15

We derive explicit expressions for the sum rules of the eigenvalues of inhomogeneous strings with arbitrary density and with different boundary conditions. We show that the sum rule of order N may be obtained in terms of a diagrammatic expansion, with (N−1)!/2 independent diagrams. These sum rules are used to derive upper and lower bounds to the energy of the fundamental mode of an inhomogeneous string; we also show that it is possible to improve these approximations taking into account the asymptotic behavior of the spectrum and applying the Shanks transformation to the sequence of approximations obtained to the differentmore » orders. We discuss three applications of these results. -- Highlights: •We derive an explicit expression for the sum rules of an inhomogeneous string. •We obtain a diagrammatic representation for the sum rules of a given order. •We obtain precise bounds on the lowest eigenvalue of the string.« less

Simplification rules for birdtrack operators

NASA Astrophysics Data System (ADS)

Alcock-Zeilinger, J.; Weigert, H.

2017-05-01

This paper derives a set of easy-to-use tools designed to simplify calculations with birdtrack operators comprised of symmetrizers and antisymmetrizers. In particular, we present cancellation rules allowing one to shorten the birdtrack expressions of operators and propagation rules identifying the circumstances under which it is possible to propagate symmetrizers past antisymmetrizers and vice versa. We exhibit the power of these simplification rules by means of a short example in which we apply the tools derived in this paper on a typical operator that can be encountered in the representation theory of 𝖲𝖴 (N ) over the product space V⊗m. These rules form the basis for the construction of compact Hermitian Young projection operators and their transition operators addressed in companion papers [J. Alcock-Zeilinger and H. Weigert, "Compact Hermitian Young projection operators," e-print arXiv:1610.10088 [math-ph] and J. Alcock-Zeilinger and H. Weigert, "Transition operators," e-print arXiv:1610.08802 [math-ph

77 FR 40951 - Medicare Program; End-Stage Renal Disease Prospective Payment System, Quality Incentive Program...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-11

...This rule proposes to update and make revisions to the End- Stage Renal Disease (ESRD) prospective payment system (PPS) for calendar year (CY) 2013. This rule also proposes to set forth requirements for the ESRD quality incentive program (QIP), including for payment year (PY) 2015 and beyond. This proposed rule will implement changes to bad debt reimbursement for all Medicare providers, suppliers, and other entities eligible to receive bad debt. (See the Table of Contents for a listing of the specific issues addressed in this proposed rule.)

Modeling non-homologous end joining.

PubMed

Li, Yongfeng; Cucinotta, Francis A

2011-08-21

Non-homologous end joining (NHEJ) is an important DNA repair pathway for DNA double-strand breaks. Several proteins, including Ku, DNA-PKcs, Artemis, XRCC4/Ligase IV and XLF, are involved in the NHEJ for the DNA damage detection, DNA free end processing and ligation. The classical model of NHEJ is a sequential model in which DNA-PKcs is first recruited by the Ku bound DNA prior to any other repair proteins. Recent experimental study (McElhinny et al., 2000; Costantini et al., 2007; Mari et al., 2006; Yano and Chen, 2008) suggested that the recruitment ordering is not crucial. In this work, by proposing a mathematical model in terms of biochemical reaction network and performing stability and related analysis, we demonstrate theoretically that if DSB repair pathway independent of DNA-PKcs exists, then the classical sequential model and new two-phase model are essentially indistinguishable in the sense that DSB can be repaired thoroughly in both models when the repair proteins are sufficient. Published by Elsevier Ltd.

N-Cadherin Attenuates High Glucose-Induced Nucleus Pulposus Cell Senescence Through Regulation of the ROS/NF-κB Pathway.

PubMed

Hou, Gang; Zhao, Huiqing; Teng, Haijun; Li, Pei; Xu, Wenbin; Zhang, Junbin; Lv, Lulu; Guo, Zhiliang; Wei, Li; Yao, Hui; Xu, Yichun

2018-01-01

Diabetes mellitus (DM) is a potential etiology of disc degeneration. N-cadherin (N-CDH) helps maintain the cell viability, cell phenotype and matrix biosynthesis of nucleus pulposus (NP) cells. Here, we mainly aimed to investigate whether N-CDH can attenuate high glucose-induced NP cell senescence and its potential mechanism. Rat NP cells were cultured in a base culture medium and base culture medium with a 0.2 M glucose concentration. Recombinant lentiviral vectors were used to enhance N-CDH expression in NP cells. Senescence-associated β-galactosidase (SA-β-Gal) activity was measured by SA-β-Gal staining. NP cell proliferation was evaluated by CCK-8 assay. Telomerase activity and intracellular reactive oxygen species (ROS) content were tested by specific chemical kits according to the manufacturer's instructions. G0/G1 cell cycle arrest was evaluated by flow cytometry. Real-time PCR and Western blotting were used to analyze mRNA and protein expressions of senescence markers (p16 and p53) and matrix macromolecules (aggrecan and collagen II). Additionally, p-NF-κB expression was also analyzed by Western blotting to evaluate NF-κB pathway activity. High glucose significantly decreased N-CDH expression, increased ROS generation and NF-κB pathway activity, and promoted NP cell senescence, which was reflected in the increase in SA-β-Gal activity and senescence marker (p16 and p53) expression, compared to the control group. High glucose decreased telomerase activity and cell proliferation potency. However, N-CDH overexpression partially attenuated NP cell senescence, decreased ROS content and inhibited the activation of the NF-κB pathway under the high glucose condition. High glucose decreases N-CDH expression and promotes NP cell senescence. N-CDH overexpression can attenuate high glucose-induced NP cell senescence through the regulation of the ROS/ NF-κB pathway. This study suggests that N-CDH is a potential therapeutic target to slow DM-mediated disc NP

Analysis of Gambierdiscus transcriptome data supports ancient origins of mixotrophic pathways in dinoflagellates.

PubMed

Price, Dana C; Farinholt, Natalie; Gates, Colin; Shumaker, Alexander; Wagner, Nicole E; Bienfang, Paul; Bhattacharya, Debashish

2016-12-01

Toxic dinoflagellates pose serious threats to human health and to fisheries. The genus Gambierdiscus is significant in this respect because its members produce ciguatoxin that accumulates in predominantly tropical marine food webs and leads to ciguatera fish poisoning. Understanding the biology of toxic dinoflagellates is crucial to developing control strategies. To this end, we generated a de novo transcriptome library from G. caribaeus and studied its growth under different culture conditions to elucidate pathways of carbon (C) and nitrogen (N) utilization. We also gathered available dinoflagellate transcriptome data to trace the evolutionary history of C and N pathways in this phylum. We find that rather than being specific adaptations to the epiphytic lifestyle in G. caribaeus, the majority of dinoflagellates share a large array of genes that putatively confer mixotrophy and the ability to use N via the ornithine-urea cycle and nitric oxide synthase production. These results suggest that prior to plastid endosymbiosis, the dinoflagellate ancestor possessed complex pathways that linked metabolism, intercellular signaling, and stress responses to environmental cues that have been maintained by extant photosynthetic species. This metabolic flexibility likely explains the success of dinoflagellates in marine ecosystems and may presage difficulties in controlling the spread of toxic species. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

‘N-of-1- pathways ’ unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: Towards precision medicine

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

Gardeux, Vincent; Achour, Ikbel; Li, Jianrong

Background: The emergence of precision medicine allowed the incorporation of individual molecular data into patient care. This research entails, DNA sequencing predicts somatic mutations in individual patients. However, these genetic features overlook dynamic epigenetic and phenotypic response to therapy. Meanwhile, accurate personal transcriptome interpretation remains an unmet challenge. Further, N-of-1 (single-subject) efficacy trials are increasingly pursued, but are underpowered for molecular marker discovery. Method: ‘N-of-1- pathways’ is a global framework relying on three principles: (i) the statistical universe is a single patient; (ii) significance is derived from geneset/biomodules powered by paired samples from the same patient; and (iii) similarity betweenmore » genesets/biomodules assesses commonality and differences, within-study and cross-studies. Thus, patient gene-level profiles are transformed into deregulated pathways. From RNA-Seq of 55 lung adenocarcinoma patients, N-of-1- pathways predicts the deregulated pathways of each patient. Results: Cross-patient N-of-1- pathways obtains comparable results with conventional genesets enrichment analysis (GSEA) and differentially expressed gene (DEG) enrichment, validated in three external evaluations. Moreover, heatmap and star plots highlight both individual and shared mechanisms ranging from molecular to organ-systems levels (eg, DNA repair, signaling, immune response). Patients were ranked based on the similarity of their deregulated mechanisms to those of an independent gold standard, generating unsupervised clusters of diametric extreme survival phenotypes (p=0.03). Conclusions: The N-of-1- pathways framework provides a robust statistical and relevant biological interpretation of individual disease-free survival that is often overlooked in conventional cross-patient studies. It enables mechanism-level classifiers with smaller cohorts as well as N-of-1 studies.« less

‘N-of-1- pathways ’ unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: Towards precision medicine

DOE PAGES

Gardeux, Vincent; Achour, Ikbel; Li, Jianrong; ...

2014-11-01

Background: The emergence of precision medicine allowed the incorporation of individual molecular data into patient care. This research entails, DNA sequencing predicts somatic mutations in individual patients. However, these genetic features overlook dynamic epigenetic and phenotypic response to therapy. Meanwhile, accurate personal transcriptome interpretation remains an unmet challenge. Further, N-of-1 (single-subject) efficacy trials are increasingly pursued, but are underpowered for molecular marker discovery. Method: ‘N-of-1- pathways’ is a global framework relying on three principles: (i) the statistical universe is a single patient; (ii) significance is derived from geneset/biomodules powered by paired samples from the same patient; and (iii) similarity betweenmore » genesets/biomodules assesses commonality and differences, within-study and cross-studies. Thus, patient gene-level profiles are transformed into deregulated pathways. From RNA-Seq of 55 lung adenocarcinoma patients, N-of-1- pathways predicts the deregulated pathways of each patient. Results: Cross-patient N-of-1- pathways obtains comparable results with conventional genesets enrichment analysis (GSEA) and differentially expressed gene (DEG) enrichment, validated in three external evaluations. Moreover, heatmap and star plots highlight both individual and shared mechanisms ranging from molecular to organ-systems levels (eg, DNA repair, signaling, immune response). Patients were ranked based on the similarity of their deregulated mechanisms to those of an independent gold standard, generating unsupervised clusters of diametric extreme survival phenotypes (p=0.03). Conclusions: The N-of-1- pathways framework provides a robust statistical and relevant biological interpretation of individual disease-free survival that is often overlooked in conventional cross-patient studies. It enables mechanism-level classifiers with smaller cohorts as well as N-of-1 studies.« less

An alternative pathway for marine nitrous oxide production at oxic-anoxic interfaces from coupled biotic-abiotic reactions

NASA Astrophysics Data System (ADS)

Glass, J. B.; Stanton, C. L.; Ochoa, H.; Haslun, J. A.; Gandhi, H.; Taillefert, M.; Dichristina, T. J.; Stewart, F. J.; Klotz, M. G.; Ostrom, N. E.

2016-02-01

Marine emissions of nitrous oxide (N2O), a potent greenhouse gas, comprise approximately a third of global sources. Recent evidence suggests that the dominant source of N2O in seawater is the activity of ammonia-oxidizing Thaumarchaeota that lack characterized N2O-generating enzymes. Nitrous oxide may arise from a novel enzyme and/or abiotic reactions between nitrification intermediates, hydroxylamine (NH2OH) and nitric oxide (NO), and redox-active metals in seawater. Isotopic site preference, or difference in δ15N between the two nitrogen atoms in N2O, has been used as tracer for microbial N2O production pathways (-10 to 0‰ for nitrifier-denitrification and denitrification vs. 30-37‰ for nitrification via NH2OH oxidation). Seawater N2O site preference falls in between these two characterized end members, suggesting simultaneous production via a combination of both microbial pathways or via a novel mechanism with intermediate site preference. Here we show significant N2O production in abiotic experiments after addition of iron to seawater containing NH2OH and NO. The N2O produced from chemical reduction of NO by Fe(II) had a site preference of 16‰ whereas N2O produced from abiotic NH2OH oxidation had a site preference of 31‰. We propose that coupled biotic-abiotic N2O production pathways could contribute significant sources of N2O at marine oxic-anoxic interfaces.

Integrating emotional and psychological support into the end-stage renal disease pathway: a protocol for mixed methods research to identify patients' lower-level support needs and how these can most effectively be addressed.

PubMed

Taylor, Francesca; Taylor, Celia; Baharani, Jyoti; Nicholas, Johann; Combes, Gill

2016-08-02

As a result of difficulties related to their illness, diagnosis and treatment, patients with end-stage renal disease experience significant emotional and psychological problems, which untreated can have considerable negative impact on their health and wellbeing. Despite evidence that patients desire improved support, management of their psychosocial problems, particularly at the lower-level, remains sub-optimal. There is limited understanding of the specific support that patients need and want, from whom, and when, and also a lack of data on what helps and hinders renal staff in identifying and responding to their patients' support needs, and how barriers to doing so might be overcome. Through this research we therefore seek to determine what, when, and how, support for patients with lower-level emotional and psychological problems should be integrated into the end-stage renal disease pathway. The research will involve two linked, multicentre studies, designed to identify and consider the perspectives of patients at five different stages of the end-stage renal disease pathway (Study 1), and renal staff working with them (Study 2). A convergent, parallel mixed methods design will be employed for both studies, with quantitative and qualitative data collected separately. For each study, the data sets will be analysed separately and the results then compared or combined using interpretive analysis. A further stage of synthesis will employ data-driven thematic analysis to identify: triangulation and frequency of themes across pathway stages; patterns and plausible explanations of effects. There is an important need for this research given the high frequency of lower-level distress experienced by end-stage renal disease patients and lack of progress to date in integrating support for their lower-level psychosocial needs into the care pathway. Use of a mixed methods design across the two studies will generate a holistic patient and healthcare professional perspective that

Defining Alcohol-Specific Rules Among Parents of Older Adolescents: Moving Beyond No Tolerance

PubMed Central

Bourdeau, Beth; Miller, Brenda; Vanya, Magdalena; Duke, Michael; Ames, Genevieve

2012-01-01

Parental beliefs and rules regarding their teen’s use of alcohol influence teen decisions regarding alcohol use. However, measurement of parental rules regarding adolescent alcohol use has not been thoroughly studied. This study used qualitative interviews with 174 parents of older teens from 100 families. From open-ended questions, themes emerged that describe explicit rules tied to circumscribed use, no tolerance, and “call me.” There was some inconsistency in explicit rules with and between parents. Responses also generated themes relating to implicit rules such as expectations and preferences. Parents described their methods of communicating their position via conversational methods, role modeling their own behavior, teaching socially appropriate use of alcohol by offering their teen alcohol, and monitoring their teens’ social activities. Findings indicate that alcohol rules are not adequately captured by current assessment measures. PMID:23204931

After the Liverpool Care Pathway—development of heuristics to guide end of life care for people with dementia: protocol of the ALCP study

PubMed Central

Davies, N; Manthorpe, J; Sampson, E L; Iliffe, S

2015-01-01

Introduction End of life care guidance for people with dementia is lacking and this has been made more problematic in England with the removal of one of the main end of life care guidelines which offered some structure, the Liverpool Care Pathway. This guidance gap may be eased with the development of heuristics (rules of thumb) which offer a fast and frugal form of decision-making. Objective To develop a toolkit of heuristics (rules of thumb) for practitioners to use when caring for people with dementia at the end of life. Method and analysis A mixed-method study using a co-design approach to develop heuristics in three phases. In phase 1, we will conduct at least six focus groups with family carers, health and social care practitioners from both hospital and community care services, using the ‘think-aloud’ method to understand decision-making processes and to develop a set of heuristics. The focus group topic guide will be developed from the findings of a previous study of 46 interviews of family carers about quality end-of-life care for people with dementia and a review of the literature. A multidisciplinary development team of health and social care practitioners will synthesise the findings from the focus groups to devise and refine a toolkit of heuristics. Phase 2 will test the use of heuristics in practice in five sites: one general practice, one community nursing team, one hospital ward and two palliative care teams working in the community. Phase 3 will evaluate and further refine the toolkit of heuristics through group interviews, online questionnaires and semistructured interviews. Ethics and dissemination This study has received ethical approval from a local NHS research ethics committee (Rec ref: 15/LO/0156). The findings of this study will be presented in peer-reviewed publications and national and international conferences. PMID:26338688

49 CFR 393.130 - What are the rules for securing heavy vehicles, equipment and machinery?

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 5 2010-10-01 2010-10-01 false What are the rules for securing heavy vehicles... heavy vehicles, equipment and machinery? (a) Applicability. The rules in this section apply to the transportation of heavy vehicles, equipment and machinery which operate on wheels or tracks, such as front end...

PIV Measurements of Gas Flow Fields from Burning End

NASA Astrophysics Data System (ADS)

Huang, Yifei; Wu, Junzhang; Zeng, Jingsong; Tang, Darong; Du, Liang

2017-12-01

To study the influence of cigarette gas on the environment, it is necessary to know the cigarette gas flow fields from burning end. By using PIV technique, in order to reveal velocity characteristics of gas flow fields, the velocities of cigarette gas flow fields was analyzed with different stepping motor frequencies corresponding to suction pressures, and the trend of velocity has been given with image fitting. The results shows that the velocities of the burning end increased with suction pressures; Between velocities of the burning end and suction pressures, the relations present polynomial rule; The cigarette gas diffusion in combustion process is faster than in the smoldering process.

Under-recognized pathways of N2O production in coastal sediments: Increased fungal and chemo-denitrification in response to elevated N loading

NASA Astrophysics Data System (ADS)

Wankel, S. D.; Ziebis, W.; Buchwald, C.; Charoenpong, C.; de Beer, D.

2016-02-01

Increasing atmospheric levels of nitrous oxide (N2O), a greenhouse gas with a 100-year global warming potential more than 300 times that of carbon dioxide, have been strongly linked to human activities - especially the dramatic increase in nitrogen loading to aquatic and marine ecosystems worldwide. While many studies have demonstrated that N2O is formed through a number of microbially mediated pathways, the factors regulating the emission of N2O to the atmosphere remain difficult to predict and the global N2O budget remains poorly constrained. In particular, coastal ecosystems, which bear much of the brunt of anthropogenically-derived nitrogen from watershed inputs and rapidly growing coastal human populations, represent large gaps in our understanding of sources and sinks of atmospheric N2O. In large part, these challenges stem from the fact that a diverse number of N2O production pathways are operative under the dynamic redox conditions encountered in coastal and estuarine sediments, complicating our ability to understand their relative roles in N2O fluxes. Here, we use whole-core sediment incubations together with a suite of conventional and novel stable isotopic tools to identify both factors influencing N2O flux as well as those underlying biogeochemical processes responding to those factors. We find that under elevated N loading to coastal sediments, an observed increase in N2O flux to the overlying water is not mediated by direct bacterial activity, but instead is catalyzed by fungal denitrification and/or abiotic interactions with reduced iron (e.g., chemodenitrification). These findings shed new light on the complexity of nitrogen cycling in coastal sedimentary environments and highlight the need for an improved understanding of eukaryotic and abiotic processes in regulating fluxes of climatically important gases such as N2O.

17 CFR 270.6d-1 - Exemption for certain closed-end investment companies.

Code of Federal Regulations, 2010 CFR

2010-04-01

...-end investment companies. 270.6d-1 Section 270.6d-1 Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION (CONTINUED) RULES AND REGULATIONS, INVESTMENT COMPANY ACT OF 1940 § 270.6d-1 Exemption for certain closed-end investment companies. (a) An application under section 6(d) of the Act shall...

Medicare program; changes to the Medicare claims appeal procedures; continuation of effectiveness and extension of timeline for publication of final rule. Interim final rule with comment period; continuation of effectiveness and extension of timeline for publication of final rule.

PubMed

2009-02-27

This notice announces the continuation of effectiveness of a Medicare interim final rule with comment period and the extension of the timeline for publication of the final rule. This notice is issued in accordance with section 1871(a)(3)(C) of the Social Security Act (the Act), which allows an interim final rule to remain in effect after the expiration of the timeline specified in section 1871(a)(3)(B) of the Act (the "regular timeline") or, if applicable, at the end of each succeeding 1-year extension to the regular timeline, if prior to the expiration of the timeline, the Secretary publishes in the Federal Register a notice of continuation and explains why the regular timeline or any subsequent extension was not complied with.

EPA, DHA, and Lipoic Acid Differentially Modulate the n-3 Fatty Acid Biosynthetic Pathway in Atlantic Salmon Hepatocytes.

PubMed

Bou, Marta; Østbye, Tone-Kari; Berge, Gerd M; Ruyter, Bente

2017-03-01

The aim of the present study was to investigate how EPA, DHA, and lipoic acid (LA) influence the different metabolic steps in the n-3 fatty acid (FA) biosynthetic pathway in hepatocytes from Atlantic salmon fed four dietary levels (0, 0.5, 1.0 and 2.0%) of EPA, DHA or a 1:1 mixture of these FA. The hepatocytes were incubated with [1- 14 C] 18:3n-3 in the presence or absence of LA (0.2 mM). Increased endogenous levels of EPA and/or DHA and LA exposure both led to similar responses in cells with reduced desaturation and elongation of [1- 14 C] 18:3n-3 to 18:4n-3, 20:4n-3, and EPA, in agreement with reduced expression of the Δ6 desaturase gene involved in the first step of conversion. DHA production, on the other hand, was maintained even in groups with high endogenous levels of DHA, possibly due to a more complex regulation of this last step in the n-3 metabolic pathway. Inhibition of the Δ6 desaturase pathway led to increased direct elongation to 20:3n-3 by both DHA and LA. Possibly the route by 20:3n-3 and then Δ8 desaturation to 20:4n-3, bypassing the first Δ6 desaturase step, can partly explain the maintained or even increased levels of DHA production. LA increased DHA production in the phospholipid fraction of hepatocytes isolated from fish fed 0 and 0.5% EPA and/or DHA, indicating that LA has the potential to further increase the production of this health-beneficial FA in fish fed diets with low levels of EPA and/or DHA.

Decomposition pathways in age hardening of Ti-Al-N films

NASA Astrophysics Data System (ADS)

Rachbauer, R.; Massl, S.; Stergar, E.; Holec, D.; Kiener, D.; Keckes, J.; Patscheider, J.; Stiefel, M.; Leitner, H.; Mayrhofer, P. H.

2011-07-01

The ability to increase the thermal stability of protective coatings under work load gives rise to scientific and industrial interest in age hardening of complex nitride coating systems such as ceramic-like Ti1-xAlxN. However, the decomposition pathway of these systems from single-phase cubic to the thermodynamically stable binary nitrides (cubic TiN and wurtzite AlN), which are essential for age hardening, are not yet fully understood. In particular, the role of decomposition kinetics still requires more detailed investigation. In the present work, the combined effect of annealing time and temperature upon the nano-structural development of Ti0.46Al0.54N thin films is studied, with a thermal exposure of either 1 min or 120 min in 100 °C steps from 500 °C to 1400 °C. The impact of chemical changes at the atomic scale on the development of micro-strain and mechanical properties is studied by post-annealing investigations using X-ray diffraction, nanoindentation, 3D-atom probe tomography and high-resolution transmission electron microscopy. The results clearly demonstrate that the spinodal decomposition process, triggering the increase of micro-strain and hardness, although taking place throughout the entire volume, is enhanced at high diffusivity paths such as grain or column boundaries and followed within the grains. Ab initio calculations further show that the early stages of wurtzite AlN precipitation are connected with increased strain formation, which is in excellent agreement with experimental observations.

Mining pathway associations for disease-related pathway activity analysis based on gene expression and methylation data.

PubMed

Lee, Hyeonjeong; Shin, Miyoung

2017-01-01

The problem of discovering genetic markers as disease signatures is of great significance for the successful diagnosis, treatment, and prognosis of complex diseases. Even if many earlier studies worked on identifying disease markers from a variety of biological resources, they mostly focused on the markers of genes or gene-sets (i.e., pathways). However, these markers may not be enough to explain biological interactions between genetic variables that are related to diseases. Thus, in this study, our aim is to investigate distinctive associations among active pathways (i.e., pathway-sets) shown each in case and control samples which can be observed from gene expression and/or methylation data. The pathway-sets are obtained by identifying a set of associated pathways that are often active together over a significant number of class samples. For this purpose, gene expression or methylation profiles are first analyzed to identify significant (active) pathways via gene-set enrichment analysis. Then, regarding these active pathways, an association rule mining approach is applied to examine interesting pathway-sets in each class of samples (case or control). By doing so, the sets of associated pathways often working together in activity profiles are finally chosen as our distinctive signature of each class. The identified pathway-sets are aggregated into a pathway activity network (PAN), which facilitates the visualization of differential pathway associations between case and control samples. From our experiments with two publicly available datasets, we could find interesting PAN structures as the distinctive signatures of breast cancer and uterine leiomyoma cancer, respectively. Our pathway-set markers were shown to be superior or very comparable to other genetic markers (such as genes or gene-sets) in disease classification. Furthermore, the PAN structure, which can be constructed from the identified markers of pathway-sets, could provide deeper insights into

Ammonia oxidation pathways and nitrifier denitrification are significant sources of N2O and NO under low oxygen availability

PubMed Central

Zhu, Xia; Burger, Martin; Doane, Timothy A.; Horwath, William R.

2013-01-01

The continuous increase of nitrous oxide (N2O) abundance in the atmosphere is a global concern. Multiple pathways of N2O production occur in soil, but their significance and dependence on oxygen (O2) availability and nitrogen (N) fertilizer source are poorly understood. We examined N2O and nitric oxide (NO) production under 21%, 3%, 1%, 0.5%, and 0% (vol/vol) O2 concentrations following urea or ammonium sulfate [(NH4)2SO4] additions in loam, clay loam, and sandy loam soils that also contained ample nitrate. The contribution of the ammonia (NH3) oxidation pathways (nitrifier nitrification, nitrifier denitrification, and nitrification-coupled denitrification) and heterotrophic denitrification (HD) to N2O production was determined in 36-h incubations in microcosms by 15N-18O isotope and NH3 oxidation inhibition (by 0.01% acetylene) methods. Nitrous oxide and NO production via NH3 oxidation pathways increased as O2 concentrations decreased from 21% to 0.5%. At low (0.5% and 3%) O2 concentrations, nitrifier denitrification contributed between 34% and 66%, and HD between 34% and 50% of total N2O production. Heterotrophic denitrification was responsible for all N2O production at 0% O2. Nitrifier denitrification was the main source of N2O production from ammonical fertilizer under low O2 concentrations with urea producing more N2O than (NH4)2SO4 additions. These findings challenge established thought attributing N2O emissions from soils with high water content to HD due to presumably low O2 availability. Our results imply that management practices that increase soil aeration, e.g., reducing compaction and enhancing soil structure, together with careful selection of fertilizer sources and/or nitrification inhibitors, could decrease N2O production in agricultural soils. PMID:23576736

Ammonia oxidation pathways and nitrifier denitrification are significant sources of N2O and NO under low oxygen availability.

PubMed

Zhu, Xia; Burger, Martin; Doane, Timothy A; Horwath, William R

2013-04-16

The continuous increase of nitrous oxide (N2O) abundance in the atmosphere is a global concern. Multiple pathways of N2O production occur in soil, but their significance and dependence on oxygen (O2) availability and nitrogen (N) fertilizer source are poorly understood. We examined N2O and nitric oxide (NO) production under 21%, 3%, 1%, 0.5%, and 0% (vol/vol) O2 concentrations following urea or ammonium sulfate [(NH4)2SO4] additions in loam, clay loam, and sandy loam soils that also contained ample nitrate. The contribution of the ammonia (NH3) oxidation pathways (nitrifier nitrification, nitrifier denitrification, and nitrification-coupled denitrification) and heterotrophic denitrification (HD) to N2O production was determined in 36-h incubations in microcosms by (15)N-(18)O isotope and NH3 oxidation inhibition (by 0.01% acetylene) methods. Nitrous oxide and NO production via NH3 oxidation pathways increased as O2 concentrations decreased from 21% to 0.5%. At low (0.5% and 3%) O2 concentrations, nitrifier denitrification contributed between 34% and 66%, and HD between 34% and 50% of total N2O production. Heterotrophic denitrification was responsible for all N2O production at 0% O2. Nitrifier denitrification was the main source of N2O production from ammonical fertilizer under low O2 concentrations with urea producing more N2O than (NH4)2SO4 additions. These findings challenge established thought attributing N2O emissions from soils with high water content to HD due to presumably low O2 availability. Our results imply that management practices that increase soil aeration, e.g., reducing compaction and enhancing soil structure, together with careful selection of fertilizer sources and/or nitrification inhibitors, could decrease N2O production in agricultural soils.

Highly scalable and robust rule learner: performance evaluation and comparison.

PubMed

Kurgan, Lukasz A; Cios, Krzysztof J; Dick, Scott

2006-02-01

Business intelligence and bioinformatics applications increasingly require the mining of datasets consisting of millions of data points, or crafting real-time enterprise-level decision support systems for large corporations and drug companies. In all cases, there needs to be an underlying data mining system, and this mining system must be highly scalable. To this end, we describe a new rule learner called DataSqueezer. The learner belongs to the family of inductive supervised rule extraction algorithms. DataSqueezer is a simple, greedy, rule builder that generates a set of production rules from labeled input data. In spite of its relative simplicity, DataSqueezer is a very effective learner. The rules generated by the algorithm are compact, comprehensible, and have accuracy comparable to rules generated by other state-of-the-art rule extraction algorithms. The main advantages of DataSqueezer are very high efficiency, and missing data resistance. DataSqueezer exhibits log-linear asymptotic complexity with the number of training examples, and it is faster than other state-of-the-art rule learners. The learner is also robust to large quantities of missing data, as verified by extensive experimental comparison with the other learners. DataSqueezer is thus well suited to modern data mining and business intelligence tasks, which commonly involve huge datasets with a large fraction of missing data.

Revised Total Coliform Rule Implementation in Wyoming and on Tribal Lands in EPA Region 8

EPA Pesticide Factsheets

The Revised Total Coliform Rule (RTCR) aims to increase public health protection through the reduction of potential pathways for fecal contamination in the distribution system of a public water system (PWS).

N-(3-Oxo-acyl)-homoserine lactone induces apoptosis primarily through a mitochondrial pathway in fibroblasts.

PubMed

Neely, Aaron M; Zhao, Guoping; Schwarzer, Christian; Stivers, Nicole S; Whitt, Aaron G; Meng, Shuhan; Burlison, Joseph A; Machen, Terry E; Li, Chi

2018-01-01

N-(3-Oxododecanoyl)-l-homoserine lactone (C12) is produced by Pseudomonas aeruginosa to function as a quorum-sensing molecule for bacteria-bacteria communication. C12 is also known to influence many aspects of human host cell physiology, including induction of cell death. However, the signalling pathway(s) leading to C12-triggered cell death is (are) still not completely known. To clarify cell death signalling induced by C12, we examined mouse embryonic fibroblasts deficient in "initiator" caspases or "effector" caspases. Our data indicate that C12 selectively induces the mitochondria-dependent intrinsic apoptotic pathway by quickly triggering mitochondrial outer membrane permeabilisation. Importantly, the activities of C12 to permeabilise mitochondria are independent of activation of both "initiator" and "effector" caspases. Furthermore, C12 directly induces mitochondrial outer membrane permeabilisation in vitro. Overall, our study suggests a mitochondrial apoptotic signalling pathway triggered by C12, in which C12 or its metabolite(s) acts on mitochondria to permeabilise mitochondria, leading to activation of apoptosis. © 2017 John Wiley & Sons Ltd.

Seasonal induction of alternative principal pathway for rose flower scent

PubMed Central

Hirata, Hiroshi; Ohnishi, Toshiyuki; Tomida, Kensuke; Ishida, Haruka; Kanda, Momoyo; Sakai, Miwa; Yoshimura, Jin; Suzuki, Hideyuki; Ishikawa, Takamasa; Dohra, Hideo; Watanabe, Naoharu

2016-01-01

Ecological adaptations to seasonal changes are often observed in the phenotypic traits of plants and animals, and these adaptations are usually expressed through the production of different biochemical end products. In this study, ecological adaptations are observed in a biochemical pathway without alteration of the end products. We present an alternative principal pathway to the characteristic floral scent compound 2-phenylethanol (2PE) in roses. The new pathway is seasonally induced in summer as a heat adaptation that uses rose phenylpyruvate decarboxylase (RyPPDC) as a novel enzyme. RyPPDC transcript levels and the resulting production of 2PE are increased time-dependently under high temperatures. The novel summer pathway produces levels of 2PE that are several orders of magnitude higher than those produced by the previously known pathway. Our results indicate that the alternative principal pathway identified here is a seasonal adaptation for managing the weakened volatility of summer roses. PMID:26831950

Integrated analysis of breast cancer cell lines reveals unique signaling pathways

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

Heiser, Laura M.; Wang, Nicholas J.; Talcott, Carolyn L.

Cancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EGFR-MAPK pathway is common in breast cancer, though the manner in which deregulation occurs varies between both individuals and cancer subtypes. We were interested in identifying subnetworks within the EGFR-MAPK pathway that are similarly deregulated across subsets of breast cancers. To that end, we mapped genomic, transcriptional and proteomic profiles for 30 breast cancer cell lines onto a curated Pathway Logic symbolic systems model of EGFR-MEK signaling. This model was comprised ofmore » 539 molecular states and 396 rules governing signaling between active states. We analyzed these models and identified several subtype specific subnetworks, including one that suggested PAK1 is particularly important in regulating the MAPK cascade when it is over-expressed. We hypothesized that PAK1 overexpressing cell lines would have increased sensitivity to MEK inhibitors. We tested this experimentally by measuring quantitative responses of 20 breast cancer cell lines to three MEK inhibitors. We found that PAK1 over-expressing luminal breast cancer cell lines are significantly more sensitive to MEK inhibition as compared to those that express PAK1 at low levels. This indicates that PAK1 over-expression may be a useful clinical marker to identify patient populations that may be sensitive to MEK inhibitors. All together, our results support the utility of symbolic system biology models for identification of therapeutic approaches that will be effective against breast cancer subsets.« less

Integrated analysis of breast cancer cell lines reveals unique signaling pathways.

PubMed

Heiser, Laura M; Wang, Nicholas J; Talcott, Carolyn L; Laderoute, Keith R; Knapp, Merrill; Guan, Yinghui; Hu, Zhi; Ziyad, Safiyyah; Weber, Barbara L; Laquerre, Sylvie; Jackson, Jeffrey R; Wooster, Richard F; Kuo, Wen Lin; Gray, Joe W; Spellman, Paul T

2009-01-01

Cancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EgfR-MAPK pathway is common in breast cancer, though the manner in which deregulation occurs varies between both individuals and cancer subtypes. We were interested in identifying subnetworks within the EgfR-MAPK pathway that are similarly deregulated across subsets of breast cancers. To that end, we mapped genomic, transcriptional and proteomic profiles for 30 breast cancer cell lines onto a curated Pathway Logic symbolic systems model of EgfR-MAPK signaling. This model was composed of 539 molecular states and 396 rules governing signaling between active states. We analyzed these models and identified several subtype-specific subnetworks, including one that suggested Pak1 is particularly important in regulating the MAPK cascade when it is over-expressed. We hypothesized that Pak1 over-expressing cell lines would have increased sensitivity to Mek inhibitors. We tested this experimentally by measuring quantitative responses of 20 breast cancer cell lines to three Mek inhibitors. We found that Pak1 over-expressing luminal breast cancer cell lines are significantly more sensitive to Mek inhibition compared to those that express Pak1 at low levels. This indicates that Pak1 over-expression may be a useful clinical marker to identify patient populations that may be sensitive to Mek inhibitors. All together, our results support the utility of symbolic system biology models for identification of therapeutic approaches that will be effective against breast cancer subsets.

Communicating eating-related rules. Suggestions are more effective than restrictions.

PubMed

Stok, F Marijn; de Vet, Emely; de Wit, John B F; Renner, Britta; de Ridder, Denise T D

2015-03-01

A common social influence technique for curbing unhealthy eating behavior is to communicate eating-related rules (e.g. 'you should not eat unhealthy food'). Previous research has shown that such restrictive rules sometimes backfire and actually increase unhealthy consumption. In the current studies, we aimed to investigate if a milder form of social influence, a suggested rule, is more successful in curbing intake of unhealthy food. We also investigated how both types of rules affected psychological reactance. Students (N = 88 in Study 1, N = 51 in Study 2) completed a creativity task while a bowl of M&M's was within reach. Consumption was either explicitly forbidden (restrictive rule) or mildly discouraged (suggested rule). In the control condition, consumption was either explicitly allowed (Study 1) or M&M's were not provided (Study 2). Measures of reactance were assessed after the creativity task. Subsequently, a taste test was administered where all participants were allowed to consume M&M's. Across both studies, consumption during the creativity task did not differ between the restrictive- and suggested-rule-conditions, indicating that both are equally successful in preventing initial consumption. Restrictive-rule-condition participants reported higher reactance and consumed more in the free-eating taste-test phase than suggested-rule-condition participants and control-group participants, indicating a negative after-effect of restriction. RESULTS show that there are more and less effective ways to communicate eating-related rules. A restrictive rule, as compared to a suggested rule, induced psychological reactance and led to greater unhealthy consumption when participants were allowed to eat freely. It is important to pay attention to the way in which eating-related rules are communicated. Copyright © 2014 Elsevier Ltd. All rights reserved.

Two distinct cytokinesis pathways drive trypanosome cell division initiation from opposite cell ends

PubMed Central

Zhou, Qing; Gu, Jianhua; Lun, Zhao-Rong; Ayala, Francisco J.; Li, Ziyin

2016-01-01

Cytokinesis in Trypanosoma brucei, an early branching protozoan, occurs along its longitudinal axis uni-directionally from the anterior tip of the new flagellum attachment zone filament toward the cell’s posterior end. However, the underlying mechanisms remain elusive. Here we report that cytokinesis in T. brucei is regulated by a concerted action of Polo-like kinase, Aurora B kinase, and a trypanosome-specific protein CIF1. Phosphorylation of CIF1 by Polo-like kinase targets it to the anterior tip of the new flagellum attachment zone filament, where it subsequently recruits Aurora B kinase to initiate cytokinesis. Consistent with its role, CIF1 depletion inhibits cytokinesis initiation from the anterior end of the cell, but, surprisingly, triggers cytokinesis initiation from the posterior end of the cell, suggesting the activation of an alternative cytokinesis from the opposite cell end. Our results reveal the mechanistic roles of CIF1 and Polo-like kinase in cytokinesis initiation and elucidate the mechanism underlying the recruitment of Aurora B kinase to the cytokinesis initiation site at late anaphase. These findings also delineate a signaling cascade controlling cytokinesis initiation from the anterior end of the cell and uncover a backup cytokinesis that is initiated from the posterior end of the cell when the typical anterior-to-posterior cytokinesis is compromised. PMID:26929336

On the fusion of tuning parameters of fuzzy rules and neural network

NASA Astrophysics Data System (ADS)

Mamuda, Mamman; Sathasivam, Saratha

2017-08-01

Learning fuzzy rule-based system with neural network can lead to a precise valuable empathy of several problems. Fuzzy logic offers a simple way to reach at a definite conclusion based upon its vague, ambiguous, imprecise, noisy or missing input information. Conventional learning algorithm for tuning parameters of fuzzy rules using training input-output data usually end in a weak firing state, this certainly powers the fuzzy rule and makes it insecure for a multiple-input fuzzy system. In this paper, we introduce a new learning algorithm for tuning the parameters of the fuzzy rules alongside with radial basis function neural network (RBFNN) in training input-output data based on the gradient descent method. By the new learning algorithm, the problem of weak firing using the conventional method was addressed. We illustrated the efficiency of our new learning algorithm by means of numerical examples. MATLAB R2014(a) software was used in simulating our result The result shows that the new learning method has the best advantage of training the fuzzy rules without tempering with the fuzzy rule table which allowed a membership function of the rule to be used more than one time in the fuzzy rule base.

Antecedents and consequences of emotional display rule perceptions.

PubMed

Diefendorff, James M; Richard, Erin M

2003-04-01

Central to all theories of emotional labor is the idea that individuals follow emotional display rules that specify the appropriate expression of emotions on the job. This investigation examined antecedents and consequences of emotional display rule perceptions. Full-time working adults (N = 152) from a variety of occupations provided self-report data, and supervisors and coworkers completed measures pertaining to the focal employees. Results using structural equation modeling revealed that job-based interpersonal requirements, supervisor display rule perceptions, and employee extraversion and neuroticism were predictive of employee display rule perceptions. Employee display rule perceptions, in turn, were related to self-reported job satisfaction and coworker ratings of employees' emotional displays on the job. Finally, neuroticism had direct negative relationships with job satisfaction and coworker ratings of employees' emotional displays.

Quantifying N2O emissions and production pathways from fresh waste during the initial stage of disposal to a landfill.

PubMed

Wang, Xiaojun; Jia, Mingsheng; Zhang, Han; Pan, Songqing; Kao, Chih Ming; Chen, Shaohua

2017-05-01

Intensive nitrous oxide (N 2 O) emissions usually occur at the working face of landfills. However, the specific amounts and contributions of the multiple pathways to N 2 O emissions are poorly understood. N 2 O emissions and the mutual conversions of N-species in both open and sealed simulated landfill reactors filled with fresh refuse were examined during a 100-h incubation period, and N 2 O sources were calculated using 15 N isotope labelling. N 2 O peak fluxes were above 70μgNkg -1 waste h -1 for both treatments. The sealed incubation reactors became a N 2 O sink when N 2 O in the ambient environment was sufficient. The total amount of N 2 O emissions under sealed conditions was 2.15±0.56mgNkg -1 waste, which was higher than that under open conditions (1.91±0.34mgNkg -1 waste). The NO 2 - peak appeared prior to the peak in N 2 O flux. The degree and duration of total nitrogen reduction in open incubations were larger and longer than those of sealed incubations and could possibly be due to oxygen supplementation. Denitrification (DF) was a major source of N 2 O generation during these incubations. The contribution of the DF pathway decreased from 89.2% to 61.3% during the open incubations. The effects of nitrification (NF) and nitrification-coupled denitrification (NCD) increased during the increasing phase and the decreasing phase of N 2 O flux, contributing 24.1-37.4% and 31.7-34.4% of total N 2 O emissions, respectively. In sealed treatments, the DF pathway accounted for more than 90% of the total N 2 O emission during the entire incubation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Correlating Temporal Rules to Time-Series Data With Rule-Based Intuition

DTIC Science & Technology

2010-03-01

t i m e o b j e c t and r e t u r n s True ( i n r u l e ) or F a l s e ( n o t i n r u l e ) . Des ign : r u l e l i s t − an a r r a y t h...e . d a t e o b j e c t s . ””” def i n i t ( s e l f , name , days , i g n o r e y e a r =True ) : s e l f . name = name s e l f . days = days 49 s...a l . tm wday == 6 r u l e l i s t . append ( Sunday ( ) ) c l a s s J a n u a r y ( TimeRule ) : ””” I s True i f i t i s January

Study of Staphylococcus aureus N315 Pathogenic Genes by Text Mining and Enrichment Analysis of Pathways and Operons.

PubMed

Yang, Chun-Feng; Gou, Wei-Hui; Dai, Xin-Lun; Li, Yu-Mei

2018-06-01

Staphylococcus aureus (S. aureus) is a versatile pathogen found in many environments and can cause nosocomial infections in the community and hospitals. S. aureus infection is an increasingly serious threat to global public health that requires action across many government bodies, medical and health sectors, and scientific research institutions. In the present study, S. aureus N315 genes that have been shown in the literature to be pathogenic were extracted using a bibliometric method for functional enrichment analysis of pathways and operons to statistically discover novel pathogenic genes associated with S. aureus N315. A total of 383 pathogenic genes were mined from the literature using bibliometrics, and subsequently a few new pathogenic genes of S. aureus N315 were identified by functional enrichment analysis of pathways and operons. The discovery of these novel S. aureus N315 pathogenic genes is of great significance to treat S. aureus induced diseases and identify potential diagnostic markers, thus providing theoretical fundamentals for epidemiological prevention.

N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes.

PubMed

Li, Qike; Schissler, A Grant; Gardeux, Vincent; Achour, Ikbel; Kenost, Colleen; Berghout, Joanne; Li, Haiquan; Zhang, Hao Helen; Lussier, Yves A

2017-05-24

Transcriptome analytic tools are commonly used across patient cohorts to develop drugs and predict clinical outcomes. However, as precision medicine pursues more accurate and individualized treatment decisions, these methods are not designed to address single-patient transcriptome analyses. We previously developed and validated the N-of-1-pathways framework using two methods, Wilcoxon and Mahalanobis Distance (MD), for personal transcriptome analysis derived from a pair of samples of a single patient. Although, both methods uncover concordantly dysregulated pathways, they are not designed to detect dysregulated pathways with up- and down-regulated genes (bidirectional dysregulation) that are ubiquitous in biological systems. We developed N-of-1-pathways MixEnrich, a mixture model followed by a gene set enrichment test, to uncover bidirectional and concordantly dysregulated pathways one patient at a time. We assess its accuracy in a comprehensive simulation study and in a RNA-Seq data analysis of head and neck squamous cell carcinomas (HNSCCs). In presence of bidirectionally dysregulated genes in the pathway or in presence of high background noise, MixEnrich substantially outperforms previous single-subject transcriptome analysis methods, both in the simulation study and the HNSCCs data analysis (ROC Curves; higher true positive rates; lower false positive rates). Bidirectional and concordant dysregulated pathways uncovered by MixEnrich in each patient largely overlapped with the quasi-gold standard compared to other single-subject and cohort-based transcriptome analyses. The greater performance of MixEnrich presents an advantage over previous methods to meet the promise of providing accurate personal transcriptome analysis to support precision medicine at point of care.

Immunofluorescence-based methods to monitor DNA end resection

PubMed Central

Mukherjee, Bipasha; Tomimatsu, Nozomi; Burma, Sandeep

2017-01-01

Summary Double-strand breaks (DSBs) are the most deleterious amongst all types of DNA damage that can occur in the cell. These breaks arise from both endogenous (for example, DNA replication stress) as well as exogenous insults (for example, ionizing radiation). DSBs are principally repaired by one of two major pathways: non-homologous end joining (NHEJ) or homologous recombination (HR). NHEJ is an error-prone process that can occur in all phases of the cell cycle, while HR is limited to the S and G2 phases of the cell cycle when a sister chromatid is available as a template for error-free repair. The first step in HR is “DNA end resection”, a process during which the broken DNA end is converted into a long stretch of 3′-ended single-stranded DNA (ssDNA). In recent years, DNA end resection has been identified as a pivotal step that controls “repair pathway choice” i.e., the appropriate choice between NHEJ and HR for DSB repair. Therefore, methods to quantitatively or semi-quantitatively assess DNA end resection have gained importance in laboratories working on DNA repair. In this chapter, we describe two simple immunofluorescence-based techniques to monitor DNA end resection in mammalian cells. The first technique involves immuno-detection of Replication Protein A (RPA), a ssDNA-binding protein that binds to resected DNA. The second technique involves labeling of genomic DNA with 5-bromo-2′-deoxyuridine (BrdU) that can be detected by anti-BrdU antibody only after the DNA becomes single stranded due to resection. These methods are not complicated, do not involve sophisticated instrumentation or reporter constructs, and can be applied to most mammalian cell lines, and therefore, should be of broad utility as simple ways of monitoring DNA end resection in vivo. PMID:25804748

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

PubMed Central

Leno-Colorado, Jordi; Hudson, Nick J.; Reverter, Antonio; Pérez-Enciso, Miguel

2017-01-01

Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig (Sus scrofa) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst) and linkage disequilibrium (nSL) statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q-value < 0.05 in Asia and Europe, respectively; five were shared across continents. In Asia, we found six significant pathways related to behavior, which involved essential neurotransmitters like dopamine and serotonin. Several significant pathways were interrelated and shared a variable percentage of genes. There were 12 genes present in >10 significant pathways (in terms of Fst), comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis), a similarly important target trait during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and breeding

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia.

PubMed

Leno-Colorado, Jordi; Hudson, Nick J; Reverter, Antonio; Pérez-Enciso, Miguel

2017-07-05

Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig ( Sus scrofa ) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst) and linkage disequilibrium (nSL) statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q -value < 0.05 in Asia and Europe, respectively; five were shared across continents. In Asia, we found six significant pathways related to behavior, which involved essential neurotransmitters like dopamine and serotonin. Several significant pathways were interrelated and shared a variable percentage of genes. There were 12 genes present in >10 significant pathways (in terms of Fst), comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis), a similarly important target trait during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and

Acentric chromosome ends are prone to fusion with functional chromosome ends through a homology-directed rearrangement

PubMed Central

Ohno, Yuko; Ogiyama, Yuki; Kubota, Yoshino; Kubo, Takuya; Ishii, Kojiro

2016-01-01

The centromeres of many eukaryotic chromosomes are established epigenetically on potentially variable tandem repeats; hence, these chromosomes are at risk of being acentric. We reported previously that artificially created acentric chromosomes in the fission yeast Schizosaccharomyces pombe can be rescued by end-to-end fusion with functional chromosomes. Here, we show that most acentric/functional chromosome fusion events in S. pombe cells harbouring an acentric chromosome I differed from the non-homologous end-joining-mediated rearrangements that result in deleterious dicentric fusions in normal cells, and were elicited by a previously unidentified homologous recombination (HR) event between chromosome end-associated sequences. The subtelomere repeats associated with the non-fusogenic ends were also destabilized in the surviving cells, suggesting a causal link between general subtelomere destabilization and acentric/functional chromosome fusion. A mutational analysis indicated that a non-canonical HR pathway was involved in the rearrangement. These findings are indicative of a latent mechanism that conditionally induces general subtelomere instability, presumably in the face of accidental centromere loss events, resulting in rescue of the fatal acentric chromosomes by interchromosomal HR. PMID:26433224

Genetic and mechanistic diversity of piRNA 3' end formation

PubMed Central

Handler, Dominik; Mohn, Fabio; Ameres, Stefan L.; Brennecke, Julius

2016-01-01

Small regulatory RNAs guide Argonaute (Ago) proteins in a sequence-specific manner to their targets and thereby play important roles in eukaryotic gene silencing1. Of the three small RNA classes, microRNAs and siRNAs are processed from double-stranded precursors into defined 21- to 23-mers by Dicer, an endoribonuclease with intrinsic ruler function. piRNAs—the 22-30 nt long guides for PIWI-clade Ago proteins that silence transposons in animal gonads—are generated Dicer-independently from single-stranded precursors2,3. piRNA 5' ends are defined either by Zucchini, a mitochondria-anchored endonuclease4,5, or by piRNA-guided target cleavage6,7. Formation of piRNA 3' ends is poorly understood. Here, we find that two genetically and mechanistically distinct pathways generate piRNA 3' ends in Drosophila. The initiating nucleases are either Zucchini or the PIWI-clade proteins Aubergine (Aub)/Ago3. While Zucchini-mediated cleavages directly define mature piRNA 3' ends8,9, Aub/Ago3-mediated cleavages liberate pre-piRNAs that require extensive resection by the 3'-to-5' exoribonuclease Nibbler/Mut-710–13. The relative activity of these two pathways dictates the extent to which piRNAs are fueled into cytoplasmic or nuclear PIWI-clade proteins and thereby sets the balance between post-transcriptional and transcriptional silencing. Strikingly, loss of both Zucchini and Nibbler reveals a minimal, Argonaute-driven small RNA biogenesis pathway where piRNA 5' and 3' ends are directly produced by closely spaced Aub/Ago3-mediated cleavage events. Our data establish a coherent blueprint for piRNA biogenesis, and set the stage for the mechanistic dissection of the processes that govern piRNA 3' end formation. PMID:27851737

Improved n-butanol production via co-expression of membrane-targeted tilapia metallothionein and the clostridial metabolic pathway in Escherichia coli.

PubMed

Chin, Wei-Chih; Lin, Kuo-Hsing; Liu, Chun-Chi; Tsuge, Kenji; Huang, Chieh-Chen

2017-04-11

N-Butanol has favorable characteristics for use as either an alternative fuel or platform chemical. Bio-based n-butanol production using microbes is an emerging technology that requires further development. Although bio-industrial microbes such as Escherichia coli have been engineered to produce n-butanol, reactive oxygen species (ROS)-mediated toxicity may limit productivity. Previously, we show that outer-membrane-targeted tilapia metallothionein (OmpC-TMT) is more effective as an ROS scavenger than human and mouse metallothioneins to reduce oxidative stress in the host cell. The host strain (BUT1-DE) containing the clostridial n-butanol pathway displayed a decreased growth rate and limited n-butanol productivity, likely due to ROS accumulation. The clostridial n-butanol pathway was co-engineered with inducible OmpC-TMT in E. coli (BUT3-DE) for simultaneous ROS removal, and its effect on n-butanol productivity was examined. The ROS scavenging ability of cells overexpressing OmpC-TMT was examined and showed an approximately twofold increase in capacity. The modified strain improved n-butanol productivity to 320 mg/L, whereas the control strain produced only 95.1 mg/L. Transcriptomic analysis revealed three major KEGG pathways that were significantly differentially expressed in the BUT3-DE strain compared with their expression in the BUT1-DE strain, including genes involved in oxidative phosphorylation, fructose and mannose metabolism and glycolysis/gluconeogenesis. These results indicate that OmpC-TMT can increase n-butanol production by scavenging ROS. The transcriptomic analysis suggested that n-butanol causes quinone malfunction, resulting in oxidative-phosphorylation-related nuo operon downregulation, which would diminish the ability to convert NADH to NAD + and generate proton motive force. However, fructose and mannose metabolism-related genes (fucA, srlE and srlA) were upregulated, and glycolysis/gluconeogenesis-related genes (pfkB, pgm) were

Comparison of metabolic pathways of different α-N-heterocyclic thiosemicarbazones.

PubMed

Pelivan, Karla; Frensemeier, Lisa M; Karst, Uwe; Koellensperger, Gunda; Heffeter, Petra; Keppler, Bernhard K; Kowol, Christian R

2018-03-01

Clinical failure of novel drugs is often related to their rapid metabolism and excretion. This highlights the importance of elucidation of their pharmacokinetic profile already at the preclinical stage of drug development. Triapine, the most prominent representative of α-N-heterocyclic thiosemicarbazones, was investigated in more than 30 clinical phase I/II trials, but the results against solid tumors were disappointing. Recent investigations from our group suggested that this is, at least partially, based on the fast metabolism and excretion. In order to establish more detailed structure/activity/metabolism relationships, herein a panel of 10 different Triapine derivatives was investigated for their metabolic pathways. From the biological point of view, the panel consists of terminally dimethylated thiosemicarbazones with nanomolar IC 50 values, derivatives with micromolar cytotoxicities comparable to Triapine and a completely inactive representative. To study the oxidative metabolism, a purely instrumental approach based on electrochemistry/mass spectrometry was applied and the results were compared to the data obtained from microsomal incubations. Overall, the investigated thiosemicarbazones underwent the phase I metabolic reactions dehydrogenation, hydroxylation, oxidative desulfuration (to semicarbazone and amidrazone) and demethylation. Notably, dehydrogenation resulted in a ring-closure reaction with formation of thiadiazoles. Although strong differences between the metabolic pathways of the different thiosemicarbazones were observed, they could not be directly correlated to their cytotoxicities. Finally, the metabolic pathways for the most cytotoxic compound were elucidated also in tissues collected from drug-treated mice, confirming the data obtained by electrochemical oxidation and microsomes. In addition, the in vivo experiments revealed a very fast metabolism and excretion of the compound. Graphical abstract Structure

Pancreatitis with normal lipase and amylase in setting of end-stage renal disease.

PubMed

Sharma, Anuj; Masood, Umair; Khan, Babar; Chawla, Kunal; Manocha, Divey

2017-09-01

Pancreatitis with normal lipase and amylase level is a rare phenomenon. This is especially true in patient with end-stage renal disease as lipase and amylase are renally excreted. Literature review reveals previous case report of pancreatitis with normal lipase and amylase level, however, none of them occurred in the setting of end-stage renal disease. Our case is the first such reported case of pancreatitis in such setting. Here we report a 30year old male with past medical history of end-stage renal disease who presented in emergency department with acute abdominal pain. Laboratory work up revealed normal lipase and amylase level. However, radiological work up was consistent with pancreatitis. This case report highlight the importance of taking the overall clinical picture rather than laboratory work up to rule in or rule out the diagnosis of pancreatitis. Furthermore, this should also serve an important reminder for clinicians to further investigate where clinical suspicion for pancreatitis is high. Copyright © 2017 Elsevier Inc. All rights reserved.

Repair of Double-Strand Breaks by End Joining

PubMed Central

Chiruvella, Kishore K.; Liang, Zhuobin; Wilson, Thomas E.

2013-01-01

Nonhomologous end joining (NHEJ) refers to a set of genome maintenance pathways in which two DNA double-strand break (DSB) ends are (re)joined by apposition, processing, and ligation without the use of extended homology to guide repair. Canonical NHEJ (c-NHEJ) is a well-defined pathway with clear roles in protecting the integrity of chromosomes when DSBs arise. Recent advances have revealed much about the identity, structure, and function of c-NHEJ proteins, but many questions exist regarding their concerted action in the context of chromatin. Alternative NHEJ (alt-NHEJ) refers to more recently described mechanism(s) that repair DSBs in less-efficient backup reactions. There is great interest in defining alt-NHEJ more precisely, including its regulation relative to c-NHEJ, in light of evidence that alt-NHEJ can execute chromosome rearrangements. Progress toward these goals is reviewed. PMID:23637284

Enhanced Formation of Methylglyoxal-Derived Advanced Glycation End Products in Arabidopsis Under Ammonium Nutrition

PubMed Central

Borysiuk, Klaudia; Ostaszewska-Bugajska, Monika; Vaultier, Marie-Noëlle; Hasenfratz-Sauder, Marie-Paule; Szal, Bożena

2018-01-01

Nitrate (NO3–) and ammonium (NH4+) are prevalent nitrogen (N) sources for plants. Although NH4+ should be the preferred form of N from the energetic point of view, ammonium nutrition often exhibits adverse effects on plant physiological functions and induces an important growth-limiting stress referred as ammonium syndrome. The effective incorporation of NH4+ into amino acid structures requires high activity of the mitochondrial tricarboxylic acid cycle and the glycolytic pathway. An unavoidable consequence of glycolytic metabolism is the production of methylglyoxal (MG), which is very toxic and inhibits cell growth in all types of organisms. Here, we aimed to investigate MG metabolism in Arabidopsis thaliana plants grown on NH4+ as a sole N source. We found that changes in activities of glycolytic enzymes enhanced MG production and that markedly elevated MG levels superseded the detoxification capability of the glyoxalase pathway. Consequently, the excessive accumulation of MG was directly involved in the induction of dicarbonyl stress by introducing MG-derived advanced glycation end products (MAGEs) to proteins. The severe damage to proteins was not within the repair capacity of proteolytic enzymes. Collectively, our results suggest the impact of MG (mediated by MAGEs formation in proteins) in the contribution to NH4+ toxicity symptoms in Arabidopsis. PMID:29881392

Tyramine Pathways in Citrus Plant Defense: Glycoconjugates of Tyramine and Its N-Methylated Derivatives.

PubMed

Servillo, Luigi; Castaldo, Domenico; Giovane, Alfonso; Casale, Rosario; D'Onofrio, Nunzia; Cautela, Domenico; Balestrieri, Maria Luisa

2017-02-01

Glucosylated forms of tyramine and some of its N-methylated derivatives are here reported for the first time to occur in Citrus genus plants. The compounds tyramine-O-β-d-glucoside, N-methyltyramine-O-β-d-glucoside, and N,N-dimethyltyramine-O-β-d-glucoside were detected in juice and leaves of sweet orange, bitter orange, bergamot, citron, lemon, mandarin, and pomelo. The compounds were identified by mass spectrometric analysis, enzymatic synthesis, and comparison with extracts of Stapelia hirsuta L., a plant belonging to the Apocynaceae family in which N,N-dimethyltyramine-O-β-d-glucoside was identified by others. Interestingly, in Stapelia hirsuta we discovered also tyramine-O-β-d-glucoside, N-methyltyramine-O-β-d-glucoside, and the tyramine metabolite, N,N,N-trimethyltyramine-O-β-glucoside. However, the latter tyramine metabolite, never described before, was not detected in any of the Citrus plants included in this study. The presence of N-methylated tyramine derivatives and their glucosylated forms in Citrus plants, together with octopamine and synephrine, also deriving from tyramine, supports the hypothesis of specific biosynthetic pathways of adrenergic compounds aimed to defend against biotic stress.

Rule-Based Event Processing and Reaction Rules

NASA Astrophysics Data System (ADS)

Paschke, Adrian; Kozlenkov, Alexander

Reaction rules and event processing technologies play a key role in making business and IT / Internet infrastructures more agile and active. While event processing is concerned with detecting events from large event clouds or streams in almost real-time, reaction rules are concerned with the invocation of actions in response to events and actionable situations. They state the conditions under which actions must be taken. In the last decades various reaction rule and event processing approaches have been developed, which for the most part have been advanced separately. In this paper we survey reaction rule approaches and rule-based event processing systems and languages.

Iron-induced oxidative injury differentially regulates PI3K/Akt/GSK3beta pathway in synaptic endings from adult and aged rats.

PubMed

Uranga, Romina María; Giusto, Norma María; Salvador, Gabriela Alejandra

2009-10-01

In this work we study the state of phosphoinositide-3-kinase/Akt/glycogen synthase kinase 3 beta (PI3K/Akt/GSK3beta) signaling during oxidative injury triggered by free iron using cerebral cortex synaptic endings isolated from adult (4-month-old) and aged (28-month-old) rats. Synaptosomes were exposed to FeSO4 (50 microM) for different periods of time and synaptosomal viability and the state of the PI3K/Akt/GSK3beta pathway were evaluated in adult and aged animals. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide reduction and lactate dehydrogenase leakage were significantly affected in both age groups. However, aged animals showed a greater susceptibility to oxidative stress. In adults, Akt was activated after a brief exposure time (5 min), whereas in aged animals activation occurred after 5 and 30 min of incubation with the metal ion. GSK3beta phosphorylation showed the same activation pattern as that observed for Akt. Both Akt and GSK3beta phosphorylation were dependent on PI3K activation. Extracellular signal-regulated kinases 1 and 2 (ERK1/2) activation was temporally coincident with Akt activation and was PI3K dependent in adults, whereas ERK1/2 activation in aged rats was higher than that observed in adults and showed no dependence on PI3K activity. We demonstrate here that synaptic endings from adult and aged animals subjected to iron-induced neurotoxicity show a differential profile in the activation of PI3K/Akt/GSK3beta. Our results strongly suggest that the increased susceptibility of aged animals to oxidative injury provokes a differential modulation of key signaling pathways involved in synaptic plasticity and neuronal survival.

49 CFR 234.305 - Remedial actions in response to reports of unsafe conditions at highway-rail and pathway grade...

Code of Federal Regulations, 2012 CFR

2012-10-01

... conditions at highway-rail and pathway grade crossings. 234.305 Section 234.305 Transportation Other... Pathway Grade Crossings § 234.305 Remedial actions in response to reports of unsafe conditions at highway-rail and pathway grade crossings. (a) General rule on response to credible report of warning system...

49 CFR 234.305 - Remedial actions in response to reports of unsafe conditions at highway-rail and pathway grade...

Code of Federal Regulations, 2014 CFR

2014-10-01

... conditions at highway-rail and pathway grade crossings. 234.305 Section 234.305 Transportation Other... Pathway Grade Crossings § 234.305 Remedial actions in response to reports of unsafe conditions at highway-rail and pathway grade crossings. (a) General rule on response to credible report of warning system...

49 CFR 234.305 - Remedial actions in response to reports of unsafe conditions at highway-rail and pathway grade...

Code of Federal Regulations, 2013 CFR

2013-10-01

... conditions at highway-rail and pathway grade crossings. 234.305 Section 234.305 Transportation Other... Pathway Grade Crossings § 234.305 Remedial actions in response to reports of unsafe conditions at highway-rail and pathway grade crossings. (a) General rule on response to credible report of warning system...

Injury of cortical neurons is caused by the advanced glycation end products-mediated pathway☆

PubMed Central

Xing, Ying; Zhang, Xu; Song, Xiangfu; Lv, Zhongwen; Hou, Lingling; Li, Fei

2013-01-01

Advanced glycation end products lead to cell apoptosis, and cause cell death by increasing endoplasmic reticulum stress. Advanced glycation end products alone may also directly cause damage to tissues and cells, but the precise mechanism remains unknown. This study used primary cultures of rat cerebral cortex neurons, and treated cells with different concentrations of glycation end products (50, 100, 200, 400 mg/L), and with an antibody for the receptor of advanced glycation end products before and after treatment with advanced glycation end products. The results showed that with increasing concentrations of glycation end products, free radical content increased in neurons, and the number of apoptotic cells increased in a dose-dependent manner. Before and after treatment of advanced glycation end products, the addition of the antibody against advanced glycation end-products markedly reduced hydroxyl free radicals, malondialdehyde levels, and inhibited cell apoptosis. This result indicated that the antibody for receptor of advanced glycation end-products in neurons from the rat cerebral cortex can reduce glycation end product-induced oxidative stress damage by suppressing glycation end product receptors. Overall, our study confirms that the advanced glycation end products-advanced glycation end products receptor pathway may be the main signaling pathway leading to neuronal damage. PMID:25206382

Computer-Assisted Synthetic Planning: The End of the Beginning.

PubMed

Szymkuć, Sara; Gajewska, Ewa P; Klucznik, Tomasz; Molga, Karol; Dittwald, Piotr; Startek, Michał; Bajczyk, Michał; Grzybowski, Bartosz A

2016-05-10

Exactly half a century has passed since the launch of the first documented research project (1965 Dendral) on computer-assisted organic synthesis. Many more programs were created in the 1970s and 1980s but the enthusiasm of these pioneering days had largely dissipated by the 2000s, and the challenge of teaching the computer how to plan organic syntheses earned itself the reputation of a "mission impossible". This is quite curious given that, in the meantime, computers have "learned" many other skills that had been considered exclusive domains of human intellect and creativity-for example, machines can nowadays play chess better than human world champions and they can compose classical music pleasant to the human ear. Although there have been no similar feats in organic synthesis, this Review argues that to concede defeat would be premature. Indeed, bringing together the combination of modern computational power and algorithms from graph/network theory, chemical rules (with full stereo- and regiochemistry) coded in appropriate formats, and the elements of quantum mechanics, the machine can finally be "taught" how to plan syntheses of non-trivial organic molecules in a matter of seconds to minutes. The Review begins with an overview of some basic theoretical concepts essential for the big-data analysis of chemical syntheses. It progresses to the problem of optimizing pathways involving known reactions. It culminates with discussion of algorithms that allow for a completely de novo and fully automated design of syntheses leading to relatively complex targets, including those that have not been made before. Of course, there are still things to be improved, but computers are finally becoming relevant and helpful to the practice of organic-synthetic planning. Paraphrasing Churchill's famous words after the Allies' first major victory over the Axis forces in Africa, it is not the end, it is not even the beginning of the end, but it is the end of the beginning for the

77 FR 52977 - Regulatory Capital Rules: Advanced Approaches Risk-Based Capital Rule; Market Risk Capital Rule

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-30

... Corporation 12 CFR Parts 324, 325 Regulatory Capital Rules: Advanced Approaches Risk-Based Capital Rule... 325 RIN 3064-AD97 Regulatory Capital Rules: Advanced Approaches Risk-Based Capital Rule; Market Risk... the agencies' current capital rules. In this NPR (Advanced Approaches and Market Risk NPR) the...

Bioethical aspects of end-of-life care.

PubMed

Zamperetti, N; Bellomo, R; Ronco, C

2008-01-01

Managing end-of-life care can be difficult because of the particular nature of intensive care support, which can separate the biological and the biographical aspects of life. Artificial organ support can temporarily delay death but, at the same time, may fail to restore a quality of life that the patient judges acceptable. For this reason, two concepts must be considered: that the mission of the healthcare system should be to care for patients according to their interests and wishes and that quality of care is related above all to the careful commitment of healthcare workers to the patient's best interests. Keeping these concepts in mind, the rule of the five Cs (competence, collegiality, communication, continuity of care and compassion) might be helpful in the management of end-of-life care. Unfortunately, neither the rule of the five Cs nor the careful use of moral principles in order to promote the patients' dignity can assure a universally acceptable decision. A reasonable level of 'moral certainty', however, might be achieved using a deliberative approach, which provides for the inclusion of all the different subjects involved in the decision-making process (patient, family, doctors, nurses and other carers), in order to reach the best possible decision in a specific situation.

Mathematical modeling of nitrous oxide (N2O) emissions from full-scale wastewater treatment plants.

PubMed

Ni, Bing-Jie; Ye, Liu; Law, Yingyu; Byers, Craig; Yuan, Zhiguo

2013-07-16

Mathematical modeling of N2O emissions is of great importance toward understanding the whole environmental impact of wastewater treatment systems. However, information on modeling of N2O emissions from full-scale wastewater treatment plants (WWTP) is still sparse. In this work, a mathematical model based on currently known or hypothesized metabolic pathways for N2O productions by heterotrophic denitrifiers and ammonia-oxidizing bacteria (AOB) is developed and calibrated to describe the N2O emissions from full-scale WWTPs. The model described well the dynamic ammonium, nitrite, nitrate, dissolved oxygen (DO) and N2O data collected from both an open oxidation ditch (OD) system with surface aerators and a sequencing batch reactor (SBR) system with bubbling aeration. The obtained kinetic parameters for N2O production are found to be reasonable as the 95% confidence regions of the estimates are all small with mean values approximately at the center. The model is further validated with independent data sets collected from the same two WWTPs. This is the first time that mathematical modeling of N2O emissions is conducted successfully for full-scale WWTPs. While clearly showing that the NH2OH related pathways could well explain N2O production and emission in the two full-scale plants studied, the modeling results do not prove the dominance of the NH2OH pathways in these plants, nor rule out the possibility of AOB denitrification being a potentially dominating pathway in other WWTPs that are designed or operated differently.

Estimating discharge and non-point source nitrate loading to streams from three end-member pathways using high-frequency water quality and streamflow data

NASA Astrophysics Data System (ADS)

Miller, M. P.; Tesoriero, A. J.; Hood, K.; Terziotti, S.; Wolock, D.

2017-12-01

The myriad hydrologic and biogeochemical processes taking place in watersheds occurring across space and time are integrated and reflected in the quantity and quality of water in streams and rivers. Collection of high-frequency water quality data with sensors in surface waters provides new opportunities to disentangle these processes and quantify sources and transport of water and solutes in the coupled groundwater-surface water system. A new approach for separating the streamflow hydrograph into three components was developed and coupled with high-frequency specific conductance and nitrate data to estimate time-variable watershed-scale nitrate loading from three end-member pathways - dilute quickflow, concentrated quickflow, and slowflow groundwater - to two streams in central Wisconsin. Time-variable nitrate loads from the three pathways were estimated for periods of up to two years in a groundwater-dominated and a quickflow-dominated stream, using only streamflow and in-stream water quality data. The dilute and concentrated quickflow end-members were distinguished using high-frequency specific conductance data. Results indicate that dilute quickflow contributed less than 5% of the nitrate load at both sites, whereas 89±5% of the nitrate load at the groundwater-dominated stream was from slowflow groundwater, and 84±13% of the nitrate load at the quickflow-dominated stream was from concentrated quickflow. Concentrated quickflow nitrate concentrations varied seasonally at both sites, with peak concentrations in the winter that were 2-3 times greater than minimum concentrations during the growing season. Application of this approach provides an opportunity to assess stream vulnerability to non-point source nitrate loading and expected stream responses to current or changing conditions and practices in watersheds.

Feasibility of automatic evaluation of clinical rules in general practice.

PubMed

Opondo, Dedan; Visscher, Stefan; Eslami, Saied; Medlock, Stephanie; Verheij, Robert; Korevaar, Joke C; Abu-Hanna, Ameen

2017-04-01

To assess the extent to which clinical rules (CRs) can be implemented for automatic evaluation of quality of care in general practice. We assessed 81 clinical rules (CRs) adapted from a subset of Assessing Care of Vulnerable Elders (ACOVE) clinical rules, against Dutch College of General Practitioners (NHG) data model. Each CR was analyzed using the Logical Elements Rule METHOD: (LERM). LERM is a stepwise method of assessing and formalizing clinical rules for decision support. Clinical rules that satisfied the criteria outlined in the LERM method were judged to be implementable in automatic evaluation in general practice. Thirty-three out of 81 (40.7%) Dutch-translated ACOVE clinical rules can be automatically evaluated in electronic medical record systems. Seven out of 7 CRs (100%) in the domain of diabetes can be automatically evaluated, 9/17 (52.9%) in medication use, 5/10 (50%) in depression care, 3/6 (50%) in nutrition care, 6/13 (46.1%) in dementia care, 1/6 (16.6%) in end of life care, 2/13 (15.3%) in continuity of care, and 0/9 (0%) in the fall-related care. Lack of documentation of care activities between primary and secondary health facilities and ambiguous formulation of clinical rules were the main reasons for the inability to automate the clinical rules. Approximately two-fifths of the primary care Dutch ACOVE-based clinical rules can be automatically evaluated. Clear definition of clinical rules, improved GP database design and electronic linkage of primary and secondary healthcare facilities can improve prospects of automatic assessment of quality of care. These findings are relevant especially because the Netherlands has very high automation of primary care. Copyright © 2017 Elsevier B.V. All rights reserved.

Pushing the rules: effects and aftereffects of deliberate rule violations.

PubMed

Wirth, Robert; Pfister, Roland; Foerster, Anna; Huestegge, Lynn; Kunde, Wilfried

2016-09-01

Most of our daily life is organized around rules and social norms. But what makes rules so special? And what if one were to break a rule intentionally? Can we simply free us from the present set of rules or do we automatically adhere to them? How do rule violations influence subsequent behavior? To investigate the effects and aftereffects of violating simple S-R rule, we conducted three experiments that investigated continuous finger-tracking responses on an iPad. Our experiments show that rule violations are distinct from rule-based actions in both response times and movement trajectories, they take longer to initiate and execute, and their movement trajectory is heavily contorted. Data not only show differences between the two types of response (rule-based vs. violation), but also yielded a characteristic pattern of aftereffects in case of rule violations: rule violations do not trigger adaptation effects that render further rule violations less difficult, but every rule violation poses repeated effort on the agent. The study represents a first step towards understanding the signature and underlying mechanisms of deliberate rule violations, they cannot be acted out by themselves, but require the activation of the original rule first. Consequently, they are best understood as reformulations of existing rules that are not accessible on their own, but need to be constantly derived from the original rule, with an add-on that might entail an active tendency to steer away from mental representations that reflect (socially) unwanted behavior.

Mechanisms of rule acquisition and rule following in inductive reasoning.

PubMed

Crescentini, Cristiano; Seyed-Allaei, Shima; De Pisapia, Nicola; Jovicich, Jorge; Amati, Daniele; Shallice, Tim

2011-05-25

Despite the recent interest in the neuroanatomy of inductive reasoning processes, the regional specificity within prefrontal cortex (PFC) for the different mechanisms involved in induction tasks remains to be determined. In this study, we used fMRI to investigate the contribution of PFC regions to rule acquisition (rule search and rule discovery) and rule following. Twenty-six healthy young adult participants were presented with a series of images of cards, each consisting of a set of circles numbered in sequence with one colored blue. Participants had to predict the position of the blue circle on the next card. The rules that had to be acquired pertained to the relationship among succeeding stimuli. Responses given by subjects were categorized in a series of phases either tapping rule acquisition (responses given up to and including rule discovery) or rule following (correct responses after rule acquisition). Mid-dorsolateral PFC (mid-DLPFC) was active during rule search and remained active until successful rule acquisition. By contrast, rule following was associated with activation in temporal, motor, and medial/anterior prefrontal cortex. Moreover, frontopolar cortex (FPC) was active throughout the rule acquisition and rule following phases before a rule became familiar. We attributed activation in mid-DLPFC to hypothesis generation and in FPC to integration of multiple separate inferences. The present study provides evidence that brain activation during inductive reasoning involves a complex network of frontal processes and that different subregions respond during rule acquisition and rule following phases.

Biofuels Fuels Technology Pathway Options for Advanced Drop-in Biofuels Production

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

Kevin L Kenney

2011-09-01

Advanced drop-in hydrocarbon biofuels require biofuel alternatives for refinery products other than gasoline. Candidate biofuels must have performance characteristics equivalent to conventional petroleum-based fuels. The technology pathways for biofuel alternatives also must be plausible, sustainable (e.g., positive energy balance, environmentally benign, etc.), and demonstrate a reasonable pathway to economic viability and end-user affordability. Viable biofuels technology pathways must address feedstock production and environmental issues through to the fuel or chemical end products. Potential end products include compatible replacement fuel products (e.g., gasoline, diesel, and JP8 and JP5 jet fuel) and other petroleum products or chemicals typically produced from a barrelmore » of crude. Considering the complexity and technology diversity of a complete biofuels supply chain, no single entity or technology provider is capable of addressing in depth all aspects of any given pathway; however, all the necessary expert entities exist. As such, we propose the assembly of a team capable of conducting an in-depth technology pathway options analysis (including sustainability indicators and complete LCA) to identify and define the domestic biofuel pathways for a Green Fleet. This team is not only capable of conducting in-depth analyses on technology pathways, but collectively they are able to trouble shoot and/or engineer solutions that would give industrial technology providers the highest potential for success. Such a team would provide the greatest possible down-side protection for high-risk advanced drop-in biofuels procurement(s).« less

Medicare program; revision to accrual basis of accounting policy. Health Care Financing Administration (HCFA), HHS. Final rule.

PubMed

1999-09-27

Medicare policy provides that payroll taxes that a provider becomes obligated to remit to governmental agencies are included in allowable costs only in the cost reporting period in which payment (upon which the payroll taxes are based) is actually made to an employee. Therefore, for payroll accrued in 1 year but not paid until the next year, the associated payroll taxes are not an allowable cost until the next year. This final rule provides for an exception when payment would be made to the employee in the current year but for the fact the regularly scheduled payment date is after the end of the year. In that case, the rule requires allowance in the current year of accrued taxes on payroll that is accrued through the end of the year but not paid until the beginning of the next year, thus allowing accrued taxes on end-of-the year payroll in the same year that the accrual of the payroll itself is allowed. The effect of this rule is not on the allowability of cost but rather only on the timing of payment; that is, the cost of payroll taxes on end-of-the-year payroll is allowable in the current period rather than in the following period.

78 FR 72155 - Medicare Program; End-Stage Renal Disease Prospective Payment System, Quality Incentive Program...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-02

...This rule updates and makes revisions to the End-Stage Renal Disease (ESRD) prospective payment system (PPS) for calendar year (CY) 2014. This rule also sets forth requirements for the ESRD quality incentive program (QIP), including for payment year (PY) 2016 and beyond. In addition, this rule clarifies the grandfathering provision related to the 3-year minimum lifetime requirement (MLR) for Durable Medical Equipment (DME), and provides clarification of the definition of routinely purchased DME. This rule also implements budget-neutral fee schedules for splints and casts, and intraocular lenses (IOLs) inserted in a physician's office. Finally, this rule makes a few technical amendments and corrections to existing regulations related to payment for durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) items and services.

Increasing Complexity in Rule-Based Clinical Decision Support: The Symptom Assessment and Management Intervention.

PubMed

Lobach, David F; Johns, Ellis B; Halpenny, Barbara; Saunders, Toni-Ann; Brzozowski, Jane; Del Fiol, Guilherme; Berry, Donna L; Braun, Ilana M; Finn, Kathleen; Wolfe, Joanne; Abrahm, Janet L; Cooley, Mary E

2016-11-08

Management of uncontrolled symptoms is an important component of quality cancer care. Clinical guidelines are available for optimal symptom management, but are not often integrated into the front lines of care. The use of clinical decision support (CDS) at the point-of-care is an innovative way to incorporate guideline-based symptom management into routine cancer care. The objective of this study was to develop and evaluate a rule-based CDS system to enable management of multiple symptoms in lung cancer patients at the point-of-care. This study was conducted in three phases involving a formative evaluation, a system evaluation, and a contextual evaluation of clinical use. In Phase 1, we conducted iterative usability testing of user interface prototypes with patients and health care providers (HCPs) in two thoracic oncology clinics. In Phase 2, we programmed complex algorithms derived from clinical practice guidelines into a rules engine that used Web services to communicate with the end-user application. Unit testing of algorithms was conducted using a stack-traversal tree-spanning methodology to identify all possible permutations of pathways through each algorithm, to validate accuracy. In Phase 3, we evaluated clinical use of the system among patients and HCPs in the two clinics via observations, structured interviews, and questionnaires. In Phase 1, 13 patients and 5 HCPs engaged in two rounds of formative testing, and suggested improvements leading to revisions until overall usability scores met a priori benchmarks. In Phase 2, symptom management algorithms contained between 29 and 1425 decision nodes, resulting in 19 to 3194 unique pathways per algorithm. Unit testing required 240 person-hours, and integration testing required 40 person-hours. In Phase 3, both patients and HCPs found the system usable and acceptable, and offered suggestions for improvements. A rule-based CDS system for complex symptom management was systematically developed and tested. The

18 CFR 385.104 - Rule of construction (Rule 104).

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Rule of construction (Rule 104). 385.104 Section 385.104 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... Definitions § 385.104 Rule of construction (Rule 104). To the extent that the text of a rule is inconsistent...

18 CFR 385.104 - Rule of construction (Rule 104).

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Rule of construction (Rule 104). 385.104 Section 385.104 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... Definitions § 385.104 Rule of construction (Rule 104). To the extent that the text of a rule is inconsistent...

Variations among Adults in Their Use of Morphemic Spelling Rules and Word-Specific Knowledge when Spelling

ERIC Educational Resources Information Center

Mitchell, Paul; Kemp, Nenagh; Bryant, Peter

2011-01-01

The purpose of this research was to examine whether adults rely on morphemic spelling rules or word-specific knowledge when spelling simple words. We examined adults' knowledge of two of the simplest and most reliable rules in English spelling concerning the morphological word ending -s. This spelling is required for regular plural nouns (e.g.,…

Phonological reduplication in sign language: Rules rule

PubMed Central

Berent, Iris; Dupuis, Amanda; Brentari, Diane

2014-01-01

Productivity—the hallmark of linguistic competence—is typically attributed to algebraic rules that support broad generalizations. Past research on spoken language has documented such generalizations in both adults and infants. But whether algebraic rules form part of the linguistic competence of signers remains unknown. To address this question, here we gauge the generalization afforded by American Sign Language (ASL). As a case study, we examine reduplication (X→XX)—a rule that, inter alia, generates ASL nouns from verbs. If signers encode this rule, then they should freely extend it to novel syllables, including ones with features that are unattested in ASL. And since reduplicated disyllables are preferred in ASL, such a rule should favor novel reduplicated signs. Novel reduplicated signs should thus be preferred to nonreduplicative controls (in rating), and consequently, such stimuli should also be harder to classify as nonsigns (in the lexical decision task). The results of four experiments support this prediction. These findings suggest that the phonological knowledge of signers includes powerful algebraic rules. The convergence between these conclusions and previous evidence for phonological rules in spoken language suggests that the architecture of the phonological mind is partly amodal. PMID:24959158

Gender-Based Behavioral Analysis for End-User Development and the "RULES" Attributes

ERIC Educational Resources Information Center

Tzafilkou, Katerina; Protogeros, Nicolaos; Karagiannidis, Charalampos; Koumpis, Adamantios

2017-01-01

This paper addresses the role of gender in End-User Development (EUD) environments and examines whether there are gender differences in performance and in correlations between performance and a set of behavioral attributes. Based on a review of the most prominent EUD-related behavioral Human Computer Interaction (HCI) theories, and the influence…

Gomisin N Inhibits Melanogenesis through Regulating the PI3K/Akt and MAPK/ERK Signaling Pathways in Melanocytes

PubMed Central

Chae, Jae Kyoung; Subedi, Lalita; Jeong, Minsun; Park, Yong Un; Kim, Chul Young; Kim, Hakwon; Kim, Sun Yeou

2017-01-01

Gomisin N, one of the lignan compounds found in Schisandra chinensis has been shown to possess anti-oxidative, anti-tumorigenic, and anti-inflammatory activities in various studies. Here we report, for the first time, the anti-melenogenic efficacy of Gomisin N in mammalian cells as well as in zebrafish embryos. Gomisin N significantly reduced the melanin content without cellular toxicity. Although it was not capable of modulating the catalytic activity of mushroom tyrosinase in vitro, Gomisin N downregulated the expression levels of key proteins that function in melanogenesis. Gomisin N downregulated melanocortin 1 receptor (MC1R), adenylyl cyclase 2, microphthalmia-associated transcription factor (MITF), tyrosinase, tyrosinase-related protein-1 (TRP-1), and tyrosinase-related protein-2 (TRP-2). In addition, Gomisin N-treated Melan-A cells exhibited increased p-Akt and p-ERK levels, which implies that the activation of the PI3K/Akt and MAPK/ERK pathways may function to inhibit melanogenesis. We also validated that Gomisin N reduced melanin production by repressing the expression of MITF, tyrosinase, TRP-1, and TRP-2 in mouse and human cells as well as in developing zebrafish embryos. Collectively, we conclude that Gomisin N inhibits melanin synthesis by repressing the expression of MITF and melanogenic enzymes, probably through modulating the PI3K/Akt and MAPK/ERK pathways. PMID:28241436

In vivo kinetic analysis of the penicillin biosynthesis pathway using PAA stimulus response experiments.

PubMed

Deshmukh, Amit T; Verheijen, Peter J T; Maleki Seifar, Reza; Heijnen, Joseph J; van Gulik, Walter M

2015-11-01

In this study we combined experimentation with mathematical modeling to unravel the in vivo kinetic properties of the enzymes and transporters of the penicillin biosynthesis pathway in a high yielding Penicillium chrysogenum strain. The experiment consisted of a step response experiment with the side chain precursor phenyl acetic acid (PAA) in a glucose-limited chemostat. The metabolite data showed that in the absence of PAA all penicillin pathway enzymes were expressed, leading to the production of a significant amount of 6-aminopenicillanic acid (6APA) as end product. After the stepwise perturbation with PAA, the pathway produced PenG within seconds. From the extra- and intracellular metabolite measurements, hypotheses for the secretion mechanisms of penicillin pathway metabolites were derived. A dynamic model of the penicillin biosynthesis pathway was then constructed that included the formation and transport over the cytoplasmic membrane of pathway intermediates, PAA and the product penicillin-G (PenG). The model parameters and changes in the enzyme levels of the penicillin biosynthesis pathway under in vivo conditions were simultaneously estimated using experimental data obtained at three different timescales (seconds, minutes, hours). The model was applied to determine changes in the penicillin pathway enzymes in time, calculate fluxes and analyze the flux control of the pathway. This led to a reassessment of the in vivo behavior of the pathway enzymes and in particular Acyl-CoA:Isopenicillin N Acyltransferase (AT). Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

A Performance Comparison Study of Uncoated and TiAlN Coated Carbide End Mill on Machining of the Al-35Zn Alloy

NASA Astrophysics Data System (ADS)

Bayraktar, S.; Hekimoglu, A. P.; Turgut, Y.; Haciosmanoglu, M.

2018-01-01

In this study, Al-35Zn alloy was produced by permanent mold casting. To investigate the cutting performance of uncoated and TiAlN coated carbide end mills on this alloy, a series of tests were carried out in the CNC vertical machining center at a constant cutting speed, feed rate and depth of cut. The results obtained from the tests showed that uncoated carbide end mill have lower cutting force and surface roughness than TiAlN coated carbide end mill. These observations are discussed in terms of the alloys properties, cutting tool surfaces, and friction and wear behavior between the cutting tool and the material.

Preschoolers can infer general rules governing fantastical events in fiction.

PubMed

Van de Vondervoort, Julia W; Friedman, Ori

2014-05-01

Young children are frequently exposed to fantastic fiction. How do they make sense of the unrealistic and impossible events that occur in such fiction? Although children could view such events as isolated episodes, the present experiments suggest that children use such events to infer general fantasy rules. In 2 experiments, 2- to 4-year-olds were shown scenarios in which 2 animals behaved unrealistically (N = 78 in Experiment 1, N = 94 in Experiment 2). When asked to predict how other animals in the fiction would behave, children predicted novel behaviors consistent with the nature of the fiction. These findings suggest that preschoolers can infer the general rules that govern the events and entities in fantastic fiction and can use these rules to predict what events will happen in the fiction. The findings also provide evidence that children may infer fantasy rules at a more superordinate level than the basic level. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

Measure in the ESRD QIP for PY 2020. Final rule.

PubMed

2017-08-04

This final rule updates the payment rates used under the prospective payment system (PPS) for skilled nursing facilities (SNFs) for fiscal year (FY) 2018. It also revises and rebases the market basket index by updating the base year from 2010 to 2014, and by adding a new cost category for Installation, Maintenance, and Repair Services. The rule also finalizes revisions to the SNF Quality Reporting Program (QRP), including measure and standardized resident assessment data policies and policies related to public display. In addition, it finalizes policies for the Skilled Nursing Facility Value-Based Purchasing Program that will affect Medicare payment to SNFs beginning in FY 2019. The final rule also clarifies the regulatory requirements for team composition for surveys conducted for investigating a complaint and aligns regulatory provisions for investigation of complaints with the statutory requirements. The final rule also finalizes the performance period for the National Healthcare Safety Network (NHSN) Healthcare Personnel (HCP) Influenza Vaccination Reporting Measure included in the End-Stage Renal Disease (ESRD) Quality Incentive Program (QIP) for Payment Year 2020.

Saccharomyces cerevisiae KTR4, KTR5 and KTR7 encode mannosyltransferases differentially involved in the N- and O-linked glycosylation pathways.

PubMed

Hernández, Nahúm V; López-Ramírez, Luz A; Díaz-Jiménez, Diana F; Mellado-Mojica, Erika; Martínez-Duncker, Iván; López, Mercedes G; Mora-Montes, Héctor M

2017-10-01

Saccharomyces cerevisiae is a model to understand basic aspects of protein glycosylation pathways. Although these metabolic routes have been thoroughly studied, there are still knowledge gaps; among them, the role of the MNT1/KRE2 gene family. This family is composed of nine members, with only six functionally characterized. The enzymes Ktr1, Ktr3, and Mnt1/Kre2 have overlapping activities in both O-linked and N-linked glycan synthesis; while Ktr2 and Yur1 participate exclusively in the elongation of the N-linked glycan outer chain. KTR6 encodes for a phosphomannosyltransferase that synthesizes the cell wall phosphomannan. Here, we aimed to establish the functional role of KTR4, KTR5 and KTR7 in the protein glycosylation pathways, by using heterologous complementation in Candida albicans null mutants lacking members of the MNT1/KRE2 gene family. The three S. cerevisiae genes restored defects in the C. albicans N-linked glycosylation pathway. KTR5 and KTR7 partially complemented a C. albicans null mutant with defects in the synthesis of O-linked glycans, and only KTR4 fully elongated the O-linked glycans like wild-type cells. Therefore, our results suggest that the three genes have a redundant activity in the S. cerevisiae N-linked glycosylation pathway, but KTR4 plays a major role in O-linked glycan synthesis. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Random walkers with extreme value memory: modelling the peak-end rule

NASA Astrophysics Data System (ADS)

Harris, Rosemary J.

2015-05-01

Motivated by the psychological literature on the ‘peak-end rule’ for remembered experience, we perform an analysis within a random walk framework of a discrete choice model where agents’ future choices depend on the peak memory of their past experiences. In particular, we use this approach to investigate whether increased noise/disruption always leads to more switching between decisions. Here extreme value theory illuminates different classes of dynamics indicating that the long-time behaviour is dependent on the scale used for reflection; this could have implications, for example, in questionnaire design.

RuleMonkey: software for stochastic simulation of rule-based models

PubMed Central

2010-01-01

Background The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen language (BNGL). A set of rules implicitly defines a (bio)chemical reaction network. The reaction network implied by a set of rules is often very large, and as a result, generation of the network implied by rules tends to be computationally expensive. Moreover, the cost of many commonly used methods for simulating network dynamics is a function of network size. Together these factors have limited application of the rule-based modeling approach. Recently, several methods for simulating rule-based models have been developed that avoid the expensive step of network generation. The cost of these "network-free" simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is now needed for the simulation and analysis of rule-based models of biochemical systems. Results Here, we present a software tool called RuleMonkey, which implements a network-free method for simulation of rule-based models that is similar to Gillespie's method. The method is suitable for rule-based models that can be encoded in BNGL, including models with rules that have global application conditions, such as rules for intramolecular association reactions. In addition, the method is rejection free, unlike other network-free methods that introduce null events, i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated. We verify that RuleMonkey produces correct simulation results, and we compare its performance against DYNSTOC, another BNGL-compliant tool for network-free simulation of rule-based models. We also compare RuleMonkey against problem-specific codes implementing network-free simulation methods. Conclusions RuleMonkey enables the simulation of

12 CFR Optional Annual Percentage... - End Plans Subject to the Requirements of § 226.5b

Code of Federal Regulations, 2012 CFR

2012-01-01

....5b Annual Optional Annual Percentage Rate Computations for Creditors Offering Open Banks and Banking... (REGULATION Z) Special Rules Applicable to Credit Card Accounts and Open-End Credit Offered to College... Creditors Offering Open-End Plans Subject to the Requirements of § 226.5b In determining the denominator of...

12 CFR Optional Annual Percentage... - End Plans Subject to the Requirements of § 226.5b

Code of Federal Regulations, 2011 CFR

2011-01-01

....5b Annual Optional Annual Percentage Rate Computations for Creditors Offering Open Banks and Banking... (REGULATION Z) Special Rules Applicable to Credit Card Accounts and Open-End Credit Offered to College... Creditors Offering Open-End Plans Subject to the Requirements of § 226.5b In determining the denominator of...

12 CFR Optional Annual Percentage... - End Plans Subject to the Requirements of § 226.5b

Code of Federal Regulations, 2013 CFR

2013-01-01

....5b Annual Optional Annual Percentage Rate Computations for Creditors Offering Open Banks and Banking... LENDING (REGULATION Z) Special Rules Applicable to Credit Card Accounts and Open-End Credit Offered to... Computations for Creditors Offering Open-End Plans Subject to the Requirements of § 226.5b In determining the...

78 FR 40835 - Medicare Program; End-Stage Renal Disease Prospective Payment System, Quality Incentive Program...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-08

...This rule proposes to update and make revisions to the End- Stage Renal Disease (ESRD) prospective payment system (PPS) for calendar year (CY) 2014. This rule also proposes to set forth requirements for the ESRD quality incentive program (QIP), including for payment year (PY) 2016 and beyond. In addition, this rule proposes to clarify the grandfathering provision related to the 3-year minimum lifetime requirement (MLR) for Durable Medical Equipment (DME). In addition, it provides clarification of the definition of routinely purchased DME. This rule also proposes the implementation of budget- neutral fee schedules for splints and casts, and intraocular lenses (IOLs) inserted in a physician's office. Finally, this rule would make a few technical amendments and corrections to existing regulations related to payment for DMEPOS items and services.

4 CFR 22.1 - Applicability of Rules [Rule 1].

Code of Federal Regulations, 2010 CFR

2010-01-01

... 4 Accounts 1 2010-01-01 2010-01-01 false Applicability of Rules [Rule 1]. 22.1 Section 22.1... ACCOUNTABILITY OFFICE CONTRACT APPEALS BOARD § 22.1 Applicability of Rules [Rule 1]. The Government... all appeals filed with the Board on or after October 1, 2007. ...

Risky business: Microhomology-mediated end joining.

PubMed

Sinha, Supriya; Villarreal, Diana; Shim, Eun Yong; Lee, Sang Eun

2016-06-01

Prevalence of microhomology (MH) at the breakpoint junctions in somatic and germ-line chromosomal rearrangements and in the programmed immune receptor rearrangements from cells deficient in classical end joining reveals an enigmatic process called MH-mediated end joining (MMEJ). MMEJ repairs DNA double strand breaks (DSBs) by annealing flanking MH and deleting genetic information at the repair junctions from yeast to humans. Being genetically distinct from canonical DNA DSB pathways, MMEJ is involved with the fusions of eroded/uncapped telomeres as well as with the assembly of chromosome fragments in chromothripsis. In this review article, we will discuss an up-to-date model representing the MMEJ process and the mechanism by which cells regulate MMEJ to limit repair-associated mutagenesis. We will also describe the possible therapeutic gains resulting from the inhibition of MMEJ in recombination deficient cancers. Lastly, we will embark on two contentious issues associated with MMEJ such as the significance of MH at the repair junction to be the hallmark of MMEJ and the relationship of MMEJ to other mechanistically related DSB repair pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

The pH dependency of N-converting enzymatic processes, pathways and microbes: effect on net N2 O production.

PubMed

Blum, Jan-Michael; Su, Qingxian; Ma, Yunjie; Valverde-Pérez, Borja; Domingo-Félez, Carlos; Jensen, Marlene Mark; Smets, Barth F

2018-05-01

Nitrous oxide (N 2 O) is emitted during microbiological nitrogen (N) conversion processes, when N 2 O production exceeds N 2 O consumption. The magnitude of N 2 O production vs. consumption varies with pH and controlling net N 2 O production might be feasible by choice of system pH. This article reviews how pH affects enzymes, pathways and microorganisms that are involved in N-conversions in water engineering applications. At a molecular level, pH affects activity of cofactors and structural elements of relevant enzymes by protonation or deprotonation of amino acid residues or solvent ligands, thus causing steric changes in catalytic sites or proton/electron transfer routes that alter the enzymes' overall activity. Augmenting molecular information with, e.g., nitritation or denitrification rates yields explanations of changes in net N 2 O production with pH. Ammonia oxidizing bacteria are of highest relevance for N 2 O production, while heterotrophic denitrifiers are relevant for N 2 O consumption at pH > 7.5. Net N 2 O production in N-cycling water engineering systems is predicted to display a 'bell-shaped' curve in the range of pH 6.0-9.0 with a maximum at pH 7.0-7.5. Net N 2 O production at acidic pH is dominated by N 2 O production, whereas N 2 O consumption can outweigh production at alkaline pH. Thus, pH 8.0 may be a favourable pH set-point for water treatment applications regarding net N 2 O production. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Slide Esophagoplasty vs End-to-End Anastomosis for Recalcitrant Esophageal Stricture after Esophageal Atresia Repair.

PubMed

Kamran, Ali; Smithers, Charles J; Manfredi, Michael A; Hamilton, Thomas E; Ngo, Peter D; Zurakowski, David; Jennings, Russell W

2018-06-01

Anastomotic stricture is a common complication after esophageal atresia (EA) repair. Patients with a recalcitrant stricture may require surgical intervention. The technique of reanastomosis after stricture resection can affect patient outcomes. Patients with EA who underwent anastomotic stricture resection, from July 2010 to February 2017, were reviewed. After stricture resection, patients who had slide esophagoplasty performed were compared with those having conventional end-to-end anastomosis. Fifty patients underwent stricture repair surgery by slide esophagoplasty (n = 12) or end-to-end (n = 38) anastomosis technique at a median age of 14 months (interquartile range [IQR] 6 to 23 months). Significantly fewer patients required dilation therapy after slide esophagoplasty: 6 of 12 (50%) compared with 32 of 38 (84%) in the end-to-end group (p = 0.02). The number of dilation sessions was significantly lower in the slide group vs the end-to-end (p = 0.004) group, with a risk ratio confirming the approximately half the number of dilations for the slide approach (risk ratio 0.57, 95% CI 0.38 to 0.86). Steroid injection was combined with dilation in 3 of 12 (25%) vs 22 of 38 (58%) in the slide and end-to-end groups, respectively (p = 0.10). Stent placement was used in none of slide cases vs 8 of 38 (21%) in the end-to-end group (p = 0.17). Stricture incision was performed in 1 of 12 (8%) in the slide group and 11 of 38 (29%) in the end-to-end group (p = 0.25). There were leak complications in fewer patients after slide esophagoplasty compared with end-to-end anastomosis: 1 of 12 (8%) vs 8 of 38 (21%) (p = 0.43). Slide esophagoplasty may be a useful technique of anastomotic configuration for selected patients with recalcitrant esophageal stricture, offering more favorable outcomes compared with end-to-end anastomosis. Copyright © 2017 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Peak and end effects in patients' daily recall of pain and fatigue: a within-subjects analysis.

PubMed

Schneider, Stefan; Stone, Arthur A; Schwartz, Joseph E; Broderick, Joan E

2011-02-01

Clinical research often relies on retrospective recall of symptom levels, but the information contained in these ratings is not well understood. The "peak-and-end rule" suggests that the most intense (peak) and final (end) moments of an experience disproportionately influence retrospective judgments, which may bias self-reports of somatic symptoms. This study examined the extent to which peak and end symptom levels systematically affect patients' day-to-day recall of pain and fatigue. Rheumatology patients (N = 97) completed 5 to 6 momentary ratings of pain and fatigue per day as well as a daily recall rating of these symptoms for 28 consecutive days. For pain, peak and end momentary ratings predicted daily recall of average pain beyond the actual average of momentary ratings. This effect was small, yet was confirmed in both between-person and within-person (repeated measures) analyses. For fatigue, neither peak nor end momentary symptoms significantly contributed to daily recall. Of note, the evidence for peak- and end-effects in recall of pain and fatigue varied significantly between individual patients. These findings suggest that peak- and end-effects create a small bias in recall reports of pain, but not fatigue. However, there are considerable individual differences in susceptibility to peak and end heuristics. The peak-end cognitive heuristic could bias end-of-day recall of pain and fatigue. An effect was shown for pain, but not for fatigue. The effects were small and were unlikely to substantially bias end-of-day assessments. Individuals were shown to differ in the degree that the heuristic was associated with recall. Copyright © 2011 American Pain Society. Published by Elsevier Inc. All rights reserved.

18 CFR 385.103 - References to rules (Rule 103).

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false References to rules (Rule 103). 385.103 Section 385.103 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... Definitions § 385.103 References to rules (Rule 103). This part cross-references its sections according to...

18 CFR 385.103 - References to rules (Rule 103).

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false References to rules (Rule 103). 385.103 Section 385.103 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... Definitions § 385.103 References to rules (Rule 103). This part cross-references its sections according to...

Analysis of the relationship between end-to-end distance and activity of single-chain antibody against colorectal carcinoma.

PubMed

Zhang, Jianhua; Liu, Shanhong; Shang, Zhigang; Shi, Li; Yun, Jun

2012-08-22

We investigated the relationship of End-to-end distance between VH and VL with different peptide linkers and the activity of single-chain antibodies by computer-aided simulation. First, we developed (G4S)n (where n = 1-9) as the linker to connect VH and VL, and estimated the 3D structure of single-chain Fv antibody (scFv) by homologous modeling. After molecular models were evaluated and optimized, the coordinate system of every protein was built and unified into one coordinate system, and End-to-end distances calculated using 3D space coordinates. After expression and purification of scFv-n with (G4S)n as n = 1, 3, 5, 7 or 9, the immunoreactivity of purified ND-1 scFv-n was determined by ELISA. A multi-factorial relationship model was employed to analyze the structural factors affecting scFv: rn=ABn-ABO2+CDn-CDO2+BCn-BCst2. The relationship between immunoreactivity and r-values revealed that fusion protein structure approached the desired state when the r-value = 3. The immunoreactivity declined as the r-value increased, but when the r-value exceeded a certain threshold, it stabilized. We used a linear relationship to analyze structural factors affecting scFv immunoreactivity.

Multiple-rule bias in the comparison of classification rules

PubMed Central

Yousefi, Mohammadmahdi R.; Hua, Jianping; Dougherty, Edward R.

2011-01-01

Motivation: There is growing discussion in the bioinformatics community concerning overoptimism of reported results. Two approaches contributing to overoptimism in classification are (i) the reporting of results on datasets for which a proposed classification rule performs well and (ii) the comparison of multiple classification rules on a single dataset that purports to show the advantage of a certain rule. Results: This article provides a careful probabilistic analysis of the second issue and the ‘multiple-rule bias’, resulting from choosing a classification rule having minimum estimated error on the dataset. It quantifies this bias corresponding to estimating the expected true error of the classification rule possessing minimum estimated error and it characterizes the bias from estimating the true comparative advantage of the chosen classification rule relative to the others by the estimated comparative advantage on the dataset. The analysis is applied to both synthetic and real data using a number of classification rules and error estimators. Availability: We have implemented in C code the synthetic data distribution model, classification rules, feature selection routines and error estimation methods. The code for multiple-rule analysis is implemented in MATLAB. The source code is available at http://gsp.tamu.edu/Publications/supplementary/yousefi11a/. Supplementary simulation results are also included. Contact: edward@ece.tamu.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21546390

Kuramoto model with uniformly spaced frequencies: Finite-N asymptotics of the locking threshold.

PubMed

Ottino-Löffler, Bertrand; Strogatz, Steven H

2016-06-01

We study phase locking in the Kuramoto model of coupled oscillators in the special case where the number of oscillators, N, is large but finite, and the oscillators' natural frequencies are evenly spaced on a given interval. In this case, stable phase-locked solutions are known to exist if and only if the frequency interval is narrower than a certain critical width, called the locking threshold. For infinite N, the exact value of the locking threshold was calculated 30 years ago; however, the leading corrections to it for finite N have remained unsolved analytically. Here we derive an asymptotic formula for the locking threshold when N≫1. The leading correction to the infinite-N result scales like either N^{-3/2} or N^{-1}, depending on whether the frequencies are evenly spaced according to a midpoint rule or an end-point rule. These scaling laws agree with numerical results obtained by Pazó [D. Pazó, Phys. Rev. E 72, 046211 (2005)PLEEE81539-375510.1103/PhysRevE.72.046211]. Moreover, our analysis yields the exact prefactors in the scaling laws, which also match the numerics.

75 FR 34626 - Rules and Regulations for Abandoned Individual Account Plans

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-18

... DEPARTMENT OF LABOR Employee Benefits Security Administration 29 CFR Part 2578 Rules and Regulations for Abandoned Individual Account Plans CFR Correction In Title 29 of the Code of Federal Regulations, Part 1927 to End, revised as of July 1, 2009, on pages 664 and 665, remove the second Appendix C...

On the kinetics of body versus end evaporation and addition of supramolecular polymers.

PubMed

Tiwari, Nitin S; van der Schoot, Paul

2017-06-01

The kinetics of the self-assembly of supramolecular polymers is dictated by how monomers, dimers, trimers etc., attach to and detach from each other. It is for this reasons that researchers have proposed a plethora of pathways to explain the kinetics of various self-assembling supramolecules, including sulfur, linear micelles, living polymers and protein fibrils. Recent observations hint at the importance of a hitherto ignored molecular aggregation pathway that we refer to as "body evaporation and addition". In this pathway, monomers can enter at or dissociate from any point along the backbone of the polymer. In this paper, we compare predictions for the well-established end evaporation and addition pathway with those that we obtained for the newly proposed body evaporation and addition model. We quantify the lag time, characteristic of nucleated reversible polymerisation, in terms of the time it takes to obtain half of the steady-state polymerised fraction and the apparent growth rate at that point, and obtain power laws for both as a function of the total monomer concentration. We find, perhaps not entirely unexpectedly, that the body evaporation and addition pathway speeds up the relaxation of the polymerised monomeric mass relative to that of the end evaporation and addition. However, the presence of the body evaporation and addition pathway does not affect the dependence of the lag time on the total monomer concentration and it remains the same as that for the case of end evaporation and addition. The scaling of the lag time with the forward rate is different for the two models, suggesting that they may be distinguished experimentally.

The Advocate-Witness Rule: Anachronism or Necessary Restraint

DTIC Science & Technology

1989-04-01

Court of Military Appeals ’ aggressive interpretation of the advocate-witness rule and reading of the Model Code provisions concerning the advocate...those federal circuits that formerly all6wed an interlocutory appeal from the denial of a motion to disqualify the opponent’s counsel. See Armstrong...the Supreme Court put an end to such interlocutory appeals in Firestone Tire & Rubber Co. v. Risjord, 449 U.S. 368 (1981)." 409. Note, The Advocate

12 CFR Appendix J to Part 226 - Annual Percentage Rate Computations for Closed-End Credit Transactions

Code of Federal Regulations, 2010 CFR

2010-01-01

... unpaid balance of the amount financed is increased by the finance charge earned during that period and is... contrast, under the United States Rule method, at the end of each payment period, the unpaid balance of the... earned, the adjustment of the unpaid balance of the amount financed is postponed until the end of the...

The Relative Emphasis of Play Rules between Experienced and Trainee Caregivers of Toddlers

ERIC Educational Resources Information Center

Gyöngy, Kinga

2017-01-01

Content analysis of a large-scale (N = 920) qualitative data set with MAXQDA12 from a nationwide questionnaire of nursery practitioners in Hungary was able to demonstrate various types of rules during free play: social, health and safety, and environment-related rules. Environment-related rules, which govern space utilisation in toddler groups,…

Signaling Pathways in Cardiac Myocyte Apoptosis

PubMed Central

Xia, Peng; Liu, Yuening

2016-01-01

Cardiovascular diseases, the number 1 cause of death worldwide, are frequently associated with apoptotic death of cardiac myocytes. Since cardiomyocyte apoptosis is a highly regulated process, pharmacological intervention of apoptosis pathways may represent a promising therapeutic strategy for a number of cardiovascular diseases and disorders including myocardial infarction, ischemia/reperfusion injury, chemotherapy cardiotoxicity, and end-stage heart failure. Despite rapid growth of our knowledge in apoptosis signaling pathways, a clinically applicable treatment targeting this cellular process is currently unavailable. To help identify potential innovative directions for future research, it is necessary to have a full understanding of the apoptotic pathways currently known to be functional in cardiac myocytes. Here, we summarize recent progress in the regulation of cardiomyocyte apoptosis by multiple signaling molecules and pathways, with a focus on the involvement of these pathways in the pathogenesis of heart disease. In addition, we provide an update regarding bench to bedside translation of this knowledge and discuss unanswered questions that need further investigation. PMID:28101515

Intrinsic honesty and the prevalence of rule violations across societies.

PubMed

Gächter, Simon; Schulz, Jonathan F

2016-03-24

Deception is common in nature and humans are no exception. Modern societies have created institutions to control cheating, but many situations remain where only intrinsic honesty keeps people from cheating and violating rules. Psychological, sociological and economic theories suggest causal pathways to explain how the prevalence of rule violations in people's social environment, such as corruption, tax evasion or political fraud, can compromise individual intrinsic honesty. Here we present cross-societal experiments from 23 countries around the world that demonstrate a robust link between the prevalence of rule violations and intrinsic honesty. We developed an index of the 'prevalence of rule violations' (PRV) based on country-level data from the year 2003 of corruption, tax evasion and fraudulent politics. We measured intrinsic honesty in an anonymous die-rolling experiment. We conducted the experiments with 2,568 young participants (students) who, due to their young age in 2003, could not have influenced PRV in 2003. We find individual intrinsic honesty is stronger in the subject pools of low PRV countries than those of high PRV countries. The details of lying patterns support psychological theories of honesty. The results are consistent with theories of the cultural co-evolution of institutions and values, and show that weak institutions and cultural legacies that generate rule violations not only have direct adverse economic consequences, but might also impair individual intrinsic honesty that is crucial for the smooth functioning of society.

Intrinsic Honesty and the Prevalence of Rule Violations across Societies

PubMed Central

Gächter, Simon; Schulz, Jonathan F.

2016-01-01

Deception is common in nature and humans are no exception1. Modern societies have created institutions to control cheating, but many situations remain where only intrinsic honesty keeps people from cheating and violating rules. Psychological2, sociological3 and economic theories4 suggest causal pathways about how the prevalence of rule violations in people's social environment such as corruption, tax evasion, or political fraud can compromise individual intrinsic honesty. Here, we present cross-societal experiments from 23 countries around the world, which demonstrate a robust link between the prevalence of rule violations and intrinsic honesty. We developed an index of the Prevalence of Rule Violations (PRV) based on country-level data of corruption, tax evasion, and fraudulent politics. We measured intrinsic honesty in an anonymous die-rolling experiment.5 We conducted the experiments at least eight years after the measurement of PRV with 2568 young participants (students) who could not influence PRV. We find individual intrinsic honesty is stronger in the subject pools of low PRV countries than those of high PRV countries. The details of lying patterns support psychological theories of honesty.6,7 The results are consistent with theories of the cultural co-evolution of institutions and values8 and show that weak institutions and cultural legacies9-11 that generate rule violations not only have direct adverse economic consequences but might also impair individual intrinsic honesty that is crucial for the smooth functioning of society. PMID:26958830

Born’s rule as signature of a superclassical current algebra

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

Fussy, S.; Mesa Pascasio, J.; Institute for Atomic and Subatomic Physics, Vienna University of Technology, Operng. 9, 1040 Vienna

2014-04-15

We present a new tool for calculating the interference patterns and particle trajectories of a double-, three- and N-slit system on the basis of an emergent sub-quantum theory developed by our group throughout the last years. The quantum itself is considered as an emergent system representing an off-equilibrium steady state oscillation maintained by a constant throughput of energy provided by a classical zero-point energy field. We introduce the concept of a “relational causality” which allows for evaluating structural interdependences of different systems levels, i.e. in our case of the relations between partial and total probability density currents, respectively. Combined with themore » application of 21st century classical physics like, e.g., modern nonequilibrium thermodynamics, we thus arrive at a “superclassical” theory. Within this framework, the proposed current algebra directly leads to a new formulation of the guiding equation which is equivalent to the original one of the de Broglie–Bohm theory. By proving the absence of third order interferences in three-path systems it is shown that Born’s rule is a natural consequence of our theory. Considering the series of one-, double-, or, generally, of N-slit systems, with the first appearance of an interference term in the double slit case, we can explain the violation of Sorkin’s first order sum rule, just as the validity of all higher order sum rules. Moreover, the Talbot patterns and Talbot distance for an arbitrary N-slit device can be reproduced exactly by our model without any quantum physics tool. -- Highlights: •Calculating the interference patterns and particle trajectories of a double-, three- and N-slit system. •Deriving a new formulation of the guiding equation equivalent to the de Broglie–Bohm one. •Proving the absence of third order interferences and thus explaining Born’s rule. •Explaining the violation of Sorkin’s order sum rules. •Classical simulation of Talbot

Influence of Lumbricus terrestris and Folsomia candida on N2 O formation pathways in two different soils - with particular focus on N2 emissions.

PubMed

Schorpp, Quentin; Riggers, Catharina; Lewicka-Szczebak, Dominika; Giesemann, Anette; Well, Reinhard; Schrader, Stefan

2016-11-15

The gaseous N losses mediated by soil denitrifiers are generally inferred by measuring N 2 O fluxes, but should include associated N 2 emissions, which may be affected by abiotic soil characteristics and biotic interactions. Soil fauna, particularly anecic earthworms and euedaphic collembola, alter the activity of denitrifiers, creating hotspots for denitrification. These soil fauna are abundant in perennial agroecosystems intended to contribute to more sustainable production of bioenergy. Two microcosm experiments were designed to evaluate gaseous N emissions from a silty loam and a sandy soil, both provided with litter from the bioenergy crop Silphium perfoliatum (cup-plant) and inoculated with an anecic earthworm (Lumbricus terrestris), which was added alone or together with an euedaphic collembola (Folsomia candida). In experiment 1, litter-derived N flux was determined by adding 15 N-labelled litter, followed by mass spectrometric analysis of N 2 and N 2 O isotopologues. In experiment 2, the δ 18 O values and 15 N site preference of N 2 O were determined by isotope ratio mass spectrometry to reveal underlying N 2 O formation pathways. Lumbricus terrestris significantly increased litter-derived N 2 emissions in the loamy soil, from 174.5 to 1019.3 μg N 2 -N kg -1 soil, but not in the sandy soil (non-significant change from 944.7 to 1054.7 μg N 2 -N kg -1 soil). Earthworm feeding on plant litter resulted in elevated N 2 O emissions in both soils, derived mainly from turnover of the soil mineral N pool during denitrification. Folsomia candida did not affect N losses but showed a tendency to redirect N 2 O formation pathways from fungal to bacterial denitrification. The N 2 O/(N 2  + N 2 O) product ratio was predominantly affected by abiotic soil characteristics (loamy soil: 0.14, sandy soil: 0.26). When feeding on S. perfoliatum litter, the anecic L. terrestris, but not the euedaphic F. candida, has the potential to cause substantial N losses. Biotic

A co-design process developing heuristics for practitioners providing end of life care for people with dementia.

PubMed

Davies, Nathan; Mathew, Rammya; Wilcock, Jane; Manthorpe, Jill; Sampson, Elizabeth L; Lamahewa, Kethakie; Iliffe, Steve

2016-08-02

The end of life for someone with dementia can present many challenges for practitioners; such as, providing care if there are swallowing difficulties. This study aimed to develop a toolkit of heuristics (rules-of-thumb) to aid practitioners making end-of-life care decisions for people with dementia. An iterative co-design approach was adopted using a literature review and qualitative methods, including; 1) qualitative interviews and focus groups with family carers and 2) focus groups with health and care professionals. Family carers were recruited from a national charity, purposively sampling those with experience of end-of-life care for a person with dementia. Health and care professionals were purposively sampled to include a broad range of expertise including; general practitioners, palliative care specialists, and geriatricians. A co-design group was established consisting of health and social care experts and family carers, to synthesise the findings from the qualitative work and produce a toolkit of heuristics to be tested in practice. Four broad areas were identified as requiring complex decisions at the end of life; 1) eating/swallowing difficulties, 2) agitation/restlessness, 3) ending life-sustaining treatment, and 4) providing "routine care" at the end of life. Each topic became a heuristic consisting of rules arranged into flowcharts. Eating/swallowing difficulties have three rules; ensuring eating/swallowing difficulties do not come as a surprise, considering if the situation is an emergency, and considering 'comfort feeding' only versus time-trialled artificial feeding. Agitation/restlessness encourages a holistic approach, considering the environment, physical causes, and the carer's wellbeing. Ending life-sustaining treatment supports practitioners through a process of considering the benefits of treatment versus quality-of-life and comfort. Finally, a heuristic on providing routine care such as bathing, prompts practitioners to consider adapting

One ring to bring them all--the role of Ku in mammalian non-homologous end joining.

PubMed

Grundy, Gabrielle J; Moulding, Hayley A; Caldecott, Keith W; Rulten, Stuart L

2014-05-01

The repair of DNA double strand breaks is essential for cell survival and several conserved pathways have evolved to ensure their rapid and efficient repair. The non-homologous end joining pathway is initiated when Ku binds to the DNA break site. Ku is an abundant nuclear heterodimer of Ku70 and Ku80 with a toroidal structure that allows the protein to slide over the broken DNA end and bind with high affinity. Once locked into placed, Ku acts as a tool-belt to recruit multiple interacting proteins, forming one or more non-homologous end joining complexes that act in a regulated manner to ensure efficient repair of DNA ends. Here we review the structure and functions of Ku and the proteins with which it interacts during non-homologous end joining. Copyright © 2014 Elsevier B.V. All rights reserved.

Substrate specificities and intracellular distributions of three N-glycan processing enzymes functioning at a key branch point in the insect N-glycosylation pathway.

PubMed

Geisler, Christoph; Jarvis, Donald L

2012-03-02

Man(α1-6)[GlcNAc(β1-2)Man(α1-3)]ManGlcNAc(2) is a key branch point intermediate in the insect N-glycosylation pathway because it can be either trimmed by a processing β-N-acetylglucosaminidase (FDL) to produce paucimannosidic N-glycans or elongated by N-acetylglucosaminyltransferase II (GNT-II) to produce complex N-glycans. N-acetylglucosaminyltransferase I (GNT-I) contributes to branch point intermediate production and can potentially reverse the FDL trimming reaction. However, there has been no concerted effort to evaluate the relationships among these three enzymes in any single insect system. Hence, we extended our previous studies on Spodoptera frugiperda (Sf) FDL to include GNT-I and -II. Sf-GNT-I and -II cDNAs were isolated, the predicted protein sequences were analyzed, and both gene products were expressed and their acceptor substrate specificities and intracellular localizations were determined. Sf-GNT-I transferred N-acetylglucosamine to Man(5)GlcNAc(2), Man(3)GlcNAc(2), and GlcNAc(β1-2)Man(α1-6)[Man(α1-3)]ManGlcNAc(2), demonstrating its role in branch point intermediate production and its ability to reverse FDL trimming. Sf-GNT-II only transferred N-acetylglucosamine to Man(α1-6)[GlcNAc(β1-2)Man(α1-3)]ManGlcNAc(2), demonstrating that it initiates complex N-glycan production, but cannot use Man(3)GlcNAc(2) to produce hybrid or complex structures. Fluorescently tagged Sf-GNT-I and -II co-localized with an endogenous Sf Golgi marker and Sf-FDL co-localized with Sf-GNT-I and -II, indicating that all three enzymes are Golgi resident proteins. Unexpectedly, fluorescently tagged Drosophila melanogaster FDL also co-localized with Sf-GNT-I and an endogenous Drosophila Golgi marker, indicating that it is a Golgi resident enzyme in insect cells. Thus, the substrate specificities and physical juxtapositioning of GNT-I, GNT-II, and FDL support the idea that these enzymes function at the N-glycan processing branch point and are major factors determining the

76 FR 24376 - Commission's Ex Parte Rules and Other Procedural Rules

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-02

...'s Ex Parte Rules and Other Procedural Rules AGENCY: Federal Communications Commission. ACTION: Final rule. SUMMARY: In this document the Commission revises certain ex parte and organizational rules. This document amends and reforms the Commission's rules on ex parte presentations made in the course of...

Loss pathways of N-nitrosodimethylamine (NDMA) in turfgrass soils.

PubMed

Arienzo, M; Gan, J; Ernst, F; Qin, S; Bondarenko, S; Sedlak, D L

2006-01-01

N-nitrosodimethylamine (NDMA) is a potent carcinogen that is often present in municipal wastewater effluents. In a previous field study, it was observed that NDMA did not leach through turfgrass soils following 4 mo of intensive irrigation with NDMA-containing wastewater effluent. To better understand the loss pathways for NDMA in landscape irrigation systems, a mass balance approach was employed using in situ lysimeters treated with 14C-NDMA. When the lysimeters were subjected to irrigation and field conditions after NDMA application, very rapid dissipation of NDMA was observed for both types of soil used in the field plots. After only 4 h, total 14C activity in the lysimeters decreased to 19.1 to 26.1% of the applied amount, and less than 1% of the activity was detected below the 20-cm depth. Analysis of plant materials showed that less than 3% of the applied 14C was incorporated into the plants, suggesting only a minor role for plant uptake in removing NDMA from the vegetated soils. The rapid dissipation and limited downward movement of NDMA in the in situ lysimeters was consistent with the negligible leaching observed in the field study, and suggests volatilization as the only significant loss pathway. This conclusion was further corroborated by rapid NDMA volatilization found from water or a thin layer of soil under laboratory conditions. In a laboratory incubation experiment, prolonged wastewater irrigation did not result in enhanced NDMA degradation in the soil. Therefore, although NDMA may be present at relatively high levels in treated wastewater, gaseous diffusion and volatilization in unsaturated soils may effectively impede significant leaching of NDMA, minimizing the potential for ground water contamination from irrigation with treated wastewater.

A Detailed Chemical Kinetic Reaction Mechanism for n-Alkane Hydrocarbons From n-Octane to n-Hexadecane

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

Westbrook, C K; Pitz, W J; Herbinet, O

2008-02-08

Detailed chemical kinetic reaction mechanisms have been developed to describe the pyrolysis and oxidation of nine n-alkanes larger than n-heptane, including n-octane (n-C{sub 8}H{sub 18}), n-nonane (n-C{sub 9}H{sub 20}), n-decane (n-C{sub 10}H{sub 22}), n-undecane (n-C{sub 11}H{sub 24}), n-dodecane (n-C{sub 12}H{sub 26}), n-tridecane (n-C{sub 13}H{sub 28}), n-tetradecane (n-C{sub 14}H{sub 30}), n-pentadecane (n-C{sub 15}H{sub 32}), and n-hexadecane (n-C{sub 16}H{sub 34}). These mechanisms include both high temperature and low temperature reaction pathways. The mechanisms are based on our previous mechanisms for the primary reference fuels n-heptane and iso-octane, using the reaction class mechanism construction first developed for n-heptane. Individual reaction class rules aremore » as simple as possible in order to focus on the parallelism between all of the n-alkane fuels included in the mechanisms, and these mechanisms will be refined further in the future to incorporate greater levels of accuracy and predictive capability. These mechanisms are validated through extensive comparisons between computed and experimental data from a wide variety of different sources. In addition, numerical experiments are carried out to examine features of n-alkane combustion in which the detailed mechanisms can be used to compare reactivities of different n-alkane fuels. The mechanisms for all of these n-alkanes are presented as a single detailed mechanism, which can be edited to produce efficient mechanisms for any of the n-alkanes included, and the entire mechanism, with supporting thermochemical and transport data, together with an explanatory glossary explaining notations and structural details, will be available for download from our web page.« less

Mathematical modelling of contact of ruled surfaces: theory and practical application

NASA Astrophysics Data System (ADS)

Panchuk, K. L.; Niteyskiy, A. S.

2016-04-01

In the theory of ruled surfaces there are well known researches of contact of ruled surfaces along their common generator line (Klein image is often used [1]). In this paper we propose a study of contact of non developable ruled surfaces via the dual vector calculus. The advantages of this method have been demonstrated by E. Study, W. Blaschke and D. N. Zeiliger in differential geometry studies of ruled surfaces in space R3 over the algebra of dual numbers. A practical use of contact is demonstrated by the example modeling of the working surface of the progressive tool for tillage.

Students' Conceptions Supporting Their Symbolization and Meaning of Function Rules

ERIC Educational Resources Information Center

Fonger, Nicole L.; Ellis, Amy; Dogan, Muhammed F.

2016-01-01

This paper explores the nature of students' quantitative reasoning and conceptions of functions supporting their ability to symbolize quadratic function rules, and the meanings students make of these rules. We analyzed middle school students' problem solving activity during a small group teaching experiment (n = 6) emphasizing quadratic growth…

Kinetics of end-to-end collision in short single-stranded nucleic acids.

PubMed

Wang, Xiaojuan; Nau, Werner M

2004-01-28

A novel fluorescence-based method, which entails contact quenching of the long-lived fluorescent state of 2,3-diazabicyclo[2.2.2]-oct-2-ene (DBO), was employed to measure the kinetics of end-to-end collision in short single-stranded oligodeoxyribonucleotides of the type 5'-DBO-(X)n-dG with X = dA, dC, dT, or dU and n = 2 or 4. The fluorophore was covalently attached to the 5' end and dG was introduced as an efficient intrinsic quencher at the 3' terminus. The end-to-end collision rates, which can be directly related to the efficiency of intramolecular fluorescence quenching, ranged from 0.1 to 9.0 x 10(6) s(-1). They were strongly dependent on the strand length, the base sequence, as well as the temperature. Oligonucleotides containing dA in the backbone displayed much slower collision rates and significantly higher positive activation energies than strands composed of pyrimidine bases, suggesting a higher intrinsic rigidity of oligoadenylate. Comparison of the measured collision rates in short single-stranded oligodeoxyribonucleotides with the previously reported kinetics of hairpin formation indicates that the intramolecular collision is significantly faster than the nucleation step of hairpin closing. This is consistent with the configurational diffusion model suggested by Ansari et al. (Ansari, A.; Kuznetsov, S. V.; Shen, Y. Proc.Natl. Acad. Sci. USA 2001, 98, 7771-7776), in which the formation of misfolded loops is thought to slow hairpin formation.

Why the Three-Point Rule Failed to Sufficiently Reduce the Number of Draws in Soccer: An Application of Prospect Theory.

PubMed

Riedl, Dennis; Heuer, Andreas; Strauss, Bernd

2015-06-01

Incentives guide human behavior by altering the level of external motivation. We apply the idea of loss aversion from prospect theory (Kahneman & Tversky, 1979) to the point reward systems in soccer and investigate the controversial impact of the three-point rule on reducing the fraction of draws in this sport. Making use of the Poisson nature of goal scoring, we compared empirical results with theoretically deduced draw ratios from 24 countries encompassing 20 seasons each (N = 118.148 matches). The rule change yielded a slight reduction in the ratio of draws, but despite adverse incentives, still 18% more matches ended drawn than expected, t(23) = 11.04, p < .001, d = 2.25, consistent with prospect theory assertions. Alternative point systems that manipulated incentives for losses yielded reductions at or below statistical expectation. This provides support for the deduced concept of how arbitrary aims, such as the reduction of draws in the world's soccer leagues, could be more effectively accomplished than currently attempted.

Classical non-homologous end-joining pathway utilizes nascent RNA for error-free double-strand break repair of transcribed genes

PubMed Central

Chakraborty, Anirban; Tapryal, Nisha; Venkova, Tatiana; Horikoshi, Nobuo; Pandita, Raj K.; Sarker, Altaf H.; Sarkar, Partha S.; Pandita, Tej K.; Hazra, Tapas K.

2016-01-01

DNA double-strand breaks (DSBs) leading to loss of nucleotides in the transcribed region can be lethal. Classical non-homologous end-joining (C-NHEJ) is the dominant pathway for DSB repair (DSBR) in adult mammalian cells. Here we report that during such DSBR, mammalian C-NHEJ proteins form a multiprotein complex with RNA polymerase II and preferentially associate with the transcribed genes after DSB induction. Depletion of C-NHEJ factors significantly abrogates DSBR in transcribed but not in non-transcribed genes. We hypothesized that nascent RNA can serve as a template for restoring the missing sequences, thus allowing error-free DSBR. We indeed found pre-mRNA in the C-NHEJ complex. Finally, when a DSB-containing plasmid with several nucleotides deleted within the E. coli lacZ gene was allowed time to repair in lacZ-expressing mammalian cells, a functional lacZ plasmid could be recovered from control but not C-NHEJ factor-depleted cells, providing important mechanistic insights into C-NHEJ-mediated error-free DSBR of the transcribed genome. PMID:27703167

7 CFR 29.1131 - Rule 25.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 2 2011-01-01 2011-01-01 false Rule 25. 29.1131 Section 29.1131 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing....” Crude or green tobacco containing 10 percent or less of oxidized shall be grade “N2.” ...

7 CFR 29.1131 - Rule 25.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Rule 25. 29.1131 Section 29.1131 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing....” Crude or green tobacco containing 10 percent or less of oxidized shall be grade “N2.” ...

Frameworks for organizing exposure and toxicity data - the Aggregate Exposure Pathway (AEP) and the Adverse Outcome Pathway (AOP)

EPA Science Inventory

The Adverse Outcome Pathway (AOP) framework organizes existing knowledge regarding a series of biological events, starting with a molecular initiating event (MIE) and ending at an adverse outcome. The AOP framework provides a biological context to interpret in vitro toxicity dat...

cfa-miR-143 Promotes Apoptosis via the p53 Pathway in Canine Influenza Virus H3N2-Infected Cells.

PubMed

Zhou, Pei; Tu, Liqing; Lin, Xi; Hao, Xiangqi; Zheng, Qingxu; Zeng, Weijie; Zhang, Xin; Zheng, Yun; Wang, Lifang; Li, Shoujun

2017-11-25

MicroRNAs regulate multiple aspects of the host response to viral infection. This study verified that the expression of cfa-miR-143 was upregulated in vivo and in vitro by canine influenza virus (CIV) H3N2 infection. To understand the role of cfa-miR-143 in CIV-infected cells, the target gene of cfa-miR-143 was identified and assessed for correlations with proteins involved in the apoptosis pathway. A dual luciferase reporter assay showed that cfa-miR-143 targets insulin-like growth factor binding protein 5 (Igfbp5). Furthermore, a miRNA agomir and antagomir of cfa-miR-143 caused the downregulation and upregulation of Igfbp5, respectively, in CIV-infected madin-darby canine kidney (MDCK) cells. This study demonstrated that cfa-miR-143 stimulated p53 and caspase3 activation and induced apoptosis via the p53 pathway in CIV H3N2-infected cells. In conclusion, CIV H3N2 induced the upregulation of cfa-miR-143, which contributes to apoptosis via indirectly activating the p53-caspase3 pathway.

Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches.

PubMed

Srivastava, Akriti; Somvanshi, Pallavi; Mishra, Bhartendu Nath

2013-06-01

Pichia pastoris is an efficient expression system for production of recombinant proteins. To understand its physiology for building novel applications it is important to understand and reconstruct its metabolic network. The metabolic reconstruction approach connects genotype with phenotype. Here, we have attempted to reconstruct carbohydrate metabolism pathways responsible for high biomass density and N-glycosylation pathways involved in the post translational modification of proteins of P. pastoris CBS7435. Both these metabolic pathways play a crucial role in heterologous protein production. We report novel, missing and unannotated enzymes involved in the target metabolic pathways. A strong possibility of cellulose and xylose metabolic processes in P. pastoris CBS7435 suggests its use in the area of biofuels. The reconstructed metabolic networks can be used for increased yields and improved product quality, for designing appropriate growth medium, for production of recombinant therapeutics and for making biofuels.

A scoping review of adult chronic kidney disease clinical pathways for primary care.

PubMed

Elliott, Meghan J; Gil, Sarah; Hemmelgarn, Brenda R; Manns, Braden J; Tonelli, Marcello; Jun, Min; Donald, Maoliosa

2017-05-01

Chronic kidney disease (CKD) affects ∼10% of the adult population. The majority of patients with CKD are managed by primary care physicians, and despite the availability of effective treatment options, the use of evidence-based interventions for CKD in this setting remains suboptimal. Clinical pathways have been identified as effective tools to guide primary care physicians in providing evidence-based care. We aimed to describe the availability, characteristics and credibility of clinical pathways for adult CKD using a scoping review methodology. We searched Medline, Embase, CINAHL and targeted Internet sites from inception to 31 October 2014 to identify studies and resources that identified adult CKD clinical pathways for primary care settings. Study selection and data extraction were independently performed by two reviewers. From 487 citations, 41 items were eligible for review: 7 published articles and 34 grey literature resources published between 2001 and 2014. Of the 41 clinical pathways, 32, 24 and 22% were from the UK, USA and Canada, respectively. The majority (66%, n = 31) of clinical pathways were static in nature (did not have an online interactive feature). The majority (76%) of articles/resources reported using one or more clinical practice guidelines as a resource to guide the clinical pathway content. Few articles described a dissemination and evaluation plan for the clinical pathway, but most reported the targeted end-users. Our scoping review synthesized available literature on CKD clinical pathways in the primary care setting. We found that existing clinical pathways are diverse in their design, content and implementation. These results can be used by researchers developing or testing new or existing clinical pathways and by practitioners and health system stakeholders who aim to implement CKD clinical pathways in clinical practice. © The Author 2016. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

Generalization of Faddeev-Popov rules in Yang-Mills theories: N = 3,4 BRST symmetries

NASA Astrophysics Data System (ADS)

Reshetnyak, Alexander

2018-01-01

The Faddeev-Popov rules for a local and Poincaré-covariant Lagrangian quantization of a gauge theory with gauge group are generalized to the case of an invariance of the respective quantum actions, S(N), with respect to N-parametric Abelian SUSY transformations with odd-valued parameters λp, p = 1,…,N and generators sp: spsq + sqsp = 0, for N = 3, 4, implying the substitution of an N-plet of ghost fields, Cp, instead of the parameter, ξ, of infinitesimal gauge transformations: ξ = Cpλ p. The total configuration spaces of fields for a quantum theory of the same classical model coincide in the N = 3 and N = 4 symmetric cases. The superspace of N = 3 SUSY irreducible representation includes, in addition to Yang-Mills fields 𝒜μ, (3 + 1) ghost odd-valued fields Cp, B̂ and 3 even-valued Bpq for p, q = 1, 2, 3. To construct the quantum action, S(3), by adding to the classical action, S0(𝒜), of an N = 3-exact gauge-fixing term (with gauge fermion), a gauge-fixing procedure requires (1 + 3 + 3 + 1) additional fields, Φ¯(3): antighost C¯, 3 even-valued Bp, 3 odd-valued B̂pq and Nakanishi-Lautrup B fields. The action of N = 3 transformations on new fields as N = 3-irreducible representation space is realized. These transformations are the N = 3 BRST symmetry transformations for the vacuum functional, Z3(0) =∫dΦ(3)dΦ¯(3)exp{(ı/ℏ)S(3)}. The space of all fields (Φ(3),Φ¯(3)) proves to be the space of an irreducible representation of the fields Φ(4) for N = 4-parametric SUSY transformations, which contains, in addition to 𝒜μ the (4 + 6 + 4 + 1) ghost-antighost, Cr = (Cp,C¯), even-valued, Brs = -Bsr = (Bpq,Bp4 = Bp), odd-valued B̂r = (B̂,B̂pq) and B fields. The quantum action is constructed by adding to S0(𝒜) an N = 4-exact gauge-fixing term with a gauge boson, F(4). The N = 4 SUSY transformations are by N = 4 BRST transformations for the vacuum functional, Z4(0) =∫dΦ(4)exp{(ı/ℏ)S(4)}. The procedures are valid for

77 FR 18106 - Award Fee for Service and End-Item Contracts

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-27

.... SUMMARY: NASA has adopted, without change, a final rule amending the NASA FAR Supplement (NFS) to update the Award Fee for Service Contracts clause (NFS 1852.216-76) to clarify that the amount of award fee... Award Fee for End-Item Contracts clause (NFS 1852.216-77) to allow the contracting officer to withhold...

Australian road rules

DOT National Transportation Integrated Search

2009-02-01

*These are national-level rules. Australian Road Rules - 2009 Version, Part 18, Division 1, Rule 300 "Use of Mobile Phones" describes restrictions of mobile phone use while driving. The rule basically states that drivers cannot make or receive calls ...

Rules and Self-Rules: Effects of Variation upon Behavioral Sensitivity to Change

ERIC Educational Resources Information Center

Baumann, Ana A.; Abreu-Rodrigues, Josele; da Silva Souza, Alessandra

2009-01-01

Four experiments compared the effects of self-rules and rules, and varied and specific schedules of reinforcement. Participants were first exposed to either several schedules (varied groups) or to one schedule (specific groups) and either were asked to generate rules (self-rule groups), were provided rules (rule groups), or were not asked nor…

Hot electron energy relaxation in lattice-matched InAlN/AlN/GaN heterostructures: The sum rules for electron-phonon interactions and hot-phonon effect

NASA Astrophysics Data System (ADS)

Zhang, J.-Z.; Dyson, A.; Ridley, B. K.

2015-01-01

Using the dielectric continuum (DC) and three-dimensional phonon (3DP) models, energy relaxation (ER) of the hot electrons in the quasi-two-dimensional channel of lattice-matched InAlN/AlN/GaN heterostructures is studied theoretically, taking into account non-equilibrium polar optical phonons, electron degeneracy, and screening from the mobile electrons. The electron power dissipation (PD) and ER time due to both half-space and interface phonons are calculated as functions of the electron temperature Te using a variety of phonon lifetime values from experiment, and then compared with those evaluated by the 3DP model. Thereby, particular attention is paid to examination of the 3DP model to use for the hot-electron relaxation study. The 3DP model yields very close results to the DC model: With no hot phonons or screening, the power loss calculated from the 3DP model is 5% smaller than the DC power dissipation, whereas slightly larger 3DP power loss (by less than 4% with a phonon lifetime from 0.1 to 1 ps) is obtained throughout the electron temperature range from room temperature to 2500 K after including both the hot-phonon effect (HPE) and screening. Very close results are obtained also for ER time with the two phonon models (within a 5% of deviation). However, the 3DP model is found to underestimate the HPE by 9%. The Mori-Ando sum rule is restored by which it is proved that the PD values obtained from the DC and 3DP models are in general different in the spontaneous phonon emission process, except when scattering with interface phonons is sufficiently weak, or when the degenerate modes condition is imposed, which is also consistent with Register's scattering rate sum rule. The discrepancy between the DC and 3DP results is found to be caused by how much the high-energy interface phonons contribute to the ER: their contribution is enhanced in the spontaneous emission process but is dramatically reduced after including the HPE. Our calculation with both phonon

A geometric constraint, the head-to-tail exclusion rule, may be the basis for the isolated-pentagon rule in fullerenes with more than 60 vertices

PubMed Central

Schein, Stan; Friedrich, Tara

2008-01-01

Carbon atoms self-assemble into the famous soccer-ball shaped Buckminsterfullerene (C60), the smallest fullerene cage that obeys the isolated-pentagon rule (IPR). Carbon atoms self-assemble into larger (n > 60 vertices) empty cages as well—but only the few that obey the IPR—and at least 1 small fullerene (n ≤ 60) with adjacent pentagons. Clathrin protein also self-assembles into small fullerene cages with adjacent pentagons, but just a few of those. We asked why carbon atoms and clathrin proteins self-assembled into just those IPR and small cage isomers. In answer, we described a geometric constraint—the head-to-tail exclusion rule—that permits self-assembly of just the following fullerene cages: among the 5,769 possible small cages (n ≤ 60 vertices) with adjacent pentagons, only 15; the soccer ball (n = 60); and among the 216,739 large cages with 60 < n ≤ 84 vertices, only the 50 IPR ones. The last finding was a complete surprise. Here, by showing that the largest permitted fullerene with adjacent pentagons is one with 60 vertices and a ring of interleaved hexagons and pentagon pairs, we prove that for all n > 60, the head-to-tail exclusion rule permits only (and all) fullerene cages and nanotubes that obey the IPR. We therefore suggest that self-assembly that obeys the IPR may be explained by the head-to-tail exclusion rule, a geometric constraint. PMID:19050075

The 1% Rule in Four Digital Health Social Networks: An Observational Study

PubMed Central

2014-01-01

Background In recent years, cyberculture has informally reported a phenomenon named the 1% rule, or 90-9-1 principle, which seeks to explain participatory patterns and network effects within Internet communities. The rule states that 90% of actors observe and do not participate, 9% contribute sparingly, and 1% of actors create the vast majority of new content. This 90%, 9%, and 1% are also known as Lurkers, Contributors, and Superusers, respectively. To date, very little empirical research has been conducted to verify the 1% rule. Objective The 1% rule is widely accepted in digital marketing. Our goal was to determine if the 1% rule applies to moderated Digital Health Social Networks (DHSNs) designed to facilitate behavior change. Methods To help gain insight into participatory patterns, descriptive data were extracted from four long-standing DHSNs: the AlcoholHelpCenter, DepressionCenter, PanicCenter, and StopSmokingCenter sites. Results During the study period, 63,990 actors created 578,349 posts. Less than 25% of actors made one or more posts. The applicability of the 1% rule was confirmed as Lurkers, Contributors, and Superusers accounted for a weighted average of 1.3% (n=4668), 24.0% (n=88,732), and 74.7% (n=276,034) of content. Conclusions The 1% rule was consistent across the four DHSNs. As social network sustainability requires fresh content and timely interactions, these results are important for organizations actively promoting and managing Internet communities. Superusers generate the vast majority of traffic and create value, so their recruitment and retention is imperative for long-term success. Although Lurkers may benefit from observing interactions between Superusers and Contributors, they generate limited or no network value. The results of this study indicate that DHSNs may be optimized to produce network effects, positive externalities, and bandwagon effects. Further research in the development and expansion of DHSNs is required. PMID:24496109

The 1% rule in four digital health social networks: an observational study.

PubMed

van Mierlo, Trevor

2014-02-04

In recent years, cyberculture has informally reported a phenomenon named the 1% rule, or 90-9-1 principle, which seeks to explain participatory patterns and network effects within Internet communities. The rule states that 90% of actors observe and do not participate, 9% contribute sparingly, and 1% of actors create the vast majority of new content. This 90%, 9%, and 1% are also known as Lurkers, Contributors, and Superusers, respectively. To date, very little empirical research has been conducted to verify the 1% rule. The 1% rule is widely accepted in digital marketing. Our goal was to determine if the 1% rule applies to moderated Digital Health Social Networks (DHSNs) designed to facilitate behavior change. To help gain insight into participatory patterns, descriptive data were extracted from four long-standing DHSNs: the AlcoholHelpCenter, DepressionCenter, PanicCenter, and StopSmokingCenter sites. During the study period, 63,990 actors created 578,349 posts. Less than 25% of actors made one or more posts. The applicability of the 1% rule was confirmed as Lurkers, Contributors, and Superusers accounted for a weighted average of 1.3% (n=4668), 24.0% (n=88,732), and 74.7% (n=276,034) of content. The 1% rule was consistent across the four DHSNs. As social network sustainability requires fresh content and timely interactions, these results are important for organizations actively promoting and managing Internet communities. Superusers generate the vast majority of traffic and create value, so their recruitment and retention is imperative for long-term success. Although Lurkers may benefit from observing interactions between Superusers and Contributors, they generate limited or no network value. The results of this study indicate that DHSNs may be optimized to produce network effects, positive externalities, and bandwagon effects. Further research in the development and expansion of DHSNs is required.

Refining the quantitative pathway of the Pathways to Mathematics model.

PubMed

Sowinski, Carla; LeFevre, Jo-Anne; Skwarchuk, Sheri-Lynn; Kamawar, Deepthi; Bisanz, Jeffrey; Smith-Chant, Brenda

2015-03-01

In the current study, we adopted the Pathways to Mathematics model of LeFevre et al. (2010). In this model, there are three cognitive domains--labeled as the quantitative, linguistic, and working memory pathways--that make unique contributions to children's mathematical development. We attempted to refine the quantitative pathway by combining children's (N=141 in Grades 2 and 3) subitizing, counting, and symbolic magnitude comparison skills using principal components analysis. The quantitative pathway was examined in relation to dependent numerical measures (backward counting, arithmetic fluency, calculation, and number system knowledge) and a dependent reading measure, while simultaneously accounting for linguistic and working memory skills. Analyses controlled for processing speed, parental education, and gender. We hypothesized that the quantitative, linguistic, and working memory pathways would account for unique variance in the numerical outcomes; this was the case for backward counting and arithmetic fluency. However, only the quantitative and linguistic pathways (not working memory) accounted for unique variance in calculation and number system knowledge. Not surprisingly, only the linguistic pathway accounted for unique variance in the reading measure. These findings suggest that the relative contributions of quantitative, linguistic, and working memory skills vary depending on the specific cognitive task. Copyright © 2014 Elsevier Inc. All rights reserved.

Mechanism of Microhomology-Mediated End-Joining Promoted by Human DNA Polymerase Theta

PubMed Central

Kent, Tatiana; Chandramouly, Gurushankar; McDevitt, Shane Michael; Ozdemir, Ahmet Y.; Pomerantz, Richard T.

2014-01-01

Microhomology-mediated end-joining (MMEJ) is an error-prone alternative double-strand break repair pathway that utilizes sequence microhomology to recombine broken DNA. Although MMEJ is implicated in cancer development, the mechanism of this pathway is unknown. We demonstrate that purified human DNA polymerase θ (Polθ) performs MMEJ of DNA containing 3’ single-strand DNA overhangs with two or more base-pairs of homology, including DNA modeled after telomeres, and show that MMEJ is dependent on Polθ in human cells. Our data support a mechanism whereby Polθ facilitates end-joining and microhomology annealing then utilizes the opposing overhang as a template in trans which stabilizes the DNA synapse. Polθ exhibits a preference for DNA containing a 5’-terminal phosphate, similar to polymerases involved in non-homologous end-joining. Lastly, we identify a conserved loop domain that is essential for MMEJ and higher-order structures of Polθ which likely promote DNA synapse formation. PMID:25643323

Use of mathematics to guide target selection in systems pharmacology; application to receptor tyrosine kinase (RTK) pathways.

PubMed

Benson, Neil; van der Graaf, Piet H; Peletier, Lambertus A

2017-11-15

A key element of the drug discovery process is target selection. Although the topic is subject to much discussion and experimental effort, there are no defined quantitative rules around optimal selection. Often 'rules of thumb', that have not been subject to rigorous exploration, are used. In this paper we explore the 'rule of thumb' notion that the molecule that initiates a pathway signal is the optimal target. Given the multi-factorial and complex nature of this question, we have simplified an example pathway to its logical minimum of two steps and used a mathematical model of this to explore the different options in the context of typical small and large molecule drugs. In this paper, we report the conclusions of our analysis and describe the analysis tool and methods used. These provide a platform to enable a more extensive enquiry into this important topic. Copyright © 2017 Elsevier B.V. All rights reserved.

The Lectin Pathway in Thrombotic Conditions-A Systematic Review.

PubMed

Larsen, Julie Brogaard; Hvas, Christine Lodberg; Hvas, Anne-Mette

2018-06-04

The lectin pathway of the complement system can activate the coagulation system in vitro, but the role of the lectin pathway in haemostatic activation and thrombosis in vivo is not clear. We performed a systematic review of the existing literature on associations between the lectin pathway and arterial and venous thrombosis, in accordance with the Assessing the Methodological Quality of Systematic Reviews guidelines. PubMed and Embase were searched from January 1990 to March 2017. We included original studies on human study populations investigating associations between the lectin pathway (protein serum levels, genotype or gene expression) and thrombotic conditions or laboratory coagulation markers. Exclusion criteria were case studies including fewer than five cases, conference abstracts or any other language than English. In total, 43 studies were included which investigated associations between the lectin pathway and cardiovascular thrombotic events (CVEs) ( n  = 22), ischaemic stroke ( n  = 9), CVE and stroke ( n  = 1) and other conditions (systemic lupus erythematosus [ n  = 6], sepsis-related coagulopathy [ n  = 3], pulmonary embolism [ n  = 1], asparaginase treatment [ n  = 1]). Studies on the lectin pathway and CVE risk reported discrepant results, as both high and low mannose-binding lectin (MBL) serum levels were found to correlate with increased CVE risk. In ischaemic stroke patients, occurrence of stroke as well as increased stroke severity and poor outcome were consistently associated with high serum MBL. For other thromboembolic conditions, only few studies were identified. In conclusion, lectin pathway activation may negatively influence outcome after ischaemic stroke and possibly contribute to CVE risk. Further research is warranted to elucidate the role of the lectin pathway in other thrombotic conditions. Schattauer GmbH Stuttgart.

Optimal Hedging Rule for Reservoir Refill Operation

NASA Astrophysics Data System (ADS)

Wan, W.; Zhao, J.; Lund, J. R.; Zhao, T.; Lei, X.; Wang, H.

2015-12-01

This paper develops an optimal reservoir Refill Hedging Rule (RHR) for combined water supply and flood operation using mathematical analysis. A two-stage model is developed to formulate the trade-off between operations for conservation benefit and flood damage in the reservoir refill season. Based on the probability distribution of the maximum refill water availability at the end of the second stage, three zones are characterized according to the relationship among storage capacity, expected storage buffer (ESB), and maximum safety excess discharge (MSED). The Karush-Kuhn-Tucker conditions of the model show that the optimality of the refill operation involves making the expected marginal loss of conservation benefit from unfilling (i.e., ending storage of refill period less than storage capacity) as nearly equal to the expected marginal flood damage from levee overtopping downstream as possible while maintaining all constraints. This principle follows and combines the hedging rules for water supply and flood management. A RHR curve is drawn analogously to water supply hedging and flood hedging rules, showing the trade-off between the two objectives. The release decision result has a linear relationship with the current water availability, implying the linearity of RHR for a wide range of water conservation functions (linear, concave, or convex). A demonstration case shows the impacts of factors. Larger downstream flood conveyance capacity and empty reservoir capacity allow a smaller current release and more water can be conserved. Economic indicators of conservation benefit and flood damage compete with each other on release, the greater economic importance of flood damage is, the more water should be released in the current stage, and vice versa. Below a critical value, improving forecasts yields less water release, but an opposing effect occurs beyond this critical value. Finally, the Danjiangkou Reservoir case study shows that the RHR together with a rolling

Analysis of the coexisting pathways for NO and N2O formation in Chernozem using the (15)N-tracer SimKIM-Advanced model.

PubMed

Stange, Claus Florian; Spott, Oliver; Russow, Rolf

2013-01-01

The nitrogen (N) cycle consists of a variety of microbial processes. These processes often occur simultaneously in soils, but respond differently to local environmental conditions due to process-specific biochemical restrictions (e.g. oxygen levels). Hence, soil nitrogen cycling (e.g. soil N gas production through nitrification and denitrification) is individually affected through these processes, resulting in the complex and highly dynamic behaviour of total soil N turnover. The development and application of methods that facilitate the quantification of individual contributions of coexisting processes is a fundamental prerequisite for (i) understanding the dynamics of soil N turnover and (ii) implementing these processes in ecosystem models. To explain the unexpected results of the triplet tracer experiment (TTE) of Russow et al. (Role of nitrite and nitric oxide in the processes of nitrification and denitrification in soil: results from (15)N tracer experiments. Soil Biol Biochem. 2009;41:785-795) the existing SimKIM model was extended to the SimKIM-Advanced model through the addition of three separate nitrite subpools associated with ammonia oxidation, oxidation of organic nitrogen (Norg), and denitrification, respectively. For the TTE, individual treatments with (15)N ammonium, (15)N nitrate, and (15)N nitrite were conducted under oxic, hypoxic, and anoxic conditions, respectively, to clarify the role of nitric oxide as a denitrification intermediate during N2O formation. Using a split nitrite pool, this analysis model explains the observed differences in the (15)N enrichments in nitric oxide (NO) and nitrous oxide (N2O) which occurred in dependence on different oxygen concentrations. The change from oxic over hypoxic to anoxic conditions only marginally increased the NO and N2O release rates (1.3-fold). The analysis using the model revealed that, under oxic and hypoxic conditions, Norg-based N2O production was the dominant pathway, contributing to 90 and 50�

Identification of altered pathways in breast cancer based on individualized pathway aberrance score.

PubMed

Shi, Sheng-Hong; Zhang, Wei; Jiang, Jing; Sun, Long

2017-08-01

The objective of the present study was to identify altered pathways in breast cancer based on the individualized pathway aberrance score (iPAS) method combined with the normal reference (nRef). There were 4 steps to identify altered pathways using the iPAS method: Data preprocessing conducted by the robust multi-array average (RMA) algorithm; gene-level statistics based on average Z ; pathway-level statistics according to iPAS; and a significance test dependent on 1 sample Wilcoxon test. The altered pathways were validated by calculating the changed percentage of each pathway in tumor samples and comparing them with pathways from differentially expressed genes (DEGs). A total of 688 altered pathways with P<0.01 were identified, including kinesin (KIF)- and polo-like kinase (PLK)-mediated events. When the percentage of change reached 50%, 310 pathways were involved in the total 688 altered pathways, which may validate the present results. In addition, there were 324 DEGs and 155 common genes between DEGs and pathway genes. DEGs and common genes were enriched in the same 9 significant terms, which also were members of altered pathways. The iPAS method was suitable for identifying altered pathways in breast cancer. Altered pathways (such as KIF and PLK mediated events) were important for understanding breast cancer mechanisms and for the future application of customized therapeutic decisions.

A toolbox model of evolution of metabolic pathways on networks of arbitrary topology.

PubMed

Pang, Tin Yau; Maslov, Sergei

2011-05-01

In prokaryotic genomes the number of transcriptional regulators is known to be proportional to the square of the total number of protein-coding genes. A toolbox model of evolution was recently proposed to explain this empirical scaling for metabolic enzymes and their regulators. According to its rules, the metabolic network of an organism evolves by horizontal transfer of pathways from other species. These pathways are part of a larger "universal" network formed by the union of all species-specific networks. It remained to be understood, however, how the topological properties of this universal network influence the scaling law of functional content of genomes in the toolbox model. Here we answer this question by first analyzing the scaling properties of the toolbox model on arbitrary tree-like universal networks. We prove that critical branching topology, in which the average number of upstream neighbors of a node is equal to one, is both necessary and sufficient for quadratic scaling. We further generalize the rules of the model to incorporate reactions with multiple substrates/products as well as branched and cyclic metabolic pathways. To achieve its metabolic tasks, the new model employs evolutionary optimized pathways with minimal number of reactions. Numerical simulations of this realistic model on the universal network of all reactions in the KEGG database produced approximately quadratic scaling between the number of regulated pathways and the size of the metabolic network. To quantify the geometrical structure of individual pathways, we investigated the relationship between their number of reactions, byproducts, intermediate, and feedback metabolites. Our results validate and explain the ubiquitous appearance of the quadratic scaling for a broad spectrum of topologies of underlying universal metabolic networks. They also demonstrate why, in spite of "small-world" topology, real-life metabolic networks are characterized by a broad distribution of pathway

Metformin Inhibits Advanced Glycation End Products-Induced Inflammatory Response in Murine Macrophages Partly through AMPK Activation and RAGE/NFκB Pathway Suppression

PubMed Central

Zhou, Zhong'e; Tang, Yong; Chen, Chengjun; Lu, Yi; Liu, Liang

2016-01-01

Advanced glycation end products (AGEs) are major inflammatory mediators in diabetes, affecting atherosclerosis progression via macrophages. Metformin slows diabetic atherosclerosis progression through mechanisms that remain to be fully elucidated. The present study of murine bone marrow derived macrophages showed that (1) AGEs enhanced proinflammatory cytokines (interleukin-1β (IL-1β), IL-6, and tumor necrosis factor-α (TNF-α)) mRNA expression, RAGE expression, and NFκB activation; (2) metformin pretreatment inhibited AGEs effects and AGEs-induced cluster designation 86 (CD86) (M1 marker) expression, while promoting CD206 (M2 marker) surface expression and anti-inflammatory cytokine (IL-10) mRNA expression; and (3) the AMPK inhibitor, Compound C, attenuated metformin effects. In conclusion, metformin inhibits AGEs-induced inflammatory response in murine macrophages partly through AMPK activation and RAGE/NFκB pathway suppression. PMID:27761470

Estimating Discharge and Nonpoint Source Nitrate Loading to Streams From Three End-Member Pathways Using High-Frequency Water Quality Data

NASA Astrophysics Data System (ADS)

Miller, Matthew P.; Tesoriero, Anthony J.; Hood, Krista; Terziotti, Silvia; Wolock, David M.

2017-12-01

The myriad hydrologic and biogeochemical processes taking place in watersheds occurring across space and time are integrated and reflected in the quantity and quality of water in streams and rivers. Collection of high-frequency water quality data with sensors in surface waters provides new opportunities to disentangle these processes and quantify sources and transport of water and solutes in the coupled groundwater-surface water system. A new approach for separating the streamflow hydrograph into three components was developed and coupled with high-frequency nitrate data to estimate time-variable nitrate loads from chemically dilute quick flow, chemically concentrated quick flow, and slowflow groundwater end-member pathways for periods of up to 2 years in a groundwater-dominated and a quick-flow-dominated stream in central Wisconsin, using only streamflow and in-stream water quality data. The dilute and concentrated quick flow end-members were distinguished using high-frequency specific conductance data. Results indicate that dilute quick flow contributed less than 5% of the nitrate load at both sites, whereas 89 ± 8% of the nitrate load at the groundwater-dominated stream was from slowflow groundwater, and 84 ± 25% of the nitrate load at the quick-flow-dominated stream was from concentrated quick flow. Concentrated quick flow nitrate concentrations varied seasonally at both sites, with peak concentrations in the winter that were 2-3 times greater than minimum concentrations during the growing season. Application of this approach provides an opportunity to assess stream vulnerability to nonpoint source nitrate loading and expected stream responses to current or changing conditions and practices in watersheds.

In TCR-Stimulated T-cells, N-ras Regulates Specific Genes and Signal Transduction Pathways

PubMed Central

Lynch, Stephen J.; Zavadil, Jiri; Pellicer, Angel

2013-01-01

It has been recently shown that N-ras plays a preferential role in immune cell development and function; specifically: N-ras, but not H-ras or K-ras, could be activated at and signal from the Golgi membrane of immune cells following a low level T-cell receptor stimulus. The goal of our studies was to test the hypothesis that N-ras and H-ras played distinct roles in immune cells at the level of the transcriptome. First, we showed via mRNA expression profiling that there were over four hundred genes that were uniquely differentially regulated either by N-ras or H-ras, which provided strong evidence in favor of the hypothesis that N-ras and H-ras have distinct functions in immune cells. We next characterized the genes that were differentially regulated by N-ras in T cells following a low-level T-cell receptor stimulus. Of the large pool of candidate genes that were differentially regulated by N-ras downstream of TCR ligation, four genes were verified in qRT-PCR-based validation experiments (Dntt, Slc9a6, Chst1, and Lars2). Finally, although there was little overlap between individual genes that were regulated by N-ras in unstimulated thymocytes and stimulated CD4+ T-cells, there was a nearly complete correspondence between the signaling pathways that were regulated by N-ras in these two immune cell types. PMID:23755101

Evidence for an Elongation/Reduction/C1-Elimination Pathway in the Biosynthesis of n-Heptane in Xylem of Jeffrey Pine.

PubMed Central

Savage, T. J.; Hristova, M. K.; Croteau, R.

1996-01-01

The biosynthetic pathway to n-heptane was investigated by examining the effect of the [beta]-keto acyl-acyl carrier protein synthase inhibitor (2R,3S)-2,3-epoxy-4-oxo-7E,10E-dodecadienamide (cerulenin), a thiol reagent ([beta]-mercaptoethanol), and an aldehydetrapping reagent (hydroxylamine) on the biosynthesis of n-[14C]heptane and putative intermediates in xylem sections of Jeffrey pine (Pinus jeffreyi Grev.& Balf.) incubated with [14C]acetate. Cerulenin inhibited C18 fatty acid biosynthesis but had relatively little effect on radiolabel incorporation into C8 fatty acyl groups and n-heptane. [beta]-Mercaptoethanol inhibited n-heptane biosynthesis, with a corresponding accumulation of radiolabel into both octanal and 1-octanol, whereas hydroxylamine inhibited both n-heptane and 1-octanol biosynthesis, with radiolabel accumulation in octyl oximes. [14C]Octanal was converted to both n-heptane and 1-octanol when incubated with xylem sections, whereas [14C]1-octanol was converted to octanal and n-heptane in a hydroxylamine-sensitive reaction. These results suggest a pathway for the biosynthesis of n-heptane whereby acetate is polymerized via a typical fatty acid synthase reaction sequence to yield a C8 thioester, which subsequently undergoes a two-electron reduction to generate a free thiol and octanal, the latter of which alternately undergoes an additional, reversible reduction to form 1-octanol or loss of C1 to generate n-heptane. PMID:12226360

Hidden overflow pathway to L-phenylalanine in Pseudomonas aeruginosa.

PubMed Central

Fiske, M J; Whitaker, R J; Jensen, R A

1983-01-01

Pseudomonas aeruginosa is representative of a large group of pseudomonad bacteria that possess coexisting alternative pathways to L-phenylalanine (as well as to L-tyrosine). These multiple flow routes to aromatic end products apparently account for the inordinate resistance of P. aeruginosa to end product analogs. Manipulation of carbon source nutrition produced a physiological state of sensitivity to p-fluorophenylalanine and m-fluorophenylalanine, each a specific antimetabolite of L-phenylalanine. Analog-resistant mutants obtained fell into two classes. One type lacked feedback sensitivity of prephenate dehydratase and was the most dramatic excretor of L-phenylalanine. The presence of L-tyrosine curbed phenylalanine excretion to one-third, a finding explained by potent early-pathway regulation of 3-deoxy-D-arabinoheptulosonate 7-phosphate (DAHP) synthase-Tyr (a DAHP synthase subject to allosteric inhibition by L-tyrosine). The second class of regulatory mutants possessed a completely feedback-resistant DAHP synthase-Tyr, the major species (greater than 90%) of two isozymes. Deregulation of DAHP synthase-Tyr resulted in the escape of most chorismate molecules produced into an unregulated overflow route consisting of chorismate mutase (monofunctional), prephenate aminotransferase, and arogenate dehydratase. In the wild type the operation of the overflow pathway is restrained by factors that restrict early-pathway flux. These factors include the highly potent feedback control of DAHP synthase isozymes by end products as well as the strikingly variable abilities of different carbon source nutrients to supply the aromatic pathway with beginning substrates. Even in the wild type, where all allosteric regulation in intact, some phenylalanine overflow was found on glucose-based medium, but not on fructose-based medium. This carbon source-dependent difference was much more exaggerated in each class of regulatory mutants. PMID:6132913

Activation of the N-Ras-PI3K-Akt-mTOR Pathway by Hepatitis C Virus: Control of Cell Survival and Viral Replication

PubMed Central

Mannová, Petra; Beretta, Laura

2005-01-01

The hepatitis C virus (HCV) replication complex is localized within detergent-resistant membranes or lipid rafts. We analyzed the protein contents of detergent-resistant fractions isolated from Huh7 cells expressing a self-replicating full-length HCV-1b genome. Using two-dimensional gel electrophoresis followed by mass spectrometry, we identified N-Ras as one of the proteins in which expression was increased in the detergent-resistant fractions from HCV genomic replicon clones compared to control cells. N-Ras is an activator of the phosphatidylinositol-3-kinase (PI3K)-Akt pathway. We found that the activities of PI3K and Akt, as well as the activity of their downstream target, mTOR, in the HCV-replicating cells were increased. Both PI3K-Akt- and mTOR-dependent pathways have been shown to promote cell survival. In agreement with this, HCV replicon cells were resistant to serum starvation-induced apoptosis. We also characterized the role of this pathway in HCV replication. Reduction of N-Ras expression by transfection of N-Ras small interfering RNA (siRNA) resulted in increased replication of HCV. We observed a similar increase in HCV replication in cells treated with the PI3K inhibitor LY294002 and in cells transfected with mTOR siRNA. Taken together, these data suggest that increased N-Ras levels in subcellular sites of HCV replication and stimulation of the prosurvival PI3K-Akt pathway and mTOR by HCV not only protect cells against apoptosis but also contribute to the maintenance of steady-state levels of HCV replication. These effects may contribute to the establishment of persistent infection by HCV. PMID:15994768

Application of Adverse Outcome Pathways to U.S. EPA’s Endocrine Disruptor Screening Program

PubMed Central

Noyes, Pamela D.; Casey, Warren M.; Dix, David J.

2017-01-01

Background: The U.S. EPA’s Endocrine Disruptor Screening Program (EDSP) screens and tests environmental chemicals for potential effects in estrogen, androgen, and thyroid hormone pathways, and it is one of the only regulatory programs designed around chemical mode of action. Objectives: This review describes the EDSP’s use of adverse outcome pathway (AOP) and toxicity pathway frameworks to organize and integrate diverse biological data for evaluating the endocrine activity of chemicals. Using these frameworks helps to establish biologically plausible links between endocrine mechanisms and apical responses when those end points are not measured in the same assay. Results: Pathway frameworks can facilitate a weight of evidence determination of a chemical’s potential endocrine activity, identify data gaps, aid study design, direct assay development, and guide testing strategies. Pathway frameworks also can be used to evaluate the performance of computational approaches as alternatives for low-throughput and animal-based assays and predict downstream key events. In cases where computational methods can be validated based on performance, they may be considered as alternatives to specific assays or end points. Conclusions: A variety of biological systems affect apical end points used in regulatory risk assessments, and without mechanistic data, an endocrine mode of action cannot be determined. Because the EDSP was designed to consider mode of action, toxicity pathway and AOP concepts are a natural fit. Pathway frameworks have diverse applications to endocrine screening and testing. An estrogen pathway example is presented, and similar approaches are being used to evaluate alternative methods and develop predictive models for androgen and thyroid pathways. https://doi.org/10.1289/EHP1304 PMID:28934726

Aβ mediates Sigma receptor degradation via CaN/NFAT pathway

PubMed Central

Fang, Min; Zhang, Pei; Zhao, Yanxin; Jin, Aiping; Liu, Xueyuan

2016-01-01

Sigma receptor is an endoplasmic reticulum protein and belongs to non-opioid receptor. Increasing evidence shows that Sigma receptor activation can significantly attenuate AD induced neurological dysfunction and the functional deficiency of Sigma receptor plays an important role in the Aβ induced neuronal loss. This study aimed to investigate the influence of extracellular accumulation of Aβ on the Sigma receptor expression. Our results showed the increase in extracellular Aβ had little influence on the mRNA expression of Sigma receptor, but gradually reduced its protein expression. Co-immunoprecipitation was employed to evaluate the interaction of Sigma receptor with other proteins. Results showed BIP could bind to Sigma receptor to affect the ubiquitination of Sigma receptor. Further investigation showed there was a NFAT binding site at the promoter of BIP. Then, Western blot assay was performed to detect NFAT expression. Results showed extracellular Aβ affected the nuclear translocation of NFAT and the CaN activity of NFAT also increased with the accumulation of extracellular Aβ. In this study, NFAT-BIP luciferase reporter gene system was constructed. Results showed NFAT was able to regulate the transcription of BIP. Thus, we speculate that extracellular Aβ accumulation may activate CaN/NFAT signaling pathway to induce chaperone BIP expression, which results in Sigma receptor ubiquitination and its degradation. PMID:27648137

Evaluation of End Mill Coatings

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

L. J. Lazarus; R. L. Hester,

2005-08-01

Milling tests were run on families of High Speed Steel (HSS) end mills to determine their lives while machining 304 Stainless Steel. The end mills tested were made from M7, M42 and T15-CPM High Speed Steels. The end mills were also evaluated with no coatings as well as with Titanium Nitride (TiN) and Titanium Carbo-Nitride (TiCN) coatings to determine which combination of HSS and coating provided the highest increase in end mill life while increasing the cost of the tool the least. We found end mill made from M42 gave us the largest increase in tool life with the leastmore » increase in cost. The results of this study will be used by Cutting Tool Engineering in determining which end mill descriptions will be dropped from our tool catalog.« less

Florida Court: Vouchers Unconstitutional--Ruling Will End Opportunity Scholarships Program for Students in State's Lowest-Rated Schools

ERIC Educational Resources Information Center

Richard, Alan

2006-01-01

Florida's voucher program for students in the lowest-rated public schools is unconstitutional, the state supreme court ruled early January 2006 in a 5-2 decision that friends and foes of private school choice are scrutinizing for its potential impact on voucher debates nationwide. Chief Justice Barbara J. Pariente of the Florida Supreme Court…

76 FR 70227 - Medicare Program; End-Stage Renal Disease Prospective Payment System and Quality Incentive...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-10

...This final rule updates and makes certain revisions to the End-Stage Renal Disease (ESRD) prospective payment system (PPS) for calendar year (CY) 2012. We are also finalizing the interim final rule with comment period published on April 6, 2011, regarding the transition budget-neutrality adjustment under the ESRD PPS,. This final rule also sets forth requirements for the ESRD quality incentive program (QIP) for payment years (PYs) 2013 and 2014. In addition, this final rule revises the ambulance fee schedule regulations to conform to statutory changes. This final rule also revises the definition of durable medical equipment (DME) by adding a 3-year minimum lifetime requirement (MLR) that must be met by an item or device in order to be considered durable for the purpose of classifying the item under the Medicare benefit category for DME. Finally, this final rule implements certain provisions of section 154 of the Medicare Improvements for Patients and Providers Act of 2008 (MIPPA) related to the durable medical equipment, prosthetics, orthotics and supplies (DMEPOS) Competitive Acquisition Program and responds to comments received on an interim final rule published January 16, 2009, that implemented these provisions of MIPPA effective April 18, 2009. (See the Table of Contents for a listing of the specific issues addressed in this final rule.)

The care pathway: concepts and theories: an introduction.

PubMed

Schrijvers, Guus; van Hoorn, Arjan; Huiskes, Nicolette

2012-01-01

This article addresses first the definition of a (care) pathway, and then follows a description of theories since the 1950s. It ends with a discussion of theoretical advantages and disadvantages of care pathways for patients and professionals. The objective of this paper is to provide a theoretical base for empirical studies on care pathways. The knowledge for this chapter is based on several books on pathways, which we found by searching in the digital encyclopedia Wikipedia. Although this is not usual in scientific publications, this method was used because books are not searchable by databases as Pubmed. From 2005, we performed a literature search on Pubmed and other literature databases, and with the keywords integrated care pathway, clinical pathway, critical pathway, theory, research, and evaluation. One of the inspirational sources was the website of the European Pathway Association (EPA) and its journal International Journal of Care Pathways. The authors visited several sites for this paper. These are mentioned as illustration of a concept or theory. Most of them have English websites with more information. The URLs of these websites are not mentioned in this paper as a reference, because the content of them changes fast, sometimes every day.

A comprehensive detailed chemical kinetic reaction mechanism for combustion of n-alkane hydrocarbons from n-octane to n-hexadecane

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

Westbrook, Charles K.; Pitz, William J.; Herbinet, Olivier

2009-01-15

Detailed chemical kinetic reaction mechanisms have been developed to describe the pyrolysis and oxidation of nine n-alkanes larger than n-heptane, including n-octane (n-C{sub 8}H{sub 18}), n-nonane (n-C{sub 9}H{sub 20}), n-decane (n-C{sub 10}H{sub 22}), n-undecane (n-C{sub 11}H{sub 24}), n-dodecane (n-C{sub 12}H{sub 26}), n-tridecane (n-C{sub 13}H{sub 28}), n-tetradecane (n-C{sub 14}H{sub 30}), n-pentadecane (n-C{sub 15}H{sub 32}), and n-hexadecane (n-C{sub 16}H{sub 34}). These mechanisms include both high temperature and low temperature reaction pathways. The mechanisms are based on previous mechanisms for the primary reference fuels n-heptane and iso-octane, using the reaction classes first developed for n-heptane. Individual reaction class rules are as simple asmore » possible in order to focus on the parallelism between all of the n-alkane fuels included in the mechanisms. These mechanisms are validated through extensive comparisons between computed and experimental data from a wide variety of different sources. In addition, numerical experiments are carried out to examine features of n-alkane combustion in which the detailed mechanisms can be used to compare reactivities of different n-alkane fuels. The mechanisms for these n-alkanes are presented as a single detailed mechanism, which can be edited to produce efficient mechanisms for any of the n-alkanes included, and the entire mechanism, with supporting thermochemical and transport data, together with an explanatory glossary explaining notations and structural details, is available for download from our web page. (author)« less

Double 90 Degrees Counterrotated End-to-End-Anastomosis: An Experimental Study of an Intestinal Anastomosis Technique.

PubMed

Holzner, Philipp; Kulemann, Birte; Seifert, Gabriel; Glatz, Torben; Chikhladze, Sophia; Höppner, Jens; Hopt, Ulrich; Timme, Sylvia; Bronsert, Peter; Sick, Olivia; Zhou, Cheng; Marjanovic, Goran

2015-06-01

The aim of the article is to investigate a new anastomotic technique compared with standardized intestinal anastomotic procedures. A total of 32 male Wistar rats were randomized to three groups. In the Experimental Group (n = 10), the new double 90 degrees inversely rotated anastomosis was used, in the End Group (n = 10) a single-layer end-to-end anastomosis, and in the Side Group (n = 12) a single-layer side-to-side anastomosis. All anastomoses were done using interrupted sutures. On postoperative day 4, rats were relaparotomized. Bursting pressure, hydroxyproline concentration, a semiquantitative adhesion score and two histological anastomotic healing scores (mucosal healing according to Chiu and overall anastomotic healing according to Verhofstad) were collected. Most data are presented as median (range). p < 0.05 was considered significant. Anastomotic insufficiency occurred only in one rat of the Side Group. Median bursting pressure in the Experimental Group was 105 mm Hg (range = 72-161 mm Hg), significantly higher in the End Group (164 mm Hg; range = 99-210 mm Hg; p = 0.021) and lower in the Side Group by trend (81 mm Hg; range = 59-122 mm Hg; p = 0.093). Hydroxyproline concentration did not differ significantly in between the groups. The adhesion score was 2.5 (range = 1-3) in the Experimental Group, 2 (range = 1-2) in the End Group, but there were significantly more adhesions in the Side Group (range = 3-4); p = 0.020 versus Experimental Group, p < 0.001 versus End Group. The Chiu Score showed the worst mucosal healing in the Experimental Group. The overall Verhofstad Score was significantly worse (mean = 2.032; standard deviation [SD] = 0.842) p = 0.031 and p = 0.002 in the Experimental Group, compared with the Side Group (mean = 1.729; SD = 0.682) and the End Group (mean = 1.571; SD = 0.612). The new anastomotic technique is feasible and did not show any relevant complication. Even though it was superior to the side-to-side anastomosis by trend with

A Combined Pathway and Regional Heritability Analysis Indicates NETRIN1 Pathway Is Associated With Major Depressive Disorder.

PubMed

Zeng, Yanni; Navarro, Pau; Fernandez-Pujals, Ana M; Hall, Lynsey S; Clarke, Toni-Kim; Thomson, Pippa A; Smith, Blair H; Hocking, Lynne J; Padmanabhan, Sandosh; Hayward, Caroline; MacIntyre, Donald J; Wray, Naomi R; Deary, Ian J; Porteous, David J; Haley, Chris S; McIntosh, Andrew M

2017-02-15

Genome-wide association studies (GWASs) of major depressive disorder (MDD) have identified few significant associations. Testing the aggregation of genetic variants, in particular biological pathways, may be more powerful. Regional heritability analysis can be used to detect genomic regions that contribute to disease risk. We integrated pathway analysis and multilevel regional heritability analyses in a pipeline designed to identify MDD-associated pathways. The pipeline was applied to two independent GWAS samples [Generation Scotland: The Scottish Family Health Study (GS:SFHS, N = 6455) and Psychiatric Genomics Consortium (PGC:MDD) (N = 18,759)]. A polygenic risk score (PRS) composed of single nucleotide polymorphisms from the pathway most consistently associated with MDD was created, and its accuracy to predict MDD, using area under the curve, logistic regression, and linear mixed model analyses, was tested. In GS:SFHS, four pathways were significantly associated with MDD, and two of these explained a significant amount of pathway-level regional heritability. In PGC:MDD, one pathway was significantly associated with MDD. Pathway-level regional heritability was significant in this pathway in one subset of PGC:MDD. For both samples the regional heritabilities were further localized to the gene and subregion levels. The NETRIN1 signaling pathway showed the most consistent association with MDD across the two samples. PRSs from this pathway showed competitive predictive accuracy compared with the whole-genome PRSs when using area under the curve statistics, logistic regression, and linear mixed model. These post-GWAS analyses highlight the value of combining multiple methods on multiple GWAS data for the identification of risk pathways for MDD. The NETRIN1 signaling pathway is identified as a candidate pathway for MDD and should be explored in further large population studies. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights

Smoke-free home and vehicle rules by tobacco use status among US adults.

PubMed

Kruger, Judy; Jama, Amal; Homa, David M; Babb, Stephen D; King, Brian A

2015-09-01

To assess the prevalence and characteristics of smoke-free home and vehicle rules by tobacco use. Data came from the 2012-2013 National Adult Tobacco Survey, a telephone survey of adults aged ≥18. Respondents who reported smoking is 'never allowed' inside their home or any family vehicle were considered to have smoke-free home and vehicle rules, respectively. Prevalence and characteristics of smoke-free rules were assessed overall and by current tobacco use (combustible only, noncombustible only, combustible and noncombustible, no current tobacco use). Assessed characteristics included: sex, age, race/ethnicity, education, marital status, income, region, and sexual orientation. Nationally, 83.7% of adults (n=48,871) had smoke-free home rules and 78.1% (n=46,183) had smoke-free vehicle rules. By tobacco use, prevalence was highest among nonusers of tobacco (homes: 90.8%; vehicles: 88.9%) and lowest among combustible-only users (homes: 53.7%; vehicles: 34.2%). Prevalence of smoke-free home and vehicle rules was higher among males, adults with a graduate degree, and adults living in the West. Most adults have smoke-free home and vehicle rules, but differences exist by tobacco use. Opportunities exist to educate adults about the dangers of secondhand smoke and the benefits of smoke-free environments, particularly among combustible tobacco users. Published by Elsevier Inc.

Qiang-Dong proper quantization rule and its applications to exactly solvable quantum systems

NASA Astrophysics Data System (ADS)

Serrano, F. A.; Gu, Xiao-Yan; Dong, Shi-Hai

2010-08-01

We propose proper quantization rule, ∫x_Ax_B k(x)dx-∫x0Ax0Bk0(x)dx=nπ, where k(x )=√2M[E -V(x)] /ℏ. The xA and xB are two turning points determined by E =V(x), and n is the number of the nodes of wave function ψ(x ). We carry out the exact solutions of solvable quantum systems by this rule and find that the energy spectra of solvable systems can be determined only from its ground state energy. The previous complicated and tedious integral calculations involved in exact quantization rule are greatly simplified. The beauty and simplicity of the rule come from its meaning—whenever the number of the nodes of ϕ(x ) or the number of the nodes of the wave function ψ(x ) increases by 1, the momentum integral ∫xAxBk(x )dx will increase by π. We apply this proper quantization rule to carry out solvable quantum systems such as the one-dimensional harmonic oscillator, the Morse potential and its generalization, the Hulthén potential, the Scarf II potential, the asymmetric trigonometric Rosen-Morse potential, the Pöschl-Teller type potentials, the Rosen-Morse potential, the Eckart potential, the harmonic oscillator in three dimensions, the hydrogen atom, and the Manning-Rosen potential in D dimensions.

75 FR 44042 - Self-Regulatory Organizations; Notice of Filing and Immediate Effectiveness of Proposed Rule...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-27

... submit order execution reports to the Exchange's Front End Systemic Capture (``FESC'') database linking... that would apply across their respective marketplaces, including a harmonized approach to riskless... approach to customer order protection rules, including how riskless principal transactions should be...

New metabolic pathway for N,N-dimethyltryptamine

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

Hryhorczuk, L.M.; Rainey, J.M. Jr.; Frohman, C.E.

1986-01-01

N,N-Dimethyltryptamine (DMT) undergoes a major structural alteration when added to whole human blood or its red blood cells in vitro. A new high-pressure liquid chromatography (HPLC) peak is present in extracts of these treated tissues. The compound responsible for this peak has been identified by ultraviolet spectrophotometry and by mass spectrometry as dimethylkynuramine (DMK). The enzyme responsible for this appears to be different from tryptophan 2,3-dioxygenase and also from indoleamine 2,3-dioxygenase.

The exoribonuclease Nibbler controls 3' end processing of microRNAs in Drosophila.

PubMed

Liu, Nan; Abe, Masashi; Sabin, Leah R; Hendriks, Gert-Jan; Naqvi, Ammar S; Yu, Zhenming; Cherry, Sara; Bonini, Nancy M

2011-11-22

MicroRNAs (miRNAs) are endogenous noncoding small RNAs with important roles in many biological pathways; their generation and activity are under precise regulation [1-3]. Emerging evidence suggests that miRNA pathways are precisely modulated with controls at the level of transcription [4-8], processing [9-11], and stability [12, 13], with miRNA deregulation linked with diseases [14] and neurodegenerative disorders [15]. In the Drosophila miRNA biogenesis pathway, long primary miRNA transcripts undergo sequential cleavage [16-18] to release the embedded miRNAs. Mature miRNAs are then loaded into Argonaute1 (Ago1) within the RNA-induced silencing complex (RISC) [19, 20]. Intriguingly, we found that Drosophila miR-34 displays multiple isoforms that differ at the 3' end, suggesting a novel biogenesis mechanism involving 3' end processing. To define the cellular factors responsible, we performed an RNA interference (RNAi) screen and identified a putative 3'→5' exoribonuclease CG9247/nibbler essential for the generation of the smaller isoforms of miR-34. Nibbler (Nbr) interacts with Ago1 and processes miR-34 within RISC. Deep sequencing analysis revealed a larger set of multi-isoform miRNAs that are controlled by nibbler. These findings suggest that Nbr-mediated 3' end processing represents a critical step in miRNA maturation that impacts miRNA diversity. Copyright © 2011 Elsevier Ltd. All rights reserved.

Kinetics and Pathways for the Debromination of Polybrominated Diphenyl Ethers by Bimetallic and Nanoscale Zerovalent Iron: Effects of Particle Properties and Catalyst

PubMed Central

Zhuang, Yuan; Jin, Luting; Luthy, Richard G.

2012-01-01

Polybrominated diphenyl ethers (PBDEs) are recognized as a new class of widely-distributed and persistent contaminants for which effective treatment and remediation technologies are needed. In this study, two kinds of commercially available nanoscale Fe° slurries (Nanofer N25 and N25S), a freeze-dried laboratory-synthesized Fe° nanoparticle (nZVI), and their palladized forms were used to investigate the effect of particle properties and catalyst on PBDE debromination kinetics and pathways. Nanofers and their palladized forms were found to debrominate PBDEs effectively. The laboratory-synthesized Fe° nanoparticles also debrominated PBDEs, but were slower due to deactivation by the freeze-drying and stabilization processes in the laboratory synthesis. An organic modifier, polyacrylic acid (PAA), bound on N25S slowed PBDE debromination by a factor of three to four compared to N25. The activity of palladized nZVI (nZVI/Pd) was optimized at 0.3 Pd/Fe wt% in our system. N25 could debrominate selected environmentally-abundant PBDEs, including BDE 209, 183, 153, 99, and 47, to end products di-BDEs, mono-BDEs and diphenyl ether (DE) in one week, while nZVI/Pd (0.3 Pd/Fe wt%) mainly resulted in DE as a final product. Step-wise major PBDE debromination pathways by unamended and palladized Fe° are described and compared. Surface precursor complex formation is an important limiting factor for palladized Fe° reduction as demonstrated by PBDE pathways where steric hindrance and rapid sequential debromination of adjacent bromines play an important role. PMID:22732301

Innovative strategy for effective critical laboratory result management: end-to-end process using automation and manual call centre.

PubMed

Ti, Lian Kah; Ang, Sophia Bee Leng; Saw, Sharon; Sethi, Sunil Kumar; Yip, James W L

2012-08-01

Timely reporting and acknowledgement are crucial steps in critical laboratory results (CLR) management. The authors previously showed that an automated pathway incorporating short messaging system (SMS) texts, auto-escalation, and manual telephone back-up improved the rate and speed of physician acknowledgement compared with manual telephone calling alone. This study investigated if it also improved the rate and speed of physician intervention to CLR and whether utilising the manual back-up affected intervention rates. Data from seven audits between November 2007 and January 2011 were analysed. These audits were carried out to assess the robustness of CLR reporting process in the authors' institution. Comparisons were made in the rate and speed of acknowledgement and intervention between the audits performed before and after automation. Using the automation audits, the authors compared intervention data between communication with SMS only and when manual intervention was required. 1680 CLR were reported during the audit periods. Automation improved the rate (100% vs 84.2%; p<0.001) and speed (median 12 min vs 23 min; p<0.001) of CLR acknowledgement. It also improved the rate (93.7% vs 84.0%, p<0.001) and speed (median 21 min vs 109 min; p<0.001) of CLR intervention. From the automation audits, the use of SMS only did not improve physician intervention rates. The automated communication pathway improved physician intervention rate and time in tandem with improved acknowledgement rate and time when compared with manual telephone calling. The use of manual intervention to augment automation did not adversely affect physician intervention rate, implying that an end-to-end pathway was more important than automation alone.

Early activation of nSMase2/ceramide pathway in astrocytes is involved in ischemia-associated neuronal damage via inflammation in rat hippocampi

PubMed Central

2013-01-01

Background Ceramide accumulation is considered a contributing factor to neuronal dysfunction and damage. However, the underlying mechanisms that occur following ischemic insult are still unclear. Methods In the present study, we established cerebral ischemia models using four-vessel occlusion and oxygen-glucose deprivation methods. The hippocampus neural cells were subjected to immunohistochemistry and immunofluorescence staining for ceramide and neutral sphingomyelinase 2 (nSMase2) levels; immunoprecipitation and immunoblot analysis for nSMase2, receptor for activated C kinase 1 (RACK1), embryonic ectoderm development (EED), p38 mitogen-activated protein kinase (p38MAPK) and phosphorylated p38MAPK expression; SMase assay for nSMase and acid sphingomyelinase (aSMase) activity; real-time reverse transcription polymerase chain reaction for cytokine expression; and Nissl, microtubule-associated protein 2 and terminal deoxynucleotidyl transferase–mediated deoxyuridine triphosphate nick-end labeling staining. Results We found considerable production of ceramide in astrocytes, but not in neurons, during early cerebral ischemia. This was accompanied by the induction of nSMase (but not aSMase) activity in the rat hippocampi. The inhibition of nSMase2 activity effectively reduced ceramide accumulation in astrocytes and alleviated neuronal damage to some extent. Meanwhile, the expression levels of proinflammatory cytokines, including tumor necrosis factor α (TNF-α), interleukin 1β (IL-1β) and IL-6, were found to be upregulated, which may have played an import role in neuronal damage mediated by the nSMase2/ceramide pathway. Although enhanced binding of nSMase2 with RACK1 and EED were also observed after cerebral ischemia, nSMase2 activity was not blocked by the TNF-α receptor inhibitor through RACK1/EED signaling. p38MAPK, but not protein kinase Cζ or protein phosphatase 2B, was able to induce nSMase2 activation after ischemia. p38MAPK can be induced by A2B adenosine

A Wnt/beta-catenin pathway antagonist Chibby binds Cenexin at the distal end of mother centrioles and functions in primary cilia formation.

PubMed

Steere, Nathan; Chae, Vanessa; Burke, Michael; Li, Feng-Qian; Takemaru, Ken-ichi; Kuriyama, Ryoko

2012-01-01

The mother centriole of the centrosome is distinguished from immature daughter centrioles by the presence of accessory structures (distal and subdistal appendages), which play an important role in the organization of the primary cilium in quiescent cells. Primary cilia serve as sensory organelles, thus have been implicated in mediating intracellular signal transduction pathways. Here we report that Chibby (Cby), a highly conserved antagonist of the Wnt/β-catenin pathway, is a centriolar component specifically located at the distal end of the mother centriole and essential for assembly of the primary cilium. Cby appeared as a discrete dot in the middle of a ring-like structure revealed by staining with a distal appendage component of Cep164. Cby interacted with one of the appendage components, Cenexin (Cnx), which thereby abrogated the inhibitory effect of Cby on β-catenin-mediated transcriptional activation in a dose-dependent manner. Cby and Cnx did not precisely align, as Cby was detected at a more distal position than Cnx. Cnx emerged earlier than Cby during the cell cycle and was required for recruitment of Cby to the mother centriole. However, Cby was dispensable for Cnx localization to the centriole. During massive centriogenesis in in vitro cultured mouse tracheal epithelial cells, Cby and Cnx were expressed in a similar pattern, which was coincident with the expression of Foxj1. Our results suggest that Cby plays an important role in organization of both primary and motile cilia in collaboration with Cnx.

Neuroma prevention by end-to-side neurorraphy: an experimental study in rats.

PubMed

Aszmann, Oskar C; Korak, Klaus J; Rab, Matthias; Grünbeck, Matthias; Lassmann, Hans; Frey, Manfred

2003-11-01

The successful treatment of painful neuromas remains a difficult goal to attain. In this report we explore the feasibility of neuroma prevention by insertion of the proximal end of a nerve through an end-to-side neurorraphy into an adjacent mixed nerve to provide a pathway and target for axons deprived of their end organ. Experiments were performed on a total of twenty 250-g Sprague-Dawley rats. Two groups of 10 animals were prepared. Group A served as an anatomic control. In group B the right saphenous nerve was transected and implanted end-to-side through an epineurial window into the tibial nerve distal to the trifurcation of the sciatic nerve. After 12 weeks the corresponding sensory neurons were identified by retrograde labeling techniques and histomorphometric analysis of the proximal and distal tibial nerve segments, and regular histology of the end-to-side site were performed. The results of the retrograde labeling of the corresponding sensory neuron pool of the saphenus nerve showed extensive labelling of the L1 to L3 spinal ganglions after intracutaneous tracer application of the planta pedis. The morphology of the end-to-side coaptation site and histomorphologic analysis prove that sensory neurons penetrate the perineurial sheath and axons regenerate along the tibial Schwann cell tubes toward their targets. Axons of a severed peripheral nerve that are provided with a pathway and target through an end-to-side coaptation will either be pruned or establish some type of end-organ contact so that a neuroma can be prevented. Whether these axons will lead to disturbing sensations such as paresthesia or dysesthesia in the newly found environment or remain silent codwellers, this experiment cannot answer. Long-term results of future clinical work will have to decide whether the prevention of the neuroma through end-to-side coaptation will be an appropriate therapy for this difficult problem.

Medicare program; revision to accrual basis of accounting policy--HCFA. Proposed rule.

PubMed

1998-05-18

Current policy provides that payroll taxes a provider becomes obligated to remit to governmental agencies are included in allowable costs under Medicare only in the cost reporting period in which payment (upon which the payroll taxes are based) is actually made to an employee. Therefore, for payroll accrued in one year but not paid until the next year, the associated payroll taxes on the payroll are not an allowable cost until the next year. This proposed rule would make one exception, in the situation where payment would be made to the employee in the current year but for the fact the regularly scheduled payment date is after the end of the year. In that case, the rule would require allowance in the current year of accrued taxes on payroll that is accrued through the end of the year but not paid until the beginning of the next year, thus allowing accrued taxes on end-of-the year payroll in the same year that the accrual of the payroll itself is allowed. The effect of this proposal is not on the allowability of cost but rather only on the timing of payment; that is, the cost of payroll taxes on and-of-the-year payroll would be allowable in the current period rather than in the following period.

Severity of influenza A 2009 (H1N1) pneumonia is underestimated by routine prediction rules. Results from a prospective, population-based study.

PubMed

Bjarnason, Agnar; Thorleifsdottir, Gudlaug; Löve, Arthur; Gudnason, Janus F; Asgeirsson, Hilmir; Hallgrimsson, Kristinn L; Kristjansdottir, Berglind S; Haraldsson, Gunnsteinn; Baldursson, Olafur; Kristinsson, Karl G; Gottfredsson, Magnus

2012-01-01

Characteristics of patients with community-acquired pneumonia (CAP) due to pandemic influenza A 2009 (H1N1) have been inadequately compared to CAP caused by other respiratory pathogens. The performance of prediction rules for CAP during an epidemic with a new infectious agent are unknown. Prospective, population-based study from November 2008-November 2009, in centers representing 70% of hospital beds in Iceland. Patients admitted with CAP underwent evaluation and etiologic testing, including polymerase chain reaction (PCR) for influenza. Data on influenza-like illness in the community and overall hospital admissions were collected. Clinical and laboratory data, including pneumonia severity index (PSI) and CURB-65 of patients with CAP due to H1N1 were compared to those caused by other agents. Of 338 consecutive and eligible patients 313 (93%) were enrolled. During the pandemic peak, influenza A 2009 (H1N1) patients constituted 38% of admissions due to CAP. These patients were younger, more dyspnoeic and more frequently reported hemoptysis. They had significantly lower severity scores than other patients with CAP (1.23 vs. 1.61, P= .02 for CURB-65, 2.05 vs. 2.87 for PSI, P<.001) and were more likely to require intensive care admission (41% vs. 5%, P<.001) and receive mechanical ventilation (14% vs. 2%, P= .01). Bacterial co-infection was detected in 23% of influenza A 2009 (H1N1) patients with CAP. Clinical characteristics of CAP caused by influenza A 2009 (H1N1) differ markedly from CAP caused by other etiologic agents. Commonly used CAP prediction rules often failed to predict admissions to intensive care or need for assisted ventilation in CAP caused by the influenza A 2009 (H1N1) virus, underscoring the importance of clinical acumen under these circumstances.

Severity of Influenza A 2009 (H1N1) Pneumonia Is Underestimated by Routine Prediction Rules. Results from a Prospective, Population-Based Study

PubMed Central

Bjarnason, Agnar; Thorleifsdottir, Gudlaug; Löve, Arthur; Gudnason, Janus F.; Asgeirsson, Hilmir; Hallgrimsson, Kristinn L.; Kristjansdottir, Berglind S.; Haraldsson, Gunnsteinn; Baldursson, Olafur; Kristinsson, Karl G.; Gottfredsson, Magnus

2012-01-01

Background Characteristics of patients with community-acquired pneumonia (CAP) due to pandemic influenza A 2009 (H1N1) have been inadequately compared to CAP caused by other respiratory pathogens. The performance of prediction rules for CAP during an epidemic with a new infectious agent are unknown. Methods Prospective, population-based study from November 2008–November 2009, in centers representing 70% of hospital beds in Iceland. Patients admitted with CAP underwent evaluation and etiologic testing, including polymerase chain reaction (PCR) for influenza. Data on influenza-like illness in the community and overall hospital admissions were collected. Clinical and laboratory data, including pneumonia severity index (PSI) and CURB-65 of patients with CAP due to H1N1 were compared to those caused by other agents. Results Of 338 consecutive and eligible patients 313 (93%) were enrolled. During the pandemic peak, influenza A 2009 (H1N1) patients constituted 38% of admissions due to CAP. These patients were younger, more dyspnoeic and more frequently reported hemoptysis. They had significantly lower severity scores than other patients with CAP (1.23 vs. 1.61, P = .02 for CURB-65, 2.05 vs. 2.87 for PSI, P<.001) and were more likely to require intensive care admission (41% vs. 5%, P<.001) and receive mechanical ventilation (14% vs. 2%, P = .01). Bacterial co-infection was detected in 23% of influenza A 2009 (H1N1) patients with CAP. Conclusions Clinical characteristics of CAP caused by influenza A 2009 (H1N1) differ markedly from CAP caused by other etiologic agents. Commonly used CAP prediction rules often failed to predict admissions to intensive care or need for assisted ventilation in CAP caused by the influenza A 2009 (H1N1) virus, underscoring the importance of clinical acumen under these circumstances. PMID:23071646

Seismic Signatures of Hydrothermal Pathways Along the East Pacific Rise Between 9°16' and 9°56'N

NASA Astrophysics Data System (ADS)

Marjanović, Milena; Fuji, Nobuaki; Singh, Satish C.; Belahi, Thomas; Escartín, Javier

2017-12-01

We apply wave equation-based techniques to 2-D seismic data to characterize the nature of zero-age upper crust at the East Pacific Rise from 9°16' to 9°56'N. The final velocity model reveals a number of low-velocity anomalies, complex in shape, extending down to 1 km below the seafloor. We attribute them to the presence of hydrothermal flow. Depending on their spatial correlation with the previously identified tectonic discontinuities in bathymetry and presence of venting, we classify them as downgoing and upgoing pathways, respectively. This distinction is not always clear; within the third-order discontinuities at 9°20' and 9°37'N, both pathways may be present. The region north of 9°44'N, known for its magmatic robustness and volcanic activity, is represented by five low-velocity perturbations. Three of these anomalies are spatially correlated with the fourth-order discontinuities and attributed to the presence of the on-axis recharge zones. The remaining two anomalies underlie two vent clusters, marked as hydrothermally active sites after the last documented eruption event. These velocity anomalies can be thus identified as the up-flow pathways or at least their remnants. By comparing our results to the available interdisciplinary data sets, we show that the interaction between the tectono-magmatic and hydrothermal processes is not straightforward due to different timescales at which they operate. However, for developing, maintaining, and driving vigorous, high-temperature hydrothermal flow, the high crustal permeability and high thermal regime must coexist in time and space.

40 CFR Appendix M to Subpart G - Unacceptable Substitutes Listed in the September 30, 2004 Final Rule, Effective November 29, 2004

Code of Federal Regulations, 2010 CFR

2010-07-01

... —Rigid polyurethane slabstock and other foams —Polystyrene extruded insulation boardstock and billet...—Unacceptable Substitutes Listed in the September 30, 2004 Final Rule, Effective November 29, 2004 Foam Blowing—Unacceptable Substitutes End-use Substitute Decision Comments All foam end-uses: HCFC-141b Unacceptable...

40 CFR Appendix M to Subpart G - Unacceptable Substitutes Listed in the September 30, 2004 Final Rule, Effective November 29, 2004

Code of Federal Regulations, 2012 CFR

2012-07-01

... —Rigid polyurethane slabstock and other foams —Polystyrene extruded insulation boardstock and billet...—Unacceptable Substitutes Listed in the September 30, 2004 Final Rule, Effective November 29, 2004 Foam Blowing—Unacceptable Substitutes End-use Substitute Decision Comments All foam end-uses: HCFC-141b Unacceptable...

40 CFR Appendix M to Subpart G - Unacceptable Substitutes Listed in the September 30, 2004 Final Rule, Effective November 29, 2004

Code of Federal Regulations, 2011 CFR

2011-07-01

... —Rigid polyurethane slabstock and other foams —Polystyrene extruded insulation boardstock and billet...—Unacceptable Substitutes Listed in the September 30, 2004 Final Rule, Effective November 29, 2004 Foam Blowing—Unacceptable Substitutes End-use Substitute Decision Comments All foam end-uses: HCFC-141b Unacceptable...

Medicare Program; End-Stage Renal Disease Prospective Payment System, Coverage and Payment for Renal Dialysis Services Furnished to Individuals With Acute Kidney Injury, End-Stage Renal Disease Quality Incentive Program, Durable Medical Equipment, Prosthetics, Orthotics and Supplies Competitive Bidding Program Bid Surety Bonds, State Licensure and Appeals Process for Breach of Contract Actions, Durable Medical Equipment, Prosthetics, Orthotics and Supplies Competitive Bidding Program and Fee Schedule Adjustments, Access to Care Issues for Durable Medical Equipment; and the Comprehensive End-Stage Renal Disease Care Model. Final rule.

PubMed

2016-11-04

This rule updates and makes revisions to the End-Stage Renal Disease (ESRD) Prospective Payment System (PPS) for calendar year 2017. It also finalizes policies for coverage and payment for renal dialysis services furnished by an ESRD facility to individuals with acute kidney injury. This rule also sets forth requirements for the ESRD Quality Incentive Program, including the inclusion of new quality measures beginning with payment year (PY) 2020 and provides updates to programmatic policies for the PY 2018 and PY 2019 ESRD QIP. This rule also implements statutory requirements for bid surety bonds and state licensure for the Durable Medical Equipment, Prosthetics, Orthotics, and Supplies (DMEPOS) Competitive Bidding Program (CBP). This rule also expands suppliers' appeal rights in the event of a breach of contract action taken by CMS, by revising the appeals regulation to extend the appeals process to all types of actions taken by CMS for a supplier's breach of contract, rather than limit an appeal for the termination of a competitive bidding contract. The rule also finalizes changes to the methodologies for adjusting fee schedule amounts for DMEPOS using information from CBPs and for submitting bids and establishing single payment amounts under the CBPs for certain groupings of similar items with different features to address price inversions. Final changes also are made to the method for establishing bid limits for items under the DMEPOS CBPs. In addition, this rule summarizes comments on the impacts of coordinating Medicare and Medicaid Durable Medical Equipment for dually eligible beneficiaries. Finally, this rule also summarizes comments received in response to a request for information related to the Comprehensive ESRD Care Model and future payment models affecting renal care.

Engineering the N-terminal end of CelA results in improved performance and growth of Caldicellulosiruptor bescii on crystalline cellulose

DOE PAGES

Kim, Sun -Ki; Chung, Daehwan; Himmel, Michael E.; ...

2016-12-26

Here, CelA is the most abundant enzyme secreted by Caldicellulosiruptor bescii and has been shown to outperform mixtures of commercially available exo- and endoglucanases in vitro. CelA contains both a glycoside hydrolase family 9 endoglucanase and a glycoside hydrolase family 48 exoglucanase known to be synergistic in their activity, connected by three cellulose-binding domains via linker peptides. Here, repeated aspartate residues were introduced into the N-terminal ends of CelA GH9 and GH48 domains to improve secretion efficiency and/or catalytic efficiency of CelA. Among several constructs, the highest activity on carboxymethylcellulose (CMC), 0.81 ± 0.03 mg/mL was observed for the C.more » bescii strain containing CelA with 5-aspartate tag at the N-terminal end of GH9 domain – an 82% increase over wild type CelA. In addition, Expression of CelA with N-terminal repeated aspartate residues in C. bescii results in a dramatic increase in its ability to grow on Avicel.« less

Leveraging Modeling Approaches: Reaction Networks and Rules

PubMed Central

Blinov, Michael L.; Moraru, Ion I.

2012-01-01

We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high resolution and/or high throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatio-temporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks – the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks. PMID:22161349

Leveraging modeling approaches: reaction networks and rules.

PubMed

Blinov, Michael L; Moraru, Ion I

2012-01-01

We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high-resolution and/or high-throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatiotemporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks - the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks.

[Subjective Level of Information and Information Needs of Patients with an Approved Rehabilitation Application and Patients at the End of Rehabilitation Results of a Written Survey].

PubMed

Walther, Anna Lena; Schreiber, Dora; Falk, Johannes; Deck, Ruth

2017-08-01

Aim The aim of the study was to identify the subjective level of information and information needs of patients with an approved rehabilitation application and patients at the end of rehabilitation with regard to preferred subjects and kind of information transfer. Method Written survey with N=283 patients with approved rehabilitation application and N=388 patients at the end of rehabilitation. Results Both groups reported high information needs particularly regarding treatments during rehabilitation, rehabilitation aftercare and rehabilitation aims. A conversation with their physician, a brochure and a website are the preferred information pathways. Conclusion Taking into account the topics for which both groups require information and the preference regarding the kind of information transfer can make a valuable contribution for the development of needs-oriented information material. © Georg Thieme Verlag KG Stuttgart · New York.

Dehydrogenation of aromatic molecules under a scanning tunneling microscope: pathways and inelastic spectroscopy simulations.

PubMed

Lesnard, Hervé; Bocquet, Marie-Laure; Lorente, Nicolas

2007-04-11

We have performed a theoretical study on the dehydrogenation of benzene and pyridine molecules on Cu(100) induced by a scanning tunneling microscope (STM). Density functional theory calculations have been used to characterize benzene, pyridine, and different dehydrogenation products. The adiabatic pathways for single and double dehydrogenation have been evaluated with the nudge elastic band method. After identification of the transition states, the analysis of the electronic structure along the reaction pathway yields interesting information on the electronic process that leads to H-scission. The adiabatic barriers show that the formation of double dehydrogenated fragments is difficult and probably beyond reach under the actual experimental conditions. However, nonadiabatic processes cannot be ruled out. Hence, in order to identify the final dehydrogenation products, the inelastic spectra are simulated and compared with the experimental ones. We can then assign phenyl (C6H5) and alpha-pyridil (alpha-C5H4N) as the STM-induced dehydrogenation products of benzene and pyridine, respectively. Our simulations permit us to understand why phenyl, pyridine, and alpha-pyridil present tunneling-active C-H stretch modes in opposition to benzene.

Parental Rule Socialization for Preventive Health and Adolescent Rule Compliance

ERIC Educational Resources Information Center

Bylund, Carma L.; Baxter, Leslie A.; Imes, Rebecca S.; Wolf, Bianca

2010-01-01

This study examined family rules about nutrition, exercise, and sun protection in 164 parent-young adult children dyads. Both parents and their young adult children independently reported on health rules that they perceived throughout their child's adolescent years and the extent to which the rules were articulated, violations sanctioned, and…

Cell Phones: Rule-Setting, Rule-Breaking, and Relationships in Classrooms

ERIC Educational Resources Information Center

Charles, Anita S.

2012-01-01

Based on a small qualitative study, this article focuses on understanding the rules for cell phones and other social networking media in schools, an aspect of broader research that led to important understandings of teacher-student negotiations. It considers the rules that schools and teachers make, the rampant breaking of these rules, the…

A Detailed Chemical Kinetic Reaction Mechanism for n-Alkane Hydrocarbons from n-Octane to n-Hexadecane

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

Westbrook, C K; Pitz, W J; Herbinet, O

2007-09-25

Detailed chemical kinetic reaction mechanisms have been developed to describe the pyrolysis and oxidation of the n-alkanes, including n-octane (n-C{sub 8}H{sub 18}), n-nonane (n-C{sub 9}H{sub 20}), n-decane (n-C{sub 10}H{sub 22}), n-undecane (n-C{sub 11}H{sub 24}), n-dodecane (n-C{sub 12}H{sub 26}), n-tridecane (n-C{sub 13}H{sub 28}), n-tetradecane (n-C{sub 14}H{sub 30}), n-pentadecane (n-C{sub 15}H{sub 32}), and n-hexadecane (n-C{sub 16}H{sub 34}). These mechanisms include both high temperature and low temperature reaction pathways. The mechanisms are based on previous mechanisms for n-heptane, using the same reaction class mechanism construction developed initially for n-heptane. Individual reaction class rules are as simple as possible in order to focus onmore » the parallelism between all of the n-alkane fuels included in the mechanisms, and there is an intent to develop these mechanisms further in the future to incorporate greater levels of accuracy and predictive capability. Several of these areas for improvement are identified and explained in detail. These mechanisms are validated through comparisons between computed and experimental data from as many different sources as possible. In addition, numerical experiments are carried out to examine features of n-alkane combustion in which the detailed mechanisms can be used to compare processes in all of the n-alkane fuels. The mechanisms for all of these n-alkanes are presented as a single detailed mechanism, which can be edited to produce efficient mechanisms for any of the n-alkanes included, and the entire mechanism, with supporting thermochemical and transport data, together with an explanatory glossary explaining notations and structural details, will be available on our web page when the paper is accepted for publication.« less