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Sample records for climate-development gordian knot

  1. Bat rabies--a Gordian knot?

    PubMed

    Freuling, Conrad; Vos, Ad; Johnson, Nicholas; Fooks, Anthony R; Müller, Thomas

    2009-01-01

    Although classical rabies is one of the earliest identified and best studied infectious diseases, there is still limited knowledge about lyssaviruses and their major natural hosts, bats. Focussing on bat rabies in Europe caused by European bat lyssaviruses 1 (EBLV-1) and 2, for instance the association of EBLV-1 to Eptesicus bats and EBLV-2 to Myotis daubentonii and M. dasycneme together with an apparent clustering of cases is one question still to be answered. Furthermore, the question whether EBLVs are less virulent or bats less susceptible is the key to the understanding of the disease. Accumulating evidence from experimental studies and field observations, however, has resulted in contradicting hypotheses. Serological surveys, using tools developed for classical rabies, are often used for bat rabies surveillance. However, such surveys are hampered by the lack of validated methods applicable for bat sera. Bats seem to play a prominent role as reservoir for viral pathogens and the unique biology of bats especially the immune response may contribute to this. Considering all known aspects, bat rabies seems to form a yet unsolvable entanglement, reminiscent of the ancient tale of the Gordian knot. In this manuscript we will not be able to untangle this knot, but we hope to offer some suggestions of where to start.

  2. Feedback in clinical education: untying the Gordian knot.

    PubMed

    Weinstein, Debra F

    2015-05-01

    Feedback is essential to clinical education, especially in the era of competencies, milestones, and entrustable professional activities. It is, however, an area where medical educators often fall short. Although educational leaders and faculty supervisors provide feedback in a variety of clinical settings, surveys show important gaps in medical student and resident satisfaction with the feedback received, suggesting lost opportunities to identify performance problems as well as to help each learner reach his or her greatest potential.In this issue of Academic Medicine, Telio and colleagues extend the empirically validated concept of a "therapeutic alliance" to propose the "educational alliance" as a framework for enhancing feedback in medical education. They highlight the importance of source credibility, which depends on the teacher-learner relationship and alignment of values, the teacher's understanding of the learner's role and goals, the teacher's direct observation of the learner, and the learner's perception of the teacher's good intentions. The author of this Commentary suggests that the educational alliance framework should prompt medical educators to reconsider feedback and explore opportunities for optimizing it. Most medical schools and graduate medical education programs are not designed in a way that supports the education alliance model, but the Commentary author offers suggestions for cultivating educational alliances, including rethinking supervisor selection criteria. Such interventions should be combined with ongoing faculty development and efforts to improve coaching and mentoring for students, residents, and fellows. Untying the Gordian knot of effective feedback will require innovative approaches, exchange of successful strategies, and continued research.

  3. Hemoglobinopathies: slicing the Gordian knot of Plasmodium falciparum malaria pathogenesis.

    PubMed

    Taylor, Steve M; Cerami, Carla; Fairhurst, Rick M

    2013-01-01

    Plasmodium falciparum malaria kills over 500,000 children every year and has been a scourge of humans for millennia. Owing to the co-evolution of humans and P. falciparum parasites, the human genome is imprinted with polymorphisms that not only confer innate resistance to falciparum malaria, but also cause hemoglobinopathies. These genetic traits--including hemoglobin S (HbS), hemoglobin C (HbC), and α-thalassemia--are the most common monogenic human disorders and can confer remarkable degrees of protection from severe, life-threatening falciparum malaria in African children: the risk is reduced 70% by homozygous HbC and 90% by heterozygous HbS (sickle-cell trait). Importantly, this protection is principally present for severe disease and largely absent for P. falciparum infection, suggesting that these hemoglobinopathies specifically neutralize the parasite's in vivo mechanisms of pathogenesis. These hemoglobin variants thus represent a "natural experiment" to identify the cellular and molecular mechanisms by which P. falciparum produces clinical morbidity, which remain partially obscured due to the complexity of interactions between this parasite and its human host. Multiple lines of evidence support a restriction of parasite growth by various hemoglobinopathies, and recent data suggest this phenomenon may result from host microRNA interference with parasite metabolism. Multiple hemoglobinopathies mitigate the pathogenic potential of parasites by interfering with the export of P. falciparum erythrocyte membrane protein 1 (PfEMP1) to the surface of the host red blood cell. Few studies have investigated their effects upon the activation of the innate and adaptive immune systems, although recent murine studies suggest a role for heme oxygenase-1 in protection. Ultimately, the identification of mechanisms of protection and pathogenesis can inform future therapeutics and preventive measures. Hemoglobinopathies slice the "Gordian knot" of host and parasite

  4. Hemoglobinopathies: Slicing the Gordian Knot of Plasmodium falciparum Malaria Pathogenesis

    PubMed Central

    Taylor, Steve M.; Cerami, Carla; Fairhurst, Rick M.

    2013-01-01

    Plasmodium falciparum malaria kills over 500,000 children every year and has been a scourge of humans for millennia. Owing to the co-evolution of humans and P. falciparum parasites, the human genome is imprinted with polymorphisms that not only confer innate resistance to falciparum malaria, but also cause hemoglobinopathies. These genetic traits—including hemoglobin S (HbS), hemoglobin C (HbC), and α-thalassemia—are the most common monogenic human disorders and can confer remarkable degrees of protection from severe, life-threatening falciparum malaria in African children: the risk is reduced 70% by homozygous HbC and 90% by heterozygous HbS (sickle-cell trait). Importantly, this protection is principally present for severe disease and largely absent for P. falciparum infection, suggesting that these hemoglobinopathies specifically neutralize the parasite's in vivo mechanisms of pathogenesis. These hemoglobin variants thus represent a “natural experiment” to identify the cellular and molecular mechanisms by which P. falciparum produces clinical morbidity, which remain partially obscured due to the complexity of interactions between this parasite and its human host. Multiple lines of evidence support a restriction of parasite growth by various hemoglobinopathies, and recent data suggest this phenomenon may result from host microRNA interference with parasite metabolism. Multiple hemoglobinopathies mitigate the pathogenic potential of parasites by interfering with the export of P. falciparum erythrocyte membrane protein 1 (PfEMP1) to the surface of the host red blood cell. Few studies have investigated their effects upon the activation of the innate and adaptive immune systems, although recent murine studies suggest a role for heme oxygenase-1 in protection. Ultimately, the identification of mechanisms of protection and pathogenesis can inform future therapeutics and preventive measures. Hemoglobinopathies slice the “Gordian knot” of host and parasite

  5. Animal abolitionism meets moral abolitionism : cutting the Gordian knot of applied ethics.

    PubMed

    Marks, Joel

    2013-12-01

    The use of other animals for human purposes is as contentious an issue as one is likely to find in ethics. And this is so not only because there are both passionate defenders and opponents of such use, but also because even among the latter there are adamant and diametric differences about the bases of their opposition. In both disputes, the approach taken tends to be that of applied ethics, by which a position on the issue is derived from a fundamental moral commitment. This commitment in turn depends on normative ethics, which investigates the various moral theories for the best fit to our moral intuitions. Thus it is that the use of animals in biomedical research is typically defended by appeal to a utilitarian theory, which legitimates harm to some for the greater good of others; while the opposition condemns that use either by appeal to the same theory, but disagreeing about the actual efficacy of animal experimentation, or by appeal to an alternative theory, such as the right of all sentient beings not to be exploited. Unfortunately, the normative issue seems likely never to be resolved, hence leaving the applied issue in limbo. The present essay seeks to circumvent this impasse by dispensing altogether with any moral claim or argument, thereby cutting the Gordian knot of animal ethics with a meta-ethical sword. The alternative schema defended is simply to advance relevant considerations, whereupon "there is nothing left but to feel." In a word, motivation replaces justification.

  6. Unravelling the Gordian knot! Key processes impacting overwintering larval survival and growth: A North Sea herring case study

    NASA Astrophysics Data System (ADS)

    Hufnagl, Marc; Peck, Myron A.; Nash, Richard D. M.; Dickey-Collas, Mark

    2015-11-01

    factors can form a Gordian knot of marine fish recruitment processes. We highlight gaps in process knowledge and recommend specific field, laboratory and modelling studies which, in our opinion, are most likely to unravel the dominant processes and advance predictive capacity of the environmental regulation of recruitment in autumn and winter-spawned fishes in temperate areas such as herring in the North Sea.

  7. Chance and time: Cutting the Gordian knot

    NASA Astrophysics Data System (ADS)

    Hagar, Amit

    One of the recurrent problems in the foundations of physics is to explain why we rarely observe certain phenomena that are allowed by our theories and laws. In thermodynamics, for example, the spontaneous approach towards equilibrium is ubiquitous yet the time-reversal-invariant laws that presumably govern thermal behaviour in the microscopic level equally allow spontaneous approach away from equilibrium to occur. Why are the former processes frequently observed while the latter are almost never reported? Another example comes from quantum mechanics where the formalism, if considered complete and universally applicable, predicts the existence of macroscopic superpositions---monstrous Schrodinger cats---and these are never observed: while electrons and atoms enjoy the cloudiness of waves, macroscopic objects are always localized to definite positions. A well-known explanatory framework due to Ludwig Boltzmann traces the rarity of "abnormal" thermodynamic phenomena to the scarcity of the initial conditions that lead to it. After all, physical laws are no more than algorithms and these are expected to generate different results according to different initial conditions, hence Boltzmann's insight that violations of thermodynamic laws are possible but highly improbable. Yet Boltzmann introduces probabilities into this explanatory scheme, and since the latter is couched in terms of classical mechanics, these probabilities must be interpreted as a result of ignorance of the exact state the system is in. Quantum mechanics has taught us otherwise. Here the attempts to explain why we never observe macroscopic superpositions have led to different interpretations of the formalism and to different solutions to the quantum measurement problem. These solutions introduce additional interpretations to the meaning of probability over and above ignorance of the definite state of the physical system: quantum probabilities may result from pure chance. Notwithstanding the success of the Boltzmannian framework in explaining the thermodynamic arrow in time it leaves us with a foundational puzzle: how can ignorance play a role in scientific explanation of objective reality? In turns out that two opposing solutions to the quantum measurement problem in which probabilities arise from the stochastic character of the underlying dynamics may scratch this explanatory itch. By offering a dynamical justification to the probabilities employed in classical statistical mechanics these two interpretations complete the Boltzmannian explanatory scheme and allow us to exorcize ignorance from scientific explanations of unobserved phenomena. In this thesis I argue that the puzzle of the thermodynamic arrow in time is closely related to the problem of interpreting quantum mechanics, i.e., to the measurement problem. We may solve one by fiat and thus solve the other, but it seems unwise to try solving them independently. I substantiate this claim by presenting two possible interpretations to non-relativistic quantum mechanics. Differing as they do on the meaning of the probabilities they introduce into the otherwise deterministic dynamics, these interpretations offer alternative explanatory schemes to the standard Boltzmannian statistical mechanical explanation of thermodynamic approach to equilibrium. I then show how notwithstanding their current empirical equivalence, the two approaches diverge at the continental divide between scientific realism and anti-realism.

  8. Hybrid Threat Center of Gravity Analysis: Cutting the Gordian Knot

    DTIC Science & Technology

    2016-04-04

    useful method for discerning a hybrid threat’s COG or omit the concept entirely. This critical deficiency in threat analysis may result in the...hybrid threat’s Center of Gravity or omit the concept entirely. This critical deficiency in threat analysis may result in the implementation of...analysis for hybrid adversaries is a critical deficiency that must be rectified if these gray zone

  9. Hybrid Threat Center of Gravity Analysis: Cutting the Gordian Knot

    DTIC Science & Technology

    2016-04-04

    government computers with a powerful exploitation tool used to access secret information.25 The cumulative effect of these disruptive actions was...Gravity earlier they could have immediately counterattacked the “little green men” in Crimea and reinforced government bases and buildings in...pressure to bear on Lebanon’s elected officials. Israeli decision makers took for granted that applying pressure on the government in Beirut would force

  10. The United States and Colombia: Untying the Gordian Knot

    DTIC Science & Technology

    2000-03-01

    replacing General Bonett with General Fernando Tapias , who removed more than a dozen other officers and ordered other personnel changes such as the...sacking of Major General Ivan Ramirez , commander of the 20th intelligence brigade-an important watershed in 13 improving the army’s intelligence collection...very costly. Although President Pastrana and Defense Minister Luis Fernando Ramirez have visited Washington to discuss additional resources for Plan

  11. Air Power’s Gordian Knot: Centralized Versus Organic Control

    DTIC Science & Technology

    1994-08-01

    the operation of US air forces without air superiority.3 FM 100-20, the document that emerged from that cam- paign experience, is the Magna Carta of...control of the Fifth Fleet until the area was secured. 72. Charles S. Nichols and Henry I. Shaw, Jr., Okinawa: Victory in the Pacific (1955; reprint. Tokyo...Aviation, 385: and Frank and Shaw. 187. 74. Morison, vol. 14, 217; Sherrod, Marine Corps Aviation, 375: Frank and Shaw, 671: and Nichols and Shaw, 263. 75

  12. Cutting the Gordian Knot: Taking Control of Assessment

    ERIC Educational Resources Information Center

    Luff, Ian

    2016-01-01

    Ian Luff recognised that in a post-levels world efforts to devise new assessment systems risked replicating old problems or creating new ones. Drawing on his many years' experience of teaching and school leadership Luff argues that for assessment in history to be truly useful to teachers and pupils it needs to be both holistic and authentic to the…

  13. The Substorm Gordian Knot: Onset Patterns and Frequencies

    NASA Astrophysics Data System (ADS)

    Sobel, E. I.; Kepko, L.

    2014-12-01

    For decades, scientists have struggled to understand what causes the aurora, and have developed two different theories to explain the phenomena. The magnetospheric and ground-based data necessary to test the two competing theories have only recently become available with the launch of NASA's THEMIS mission in 2007 and the Canadian Space Agency's (CSA) deployment of an all-sky imaging network. We present research testing the "Auroral Streamer" hypothesis given by Nishimura, Lyons, et al. in their various papers from 2010 to present. We compiled a list of all their published events (numbering 455, and covering a span from 2007 to 2011) and reviewed ground-based white- and red-light image files, THEMIS satellite bulk plasma velocity and magnetic field strength measurements, ground-based magnetometer observations, and 1-minute Auroral Electrojet (AL) index data. We visually categorized the events by auroral phenomenology, separating events with auroral streamers from those without, and analyzed the characteristics of the events with superposed epoch analyses. Although Nishimura, Lyons et al. argued that every event in their onset list constituted an "Auroral Streamer" onset, our results show that most events in the list are not poleward boundary intensifications (PBIs). In contrast to these previous studies, the results suggest that the "auroral streamer" model is not widely applicable. This is the first time these events have been analyzed with such detail, and call into question fundamental aspects of this model.

  14. The real gordian knot: racemic mixtures versus pure enantiomers.

    PubMed

    Szelenyi, I; Geisslinger, G; Polymeropoulos, E; Paul, W; Herbst, M; Brune, K

    1998-04-01

    Many drugs exist as asymmetric three-dimensional (chiral) molecules and will therefore have several stereoisomers. There are often pharmacodynamic, pharmacokinetic and/or toxicological differences between enantiomers. The choice between developing a racemate or single enantiomers depends on therapeutic advances and developmental costs involved. Regarding the target environment for drug intervention, even if natural physiological mediators are achiral, their receptors may demonstrate a preference for the (-)- or (+)-enantiomer of agonists or antagonists. It is also obvious that the majority of enzymes and channels are stereospecific, at least to a variable extent. From a pharmacokinetics point of view, chirality can have an influence on drug absorption, distribution, metabolism and elimination. With a few exceptions, toxicological differences between isomers of known drugs are less dramatic than thought to be and only seldom substantiate the necessity of a racemic switch. The pharmaceutical industry is currently very interested in the so-called "racemic switch." Before proceeding to a racemic switch it is necessary to determine if 1) it is chemically feasible to produce a single enantiomer; 2) a clinical advantage is obtainable through a racemic switch; and 3) a marketing advantage is obtainable. The real goal of a racemic switch should be the rational development of compounds that are profitable for the company and--first of all--beneficial for the patient.

  15. Cutting Gordian Knots: Reducing Prejudice Through Attachment Security.

    PubMed

    Saleem, Muniba; Prot, Sara; Cikara, Mina; Lam, Ben C P; Anderson, Craig A; Jelic, Margareta

    2015-11-01

    The positive role of secure attachment in reducing intergroup biases has been suggested in prior studies. We extend this work by testing the effects of secure attachment primes on negative emotions and aggressive behaviors toward outgroup members across four experiments. Results from Studies 1A and 1B reveal that secure attachment prime, relative to neutral, can reduce negative outgroup emotions. In addition, Studies 1B and 3 results rule out positive mood increase as an alternative explanation for the observed effects. Results from Studies 2 and 3 reveal that secure attachment primes can reduce aggressive behavior toward an outgroup member. The effect of secure attachment primes on outgroup harm was found to be fully mediated by negative emotions in Studies 2 and 3. An interaction between secure attachment primes and ingroup identification in Study 2 indicated that the positive effects of secure attachment in reducing outgroup harm may be especially beneficial for highly identified ingroup members.

  16. Serum uric acid levels and cardiovascular disease: the Gordian knot

    PubMed Central

    Tugores, Antonio; Rodríguez-González, Fayna

    2016-01-01

    Hyperuricemia is defined as serum uric acid level of more than 7 mg/dL and blood levels of uric acid are causally associated with gout, as implicated by evidence from randomized clinical trials using urate lowering therapies. Uric acid as a cardiovascular risk factor often accompanies metabolic syndrome, hypertension, diabetes, dyslipidemia, chronic renal disease, and obesity. Despite the association of hyperuricemia with cardiovascular risk factors, it has remained controversial as to whether uric acid is an independent predictor of cardiovascular disease. To settle this issue, and in the absence of large randomized controlled trials, Mendelian randomization analysis in which the exposure is defined based on the presence or absence of a specific allele that influences a risk factor of interest have tried to shed light on this. PMID:28066631

  17. Recreating the Research University: Cutting the Gordian Knot.

    ERIC Educational Resources Information Center

    Carothers, Robert L.

    This paper consists of a speech delivered on the occasion of the 100th anniversary of the University of Rhode Island (URI) that proposes a new structure for the future of that institution. The paper opens by describing the questions and discussion raised in the past year by the onset of the anniversary. Also touched on is the early history of the…

  18. Cutting the Gordian Knot: Taking Control of Assessment

    ERIC Educational Resources Information Center

    Luff, Ian

    2016-01-01

    Ian Luff recognised that in a post-levels world efforts to devise new assessment systems risked replicating old problems or creating new ones. Drawing on his many years' experience of teaching and school leadership Luff argues that for assessment in history to be truly useful to teachers and pupils it needs to be both holistic and authentic to the…

  19. Molecular Knots

    PubMed Central

    Fielden, Stephen D. P.; Woltering, Steffen L.

    2017-01-01

    Abstract The first synthetic molecular trefoil knot was prepared in the late 1980s. However, it is only in the last few years that more complex small‐molecule knot topologies have been realized through chemical synthesis. The steric restrictions imposed on molecular strands by knotting can impart significant physical and chemical properties, including chirality, strong and selective ion binding, and catalytic activity. As the number and complexity of accessible molecular knot topologies increases, it will become increasingly useful for chemists to adopt the knot terminology employed by other disciplines. Here we give an overview of synthetic strategies towards molecular knots and outline the principles of knot, braid, and tangle theory appropriate to chemistry and molecular structure. PMID:28477423

  20. Fused micro-knots

    NASA Astrophysics Data System (ADS)

    Shahal, Shir; Linzon, Yoav; Fridman, Moti

    2017-02-01

    We present fusing of fiber micro-knot by CO2 laser which fixes the micro-fibers in place and stabilizing the micro-knot shape, size and orientation. This fusing enables tuning of the coupling strength, the free-spectral range and the birefringence of the fiber micro-knot. Fused micro-knots are superior over regular micro-knots and we believe that fusing of micro-knots should be a standard procedure in fabricating fiber micro-knots.

  1. A Midsummer Knot's Dream

    ERIC Educational Resources Information Center

    Henrich, A.; MacNaughton, N.; Narayan, S.; Pechenik, O.; Silversmith, R.; Townsend, J.

    2011-01-01

    We introduce playing games on the shadows of knots and demonstrate two novel games, namely, "To Knot or Not to Knot" and "Much Ado about Knotting." We discuss winning strategies for these games on certain families of knot shadows and go on to suggest variations of these games for further study.

  2. Untangling the Gordian Knot The Socio-Cultural Challenge of Syria

    DTIC Science & Technology

    2015-10-30

    the Syrian Civil War to seize territory and build support for transnational jihadist terrorism . This paper seeks to illuminate the socio-cultural...nationalism provide the strongest counter narrative to ISIL’s jihadi-Islamism. 15. SUBJECT TERMS Terrorism , Syria, Islamic State of Iraq and the Levant...the Syrian Civil War to seize territory and build support for transnational jihadist terrorism . This paper seeks to illuminate the socio-cultural

  3. Proliferation and Polarity in Breast Cancer: Untying the GordianKnot

    SciTech Connect

    Liu, Hong; Radisky, Derek C.; Bissell, Mina J.

    2005-05-09

    Epithelial cancers are associated with genomic instability and alterations in signaling pathways that affect proliferation, apoptosis, and integrity of tissue structure. Overexpression of a number of oncogenic protein kinases has been shown to malignantly transform cells in culture and to cause tumors in vivo, but the interconnected signaling events induced by transformation still awaits detailed dissection. We propose that the network of cellular signaling pathways can be classified into functionally distinct branches, and that these pathways are rewired in transformed cells and tissues after they lose tissue-specific architecture to favor tumor expansion and invasion. Using three-dimensional (3D) culture systems, we recently demonstrated that polarity and proliferation of human mammary epithelial cancer cells were separable consequences of signaling pathways downstream of PI3 kinase.These, and results from a number of other laboratories are beginning to provide insight into how different signaling pathways may become interconnected in normal tissues to allow homeostasis, and how they are disrupted during malignant progression.

  4. Procedural vs. substantive in the NEPA law: Cutting the Gordian knot

    SciTech Connect

    Boggs, J.P. . Dept. of Anthropology)

    1993-01-01

    The debate whether the National Environmental Policy Act (NEPA) is procedural or substantive has become central both to agency implementation of the act and to court review of agency compliance. While NEPA mandates both procedural and substantive reform as a means to improve environmental quality, NEPA also focuses on cognitive reform--the improved utilization of knowledge in public affairs. Choices about what knowledge to base public decisions on, and how that knowledge will be used, build the social realities that shape lives. Thus, NEPA's mandates for the creation and use of public knowledge activate fundamentally conflicting values and visions of social order. However, debate about the procedural and substantive provisions of NEPA cannot resolve the conflict about values that actually motivates the debate, and this constrictive debate impoverishes public discussion about NEPA implementation and judicial review. This paper links the present debate with the values issues that underlie it, suggesting a more direct language for characterizing NEPA and a broader framework of legal theory for debating the issues it raises. This paper also finds that environmental and social science practitioners are strategically positioned to contribute materially to the issues raised by a NEPA properly understood as law that mandates knowledge utilization.

  5. Rural and remote early psychosis intervention services: the Gordian knot of early intervention.

    PubMed

    Cheng, Chiachen; Dewa, Carolyn S; Langill, Gord; Fata, Mirella; Loong, Desmond

    2014-11-01

    One of the basic challenges of Early Psychosis Intervention (EPI) programs for rural populations is translating best practice which developed for urban high-population density areas to rural and remote settings. This paper presents data from two different models (hub and spoke and specialist outreach) of rural EPI practice in Ontario, Canada. This cross-sectional study used a convenience sample of clients from two rural EPI programs between 2005 and 2007. Data about client outcomes specific to general functioning, admissions to hospital and emergency room (ER) visits were collected. For all dichotomous variables, chi-square tests were used to test differences between two groups. The total clients served in hub and spoke were 457 compared to 91 in specialist outreach. Although not statistically significant, the hub and spoke group showed better functioning in the community. There was a significant difference between the two groups with regard to hospital admissions. Although not significant, there was a greater percentage (58.3%) of specialist outreach clients who visited the ER in the previous 12 months as compared to clients serviced by the hub and spoke model (34.9%). The observed data from these two rural models suggest that there may be differing outcomes. There are limitations to this study, and this paper does not address why there are differences. Future work needs to continue to further explore why differences exist and whether they persist so we can provide equity and quality care for rural and remote populations. © 2013 Wiley Publishing Asia Pty Ltd.

  6. Diagnosing and attributing neuropsychiatric events to systemic lupus erythematosus: time to untie the Gordian knot?

    PubMed

    Tay, Sen Hee; Mak, Anselm

    2016-10-15

    Neurological and psychiatric syndromes, collectively referred to as NPSLE, occur frequently in SLE. The frequency of NPSLE varies from 21 to 95%; however, only 13-38% of neuropsychiatric (NP) events could be attributable to SLE in the NPSLE SLICC inception cohort. This variability in the frequency of NPSLE is attributable to the low specificity of the ACR case definitions for SLE-attributed NP syndromes, inclusion of minor NP events in the ACR nomenclature, difficulty in ascertainment of NP events and diverse experience of rheumatologists in the clinical assessment of NP events. Making the correct and early attribution of NP events to SLE is important to institute appropriate immunosuppressive treatment for favourable outcomes. Various attribution models using composite decision rules have been developed and used to ascribe NP events to SLE. This review will focus on the various clinical presentations, diagnostic work-up and attributions of the common NPSLE syndromes, including other NP events not included in the ACR nomenclature but which have come to attention in recent years.

  7. Untangling Gordian knots: improving tuberculosis control through the development of 'programme theories'.

    PubMed

    Coker, R; Atun, R; McKee, M

    2004-01-01

    We argue that if the lessons from tuberculosis control programmes are to be drawn effectively then a more nuanced understanding is needed that takes account of the complex health system environment within which they sit. We suggest that a conceptual framework that draws upon the World Health Organization's DOTS strategy can be harnessed to assist the systematic analysis of programmes in a way that links this vertical, disease specific strategy to horizontal health system factors so that comparisons can be made. This multi-disciplinary, multi-method approach to the evaluation builds upon the work of others including Pawson and Tilley and their 'programmes theories'. This work has informed the application of an evaluation toolkit which has been successfully applied in a number of settings and assisted in the sustainable implementation of a DOTS strategy in Russia.

  8. Unraveling the Gordian knot: red blood cell storage lesion and transfusion outcomes

    PubMed Central

    Tzounakas, Vassilis L.; Kriebardis, Anastasios G.; Seghatchian, Jerard; Papassideri, Issidora S.; Antonelou, Marianna H.

    2017-01-01

    What is following the impressive progress that has been made? During the last couple of years several tremors have shaken the field of Transfusion Medicine. The epicentres of those tremors were located on novel insights into the RBC storage lesion, on emerging connections between storage lesion and post-transfusion performance and effects, and on acknowledging that storage time is only one (rather than the most prominent) of the parameters which contribute to the progression of storage lesion in any given unit of blood. The optimisation of bio-preservation conditions emerged at the same time with all-new scientific knowledge gained by advances in research tools, implementation of technological innovations, and application of elegant in vitro and in vivo models of transfusion. Simultaneously, one after another, all the reported randomised clinical trials concluded, with spectacular consensus, that there is no significant difference in the rate of adverse clinical events (including death) among patients who underwent transfusion with fresh (and presumably good) or standard of care (and presumably bad) blood. The comparative analysis and comprehension of the aforementioned data would set the context for the next generation of research in blood transfusion science, since the need for safer and more efficient transfusions remains. PMID:28263169

  9. Breaking the Gordian Knot in the Structural Chemistry of Polyoxometalates: Copper(II)-Oxo/Hydroxo Clusters.

    PubMed

    Kondinski, Aleksandar; Monakhov, Kirill Yu

    2017-06-12

    This Concept article provides insights into the molecular design and construction aspects of polyoxocuprates (POCus), an emerging class of polyoxometalate (POM)-like architectures featuring low-to-high nuclearity copper(II)-oxo/hydroxo skeletons. POCus have been identified to adopt the structural principles of classical POMs consisting of early transition metals. Their potential to afford motifs of the noble-metal-based POMs is exploited. "Cross-structural topological transformation" is introduced to generalize skeletal relationships between POCus and POMs. The study opens up strategies toward the brand-new structural chemistry of POCus with relevance to homogeneous photocatalysis, medicinal chemistry, molecular magnetism, and quantum computing. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. The Gordian Knot: Analysis of United States Support to Ethnic-Based "Resistance" Movements

    DTIC Science & Technology

    2002-04-09

    Conflict. The name alone conjures forth CNN-provided visions of angry camouflaged youths with guns, crying old women with dead children, streams of refugees...York: Puebla Institute, 1987); Nina H. Shea, "Testimony for Nicaraguan Refugees," Nicaragua in Focus, Vol. 1, No. 4, Joseph E. Davis, ed. (New York... Puebla Institute, 1987), 16-23; and Congress, Senate, Republican Policy Committee, Turmoil in Central America (Washington, D.C.: Government Printing

  11. Informed consent in Italy-traditional versus the law: a gordian knot.

    PubMed

    Turillazzi, Emanuela; Neri, Margherita; Riezzo, Irene; Frati, Paola; Fineschi, Vittorio

    2014-08-01

    Italian law no. 86 of 5 June 2012, which establishes a set of rules on the matter of breast implants, came into effect in July 2012. The law is at the center of a widespread and animated cultural debate that in recent years has been taking place in Italy. The fundamental prohibition imposed by the law concerns the age limit. Breast implants for exclusively aesthetic purposes are allowed only if the legal age (18 years) has been reached. This prohibition does not apply in cases of severe congenital malformations certified by a physician operating within the National Health Service or by a public health care institution. The legal imposition of an age limit raises a number of perplexities: one at a bioethical level and one that is strictly juridical. In fact, it is impossible to deal with this issue unless the wider debate concerning the self-determination and autonomy of underage patients in biomedical matters is considered. It appears, then, that the issue is again exclusively related to the peculiarity of cosmetic surgery, which when aimed at correcting "only" the pathologic experiences of self-image, does not acquire the dignity of therapy. If, however, the improvement of self-image serves to achieve a better psycho-emotional balance and favors the development of social relations undermined by evident physical defects, age restrictions can be disregarded. The authors believe the real risk is that the law imposed by the Italian state is based on assumptions and preformed value judgments. Furthermore, in the understanding of needs, legislation often is biased toward objective biophysical problems without attaching due importance to subjective psychological and social problems. While acknowledging the seriousness of the issue, the authors do not agree with the legislature's rigidity. However, plastic surgeons must form a plan for addressing the concerns about breast implants and evaluating whether they are appropriate for adolescents, taking into account the unique psychological and developmental considerations of adolescent cosmetic surgery patients. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

  12. Reweaving the Gordian Knot: Developing a Comprehensive Strategy for the United States in Afghanistan

    DTIC Science & Technology

    2008-01-01

    that its citizens are fed is an inadequate one. Drugs One of the principal difficulties in building effective governance at all levels in...levels, and provides a level of income much of the rural populace could not earn legitimately. Less tangible, but equally insidious is the effect of...policy for weaning Afghanistan of its opium addiction . Paralyzed by disagreement upon the best way to approach the problem at the political level, NATO

  13. Unraveling the Gordian knot: red blood cell storage lesion and transfusion outcomes.

    PubMed

    Tzounakas, Vassilis L; Kriebardis, Anastasios G; Seghatchian, Jerard; Papassideri, Issidora S; Antonelou, Marianna H

    2017-03-01

    What is following the impressive progress that has been made? During the last couple of years several tremors have shaken the field of Transfusion Medicine. The epicentres of those tremors were located on novel insights into the RBC storage lesion, on emerging connections between storage lesion and post-transfusion performance and effects, and on acknowledging that storage time is only one (rather than the most prominent) of the parameters which contribute to the progression of storage lesion in any given unit of blood. The optimisation of bio-preservation conditions emerged at the same time with all-new scientific knowledge gained by advances in research tools, implementation of technological innovations, and application of elegant in vitro and in vivo models of transfusion. Simultaneously, one after another, all the reported randomised clinical trials concluded, with spectacular consensus, that there is no significant difference in the rate of adverse clinical events (including death) among patients who underwent transfusion with fresh (and presumably good) or standard of care (and presumably bad) blood. The comparative analysis and comprehension of the aforementioned data would set the context for the next generation of research in blood transfusion science, since the need for safer and more efficient transfusions remains.

  14. Haeckel or Hennig? The Gordian Knot of Characters, Development, and Procedures in Phylogeny.

    ERIC Educational Resources Information Center

    Dupuis, Claude

    1984-01-01

    Discusses the conditions for validating customary phylogenetic procedures. Concludes that the requisites of homogeneity and completeness for proved short lineages seem satisfied by the Hennigian but not the Haeckelian procedure. The epistemological antinomy of the two procedures is emphasized for the first time. (Author/RH)

  15. Untying the Gordian knot: policies, practices, and ethical issues related to banking of umbilical cord blood

    PubMed Central

    Kurtzberg, Joanne; Lyerly, Anne Drapkin; Sugarman, Jeremy

    2005-01-01

    Since the first successful transplantation of umbilical cord blood in 1988, cord blood has become an important source of hematopoietic stem and progenitor cells for the treatment of blood and genetic disorders. Significant progress has been accompanied by challenges for scientists, ethicists, and health policy makers. With the recent recognition of the need for a national system for the collection, banking, distribution, and use of cord blood and the increasing focus on cord blood as an alternative to embryos as a source of tissue for regenerative medicine, cord blood has garnered significant attention. We review the development of cord blood banking and transplantation and then discuss the scientific and ethical issues influencing both established and investigational practices surrounding cord blood collection, banking, and use. PMID:16200191

  16. Untying the Gordian knot of creation: metaphors for the Human Genome Project in Greek newspapers.

    PubMed

    Gogorosi, Eleni

    2005-12-01

    This article studies the metaphorical expressions used by newspapers to present the near completion of the Human Genome Project (HGP) to the Greek public in the year 2000. The analysis, based on cognitive metaphor theory, deals with the most frequent or captivating metaphors used to refer to the human genome, which give rise to both conventional and novel expressions. The majority of creative metaphorical expressions participate in the discourse of hope and promise propagated by the Greek media in an attempt to present the HGP and its outcome in a favorable light. Instances of the competing discourse of fear and danger are much rarer but can also be found in creative metaphorical expressions. Metaphors pertaining to the Greek culture or to ancient Greek mythology tend to carry a special rhetorical force. However, it will be shown that the Greek press strategically used most of the metaphors that circulated globally at the time, not only culture specific ones.

  17. Haeckel or Hennig? The Gordian Knot of Characters, Development, and Procedures in Phylogeny.

    ERIC Educational Resources Information Center

    Dupuis, Claude

    1984-01-01

    Discusses the conditions for validating customary phylogenetic procedures. Concludes that the requisites of homogeneity and completeness for proved short lineages seem satisfied by the Hennigian but not the Haeckelian procedure. The epistemological antinomy of the two procedures is emphasized for the first time. (Author/RH)

  18. Length of excitable knots

    NASA Astrophysics Data System (ADS)

    Maucher, Fabian; Sutcliffe, Paul

    2017-07-01

    In this paper, we present extensive numerical simulations of an excitable medium to study the long-term dynamics of knotted vortex strings for all torus knots up to crossing number 11. We demonstrate that FitzHugh-Nagumo evolution preserves the knot topology for all the examples presented, thereby providing a field theory approach to the study of knots. Furthermore, the evolution yields a well-defined minimal length for each knot that is comparable to the ropelength of ideal knots. We highlight the role of the medium boundary in stabilizing the length of the knot and discuss the implications beyond torus knots. We also show that there is not a unique attractor within a given knot topology.

  19. Parity in knot theory

    SciTech Connect

    Manturov, Vassily O

    2010-06-29

    In this work we study knot theories with a parity property for crossings: every crossing is declared to be even or odd according to a certain preassigned rule. If this rule satisfies a set of simple axioms related to the Reidemeister moves, then certain simple invariants solving the minimality problem can be defined, and invariant maps on the set of knots can be constructed. The most important example of a knot theory with parity is the theory of virtual knots. Using the parity property arising from Gauss diagrams we show that even a gross simplification of the theory of virtual knots, namely, the theory of free knots, admits simple and highly nontrivial invariants. This gives a solution to a problem of Turaev, who conjectured that all free knots are trivial. In this work we show that free knots are generally not invertible, and provide invariants which detect the invertibility of free knots. The passage to ordinary virtual knots allows us to strengthen known invariants (such as the Kauffman bracket) using parity considerations. We also discuss other examples of knot theories with parity. Bibliography: 27 items.

  20. A Stevedore's Protein Knot

    PubMed Central

    Hsu, Hsiao-Ping; Mirny, Leonid A.; Kardar, Mehran; Onuchic, José N.; Virnau, Peter

    2010-01-01

    Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered α-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified protein fragment that consists of only 92 amino acids. The topological complexity of the Stevedore knot presents a puzzle as to how it could possibly fold. To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possible mechanism by which the knot forms in a single loop flip. PMID:20369018

  1. Lattice invariants for knots

    SciTech Connect

    Janse Van Rensburg, E.J.

    1996-12-31

    The geometry of polygonal knots in the cubic lattice may be used to define some knot invariants. One such invariant is the minimal edge number, which is the minimum number of edges necessary (and sufficient) to construct a lattice knot of given type. In addition, one may also define the minimal (unfolded) surface number, and the minimal (unfolded) boundary number; these are the minimum number of 2-cells necessary to construct an unfolded lattice Seifert surface of a given knot type in the lattice, and the minimum number of edges necessary in a lattice knot to guarantee the existence of an unfolded lattice Seifert surface. In addition, I derive some relations amongst these invariants. 8 refs., 5 figs., 2 tabs.

  2. The Wiese Knot: A Sliding-Locking Arthroscopic Knot.

    PubMed

    Parada, Stephen A; Shaw, K Aaron; Eichinger, Josef K; Boykin, Nathan T; Gloystein, David M; Ledford, Cheryl L; Arrington, Edward D; Wiese, Paul T

    2017-02-01

    Despite recent advances in knotless suture devices for arthroscopic surgical procedures, arthroscopic knot tying remains a necessary skill for the arthroscopic surgeon. Successful completion of arthroscopic knot tying relies on a thorough understanding of the chosen technique, proper suture management, adequate knot tensioning and securement, and the ability to reproducibly create the knot. We introduce a technique that serves as both a sliding and locking knot while being simple to master and reproducible to perform.

  3. Tabulating knot polynomials for arborescent knots

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.; Morozov, A.; Ramadevi, P.; Singh, Vivek Kumar; Sleptsov, A.

    2017-02-01

    Arborescent knots are those which can be represented in terms of double fat graphs or equivalently as tree Feynman diagrams. This is the class of knots for which the present knowledge is sufficient for lifting topological description to the level of effective analytical formulas. The paper describes the origin and structure of the new tables of colored knot polynomials, which will be posted at the dedicated site (http://knotebook.org). Even if formal expressions are known in terms of modular transformation matrices, the computation in finite time requires additional ideas. We use the ‘family’ approach, suggested in Mironov and Morozov (2015 Nucl. Phys. B 899 395–413), and apply it to arborescent knots in the Rolfsen table by developing a Feynman diagram technique, associated with an auxiliary matrix model field theory. Gauge invariance in this theory helps to provide meaning to Racah matrices in the case of non-trivial multiplicities and explains the need for peculiar sign prescriptions in the calculation of [21]-colored HOMFLY-PT polynomials.

  4. Knotting pathways in proteins.

    PubMed

    Sułkowska, Joanna I; Noel, Jeffrey K; Ramírez-Sarmiento, César A; Rawdon, Eric J; Millett, Kenneth C; Onuchic, José N

    2013-04-01

    Most proteins, in order to perform their biological function, have to fold to a compact native state. The increasing number of knotted and slipknotted proteins identified suggests that proteins are able to manoeuvre around topological barriers during folding. In the present article, we review the current progress in elucidating the knotting process in proteins. Although we concentrate on theoretical approaches, where a knotted topology can be unambiguously detected, comparison with experiments is also reviewed. Numerical simulations suggest that the folding process for small knotted proteins is composed of twisted loop formation and then threading by either slipknot geometries or flipping. As the size of the knotted proteins increases, particularly for more deeply threaded termini, the prevalence of traps in the free energy landscape also increases. Thus, in the case of longer knotted and slipknotted proteins, the folding mechanism is probably supported by chaperones. Overall, results imply that knotted proteins can be folded efficiently and survive evolutionary pressure in order to perform their biological functions.

  5. The effect of an air knot on surgical knot integrity.

    PubMed

    Shatkin-Margolis, Abigail; Kow, Nathan; Patonai, Nicolas; Boin, Michael; Muffly, Tyler M

    2015-01-01

    Surgical trainees may tie air knots, which have a questionable tensile strength and rate of untying. The purpose of this study was to determine the effect of an air knot on knot integrity. The 5 suture materials tested were 0-0 gauge coated polyethylene, polyglyconate, glycolide/lactide, polypropylene, and silk. The suture was tied between 2 hex screws 50 mm on center. The strands were tied using 5 square throws, and the knot tails were cut at 3-mm length. To create a standardized air knot, a round common nail measuring 3 mm in diameter was inserted between throws before tying square throw #3. The suture loop was positioned around the upper and lower hooks of the tensiometer so the location of the knot was roughly equidistant from the hooks. Ultimately, either the loop broke or the knot slipped. At that time, the peak tensile force as well as the outcome of the knot were recorded. A total of 480 knots were tied. The presence of an air knot significantly lowered the tension at knot failure in the glycolide/lactide (P = 0.0003), polypropylene (P = 0.0005), and silk (P = 0.0001) knot configurations. Air knots had the same integrity as surgical knots when coated polyethylene and polyglyconate suture were used. Linear regression was performed and identified both suture material (P < 0.0001) and presence of an air knot (P < 0.0001) to be independently associated with a lower tension at failure. Under laboratory conditions, an air knot may contribute to a lower tensile strength at failure for certain suture materials.

  6. Knotted fields and explicit fibrations for lemniscate knots

    NASA Astrophysics Data System (ADS)

    Bode, B.; Dennis, M. R.; Foster, D.; King, R. P.

    2017-06-01

    We give an explicit construction of complex maps whose nodal lines have the form of lemniscate knots. We review the properties of lemniscate knots, defined as closures of braids where all strands follow the same transverse (1, ℓ) Lissajous figure, and are therefore a subfamily of spiral knots generalizing the torus knots. We then prove that such maps exist and are in fact fibrations with appropriate choices of parameters. We describe how this may be useful in physics for creating knotted fields, in quantum mechanics, optics and generalizing to rational maps with application to the Skyrme-Faddeev model. We also prove how this construction extends to maps with weakly isolated singularities.

  7. Knotted fields and explicit fibrations for lemniscate knots.

    PubMed

    Bode, B; Dennis, M R; Foster, D; King, R P

    2017-06-01

    We give an explicit construction of complex maps whose nodal lines have the form of lemniscate knots. We review the properties of lemniscate knots, defined as closures of braids where all strands follow the same transverse (1, ℓ) Lissajous figure, and are therefore a subfamily of spiral knots generalizing the torus knots. We then prove that such maps exist and are in fact fibrations with appropriate choices of parameters. We describe how this may be useful in physics for creating knotted fields, in quantum mechanics, optics and generalizing to rational maps with application to the Skyrme-Faddeev model. We also prove how this construction extends to maps with weakly isolated singularities.

  8. Transcranial Alternating Current Stimulation in Patients with Chronic Disorder of Consciousness: A Possible Way to Cut the Diagnostic Gordian Knot?

    PubMed

    Naro, Antonino; Bramanti, Placido; Leo, Antonino; Russo, Margherita; Calabrò, Rocco Salvatore

    2016-07-01

    Unresponsive wakefulness syndrome (UWS) is a chronic disorder of consciousness (DOC) characterized by a lack of awareness and purposeful motor behaviors, owing to an extensive brain connectivity impairment. Nevertheless, some UWS patients may retain residual brain connectivity patterns, which may sustain a covert awareness, namely functional locked-in syndrome (fLIS). We evaluated the possibility of bringing to light such residual neural networks using a non-invasive neurostimulation protocol. To this end, we enrolled 15 healthy individuals and 26 DOC patients (minimally conscious state-MCS- and UWS), who underwent a γ-band transcranial alternating current stimulation (tACS) over the right dorsolateral prefrontal cortex. We measured the effects of tACS on power and partial-directed coherence within local and long-range cortical networks, before and after the protocol application. tACS was able to specifically modulate large-scale cortical effective connectivity and excitability in all the MCS participants and some UWS patients, who could be, therefore, considered as suffering from fLIS. Hence, tACS could be a useful approach in supporting a DOC differential diagnosis, depending on the level of preservation of the cortical large-scale effective connectivity.

  9. Allopatry as a Gordian Knot for Taxonomists: Patterns of DNA Barcode Divergence in Arctic-Alpine Lepidoptera

    PubMed Central

    Mutanen, Marko; Hausmann, Axel; Hebert, Paul D. N.; Landry, Jean-François; de Waard, Jeremy R.; Huemer, Peter

    2012-01-01

    Many cold adapted species occur in both montane settings and in the subarctic. Their disjunct distributions create taxonomic complexity because there is no standardized method to establish whether their allopatric populations represent single or different species. This study employs DNA barcoding to gain new perspectives on the levels and patterns of sequence divergence among populations of 122 arctic-alpine species of Lepidoptera from the Alps, Fennoscandia and North America. It reveals intraspecific variability in the barcode region ranging from 0.00–10.08%. Eleven supposedly different species pairs or groups show close genetic similarity, suggesting possible synonymy in many cases. However, a total of 33 species show evidence of cryptic diversity as evidenced by the presence of lineages with over 2% maximum barcode divergence in Europe, in North America or between the two continents. Our study also reveals cases where taxonomic names have been used inconsistently between regions and exposes misidentifications. Overall, DNA barcodes have great potential to both increase taxonomic resolution and to make decisions concerning the taxonomic status of allopatric populations more objective. PMID:23071761

  10. Allopatry as a gordian knot for taxonomists: patterns of DNA barcode divergence in arctic-alpine lepidoptera.

    PubMed

    Mutanen, Marko; Hausmann, Axel; Hebert, Paul D N; Landry, Jean-François; de Waard, Jeremy R; Huemer, Peter

    2012-01-01

    Many cold adapted species occur in both montane settings and in the subarctic. Their disjunct distributions create taxonomic complexity because there is no standardized method to establish whether their allopatric populations represent single or different species. This study employs DNA barcoding to gain new perspectives on the levels and patterns of sequence divergence among populations of 122 arctic-alpine species of Lepidoptera from the Alps, Fennoscandia and North America. It reveals intraspecific variability in the barcode region ranging from 0.00-10.08%. Eleven supposedly different species pairs or groups show close genetic similarity, suggesting possible synonymy in many cases. However, a total of 33 species show evidence of cryptic diversity as evidenced by the presence of lineages with over 2% maximum barcode divergence in Europe, in North America or between the two continents. Our study also reveals cases where taxonomic names have been used inconsistently between regions and exposes misidentifications. Overall, DNA barcodes have great potential to both increase taxonomic resolution and to make decisions concerning the taxonomic status of allopatric populations more objective.

  11. Cutting the Gordian Knot: Identifiability of anaplerotic reactions in Corynebacterium glutamicum by means of (13) C-metabolic flux analysis.

    PubMed

    Kappelmann, Jannick; Wiechert, Wolfgang; Noack, Stephan

    2016-03-01

    Corynebacterium glutamicum is the major workhorse for the microbial production of several amino and organic acids. As long as these derive from tricarboxylic acid cycle intermediates, the activity of anaplerotic reactions is pivotal for a high biosynthetic yield. To determine single anaplerotic activities (13) C-Metabolic Flux Analysis ((13) C-MFA) has been extensively used for C. glutamicum, however with different network topologies, inconsistent or poorly determined anaplerotic reaction rates. Therefore, in this study we set out to investigate whether a focused isotopomer model of the anaplerotic node can at all admit a unique solution for all fluxes. By analyzing different scenarios of active anaplerotic reactions, we show in full generality that for C. glutamicum only certain anaplerotic deletion mutants allow to uniquely determine the anaplerotic fluxes from (13) C-isotopomer data. We stress that the result of this analysis for different assumptions on active enzymes is directly transferable to other compartment-free organisms. Our results demonstrate that there exist biologically relevant metabolic network topologies for which the flux distribution cannot be inferred by classical (13) C-MFA.

  12. Development of biomarkers to chart all Alzheimer's disease stages: the royal road to cutting the therapeutic Gordian Knot.

    PubMed

    Hampel, Harald; Lista, Simone; Khachaturian, Zaven S

    2012-07-01

    The aim of this perspective article is to stimulate radical shifts in thinking and foster further discussion on the effective discovery, development, validation, and qualification process of biological markers derived from all available technical modalities that meet the complex conceptual and pathophysiological challenges across all stages of the complex, nonlinear, dynamic, and chronically progressive sporadic Alzheimer's disease (AD). This perspective evaluates the current state of the science regarding a broad spectrum of hypothesis-driven and exploratory technologies and "markers" as candidates for all required biomarker functions, in particular, surrogate indicators of adaptive to maladaptive and compensatory to decompensatory, reversible to irreversible brain "systems failure." We stress the future importance of the systems biology (SB) paradigm (next to the neural network paradigm) for substantial progress in AD research. SB represents an integrated and deeper investigation of interacting biomolecules within cells and organisms. This approach has only recently become feasible as high-throughput technologies and mass spectrometric analyses of proteins and lipids, together with rigorous bioinformatics, have evolved. Existing high-content data derived from clinically and experimentally derived neural tissues point to convergent pathophysiological pathways during the course of AD, transcending traditional descriptive studies to reach a more integrated and comprehensive understanding of AD pathophysiology, derived systems biomarkers, and "druggable" system nodes. The discussion is continued on the premise that the lack of integration of advanced biomarker technologies and transfertilization from more mature translational research fields (e.g., oncology, immunology, cardiovascular), which satisfy regulatory requirements for an accurate, sensitive, and well-validated surrogate marker of specific pathophysiological processes and/or clinical outcomes, is a major rate-limiting factor for the successful development and approval of effective treatments for AD prevention. We consider the conceptual, scientific, and technical challenges for the discovery-development-validation-qualification process of biomarker tools and analytical algorithms for detection of the earliest pathophysiological processes in asymptomatic individuals at elevated risk during preclinical stages of AD. The most critical need for rapid translation of putative markers into validated (performance) and standardized (harmonized standard operating procedures) biomarker tools that fulfill regulatory requirements (qualify for use in treatment trials: e.g., safety, target engagement, mechanism of action, enrichment, stratification, secondary and primary outcome, surrogate outcome) is the availability of a large-scale worldwide comprehensive longitudinal database that includes the following cohorts: (a) healthy aging, (b) people at elevated risks (genetic/epigenetic/lifestyle/comorbid conditions), and (c) asymptomatic-preclinical/prodromal-mild cognitive impairment/syndromal mild, moderate, or severe AD. Our proposal, as initial strategic steps for integrating markers into future development of diagnostic and therapy trial technologies, is to work toward: (a) creating the essential research and development infrastructure as an international shared resource, (b) building the organizational structure for managing such a multinational shared resource, and (c) establishing an integrated transsectoral multidisciplinary global network of collaborating investigators to help build and use the shared research resource. Copyright © 2012 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

  13. Sampling and analysis validates acceptable knowledge on LANL transuranic, heterogeneous, debris waste, or ``Cutting the Gordian knot that binds WIPP``

    SciTech Connect

    Kosiewicz, S.T.; Triay, I.R.; Souza, L.A.; Michael, D.I.; Black, P.K.

    1999-02-01

    Through sampling and toxicity characteristic leaching procedure (TCLP) analyses, LANL and the DOE validated that a LANL transuranic (TRU) waste (TA-55-43, Lot No. 01) was not a Resource Recovery and Conservation Act (RCRA) hazardous waste. This paper describes the sampling and analysis project as well as the statistical assessment of the analytical results. The analyses were conducted according to the requirements and procedures in the sampling and analysis plan approved by the New Mexico Environmental Department. The plan used a statistical approach that was consistent with the stratified, random sampling requirements of SW-846. LANL adhered to the plan during sampling and chemical analysis of randomly selected items of the five major types of materials in this heterogeneous, radioactive, debris waste. To generate portions of the plan, LANL analyzed a number of non-radioactive items that were representative of the mix of items present in the waste stream. Data from these cold surrogates were used to generate means and variances needed to optimize the design. Based on statistical arguments alone, only two samples from the entire waste stream were deemed necessary, however a decision was made to analyze at least two samples of each of the five major waste types. To obtain these samples, nine TRU waste drums were opened. Sixty-six radioactively contaminated and four non-radioactive grab samples were collected. Portions of the samples were composited for chemical analyses. In addition, a radioactively contaminated sample of rust-colored powder of interest to the New Mexico Environment Department (NMED) was collected and qualitatively identified as rust.

  14. Knot theory in modern chemistry.

    PubMed

    Horner, Kate E; Miller, Mark A; Steed, Jonathan W; Sutcliffe, Paul M

    2016-11-21

    Knot theory is a branch of pure mathematics, but it is increasingly being applied in a variety of sciences. Knots appear in chemistry, not only in synthetic molecular design, but also in an array of materials and media, including some not traditionally associated with knots. Mathematics and chemistry can now be used synergistically to identify, characterise and create knots, as well as to understand and predict their physical properties. This tutorial review provides a brief introduction to the mathematics of knots and related topological concepts in the context of the chemical sciences. We then survey the broad range of applications of the theory to contemporary research in the field.

  15. Proteins analysed as virtual knots

    PubMed Central

    Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.

    2017-01-01

    Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important. PMID:28205562

  16. Proteins analysed as virtual knots

    NASA Astrophysics Data System (ADS)

    Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.

    2017-02-01

    Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.

  17. The "wilderness knot"

    Treesearch

    Haydn G. Washington

    2007-01-01

    The word “wilderness” is beset by a tangle of meanings. This “knot” is made of five strands: philosophical, political, cultural, justice and exploitation. Wilderness has a unique philosophical position—being disliked by both Modernism and Postmodernism. Eight key criticisms of wilderness are identified, and two different meanings discussed—“wasteland” and “large...

  18. YS knot: A new technique for a tension-controlled slip knot using a trocar

    PubMed Central

    Lee, Yoon Hee; Kim, Mi Jeong; Chong, Gun Oh; Hong, Dae Gy; Lee, Juhun

    2015-01-01

    The Yoon Soon (YS) knot is a laparoscopic extracorporeal slip knot that is easy to learn and apply. Our new technique, which uses the trocar as a knot pusher, is simpler, faster, and has more tension than conventional knot methods. The YS knot will help surgeons save operative time and perform tension-controlled knot-tying during laparoscopic surgery. PMID:25798432

  19. Metastable Tight Knots in DNA

    NASA Astrophysics Data System (ADS)

    Dai, Liang; Renner, C. Benjamin; Doyle, Patrick

    2015-03-01

    Knotted structures can spontaneously occur in polymers such as DNA and proteins, and the formation of knots affects biological functions, mechanical strength and rheological properties. In this work, we calculate the equilibrium size distribution of trefoil knots in linear DNA using off-lattice simulations. We observe metastable knots on DNA, as predicted by Grosberg and Rabin. Furthermore, we extend their theory to incorporate the finite width of chains and show an agreement between our simulations and the modified theory for real chains. Our results suggest localized knots spontaneously occur in long DNA and the contour length in the knot ranges from 600 to 1800 nm. This research was supported by the National Research Foundation Singapore through the Singapore MIT Alliance for Research and Technology's research program in BioSystems and Micromechanics, the National Science Foundation (Grant No. 1335938).

  20. Untangling of knotted urethral catheters.

    PubMed

    Sambrook, Andrew J; Todd, Alistair

    2007-04-01

    Intravesical catheter knotting during micturating cystourethrography is a rare but recognized complication of the procedure. We were able to untangle a knot utilizing a fluoroscopically guided vascular guidewire. Following this success, a small study was performed using a model. Various types of guidewires and techniques were tested for different diameters of knots in order to predict the likelihood of success in this type of situation.

  1. How superfluid vortex knots untie

    NASA Astrophysics Data System (ADS)

    Kleckner, Dustin; Kauffman, Louis H.; Irvine, William T. M.

    2016-07-01

    Knots and links often occur in physical systems, including shaken strands of rope and DNA (ref. ), as well as the more subtle structure of vortices in fluids and magnetic fields in plasmas. Theories of fluid flows without dissipation predict these tangled structures persist, constraining the evolution of the flow much like a knot tied in a shoelace. This constraint gives rise to a conserved quantity known as helicity, offering both fundamental insights and enticing possibilities for controlling complex flows. However, even small amounts of dissipation allow knots to untie by means of `cut-and-splice’ operations known as reconnections. Despite the potentially fundamental role of these reconnections in understanding helicity--and the stability of knotted fields more generally--their effect is known only for a handful of simple knots. Here we study the evolution of 322 elemental knots and links in the Gross-Pitaevskii model for a superfluid, and find that they universally untie. We observe that the centreline helicity is partially preserved even as the knots untie, a remnant of the perfect helicity conservation predicted for idealized fluids. Moreover, we find that the topological pathways of untying knots have simple descriptions in terms of minimal two-dimensional knot diagrams, and tend to concentrate in states which are twisted in only one direction. These results have direct analogies to previous studies of simple knots in several systems, including DNA recombination and classical fluids. This similarity in the geometric and topological evolution suggests there are universal aspects in the behaviour of knots in dissipative fields.

  2. Five Uncommon but Useful Knots.

    ERIC Educational Resources Information Center

    Chisnall, Rob

    1997-01-01

    Describes five useful, little-known knots: mooring hitch for securing a line to a stump or post; highwayman's cutaway for securing canoe lines or horses' reins; taut-line hitch or midshipman's hitch for securing tent guys; and Hedden knot and C&F belay hitch, used by rock climbers and mountaineers, which combine in a simple rescue haul system.…

  3. Knots in electromagnetism

    NASA Astrophysics Data System (ADS)

    Arrayás, M.; Bouwmeester, D.; Trueba, J. L.

    2017-01-01

    Maxwell equations in vacuum allow for solutions with a non-trivial topology in the electric and magnetic field line configurations at any given moment in time. One example is a space filling congruence of electric and magnetic field lines forming circles lying on the surfaces of nested tori. In this example the electric, magnetic and Poynting vector fields are orthogonal everywhere. As time evolves the electric and magnetic fields expand and deform without changing the topology and energy, while the Poynting vector structure remains unchanged while propagating with the speed of light. The topology is characterized by the concept of helicity of the field configuration. Helicity is an important fundamental concept and for massless fields it is a conserved quantity under conformal transformations. We will review several methods by which linked and knotted electromagnetic (spin-1) fields can be derived. A first method, introduced by A. Rañada, uses the formulation of the Maxwell equations in terms of differential forms combined with the Hopf map from the three-sphere S3 to the two-sphere S2. A second method is based on spinor and twistor theory developed by R. Penrose in which elementary twistor functions correspond to the family of electromagnetic torus knots. A third method uses the Bateman construction of generating null solutions from complex Euler potentials. And a fourth method uses special conformal transformations, in particular conformal inversion, to generate new linked and knotted field configurations from existing ones. This fourth method is often accompanied by shifting singularities in the field to complex space-time points. Of course the various methods must be closely related to one another although they have been developed largely independently and they suggest different directions in which to expand the study of topologically non-trivial field configurations. It will be shown how the twistor formulation allows for a direct extension to massless

  4. Beyond the Square Knot: A Novel Knotting Technique for Surgical Use

    PubMed Central

    Zhao, Chunfeng; Hsu, Chung-Chen; Moriya, Tamami; Thoreson, Andrew R.; Cha, Steven S.; Moran, Steven L.; An, Kai-Nan; Amadio, Peter C.

    2013-01-01

    Background: Knot holding strength is essential to maintain wound closure and ensure tissue contact for healing. Knot unraveling can lead to severe complications, especially for high-tension closures such as tendon repairs, which have recently been reported to have knot unraveling rates as high as 86%. In the current study, a novel surgical knot, the two-strand-overhand locking (TSOL) knot, was designed and mechanically evaluated with use of different suture materials and knot configurations and in actual tendon repairs. Methods: The knot holding strength of the TSOL knot was compared with that of a 4-throw square knot with use of three different suture materials that are in common clinical use. With use of braided polyblend suture, the TSOL knot was also compared with five other surgical knot configurations. Finally, the strength of tendon repairs performed with use of the TSOL knot and a 4-throw square knot was studied. Results: Compared with the 4-throw square knot, the holding strength of the TSOL knot was 143% greater for braided polyblend, 216% greater for polydioxanone, and 118% greater for polyester suture, with a significantly lower knot unraveling rate compared with that of the 4-throw square knot regardless of suture material. The TSOL knot holding strength was also greater than that of the other surgical knot configurations. The strength and stiffness of tendon repairs with a TSOL knot were significantly increased over those of repairs with a 4-throw square knot. Conclusions: The TSOL knot provided superior knot holding strength compared with some commonly used surgical knots. Clinical Relevance: The TSOL knot has potential clinical applications, especially when knot security is important and high loads are expected, as in tendon or ligament repairs. PMID:23780540

  5. Periodic forces trigger knot untying during translocation of knotted proteins.

    PubMed

    Szymczak, Piotr

    2016-03-21

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process, jamming the pore, since the diameter of the pore is smaller than the size of maximally tightened knot. The jamming probability dramatically increases as the magnitude of the driving force exceeds a critical value, Fc. In this numerical study, we show that for deep knots Fc lies below the force range over which molecular import motors operate, which suggest that in these cases the knots will tighten and block the pores. Next, we show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other molecular motors transforms chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character.

  6. Periodic forces trigger knot untying during translocation of knotted proteins

    PubMed Central

    Szymczak, Piotr

    2016-01-01

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process, jamming the pore, since the diameter of the pore is smaller than the size of maximally tightened knot. The jamming probability dramatically increases as the magnitude of the driving force exceeds a critical value, Fc. In this numerical study, we show that for deep knots Fc lies below the force range over which molecular import motors operate, which suggest that in these cases the knots will tighten and block the pores. Next, we show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other molecular motors transforms chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character. PMID:26996878

  7. Periodic forces trigger knot untying during translocation of knotted proteins

    NASA Astrophysics Data System (ADS)

    Szymczak, Piotr

    2016-03-01

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process, jamming the pore, since the diameter of the pore is smaller than the size of maximally tightened knot. The jamming probability dramatically increases as the magnitude of the driving force exceeds a critical value, Fc. In this numerical study, we show that for deep knots Fc lies below the force range over which molecular import motors operate, which suggest that in these cases the knots will tighten and block the pores. Next, we show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other molecular motors transforms chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character.

  8. Knot invariants from Virasoro related representation and pretzel knots

    NASA Astrophysics Data System (ADS)

    Galakhov, D.; Melnikov, D.; Mironov, A.; Morozov, A.

    2015-10-01

    We remind the method to calculate colored Jones polynomials for the plat representations of knot diagrams from the knowledge of modular transformation (monodromies) of Virasoro conformal blocks with insertions of degenerate fields. As an illustration we use a rich family of pretzel knots, lying on a surface of arbitrary genus g, which was recently analyzed by the evolution method. Further generalizations can be to generic Virasoro modular transformations, provided by integral kernels, which can lead to the Hikami invariants.

  9. Biomechanical characteristics of 9 arthroscopic knots.

    PubMed

    Dahl, Kevin A; Patton, Daniel J; Dai, Qiang; Wongworawat, Montri D

    2010-06-01

    To determine the optimal arthroscopic slipknot through comparison of ease of placement, loop security, knot security, and amount of suture material needed using a new suture material. Nine commonly used arthroscopic knots (Dines, Field, Nicky, Hu, San Diego, Snyder, Tennessee slider, Triad, and Tuckahoe) were tested by use of modern suture material, FiberWire (Arthrex, Naples, FL), with the Instron materials testing machine (Instron, Norwood, MA) for ease of knot placement (forward and backward sliding), loop security, and knot security. The amount of suture material needed to create the knot was compared by use of the knot weight. Analysis of variance with Kruskal-Wallis analysis and Bonferroni correction (alpha < .01) was used to compare different knots. The Tennessee slider knot sustained the greatest force at failure (269 N), the greatest knot resistance (32 N), and the smallest mass (8.5 mg). The Dines was the only knot superior in all 3 knot placement categories. The Nicky held the most loop force (66 N), and the Tuckahoe had the greatest loop resistance (20 N) (P < .01 for all except mass [P < .05]). Our study comprehensively presents ease-of-placement and security characteristics of 9 common and new arthroscopic knots using modern FiberWire suture. The Tennessee slider knot showed superior characteristics in knot security and knot mass. The Dines knot was the most ideal knot to place. However, the surgeon will need to review the individual knot characteristics and select the knot most suited to application. This study analyzed 9 arthroscopic knots with modern suture material and identified those with superior characteristics. Copyright (c) 2010 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

  10. Weaving Knotted Vector Fields with Tunable Helicity.

    PubMed

    Kedia, Hridesh; Foster, David; Dennis, Mark R; Irvine, William T M

    2016-12-30

    We present a general construction of divergence-free knotted vector fields from complex scalar fields, whose closed field lines encode many kinds of knots and links, including torus knots, their cables, the figure-8 knot, and its generalizations. As finite-energy physical fields, they represent initial states for fields such as the magnetic field in a plasma, or the vorticity field in a fluid. We give a systematic procedure for calculating the vector potential, starting from complex scalar functions with knotted zero filaments, thus enabling an explicit computation of the helicity of these knotted fields. The construction can be used to generate isolated knotted flux tubes, filled by knots encoded in the lines of the vector field. Lastly, we give examples of manifestly knotted vector fields with vanishing helicity. Our results provide building blocks for analytical models and simulations alike.

  11. Universal Racah matrices and adjoint knot polynomials: Arborescent knots

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.

    2016-04-01

    By now it is well established that the quantum dimensions of descendants of the adjoint representation can be described in a universal form, independent of a particular family of simple Lie algebras. The Rosso-Jones formula then implies a universal description of the adjoint knot polynomials for torus knots, which in particular unifies the HOMFLY (SUN) and Kauffman (SON) polynomials. For E8 the adjoint representation is also fundamental. We suggest to extend the universality from the dimensions to the Racah matrices and this immediately produces a unified description of the adjoint knot polynomials for all arborescent (double-fat) knots, including twist, 2-bridge and pretzel. Technically we develop together the universality and the ;eigenvalue conjecture;, which expresses the Racah and mixing matrices through the eigenvalues of the quantum R-matrix, and for dealing with the adjoint polynomials one has to extend it to the previously unknown 6 × 6 case. The adjoint polynomials do not distinguish between mutants and therefore are not very efficient in knot theory, however, universal polynomials in higher representations can probably be better in this respect.

  12. Stabilizing effect of knots on proteins.

    PubMed

    Sułkowska, Joanna I; Sulkowski, Piotr; Szymczak, P; Cieplak, Marek

    2008-12-16

    Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot.

  13. Stabilizing effect of knots on proteins

    PubMed Central

    Sułkowska, Joanna I.; Sułkowski, Piotr; Szymczak, P.; Cieplak, Marek

    2008-01-01

    Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot. PMID:19064918

  14. On ambiguity in knot polynomials for virtual knots

    NASA Astrophysics Data System (ADS)

    Morozov, A.; Morozov, And.; Popolitov, A.

    2016-06-01

    We claim that HOMFLY polynomials for virtual knots, defined with the help of the matrix-model recursion relations, contain more parameters, than just the usual q and A =qN. These parameters preserve topological invariance and do not show up in the case of ordinary (non-virtual) knots and links. They are most conveniently observed in the hypercube formalism: then they substitute q-dimensions of certain fat graphs, which are not constrained by recursion and can be chosen arbitrarily. The number of these new topological invariants seems to grow fast with the number of non-virtual crossings: 0, 1, 1, 5, 15, 91, 784, 9160, ... This number can be decreased by imposing the factorization requirement for composites, in addition to topological invariance - still freedom remains. None of these new parameters, however, appears in HOMFLY for Kishino unknot, which thus remains unseparated from the ordinary unknots even by this enriched set of knot invariants.

  15. Spontaneous knotting of an agitated string.

    PubMed

    Raymer, Dorian M; Smith, Douglas E

    2007-10-16

    It is well known that a jostled string tends to become knotted; yet the factors governing the "spontaneous" formation of various knots are unclear. We performed experiments in which a string was tumbled inside a box and found that complex knots often form within seconds. We used mathematical knot theory to analyze the knots. Above a critical string length, the probability P of knotting at first increased sharply with length but then saturated below 100%. This behavior differs from that of mathematical self-avoiding random walks, where P has been proven to approach 100%. Finite agitation time and jamming of the string due to its stiffness result in lower probability, but P approaches 100% with long, flexible strings. We analyzed the knots by calculating their Jones polynomials via computer analysis of digital photos of the string. Remarkably, almost all were identified as prime knots: 120 different types, having minimum crossing numbers up to 11, were observed in 3,415 trials. All prime knots with up to seven crossings were observed. The relative probability of forming a knot decreased exponentially with minimum crossing number and Möbius energy, mathematical measures of knot complexity. Based on the observation that long, stiff strings tend to form a coiled structure when confined, we propose a simple model to describe the knot formation based on random "braid moves" of the string end. Our model can qualitatively account for the observed distribution of knots and dependence on agitation time and string length.

  16. Spontaneous knotting of an agitated string

    PubMed Central

    Raymer, Dorian M.; Smith, Douglas E.

    2007-01-01

    It is well known that a jostled string tends to become knotted; yet the factors governing the “spontaneous” formation of various knots are unclear. We performed experiments in which a string was tumbled inside a box and found that complex knots often form within seconds. We used mathematical knot theory to analyze the knots. Above a critical string length, the probability P of knotting at first increased sharply with length but then saturated below 100%. This behavior differs from that of mathematical self-avoiding random walks, where P has been proven to approach 100%. Finite agitation time and jamming of the string due to its stiffness result in lower probability, but P approaches 100% with long, flexible strings. We analyzed the knots by calculating their Jones polynomials via computer analysis of digital photos of the string. Remarkably, almost all were identified as prime knots: 120 different types, having minimum crossing numbers up to 11, were observed in 3,415 trials. All prime knots with up to seven crossings were observed. The relative probability of forming a knot decreased exponentially with minimum crossing number and Möbius energy, mathematical measures of knot complexity. Based on the observation that long, stiff strings tend to form a coiled structure when confined, we propose a simple model to describe the knot formation based on random “braid moves” of the string end. Our model can qualitatively account for the observed distribution of knots and dependence on agitation time and string length. PMID:17911269

  17. Colored knot polynomials for arbitrary pretzel knots and links

    DOE PAGES

    Galakhov, D.; Melnikov, D.; Mironov, A.; ...

    2015-04-01

    A very simple expression is conjectured for arbitrary colored Jones and HOMFLY polynomials of a rich (g+1)-parametric family of pretzel knots and links. The answer for the Jones and HOMFLY is fully and explicitly expressed through the Racah matrix of Uq(SUN), and looks related to a modular transformation of toric conformal block. Knot polynomials are among the hottest topics in modern theory. They are supposed to summarize nicely representation theory of quantum algebras and modular properties of conformal blocks. The result reported in the present letter, provides a spectacular illustration and support to this general expectation.

  18. Skyrmion Knots in Frustrated Magnets

    NASA Astrophysics Data System (ADS)

    Sutcliffe, Paul

    2017-06-01

    A magnetic Skyrmion is a stable two-dimensional nanoparticle describing a localized winding of the magnetization in certain magnetic materials. Skyrmions are the subject of intense experimental and theoretical investigation and have potential technological spintronic applications. Here we show that numerical computations of frustrated magnets predict that Skyrmions can be tied into knots to form new stable three-dimensional nanoparticles. These stable equilibria of twisted loops of Skyrmion strings have an integer-valued topological charge, known as the Hopf charge, that counts the number of particles. Rings are formed for low values of this charge, but for higher values it is energetically favorable to form links and then knots. This computational study provides a novel impetus for future experimental work on these nanoknots and an exploration of the potential technological applications of three-dimensional nanoparticles encoding knotted magnetization.

  19. Skyrmion Knots in Frustrated Magnets.

    PubMed

    Sutcliffe, Paul

    2017-06-16

    A magnetic Skyrmion is a stable two-dimensional nanoparticle describing a localized winding of the magnetization in certain magnetic materials. Skyrmions are the subject of intense experimental and theoretical investigation and have potential technological spintronic applications. Here we show that numerical computations of frustrated magnets predict that Skyrmions can be tied into knots to form new stable three-dimensional nanoparticles. These stable equilibria of twisted loops of Skyrmion strings have an integer-valued topological charge, known as the Hopf charge, that counts the number of particles. Rings are formed for low values of this charge, but for higher values it is energetically favorable to form links and then knots. This computational study provides a novel impetus for future experimental work on these nanoknots and an exploration of the potential technological applications of three-dimensional nanoparticles encoding knotted magnetization.

  20. Relation between strings and ribbon knots

    NASA Astrophysics Data System (ADS)

    Ahmed, E.; El-Rifai, E. A.; Abdellatif, R. A.

    1991-02-01

    A ribbon knot can be represented as the propagation of an open string in (Euclidean) space-time. By imposing physical conditions plus an ansatz on the string scattering amplitude, we get invariant polynomials of ribbon knots which correspond to Jones and Wadati et al. polynomials for ordinary knots. Motivated by the string scattering vertices, we derive an algebra which is a generalization of Hecke and Murakami-Birman-Wenzel (BMW) algebras of knots.

  1. Second IBEX Map Unties the Knot

    NASA Image and Video Library

    One of the clear features visible in the IBEX maps is an apparent knot in the ribbon. The second map showed that the knot in the ribbon somehow spread out. It is as if the knot in the ribbon was li...

  2. Colored knot polynomials for arbitrary pretzel knots and links

    NASA Astrophysics Data System (ADS)

    Galakhov, D.; Melnikov, D.; Mironov, A.; Morozov, A.; Sleptsov, A.

    2015-04-01

    A very simple expression is conjectured for arbitrary colored Jones and HOMFLY polynomials of a rich (g + 1)-parametric family of pretzel knots and links. The answer for the Jones and HOMFLY is fully and explicitly expressed through the Racah matrix of Uq (SUN), and looks related to a modular transformation of toric conformal block.

  3. Biomechanical performance of traditional arthroscopic knots versus slippage-proof knots.

    PubMed

    Clark, Randy R; Dierckman, Brian; Sampatacos, Nels; Sampaticos, Nels; Snyder, Stephen

    2013-07-01

    To compare the biomechanical, time, and profile characteristics of a new sliding locking knot termed the slippage-proof knot (SPK) and a modified slippage-proof knot (MSPK) with those of traditional arthroscopic knots. We evaluated the Samsung Medical Center (SMC) knot, Revo knot, SPK, and MSPK (an SPK with a single added half-hitch) tied with high-strength suture, with 11 trials of each cycled 1,000 times between 10 and 45 N and then loaded to failure. Total displacement during cyclical testing, maximal load to failure, and mode of failure were recorded for each knot. We also measured the dimensions of the knots and the time required to tie each knot. On load-to-failure testing, no difference in strength was found between the SMC and Revo knots (P = .082). The Revo knot and MSPK were also of equivalent strength (P = .183), and the SMC knot was 11% stronger than the MSPK (P = .017). All 3 of these knots were stronger than the SPK. On cyclical testing, the SMC knot, Revo knot, and MSPK allowed equivalent total displacement and allowed statistically less total displacement than the SPK. All SMC knots, Revo knots, and MSPKs failed by suture breakage, whereas the SPKs all slipped at failure. We found that the SPKs and MSPKs are tied more quickly than traditional knots. The SPK and MSPK dimensions are wider yet shorter than those of the other knots in the study. Our results indicate that the MSPK has biomechanical properties comparable to the SMC and Revo knots despite only requiring 1 added half-hitch, whereas the SPK was found to be significantly inferior to the other knots tested. We found that the slippage-proof knots (SPK and MSPK) were tied more quickly and have shorter, wider profiles than traditional knots. The MSPK has knot security comparable to the SMC and Revo knots while requiring only 1 added half-hitch, and it may be most beneficial in cases in which a large number of knots will be tied because the fewer required half-hitches reduces the surgical time

  4. Biomechanical evaluation of the Nice knot

    PubMed Central

    Hill, Shannon W.; Chapman, Christopher R.; Adeeb, Samer; Duke, Kajsa; Beaupre, Lauren; Bouliane, Martin J.

    2016-01-01

    Background: The Nice knot is a bulky double-stranded knot. Biomechanical data supporting its use as well as the number of half hitches required to ensure knot security is lacking. Materials and Methods: Nice knots with, one, two, or three half-hitches were compared with the surgeon's and Tennessee slider knots with three half hitches. Each knot was tied 10 times around a fixed diameter using four different sutures: FiberWire (Arthrex, Naples, FL), Ultrabraid (Smith and Nephew, Andover, MA), Hi-Fi (ConMed Linvatec, Largo, FL) and Force Fiber (Teleflex Medical OEM, Gurnee, IL). Cyclic testing was performed for 10 min between 10N and 45N, resulting in approximately 1000 cycles. Displacement from an initial 10N load was recorded. Knots surviving cyclic testing were subjected to a load to failure test at a rate of 60 mm/min. Load at clinical failure: 3 mm slippage or opening of the suture loop was recorded. Bulk, mode of ultimate failure, opening of the loop past clinical failure, was also recorded. Results: During cyclic testing, the Nice knots with one or more half-hitches performed the best, slipping significantly less than the surgeon's and Tennessee Slider (P < 0.002). After one half-hitch, the addition of half-hitches did not significantly improve Nice knot performance during cyclic testing (P > 0.06). The addition of half-hitches improved the strength of the Nice knot during the force to failure test, however after two half-hitches, increase of strength was not significant (P = 0.59). While FiberWire was the most bulky of the sutures tested, it also performed the best, slipping the least. Conclusion: The Nice knot, especially using FiberWire, is biomechanically superior to the surgeon's and Tennessee slider knots. Two half hitches are recommended to ensure adequate knot security. PMID:26980985

  5. KnotPad: Visualizing and Exploring Knot Theory with Fluid Reidemeister Moves.

    PubMed

    Zhang, Hui; Weng, Jianguang; Jing, Lin; Zhong, Yiwen

    2012-12-01

    We present KnotPad, an interactive paper-like system for visualizing and exploring mathematical knots; we exploit topological drawing and math-aware deformation methods in particular to enable and enrich our interactions with knot diagrams. Whereas most previous efforts typically employ physically based modeling to simulate the 3D dynamics of knots and ropes, our tool offers a Reidemeister move based interactive environment that is much closer to the topological problems being solved in knot theory, yet without interfering with the traditional advantages of paper-based analysis and manipulation of knot diagrams. Drawing knot diagrams with many crossings and producing their equivalent is quite challenging and error-prone. KnotPad can restrict user manipulations to the three types of Reidemeister moves, resulting in a more fluid yet mathematically correct user experience with knots. For our principal test case of mathematical knots, KnotPad permits us to draw and edit their diagrams empowered by a family of interactive techniques. Furthermore, we exploit supplementary interface elements to enrich the user experiences. For example, KnotPad allows one to pull and drag on knot diagrams to produce mathematically valid moves. Navigation enhancements in KnotPad provide still further improvement: by remembering and displaying the sequence of valid moves applied during the entire interaction, KnotPad allows a much cleaner exploratory interface for the user to analyze and study knot equivalence. All these methods combine to reveal the complex spatial relationships of knot diagrams with a mathematically true and rich user experience.

  6. KnotProt: a database of proteins with knots and slipknots

    PubMed Central

    Jamroz, Michal; Niemyska, Wanda; Rawdon, Eric J.; Stasiak, Andrzej; Millett, Kenneth C.; Sułkowski, Piotr; Sulkowska, Joanna I.

    2015-01-01

    The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints. PMID:25361973

  7. Knot security in laparoscopic surgery. A comparative study with conventional knots.

    PubMed

    Amortegui, J D; Restrepo, H

    2002-11-01

    Few comparative studies have evaluated conventional and laparoscopic knots. The objective of this study was to evaluate laparoscopic knot reliability and identify which type of knot is most secure. Seven types of knots were compared; each one was conventionally tied with four and six throws and similarly by laparoscopy. Dinsmore nomenclature for knots was used. A tension meter was used to evaluate knot reliability, using the loop method, and percentage of failure by slipping and tensile strength was calculated for each group. When S=S=S=S and S=S=S=S=S=S geometry are excluded, there was no difference between laparoscopic and conventional knot. A significant difference between four- and six-throw knots was shown. Excluding S=S=S=S=S=S geometry, all knots in the conventional six-throw group were secure. Intracorporeal 2X1X1X1X1 and 1X1X1X1X1X1 and extracorporeal SXS#SXS#SXS six-throw laparoscopic group knots were secure. Laparoscopic knots are as secure as conventional knots. All knots must be made with six throws because security is maximized.

  8. Translocation of knotted proteins through a pore

    NASA Astrophysics Data System (ADS)

    Szymczak, P.

    2014-09-01

    We report the results of molecular dynamics simulations of translocation of knotted proteins through pores. The protein is pulled into the pore with a constant force, which in many cases leads to the tightening of the knot. Since the radius of tightened knot is larger than that of the pore opening, the tight knot can block the pore thus preventing further translocation of the chain. Analyzing six different proteins, we show that the stuck probability increases with the applied force and that final positions of the tightened knot along the protein backbone are not random but are usually associated with sharp turns in the polypeptide chain. The combined effect of the confining geometry of the pore and the inhomogeneous character of the protein chain leads thus to the appearance of topological traps, which can immobilize the knot and lead to the jamming of the pore.

  9. Vortex knots in tangled quantum eigenfunctions.

    PubMed

    Taylor, Alexander J; Dennis, Mark R

    2016-07-29

    Tangles of string typically become knotted, from macroscopic twine down to long-chain macromolecules such as DNA. Here, we demonstrate that knotting also occurs in quantum wavefunctions, where the tangled filaments are vortices (nodal lines/phase singularities). The probability that a vortex loop is knotted is found to increase with its length, and a wide gamut of knots from standard tabulations occur. The results follow from computer simulations of random superpositions of degenerate eigenstates of three simple quantum systems: a cube with periodic boundaries, the isotropic three-dimensional harmonic oscillator and the 3-sphere. In the latter two cases, vortex knots occur frequently, even in random eigenfunctions at relatively low energy, and are constrained by the spatial symmetries of the modes. The results suggest that knotted vortex structures are generic in complex three-dimensional wave systems, establishing a topological commonality between wave chaos, polymers and turbulent Bose-Einstein condensates.

  10. Characteristic length of the knotting probability revisited

    NASA Astrophysics Data System (ADS)

    Uehara, Erica; Deguchi, Tetsuo

    2015-09-01

    We present a self-avoiding polygon (SAP) model for circular DNA in which the radius of impermeable cylindrical segments corresponds to the screening length of double-stranded DNA surrounded by counter ions. For the model we evaluate the probability for a generated SAP with N segments having a given knot K through simulation. We call it the knotting probability of a knot K with N segments for the SAP model. We show that when N is large the most significant factor in the knotting probability is given by the exponentially decaying part exp(-N/NK), where the estimates of parameter NK are consistent with the same value for all the different knots we investigated. We thus call it the characteristic length of the knotting probability. We give formulae expressing the characteristic length as a function of the cylindrical radius rex, i.e. the screening length of double-stranded DNA.

  11. Endoscopic Release of Master Knot of Henry.

    PubMed

    Lui, Tun Hing

    2015-12-01

    A post-traumatic partial tear of the flexor hallucis longus tendon at the master knot of Henry and the resultant fibrosis of the knot can result in pain at the medial foot arch or posteromedial ankle pain with trigger hallux. Open debridement of the master knot of Henry is indicated if the symptoms do not improve with nonoperative treatment. The open procedure requires extensive soft-tissue dissection because the master knot of Henry is a deep structure. Endoscopic release of the master knot of Henry is an alternative to the open procedure and has the advantage of less surgical trauma and potential for less chance of recurrence of fibrosis of the master knot of Henry.

  12. Vortex knots in tangled quantum eigenfunctions

    PubMed Central

    Taylor, Alexander J.; Dennis, Mark R.

    2016-01-01

    Tangles of string typically become knotted, from macroscopic twine down to long-chain macromolecules such as DNA. Here, we demonstrate that knotting also occurs in quantum wavefunctions, where the tangled filaments are vortices (nodal lines/phase singularities). The probability that a vortex loop is knotted is found to increase with its length, and a wide gamut of knots from standard tabulations occur. The results follow from computer simulations of random superpositions of degenerate eigenstates of three simple quantum systems: a cube with periodic boundaries, the isotropic three-dimensional harmonic oscillator and the 3-sphere. In the latter two cases, vortex knots occur frequently, even in random eigenfunctions at relatively low energy, and are constrained by the spatial symmetries of the modes. The results suggest that knotted vortex structures are generic in complex three-dimensional wave systems, establishing a topological commonality between wave chaos, polymers and turbulent Bose–Einstein condensates. PMID:27468801

  13. Knotted solitons in nonlinear magnetic metamaterials.

    PubMed

    Rosanov, Nikolay N; Vysotina, Nina V; Shatsev, Anatoly N; Desyatnikov, Anton S; Kivshar, Yuri S

    2012-03-30

    We demonstrate that nonlinear magnetic metamaterials comprised of a lattice of weakly coupled split-ring resonators driven by an external electromagnetic field may support entirely new classes of spatially localized modes--knotted solitons, which are stable self-localized dissipative structures in the form of closed knotted chains. We demonstrate different topological types of stable knots for the subcritical coupling between resonators and instability-induced breaking of the chains for the supercritical coupling.

  14. Chirality modifies the interaction between knots

    NASA Astrophysics Data System (ADS)

    Najafi, Saeed; Tubiana, Luca; Podgornik, Rudolf; Potestio, Raffaello

    2016-06-01

    In this study we consider an idealization of a typical optical tweezers experiment involving a semiflexible double-knotted polymer, with steric hindrance and persistence length matching those of dsDNA in high salt concentration, under strong stretching. Using exhaustive molecular-dynamics simulations we show that not only does a double-knotted dsDNA filament under tension possess a free-energy minimum when the two knots are intertwined, but also that the depth of this minimum depends on the relative chirality of the two knots. We rationalize this dependence of the effective interaction on the chirality in terms of a competition between chain entropy and bending energy.

  15. Arthroscopic knot tying: the role of instrumentation in achieving knot security.

    PubMed

    Milia, Marc J; Peindl, Richard D; Connor, Patrick M

    2005-01-01

    To determine the role of arthroscopic knot-tying instrumentation in achieving knot security. Biomechanical study. The security achieved by 3 different commercially available knot-tying instruments using No. 2 braided suture and a standardized knot configuration was compared. Instrumentation included (1) a single-hole knot pusher, (2) a cannulated double-diameter knot pusher, and (3) a mechanical end-splitting knot tightener. Hand-tied knots served as controls. Testing included both cyclic loading and load to failure parameters using the Bionix 858 (MTS Inc, Eden Prairie, MN) and Instron Mini 44 (Instron, Canton, MA) materials testing systems, respectively. An experienced arthroscopic shoulder surgeon and a less experienced junior-level orthopaedic resident surgeon performed tying. Knot displacement after cyclic loading was smallest for the mechanical end-splitting knot tightener (average, 0.054 mm) and did not differ statistically from hand-tied knots (average, 0.058 mm). Knots tied with this device also withstood the greatest load to failure (average, 126.0 N) and were statistically similar to hand-tied knots (average, 134.1 N). The single-hole pusher had an average cyclic loading displacement of 0.095 mm and failed at 108.6 N. The cannulated double-diameter pushers had an average cyclic loading displacement of 0.106 mm and failed at 93.1 N. Both were statistically less secure than hand-tied knots or those tied with the end-splitting tightener. Investigator experience did not affect knot security with those tied by the mechanical end-splitting tightener or hand-tied knots. The end-splitting tightener provided the most secure arthroscopic knots that were statistically as secure as those tied by hand for both investigators. The knot-tying instrument used in arthroscopic shoulder surgery may be an important consideration with potential clinical implications based on knot security. The specific knot tying instrument that is selected for use in arthroscopic shoulder

  16. Untying the gordian knot: what we do and don't know about gender-specific medicine-keynote address for the 2014 Academic Emergency Medicine Consensus Conference.

    PubMed

    Legato, Marianne

    2014-12-01

    Over the past two decades, a burgeoning interest in women's health, the direct consequence of the feminist movement, has inspired a worldwide interest in the differences between the normal function of men and women and their unique experiences of the same illnesses. The scope and significance of what we have discovered and continue to find has fundamentally changed the way we prevent, diagnose, and treat diseases. Important questions remain, however, and deserve specific investigation and analysis.

  17. Amoralist rationalism? A response to Joel Marks: commentary on "Animal abolitionism meets moral abolitionism: cutting the Gordian knot of applied ethics" by Joel Marks.

    PubMed

    Lederman, Zohar

    2014-06-01

    In a recent article, Joel Marks presents the amoralist argument against vivisection, or animal laboratory experimentation. He argues that ethical theories that seek to uncover some universal morality are in fact useless and unnecessary for ethical deliberations meant to determine what constitutes an appropriate action in a specific circumstance. I agree with Marks' conclusion. I too believe that vivisection is indefensible, both from a scientific and philosophical perspective. I also believe that we should become vegan (unfortunately, like the two philosophers mentioned by Marks, I too am still struggling to reduce my meat and dairy consumption). However, I am in the dark as to Marks' vision of normative deliberations in the spirit of amoralism and desirism.

  18. Sedimentation of macroscopic rigid knots and its relation to gel electrophoretic mobility of DNA knots.

    PubMed

    Weber, Cédric; Carlen, Mathias; Dietler, Giovanni; Rawdon, Eric J; Stasiak, Andrzej

    2013-01-01

    We address the general question of the extent to which the hydrodynamic behaviour of microscopic freely fluctuating objects can be reproduced by macrosopic rigid objects. In particular, we compare the sedimentation speeds of knotted DNA molecules undergoing gel electrophoresis to the sedimentation speeds of rigid stereolithographic models of ideal knots in both water and silicon oil. We find that the sedimentation speeds grow roughly linearly with the average crossing number of the ideal knot configurations, and that the correlation is stronger within classes of knots. This is consistent with previous observations with DNA knots in gel electrophoresis.

  19. Scissor-Knot-Pusher: An Instrument for Simplified Laparoscopic Extracorporeal Knotting

    PubMed Central

    Croce, Enrico

    2003-01-01

    This paper describes the “scissor-knot-pusher,” an instrument that greatly facilitates the execution of knot tying during laparoscopic operations. The instrument acts in essence as an extension of the surgeon's hand and, given its rigid structure, allows the surgeon full control of the process of knot tying. Additionally, after the knot has been tightened, it is possible to cut the suture without using a different instrument. As a result, this technical device simplifies knot tying and may help to reduce the frustration and the time often associated with intracorporeal suturing during laparoscopic surgery. PMID:14558722

  20. Diagnosis of true umbilical cord knot.

    PubMed

    Guzikowski, Wojciech; Kowalczyk, Dariusz; Więcek, Jacek

    2014-02-24

    Many abnormalities are observed in the morphology and pathology of the umbilical cord. The aim of the study was to assess the role of 3D sonography in pathology of true umbilical cord knots. In our materials we observed 10 cases of true umbilical cord knots in a population of 2,864 deliveries. The 2-dimensional transverse scan of the umbilical cord was shown in 3- and 4-dimensional volume scan in order to get a precise image. Four knots were diagnosed prenatally, 3 knots were not diagnosed before the delivery and in the 3 remaining cases ultrasound examinations were not undertaken because the patients were in the course of delivery. In the pregnant subjects with diagnosed true umbilical cord knot once a week the Doppler blood flow indices were examined in the umbilical cord sections before and after the knot. In the three shown cases there were no signs of constriction or tightening of the knot. Four newborns were delivered spontaneously and five by caesarean section. In none of the cases was a pathological FHR trace an indication for emergency delivery. Four-dimensional and Color Doppler examination is very important to diagnose a true umbilical cord. To make a precise diagnosis a longer observation of the abnormality is necessary and its repeated confirmation by color Doppler and power Doppler. This diagnosis requires strict monitoring of fetal wellbeing during pregnancy and the delivery. Perfection of true umbilical cord knot diagnoses may reduce sudden and unforeseen fetal distress.

  1. Spline curve matching with sparse knot sets

    Treesearch

    Sang-Mook Lee; A. Lynn Abbott; Neil A. Clark; Philip A. Araman

    2004-01-01

    This paper presents a new curve matching method for deformable shapes using two-dimensional splines. In contrast to the residual error criterion, which is based on relative locations of corresponding knot points such that is reliable primarily for dense point sets, we use deformation energy of thin-plate-spline mapping between sparse knot points and normalized local...

  2. Knot strength of nylon-band cerclage.

    PubMed

    Kirby, B M; Wilson, J W

    1989-12-01

    Nylon bands of five sizes were tested to failure using a splint circular jaw mounted on a tensile testing machine. Four treatment groups of each of the five sizes were tested: as supplied by the manufacturer, ethylene oxide sterilized, autoclave sterilized, and saline-soaked. Comparisons were made between groups and to previously reported results of similar testing of stainless steel wire of three sizes. All the bands failed at the lock mechanism. Knot strength increased with increased size of nylon band. There was no difference between untreated and ethylene oxide sterilized bands, whereas bands subjected to autoclaving or saline soaking failed at less force. The knot strength of all the treatment groups in the three smaller sizes of bands was less than twist-knotted 0.8-mm wire cerclage; and when soaked in saline for 24 hours, the knot strength of the two largest size bands dropped to less than 1.2-mm twist-knotted wire.

  3. A pseudo-haptic knot diagram interface

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Weng, Jianguang; Hanson, Andrew J.

    2011-01-01

    To make progress in understanding knot theory, we will need to interact with the projected representations of mathematical knots which are of course continuous in 3D but significantly interrupted in the projective images. One way to achieve such a goal would be to design an interactive system that allows us to sketch 2D knot diagrams by taking advantage of a collision-sensing controller and explore their underlying smooth structures through a continuous motion. Recent advances of interaction techniques have been made that allow progress to be made in this direction. Pseudo-haptics that simulates haptic effects using pure visual feedback can be used to develop such an interactive system. This paper outlines one such pseudo-haptic knot diagram interface. Our interface derives from the familiar pencil-and-paper process of drawing 2D knot diagrams and provides haptic-like sensations to facilitate the creation and exploration of knot diagrams. A centerpiece of the interaction model simulates a "physically" reactive mouse cursor, which is exploited to resolve the apparent conflict between the continuous structure of the actual smooth knot and the visual discontinuities in the knot diagram representation. Another value in exploiting pseudo-haptics is that an acceleration (or deceleration) of the mouse cursor (or surface locator) can be used to indicate the slope of the curve (or surface) of whom the projective image is being explored. By exploiting these additional visual cues, we proceed to a full-featured extension to a pseudo-haptic 4D visualization system that simulates the continuous navigation on 4D objects and allows us to sense the bumps and holes in the fourth dimension. Preliminary tests of the software show that main features of the interface overcome some expected perceptual limitations in our interaction with 2D knot diagrams of 3D knots and 3D projective images of 4D mathematical objects.

  4. In Search of Functional Advantages of Knots in Proteins

    PubMed Central

    Dabrowski-Tumanski, Pawel; Sulkowska, Joanna I.

    2016-01-01

    We analysed the structure of deeply knotted proteins representing three unrelated families of knotted proteins. We looked at the correlation between positions of knotted cores in these proteins and such local structural characteristics as the number of intra-chain contacts, structural stability and solvent accessibility. We observed that the knotted cores and especially their borders showed strong enrichment in the number of contacts. These regions showed also increased thermal stability, whereas their solvent accessibility was decreased. Interestingly, the active sites within these knotted proteins preferentially located in the regions with increased number of contacts that also have increased thermal stability and decreased solvent accessibility. Our results suggest that knotting of polypeptide chains provides a favourable environment for the active sites observed in knotted proteins. Some knotted proteins have homologues without a knot. Interestingly, these unknotted homologues form local entanglements that retain structural characteristics of the knotted cores. PMID:27806097

  5. The Length Scale of 3-Space Knots, Ephemeral Knots, and Slipknots in Random Walks

    NASA Astrophysics Data System (ADS)

    Millett, K. C.

    The probability that a random walk or polygon in the 3-space or in the simple cubic lattice contains a small knot, an ephemeral knot, or a slipknot goes to one as the length goes to infinity. The probability that a polygon or walk contains a ``global'' knot also goes to one as the length goes to infinity. What immerges is a highly complex picture of the length scale of knotting in polygons and walks. Here we study the average scale of knots, ephemeral knots, and slipknots in 3-space random walks, paying special attention to the probability of their occurance and to the growth of their average sizes as a function of the length of the walk.

  6. Molecular knots in biology and chemistry

    NASA Astrophysics Data System (ADS)

    Lim, Nicole C. H.; Jackson, Sophie E.

    2015-09-01

    Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.

  7. A knotted free minicircle in kinetoplast DNA.

    PubMed

    Ryan, K A; Shapiro, T A; Rauch, C A; Griffith, J D; Englund, P T

    1988-08-01

    Kinetoplast DNA, the mitochondrial DNA of trypanosomes, is a network containing thousands of minicircles that are topologically interlocked. The minicircle replication intermediates are free molecules that have been released from the network. We report here that one form of free minicircles is a trefoil knot. Identification of this knotted structure is based on its electrophoretic and sedimentation properties, its response to treatments with restriction enzymes or topoisomerase II, and its appearance by electron microscopy. Except for its topology, the knotted minicircle closely resembles a previously described replication intermediate with a unique gap in the newly synthesized L strand.

  8. Energy functions for knots: Beginning to predict physical behavior

    SciTech Connect

    Simon, J.

    1996-12-31

    Several definitions have been proposed for the {open_quotes}energy{close_quotes} of a knot. The intuitive goal is to define a number u(K) that somehow measures how {open_quotes}tangled{close_quotes} or {open_quotes}crumpled{close_quotes} a knot K is. Typically, one starts with the idea that a small piece of the knot somehow repels other pieces, and then adds up the contributions from all the pieces. From a purely mathematical standpoint, one may hope to define new knot-type invariants, e.g by considering the minimum of u(K) as K ranges over all the knots of a given knot-type. We also are motivated by the desire to understand and predict how knot-type affects the behavior of physically real knots, in particular DNA loops in gel electrophoresis or random knotting experiments. Despite the physical naivete of recently studied knot energies, there now is enough laboratory data on relative gel velocity, along with computer calculations of idealized knot energies, to justify the assertion that knot energies can predict relative knot behavior in physical systems. The relationships between random knot frequencies and either gel velocities or knot energies is less clear at this time. 50 refs., 8 figs., 2 tabs.

  9. Knot theory realizations in nematic colloids

    PubMed Central

    Čopar, Simon; Tkalec, Uroš; Muševič, Igor; Žumer, Slobodan

    2015-01-01

    Nematic braids are reconfigurable knots and links formed by the disclination loops that entangle colloidal particles dispersed in a nematic liquid crystal. We focus on entangled nematic disclinations in thin twisted nematic layers stabilized by 2D arrays of colloidal particles that can be controlled with laser tweezers. We take the experimentally assembled structures and demonstrate the correspondence of the knot invariants, constructed graphs, and surfaces associated with the disclination loop to the physically observable features specific to the geometry at hand. The nematic nature of the medium adds additional topological parameters to the conventional results of knot theory, which couple with the knot topology and introduce order into the phase diagram of possible structures. The crystalline order allows the simplified construction of the Jones polynomial and medial graphs, and the steps in the construction algorithm are mirrored in the physics of liquid crystals. PMID:25624467

  10. Cotranslational folding of deeply knotted proteins

    NASA Astrophysics Data System (ADS)

    Chwastyk, Mateusz; Cieplak, Marek

    2015-09-01

    Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.

  11. Cotranslational folding of deeply knotted proteins.

    PubMed

    Chwastyk, Mateusz; Cieplak, Marek

    2015-09-09

    Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.

  12. Size of knots in ring polymers.

    PubMed

    Marcone, B; Orlandini, E; Stella, A L; Zonta, F

    2007-04-01

    We give two different, statistically consistent definitions of the length l of a prime knot tied into a polymer ring. In the good solvent regime the polymer is modeled by a self avoiding polygon of N steps on cubic lattice and l is the number of steps over which the knot "spreads" in a given configuration. An analysis of extensive Monte Carlo data in equilibrium shows that the probability distribution of l as a function of N obeys a scaling of the form p(l,N) approximately l(-c)f(l/N(D)) , with c approximately equal to 1.25 and D approximately equal to 1. Both D and c could be independent of knot type. As a consequence, the knot is weakly localized, i.e., approximately N(t) , with t=2-c approximately equal to 0.75 . For a ring with fixed knot type, weak localization implies the existence of a peculiar characteristic length l(nu) approximately N(tnu) . In the scaling approximately N(nu) (nu approximately equal to 0.58) of the radius of gyration of the whole ring, this length determines a leading power law correction which is much stronger than that found in the case of unrestricted topology. The existence of this correction is confirmed by an analysis of extensive Monte Carlo data for the radius of gyration. The collapsed regime is studied by introducing in the model sufficiently strong attractive interactions for nearest neighbor sites visited by the self-avoiding polygon. In this regime knot length determinations can be based on the entropic competition between two knotted loops separated by a slip link. These measurements enable us to conclude that each knot is delocalized (t approximately equal to 1) .

  13. On rectangular HOMFLY for twist knots

    NASA Astrophysics Data System (ADS)

    Kononov, Ya.; Morozov, A.

    2016-11-01

    As a new step in the study of rectangularly-colored knot polynomials, we reformulate the prescription [A. Morozov, arXiv:1606.06015v8] for twist knots in the double-column representations R = [rr] in terms of skew Schur polynomials. These, however, are mysteriously shifted from the standard topological locus, which makes further generalization to arbitrary R = [rs] not quite straightforward.

  14. Diagnosis of true umbilical cord knot

    PubMed Central

    Kowalczyk, Dariusz; Więcek, Jacek

    2013-01-01

    Introduction Many abnormalities are observed in the morphology and pathology of the umbilical cord. The aim of the study was to assess the role of 3D sonography in pathology of true umbilical cord knots. Material and methods In our materials we observed 10 cases of true umbilical cord knots in a population of 2,864 deliveries. The 2-dimensional transverse scan of the umbilical cord was shown in 3- and 4-dimensional volume scan in order to get a precise image. Results Four knots were diagnosed prenatally, 3 knots were not diagnosed before the delivery and in the 3 remaining cases ultrasound examinations were not undertaken because the patients were in the course of delivery. In the pregnant subjects with diagnosed true umbilical cord knot once a week the Doppler blood flow indices were examined in the umbilical cord sections before and after the knot. In the three shown cases there were no signs of constriction or tightening of the knot. Four newborns were delivered spontaneously and five by caesarean section. In none of the cases was a pathological FHR trace an indication for emergency delivery. Conclusions Four-dimensional and Color Doppler examination is very important to diagnose a true umbilical cord. To make a precise diagnosis a longer observation of the abnormality is necessary and its repeated confirmation by color Doppler and power Doppler. This diagnosis requires strict monitoring of fetal wellbeing during pregnancy and the delivery. Perfection of true umbilical cord knot diagnoses may reduce sudden and unforeseen fetal distress. PMID:24701220

  15. Magnetic surface topology in decaying plasma knots

    NASA Astrophysics Data System (ADS)

    Smiet, C. B.; Thompson, A.; Bouwmeester, P.; Bouwmeester, D.

    2017-02-01

    Torus-knot solitons have recently been formulated as solutions to the ideal incompressible magnetohydrodynamics (MHD) equations. We investigate numerically how these fields evolve in resistive, compressible, and viscous MHD. We find that certain decaying plasma torus knots exhibit magnetic surfaces that are topologically distinct from a torus. The evolution is predominantly determined by a persistent zero line in the field present when the poloidal winding number {n}{{p}}\

  16. Counterexamples to Moffatt's statements on vortex knots.

    PubMed

    Bogoyavlenskij, Oleg

    2017-04-01

    One of the well-known problems of hydrodynamics is studied: the problem of classification of vortex knots for ideal fluid flows. In the literature there are known Moffatt statements that all torus knots K_{m,n} for all rational numbers m/n (0knots for each one of the considered axisymmetric fluid flows. We prove that actually such a uniformity does not exist because it does not correspond to the facts. Namely, we derive a complete classification of all vortex knots realized for the fluid flows studied by Moffatt and demonstrate that the real structure of vortex knots is much more rich because the sets of mutually nonisotopic vortex knots realized for different axisymmetric fluid flows are all different. An exact formula for the limit of the hydrodynamic safety factor q_{h} at a vortex axis is derived for arbitrary axisymmetric fluid equilibria. Another exact formula is obtained for the limit of the magnetohydrodynamics safety factor q at a magnetic axis for the general axisymmetric plasma equilibria.

  17. Counterexamples to Moffatt's statements on vortex knots

    NASA Astrophysics Data System (ADS)

    Bogoyavlenskij, Oleg

    2017-04-01

    One of the well-known problems of hydrodynamics is studied: the problem of classification of vortex knots for ideal fluid flows. In the literature there are known Moffatt statements that all torus knots Km ,n for all rational numbers m /n (0 knots for each one of the considered axisymmetric fluid flows. We prove that actually such a uniformity does not exist because it does not correspond to the facts. Namely, we derive a complete classification of all vortex knots realized for the fluid flows studied by Moffatt and demonstrate that the real structure of vortex knots is much more rich because the sets of mutually nonisotopic vortex knots realized for different axisymmetric fluid flows are all different. An exact formula for the limit of the hydrodynamic safety factor qh at a vortex axis is derived for arbitrary axisymmetric fluid equilibria. Another exact formula is obtained for the limit of the magnetohydrodynamics safety factor q at a magnetic axis for the general axisymmetric plasma equilibria.

  18. Self-assembly of knots and links

    NASA Astrophysics Data System (ADS)

    Orlandini, Enzo; Polles, Guido; Marenduzzo, Davide; Micheletti, Cristian

    2017-03-01

    Guiding the self-assembly of identical building blocks towards complex three-dimensional structures with a set of desired properties is a major goal in material science, chemistry and physics. A particularly challenging problem, especially explored in synthetic chemistry, is that of self-assembling closed structures with a target topology starting by simple geometrical templates. Here we overview and revisit recent advancements, based on stochastic simulations, where the geometry of rigid helical templates with functionalised sticky ends has been designed for self-assembling efficiently and reproducibly into a wide range of three-dimensional closed structures. Notably, these include non trivial topologies of links and knots, including the 819 knot that we had predicted to be highly encodable and that has only recently been obtained experimentally. By appropriately tuning the parameters that define the template shape, we show that, for fixed concentration of templates, the assembly process can be directed towards the formation of specific knotted and linked structures such as the trefoils, pentafoil knots, Hopf and Solomon links. More exotic and unexpected knots and links are also found. Our results should be relevant to the design of new protocols that can both increase and broaden the population of synthetise molecular knots and catenanes.

  19. Absence of knots in known RNA structures

    PubMed Central

    Micheletti, Cristian; Di Stefano, Marco; Orland, Henri

    2015-01-01

    The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also, abound in viral DNA packaged inside bacteriophages. RNA molecules, however, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the several thousand RNA structures present in the Protein Data Bank (PDB). The search identified no more than three deeply knotted RNA molecules. These entries are rRNAs of about 3,000 nt solved by cryo-EM. Their genuine knotted state is, however, doubtful based on the detailed structural comparison with homologs of higher resolution, which are all unknotted. Compared with the case of proteins and viral DNA, the observed incidence of knots in available RNA structures is, therefore, practically negligible. This fact suggests that either evolutionary selection or thermodynamic and kinetic folding mechanisms act toward minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. A possible general strategy for designing synthetic RNA sequences capable of self-tying in a twist-knot fold is finally proposed. PMID:25646433

  20. Arthroscopic suture material and knot type: an updated biomechanical analysis.

    PubMed

    Swan, Kenneth G; Baldini, Todd; McCarty, Eric C

    2009-08-01

    Several new arthroscopic suture materials are available. It is important for surgeons to know which suture-knot combination provides the strongest construct. The newer, polyblend sutures have dissimilar load-to-failure characteristics. Controlled laboratory study. The load to failure of 4 knots was evaluated (surgeon's, Duncan loop, Samsung Medical Center [SMC], and Roeder) using 5 No. 2 suture materials (Ethibond, Ticron, FiberWire, ForceFiber, MaxBraid). One surgeon tied all knots. Fifteen samples were tested for each suture-knot configuration. Knots were pretensioned to 10 N, then loaded to failure at a rate of 1.0 mm/s. Failure load recorded was the maximum load applied between 0 and 3 mm of displacement. Cyclic loading of suture-knot samples was performed on 3 knots (surgeon's, Duncan loop, and SMC) using 4 suture materials (Ethibond, FiberWire, ForceFiber, MaxBraid). Six samples were tested for each suture-knot configuration. Knots were cyclically loaded from 5 to 40 N at 0.5 Hz for 1000 cycles, then loaded to failure. Data were compared with analysis of variance and the Tukey multiple range test and considered significant at P < .05. The surgeon's and SMC knots were strongest, particularly if tied using MaxBraid or ForceFiber. With single load-to-failure testing, MaxBraid was significantly stronger than Ethibond, Ticron, or FiberWire, regardless of knot type used. ForceFiber was stronger than Ethibond and Ticron with any knot type, and stronger than FiberWire when tied with a surgeon's knot or Roeder knot. The MaxBraid surgeon's knot (246 N) and MaxBraid SMC knot (239 N) were more than twice as strong as the Ethibond surgeon's knot (111 N) and Ethibond SMC (118 N). With cyclic loading, MaxBraid and ForceFiber were stronger than FiberWire and Ethibond, regardless of knot type tied. The SMC knot using MaxBraid withstood the highest load, and was stronger than the Duncan loop tied with MaxBraid. When stricter criteria (1-mm and 2-mm displacement) for failure

  1. Statistics of knots, geometry of conformations, and evolution of proteins.

    PubMed

    Lua, Rhonald C; Grosberg, Alexander Y

    2006-05-01

    Like shoelaces, the backbones of proteins may get entangled and form knots. However, only a few knots in native proteins have been identified so far. To more quantitatively assess the rarity of knots in proteins, we make an explicit comparison between the knotting probabilities in native proteins and in random compact loops. We identify knots in proteins statistically, applying the mathematics of knot invariants to the loops obtained by complementing the protein backbone with an ensemble of random closures, and assigning a certain knot type to a given protein if and only if this knot dominates the closure statistics (which tells us that the knot is determined by the protein and not by a particular method of closure). We also examine the local fractal or geometrical properties of proteins via computational measurements of the end-to-end distance and the degree of interpenetration of its subchains. Although we did identify some rather complex knots, we show that native conformations of proteins have statistically fewer knots than random compact loops, and that the local geometrical properties, such as the crumpled character of the conformations at a certain range of scales, are consistent with the rarity of knots. From these, we may conclude that the known "protein universe" (set of native conformations) avoids knots. However, the precise reason for this is unknown--for instance, if knots were removed by evolution due to their unfavorable effect on protein folding or function or due to some other unidentified property of protein evolution.

  2. Tight knots in proteins: can they block the mitochondrial pores?

    PubMed

    Szymczak, Piotr

    2013-04-01

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process since the diameter of the pore is smaller than the size of maximally tightened knot. In the present article, I briefly review the experimental and numerical studies of tight knots in proteins, with a particular emphasis on the estimates of the size of these knots. Next, I discuss the process of protein translocation through the mitochondrial pores and report the results of molecular dynamics simulations of knotted protein translocation, which show how the knot can indeed block the pore.

  3. Origin of metastable knots in single flexible chains.

    PubMed

    Dai, Liang; Renner, C Benjamin; Doyle, Patrick S

    2015-01-23

    Recent theoretical progress has explained the physics of knotting of semiflexible polymers, yet knotting of flexible polymers is relatively unexplored. We herein develop a new theory for the size distribution of knots on a flexible polymer and the existence of metastable knots. We show the free energy of a flexible molecule in a tube can be mapped to quantitatively reproduce the free energy distribution of a knot on a flexible chain. The size distribution of knots on flexible chains is expected to be universal and might be observed at a macroscopic scale, such as a string of hard balls.

  4. Comparing models of Red Knot population dynamics

    USGS Publications Warehouse

    McGowan, Conor

    2015-01-01

    Predictive population modeling contributes to our basic scientific understanding of population dynamics, but can also inform management decisions by evaluating alternative actions in virtual environments. Quantitative models mathematically reflect scientific hypotheses about how a system functions. In Delaware Bay, mid-Atlantic Coast, USA, to more effectively manage horseshoe crab (Limulus polyphemus) harvests and protect Red Knot (Calidris canutus rufa) populations, models are used to compare harvest actions and predict the impacts on crab and knot populations. Management has been chiefly driven by the core hypothesis that horseshoe crab egg abundance governs the survival and reproduction of migrating Red Knots that stopover in the Bay during spring migration. However, recently, hypotheses proposing that knot dynamics are governed by cyclical lemming dynamics garnered some support in data analyses. In this paper, I present alternative models of Red Knot population dynamics to reflect alternative hypotheses. Using 2 models with different lemming population cycle lengths and 2 models with different horseshoe crab effects, I project the knot population into the future under environmental stochasticity and parametric uncertainty with each model. I then compare each model's predictions to 10 yr of population monitoring from Delaware Bay. Using Bayes' theorem and model weight updating, models can accrue weight or support for one or another hypothesis of population dynamics. With 4 models of Red Knot population dynamics and only 10 yr of data, no hypothesis clearly predicted population count data better than another. The collapsed lemming cycle model performed best, accruing ~35% of the model weight, followed closely by the horseshoe crab egg abundance model, which accrued ~30% of the weight. The models that predicted no decline or stable populations (i.e. the 4-yr lemming cycle model and the weak horseshoe crab effect model) were the most weakly supported.

  5. The inner knot of the Crab nebula

    NASA Astrophysics Data System (ADS)

    Lyutikov, Maxim; Komissarov, Serguei S.; Porth, Oliver

    2016-02-01

    We model the inner knot of the Crab nebula as a synchrotron emission coming from the non-spherical MHD termination shock of relativistic pulsar wind. The post-shock flow is mildly relativistic; as a result the Doppler beaming has a strong impact on the shock appearance. The model can reproduce the knot location, size, elongation, brightness distribution, luminosity and polarization provided the effective magnetization of the section of the pulsar wind producing the knot is low, σ ≤ 1. In the striped wind model, this implies that the striped zone is rather wide, with the magnetic inclination angle of the Crab pulsar ≥45°; this agrees with the previous model-dependent estimate based on the gamma-ray emission of the pulsar. We conclude that the tiny knot is indeed a bright spot on the surface of a quasi-stationary magnetic relativistic shock and that this shock is a site of efficient particle acceleration. On the other hand, the deduced low magnetization of the knot plasma implies that this is an unlikely site for the Crab's gamma-ray flares, if they are related to the fast relativistic magnetic reconnection events.

  6. Conservation of complex knotting and slipknotting patterns in proteins.

    PubMed

    Sułkowska, Joanna I; Rawdon, Eric J; Millett, Kenneth C; Onuchic, Jose N; Stasiak, Andrzej

    2012-06-26

    While analyzing all available protein structures for the presence of knots and slipknots, we detected a strict conservation of complex knotting patterns within and between several protein families despite their large sequence divergence. Because protein folding pathways leading to knotted native protein structures are slower and less efficient than those leading to unknotted proteins with similar size and sequence, the strict conservation of the knotting patterns indicates an important physiological role of knots and slipknots in these proteins. Although little is known about the functional role of knots, recent studies have demonstrated a protein-stabilizing ability of knots and slipknots. Some of the conserved knotting patterns occur in proteins forming transmembrane channels where the slipknot loop seems to strap together the transmembrane helices forming the channel.

  7. On the character variety of periodic knots and links

    NASA Astrophysics Data System (ADS)

    Hilden, Hugh M.; Lozano, María Teresa; Montesinos-Amilibia, José María

    2000-11-01

    For a hyperbolic knot, the excellent component of the character curve is the one containing the complete hyperbolic structure on the complement of the knot. In this paper we explain a method to compute the excellent component of the character variety of periodic knots. We apply the method to those knots obtained as the preimage of one component of a 2-bridge link by a cyclic covering of S3 branched on the other component. We call these knots periodic knots with rational quotient. Among this class of knots are the ‘Turk's head knots’. Finally we give some invariants deduced from the excellent component of the character curve, such as the h-polynomial and the limit of hyperbolicity for all the periodic knots with rational quotient, up to 10 crossings, which are not 2-bridge or toroidal.

  8. Untangling the Influence of a Protein Knot on Folding.

    PubMed

    Capraro, Dominique T; Jennings, Patricia A

    2016-03-08

    Entanglement and knots occur across all aspects of the physical world. Despite the common belief that knots are too complicated for incorporation into proteins, knots have been identified in the native fold of a growing number of proteins. The discovery of proteins with this unique backbone characteristic has challenged the preconceptions about the complexity of biological structures, as well as current folding theories. Given the intricacies of the knotted geometry, the interplay between a protein's fold, structure, and function is of particular interest. Interestingly, for most of these proteins, the knotted region appears critical both in folding and function, although full understanding of these contributions is still incomplete. Here, we experimentally reveal the impact of the knot on the landscape, the origin of the bistable nature of the knotted protein, and broaden the view of knot formation as uniquely decoupled from folding.

  9. Nonlinear electrodynamics is skilled with knots

    NASA Astrophysics Data System (ADS)

    Goulart, E.

    2016-07-01

    The aim of this letter is threefold: First is to show that nonlinear generalizations of electrodynamics support various types of knotted solutions in vacuum. The solutions are universal in the sense that they do not depend on the specific Lagrangian density, at least if the latter gives rise to a well-posed theory. Second, is to describe the interaction between probe waves and knotted background configurations. We show that the qualitative behaviour of this interaction may be described in terms of Robinson congruences, which appear explicitly in the causal structure of the theory. Finally, we argue that optical arrangements endowed with intense background fields could be the natural place to look for the knots experimentally.

  10. Are there p-adic knot invariants?

    NASA Astrophysics Data System (ADS)

    Morozov, A. Yu.

    2016-04-01

    We suggest using the Hall-Littlewood version of the Rosso-Jones formula to define the germs of p-adic HOMFLY-PT polynomials for torus knots [ m, n] as coefficients of superpolynomials in a q-expansion. In this form, they have at least the [ m, n] ↔ [ n, m] topological invariance. This opens a new possibility to interpret superpolynomials as p-adic deformations of HOMFLY polynomials and poses a question of generalizing to other knot families, which is a substantial problem for several branches of modern theory.

  11. The Miller׳s knot as an alternative to the surgical knotting? Characterization of the mechanical behavior.

    PubMed

    Ortillés, A; Rodríguez, J; Calvo, B

    2014-10-01

    Several types of materials and surgical suture patterns are used in conventional surgery. Their combination with an appropriate knot is the basis for correct tissue apposition and healing. Knot security is essential to prevent loosening or slipping before the suture line is completely closed. Nevertheless, the knot itself is the weakest link in any surgical handling. The aim of this study is to determine and compare the mechanical behavior of four surgical knot types (square knot, surgeon׳s knot, square slipknot and Miller׳s knot) performed with three different suture materials (absorbable monofilament glyconate, non-absorbable monofilament polyamide and absorbable braided polyglycolic acid) in a non-biological experimental in vitro model (a tube of synthetic material with non-linear mechanical behavior). The mechanical properties of each suture material are also compared. Ten samples were mechanically tested for each suture and knot using a uniaxial tensile test until complete sample rupture. The failure Cauchy stress and stretch were calculated. The Cauchy stress at 5%, 10% and 15% strain and standard deviation were compared for each suture and knot type. The results demonstrated that all the suture materials had statistically significant differences in their non-linear mechanical behavior. Absorbable monofilament glyconate was the most compliant suture with the greatest tensile strength, while absorbable braided polyglycolic acid was the stiffest. Regardless of the suture type used, the Miller׳s knot had the greatest failure Cauchy stress and stretch, while the square, surgeon׳s and square slipknot had the lowest. In all cases, the Miller׳s knot was more compliant and had greater tensile strength than the other knots. The square knot, surgeon׳s knot, and square slipknot had statistically significant similarities in their mechanical behavior. Therefore, the Miller׳s knot could be classified as the gold standard and an alternative to the surgical knotting

  12. Heat treatment of arthroscopic knots and its effect on knot security.

    PubMed

    Williams, Derfel Pari; Hughes, Peter J; Fisher, Anthony C; Doherty, Patrick

    2008-01-01

    The purpose of this study was to investigate heat application to arthroscopic knots as a method of improving knot security. Heat treatment was assessed on 4 suture materials--Ethibond (Ethicon, Somerville, NJ), PDS (Ethicon), Orthocord (DePuy Mitek, Raynham, MA), and FiberWire (Arthrex, Naples, FL)--tied by use of the Duncan loop, compared with untreated controls. A hand-tied surgeon's knot with Ethibond was included as the gold standard. Knots were tied around a plastic rod immersed in a saline solution-filled water bath at 37 degrees C, with heat treatment performed by use of the Mitek VAPR 3 electrosurgical unit and VAPR S(90) electrode (DePuy Mitek), applied directly to the knot body. Loops were subjected to a 5-N preload, followed by loading to clinical failure (>3 mm of displacement) and ultimate (breaking) failure by use of a tensile tester. Load to ultimate failure was significantly higher in the FiberWire 1-second heat treatment arm (26.0% increase, 234.25 +/- 62.34 N, P < .03), Orthocord 1-second heat treatment arm (55.6% increase, 204.72 +/- 78.47 N, P < .03), and Orthocord 5-second heat treatment arm (69.2% increase, 222.58 +/- 56.57 N, P < .001) than in controls. Load to clinical failure was significantly higher in the Orthocord 10-second heat treatment arm (34.7% increase, 78.58 +/- 13.88 N, P < .0001) when compared with controls. The FiberWire 5- and 10-second heat treatment arms showed lower load to clinical and ultimate failure (P < .001). Ethibond, Orthocord, and FiberWire showed higher load to clinical failure than PDS (P < .0001). Ethibond and Orthocord knots were more likely to fail through knot slippage after heat treatment compared with controls (P < .01). Heat treatment resulted in greater knot security when combined with Orthocord and FiberWire suture materials. Heat-treated Ethibond and Orthocord knots were more likely to fail through suture breakage than knot slippage. This study presents a simple and novel technique of improving knot

  13. Knotting probability of a shaken ball-chain.

    PubMed

    Hickford, J; Jones, R; du Pont, S Courrech; Eggers, J

    2006-11-01

    We study the formation of knots on a macroscopic ball chain, which is shaken on a horizontal plate at 12 times the acceleration of gravity. We find that above a certain critical length, the knotting probability is independent of chain length, while the time to shake out a knot increases rapidly with chain length. The probability of finding a knot after a certain time is the result of the balance of these two processes. In particular, the knotting probability tends to a constant for long chains.

  14. Knotted proteins: A tangled tale of Structural Biology

    PubMed Central

    Faísca, Patrícia F.N.

    2015-01-01

    Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research. PMID:26380658

  15. Vortex knots in a Bose-Einstein condensate.

    PubMed

    Proment, Davide; Onorato, Miguel; Barenghi, Carlo F

    2012-03-01

    We present a method for numerically building a vortex knot state in the superfluid wave function of a Bose-Einstein condensate. We integrate in time the governing Gross-Pitaevskii equation to determine evolution and shape preservation of the two (topologically) simplest vortex knots which can be wrapped over a torus. We find that the velocity of a vortex knot depends on the ratio of poloidal and toroidal radius: for smaller ratio, the knot travels faster. Finally, we show how vortex knots break up into vortex rings.

  16. "Knots on a Counting Rope": Teaching Stories.

    ERIC Educational Resources Information Center

    Key, Daphne

    2001-01-01

    Argues that reflecting on important "marker" stories in people's lives by using counting ropes (based on the children's book "Knots on a Counting Rope" by Bill Martin Jr. and John Archambault) helps students and teachers make sense of their complex worlds. Describes how they are used in the author's language arts methods course. Describes a…

  17. The constrictor knot is the best ligature.

    PubMed

    Taylor, H; Grogono, A W

    2014-03-01

    An ideal ligature should tighten readily and remain tight. Ligature failure can be a critical complication of invasive procedures in human and veterinary surgical practice. Previous studies have tested various knots but not the constrictor knot. A new test bench was employed to compare six ligatures using four suture materials. As tension in a ligature is not readily measured, the study employed a surrogate measurement: the force required to slide a ligature along a rod. Benchmark values tested each suture material wrapped around the rod to establish the ratio between this force and the ligature tension for each material. Each ligature was tested first during tightening and then again afterwards. The benchmark ratios were employed to calculate the tensions to evaluate which ligature and which suture material retained tension best. The model provided consistent linear relationships between the tension in the suture and the force required to pull the ligature along the rod. The constrictor knot retained tension in the ligature best (55-107% better than the next best ligature). Among the suture materials, polydioxanone had the greatest ability to retain the tension in a ligature and polyglactin the least. The constrictor knot showed superior characteristics for use as a ligature, and should be introduced into teaching and clinical practice for human and veterinary surgery. The new test bench is recommended for future testing of ligatures as well as objective comparison of suture materials.

  18. A preliminary design of a knot undulator.

    PubMed

    Xi, Fuchun; Shi, Tan; Fan, Qingyan; Prestemon, Soren; Wan, Weishi; An, Zhenghua; Qiao, S

    2013-01-01

    The magnetic field configuration of the previously proposed knot undulator [Qiao et al. (2009). Rev. Sci. Instrum. 80, 085108] is realised in the design of a hybridized elliptically polarized undulator, which is presented. Although the details of the field distribution are not the same as those in the theoretical proposal, it is demonstrated that the practical knot undulator could work perfectly. In order to understand the minor discrepancies of the two, mathematical formulae of the synchrotron radiation are derived based on the Fourier transform of the magnetic field. From the results of calculations by simulation program, the discrepancies could be well interpreted by the corresponding formulae. The results show the importance of optimization of the end sections of the knot undulator to suppress the on-axis heat load. Furthermore, a study of the impact of the undulator on beam dynamics of the storage ring was conducted using the Shanghai Synchrotron Radiation Facility as an example and the results show that the knot undulator has little effect on the beam.

  19. Decay of helical and nonhelical magnetic knots

    NASA Astrophysics Data System (ADS)

    Candelaresi, Simon; Brandenburg, Axel

    2011-07-01

    We present calculations of the relaxation of magnetic field structures that have the shape of particular knots and links. A set of helical magnetic flux configurations is considered, which we call n-foil knots of which the trefoil knot is the most primitive member. We also consider two nonhelical knots; namely, the Borromean rings as well as a single interlocked flux rope that also serves as the logo of the Inter-University Centre for Astronomy and Astrophysics in Pune, India. The field decay characteristics of both configurations is investigated and compared with previous calculations of helical and nonhelical triple-ring configurations. Unlike earlier nonhelical configurations, the present ones cannot trivially be reduced via flux annihilation to a single ring. For the n-foil knots the decay is described by power laws that range form t-2/3 to t-1/3, which can be as slow as the t-1/3 behavior for helical triple-ring structures that were seen in earlier work. The two nonhelical configurations decay like t-1, which is somewhat slower than the previously obtained t-3/2 behavior in the decay of interlocked rings with zero magnetic helicity. We attribute the difference to the creation of local structures that contain magnetic helicity which inhibits the field decay due to the existence of a lower bound imposed by the realizability condition. We show that net magnetic helicity can be produced resistively as a result of a slight imbalance between mutually canceling helical pieces as they are being driven apart. We speculate that higher order topological invariants beyond magnetic helicity may also be responsible for slowing down the decay of the two more complicated nonhelical structures mentioned above.

  20. Effect of knots on binding of intercalators to DNA

    NASA Astrophysics Data System (ADS)

    Medalion, Shlomi; Rabin, Yitzhak

    2014-05-01

    We study the effect of knots in circular dsDNA molecules on the binding of intercalating ligands. Using Monte Carlo simulations we show that depending on their handedness, the presence of knots can either suppress or enhance intercalation in supercoiled DNA. When the occupancy of intercalators on DNA is low, the effect of knots on intercalation can be captured by introducing a shift in the mean writhe of the chain that accounts for the writhe of the corresponding ideal knot. In the limit of high intercalator occupancy, the writhe distribution of different knots is strongly affected by excluded volume effects and therefore by salt concentration. Based on the finding that different knots yield well-separated probability distributions of bound intercalators, we propose a new experimental approach to determine DNA topology by monitoring the intensity of fluorescence emitted by dye molecules intercalated into knotted DNA molecules.

  1. In vitro comparison of secure Aberdeen and square knots with plasma- and fat-coated polydioxanone.

    PubMed

    Schaaf, Olaf; Glyde, Mark; Day, Robert E

    2010-07-01

    To determine (1) the minimum number of throws to form secure Aberdeen (AB) and square knots to start (SS) and end (SE) continuous patterns, in fat- and plasma-coated polydioxanone; and (2) compare relative knot security (RKS) and knot volumes of these secure SS, SE, and AB knots. In vitro experimental materials testing. Polydioxanone suture material (3 metric). Each knot was tested 20 times, and throws incrementally added until secure SS, SE, and AB knots were found. RKS and knot volumes were calculated for SS, SE, and AB knots. Secure SE knots needed 5 throws in plasma or fat. Secure SS knots needed 4 throws in plasma, but 5 in fat. The minimum AB configuration that was secure in plasma or fat was 3+1, however, the 4+1 AB knot was also secure in fat. Mean (SD) RKS of secure knots were: SE 59.69% (5.91), SS 67.92% (12.50), AB 81.08% (8.99). AB knots had significantly higher mean RKS than any SS or SE knot in plasma or fat (P<.001). Mean knot volume of 3+1 AB knot was significantly smaller than any secure SS or SE knots by 22.6-69.4% (P<.0001). Mean knot volume of 4+1 AB knots was significantly smaller than all fat secure SS and SE knots by 19.9-57.5% (P=.0001). The knot security of the SS knot was decreased by fat coating polydioxanone suture, requiring an additional throw to keep it secure. Secure AB knots had a higher breaking strength and smaller knot volume than secure SS and SE knots. The AB may be preferable to square knots in continuous closures. As many body fluids contain lipid, surgeons should tie knot configurations considered secure in fat. We advise tying a 4+1 AB and placing a minimum of 5 throws to tie SS and SE knots using 3 metric polydioxanone.

  2. Twist knot cerclage wire: the appropriate wire tension for knot construction and fracture stability.

    PubMed

    Harnroongroj, Thossart

    1998-09-01

    OBJECTIVE: The aim was to find the best wire tension in order to permit a reliable first twist and simultaneously provide the best stability of fracture fixation from the twist knot cerclage wire. DESIGN: Wires at different distal tensions, looped around the fracture, were measured during twist and compared with the yield strength of the wire. Then, the fracture stability of the twist knot cerclage wire was determined from the pull-out strength. METHODS: In order to measure wire tension during twist knot construction, an instrument was designed using the tension load cell of a universal testing machine, a 15 degrees oblique osteotomy femoral shaft and 1.25 mm diameter wire. A wire tensioner and a pair of extraction grips were then used for measuring the pull-out strength of the cerclage wire fixation. RESULT: Three wire tensions (160, 200 and 240 N) were used as looped wire for the first twist knot construction. The 200 N tension cerclage wire provided the best fracture stability. CONCLUSION: It was found that 200 N was the best wire tension for the construction of a twist knot cerclage wire. RELEVANCE: When a cerclage wire is twisted at a femoral shaft using 1.25 mm diameter wire, a wire tension of 200 N should be used to achieve a reliable first twist and the best stability of fracture fixation.

  3. Parity and cobordism of free knots

    SciTech Connect

    Manturov, Vassily O

    2012-02-28

    A simple invariant is constructed which obstructs a free knot to be truncated. In particular, this invariant provides an obstruction to the truncatedness of curves immersed in two-dimensional surfaces. A curve on an oriented two-dimensional surface S{sub g} is referred to as truncated (null-cobordant) if there exists a three-dimensional manifold M with boundary S{sub g} and a smooth proper map of a two-disc to M such that the image of the boundary of the disc coincides with the curve. The problem of truncatedness for free knots is solved in this paper using the notion of parity recently introduced by the author. Bibliography: 12 titles.

  4. Topological knots and links in proteins

    PubMed Central

    Dabrowski-Tumanski, Pawel; Sulkowska, Joanna I.

    2017-01-01

    Twenty years after their discovery, knots in proteins are now quite well understood. They are believed to be functionally advantageous and provide extra stability to protein chains. In this work, we go one step further and search for links—entangled structures, more complex than knots, which consist of several components. We derive conditions that proteins need to meet to be able to form links. We search through the entire Protein Data Bank and identify several sequentially nonhomologous chains that form a Hopf link and a Solomon link. We relate topological properties of these proteins to their function and stability and show that the link topology is characteristic of eukaryotes only. We also explain how the presence of links affects the folding pathways of proteins. Finally, we define necessary conditions to form Borromean rings in proteins and show that no structure in the Protein Data Bank forms a link of this type. PMID:28280100

  5. Topological knots and links in proteins.

    PubMed

    Dabrowski-Tumanski, Pawel; Sulkowska, Joanna I

    2017-03-28

    Twenty years after their discovery, knots in proteins are now quite well understood. They are believed to be functionally advantageous and provide extra stability to protein chains. In this work, we go one step further and search for links-entangled structures, more complex than knots, which consist of several components. We derive conditions that proteins need to meet to be able to form links. We search through the entire Protein Data Bank and identify several sequentially nonhomologous chains that form a Hopf link and a Solomon link. We relate topological properties of these proteins to their function and stability and show that the link topology is characteristic of eukaryotes only. We also explain how the presence of links affects the folding pathways of proteins. Finally, we define necessary conditions to form Borromean rings in proteins and show that no structure in the Protein Data Bank forms a link of this type.

  6. The Vale knot: an intracorporeal slipknot.

    PubMed

    Campbell, D F; Nassar, A H; Tamijmarane, A

    2000-01-01

    Mastering intracorporeal ligation and suturing is an essential skill for the performance of most advanced endoscopic surgical procedures. Although many disposable instruments have become available for various tasks necessitating the construction of sutures and knots; issues of performance, safety, and cost-efficiency remain to be settled. The authors believe that training should aim at the development of manual skills that could realize the clinical and cost-efficiency benefits of using conventional surgical tasks in the endoscopic setting.

  7. Induction effects of torus knots and unknots

    NASA Astrophysics Data System (ADS)

    Oberti, Chiara; Ricca, Renzo L.

    2017-09-01

    Geometric and topological aspects associated with induction effects of field lines in the shape of torus knots/unknots are examined and discussed in detail. Knots are assumed to lie on a mathematical torus of circular cross-section and are parametrized by standard equations. The induced field is computed by direct integration of the Biot-Savart law. Field line patterns of the induced field are obtained and several properties are examined for a large family of knots/unknots up to 51 crossings. The intensity of the induced field at the origin of the reference system (center of the torus) is found to depend linearly on the number of toroidal coils and reaches maximum values near the boundary of the mathematical torus. New analytical estimates and bounds on energy and helicity are established in terms of winding number and minimum crossing number. These results find useful applications in several contexts when the source field is either vorticity, electric current or magnetic field, from vortex dynamics to astrophysics and plasma physics, where highly braided magnetic fields and currents are present.

  8. Stretching Response of Knotted and Unknotted Polymer Chains

    NASA Astrophysics Data System (ADS)

    Caraglio, Michele; Micheletti, Cristian; Orlandini, Enzo

    2015-10-01

    Recent theoretical and experimental advances have clarified the major effects of knotting on the properties of stretched chains. Yet, how knotted chains respond to weak mechanical stretching and how this behavior differs from the unknotted case are still open questions and we address them here by profiling the complete stretching response of chains of hundreds of monomers and different topology. We find that the ratio of the knotted and unknotted chain extensions varies nonmonotonically with the applied force. This surprising feature is shown to be a signature of the crossover between the well-known high-force stretching regime and the previously uncharacterized low-force one. The observed differences of knotted and unknotted chain response increases with knot complexity and are sufficiently marked that they could be harnessed in single-molecule contexts to infer the presence and complexity of physical knots in micron-long biomolecules.

  9. Stable knots in the trapped Bose-Einstein condensates

    NASA Astrophysics Data System (ADS)

    Liu, Yong-Kai; Feng, Shiping; Yang, Shi-Jie

    2014-06-01

    The knot of the spin-texture is studied within the two-component Bose-Einstein condensates which are described by the nonlinear Gross-Pitaevskii equations. We start from the noninteracting equations including an axisymmetric harmonic trap to obtain an exact solution, which exhibits a nontrivial topological structure. The spin-texture is a knot with an integral Hopf invariant. The stability of the knot is verified by numerically evolving the nonlinear Gross-Pitaevskii equations along imaginary time.

  10. Effect of knots on stress waves in lumber

    Treesearch

    C.C. Gerhards

    1982-01-01

    An impact stress wave was induced in the end of 2 by 6 lumber containing knots. Rather than a normal, perpendicular-to-the-axis profile in transiting by a knot, the stress wave tended to Iead in zones of clear wood in the direction of the slope of grain or slope of the annual rings and to lag behind the knot. Of three methods evaluated to time the stress wave, the...

  11. Experimental detection of knotted conformations in denatured proteins.

    PubMed

    Mallam, Anna L; Rogers, Joseph M; Jackson, Sophie E

    2010-05-04

    Structures that contain a knot formed by the path of the polypeptide backbone represent some of the most complex topologies observed in proteins. How or why these topological knots arise remains unclear. By developing a method to experimentally trap and detect knots in nonnative polypeptide chains, we find that two knotted methyltransferases, YibK and YbeA, can exist in a trefoil-knot conformation even in their chemically unfolded states. The unique denatured-state topology of these molecules explains their ability to efficiently fold to their native knotted structures in vitro and offers insights into the potential role of knots in proteins. Furthermore, the high prevalence of the denatured-state knots identified here suggests that they are either difficult to untie or that threading of any untied molecules is rapid and spontaneous. The occurrence of such knotted topologies in unfolded polypeptide chains raises the possibility that they could play an important, and as yet unexplored, role in folding and misfolding processes in vivo.

  12. Escape of a knot from a DNA molecule in flow

    NASA Astrophysics Data System (ADS)

    Renner, Benjamin; Doyle, Patrick

    2014-03-01

    Macroscale knots are an everyday occurrence when trying to unravel an unorganized flexible string (e.g. an iPhone cord taken out of your pocket). In nature, knots are found in proteins and viral capsid DNA, and the properties imbued by their topologies are thought to have biological significance. Unlike their macroscale counterparts, thermal fluctuations greatly influence the dynamics of polymer knots. Here, we use Brownian Dynamics simulations to study knot diffusion along a linear polymer chain. The model is parameterized to dsDNA, a model polymer used in previous simulation and experimental studies of knot dynamics. We have used this model to study the process of knot escape and transport along a dsDNA strand extended by an elongational flow. For a range of knot topologies and flow strengths, we show scalings that result in collapse of the data onto a master curve. We show a topologically mediated mode of transport coincides with observed differences in rates of knot transport, and we provide a simple mechanistic explanation for its effect. We anticipate these results will build on the growing body of fundamental studies of knotted polymers and inform future experimental study. This work is supported by the Singapore-MIT Alliance for Research and Technology (SMART) and National Science Foundation (NSF) grant CBET-0852235.

  13. Mechanically tightening a protein slipknot into a trefoil knot.

    PubMed

    He, Chengzhi; Lamour, Guillaume; Xiao, Adam; Gsponer, Joerg; Li, Hongbin

    2014-08-27

    The knotted/slipknotted polypeptide chain is one of the most surprising topological features found in certain proteins. Understanding how knotted/slipknotted proteins overcome the topological difficulty during the folding process has become a challenging problem. By stretching a knotted/slipknotted protein, it is possible to untie or tighten a knotted polypeptide and even convert a slipknot to a true knot. Here, we use single molecule force spectroscopy as well as steered molecular dynamics (SMD) simulations to investigate how the slipknotted protein AFV3-109 is transformed into a tightened trefoil knot by applied pulling force. Our results show that by pulling the N-terminus and the threaded loop of AFV3-109, the protein can be unfolded via multiple pathways and the slipknot can be transformed into a tightened trefoil knot involving ∼13 amino acid residues as the polypeptide chain is apparently shortened by ∼4.7 nm. The SMD simulation results are largely consistent with our experimental findings, providing a plausible and detailed molecular mechanism of mechanical unfolding and knot tightening of AFV3-109. These simulations reveal that interactions between shearing β-strands on the threaded and knotting loops provide high mechanical resistance during mechanical unfolding.

  14. Large N Duality, Lagrangian Cycles, and Algebraic Knots

    NASA Astrophysics Data System (ADS)

    Diaconescu, D.-E.; Shende, V.; Vafa, C.

    2013-05-01

    We consider knot invariants in the context of large N transitions of topological strings. In particular we consider aspects of Lagrangian cycles associated to knots in the conifold geometry. We show how these can be explicitly constructed in the case of algebraic knots. We use this explicit construction to explain a recent conjecture relating study of stable pairs on algebraic curves with HOMFLY polynomials. Furthermore, for torus knots, using the explicit construction of the Lagrangian cycle, we also give a direct A-model computation and recover the HOMFLY polynomial for this case.

  15. Minimum number of throws needed for knot security.

    PubMed

    Muffly, Tyler M; Kow, Nathan; Iqbal, Imran; Barber, Matthew D

    2011-01-01

    The purpose of the study was to determine the optimal number of throws to ensure knot security. Knots were tied with 3, 4, 5, or 6 square throws with 0-gauge coated polyester, polydioxanone, polypropylene, and polyglactin 910. The suture was soaked in 0.9% sodium chloride and subsequently transferred to a tensiometer and broken. A total of 225 knots were tied. Regardless of the suture type, tension at failure for knots with 4 throws, 5 throws, and 6 throws was higher than tension at failure of knots with only 3 throws (p < 0.05 for each). We found no difference in the tensile strength between knots with 4, 5, or 6 throws (p > 0.05 for each). Knots with 4 throws were significantly more likely to come untied than knots with 5 or 6 throws (p < 0.01). Under laboratory conditions, the ideal knot has 5 throws to maximize tensile strength and rate of untying. This finding does not seem to vary by type of suture material. Copyright © 2011 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

  16. Objective Assessment of Knot-Tying Proficiency With the Fundamentals of Arthroscopic Surgery Training Program Workstation and Knot Tester.

    PubMed

    Pedowitz, Robert A; Nicandri, Gregg T; Angelo, Richard L; Ryu, Richard K N; Gallagher, Anthony G

    2015-10-01

    To assess a new method for biomechanical assessment of arthroscopic knots and to establish proficiency benchmarks using the Fundamentals of Arthroscopic Surgery Training (FAST) Program workstation and knot tester. The first study group included 20 faculty at an Arthroscopy Association of North America resident arthroscopy course (19.9 ± 8.25 years in practice). The second group comprised 30 experienced surgeons attending an Arthroscopy Association of North America fall course (17.1 ± 19.3 years in practice). The training group included 44 postgraduate year 4 or 5 orthopaedic residents in a randomized, prospective study of proficiency-based training, with 3 subgroups: group A, standard training (n = 14); group B, workstation practice (n = 14); and group C, proficiency-based progression using the knot tester (n = 16). Each subject tied 5 arthroscopic knots backed up by 3 reversed hitches on alternating posts. Knots were tied under video control around a metal mandrel through a cannula within an opaque dome (FAST workstation). Each suture loop was stressed statically at 15 lb for 15 seconds. A calibrated sizer measured loop expansion. Knot failure was defined as 3 mm of loop expansion or greater. In the faculty group, 24% of knots "failed" under load. Performance was inconsistent: 12 faculty had all knots pass, whereas 2 had all knots fail. In the second group of practicing surgeons, 21% of the knots failed under load. Overall, 56 of 250 knots (22%) tied by experienced surgeons failed. For the postgraduate year 4 or 5 residents, the aggregate knot failure rate was 26% for the 220 knots tied. Group C residents had an 11% knot failure rate (half the overall faculty rate, P = .013). The FAST workstation and knot tester offer a simple and reproducible educational approach for enhancement of arthroscopic knot-tying skills. Our data suggest that there is significant room for improvement in the quality and consistency of these important arthroscopic skills, even for

  17. Optical knots and contact geometry II. From Ranada dyons to transverse and cosmetic knots

    SciTech Connect

    Kholodenko, Arkady L.

    2016-08-15

    Some time ago Ranada (1989) obtained new nontrivial solutions of the Maxwellian gauge fields without sources. These were reinterpreted in Kholodenko (2015) [10] (part I) as particle-like (monopoles, dyons, etc.). They were obtained by the method of Abelian reduction of the non-Abelian Yang–Mills functional. The developed method uses instanton-type calculations normally employed for the non-Abelian gauge fields. By invoking the electric–magnetic duality it then becomes possible to replace all known charges/masses by the particle-like solutions of the source-free Abelian gauge fields. To employ these results in high energy physics, it is essential to extend Ranada’s results by carefully analyzing and classifying all dynamically generated knotted/linked structures in gauge fields, including those discovered by Ranada. This task is completed in this work. The study is facilitated by the recent progress made in solving the Moffatt conjecture. Its essence is stated as follows: in steady incompressible Euler-type fluids the streamlines could have knots/links of all types. By employing the correspondence between the ideal hydrodynamics and electrodynamics discussed in part I and by superimposing it with the already mentioned method of Abelian reduction, it is demonstrated that in the absence of boundaries only the iterated torus knots and links could be dynamically generated. Obtained results allow to develop further particle-knot/link correspondence studied in Kholodenko (2015) [13].

  18. Optical knots and contact geometry II. From Ranada dyons to transverse and cosmetic knots

    NASA Astrophysics Data System (ADS)

    Kholodenko, Arkady L.

    2016-08-01

    Some time ago Ranada (1989) obtained new nontrivial solutions of the Maxwellian gauge fields without sources. These were reinterpreted in Kholodenko (2015) [10] (part I) as particle-like (monopoles, dyons, etc.). They were obtained by the method of Abelian reduction of the non-Abelian Yang-Mills functional. The developed method uses instanton-type calculations normally employed for the non-Abelian gauge fields. By invoking the electric-magnetic duality it then becomes possible to replace all known charges/masses by the particle-like solutions of the source-free Abelian gauge fields. To employ these results in high energy physics, it is essential to extend Ranada's results by carefully analyzing and classifying all dynamically generated knotted/linked structures in gauge fields, including those discovered by Ranada. This task is completed in this work. The study is facilitated by the recent progress made in solving the Moffatt conjecture. Its essence is stated as follows: in steady incompressible Euler-type fluids the streamlines could have knots/links of all types. By employing the correspondence between the ideal hydrodynamics and electrodynamics discussed in part I and by superimposing it with the already mentioned method of Abelian reduction, it is demonstrated that in the absence of boundaries only the iterated torus knots and links could be dynamically generated. Obtained results allow to develop further particle-knot/link correspondence studied in Kholodenko (2015) [13].

  19. Heraklas on knots: sixteen surgical nooses and knots from the first century A.D.

    PubMed

    Hage, J Joris

    2008-04-01

    In the first century of our common era, the Greek physician Heraklas wrote a brief essay on how to tie 16 knots and nooses for surgical and orthopedic purposes. His work is reintroduced and discussed here because its place in the origin and evolution of surgery needs to be properly acknowledged and recorded in the current medical literature. To do so, Raeder's definitive Greek edition of the oldest extant manuscripts of Heraklas' essay was studied along with the various illustrated interpretations of his text published over the last six centuries. Moreover, the contemporary literature was searched for current applications of Heraklas' knots by use of a database of surgical knots. It was found that seven of Heraklas' 16 knots and nooses were still applied surgically of late, and that four of these have even been recently rediscovered for such applications. Therefore, it is concluded that Hellenistic, Roman, and Byzantine medicine had a rich knowledge and high standards. Contemporary surgical techniques may be found to be truly ancient if we search deep enough, far enough, and long enough.

  20. Ventriculoperitoneal Shunt Peritoneal Catheter Knot Formation

    PubMed Central

    Ul-Haq, Anwar; Al-Otaibi, Faisal; Alshanafey, Saud; Sabbagh, Mohamed Diya; Al Shail, Essam

    2013-01-01

    The ventriculoperitoneal (VP) shunt is a common procedure in pediatric neurosurgery that carries a risk of complications at cranial and abdominal sites. We report on the case of a child with shunt infection and malfunction. The peritoneal catheter was tethered within the abdominal cavity, precluding its removal. Subsequently, laparoscopic exploration identified a knot at the distal end of the peritoneal catheter around the omentum. A new VP shunt was inserted after the infection was healed. This type of complication occurs rarely, so there are a limited number of case reports in the literature. This report is complemented by a literature review. PMID:24109528

  1. Factorization of differential expansion for antiparallel double-braid knots

    NASA Astrophysics Data System (ADS)

    Morozov, A.

    2016-09-01

    Continuing the quest for exclusive Racah matrices, which are needed for evaluation of colored arborescent-knot polynomials in Chern-Simons theory, we suggest to extract them from a new kind of a double-evolution — that of the antiparallel double-braids, which is a simple two-parametric family of two-bridge knots, generalizing the one-parametric family of twist knots. In the case of rectangular representations R = [ r s ] we found an evidence that the corresponding differential expansion miraculously factorizes and can be obtained from that for the twist knots. This reduces the problem of rectangular exclusive Racah to constructing the answers for just a few twist knots. We develop a recent conjecture on the structure of differential expansion for the simplest members of this family (the trefoil and the figure-eight knot) and provide the exhaustive answer for the first unknown case of R = [33]. The answer includes HOMFLY of arbitrary twist and double-braid knots and Racah matrices overline{S} and S — what allows to calculate [33]-colored polynomials for arbitrary arborescent (double-fat) knots. For generic rectangular representations fully described are only the contributions of the single-floor pyramids. One step still remains to be done.

  2. Lanthanide template synthesis of a molecular trefoil knot.

    PubMed

    Ayme, Jean-François; Gil-Ramírez, Guzmán; Leigh, David A; Lemonnier, Jean-François; Markevicius, Augustinas; Muryn, Christopher A; Zhang, Gen

    2014-09-24

    We report on a complex featuring three 2,6-pyridinedicarboxamide ligands entwined around a lanthanide (Ln(3+)) ion. The ligand strands can be cyclized by ring-closing olefin metathesis to form a molecular trefoil knot in 58% yield. Demetalation with tetraethylammonium fluoride quantitatively generates the wholly organic 81-atom-loop trefoil knot.

  3. Structural recognition and nomenclature standardization in forensic knot analysis.

    PubMed

    Chisnall, Robert Charles

    2016-07-01

    The analysis of knots during civil and criminal investigations is characterized by two fundamental challenges: the precise recognition of all structural nuances and the application of accurate, universally recognized terms. These challenges are exacerbated by inconsistencies, contradictions and regional terminology, which occur in common practice and in mainstream books as well as within forensic science. Some knots bear multiple or value-laden names, even misnomers, and some terms have manifold applications. This can lead to ambiguity and confusion. Additionally, many topological concepts and terms are applicable to practical knot-tying, despite the differences between real-world and theoretical knots, but the esoterica of topology are inaccessible to anyone unfamiliar with that branch of mathematics. To highlight these challenges some examples of knots encountered in case work are presented. Significantly, an overview of a few previously ignored issues is examined and several new concepts are introduced. An emphasis is placed on identifying structural variations, standardized nomenclature is outlined, and recommended terminology is derived from fields such as forensic science, chemistry, archaeology, topology and the textile industry. Greater precision in knot identifications, characterizations and descriptions can assist investigators in linking specific tying practises to potential suspects, analysing the manner in which knotted evidence was tied, and understanding how knots and ligatures perform in given scenarios.

  4. Root-knot nematode resistant rootstocks for grafted watermelon

    USDA-ARS?s Scientific Manuscript database

    Rootstock lines of wild watermelon (Citrullus lanatus var. citroides) with resistance to root-knot nematodes (RKN) were developed by our team at the U.S. Vegetable Laboratory. Rootstock lines RKVL 301, RKVL 316, and RKVL 318 (RKVL = Root Knot Vegetable Laboratory) were compared to wild tinda (Praec...

  5. Cystine knot growth factors and their functionally versatile proregions.

    PubMed

    Schwarz, Elisabeth

    2017-09-05

    The cystine knot disulfide pattern has been found to be widespread in nature, since it has been detected in proteins from plants, marine snails, spiders and mammals. Cystine knot proteins are secreted proteins. Their functions range from defense mechanisms as toxins, e.g. ion channel or enzyme inhibitors, to hormones, blood factors and growth factors. Cystine knot proteins can be divided into two superordinate groups. (i) The cystine knot peptides, also referred to - with other non-cystine knot proteins - as knottins, with linear and cyclic polypeptide chains. (ii) The cystine knot growth factor family, which is in the focus of this article. The disulfide ring structure of the cystine knot peptides is made up by the half-cystines 1-4 and 2-5, and the threading disulfide bond is formed by the half-cystines, 3-6. In the growth factor group, the disulfides of half-cystines 1 and 4 pass the ring structure formed by the half-cystines 2-5 and 3-6. In this review, special emphasis will be devoted to the growth factor cystine knot proteins and their proregions. The latter have shifted into the focus of scientific interest as their important biological roles are just to be unravelled.

  6. Using more of what trees provide - why not knots?

    Treesearch

    Matthew Bumgardner

    2003-01-01

    We are all familiar with furniture and paneling made from "knotty" pine. In fact, we expect pine to be knotty and such knots add a certain degree of warmness and authenticity. But have you ever wondered why there isn't more knotty oak furniture! Or knotty cherry cabinets? The fact is that most knot distortions and visual defects such as color streaks and...

  7. Lanthanide Template Synthesis of Trefoil Knots of Single Handedness.

    PubMed

    Zhang, Gen; Gil-Ramírez, Guzmán; Markevicius, Augustinas; Browne, Colm; Vitorica-Yrezabal, Iñigo J; Leigh, David A

    2015-08-19

    We report on the assembly of 2,6-pyridinedicarboxamide ligands (1) with point chirality about lanthanide metal ion (Ln(3+)) templates, in which the helical chirality of the resulting entwined 3:1 ligand:metal complexes is covalently captured by ring-closing olefin metathesis to form topologically chiral molecular trefoil knots of single handedness. The ligands do not self-sort (racemic ligands form a near-statistical mixture of homoleptic and heteroleptic lanthanide complexes), but the use of only (R,R)-1 leads solely to a trefoil knot of Λ-handedness, whereas (S,S)-1 forms the Δ-trefoil knot with complete stereoselectivity. The knots and their isomeric unknot macrocycles were characterized by NMR spectroscopy, mass spectrometry, and X-ray crystallography and the expression of the chirality that results from the topology of the knots studied by circular dichroism.

  8. UNEXPECTED IONIZATION STRUCTURE IN ETA CARINAE'S ''WEIGELT KNOTS''

    SciTech Connect

    Remmen, Grant N.; Davidson, Kris; Mehner, Andrea

    2013-08-10

    The Weigelt knots, dense slow-moving ejecta near {eta} Carinae, are mysterious in structure as well as in origin. Using spatially dithered spectrograms obtained with the Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS), we have partially resolved the ionization zones of one knot. Contrary to simple models, higher ionization levels occur on the outer side, i.e., farther from the star. They cannot represent a bow shock, and no satisfying explanation is yet available-though we sketch one qualitative possibility. STIS spectrograms provide far more reliable spatial measurements of the Weigelt knots than HST images do, and this technique can also be applied to the knots' proper motion problem. Our spatial measurement accuracy is about 10 mas, corresponding to a projected linear scale of the order of 30 AU, which is appreciably smaller than the size of each Weigelt knot.

  9. New suture: tail clinch knot for transabdominal preperitoneal hernia repair.

    PubMed

    Uchida, Kazunori; Morimoto, Hiroshi; Tashiro, Hirotaka; Ohdan, Hideki; Yamamoto, Manabu

    2015-02-01

    There is some controversy regarding the proper surgical method for inguinal hernia repair and whether transabdominal preperitoneal or totally extraperitoneal repair should be used. The greatest difference between these procedures is the need for absorbable sutures to close the peritoneal incision. The clinch knot is a kind of slip knot that is used for securing a fishing lure, hook, or swivel to a fishing line. This knot is used by fishermen and has historically proven to be secure. When a clinch knot is placed at the tail end of a suture thread, a running suture can be started without knot tying. © 2015 Japan Society for Endoscopic Surgery, Asia Endosurgery Task Force and Wiley Publishing Asia Pty Ltd.

  10. Knot polynomials in the first non-symmetric representation

    NASA Astrophysics Data System (ADS)

    Anokhina, A.; Mironov, A.; Morozov, A.; Morozov, And.

    2014-05-01

    We describe the explicit form and the hidden structure of the answer for the HOMFLY polynomial for the figure-8 and some other 3-strand knots in representation [21]. This is the first result for non-torus knots beyond (anti)symmetric representations, and its evaluation is far more complicated. We provide a whole variety of different arguments, allowing one to guess the answer for the figure-8 knot, which can be also partly used in more complicated situations. Finally we report the result of exact calculation for figure-8 and some other 3-strand knots based on the previously developed sophisticated technique of multi-strand calculations. We also discuss a formula for the superpolynomial in representation [21] for the figure-8 knot, which heavily relies on the conjectural form of superpolynomial expansion nearby the special polynomial point. Generalizations and details will be presented elsewhere.

  11. Knot Solitons in Spinor Bose-Einstein Condensates

    NASA Astrophysics Data System (ADS)

    Hall, David; Ray, Michael; Tiurev, Konstantin; Ruokokoski, Emmi; Gheorghe, Andrei Horia; Möttönen, Mikko

    2016-05-01

    Knots are familiar entities that appear at a captivating nexus of art, technology, mathematics and science. Following a lengthy period of theoretical investigation and development, they have recently attracted great experimental interest in classical contexts ranging from knotted DNA and nanostructures to vortex knots in fluids. We demonstrate here the controlled creation and detection of knot solitons in the quantum-mechanical order parameter of a spinor Bose-Einstein condensate. Images of the superfluid reveal the circular shape of the soliton core and its associated linked rings. Our observations of the knot soliton establish an experimental foundation for future studies of their stability, dynamics and applications within quantum systems. Supported in part by NSF Grant PHY-1205822.

  12. Intracorporal knot tying techniques - which is the right one?

    PubMed

    Romero, Philipp; Nickel, Felix; Mantel, Maisha; Frongia, Giovanni; Rossler, Alina; Kowalewski, Karl-Friedrich; Müller-Stich, Beat Peter; Günther, Patrick

    2017-04-01

    Intracorporal knot tying (ICKT) and suturing in minimal invasive surgery (MIS) represent a key skill for advanced procedures such as Nissen fundoplication. Suture placement under tension is particularly challenging during MIS. The aim of this study was to compare ICKT of the common surgical square knot and the slipping knot on a simulated suture placement under tension. Furthermore, we objectively assessed the surgical skill of ICKT following 3hours of hands-on training. A box trainer was used for laparoscopic knot tying with predefined openings. A 12cm suture was placed in central view. We used a standardized silicon suture pad with a defined wound dehiscence of 0.5cm and marked needle entrance and exit targets next to the incision. Twenty participants were divided among three groups in this study. The first group (n=5) consisted of senior physicians. The second group (n=5) was made up of surgical residents in the first to fourth year of residency training. The third group (n=10) contained medical students between their third and sixth year of study without any prior experience in laparoscopic surgery. Residents and students received a 3-hour hands-on training in surgical square and slipping knot tying. Each participant tied two of each knot types before and after the hands-on training. Knot quality, performance, total time and suture placement accuracy were the parameters for assessment in this study. The knot quality was greater for the slipping knot compared with the square knot in all groups. There were no significant intragroup differences in knot tying performance, task time and accuracy of both suture methods. Students and residents improved in all categories for both ICKT techniques after training. We compared ICKT of the surgical square knot with the slipping knot on a simulated suture placement under tension during a standardized training program for medical students and surgical residents. In our study, the average quality of the slipping knot was

  13. Design principles for rapid folding of knotted DNA nanostructures.

    PubMed

    Kočar, Vid; Schreck, John S; Čeru, Slavko; Gradišar, Helena; Bašić, Nino; Pisanski, Tomaž; Doye, Jonathan P K; Jerala, Roman

    2016-02-18

    Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the 'free-end' rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins.

  14. Knotting probability of self-avoiding polygons under a topological constraint

    NASA Astrophysics Data System (ADS)

    Uehara, Erica; Deguchi, Tetsuo

    2017-09-01

    We define the knotting probability of a knot K by the probability for a random polygon or self-avoiding polygon (SAP) of N segments having the knot type K. We show fundamental and generic properties of the knotting probability particularly its dependence on the excluded volume. We investigate them for the SAP consisting of hard cylindrical segments of unit length and radius rex. For various prime and composite knots, we numerically show that a compact formula describes the knotting probabilities for the cylindrical SAP as a function of segment number N and radius rex. It connects the small-N to the large-N behavior and even to lattice knots in the case of large values of radius. As the excluded volume increases, the maximum of the knotting probability decreases for prime knots except for the trefoil knot. If it is large, the trefoil knot and its descendants are dominant among the nontrivial knots in the SAP. From the factorization property of the knotting probability, we derive a sum rule among the estimates of a fitting parameter for all prime knots, which suggests the local knot picture and the dominance of the trefoil knot in the case of large excluded volumes. Here we remark that the cylindrical SAP gives a model of circular DNA which is negatively charged and semiflexible, where radius rex corresponds to the screening length.

  15. Knotting probability of self-avoiding polygons under a topological constraint.

    PubMed

    Uehara, Erica; Deguchi, Tetsuo

    2017-09-07

    We define the knotting probability of a knot K by the probability for a random polygon or self-avoiding polygon (SAP) of N segments having the knot type K. We show fundamental and generic properties of the knotting probability particularly its dependence on the excluded volume. We investigate them for the SAP consisting of hard cylindrical segments of unit length and radius rex. For various prime and composite knots, we numerically show that a compact formula describes the knotting probabilities for the cylindrical SAP as a function of segment number N and radius rex. It connects the small-N to the large-N behavior and even to lattice knots in the case of large values of radius. As the excluded volume increases, the maximum of the knotting probability decreases for prime knots except for the trefoil knot. If it is large, the trefoil knot and its descendants are dominant among the nontrivial knots in the SAP. From the factorization property of the knotting probability, we derive a sum rule among the estimates of a fitting parameter for all prime knots, which suggests the local knot picture and the dominance of the trefoil knot in the case of large excluded volumes. Here we remark that the cylindrical SAP gives a model of circular DNA which is negatively charged and semiflexible, where radius rex corresponds to the screening length.

  16. Knot Invariants from Topological Recursion on Augmentation Varieties

    NASA Astrophysics Data System (ADS)

    Gu, Jie; Jockers, Hans; Klemm, Albrecht; Soroush, Masoud

    2015-06-01

    Using the duality between Wilson loop expectation values of SU( N) Chern-Simons theory on S 3 and topological open-string amplitudes on the local mirror of the resolved conifold, we study knots on S 3 and their invariants encoded in colored HOMFLY polynomials by means of topological recursion. In the context of the local mirror Calabi-Yau threefold of the resolved conifold, we generalize the topological recursion of the remodelled B-model in order to study branes beyond the class of toric Harvey-Lawson special Lagrangians—as required for analyzing non-trivial knots on S 3. The basic ingredients for the proposed recursion are the spectral curve, given by the augmentation variety of the knot, and the calibrated annulus kernel, encoding the topological annulus amplitudes associated to the knot. We present an explicit construction of the calibrated annulus kernel for torus knots and demonstrate the validity of the topological recursion. We further argue that—if an explicit form of the calibrated annulus kernel is provided for any other knot—the proposed topological recursion should still be applicable. We study the implications of our proposal for knot theory, which exhibit interesting consequences for colored HOMFLY polynomials of mutant knots.

  17. A machine vision based approach for timber knots detection

    NASA Astrophysics Data System (ADS)

    Hittawe, Mohamad Mazen; Sidibé, Désiré; Mériaudeau, Fabrice

    2015-04-01

    Wood singularities detection is a primary step in wood grading enhancement. Our approach is purely machine vision based. The main objective is to compute physical properties like density, modulus of elasticity (MOE) and modulus of rupture (MOR) given wood surface images. Knots are one of the main singularities which directly affect the wood strength. Hence, our target is to detect knots and classify them into transverse and non-transverse ones. Then the Knots Depth Ratio (KDR) is computed based on all found transverse knots. Afterwards, KDR is used for the wood mechanical model improvement. Our technique is based on colour image analysis where the knots are detected by means of contrast intensity transformation and morphological operations. Then KDR computations are based on transverse knots and clear wood densities. Finally, MOE and MOR are computed using KDR images. The accuracy of number of knots found, their locations, MOE and MOR has been validated using a dataset of 252 images. In our dataset, these values were manually calculated. To the best of our knowledge our approach is the first purely machine vision based method to compute KDR, MOE and MOR.

  18. Bioactive properties of wood knot extracts on cultured human cells.

    PubMed

    Phelan, Martha; Aherne, S Aisling; Wong, Alfred; O'Brien, Nora M

    2009-12-01

    Not all felled wood is converted to timber or pulp, with the remaining material being a rich source of relatively unexplored and unexploited potentially novel bioactive compounds. Therefore the potential bioactive effects of two softwood knot (the part of the branch encased in the tree stem) extracts--namely, Pinus banksiana Lamb. (Jack pine) and Picea sitchensis (Bong.) Carr. (Sitka spruce)--were investigated by (1) determining their effects on the viability and antioxidant status of human Jurkat T cells, (2) investigating potential cytoprotective and genoprotective effects against oxidative stress in cultured cells, and (3) assessing their effects on concanavalin A (ConA)-induced interleukin-2 (IL-2) production. Initially, both Jack pine knot and Sitka spruce knot extracts were shown to possess strong antioxidant activity as determined by the ferric reducing antioxidant power assay. When added to Jurkat cells, Jack pine knot extract was more toxic compared with Sitka spruce knot extract, with concentrations that resulted in 50% cell death of 153.0 microg/mL and 376.1 microg/mL, respectively. Supplementation of Jurkat cells with wood knot extracts did not affect their glutathione content or catalase activity. Pretreatment of Jurkat cells with Sitka spruce or Jack pine knot extracts protected against H(2)O(2)-induced cell injury. However, none of the extracts protected against H(2)O(2)-induced DNA damage. Jack pine knots, at a concentration of 30 microg/mL, significantly suppressed ConA-induced IL-2 production. Although total phenol content did not differ between the two extracts, gas chromatography analysis did show variation in the types of constituents present. Further research is warranted to elucidate the selective bioactive properties of these softwood knot extracts.

  19. EJECTA KNOT FLICKERING, MASS ABLATION, AND FRAGMENTATION IN CASSIOPEIA A

    SciTech Connect

    Fesen, Robert A.; Zastrow, Jordan A.; Hammell, Molly C.; Shull, J. Michael; Silvia, Devin W.

    2011-08-01

    Ejecta knot flickering, ablation tails, and fragmentation are expected signatures associated with the gradual dissolution of high-velocity supernova (SN) ejecta caused by their passage through an inhomogeneous circumstellar medium or interstellar medium (ISM). Such phenomena mark the initial stages of the gradual merger of SN ejecta with and the enrichment of the surrounding ISM. Here we report on an investigation of this process through changes in the optical flux and morphology of several high-velocity ejecta knots located in the outskirts of the young core-collapse SN remnant Cassiopeia A using Hubble Space Telescope images. Examination of WFPC2 F675W and combined ACS F625W + F775W images taken between 1999 June and 2004 December of several dozen debris fragments in the remnant's northeast ejecta stream and along the remnant's eastern limb reveal substantial emission variations ('flickering') over timescales as short as nine months. Such widespread and rapid variability indicates knot scale lengths {approx_equal} 10{sup 15} cm and a highly inhomogeneous surrounding medium. We also identify a small percentage of ejecta knots located all around the remnant's outer periphery which show trailing emissions typically 0.''2-0.''7 in length aligned along the knot's direction of motion suggestive of knot ablation tails. We discuss the nature of these trailing emissions as they pertain to ablation cooling, knot disruption, and fragmentation, and draw comparisons to the emission 'strings' seen in {eta} Car. Finally, we identify several tight clusters of small ejecta knots which resemble models of shock-induced fragmentation of larger SN ejecta knots caused by a high-velocity interaction with a lower density ambient medium.

  20. Intracorporeal knotting of a femoral nerve catheter.

    PubMed

    Ghanem, Mohamed; Schnoor, Jörg; Wiegel, Martin; Josten, Christoph; Reske, Andreas W

    2015-01-01

    Peripheral nerve catheters are effective and well-established tools to provide postoperative analgesia to patients undergoing orthopedic surgery. The performance of these techniques is usually considered safe. However, placement of nerve catheters may be associated with a considerable number of side effects and major complications have repeatedly been published. In this work, we report on a patient who underwent total knee replacement with spinal anesthesia and preoperative insertion of femoral and sciatic nerve catheters for postoperative analgesia. During insertion of the femoral catheter, significant resistance was encountered upon retracting the catheter. This occurred due to knotting of the catheter. The catheter had to be removed by operative intervention which has to be considered a major complication. The postoperative course was uneventful. The principles for removal of entrapped peripheral catheters are not well established, may differ from those for neuroaxial catheters, and range from cautious manipulation up to surgical intervention.

  1. Intracorporeal knotting of a femoral nerve catheter

    PubMed Central

    Ghanem, Mohamed; Schnoor, Jörg; Wiegel, Martin; Josten, Christoph; Reske, Andreas W.

    2015-01-01

    Peripheral nerve catheters are effective and well-established tools to provide postoperative analgesia to patients undergoing orthopedic surgery. The performance of these techniques is usually considered safe. However, placement of nerve catheters may be associated with a considerable number of side effects and major complications have repeatedly been published. In this work, we report on a patient who underwent total knee replacement with spinal anesthesia and preoperative insertion of femoral and sciatic nerve catheters for postoperative analgesia. During insertion of the femoral catheter, significant resistance was encountered upon retracting the catheter. This occurred due to knotting of the catheter. The catheter had to be removed by operative intervention which has to be considered a major complication. The postoperative course was uneventful. The principles for removal of entrapped peripheral catheters are not well established, may differ from those for neuroaxial catheters, and range from cautious manipulation up to surgical intervention. PMID:26504733

  2. Knots and Coils in Superfluid Vortices

    NASA Astrophysics Data System (ADS)

    Kleckner, Dustin; Proment, Davide; Scheeler, Martin; Irvine, William T. M.

    2014-11-01

    Recent work has demonstrated that linked and knotted vortices will spontaneously unknot or untie in both classical fluids and superfluids. This effect would appear to jeopardize any notion of conservation of fluid topology (helicity), but this need not be the case: vortices can transfer their knottedness to helical coils, preserving some measure of the original topology. By simulating superfluid vortices in the Gross-Pitaevskii equation, we find a geometric mechanism for efficiently transferring helicity in exactly this manner. Remarkably, the same transfer of topology to geometry also appears in viscous fluid vortices, suggesting it is a generic feature of non-ideal fluids. This work was supported by the NSF MRSEC shared facilities at the University of Chicago (DMR-0820054) and an NSF CAREER Award (DMR-1351506). W.T.M.I. further acknowledges support from the A.P. Sloan Foundation and the Packard Foundation.

  3. Two Adhesive Sites Can Enhance the Knotting Probability of DNA

    PubMed Central

    2015-01-01

    Self-entanglement, or knotting, is entropically favored in long polymers. Relatively short polymers such as proteins can knot as well, but in this case the entanglement is mainly driven by fine-tuned, sequence-specific interactions. The relation between the sequence of a long polymer and its topological state is here investigated by means of a coarse-grained model of DNA. We demonstrate that the introduction of two adhesive regions along the sequence of a self-avoiding chain substantially increases the probability of forming a knot. PMID:26136125

  4. Intraoperative wide bore nasogastric tube knotting: A rare incidence

    PubMed Central

    Lamba, Sangeeta; Sethi, Surendra K.; Khare, Arvind; Saini, Sudheendra

    2016-01-01

    Nasogastric tubes are commonly used in anesthetic practice for gastric decompression in surgical patients intraoperatively. The indications for its use are associated with a number of potential complications. Knotting of small-bore nasogastric tubes is usually common both during insertion and removal as compared to wide bore nasogastric tubes. Knotting of wide bore nasogastric tube is a rare complication and if occurs usually seen in long standing cases. We hereby report a case of incidental knotting of wide bore nasogastric tube that occurred intraoperatively. PMID:26957700

  5. Pinus pinaster Knot: A Source of Polyphenols against Plasmopara viticola.

    PubMed

    Gabaston, Julien; Richard, Tristan; Cluzet, Stéphanie; Palos Pinto, Antonio; Dufour, Marie-Cécile; Corio-Costet, Marie-France; Mérillon, Jean-Michel

    2017-09-29

    Pine knot extract from Pinus pinaster byproducts was characterized by UHPLC-DAD-MS and NMR. Fourteen polyphenols divided into four classes were identified as follows: lignans (nortrachelogenin, pinoresinol, matairesinol, isolariciresinol, secoisolariciresinol), flavonoids (pinocembrin, pinobanksin, dihydrokaempferol, taxifolin), stilbenes (pinosylvin, pinosylvin monomethyl ether, pterostilbene), and phenolic acids (caffeic acid, ferulic acid). The antifungal potential of pine knot extract, as well as the main compounds, was tested in vitro against Plasmopara viticola. The ethanolic extract showed a strong antimildew activity. In addition, pinosylvins and pinocembrin demonstrated significant inhibition of zoospore mobility and mildew development. These findings strongly suggest that pine knot is a potential biomass that could be used as a natural antifungal product.

  6. On the Construction and Dynamics of Knotted Fields

    NASA Astrophysics Data System (ADS)

    Kedia, Hridesh

    Representing a physical field in terms of its field lines has often enabled a deeper understanding of complex physical phenomena, from Faraday's law of magnetic induction, to the Helmholtz laws of vortex motion, to the free energy density of liquid crystals in terms of the distortions of the lines of the director field. At the same time, the application of ideas from topology--the study of properties that are invariant under continuous deformations--has led to robust insights into the nature of complex physical systems from defects in crystal structures, to the earth's magnetic field, to topological conservation laws. The study of knotted fields, physical fields in which the field lines encode knots, emerges naturally from the application of topological ideas to the investigation of the physical phenomena best understood in terms of the lines of a field. A knot--a closed loop tangled with itself which can not be untangled without cutting the loop--is the simplest topologically non-trivial object constructed from a line. Remarkably, knots in the vortex (magnetic field) lines of a dissipationless fluid (plasma), persist forever as they are transported by the flow, stretching and rotating as they evolve. Moreover, deeply entwined with the topology-preserving dynamics of dissipationless fluids and plasmas, is an additional conserved quantity--helicity, a measure of the average linking of the vortex (magnetic field) lines in a fluid (plasma)--which has had far-reaching consequences for fluids and plasmas. Inspired by the persistence of knots in dissipationless flows, and their far-reaching physical consequences, we seek to understand the interplay between the dynamics of a field and the topology of its field lines in a variety of systems. While it is easy to tie a knot in a shoelace, tying a knot in the the lines of a space-filling field requires contorting the lines everywhere to match the knotted region. The challenge of analytically constructing knotted field

  7. Analysis of the tractive force pattern on a knot by force measurement during laparoscopic knot tying.

    PubMed

    Takayasu, Kenta; Yoshida, Kenji; Kinoshita, Hidefumi; Yoshimoto, Syunsuke; Oshiro, Osamu; Matsuda, Tadashi

    2017-07-19

    Quantifying surgical skills assists novice surgeons when learning operative techniques. We measured the interaction force at a ligation point and clarified the features of the force pattern among surgeons with different skill levels during laparoscopic knot tying. Forty-four surgeons were divided into three groups based on experience: 13 novice (0-5 years), 16 intermediate (6-15 years), and 15 expert (16-30 years). To assess the tractive force direction and volume during knot tying, we used a sensor that measures six force-torque values (x-axis: Fx, y-axis: Fy, z-axis: Fz, and xy-axis: Fxy) attached to a slit Penrose drain. All participants completed one double knot and five single knot sequences. We recorded completion time, force volume (FV), maximum force (MF), time over 1.5 N, duration of non-zero force, and percentage time when vertical force exceeded horizontal force (PTz). There was a significant difference between groups for completion time (p = 0.007); FV (total: p = 0.002; Fx: p = 0.004, Fy: p = 0.007, Fxy: p = 0.004, Fz: p < 0.001, Fxy/Fz: p = 0.003), MF (total: p = 0.004; Fx: p = 0.015, Fy: p = 0.035, Fxy: p = 0.009, Fz: p = 0.001, Fxy/Fz: p = 0.041); time over 1.5 N (p = 0.002); duration of non-zero force (p = 0.029); and PTz (p < 0.001). PTz showed the only significant difference comparing intermediates with experts (intermediates: 13.7 ± 9.0, experts: 4.9 ± 3.2; p < 0.001). We clarified the characteristics of the force pattern at the ligation point during suturing by surgeons with three levels of experience using a force measurement system. We revealed that both force volume and force direction differed depending on surgeons' skill level during knot tying. Copyright © 2017. Published by Elsevier Inc.

  8. A comparison of the strength of knots tied by hand and at laparoscopy.

    PubMed

    Kadirkamanathan, S S; Shelton, J C; Hepworth, C C; Laufer, J G; Swain, C P

    1996-01-01

    The strength of knots tied at laparoscopy was compared with that of hand-tied knots. The force needed to undo or break eight types of knots that were tied in fresh postmortem human stomachs was measured. The knotting performance of nylon, polyglactin 910, braided silk, polytetrafluoroethylene, braided polyester fiber, braided polyester suture, polyamide 66, and polydiaxone was also compared. Measurements of knot strength of two to six half hitches (hand tied) showed that four half hitches were necessary to tie a secure nonslipping knot with most monofilament threads (nylon, polytetrafluoroethylene, braided polyester suture, and polyamide 66), while three half hitches were adequate to secure a knot when polyglactin 910, braided polyester fiber, silk, and polydiaxone were used. Additional throws did not increase knot strength once the knot no longer slipped (p = NS). Some commonly tied knots, three half hitches and surgical knots at laparoscopy were weaker than the same hand-tied knots (p < 0.05) but an additional throw increased knot security (p < 0.01). Differences between laparoscopic and hand-tied knot strengths were greater for monofilament than multifilament threads. There was a wider distribution of strengths for laparoscopically tied than hand-tied knots. Four half hitches were the most secure configuration for laparoscopically tied knots and were significantly stronger than three half hitches and surgical knots (p < 0.01). The extracorporeally tied slipknot (Roeder loop) was significantly less secure than four half hitches (p < 0.05). This study demonstrates that laparoscopically formed knots may be weaker than those tied by hand and shows that improvements in knot strength at laparoscopy can be achieved by choice of optimal knot configuration for different suture materials.

  9. Intracardiac migration and knotting of a ventriculoperitoneal shunt.

    PubMed

    Frahm-Jensen, Gert; Newton, Peter R; Drummond, Katharine J; Wagner, Tim P; Mees, Barend M E

    2015-04-01

    We report a patient with delayed migration of the distal ventriculoperitoneal shunt catheter from the peritoneum to the right atrium with associated knotting of the catheter complicating removal. We also review the literature on this topic.

  10. Knotted optical vortices in exact solutions to Maxwell's equations

    NASA Astrophysics Data System (ADS)

    de Klerk, Albertus J. J. M.; van der Veen, Roland I.; Dalhuisen, Jan Willem; Bouwmeester, Dirk

    2017-05-01

    We construct a family of exact solutions to Maxwell's equations in which the points of zero intensity form knotted lines topologically equivalent to a given but arbitrary algebraic link. These lines of zero intensity, more commonly referred to as optical vortices, and their topology are preserved as time evolves and the fields have finite energy. To derive explicit expressions for these new electromagnetic fields that satisfy the nullness property, we make use of the Bateman variables for the Hopf field as well as complex polynomials in two variables whose zero sets give rise to algebraic links. The class of algebraic links includes not only all torus knots and links thereof, but also more intricate cable knots. While the unknot has been considered before, the solutions presented here show that more general knotted structures can also arise as optical vortices in exact solutions to Maxwell's equations.

  11. Knots cascade detected by a monotonically decreasing sequence of values

    PubMed Central

    Liu, Xin; Ricca, Renzo L.

    2016-01-01

    Due to reconnection or recombination of neighboring strands superfluid vortex knots and DNA plasmid torus knots and links are found to undergo an almost identical cascade process, that tend to reduce topological complexity by stepwise unlinking. Here, by using the HOMFLYPT polynomial recently introduced for fluid knots, we prove that under the assumption that topological complexity decreases by stepwise unlinking this cascade process follows a path detected by a unique, monotonically decreasing sequence of numerical values. This result holds true for any sequence of standardly embedded torus knots T(2, 2n + 1) and torus links T(2, 2n). By this result we demonstrate that the computation of this adapted HOMFLYPT polynomial provides a powerful tool to measure topological complexity of various physical systems. PMID:27052386

  12. Linked and knotted chimera filaments in oscillatory systems

    NASA Astrophysics Data System (ADS)

    Lau, Hon Wai; Davidsen, Jörn

    2016-07-01

    While the existence of stable knotted and linked vortex lines has been established in many experimental and theoretical systems, their existence in oscillatory systems and systems with nonlocal coupling has remained elusive. Here, we present strong numerical evidence that stable knots and links such as trefoils and Hopf links do exist in simple, complex, and chaotic oscillatory systems if the coupling between the oscillators is neither too short ranged nor too long ranged. In this case, effective repulsive forces between vortex lines in knotted and linked structures stabilize curvature-driven shrinkage observed for single vortex rings. In contrast to real fluids and excitable media, the vortex lines correspond to scroll wave chimeras [synchronized scroll waves with spatially extended (tubelike) unsynchronized filaments], a prime example of spontaneous synchrony breaking in systems of identical oscillators. In the case of complex oscillatory systems, this leads to a topological superstructure combining knotted filaments and synchronization defect sheets.

  13. Knots cascade detected by a monotonically decreasing sequence of values

    NASA Astrophysics Data System (ADS)

    Liu, Xin; Ricca, Renzo L.

    2016-04-01

    Due to reconnection or recombination of neighboring strands superfluid vortex knots and DNA plasmid torus knots and links are found to undergo an almost identical cascade process, that tend to reduce topological complexity by stepwise unlinking. Here, by using the HOMFLYPT polynomial recently introduced for fluid knots, we prove that under the assumption that topological complexity decreases by stepwise unlinking this cascade process follows a path detected by a unique, monotonically decreasing sequence of numerical values. This result holds true for any sequence of standardly embedded torus knots T(2, 2n + 1) and torus links T(2, 2n). By this result we demonstrate that the computation of this adapted HOMFLYPT polynomial provides a powerful tool to measure topological complexity of various physical systems.

  14. Linked and knotted chimera filaments in oscillatory systems.

    PubMed

    Lau, Hon Wai; Davidsen, Jörn

    2016-07-01

    While the existence of stable knotted and linked vortex lines has been established in many experimental and theoretical systems, their existence in oscillatory systems and systems with nonlocal coupling has remained elusive. Here, we present strong numerical evidence that stable knots and links such as trefoils and Hopf links do exist in simple, complex, and chaotic oscillatory systems if the coupling between the oscillators is neither too short ranged nor too long ranged. In this case, effective repulsive forces between vortex lines in knotted and linked structures stabilize curvature-driven shrinkage observed for single vortex rings. In contrast to real fluids and excitable media, the vortex lines correspond to scroll wave chimeras [synchronized scroll waves with spatially extended (tubelike) unsynchronized filaments], a prime example of spontaneous synchrony breaking in systems of identical oscillators. In the case of complex oscillatory systems, this leads to a topological superstructure combining knotted filaments and synchronization defect sheets.

  15. Expanded Polytetrafluoroethylene for Chordal Replacement: Preventing Knot Failure.

    PubMed

    Miller, Jacob R; Deeken, Corey R; Ray, Shuddhadeb; Henn, Matthew C; Lancaster, Timothy S; Schuessler, Richard B; Damiano, Ralph J; Melby, Spencer J

    2015-12-01

    Expanded polytetrafluoroethylene suture is commonly used for chordal replacement in mitral valve repair, but due to material characteristics, knots can unravel. Our aim was to determine the knot security, including how many throws are necessary to prevent knot failure, with Gore-Tex (W.L. Gore and Associates, Elkton, MD) and the newly available Chord-X (On-X Life Technologies Inc, Austin, TX). Knots were evaluated for maximal load based on: number of throws (6, 8, 10, and 12), tension to secure each throw (10%, 50%, and 85%) and suture type (Gore-Tex CV-5 and Chord-X 3-0). A physiologic force of 2 N was used for comparison. We evaluated 240 knots. For all knots, the mean load to failure was 11.1 ± 5.8 N. Failure occurred due to unraveling in 141 knots (59%) at 7.1 ± 4.1 N and to breaking in 99 (41%) at 16.7 ± 2.0 N (p < 0.01). Gore-Tex failed at higher loads (12.6 ± 6.0 N vs 9.5 ± 5.2 N, p < 0.01); however, an equivalent number, 6 Gore-Tex and 6 Chord-X, unraveled at 2 N, all with fewer than 10 throws. Expanded polytetrafluoroethylene has adequate strength to prevent breakage; however, a risk of knot unraveling at physiologic conditions exists when fewer than 10 throws are performed. Copyright © 2015 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  16. Flexor Tendon Repair With Looped Suture: 1 Versus 2 Knots.

    PubMed

    Gil, Joseph A; Skjong, Christian; Katarincic, Julia A; Got, Christopher

    2016-03-01

    To assess the strength of flexor tendon repair with looped suture. We hypothesized that, after passing the intact looped suture in the desired repair configuration, splitting the loop and tying 2 independent knots would increase the strength of flexor tendon repair. Thirty-two flexor tendons were harvested and were sharply transected in zone II. The tendons were repaired with a 4-strand core suture repair using 3-0 looped nonabsorbable nylon suture. The harvested tendons were randomly assigned and repaired with either a 1- or a 2-knot construct. The repaired flexor tendons were fixed in a servohydraulic material testing system and were loaded to failure either with uniaxial tension or cyclically. The average force at failure was 43 N for the 1-knot repair and 28 N for the 2-knot repair. The mode of failure of 15 of the flexor tendon repairs that were cyclically loaded to failure was suture pull-out. The average number of cycles and force in cyclic testing that caused failure of flexor tendon repairs was 134 cycles and 31 N for tendons repaired with looped 3-0 suture tied with 1 knot and 94 cycles and 33 N for tendons repaired with looped 3-0 suture tied with 2 knots. Our hypothesis was disproved by the results of this study. This study suggests that, when using looped suture, tying 2 independent knots instead of tying a single knot does not increase the strength of the flexor tendon repair. Copyright © 2016 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

  17. The beauty of knots at the molecular level.

    PubMed

    Sauvage, Jean-Pierre; Amabilino, David B

    2012-01-01

    What makes a given object look beautiful to the observer, be it in the macroscopic world or at the molecular level? This very general question will be briefly addressed at the beginning of this essay, in relation to contemporary molecular chemistry and biology, leading to the general statement that, most of the time, beauty is tightly connected to function as well as to the cultural background of the observer. The main topic of the present article will be that of topologically non-trivial molecules or molecular ensembles and the fascination that such species have exerted on molecular or solid state chemists. Molecules with a graph identical to Kuratowski's K₅ or K₃,₃ graphs are indeed highly attractive from an aesthetical viewpoint, but perhaps even more fascinating and beautiful are molecular knots. A general discussion will be devoted to these compounds, which are still considered as exotic species because of the very limited number of efficient synthetic strategies leading to their preparation. Particularly efficient are templated approaches based either on transition metals such as copper(I) or on organic groups able to form hydrogen bonds or acceptor-donor stacks. A particularly noteworthy property of knots, and in particular of the trefoil knot, is their topological chirality. The isolation of both enantiomers of the trefoil knot (3₁) could be achieved and showed that such species have fascinating chiroptical properties. Finally, various routes to more complex and beautiful knots than the trefoil knot, which is the simplest non-trivial knot, will be discussed in line with the remarkable ability of transition metals to gather and orient in a very precise fashion several organic components in their coordination spheres, thus leading to synthetic precursors displaying geometries which are perfectly well adapted to the preparation of the desired knots or links.

  18. Moduli spaces of vortex knots for an exact fluid flow

    NASA Astrophysics Data System (ADS)

    Bogoyavlenskij, Oleg

    2017-01-01

    The moduli spaces S ( D ) of non-isotopic vortex knots are introduced for the ideal fluid flows in invariant domains D . The analogous moduli spaces of the magnetic fields B knots are defined. We derive and investigate new exact fluid flows (and analogous plasma equilibria) satisfying the Beltrami equation which have nested invariant balls Bk 3 with radii Rk ≈ (k + 1) π, k⟶∞. The first flow is z-axisymmetric; the other ones do not possess any rotational symmetries. The axisymmetric flow has an invariant plane z = 0. Due to an involutive symmetry of the flow, its vortex knots in the invariant half-spaces z > 0 and z < 0 are equivalent. It is demonstrated that the moduli space 𝒮(ℝ3) for the derived fluid flow in ℝ3 is naturally isomorphic to the set of all rational numbers p/q in the interval J 1 : 0 . 25 < q < M ˜ 1 ≈ 0 . 5847 , where q is the safety factor. For the fluid flow in the first invariant ball B1 3 , it is shown that all values of the safety factor q belong to a small interval of length ℓ ≈ 0.1261. It is established that only torus knots Kp,q with 0.25 < p/q < 0.5847 are realized as vortex knots for the constructed flow in ℝ3. Each torus knot Kp,q with 0.25 < p/q < 0.5 is realized on countably many invariant tori Tk 2 located between the invariant spheres Sk 2 and Sk + 1 2 , while torus knots with 0 . 5 < p / q < M ˜ 1 are realized only on finitely many invariant tori. The moduli spaces S m ( Ba 3 ) ( m = 1 , 2 , … ) of vortex knots are constructed for some axisymmetric steady fluid flows that are solutions to the boundary eigenvalue problem for the curl operator on a ball Ba 3 .

  19. Topological Strings, Double Affine Hecke Algebras, and Exceptional Knot Homology

    NASA Astrophysics Data System (ADS)

    Elliot, Ross F.

    In this thesis, we consider two main subjects: refined, composite invariants and exceptional knot homologies of torus knots. The main technical tools are double affine Hecke algebras ("DAHA") and various insights from topological string theory. In particular, we define and study the composite DAHA-superpolynomials of torus knots, which depend on pairs of Young diagrams and generalize the composite HOMFLY-PT polynomials from the full HOMFLY-PT skein of the annulus. We also describe a rich structure of differentials that act on homological knot invariants for exceptional groups. These follow from the physics of BPS states and the adjacencies/spectra of singularities associated with Landau-Ginzburg potentials. At the end, we construct two DAHA-hyperpolynomials which are closely related to the Deligne-Gross exceptional series of root systems. In addition to these main themes, we also provide new results connecting DAHA-Jones polynomials to quantum torus knot invariants for Cartan types A and D, as well as the first appearance of quantum E6 knot invariants in the literature.

  20. Colored HOMFLY polynomials of knots presented as double fat diagrams

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.; Morozov, An.; Ramadevi, P.; Singh, Vivek Kumar

    2015-07-01

    Many knots and links in S 3 can be drawn as gluing of three manifolds with one or more four-punctured S 2 boundaries. We call these knot diagrams as double fat graphs whose invariants involve only the knowledge of the fusion and the braiding matrices of four -strand braids. Incorporating the properties of four-point conformal blocks in WZNW models, we conjecture colored HOMFLY polynomials for these double fat graphs where the color can be rectangular or non-rectangular representation. With the recent work of Gu-Jockers, the fusion matrices for the non-rectangular [21] representation, the first which involves multiplicity is known. We verify our conjecture by comparing with the [21] colored HOMFLY of many knots, obtained as closure of three braids. The conjectured form is computationally very effective leading to writing [21]-colored HOMFLY polynomials for many pretzel type knots and non-pretzel type knots. In particular, we find class of pretzel mutants which are distinguished and another class of mutants which cannot be distinguished by [21] representation. The difference between the [21]-colored HOMFLY of two mutants seems to have a general form, with A-dependence completely defined by the old conjecture due to Morton and Cromwell. In particular, we check it for an entire multi-parametric family of mutant knots evaluated using evolution method.

  1. Shunt insufficiency due to knot formation in the peritoneal catheter.

    PubMed

    Fekete, Gábor; Nagy, Andrea; Pataki, István; Bognar, László; Novák, László

    2013-07-30

    The authors report a rare case of the peripheral obstruction of a ventriculoperitoneal shunt. Premature baby was operated on hydrocephalus due to germinal matrix bleeding. After two months of implantation of venticuloperitoneal shunt peripheral insufficiency of the system was emerged. During the shunt revision extensive knot formation became visible. We simply cut the catheter above the knot and the working shunt was replaced into the abdominal cavity. The postoperative course was uneventful and the baby was free of complaints for more than one year. The pathomechanism of knot formation is not clear thus the discovery of the problem during the operation is an unexpected event. In our opinion tight knot cannot be spontaneously formed intraabdominally. Loose knots can be developed and can reduce the capacity of liquor flow. We think that the knot tightens during pulling out. Longer peritoneal catheters can precipitate multiple looping and/or axial torquations and increase the peripheral resistance of the shunt. In such cases when the pulling out is challenged conversion to laparotomy is suggested.

  2. Knots can impair protein degradation by ATP-dependent proteases.

    PubMed

    San Martín, Álvaro; Rodriguez-Aliaga, Piere; Molina, José Alejandro; Martin, Andreas; Bustamante, Carlos; Baez, Mauricio

    2017-09-12

    ATP-dependent proteases translocate proteins through a narrow pore for their controlled destruction. However, how a protein substrate containing a knotted topology affects this process remains unknown. Here, we characterized the effects of the trefoil-knotted protein MJ0366 from Methanocaldococcus jannaschii on the operation of the ClpXP protease from Escherichia coli ClpXP completely degrades MJ0366 when pulling from the C-terminal ssrA-tag. However, when a GFP moiety is appended to the N terminus of MJ0366, ClpXP releases intact GFP with a 47-residue tail. The extended length of this tail suggests that ClpXP tightens the trefoil knot against GFP, which prevents GFP unfolding. Interestingly, if the linker between the knot core of MJ0366 and GFP is longer than 36 residues, ClpXP tightens and translocates the knot before it reaches GFP, enabling the complete unfolding and degradation of the substrate. These observations suggest that a knot-induced stall during degradation of multidomain proteins by AAA proteases may constitute a novel mechanism to produce partially degraded products with potentially new functions.

  3. Antiviral Cystine Knot α-Amylase Inhibitors from Alstonia scholaris*

    PubMed Central

    Nguyen, Phuong Quoc Thuc; Ooi, Justin Seng Geap; Nguyen, Ngan Thi Kim; Wang, Shujing; Huang, Mei; Liu, Ding Xiang; Tam, James P.

    2015-01-01

    Cystine knot α-amylase inhibitors are cysteine-rich, proline-rich peptides found in the Amaranthaceae and Apocynaceae plant species. They are characterized by a pseudocyclic backbone with two to four prolines and three disulfides arranged in a knotted motif. Similar to other knottins, cystine knot α-amylase inhibitors are highly resistant to degradation by heat and protease treatments. Thus far, only the α-amylase inhibition activity has been described for members of this family. Here, we show that cystine knot α-amylase inhibitors named alstotides discovered from the Alstonia scholaris plant of the Apocynaceae family display antiviral activity. The alstotides (As1–As4) were characterized by both proteomic and genomic methods. All four alsotides are novel, heat-stable and enzyme-stable and contain 30 residues. NMR determination of As1 and As4 structures reveals their conserved structural fold and the presence of one or more cis-proline bonds, characteristics shared by other cystine knot α-amylase inhibitors. Genomic analysis showed that they contain a three-domain precursor, an arrangement common to other knottins. We also showed that alstotides are antiviral and cell-permeable to inhibit the early phase of infectious bronchitis virus and Dengue infection, in addition to their ability to inhibit α-amylase. Taken together, our results expand membership of cystine knot α-amylase inhibitors in the Apocynaceae family and their bioactivity, functional promiscuity that could be exploited as leads in developing therapeutics. PMID:26546678

  4. Methyl Transfer by Substrate Signaling from a Knotted Protein Fold

    PubMed Central

    Christian, Thomas; Sakaguchi, Reiko; Perlinska, Agata P.; Lahoud, Georges; Ito, Takuhiro; Taylor, Erika A.; Yokoyama, Shigeyuki; Sulkowska, Joanna I.; Hou, Ya-Ming

    2017-01-01

    Proteins with knotted configurations are restricted in conformational space relative to unknotted proteins. Little is known if knotted proteins have sufficient dynamics to communicate between spatially separated substrate-binding sites. In bacteria, TrmD is a methyl transferase that uses a knotted protein fold to catalyze methyl transfer from S-adenosyl methionine (AdoMet) to G37-tRNA. The product m1G37-tRNA is essential for life as a determinant to maintain protein synthesis reading-frame. Using an integrated approach of structure, kinetic, and computational analysis, we show here that the structurally constrained TrmD knot is required for its catalytic activity. Unexpectedly, the TrmD knot has complex internal movements that respond to AdoMet binding and signaling. Most of the signaling propagates the free energy of AdoMet binding to stabilize tRNA binding and to assemble the active site. This work demonstrates new principles of knots as an organized structure that captures the free energies of substrate binding to facilitate catalysis. PMID:27571175

  5. Comparison of tensile strength of slip knots with that of 3-1-1 knots using 10-0 nylon sutures.

    PubMed

    Lutchman, Carla R; Leung, Linus H; Moineddin, Rahim; Chew, Hall F

    2014-04-01

    The aim of this study was to compare the tensile strength of slip knots with that of 3-1-1 knots using 10-0 nylon sutures. In vitro, destructive materials testing was used. By adhering to the American Standard for Testing and Materials standards for testing of suture materials, slip knots were compared with 3-1-1 knots using 10-0 nylon suture material. Tensile testing was performed on each knot type using the Instron Microtester (Model 5848 Norwood, MA). Scanning electron microscopy was used to analyze all sutures tested to failure. The main outcome measure was the maximum load (newtons) or ultimate tensile strength before which each knot failed by breakage or by unraveling. The mean force resulting in failure by breakage of the 3-1-1 knot and slip knot was 0.71 and 0.64 N, respectively (P = 0.048). The mean force resulting in failure by the unraveling of the 3-1-1 knot and slip knot was 0.48 and 0.37 N, respectively (P = 0.022). In 10-0 nylon sutures, the 3-1-1 knot has a statistically significant greater tensile strength than the slip knot has in conditions wherein they fail by either breakage or unraveling.

  6. Knot Security- How is it Affected by Suture Technique, Material, Size, and Number of Throws?

    PubMed

    Silver, Eric; Wu, Rong; Grady, James; Song, Liansheng

    2016-07-01

    To measure knot security in relation to different surgical knotting techniques, suture materials, suture sizes, and number of throws commonly used in oral and maxillofacial surgery. Three surgical tying techniques were tested: square, surgeon's, and sliding knots. Suture materials included chromic gut, nylon, silk, and Vicryl (polyglycolic acid). Suture diameter sizes 3-0, 4-0, and 5-0 were tested. Ten trials were undertaken for each combination of material, size, and technique using 2, 3, 4, 5, and 6 throws (ties). Suture materials were presoaked in 0.9% saline solution for 15 minutes to simulate the environment of the oral cavity. A standard knot-tying force for each throw was applied to each combination. Knot security satisfaction was set from pilot experimental trials at less than 1.8-mm slippage from the center of the knot while testing. The dichotomous outcome of knot slippage (stable or unstable) was analyzed using logistic regression analysis and odds ratios with Tukey-adjusted 95% confidence intervals. Knot security depended on suture technique, material, and number of throws but did not depend on suture size. In general, 4 throws were required for surgeon's and square knots, whereas 5 throws were required for sliding knots. After 5 throws, tying an additional throw did not contribute to knot security. Surgeon's knots were stronger than square knots and sliding knots (P < .0001 and P < .0001). Square knots were stronger than sliding knots (P = .01). Vicryl had the greatest knot security, followed by chromic gut, nylon, and silk. This study showed that knot security depends on suture material, tying technique, and number of throws, but is independent of suture size. Surgeon's knot security was greater than that for square and sliding knots when using sutures commonly used in the oral cavity. Vicryl had the greatest knot security and silk had the least. For surgeon's and square knots, at least 4 throws were generally indicated to achieve knot security; for

  7. Knots Untie: Molecular Determinants Involved in Knot Formation Induced by Pseudomonas savastanoi in Woody Hosts

    PubMed Central

    Caballo-Ponce, Eloy; Murillo, Jesús; Martínez-Gil, Marta; Moreno-Pérez, Alba; Pintado, Adrián; Ramos, Cayo

    2017-01-01

    The study of the molecular basis of tree diseases is lately receiving a renewed attention, especially with the emerging perception that pathogens require specific pathogenicity and virulence factors to successfully colonize woody hosts. Pathosystems involving woody plants are notoriously difficult to study, although the use of model bacterial strains together with genetically homogeneous micropropagated plant material is providing a significant impetus to our understanding of the molecular determinants leading to disease. The gammaproteobacterium Pseudomonas savastanoi belongs to the intensively studied Pseudomonas syringae complex, and includes three pathogenic lineages causing tumorous overgrowths (knots) in diverse economically relevant trees and shrubs. As it occurs with many other bacteria, pathogenicity of P. savastanoi is dependent on a type III secretion system, which is accompanied by a core set of at least 20 effector genes shared among strains isolated from olive, oleander, and ash. The induction of knots of wild-type size requires that the pathogen maintains adequate levels of diverse metabolites, including the phytohormones indole-3-acetic acid and cytokinins, as well as cyclic-di-GMP, some of which can also regulate the expression of other pathogenicity and virulence genes and participate in bacterial competitiveness. In a remarkable example of social networking, quorum sensing molecules allow for the communication among P. savastanoi and other members of the knot microbiome, while at the same time are essential for tumor formation. Additionally, a distinguishing feature of bacteria from the P. syringae complex isolated from woody organs is the possession of a 15 kb genomic island (WHOP) carrying four operons and three other genes involved in degradation of phenolic compounds. Two of these operons mediate the catabolism of anthranilate and catechol and, together with another operon, are required for the induction of full-size tumors in woody hosts

  8. To Knot or Not-That is the Question: A Nanofluidic Knot Factory based on Compression of Single DNA Molecules against Slit Barriers in Nanochannels

    NASA Astrophysics Data System (ADS)

    Amin, Susan; Khorshid, Ahmed; Zeng, Lili; Zimny, Philip; Reisner, Walter

    Knots can form during DNA packaging in chromosome and obstruct mapping of DNA in nanochannels. Studies have focused on theoretical and numerical studies of knots, but an efficient and fully controlled means of knotting has not yet been explored. Here, we introduce a knot factory on chip based on pneumatic compression of single T4 DNA against a slit barrier in a nanochannel. The DNA are compressed to a well-defined fraction of their initial equilibrium extension. The pressure is then released and the DNA molecules relax back to their equilibrium extension; knots are present along the relaxed DNA, visualized as sharply localized regions of high intensity. Via repeated compression and relaxation, we can measure the probabilities of forming single and multiple knot states and the distribution of knot sizes as a function of fractional compression and waiting time in the compressed state. We show that the total probability of knot formation increases with greater compression and waiting time.These findings are well described via a knot formation free energy derived from scaling arguments, suggesting that the enhanced knotting probability at high compression arises from avoiding the free energy cost due to self-exclusion interactions that would arise from contour stored in the knot.

  9. Velocity dispersions of knots in Vela X and Puppis A

    NASA Technical Reports Server (NTRS)

    Shull, P., Jr.

    1983-01-01

    Very high resolution spectroscopy of optical emission lines indicates that the velocity dispersions of knots in Vela X and Puppis A result primarily from turbulence within the emitting regions. Line-of-sight velocity dispersions (half-widths at half-maximum) for the observed knots in both remnants are about 20-30 km/s. In Vela X, these include thermal velocity dispersions of roughly 16 km/s for hydrogen and 4 km/s for nitrogen. The knots themselves move randomly relative to each other, with speeds up to 30 km/s in Vela X and between 30-80 km/s in Puppis A. Occasionally, diffuse components of the filaments are observed in Puppis A. These diffuse components have velocity dispersions between 55 and 80 km/s, but the relative contributions of turbulent and thermal motions to the dispersions are unknown. The results are compared with theory and previous observations. Direct photographs may be able to show if the forbidden O III knots are less spatially dispersed than the forbidden N II, forbidden S II, forbidden O II, and H I knots.

  10. Equations on knot polynomials and 3d/5d duality

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.

    2012-10-01

    We briefly review the current situation with various relations between knot/braid polynomials (Chern-Simons correlation functions), ordinary and extended, considered as functions of the representation and of the knot topology. These include linear skein relations, quadratic Plucker relations, as well as "differential" and (quantum) ̂A-polynomial structures. We pay a special attention to identity between the ̂A-polynomial equations for knots and Baxter equations for quantum relativistic integrable systems, related through Seiberg-Witten theory to 5d super-Yang-Mills models and through the AGT relation to the q-Virasoro algebra. This identity is an important ingredient of emerging a 3d - 5d generalization of the AGT relation. The shape of the Baxter equation (including the values of coefficients) depend on the choice of the knot/braid. Thus, like the case of KP integrability, where (some, so far torus) knots parameterize particular points of the Universal Grassmannian, in this relation they parameterize particular points in the moduli space of many-body integrable systems of relativistic type.

  11. Equations on knot polynomials and 3d/5d duality

    SciTech Connect

    Mironov, A.; Morozov, A.

    2012-09-24

    We briefly review the current situation with various relations between knot/braid polynomials (Chern-Simons correlation functions), ordinary and extended, considered as functions of the representation and of the knot topology. These include linear skein relations, quadratic Plucker relations, as well as 'differential' and (quantum) A-polynomial structures. We pay a special attention to identity between the A-polynomial equations for knots and Baxter equations for quantum relativistic integrable systems, related through Seiberg-Witten theory to 5d super-Yang-Mills models and through the AGT relation to the q-Virasoro algebra. This identity is an important ingredient of emerging a 3d- 5d generalization of the AGT relation. The shape of the Baxter equation (including the values of coefficients) depend on the choice of the knot/braid. Thus, like the case of KP integrability, where (some, so far torus) knots parameterize particular points of the Universal Grassmannian, in this relation they parameterize particular points in the moduli space of many-body integrable systems of relativistic type.

  12. Explicit formulae for Chern-Simons invariants of the twist-knot orbifolds and edge polynomials of twist knots

    NASA Astrophysics Data System (ADS)

    Ham, J.-Y.; Lee, J.

    2016-09-01

    We calculate the Chern-Simons invariants of twist-knot orbifolds using the Schläfli formula for the generalized Chern-Simons function on the family of twist knot cone-manifold structures. Following the general instruction of Hilden, Lozano, and Montesinos-Amilibia, we here present concrete formulae and calculations. We use the Pythagorean Theorem, which was used by Ham, Mednykh and Petrov, to relate the complex length of the longitude and the complex distance between the two axes fixed by two generators. As an application, we calculate the Chern-Simons invariants of cyclic coverings of the hyperbolic twist-knot orbifolds. We also derive some interesting results. The explicit formulae of the A-polynomials of twist knots are obtained from the complex distance polynomials. Hence the edge polynomials corresponding to the edges of the Newton polygons of the A-polynomials of twist knots can be obtained. In particular, the number of boundary components of every incompressible surface corresponding to slope -4n+2 turns out to be 2. Bibliography: 39 titles.

  13. Knots, Braids and Hedgehogs from the Eikonal Equation

    NASA Astrophysics Data System (ADS)

    Wereszczyński, A.

    The complex eikonal equation in the three space dimensions is considered. We show that apart from the recently found torus knots, this equation can also generate other topological configurations with a nontrivial value of the π2(S2) index: braided open strings as well as hedgehogs. In particular, cylindric strings, i.e. string solutions located on a cylinder with a constant radius are found. Moreover, solutions describing strings lying on an arbitrary surface topologically equivalent to cylinder are presented. We discuss them in the context of the eikonal knots. The physical importance of the results originates in the fact that the eikonal knots have been recently used to approximate the Faddeev-Niemi hopfions.

  14. Classification of knotted tori in 2-metastable dimension

    SciTech Connect

    Cencelj, Matija; Repovs, Dusan; Skopenkov, Mihail B

    2012-11-30

    This paper is devoted to the classical Knotting Problem: for a given manifold N and number m describe the set of isotopy classes of embeddings N{yields}S{sup m}. We study the specific case of knotted tori, that is, the embeddings S{sup p} Multiplication-Sign S{sup q}{yields}S{sup m}. The classification of knotted tori up to isotopy in the metastable dimension range m {>=} p + 3/2q + 2, p{<=}q, was given by Haefliger, Zeeman and A. Skopenkov. We consider the dimensions below the metastable range and give an explicit criterion for the finiteness of this set of isotopy classes in the 2-metastable dimension. Bibliography: 35 titles.

  15. BPS states in the Ω-background and torus knots

    NASA Astrophysics Data System (ADS)

    Bulycheva, K.; Gorsky, A.

    2014-04-01

    We clarify some issues concerning the central charges saturated by the extended objects in the SUSY U(1) 4 d gauge theory in the Ω-background. The configuration involving the monopole localized at the domain wall is considered in some details. At the rational ratio the trajectory of the monopole provides the torus ( p,q) knot in the squashed three-sphere. Using the relation between the integrable systems of Calogero type at the rational couplings and the torus knots we interpret this configuration in terms of the auxiliary 2 d quiver theory or 3 d theory with nontrivial boundary conditions. This realization can be considered as the AGT-like representation of the torus knot invariants.

  16. Emission Knots and Polarization Swings of Swinging Jets

    NASA Astrophysics Data System (ADS)

    Lyutikov, Maxim; Kravchenko, Evgeniya

    2016-12-01

    Knots (emission features in jets of active galactic nuclei) often show non-ballistic dynamics and variable emission/polarization properties. We model these features as emission pattern propagating in a jet that carries helical magnetic field and is launched along a changing direction. The model can reproduce a wide range of phenomena observed in the motion of knots: non-ballistic motion (both smooth and occasional sudden change of direction, and/or oscillatory behavior), variable brightness, confinement of knots' motion within an overlaying envelope. The model also reproduces smooth large polarization angle swings, and at the same time allows for the seemingly random behavior of synchrotron fluxes, polarization fraction and occasional $\\pi/2$ polarization jumps.

  17. Sorting ring polymers by knot type with modulated nanochannels.

    PubMed

    Marenda, Mattia; Orlandini, Enzo; Micheletti, Cristian

    2017-01-25

    In this theoretical study we discuss a novel method for sorting ring polymers according to their topological, knotted state. The proposed approach harnesses the rich dynamical behaviour of polymers confined inside spatially-modulated nanochannels. The longitudinal mobility of the rings is shown to have two key properties that are ideally suited for knot sorting. First, at fixed topology, the mobility has an intriguing oscillatory dependence on chain length. Second, the mobility ranking of different knot types is inverted upon increasing the chain length. We show that this complex interplay of channel geometry, chain length and topology can be rationalised within a simple theoretical framework based on Fick-Jacobs's diffusive theory. The results and the interpretative scheme ought to be useful for designing microfluidic devices with optimal topological sorting capabilities.

  18. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings

    NASA Astrophysics Data System (ADS)

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-01

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.

  19. Extraordinary line-emitting knots in the Crab Nebula

    NASA Technical Reports Server (NTRS)

    Macalpine, Gordon M.; Lawrence, Stephen S.; Brown, Beth A.; Uomoto, Alan; Woodgate, Bruce E.; Brown, Larry W.; Oliversen, Ronald J.; Lowenthal, James D.; Liu, Charles

    1994-01-01

    Extraordinary, semistellar, line-emitting knots are apparent in images of the Crab Nebula which were obtained with the Goddard Fabry-Perot imager at the Michigan-Dartmouth-MIT Observatory. The knots are most prominent for (O III) lambda 5007 emission through a 5.3 A (Full Width at Half Maximum (FWHM)) bandpass centered at 5015.3 A, with representative fluxes of roughly 10(exp -14) ergs/sq cm. They are aligned in arcs, seven to the north and four to the south, from the pulsar. The northern group appears to be in a bounded corridor through the filamentary structure. Measurements over a 2 year baseline yield proper motions of order 0.1 sec/yr, corresponding to transverse velocities of order 900 km/s for a distance of 1830 pc. The knots are characterized by remarkably strong (Ar III) emission, possibly indicating high argon abundances, high gas temperatures, or anomalous physical processes.

  20. The average shape of the closed trefoil knot fluctuating on a floppy rope.

    PubMed

    Modlinski, Marcin; Przybyl, Sylwester; Pieranski, Piotr

    2013-05-01

    The average shape of the trefoil knot tied on a floppy, hard rope subject to thermal fluctuations has been determined. The fluctuations of the shape of knots were performed by random bending. As a result of the changing shape procedure large sets of deformed conformations of the initial knot were obtained. Afterwards, these sets were subject to the shape-fitting procedure. It has been found that the conformation is different from the ideal conformation of the knot.

  1. In vitro evaluation of square and surgeon's knots in large gauge suture.

    PubMed

    Gillen, Alex M; Munsterman, Amelia S; Farag, Ramsis; Coleridge, Matthew O D; Hanson, R Reid

    2017-02-01

    To investigate the strength and size of surgeon's and square knots for starting and ending continuous suture lines using large gauge suture. In vitro mechanical study. Knotted suture. Surgeon's and square knots were tested using 2 and 3 USP polyglactin 910 and 2 USP polydioxanone under linear tension on a universal testing machine. Failure mode and knot holding capacity (KHC) were recorded, and relative knot security (RKS) was calculated as a percentage of KHC. Comparisons were made between number of throws, suture size, suture type, and knot types. Knot volume and weight were assessed by a digital micrometer and balance, respectively. There were no significant differences in KHC (P = .295), RKS (P = .307), volume (P = .128), or weight (P = .310) between square and surgeon's knots at the start or end of suture lines with the same number of throws and suture type. A minimum of 6 throws were required for start knots and 7 throws at end knots to prevent unraveling. Knots tied with 3 polyglactin 910 were strongest (P < .001) and 2 polyglactin 910 produced knots with higher KHC and RKS than 2 polydioxanone (P < .001). No consistent differences were detected between knots types tied with the same suture material; however, number of throws affected KHC and RKS up to 6 throws in start or 7 throws in end knots. The configuration of square and surgeon's knots performed at the end of a continuous line alters their KHC, supporting the use of additional throws for knot security. © 2017 The American College of Veterinary Surgeons.

  2. Antiviral Cystine Knot α-Amylase Inhibitors from Alstonia scholaris.

    PubMed

    Nguyen, Phuong Quoc Thuc; Ooi, Justin Seng Geap; Nguyen, Ngan Thi Kim; Wang, Shujing; Huang, Mei; Liu, Ding Xiang; Tam, James P

    2015-12-25

    Cystine knot α-amylase inhibitors are cysteine-rich, proline-rich peptides found in the Amaranthaceae and Apocynaceae plant species. They are characterized by a pseudocyclic backbone with two to four prolines and three disulfides arranged in a knotted motif. Similar to other knottins, cystine knot α-amylase inhibitors are highly resistant to degradation by heat and protease treatments. Thus far, only the α-amylase inhibition activity has been described for members of this family. Here, we show that cystine knot α-amylase inhibitors named alstotides discovered from the Alstonia scholaris plant of the Apocynaceae family display antiviral activity. The alstotides (As1-As4) were characterized by both proteomic and genomic methods. All four alsotides are novel, heat-stable and enzyme-stable and contain 30 residues. NMR determination of As1 and As4 structures reveals their conserved structural fold and the presence of one or more cis-proline bonds, characteristics shared by other cystine knot α-amylase inhibitors. Genomic analysis showed that they contain a three-domain precursor, an arrangement common to other knottins. We also showed that alstotides are antiviral and cell-permeable to inhibit the early phase of infectious bronchitis virus and Dengue infection, in addition to their ability to inhibit α-amylase. Taken together, our results expand membership of cystine knot α-amylase inhibitors in the Apocynaceae family and their bioactivity, functional promiscuity that could be exploited as leads in developing therapeutics. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. The reality principle, tragic knots, and the analytic process.

    PubMed

    Schafer, Roy

    2007-01-01

    Civilization and Its Discontents is shown to occupy a special place in Freud's development of psychoanalytic theory and technique. Especially emphasized is its implications for an inclusive understanding of the reality principle. The concept tragic knots is then defined and used to emphasize Freud's readiness to include tragic elements in that principle. An extended section then illustrates the spread of tragic knots into several diverse aspects of human existence: victimization, intimacy, and maintaining privacy. Finally, implications are drawn for the clinical assessment of working through unconscious conflicts.

  4. A plasmon model for the knots of M 87

    NASA Astrophysics Data System (ADS)

    Qian, S.-J.

    1983-12-01

    A plasmon model of the optical-radio knots of M 87 is discussed in terms of the observed characteristics of the galactic jet. The physical properties of the jet are summarized, and the spectral evolution of the jet and knots is studied, taking expansion, Fermi acceleration, and synchrotron radiation into account. A Fermi acceleration coefficient of about 10 to the 9th/s is obtained, and it is shown that a spectral break should occur at about 5 x 10 to the 14th Hz and should vary quite slowly with time, in agreement with observations.

  5. Affine reflection groups for tiling applications: Knot theory and DNA

    NASA Astrophysics Data System (ADS)

    Bodner, M.; Patera, J.; Peterson, M.

    2012-01-01

    We present in this paper some non-conventional applications of affine Weyl groups Waff of rank 2, the symmetry group of the tiling/lattice. We first develop and present the tools for applications requiring tilings of a real Euclidean plane {R}^2. We then elucidate the equivalence of these tilings with 2D projections of knots. The resulting mathematical structure provides a framework within which is encompassed recent work utilizing knot theory for modeling the structure and function of genetic molecules, specifically the action of particular enzymes in altering the topology of DNA in site-specific recombination.

  6. Knots and physics: Old wine in new bottles

    NASA Astrophysics Data System (ADS)

    Hirshfeld, Allen C.

    1998-12-01

    The history of the interplay between physics and mathematics in the theory of knots is briefly reviewed. In particular, Gauss' original definition of the linking number in the context of electromagnetism is presented, along with analytical, algebraical, and geometrical derivations. In a modern context, the linking number appears in the first-order term in the perturbation expansion of a Wilson loop in Chern-Simons quantum field theory. New knot invariants, the Vassiliev numbers, arise in higher-order terms of the expansion, and can be written in a form which shows them to be generalizations of the linking number.

  7. Influence of a knot on the stretching-induced crystallization of a polymer

    NASA Astrophysics Data System (ADS)

    Saitta, A. Marco; Klein, Michael L.

    2002-04-01

    The effect of stretching a polymer sample containing a single trefoil knot has been studied by computer simulation molecular dynamics calculations. Under axial load that approximates a fiber extrusion process, the knot is found to nucleate crystallization of the sample, which occurs on the ns time scale. The extension of the strain field associated with the knot has been quantified.

  8. A Comparative Study in Learning Curves of Two Different Intracorporeal Knot Tying Techniques.

    PubMed

    Thiyagarajan, Manuneethimaran; Ravindrakumar, Chandru

    2016-01-01

    Objectives. In our study we are aiming to analyse the learning curves in our surgical trainees by using two standard methods of intracorporeal knot tying. Material and Method. Two randomized groups of trainees are trained with two different intracorporeal knot tying techniques (loop and winding) by single surgeon for eight sessions. In each session participants were allowed to make as many numbers of knots in thirty minutes. The duration for each set of knots and the number of knots for each session were calculated. At the end each session, participants were asked about their frustration level, difficulty in making knot, and dexterity. Results. In winding method the number of knots tied was increasing significantly in each session with less frustration and less difficulty level. Discussion. The suturing and knotting skill improved in every session in both groups. But group B (winding method) trainees made significantly higher number of knots and they took less time for each set of knots than group A (loop method). Although both knotting methods are standard methods, the learning curve is better in loop method. Conclusion. The winding method of knotting is simpler and easier to perform, especially for the surgeons who have limited laparoscopic experience.

  9. Knot, heartwood, and sapwood extractives related to VOCs from drying southern pine lumber

    Treesearch

    Leonard L. Ingram; M. Curry Templeton; G. Wayne McGraw; Richard W. Hemingway

    2000-01-01

    The presence of knots or heartwood influences the amount and composition of volatile organic compound (VOC) emissions associated with drying of southern pine lumber. Experimental kiln charges of lumber containing 0 to 5% of knot volume gave VOC emissions ranging from 2.86 to 4.25 lb of carbonldry ton of wood. Studies of emissions from sapwood and knots showed that...

  10. Tying a Molecular Overhand Knot of Single Handedness and Asymmetric Catalysis with the Corresponding Pseudo-D3-Symmetric Trefoil Knot

    PubMed Central

    2016-01-01

    We report the stereoselective synthesis of a left-handed trefoil knot from a tris(2,6-pyridinedicarboxamide) oligomer with six chiral centers using a lanthanide(III) ion template. The oligomer folds around the lanthanide ion to form an overhand knot complex of single handedness. Subsequent joining of the overhand knot end groups by ring-closing olefin metathesis affords a single enantiomer of the trefoil knot in 90% yield. The knot topology and handedness were confirmed by NMR spectroscopy, mass spectrometry, and X-ray crystallography. The pseudo-D3-symmetric knot was employed as an asymmetric catalyst in Mukaiyama aldol reactions, generating enantioselectivities of up to 83:17 er, which are significantly higher than those obtained with a comparable unknotted ligand complex. PMID:27667319

  11. Comparing the tensile strength of square and reversing half-hitch alternating post knots

    PubMed Central

    Wu, Vincent; Sykes, Edward A.; Mercer, Dale; Hopman, Wilma M.; Tang, Ephraim

    2017-01-01

    Background Square knots are the gold standard in hand-tie wound closure, but are difficult to reproduce in deep cavities, inadvertently resulting in slipknots. The reversing half-hitch alternating post (RHAP) knot has been suggested as an alternative owing to its nonslip nature and reproducibility in limited spaces. We explored whether the RHAP knot is noninferior to the square knot by assessing tensile strength. Methods We conducted 10 trials for each baseline and knot configuration, using 3–0 silk and 3–0 polyglactin 910 sutures. We compared tensile strength between knot configurations at the point of knot failure between slippage and breakage. Results Maximal failure strength (mean ± SD) in square knots was reached with 4-throw in both silk (30 ± 1.5 N) and polyglactin 910 (39 ± 12 N). For RHAP knots, maximal failure strength was reached at 5-throw for both silk (31 ± 1.5 N) and polyglactin 910 (41 ± 13 N). In both sutures, there were no strength differences between 3-throw square and 4-throw RHAP, between 4-throw square and 5-throw RHAP, or between 5-throw square and 6-throw RHAP knots. Polyglactin 910 sutures, in all knot configurations, were more prone to slippage than silk sutures (p < 0.001). Conclusion The difference in mean tensile strength could be attributed to the proportion of knot slippage versus breakage, which is material-dependent. Future studies can re-evaluate findings in monofilament sutures and objectively assess the reproducibility of square and RHAP knots in deep cavities. Our results indicate that RHAP knots composed of 1 extra throw provide equivalent strength to square knots and may be an alternative when performing hand-ties in limited cavities with either silk or polyglactin 910 sutures. PMID:28327276

  12. Comparing the tensile strength of square and reversing half-hitch alternating post knots.

    PubMed

    Wu, Vincent; Sykes, Edward A; Mercer, Dale; Hopman, Wilma M; Tang, Ephraim

    2017-06-01

    Square knots are the gold standard in hand-tie wound closure, but are difficult to reproduce in deep cavities, inadvertently resulting in slipknots. The reversing half-hitch alternating post (RHAP) knot has been suggested as an alternative owing to its nonslip nature and reproducibility in limited spaces. We explored whether the RHAP knot is noninferior to the square knot by assessing tensile strength. We conducted 10 trials for each baseline and knot configuration, using 3-0 silk and 3-0 polyglactin 910 sutures. We compared tensile strength between knot configurations at the point of knot failure between slippage and breakage. Maximal failure strength (mean ± SD) in square knots was reached with 4-throw in both silk (30 ± 1.5 N) and polyglactin 910 (39 ± 12 N). For RHAP knots, maximal failure strength was reached at 5-throw for both silk (31 ± 1.5 N) and polyglactin 910 (41 ± 13 N). In both sutures, there were no strength differences between 3-throw square and 4-throw RHAP, between 4-throw square and 5-throw RHAP, or between 5-throw square and 6-throw RHAP knots. Polyglactin 910 sutures, in all knot configurations, were more prone to slippage than silk sutures (p < 0.001). The difference in mean tensile strength could be attributed to the proportion of knot slippage versus breakage, which is material-dependent. Future studies can re-evaluate findings in monofilament sutures and objectively assess the reproducibility of square and RHAP knots in deep cavities. Our results indicate that RHAP knots composed of 1 extra throw provide equivalent strength to square knots and may be an alternative when performing hand-ties in limited cavities with either silk or polyglactin 910 sutures.

  13. Knot-Controlled Ejection of a Polymer from a Virus Capsid

    NASA Astrophysics Data System (ADS)

    Matthews, Richard; Louis, A. A.; Yeomans, J. M.

    2009-02-01

    We present a numerical study of the effect of knotting on the ejection of flexible and semiflexible polymers from a spherical, viruslike capsid. The polymer ejection rate is primarily controlled by the knot, which moves to the hole in the capsid and then acts as a ratchet. Polymers with more complex knots eject more slowly and, for large knots, the knot type, and not the flexibility of the polymer, determines the rate of ejection. We discuss the relation of our results to the ejection of DNA from viral capsids and conjecture that this process has the biological advantage of unknotting the DNA before it enters a cell.

  14. Wall-crossing invariants: from quantum mechanics to knots

    SciTech Connect

    Galakhov, D. E-mail: galakhov@physics.rutgers.edu; Mironov, A. Morozov, A.

    2015-03-15

    We offer a pedestrian-level review of the wall-crossing invariants. The story begins from the scattering theory in quantum mechanics where the spectrum reshuffling can be related to permutations of S-matrices. In nontrivial situations, starting from spin chains and matrix models, the S-matrices are operatorvalued and their algebra is described in terms of R- and mixing (Racah) U-matrices. Then the Kontsevich-Soibelman (KS) invariants are nothing but the standard knot invariants made out of these data within the Reshetikhin-Turaev-Witten approach. The R and Racah matrices acquire a relatively universal form in the semiclassical limit, where the basic reshufflings with the change of moduli are those of the Stokes line. Natural from this standpoint are matrices provided by the modular transformations of conformal blocks (with the usual identification R = T and U = S), and in the simplest case of the first degenerate field (2, 1), when the conformal blocks satisfy a second-order Shrödinger-like equation, the invariants coincide with the Jones (N = 2) invariants of the associated knots. Another possibility to construct knot invariants is to realize the cluster coordinates associated with reshufflings of the Stokes lines immediately in terms of check-operators acting on solutions of the Knizhnik-Zamolodchikov equations. Then the R-matrices are realized as products of successive mutations in the cluster algebra and are manifestly described in terms of quantum dilogarithms, ultimately leading to the Hikami construction of knot invariants.

  15. Untangling Some Knots in K-8 Writing Instruction.

    ERIC Educational Resources Information Center

    Peterson, Shelley, Ed.

    This book brings together the perspectives of teachers, administrators, consultants, and researchers on teaching writing to create a bridge between theory and practice. The book's 11 chapters are organized into three sections that tackle some persistent knots of writing instruction and assessment. Under Section I-Students' and Teachers' Learning…

  16. Material Properties of Hagfish Skin, with Insights into Knotting Behaviors.

    PubMed

    Clark, Andrew J; Crawford, Callie H; King, Brooke D; Demas, Andrew M; Uyeno, Theodore A

    2016-06-01

    Hagfishes (Myxinidae) often integrate whole-body knotting movements with jawless biting motions when reducing large marine carcasses to ingestible items. Adaptations for these behaviors include complex arrangements of axial muscles and flexible, elongate bodies without vertebrae. Between the axial muscles and the hagfish skin is a large, blood-filled subcutaneous sinus devoid of the intricate, myoseptal tendon networks characteristic of the taut skins of other fishes. We propose that the loose-fitting skin of the hagfish facilitates the formation and manipulation of body knots, even if it is of little functional significance to steady swimming. Hagfish skin is a relatively thick, anisotropic, multilayered composite material comprising a superficial, thin, and slimy epidermis, a middle dermal layer densely packed with fibrous tissues, and a deep subdermal layer comprised of adipose tissue. Hagfish skin is stiffer when pulled longitudinally than circumferentially. Stress-strain data from uniaxial tensile tests show that hagfish skins are comparable in tensile strength and stiffness to the taut skins of elongate fishes that do not engage in knotting behaviors (e.g., sea lamprey and penpoint gunnel). Sheath-core-constructed ropes, which serve as more accurate models for hagfish bodies, demonstrate that loose skin (extra sheathing) enhances flexibility of the body (rope). Along with a loose-fitting skin, the morphologies of hagfish skin parallel those of moray eels, which are also known for generating and manipulating figure-eight-style body knots when struggling with prey. © 2016 Marine Biological Laboratory.

  17. Factorization of colored knot polynomials at roots of unity

    NASA Astrophysics Data System (ADS)

    Kononov, Ya.; Morozov, A.

    2015-07-01

    HOMFLY polynomials are the Wilson-loop averages in Chern-Simons theory and depend on four variables: the closed line (knot) in 3d space-time, representation R of the gauge group SU (N) and exponentiated coupling constant q. From analysis of a big variety of different knots we conclude that at q, which is a 2m-th root of unity, q2m = 1, HOMFLY polynomials in symmetric representations [ r ] satisfy recursion identity: Hr+m =Hr ṡHm for any A =qN, which is a generalization of the property Hr = H1r for special polynomials at m = 1. We conjecture a further generalization to arbitrary representation R, which, however, is checked only for torus knots. Next, Kashaev polynomial, which arises from HR at q2 = e 2 πi / | R |, turns equal to the special polynomial with A substituted by A| R |, provided R is a single-hook representations (including arbitrary symmetric) - what provides a q - A dual to the similar property of Alexander polynomial. All this implies non-trivial relations for the coefficients of the differential expansions, which are believed to provide reasonable coordinates in the space of knots - existence of such universal relations means that these variables are still not unconstrained.

  18. Coaxial rings and H2 knots in Hubble 12

    NASA Astrophysics Data System (ADS)

    Hsia, Chih-Hao; Kwok, Sun; Chau, Wayne; Zhang, Yong

    2016-07-01

    Hubble 12 (Hb 12) is a young planetary nebula (PN) exhibiting nested shells. We present new near-infrared narrow-band imaging observations of Hb 12 using the Canada-France- Hawaii Telescope (CFHT). A number of co-axial rings aligned with the bipolar lobes and two pairs of separate H2 knots with different orientations are detected.

  19. Coil Knotting during Endovascular Coil Embolization for Ruptured MCA Aneurysm

    PubMed Central

    Kwon, S.C.; Lyo, I.U.; Shin, S.H.; Park, J.B.; Kim, Y.

    2008-01-01

    Summary Complications during coil embolization of cerebral aneurysms include thromboembolic events, hemorrhagic complications related to procedural aneurysmal rupture and parent vessel perforation, and coil-related complications. The present report describes a rare coil-related complication involving spontaneous coil knotting. PMID:20557732

  20. Management of root-knot nematode, Meloidogyne incognita in carrot.

    PubMed

    Pedroche, Nordalyn B; Villanueva, Luciana M; De Waele, Dirk

    2009-01-01

    The root-knot nematode, Meloidogyne incognito, remains to be one of the most important constraints in agricultural production worldwide. However, reports showed that root-knot nematode (RKN) population can be suppressed by addition of organic amendments. A greenhouse microplot experiment was conducted to determine if locally available organic amendments would reduce RKN population and improve the growth and yield of more susceptible and less susceptible carrot cultivars in comparison with the farmers' practice. Residues of broccoli, chicken manure and Trichoderma inoculant were incorporated into the soil artificially infested with root-knot nematodes. Untreated microplots were provided as controls. Three months after transplanting, nematodes were recovered from the soil using the modified Baermann-tray technique and from the roots using staining technique. The number of root-knot nematodes was counted under the stereoscopic microscope. In the more susceptible cultivar New Kuroda, significantly lowest number of second stage juveniles (J2's) was recovered from the soil incorporated with broccoli left-over materials and Trichoderma inoculant while chicken manure-amended soil had the most number of J2's. Galls and egg masses in secondary roots were highest in unamended-inoculated soil which was significantly different from broccoli-amended soil with solarisation and Trichoderma inoculant. No significant differences were obtained among the treatments in the less susceptible cultivar Chunhong. The yield was significantly highest in broccoli-amended soil with solarisation and Trichoderma inoculant but no significant difference existed between the two cultivars tested. In general, the treatments with broccoli residues and Trichoderma inoculant were able to decrease root-knot nematode population and significantly increase the yield relative to untreated soil, however, differences between the two cultivars were not significant.

  1. The roles of impact and inertia in the failure of a shoelace knot

    NASA Astrophysics Data System (ADS)

    Daily-Diamond, Christopher A.; Gregg, Christine E.; O'Reilly, Oliver M.

    2017-04-01

    The accidental untying of a shoelace while walking often occurs without warning. In this paper, we discuss the series of events that lead to a shoelace knot becoming untied. First, the repeated impact of the shoe on the floor during walking serves to loosen the knot. Then, the whipping motions of the free ends of the laces caused by the leg swing produce slipping of the laces. This leads to eventual runaway untangling of the knot. As demonstrated using slow-motion video footage and a series of experiments, the failure of the knot happens in a matter of seconds, often without warning, and is catastrophic. The controlled experiments showed that increasing inertial effects of the swinging laces leads to increased rate of knot untying, that the directions of the impact and swing influence the rate of failure, and that the knot structure has a profound influence on a knot's tendency to untie under cyclic impact loading.

  2. Constructing a polynomial whose nodal set is the three-twist knot 52

    NASA Astrophysics Data System (ADS)

    Dennis, Mark R.; Bode, Benjamin

    2017-06-01

    We describe a procedure that creates an explicit complex-valued polynomial function of three-dimensional space, whose nodal lines are the three-twist knot 52. The construction generalizes a similar approach for lemniscate knots: a braid representation is engineered from finite Fourier series and then considered as the nodal set of a certain complex polynomial which depends on an additional parameter. For sufficiently small values of this parameter, the nodal lines form the three-twist knot. Further mathematical properties of this map are explored, including the relationship of the phase critical points with the Morse-Novikov number, which is nonzero as this knot is not fibred. We also find analogous functions for other simple knots and links. The particular function we find, and the general procedure, should be useful for designing knotted fields of particular knot types in various physical systems.

  3. A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains

    PubMed Central

    Rieger, Florian C.; Virnau, Peter

    2016-01-01

    We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on experimental knotting probabilities of short DNA strands, it reproduces the correct persistence length of DNA. This indicates that knots are not only a fine gauge for structural properties, but a promising tool for the design of polymer models. PMID:27631891

  4. Chemical signals from plants previously infected with root knot nematodes affect behavior of infective juvenile root knot nematodes

    USDA-ARS?s Scientific Manuscript database

    Nematodes are a worldwide problem in agriculture, with losses estimated to $100 billion per year in the US. Damage caused by root-knot nematodes (Meloidogyne spp.) (RKN) disrupts the flow of water and nutrients to the plant and increases the plant’s vulnerability to other pathogens. While studies ...

  5. Variation in pin knot frequency in black walnut lumber cut from a small provenance/progeny test

    Treesearch

    Peter Y. S. Chen; Robert E. Bodkin; J. W. Van Sambeek

    1995-01-01

    This small study examined the frequency of knots (> 1 growth ring), pin knots (latent or suppressed buds), and pin knot clusters in 414 black walnut (Juglans nigra L.) lumber from 42 logs. 18 to 21 cm dbh, cut from a 14-year-old provenance/progeny test. Two boards from opposite sides of each log were analyzed for number of knots, pin knots, and...

  6. Direct observation of DNA knots using a solid-state nanopore

    NASA Astrophysics Data System (ADS)

    Plesa, Calin; Verschueren, Daniel; Pud, Sergii; van der Torre, Jaco; Ruitenberg, Justus W.; Witteveen, Menno J.; Jonsson, Magnus P.; Grosberg, Alexander Y.; Rabin, Yitzhak; Dekker, Cees

    2016-12-01

    Long DNA molecules can self-entangle into knots. Experimental techniques for observing such DNA knots (primarily gel electrophoresis) are limited to bulk methods and circular molecules below 10 kilobase pairs in length. Here, we show that solid-state nanopores can be used to directly observe individual knots in both linear and circular single DNA molecules of arbitrary length. The DNA knots are observed as short spikes in the nanopore current traces of the traversing DNA molecules and their detection is dependent on a sufficiently high measurement resolution, which can be achieved using high-concentration LiCl buffers. We study the percentage of molecules with knots for DNA molecules of up to 166 kilobase pairs in length and find that the knotting occurrence rises with the length of the DNA molecule, consistent with a constant knotting probability per unit length. Our experimental data compare favourably with previous simulation-based predictions for long polymers. From the translocation time of the knot through the nanopore, we estimate that the majority of the DNA knots are tight, with remarkably small sizes below 100 nm. In the case of linear molecules, we also observe that knots are able to slide out on application of high driving forces (voltage).

  7. Toward U(N|M) knot invariant from ABJM theory

    NASA Astrophysics Data System (ADS)

    Eynard, Bertrand; Kimura, Taro

    2017-02-01

    We study U(N|M) character expectation value with the supermatrix Chern-Simons theory, known as the ABJM matrix model, with emphasis on its connection to the knot invariant. This average just gives the half-BPS circular Wilson loop expectation value in ABJM theory, which shall correspond to the unknot invariant. We derive the determinantal formula, which gives U(N|M) character expectation values in terms of U(1|1) averages for a particular type of character representations. This means that the U(1|1) character expectation value is a building block for the U(N|M) averages and also, by an appropriate limit, for the U(N) invariants. In addition to the original model, we introduce another supermatrix model obtained through the symplectic transform, which is motivated by the torus knot Chern-Simons matrix model. We obtain the Rosso-Jones-type formula and the spectral curve for this case.

  8. Knotting of vortex tangle in three-dimensional random waves

    NASA Astrophysics Data System (ADS)

    Taylor, Alexander; Dennis, Mark

    2014-03-01

    Quantised vortices are fundamental to the description of disordered 3D complex scalar fields such as turbulent superfluids or BECs, but also a wide range of other phenomena including optical volume speckle, the quantum eigenfunctions of chaotic 3D cavities, and liquid crystal phases. These systems all exhibit statistically random large scale vortex tangles that are difficult to describe analytically, but certain properties appear universal despite the physically different origin of complexity. We track vortex tangle in numerical simulations of the random wave model of chaotic eigenfunctions, where the waves are linear, but the zeros themselves are very nonlinear features forming a dense tangle of filaments whose geometry and topology we analyse numerically. We observe that while many standard quantities reveal only a common statistical scaling on the large scale, the topology - particularly the occurrence of knots in vortex loops - discriminates between tangles with different origins. In fact, knotting is surprisingly rare when compared to standard random walk models.

  9. Unexpected connections between Burnside groups and knot theory

    PubMed Central

    Dabkowski, Mieczyslaw K.; Przytycki, Józef H.

    2004-01-01

    In classical knot theory and the theory of quantum invariants substantial effort was directed toward the search for unknotting moves on links. We solve, in this article, several classical problems concerning unknotting moves. Our approach uses a concept, Burnside groups of links, that establishes an unexpected relationship between knot theory and group theory. Our method has the potential to be used in computational biology in the analysis of DNA via tangle embedding theory, as developed by D. W. Sumners [Sumners, D. W., ed. (1992) New Scientific Applications of Geometry and Topology (Am Math. Soc., Washington, DC) and Ernst, C. & Sumners, D. W. (1999) Math. Proc. Cambridge Philos. Soc. 126, 23–36]. PMID:15576510

  10. Self-Organizing Knotted Magnetic Structures in Plasma

    NASA Astrophysics Data System (ADS)

    Smiet, C. B.; Candelaresi, S.; Thompson, A.; Swearngin, J.; Dalhuisen, J. W.; Bouwmeester, D.

    2015-08-01

    We perform full-magnetohydrodynamics simulations on various initially helical configurations and show that they reconfigure into a state where the magnetic field lines span nested toroidal surfaces. This relaxed configuration is not a Taylor state, as is often assumed for relaxing plasma, but a state where the Lorentz force is balanced by the hydrostatic pressure, which is lowest on the central ring of the nested tori. Furthermore, the structure is characterized by a spatially slowly varying rotational transform, which leads to the formation of a few magnetic islands at rational surfaces. We then obtain analytic expressions that approximate the global structure of the quasistable linked and knotted plasma configurations that emerge, using maps from S3 to S2 of which the Hopf fibration is a special case. The knotted plasma configurations have a highly localized magnetic energy density and retain their structure on time scales much longer than the Alfvénic time scale.

  11. Toward {U}(N|M) knot invariant from ABJM theory

    NASA Astrophysics Data System (ADS)

    Eynard, Bertrand; Kimura, Taro

    2017-06-01

    We study {U}(N|M) character expectation value with the supermatrix Chern-Simons theory, known as the ABJM matrix model, with emphasis on its connection to the knot invariant. This average just gives the half-BPS circular Wilson loop expectation value in ABJM theory, which shall correspond to the unknot invariant. We derive the determinantal formula, which gives {U}(N|M) character expectation values in terms of {U}(1|1) averages for a particular type of character representations. This means that the {U}(1|1) character expectation value is a building block for the {U}(N|M) averages and also, by an appropriate limit, for the {U}(N) invariants. In addition to the original model, we introduce another supermatrix model obtained through the symplectic transform, which is motivated by the torus knot Chern-Simons matrix model. We obtain the Rosso-Jones-type formula and the spectral curve for this case.

  12. Dodging the crisis of folding proteins with knots.

    PubMed

    Sułkowska, Joanna I; Sułkowski, Piotr; Onuchic, José

    2009-03-03

    Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, that involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in approximately 1-2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies.

  13. Dodging the crisis of folding proteins with knots

    NASA Astrophysics Data System (ADS)

    Sulkowska, Joanna

    2009-03-01

    Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, which involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in around 1-2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies.

  14. Dodging the crisis of folding proteins with knots

    PubMed Central

    Sułkowska, Joanna I.; Sułkowski, Piotr; Onuchic, José

    2009-01-01

    Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, that involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in ≈1–2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies. PMID:19211785

  15. Knots and Random Walks in Vibrated Granular Chains

    NASA Astrophysics Data System (ADS)

    Ben-Naim, Eli

    2002-03-01

    We study experimentally and theoretically statistical properties of the opening times of knots in vertically vibrated granular chains. Our measurements are in good qualitative and quantitative agreement with a theoretical model involving three random walks interacting via hard-core exclusion in one spatial dimension. In particular, the knot survival probability follows a universal scaling function which is independent of the chain length, with a corresponding diffusive characteristic time scale. Both the large-exit-time and the small-exit-time tails of the distribution are suppressed exponentially, and the corresponding decay coefficients are in excellent agreement with theoretical values. E. Ben-Naim, Z. A. Daya, P. Vorobieff, and R. E. Ecke, Phys. Rev. Lett. 86, 1414 (2001).

  16. BPS counting for knots and combinatorics on words

    NASA Astrophysics Data System (ADS)

    Kucharski, Piotr; Sułkowski, Piotr

    2016-11-01

    We discuss relations between quantum BPS invariants defined in terms of a product decomposition of certain series, and difference equations (quantum A-polynomials) that annihilate such series. We construct combinatorial models whose structure is encoded in the form of such difference equations, and whose generating functions (Hilbert-Poincaré series) are solutions to those equations and reproduce generating series that encode BPS invariants. Furthermore, BPS invariants in question are expressed in terms of Lyndon words in an appropriate language, thereby relating counting of BPS states to the branch of mathematics referred to as combinatorics on words. We illustrate these results in the framework of colored extremal knot polynomials: among others we determine dual quantum extremal A-polynomials for various knots, present associated combinatorial models, find corresponding BPS invariants (extremal Labastida-Mariño-Ooguri-Vafa invariants) and discuss their integrality.

  17. Helicity Injection by Knotted Antennas into Electron Magnetohydrodynamical Plasmas

    NASA Astrophysics Data System (ADS)

    Rousculp, C. L.; Stenzel, R. L.

    1997-08-01

    A fully three-dimensional computer simulation of an ideal electron magnetohydrodynamical plasma is performed. By introducing various pulsed inductive antenna sources, magnetic helicity ( H = A˙B dV) injection is studied. Confirming experimental results, a simple loop provides no net helicity injection. Linked and knotted antennas, however, do inject helicity and preferentially radiate whistler wave packets parallel or antiparallel to the ambient magnetic field. Relative efficiencies of these antennas are reported as well as their unique directional properties.

  18. Knotted nasogastric tube in the posterior nasopharynx: A case report.

    PubMed

    Hirwa, Kagabo D; Toshniwal, Naresh

    2016-01-01

    Nasogastric tubes are widely used for enteral feeding and administration of medication but unexpected complications can arise during their insertion or removal. There are no standardized ways of dealing with such complications and the safer methods of insertion available are mostly expensive. We present here a case of knotted nasogastric tube and the different approaches that were used to remove it. A brief review of the literature on nasogastric position confirmation techniques is also presented.

  19. Knotted nasogastric tube in the posterior nasopharynx: A case report

    PubMed Central

    Hirwa, Kagabo D.; Toshniwal, Naresh

    2016-01-01

    Nasogastric tubes are widely used for enteral feeding and administration of medication but unexpected complications can arise during their insertion or removal. There are no standardized ways of dealing with such complications and the safer methods of insertion available are mostly expensive. We present here a case of knotted nasogastric tube and the different approaches that were used to remove it. A brief review of the literature on nasogastric position confirmation techniques is also presented. PMID:28058233

  20. Zeros of Jones polynomials for families of knots and links

    NASA Astrophysics Data System (ADS)

    Chang, S.-C.; Shrock, R.

    2001-12-01

    We calculate Jones polynomials VL( t) for several families of alternating knots and links by computing the Tutte polynomials T( G, x, y) for the associated graphs G and then obtaining VL( t) as a special case of the Tutte polynomial. For each of these families we determine the zeros of the Jones polynomial, including the accumulation set in the limit of infinitely many crossings. A discussion is also given of the calculation of Jones polynomials for non-alternating links.

  1. Hypermagnetic knots and gravitational radiation at intermediate frequencies

    NASA Astrophysics Data System (ADS)

    Giovannini, Massimo

    2017-07-01

    The maximally gyrotropic configurations of the hypermagnetic field at the electroweak epoch can induce a stochastic background of relic gravitational waves with comoving frequencies ranging from the μHz to the kHz. Using two complementary approaches we construct a physical template family for the emission of the gravitational radiation produced by the hypermagnetic knots. The current constraints and the presumed sensitivities of the advanced wide-band interferometers (both terrestrial and space-borne) are combined to infer that the lack of observations at intermediate frequencies may invalidate the premise of baryogenesis models based (directly or indirectly) on the presence of gyrotropic configurations of the hypermagnetic field at the electroweak epoch. Over the intermediate frequency range the spectral energy density of the gravitational waves emitted by the hypermagnetic knots at the electroweak scale can exceed the inflationary signal even by nine orders of magnitude without affecting the standard bounds applicable on the stochastic backgrounds of gravitational radiation. The signal of hypermagnetic knots can be disambiguated, at least in principle, since the the produced gravitational waves are polarized.

  2. Protein knotting through concatenation significantly reduces folding stability

    PubMed Central

    Hsu, Shang-Te Danny

    2016-01-01

    Concatenation by covalent linkage of two protomers of an intertwined all-helical HP0242 homodimer from Helicobacter pylori results in the first example of an engineered knotted protein. While concatenation does not affect the native structure according to X-ray crystallography, the folding kinetics is substantially slower compared to the parent homodimer. Using NMR hydrogen-deuterium exchange analysis, we showed here that concatenation destabilises significantly the knotted structure in solution, with some regions close to the covalent linkage being destabilised by as much as 5 kcal mol−1. Structural mapping of chemical shift perturbations induced by concatenation revealed a pattern that is similar to the effect induced by concentrated chaotrophic agent. Our results suggested that the design strategy of protein knotting by concatenation may be thermodynamically unfavourable due to covalent constrains imposed on the flexible fraying ends of the template structure, leading to rugged free energy landscape with increased propensity to form off-pathway folding intermediates. PMID:27982106

  3. Helicity conservation in classical vortex knots and links

    NASA Astrophysics Data System (ADS)

    Scheeler, Martin W.; Kleckner, Dustin; Kindlmann, Gordon L.; Irvine, William T. M.

    2014-11-01

    Vortex knots and links in an ideal fluid remain knotted or linked, ensuring that the topology of the vortex field lines is conserved. For a real fluid, however, this conservation is jeopardized by the presence of reconnection events, which allow vortex tubes to reconfigure their global topology; indeed, it has recently been observed that knotted and linked vortex tubes in classical fluids unknot or untie themselves via a series of these reconnection events. Remarkably, we observe that these reconnection processes conserve a measure of the vortex line topology (helicity) and do so through a geometric mechanism that efficiently transfers this topology across scales. The geometric nature of this topology transfer, along with its recent observation in superfluid vortices, suggests that helicity conservation may be a robust and generic feature of non-ideal flows. This work was supported by the NSF MRSEC shared facilities at the University of Chicago (DMR-0820054) and an NSF CAREER award (DMR-1351506). W.T.M.I. further acknowledges support from the A.P. Sloan Foundation and the Packard Foundation.

  4. Insecticidal plant cyclotides and related cystine knot toxins.

    PubMed

    Gruber, Christian W; Cemazar, Masa; Anderson, Marilyn A; Craik, David J

    2007-03-15

    Cyclotides are small disulphide-rich peptides found in plants from the violet (Violaceae), coffee (Rubiaceae) and cucurbit (Cucurbitaceae) families. They have the distinguishing structural features of a macrocyclic peptide backbone and a cystine knot made up of six conserved cysteine residues, which makes cyclotides exceptionally stable. Individual plants express a suite of cyclotides in a wide range of tissue types, including leaves, flowers, stems and roots and it is thought that their natural function in plants is as defence agents. This proposal is supported by their high expression levels in plants and their toxic and growth retardant activity in feeding trials against Helicoverpa spp. insect pests. This review describes the structures and activities of cyclotides with specific reference to their insecticidal activity and compares them with structurally similar cystine knot proteins from peas (Pisum sativum) and an amaranthus crop plant (Amaranthus hypocondriancus). More broadly, cystine knot proteins are common in a wide range of organisms from fungi to mammals, and it appears that this interesting structural motif has evolved independently in different organisms as a stable protein framework that has a variety of biological functions.

  5. The Effect of Instrumentation on Suture Tensile Strength and Knot Pullout Strength of Common Suture Materials.

    PubMed

    Johnson, Peter C; Roberts, Aaron D; Hire, Justin M; Mueller, Terry L

    2016-01-01

    To determine the effect of instrumentation of suture material on knot security and tensile strength. In all, 5 types of suture material were used; 10 knots were tied without any instrumentation and 10 knots were tied with a hemostat holding tension on the first throw while the second throw was made for each suture type. Each group was tested to failure with the maximum load and mode of failure recorded. The maximum load between groups of each suture type was compared; frequency of failure through knot slippage vs material fracture was also compared between groups. There was no significant difference observed in the maximum load to failure for any suture type between instrumented and noninstrumented groups. Additionally, there was no difference between any instrumented and noninstrumented groups for material failure vs failure due to knot slippage. Instrumentation of suture material during two-hand tying does not affect the strength of suture material or knot security. Published by Elsevier Inc.

  6. T7 RNA polymerase cannot transcribe through a highly knotted DNA template.

    PubMed Central

    Portugal, J; Rodríguez-Campos, A

    1996-01-01

    The ability of T7 RNA polymerase to transcribe a plasmid DNA in vitro in its linear, supercoiled, relaxed and knotted forms was analysed. Similar levels of transcription were found on each template with the exception of plasmids showing varying degrees of knotting (obtained using stoichiometric amounts of yeast topoisomerase II). A purified fraction of knotted DNA with a high number of nodes (crosses) was found to be refractory to transcription. The unknotting of the knotted plasmids, using catalytic amounts of topoisomerase II, restored their capacity as templates for transcription to levels similar to those obtained for the other topological forms. These results demonstrate that highly knotted DNA is the only topological form of DNA that is not a template for transcription. We suggest that the regulation of transcription, which depends on the topological state of the template, might be related to the presence of knotted DNA with different number of nodes. PMID:9016657

  7. Knotted bowel: small-bowel obstruction from coiled peritoneal shunt catheters. Report of two cases.

    PubMed

    Sanan, A; Haines, S J; Nyberg, S L; Leonard, A S

    1995-06-01

    Knotting of a peritoneal catheter around a loop of bowel is a rare occurrence, which may lead to bowel obstruction. The incomplete removal of two ventriculoperitoneal shunts resulted in two cases of iatrogenically knotted peritoneal catheters. One patient underwent a laparotomy for relief of obstruction and the other was successfully treated by uncoiling the catheter by means of a wire passed into its lumen. A plan for management of a knotted peritoneal catheter is outlined.

  8. Computational study on the progressive factorization of composite polymer knots into separated prime components.

    PubMed

    Tubiana, Luca

    2014-05-01

    Using Monte Carlo simulations and advanced knot localization methods, we analyze the length and distribution of prime components in composite knots tied on freely jointed rings. For increasing contour length, we observe the progressive factorization of composite knots into separated prime components. However, we observe that a complete factorization, equivalent to the "decorated ring" picture, is not obtained even for rings of contour lengths N ≃ 3 N(0), about tens of times the most probable length of the prime knots tied on the rings. The decorated ring hypothesis has been used in the literature to justify the factorization of composite knot probabilities into the knotting probabilities of their prime components. Following our results, we suggest that such a hypothesis may not be necessary to explain the factorization of the knotting probabilities, at least when polymers excluding volume is not relevant. We rationalize the behavior of the system through a simple one-dimensional model in which prime knots are replaced by slip links randomly placed on a circle, with the only constraint being that the length of the loops has the same distribution as that of the length of the corresponding prime knots.

  9. Backbone NMR assignments of a topologically knotted protein in urea-denatured state.

    PubMed

    Hsieh, Shu-Ju Micky; Mallam, Anna L; Jackson, Sophie E; Hsu, Shang-Te Danny

    2014-10-01

    YbeA is a 3-methylpseudoridine methyltransferase from Escherichia coli that forms a stable homodimer in solution. It is one of the deeply trefoil 31 knotted proteins, of which the knot encompasses the C-terminal helix that threads through a long loop. Recent studies on the knotted protein folding pathways using YbeA have suggested that the protein knot remains present under chemically denaturing conditions. Here, we report (1)H, (13)C and (15)N chemical shift assignments for urea-denatured YbeA, which will serve as the basis for further structural characterisations using solution state NMR spectroscopy with paramagnetic spin labeled and partial alignment media.

  10. Dielectric Detection of Knots in Green Red Oak and Southern Pine Lumber

    NASA Astrophysics Data System (ADS)

    Cooper, Jerome E.; Steele, Philip H.; Mitchell, Brian

    2007-03-01

    Forest products industry automation requires accurate detection of knots in lumber. A radio frequency system has been patented and commercialized that relies on signal attenuation to detect knots in green softwood lumber. Signal attenuation has proven less reliable for hardwood species and for application to green lumber where moisture content may range from 60 to 150 percent. This paper reports on knot detection in green southern yellow pine and red oak lumber with a system that utilizes phase shift data to supplement attenuation data. Phase shift was found to be considerably more reliable than signal attenuation for knot detection in green lumber.

  11. Slipknotting upon native-like loop formation in a trefoil knot protein.

    PubMed

    Noel, Jeffrey K; Sułkowska, Joanna I; Onuchic, José N

    2010-08-31

    Protein knots and slipknots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Recent experimental results show that knotting, starting from a fully extended polypeptide, has not yet been observed. Understanding the nucleation process of folding knots is thus a natural challenge for both experimental and theoretical investigation. In this study, we employ energy landscape theory and molecular dynamics to elucidate the entire folding mechanism. The full free energy landscape of a knotted protein is mapped using an all-atom structure-based protein model. Results show that, due to the topological constraint, the protein folds through a three-state mechanism that contains (i) a precise nucleation site that creates a correctly twisted native loop (first barrier) and (ii) a rate-limiting free energy barrier that is traversed by two parallel knot-forming routes. The main route corresponds to a slipknot conformation, a collapsed configuration where the C-terminal helix adopts a hairpin-like configuration while threading, and the minor route to an entropically limited plug motion, where the extended terminus is threaded as through a needle. Knot formation is a late transition state process and results show that random (nonspecific) knots are a very rare and unstable set of configurations both at and below folding temperature. Our study shows that a native-biased landscape is sufficient to fold complex topologies and presents a folding mechanism generalizable to all known knotted protein topologies: knotting via threading a native-like loop in a preordered intermediate.

  12. Sequence-specific size, structure, and stability of tight protein knots.

    PubMed

    Dzubiella, Joachim

    2009-02-01

    Approximately 1% of known protein structures display knotted configurations in their native fold, but the function of these configurations is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport, e.g., as in cellular threading or translocation processes through narrow biological pores. Protein knot manipulation, e.g., knot tightening and localization, has become possible in single-molecule experiments. Here, we investigate tight peptide knot (TPK) characteristics in detail by pulling selected 3(1) and 4(1)-knotted peptides using all-atom molecular dynamics computer simulations. We find that the 3(1)- and 4(1)-TPK lengths are typically Deltal approximately 47+/- 4 A and 69 +/- 4 A, respectively, for a wide range of tensions (0.1 nN less, similarF less, similar 1.5 nN). The 4(1)-knot length is in agreement with recent atomic force microscopy pulling experiments. Calculated TPK radii of gyration point to a pore diameter of approximately 20 A, below which a translocated knotted protein might get stuck. TPK characteristics, however, may be sequence-specific: we find a different size and structural behavior in polyglycines, and, strikingly, a strong hydrogen bonding and water trapping capability of hydrophobic TPKs. Water capture and release is found to be controllable by the tightening force in a few cases. These mechanisms result in a sequence-specific "locking" and metastability of TPKs, which might lead to a blocking of knotted peptide transport at designated sequence positions. We observe that macroscopic tight 4(1)-knot structures are reproduced microscopically ("figure of eight" versus the "pretzel") and can be tuned by sequence, in contrast to mathematical predictions. Our findings may explain a function of knots in native proteins, challenge previous studies on macromolecular knots, and prove useful in bio- and nanotechnology.

  13. Sequence-Specific Size, Structure, and Stability of Tight Protein Knots

    PubMed Central

    Dzubiella, Joachim

    2009-01-01

    Approximately 1% of known protein structures display knotted configurations in their native fold, but the function of these configurations is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport, e.g., as in cellular threading or translocation processes through narrow biological pores. Protein knot manipulation, e.g., knot tightening and localization, has become possible in single-molecule experiments. Here, we investigate tight peptide knot (TPK) characteristics in detail by pulling selected 31 and 41-knotted peptides using all-atom molecular dynamics computer simulations. We find that the 31- and 41-TPK lengths are typically Δl ≈ 47± 4 Å and 69 ± 4 Å, respectively, for a wide range of tensions (0.1 nN ≲ F ≲ 1.5 nN). The 41-knot length is in agreement with recent atomic force microscopy pulling experiments. Calculated TPK radii of gyration point to a pore diameter of ∼20 Å, below which a translocated knotted protein might get stuck. TPK characteristics, however, may be sequence-specific: we find a different size and structural behavior in polyglycines, and, strikingly, a strong hydrogen bonding and water trapping capability of hydrophobic TPKs. Water capture and release is found to be controllable by the tightening force in a few cases. These mechanisms result in a sequence-specific “locking” and metastability of TPKs, which might lead to a blocking of knotted peptide transport at designated sequence positions. We observe that macroscopic tight 41-knot structures are reproduced microscopically (“figure of eight” versus the “pretzel”) and can be tuned by sequence, in contrast to mathematical predictions. Our findings may explain a function of knots in native proteins, challenge previous studies on macromolecular knots, and prove useful in bio- and nanotechnology. PMID:19186124

  14. The Nature of Cometary Knots in the Helix Nebula

    NASA Astrophysics Data System (ADS)

    Burkert, A.; O'dell, C. R.

    1996-12-01

    Recent HST observations have revealed heretofore unseen fine scale structure in the Helix Nebula. Thousands of well resolved neutral dark cores have been detected in extinction against the background emission of the nebula. These Cometary Knots (CK) have a remarkably uniform appearance with photoionized cusps and tails trailing away from the cusps on almost radial lines. The total mass of the CK is similar to the total mass of the ionized diffuse gas in the ring which means that they represent an important component of the nebula. We discuss the origin and future of the CK in the Helix. It has been suggested that the CK result from Rayleigh-Taylor instabilities arising at the ionization front of the nebula (Capriotti 1973, 1996). Our hydrodynamical simulations indicate that indeed Rayleigh-Taylor instabilities could lead to filamentary structures within planetary nebulae. The substructure of these fingers differs, however, from the observations in important ways. The observed CK therefore must have a different origin. The knots might represent local density fluctuations which remained behind and were compressed as the main ionization front advanced into the neutral material. Another formation scenario is a thin shell instability which results from the interaction of the nebula with a fast stellar wind. Although no stellar wind features have been detected so far, the brightness distribution of the ionized cusps of the knots indicates that this gas is in pressure equilibrium with a high-temperature surrounding gas which could be generated by a shocked stellar wind. If such a wind would have high velocities and low densities it could fall beneath the threshold for spectroscopic detection although it could be important for understanding the formation and structure of the CK. Detailed high-resolution numerical simulations which take into account a fast wind phase as well as the time variation of the Central Star's UV photon flux are presented.

  15. The validation of an instrumented simulator for the assessment of performance and outcome of knot tying skill: a pilot study.

    PubMed

    Rojas, David; Cristancho, Sayra; Rueda, Claudia; Grierson, Lawrence; Monclou, Alex; Dubrowski, Adam

    2011-01-01

    The construct validity of a surgical bench-top simulator with built-in computer acquired assessments was examined. It features two parallel elastic tubes instrumented with flexion sensors that simulate the walls of a wound. Participants from three groups (9 novices, 7 intermediates, 9 experts) performed 10 two-handed, double square knots. The peak tensions at the initiation of the first knot, the completion of the first knot and the completion of the second knot, as well as measures of movement economy indicated technical performance. Product quality was indicated by knot stability defined as the amount of slippage of the knot under the tension. There were significant differences between experts and novices for peak tension on first knot (p=.03), movement economy (p=.02), and knot stability (p=.002). The results support the construct validity of these objective measures.

  16. An unusual ventriculoperitoneal shunt complication: spontaneous knot formation.

    PubMed

    Borcek, Alp Ozgun; Civi, Soner; Golen, Mustafa; Emmez, Hakan; Baykaner, M Kemali

    2012-01-01

    This article aims to describe an extraordinary complication of a ventriculoperitoneal shunt system that formed a knot spontaneously and lead to a shunt malfunction. A 3-year-old male patient was operated due to posttraumatic hydrocephalus. After an uneventful follow-up period of 34 months, he presented with shunt malfunction. During the shunt revision surgery, the peritoneal catheter was found to form a loop over itself. There are various complications of ventriculoperitoneal shunt systems. Migration to body cavities is among the most interesting ones. This is the fifth report describing this rare complication. Hydrocephalic patients should be closely followed up after shunt surgery for various extraordinary complications.

  17. Helicity Injection by Knotted Antennas into Electron Magnetohydrodynamical Plasmas

    SciTech Connect

    Rousculp, C.L.; Stenzel, R.L.

    1997-08-01

    A fully three-dimensional computer simulation of an ideal electron magnetohydrodynamical plasma is performed. By introducing various pulsed inductive antenna sources, magnetic helicity (H={bold A}{center_dot}{bold B}dV) injection is studied. Confirming experimental results, a simple loop provides no net helicity injection. Linked and knotted antennas, however, do inject helicity and preferentially radiate whistler wave packets parallel or antiparallel to the ambient magnetic field. Relative efficiencies of these antennas are reported as well as their unique directional properties. {copyright} {ital 1997} {ital The American Physical Society}

  18. Buoyant vortex rings and knots with thin core

    NASA Astrophysics Data System (ADS)

    Chang, Ching; Llewellyn Smith, Stefan

    2016-11-01

    One challenge of studying the motion of vortex filaments arises from the singular nature of the Biot-Savart integral. We employ the momentum balance investigated by Moore and Saffman for thin-core vortex filaments to obtain the self-induced velocity of filaments, rings and knots. A key feature of the approach is the possibility of incorporating buoyancy forces. The numerical scheme used is discussed and compared to previous analytical and numerical results in the literature. The effect of geometry and buoyancy on the motion of such vortices is examined.

  19. Geometric Knot Selection for Radial Scattered Data Approximation

    DTIC Science & Technology

    2001-07-01

    approximated by means of radial basis functions with compact support and the related knot selection is based on the information given by the discrete Gaussian...obtaining important shape information. Thus we get some suggestions for determining the supports of the local ra- dial basis functions [8] used in the...be defined in order to obtain a reliable estimate of the Gaussian curvature from (2.1). 0.3 S -A.- 02 0.1 -2 0.W 0 • 0. 0 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7

  20. Knot Theory and Topologically Massive Yang-Mills Theory

    NASA Astrophysics Data System (ADS)

    Yildirim, Tuna; Rodgers, Vincent; Nair, Parameswaran; Carter, Suzanne

    2013-04-01

    In 2+1 dimensions, we study Yang-Mills(YM) + Chern-Simons(CS) theory also known as topologically massive Yang-Mills(TMYM) theory. Using geometric quantization method we calculate the Wilson Loop expectation values of TMYM theory. At large distances, where only the topological theory survives, we obtain a condition that makes skein relations of knot theory useful to calculate Wilson loop expectation values of TMYM theory. These link invariants may lead to a better understanding of mass gap in 2+1 dimensions.

  1. Design and performance of the APPLE-Knot undulator.

    PubMed

    Ji, Fuhao; Chang, Rui; Zhou, Qiaogen; Zhang, Wei; Ye, Mao; Sasaki, Shigemi; Qiao, Shan

    2015-07-01

    Along with the development of accelerator technology, synchrotron emittance has continuously decreased. This results in increased brightness, but also causes a heavy heat load on beamline optics. Recently, optical surfaces with 0.1 nm micro-roughness and 0.05 µrad slope error (r.m.s.) have become commercially available and surface distortions due to heat load have become a key factor in determining beamline performance, and heat load has become a serious problem at modern synchrotron radiation facilities. Here, APPLE-Knot undulators which can generate photons with arbitrary polarization, with low on-axis heat load, are reported.

  2. Design and performance of the APPLE-Knot undulator

    PubMed Central

    Ji, Fuhao; Chang, Rui; Zhou, Qiaogen; Zhang, Wei; Ye, Mao; Sasaki, Shigemi; Qiao, Shan

    2015-01-01

    Along with the development of accelerator technology, synchrotron emittance has continuously decreased. This results in increased brightness, but also causes a heavy heat load on beamline optics. Recently, optical surfaces with 0.1 nm micro-roughness and 0.05 µrad slope error (r.m.s.) have become commercially available and surface distortions due to heat load have become a key factor in determining beamline performance, and heat load has become a serious problem at modern synchrotron radiation facilities. Here, APPLE-Knot undulators which can generate photons with arbitrary polarization, with low on-axis heat load, are reported. PMID:26134793

  3. Ball lightning as a force-free magnetic knot

    PubMed

    Ranada; Soler; Trueba

    2000-11-01

    The stability of fireballs in a recent model of ball lightning is studied. It is shown that the balls shine while relaxing in an almost quiescent expansion, and that three effects contribute to their stability: (i) the formation in each one during a process of Taylor relaxation of a force-free magnetic field, a concept introduced in 1954 in order to explain the existence of large magnetic fields and currents in stable configurations of astrophysical plasmas; (ii) the so called Alfven conditions in magnetohydrodynamics; and (iii) the approximate conservation of the helicity integral. The force-free fields that appear are termed "knots" because their magnetic lines are closed and linked.

  4. Cotton Cultivar Response to Root-Knot Nematodes in Two Tillage Regimes, 2008

    USDA-ARS?s Scientific Manuscript database

    Six cotton cultivars were evaluated for yield response to the root-knot nematode in a naturally infested field at E. V. Smith Research and Extension Center, near Shorter, Alabama. The field had a long history of root-knot nematode infestation, and the soil type was classified as a sandy loam. Plots ...

  5. Ethnomathematics in Arfak (West Papua-Indonesia): Hidden Mathematics on Knot of Rumah Kaki Seribu

    ERIC Educational Resources Information Center

    Haryanto; Nusantara, Toto; Subanji; Abadyo

    2016-01-01

    This ethnomathematics article focused on the models of knot which is used in the frame of "Rumah Kaki Seribu." The knot model itself was studied mathematically. The results of this study revealed the way Arfak tribal communities think mathematically. This article uses exploration, documentation, interview, experiments and literature…

  6. Use of gadolinium chloride as a contrast agent for imaging spruce knots by magnetic resonance

    Treesearch

    Thomas L. Eberhardt; Chi-Leung So; Amy H. Herlihy; Po-Wah So

    2006-01-01

    Treatments of knot-containing spruce wood blocks with a paramagnetic salt, gadolinium (III) chloride, in combination with solvent pretreatments, were evaluated as strategies to enhance the visualization of wood features by magnetic resonance imaging (MRI). Initial experiments with clear wood and excised knot samples showed differences in moisture uptake after...

  7. [Suprapubic cystostomy catheter knotting. Presentation of the first national case and review of the literature].

    PubMed

    Romero Pérez, Pedro; Lapuerta Torres, F Eduardo; Amat Cecilia, Manuel; Merenciano Cortina, Francisco José; Gordo Flores, Maria Esther; Navarro Antón, Jose Antonio; Ferrero, Roberto

    2013-03-01

    This study presents the first Spanish case of a spontaneous knot in the catheter of a suprapubic cystostomy and review the national and international literature. The case of an 87-year-old patient who was diagnosed with adenocarcinoma of the prostate is presented. A suprapubic vesical puncture for urinary retention was urgently performed in this patient because of the impossibility of urethral catheterisation. A spontaneous knot in the catheter was detected upon removal; the tightened knot could be removed by gentle and sustained traction without surgery. Knotting or calcification of the catheter was suspected when the catheter remained anchored in the bladder during a removal attempt 5 days after initial catheterisation. Plain pelvis x-ray was taken, but no calcification or knots were observed because the catheter was radiolucent. An ultrasound would have offered more information, but it was not requested. Gentle and sustained traction of the catheter reduced the knot size and allowed catheter removal without complications. Worldwide cases and national publications were reviewed. The formation of spontaneous or manipulation-induced knots in urinary cystostomy catheters is an extremely rare complication. The presented case is the first Spanish case of catheter knotting; it is only the 17th reported case worldwide.

  8. A summary of modulus of elasticity and knot size surveys for laminating grades of lumber

    Treesearch

    R. W. Wolfe; R. C. Moody

    1981-01-01

    A summary of modulus of elasticity (MOE) and knot data is presented for grades of lumber commonly used to manufacture glued-laminated (glulam) timber by the laminating Industry. Tabulated values represent 30 different studies covering a time span of over 16 years. Statistical estimates of average and near-maximum knot sizes as well as mean and coefficient of variation...

  9. Expression of almond KNOTTED1 homologue (PdKn1) anticipates adventitious shoot initiation

    USDA-ARS?s Scientific Manuscript database

    Background and Aims: The transcription factor encoded by the gene Knotted1 is a nuclear homeodomain protein, regulating meristematic cells at the shoot apical meristem. It has been proven that Knotted1 (KN1) has a role in the switch from an indeterminate to determinate cell fate and as such this gen...

  10. Percutaneous Retrieval of a Pulmonary Artery Catheter Knot in Pacing Electrodes

    SciTech Connect

    Valenzuela-Garcia, Luis Felipe Almendro-Delia, Manuel; Gonzalez-Valdayo, Miguel; Munoz-Campos, Juan; Dorado-Garcia, Jose C.; Gomez-Rosa, Francisco; Vazquez-Garcia, Rafael; Calderon-Leal, Jose M.

    2007-09-15

    To illustrate a successful approach to resolving a pulmonary artery catheter knot in the pacing leads of a cardiac resynchronization device. When planning invasive monitoring for patients having right chamber electrodes, fluoroscopic-guided catheter insertion and extraction is advisable. In the event of coiling or knotting, an interventional radiologist should be contacted as soon as possible to avoid serious complications.

  11. [Methodologic procedure in the removal of a knotted intravascular pulmonary artery catheter].

    PubMed

    Kaltenborn, H A; Klose, K J

    1990-01-01

    Distal knotting of a pulmonary artery catheter that had been introduced via the subclavian or jugular vein, is a possible complication. To avoid venous dissection in the thoracic or cervical regions, removal via a transfemoral approach should be considered as a feasible alternative. The article report on the extraction of two knotted pulmonary artery catheters, effected transfemorally.

  12. Long-term safety of polypropylene knots under scleral flaps for transsclerally sutured posterior chamber lenses.

    PubMed Central

    Van Meter, W S

    1997-01-01

    PURPOSE: To evaluate the safety of polypropylene knots used in TS-SPCL combined with PK and AV over time. METHOD: A retrospective review of 26 consecutive cases of TS-SPCL by one surgeon (WSVM) with at least 12 months follow-up (mean 26, range 12-62). All patients had a double strand polypropylene knot buried under partial thickness scleral flaps at 2 and 8 o'clock. Knots were rotated into the globe (R) in 10 cases, and could not be buried (N) in 13 cases, and in 3 cases 1 knot was buried. RESULTS: No cases of suture erosion occurred in R or N. One or more polypropylene sutures were visible in 17 patients (8 R, 9 T) at last exam. Twenty-three of 52 knots were rotated into the globe, and 70% of rotated knots were not even visible at the slit lamp at final visit. There was no evidence of conjunctival erosion in any patient. There was no lens dislocation and no endophthalmitis. CONCLUSION: The combination of partial thickness scleral flaps with double strand polypropylene knots reduces the incidence of suture erosion through the conjunctive if knots cannot be rotated into the globe. Images FIGURE 1 FIGURE 2 FIGURE 3 PMID:9440177

  13. Predicting internal lumber grade from log surface knots: actual and simulated results.

    Treesearch

    Christine Todoroki; Robert A. Monserud; Dean L. Parry

    2005-01-01

    The purpose of this study was threefold: 1) compare actual with simulated lumber yields; 2) examine the effect of measurement errors associated with knot angles and morphology. on lumber grade; and 3) investigate methods for predicting lumber quality within unsawn logs from surface knots. Twenty-eight Douglas-fir (Pseudotsuga menziesii(Mii irb.)...

  14. Translocation dynamics of knotted polymers under a constant or periodic external field.

    PubMed

    Narsimhan, Vivek; Renner, C Benjamin; Doyle, Patrick S

    2016-06-14

    We perform Brownian dynamics simulations to examine how knots alter the dynamics of polymers moving through nanopores under an external field. In the first part of this paper, we study the situation when the field is constant. Here, knots halt translocation above a critical force with jamming occurring at smaller forces for twist topologies compared to non-twist topologies. Slightly below the jamming transition, the polymer's transit times exhibit large fluctuations. This phenomenon is an example of the knot's molecular individualism since the conformation of the knot plays a large role in the chain's subsequent dynamics. In the second part of the paper, we study the motion of the chain when one cycles the field on and off. If the off time is comparable to the knot's relaxation time, one can adjust the swelling of the knot at the pore and hence design strategies to ratchet the polymer in a controllable fashion. We examine how the off time affects the ratcheting dynamics. We also examine how this strategy alters the fluctuations in the polymer's transit time. We find that cycling the force field can reduce fluctuations near the knot's jamming transition, but can enhance the fluctuations at very high forces since knots get trapped in metastable states during the relaxation process. The latter effect appears to be more prominent for non-torus topologies than torus ones. We conclude by discussing the feasibility of this approach to control polymer motion in biotechnology applications such as sequencing.

  15. Topological semimetals carrying arbitrary Hopf numbers: Fermi surface topologies of a Hopf link, Solomon's knot, trefoil knot, and other linked nodal varieties

    NASA Astrophysics Data System (ADS)

    Ezawa, Motohiko

    2017-07-01

    We propose a type of Hopf semimetal indexed by a pair of numbers (p ,q ) , where the Hopf number is given by p q . The Fermi surface is given by a preimage of the Hopf map, which consists of loops nontrivially linked for a nonzero Hopf number. The Fermi surface forms a torus link, whose examples are a Hopf link indexed by (1 ,1 ) , Solomon's knot (2 ,1 ) , a double Hopf link (2 ,2 ) , and a double trefoil knot (3 ,2 ) . We may choose p or q to be a half integer, where the Fermi surface is a torus knot, such as a trefoil knot (3 /2 ,1 ) . It is even possible to make the Hopf number an arbitrary rational number, where a semimetal whose Fermi surface forms open strings is generated.

  16. [Mechanical behaviour of three types of surgical knots using 4/0 monofilament].

    PubMed

    Gil Santos, Luis; Más-Estellés, Jorge; Salmerón Sánchez, Manuel; Barrios, Carlos

    2012-01-01

    To experimentally study the behaviour of 4 types of monofilament with 3 knotting techniques, very often used in surgery, employing mechanical tests. Four 4/0 monofilaments were chosen, two of nylon, and the other two of polypropylene. Three types of knot designs were made with each thread. The first design (D-S-S) consisted of a double half-knot (D) followed by one single (S) in the opposite direction, a third S in turn in the opposite direction. The configuration of the second design was D-S-D, and the third, S-S-D. A mechanical fracture test was performed by stretching the thread at a rate of 4N/s, the force and deformation being recorded at intervals of 100 ms. There was a decrease in the force and deformation in the tests on threads with knots compared to threads without knots. In all cases the rupture of the thread occurred in the knot area, presumably due to damage caused to the thread during the knotting process. The D-S-D knot had the greatest resistance with polypropylene threads, and S-S-D provided the greatest resistance with nylon threads Polypropylene threads, with D-S-D knots, should be more indicated to suture tissues that have to support great forces and with little deformation of the suture (e.g., tendons). Nylon threads, with S-S-D knots, would be better indicated for tissues that have to support smaller forces and that require greater elasticity (e.g., skin). Copyright © 2011 AEC. Published by Elsevier Espana. All rights reserved.

  17. KnotSeeker: heuristic pseudoknot detection in long RNA sequences.

    PubMed

    Sperschneider, Jana; Datta, Amitava

    2008-04-01

    Pseudoknots are folded structures in RNA molecules that perform essential functions as part of cellular transcription machinery and regulatory processes. The prediction of these structures in RNA molecules has important implications in antiviral drug design. It has been shown that the prediction of pseudoknots is an NP-complete problem. Practical structure prediction algorithms based on free energy minimization employ a restricted problem class and dynamic programming. However, these algorithms are computationally very expensive, and their accuracy deteriorates if the input sequence containing the pseudoknot is too long. Heuristic methods can be more efficient, but do not guarantee an optimal solution in regards to the minimum free energy model. We present KnotSeeker, a new heuristic algorithm for the detection of pseudoknots in RNA sequences as a preliminary step for structure prediction. Our method uses a hybrid sequence matching and free energy minimization approach to perform a screening of the primary sequence. We select short sequence fragments as possible candidates that may contain pseudoknots and verify them by using an existing dynamic programming algorithm and a minimum weight independent set calculation. KnotSeeker is significantly more accurate in detecting pseudoknots compared to other common methods as reported in the literature. It is very efficient and therefore a practical tool, especially for long sequences. The algorithm has been implemented in Python and it also uses C/C++ code from several other known techniques. The code is available from http://www.csse.uwa.edu.au/~datta/pseudoknot.

  18. RGS Spectroscopy of the Cygnus Loop XA Knot

    NASA Technical Reports Server (NTRS)

    Mushotzky, Richard F. (Technical Monitor); Gaetz, Terrance J.

    2004-01-01

    The observations were performed at the end of April 2002, and the data were received in July 2002. Unfortunately, the observations were badly compromised by high levels of background radiation; one of the three observations was lost entirely. Two replacement observations were scheduled for November 2002, and were only made available in January of 2003. A preliminary analysis of the RGS data has been performed. Analysis of these data is complicated by the extended nature of the source, and the limited statistics. Nevertheless, examination of the 'm lambda' vs. 'xdsp-corr' data shows that the bright knot is visible in C VI Ly-alpha and Ly-beta, the O VII triplet and He-beta, and O VIII Ly-alpha. The dispersed C VI Ly-alpha image is the first image of the remnant at that energy. The F, I, R components of the O VII triplet can be seen, and the 0 VII He-beta is distinct from the O VIII Ly-alpha (although the dispersed diffuse emission provides a pseudo-continuum). Trial-and-error adjustment of the rgsproc parameters allowed the extraction of a narrow (approx. 1 arcmin wide) region centered on the knot; corresponding background spectra were extracted from the sky background data sets. The xspec rgsxsrc model was used to convolve the response with a Chandra spatial image. Because the spatial distribution of the emission is energy-dependent, the use of a single convolution kernel is only approximate.

  19. High Proteolytic Resistance of Spider-Derived Inhibitor Cystine Knots

    PubMed Central

    Kikuchi, Kyoko; Sugiura, Mika; Kimura, Tadashi

    2015-01-01

    Proteolytic stability in gastrointestinal tract and blood plasma is the major obstacle for oral peptide drug development. Inhibitor cystine knots (ICKs) are linear cystine knot peptides which have multifunctional properties and could become promising drug scaffolds. ProTx-I, ProTx-II, GTx1-15, and GsMTx-4 were spider-derived ICKs and incubated with pepsin, trypsin, chymotrypsin, and elastase in physiological conditions to find that all tested peptides were resistant to pepsin, and ProTx-II, GsMTx-4, and GTx1-15 showed resistance to all tested proteases. Also, no ProTx-II degradation was observed in rat blood plasma for 24 hours in vitro and ProTx-II concentration in circulation decreased to half in 40 min, indicating absolute stability in plasma and fast clearance from the system. So far, linear peptides are generally thought to be unsuitable in vivo, but all tested ICKs were not degraded by pepsin and stomach could be selected for the alternative site of drug absorption for fast onset of the drug action. Since spider ICKs are selective inhibitors of various ion channels which are related to the pathology of many diseases, engineered ICKs will make a novel class of peptide medicines which can treat variety of bothering symptoms. PMID:26843868

  20. An Indwelling Urethral Catheter Knotted Around a Double-J Ureteral Stent: An Unusual Complication after Kidney Transplantation

    PubMed Central

    Warmerdam, E. G.; Toorop, R. J.; Abrahams, A. C.; Berger, P.

    2011-01-01

    Urethral catheterization is a common procedure with a relatively low complication rate. Knotting of an indwelling urethral catheter is a very rare complication, and there are only a few case reports on knotted catheters, most of them concerning children. We report an especially rare case where a urethral catheter formed a knot around a double-J ureteral stent after a kidney transplantation. We will discuss the various risk factors for knotting of a catheter and the methods to untangle a knot. PMID:24533194

  1. Effects of horseshoe crab harvest in delaware bay on red knots: Are harvest restrictions working?

    USGS Publications Warehouse

    Niles, L.J.; Bart, J.; Sitters, H.P.; Dey, A.D.; Clark, K.E.; Atkinson, P.W.; Baker, Allan J.; Bennett, K.A.; Kalasz, K.S.; Clark, N.A.; Clark, J.; Gillings, S.; Gates, A.S.; Gonzalez, P.M.; Hernandez, D.E.; Minton, C.D.T.; Morrison, R.I.G.; Porter, R.R.; Ross, R.K.; Veitch, C.R.

    2009-01-01

    Each May, red knots (Calidris canutus rufa) congregate in Delaware Bay during their northward migration to feed on horseshoe crab eggs (Limulus polyphemus) and refuel for breeding in the Arctic. During the 1990s, the Delaware Bay harvest of horseshoe crabs for bait increased 10-fold, leading to a more than 90% decline in the availability of their eggs for knots. The proportion of knots achieving weights of more than 180 grams by 26-28 May, their main departure period, dropped from 0.6-0.8 to 0.14-0.4 over 1997-2007. During the same period, the red knot population stopping in Delaware Bay declined by more than 75%, in part because the annual survival rate of adult knots wintering in Tierra del Fuego declined. Despite restrictions, the 2007 horseshoe crab harvest was still greater than the 1990 harvest, and no recovery of knots was detectable. We propose an adaptive management strategy with recovery goals and annual monitoring that, if adopted, will both allow red knot and horseshoe crab populations to recover and permit a sustainable harvest of horseshoe crabs.

  2. Learning to tie the knot: The acquisition of functional object representations by physical and observational experience.

    PubMed

    Cross, Emily S; Hamilton, Antonia F de C; Cohen, Nichola Rice; Grafton, Scott T

    2017-01-01

    Here we examined neural substrates for physically and observationally learning to construct novel objects, and characterized brain regions associated with each kind of learning using fMRI. Each participant was assigned a training partner, and for five consecutive days practiced tying one group of knots ("tied" condition) or watched their partner tie different knots ("watched" condition) while a third set of knots remained untrained. Functional MRI was obtained prior to and immediately following the week of training while participants performed a visual knot-matching task. After training, a portion of left superior parietal lobule demonstrated a training by scan session interaction. This means this parietal region responded selectively to knots that participants had physically learned to tie in the post-training scan session but not the pre-training scan session. A conjunction analysis on the post-training scan data showed right intraparietal sulcus and right dorsal premotor cortex to respond when viewing images of knots from the tied and watched conditions compared to knots that were untrained during the post-training scan session. This suggests that these brain areas track both physical and observational learning. Together, the data provide preliminary evidence of engagement of brain regions associated with hand-object interactions when viewing objects associated with physical experience, and with observational experience without concurrent physical practice.

  3. Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

    PubMed Central

    Li, Wenfei; Terakawa, Tsuyoshi; Wang, Wei; Takada, Shoji

    2012-01-01

    While fast folding of small proteins has been relatively well characterized by experiments and theories, much less is known for slow folding of larger proteins, for which recent experiments suggested quite complex and rich folding behaviors. Here, we address how the energy landscape theory can be applied to these slow folding reactions. Combining the perfect-funnel approximation with a multiscale method, we first extended our previous atomic-interaction based coarse grained (AICG) model to take into account local flexibility of protein molecules. Using this model, we then investigated the energy landscapes and folding routes of two proteins with complex topologies: a multidomain protein adenylate kinase (AKE) and a knotted protein 2ouf-knot. In the AKE folding, consistent with experimental results, the kinetic free energy surface showed several substates between the fully unfolded and native states. We characterized the structural features of these substates and transitions among them, finding temperature-dependent multiroute folding. For protein 2ouf-knot, we found that the improved atomic-interaction based coarse-grained model can spontaneously tie a knot and fold the protein with a probability up to 96%. The computed folding rate of the knotted protein was much slower than that of its unknotted counterpart, in agreement with experimental findings. Similar to the AKE case, the 2ouf-knot folding exhibited several substates and transitions among them. Interestingly, we found a dead-end substate that lacks the knot, thus suggesting backtracking mechanisms. PMID:22753508

  4. Freely Expanding X-ray Ejecta Knots in Kepler's Supernova Remnant

    NASA Astrophysics Data System (ADS)

    Hughes, John Patrick; Sato, Toshiki

    2017-08-01

    Using archival data from the Chandra X-ray Observatory, we measure the proper motions and radial velocities of compact X-ray bright knots in Kepler's supernova remnant (SNR). The high speed ejecta knots are morphologically and kinematically distinct from the rest of the ejecta and appear only in specific, limited locations. The highest speed knots show both large proper motions and high radial velocities with estimated space velocities of 10,000 km/s, similar to the typical Si velocity seen in Type Ia supernovae near maximum light. The proper motions of five knots extrapolate back over the age of the remnant to a consistent central position, defining a kinematic center for Kepler's SNR. Our new explosion center agrees well with previous determinations, but suffers less from systematic uncertainty. These five knots are expanding at close to the free expansion rate (expansion indices of 0.75 < m < 1.0), while other knots show slower speeds and expansion indices consistent with decelerated ejecta knots. The differences in the expansion rates are likely a function of differences in the ambient medium density surrounding Kepler’s SNR.

  5. Slipknotting upon native-like loop formation in a trefoil knot protein

    PubMed Central

    Noel, Jeffrey K.; Sułkowska, Joanna I.; Onuchic, José N.

    2010-01-01

    Protein knots and slipknots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Recent experimental results show that knotting, starting from a fully extended polypeptide, has not yet been observed. Understanding the nucleation process of folding knots is thus a natural challenge for both experimental and theoretical investigation. In this study, we employ energy landscape theory and molecular dynamics to elucidate the entire folding mechanism. The full free energy landscape of a knotted protein is mapped using an all-atom structure-based protein model. Results show that, due to the topological constraint, the protein folds through a three-state mechanism that contains (i) a precise nucleation site that creates a correctly twisted native loop (first barrier) and (ii) a rate-limiting free energy barrier that is traversed by two parallel knot-forming routes. The main route corresponds to a slipknot conformation, a collapsed configuration where the C-terminal helix adopts a hairpin-like configuration while threading, and the minor route to an entropically limited plug motion, where the extended terminus is threaded as through a needle. Knot formation is a late transition state process and results show that random (nonspecific) knots are a very rare and unstable set of configurations both at and below folding temperature. Our study shows that a native-biased landscape is sufficient to fold complex topologies and presents a folding mechanism generalizable to all known knotted protein topologies: knotting via threading a native-like loop in a preordered intermediate. PMID:20702769

  6. Near-Infrared Knots and Dense Fe Ejecta in the Cassiopeia A Supernova Remnant

    NASA Astrophysics Data System (ADS)

    Lee, Yong-Hyun; Koo, Bon-Chul; Moon, Dae-Sik; Burton, Michael G.; Lee, Jae-Joon

    2017-03-01

    We report the results of broadband (0.95–2.46 μm) near-infrared spectroscopic observations of the Cassiopeia A supernova remnant. Using a clump-finding algorithm in two-dimensional dispersed images, we identify 63 “knots” from eight slit positions and derive their spectroscopic properties. All of the knots emit [Fe ii] lines together with other ionic forbidden lines of heavy elements, and some of them also emit H and He lines. We identify 46 emission line features in total from the 63 knots and measure their fluxes and radial velocities. The results of our analyses of the emission line features based on principal component analysis show that the knots can be classified into three groups: (1) He-rich, (2) S-rich, and (3) Fe-rich knots. The He-rich knots have relatively small, ≲ 200 {km} {{{s}}}-1, line-of-sight speeds and radiate strong He i and [Fe ii] lines resembling closely optical quasi-stationary flocculi of circumstellar medium, while the S-rich knots show strong lines from O-burning material with large radial velocities up to ∼ 2000 {km} {{{s}}}-1 indicating that they are supernova ejecta material known as fast-moving knots. The Fe-rich knots also have large radial velocities but show no lines from O-burning material. We discuss the origin of the Fe-rich knots and conclude that they are most likely “pure” Fe ejecta synthesized in the innermost region during the supernova explosion. The comparison of [Fe ii] images with other waveband images shows that these dense Fe ejecta are mainly distributed along the southwestern shell just outside the unshocked 44Ti in the interior, supporting the presence of unshocked Fe associated with 44Ti.

  7. Reconstruction-induced trefoil knot Fermi contour of Au(111)

    NASA Astrophysics Data System (ADS)

    Dendzik, Maciej; Bianchi, Marco; Michiardi, Matteo; Sanders, Charlotte E.; Hofmann, Philip

    2016-11-01

    Using angle-resolved photoemission spectroscopy (ARPES), we study the effect of the so-called herringbone reconstruction of Au(111) on the dispersion of the free-electron-like surface state. While earlier ARPES investigations have only reported a minor interplay of the surface state dispersion and the underlying reconstruction, we show that the uniaxial lattice distortion and the thereby changed reciprocal lattice for the first atomic layer lead to distinct surface state dispersions around the first-order reciprocal lattice points of the three domains, creating a constant energy surface resembling a trefoil knot. The findings resolve the long-standing discrepancy between, on one hand, the reconstruction-induced surface state modifications reported in scanning tunneling microscopy and first principles calculations and, on the other hand, their conspicuous absence in photoemission.

  8. Nematicides and nonconventional soil amendments in the management of root-knot nematode on cotton.

    PubMed

    Jorgenson, E C

    1984-04-01

    Granular and liquid commercial humates, with micronutrients, and a microbial fermentation product were compared in several combinations with nematicides for their effects on cotton lint yield and root-knot nematode suppression. Fumigant nematicides effectively reduced cotton root galling caused by root-knot nematodes, and cotton lint yields increased. Organophosphates and carbamates were not effective. Occasionally, cotton lint yields were increased or maintained with combination treatments o f humates, micronutrients, and a microbial fermentation product, but galling o f cotton roots by root-knot nematodes was usually not reduced by these treatments.

  9. Multiple folding pathways of proteins with shallow knots and co-translational folding

    NASA Astrophysics Data System (ADS)

    Chwastyk, Mateusz; Cieplak, Marek

    2015-07-01

    We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding.

  10. Knotted and topologically complex proteins as models for studying folding and stability

    PubMed Central

    Yeates, Todd O.; Norcross, Todd S.; King, Neil P.

    2008-01-01

    SUMMARY Among proteins of known three dimensional structure, only a few possess complex topological features such as knotted or interlinked (catenated) protein backbones. Such unusual proteins offer potentially unique insights into folding pathways and stabilization mechanisms. They also present special challenges for both theorists and computational scientists interested in understanding and predicting protein folding behavior. Here we review complex topological features in proteins with a focus on recent progress on the identification and characterization of knotted and interlinked protein systems. Also, an approach is described for designing an expanded set of knotted proteins. PMID:17967433

  11. TOPICAL REVIEW: Knot theory and a physical state of quantum gravity

    NASA Astrophysics Data System (ADS)

    Liko, Tomás; Kauffman, Louis H.

    2006-02-01

    We discuss the theory of knots, and describe how knot invariants arise naturally in gravitational physics. The focus of this review is to delineate the relationship between knot theory and the loop representation of non-perturbative canonical quantum general relativity (loop quantum gravity). This leads naturally to a discussion of the Kodama wavefunction, a state which is conjectured to be the ground state of the gravitational field with positive cosmological constant. This review can serve as a self-contained introduction to loop quantum gravity and related areas. Our intent is to make the paper accessible to a wider audience that may include topologists, knot theorists, and other persons innocent of the physical background to this approach to quantum gravity.

  12. Tightening slip knots in raw and degummed silk to increase toughness without losing strength

    PubMed Central

    Pantano, Maria F.; Berardo, Alice; Pugno, Nicola M.

    2016-01-01

    Knots are fascinating topological elements, which can be found in both natural and artificial systems. While in most of the cases, knots cannot be loosened without breaking the strand where they are tightened, herein, attention is focused on slip or running knots, which on the contrary can be unfastened without compromising the structural integrity of their hosting material. Two different topologies are considered, involving opposite unfastening mechanisms, and their influence on the mechanical properties of natural fibers, as silkworm silk raw and degummed single fibers, is investigated and quantified. Slip knots with optimized shape and size result in a significant enhancement of fibers energy dissipation capability, up to 300–400%, without affecting their load bearing capacity. PMID:26868855

  13. Ileo-ileal knot: a rare case of acute strangulated intestinal obstruction

    PubMed Central

    Taniguchi, Kohei; Iida, Ryo; Watanabe, Tomohiko; Nitta, Masahiko; Tomioka, Masao; Uchiyama, Kazuhisa; Takasu, Akira

    2017-01-01

    ABSTRACT Strangulated intestinal obstruction is one of the most common types of acute abdomen and requires urgent surgical treatment. Herein, we report a very rare case of strangulated intestinal obstruction caused by an ileo-ileal knot. An 80-year-old woman was admitted to our hospital with suspicion of strangulation ileus and underwent emergency laparotomy after investigation by exploratory single-port laparoscopy. During surgery, a small bowel gangrene caused by an ileo-ileal knot was found. The gangrenous segment was resected, and primary anastomosis was performed. Post-operative recovery was uneventful except for a minor wound infection. Our extensive search of the literature found only 7 case reports of ileo-ileal knot including ours. An ileo-ileal knot should be considered in the differential diagnosis of acute intestinal obstruction, because this rare phenomenon requires urgent surgical treatment; and some complications should be considered during or after surgery. PMID:28303069

  14. Splitting, linking, knotting, and solitonic escape of topological defects in nematic drops with handles.

    PubMed

    Tasinkevych, Mykola; Campbell, Michael G; Smalyukh, Ivan I

    2014-11-18

    Topologically nontrivial field excitations, including solitonic, linked, and knotted structures, play important roles in physical systems ranging from classical fluids and liquid crystals, to electromagnetism, classic, and quantum field theories. These excitations can appear spontaneously during symmetry-breaking phase transitions. For example, in cosmological theories, cosmic strings may have formed knotted configurations influencing the Early Universe development, whereas in liquid crystals transient tangled defect lines were observed during isotropic-nematic transitions, eventually relaxing to defect-free states. Knotted and solitonic fields and defects were also obtained using optical manipulation, complex-shaped colloids, and frustrated cholesterics. Here we use confinement of nematic liquid crystal by closed surfaces with varied genus and perpendicular boundary conditions for a robust control of appearance and stability of such field excitations. Theoretical modeling and experiments reveal structure of defect lines as a function of the surface topology and material and geometric parameters, establishing a robust means of controlling solitonic, knotted, linked, and other field excitations.

  15. Quandle coloring and cocycle invariants of composite knots and abelian extensions

    PubMed Central

    Clark, W. Edwin; Saito, Masahico; Vendramin, Leandro

    2016-01-01

    Quandle colorings and cocycle invariants are studied for composite knots, and applied to chirality and abelian extensions. The square and granny knots, for example, can be distinguished by quandle colorings, so that a trefoil and its mirror can be distinguished by quandle coloring of composite knots. We investigate this and related phenomena. Quandle cocycle invariants are studied in relation to quandle coloring of the connected sum, and formulas are given for computing the cocycle invariant from the number of colorings of composite knots. Relations to corresponding abelian extensions of quandles are studied, and extensions are examined for the table of small connected quandles, called Rig quandles. Computer calculations are presented, and summaries of outputs are discussed. PMID:27346904

  16. Quandle coloring and cocycle invariants of composite knots and abelian extensions.

    PubMed

    Clark, W Edwin; Saito, Masahico; Vendramin, Leandro

    2016-04-01

    Quandle colorings and cocycle invariants are studied for composite knots, and applied to chirality and abelian extensions. The square and granny knots, for example, can be distinguished by quandle colorings, so that a trefoil and its mirror can be distinguished by quandle coloring of composite knots. We investigate this and related phenomena. Quandle cocycle invariants are studied in relation to quandle coloring of the connected sum, and formulas are given for computing the cocycle invariant from the number of colorings of composite knots. Relations to corresponding abelian extensions of quandles are studied, and extensions are examined for the table of small connected quandles, called Rig quandles. Computer calculations are presented, and summaries of outputs are discussed.

  17. Syncytial knots and intervillous bridges in the human placenta: an ultrastructural study.

    PubMed Central

    Jones, C J; Fox, H

    1977-01-01

    An electron microscopic study has shown that the syncytial knots of the villi of the human placenta contain aggregated nuclei which exhibit marked degenerative changes; within the cytoplasm there is an abundance of cytoplasmic filaments and many stacks of annulate lamellae. It is suggested that syncytial knots are a sequestration phenomenon in which senescent nuclear material is aggregated and removed from metabolically active areas of the syncytiotrophoblast. Intervillous bridges appear to be formed chiefly by fusion of syncytial knots from adjacent villi, and it seems reasonable that the effete material in a syncytial knot should be used for this purpose. The intervillous bridges hava a fine structure which suggests that they have a mechanical function, and this lends support to the theory that they form an internal strut system within the placenta. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 Fig. 9 PMID:591426

  18. Tightening slip knots in raw and degummed silk to increase toughness without losing strength

    NASA Astrophysics Data System (ADS)

    Pantano, Maria F.; Berardo, Alice; Pugno, Nicola M.

    2016-02-01

    Knots are fascinating topological elements, which can be found in both natural and artificial systems. While in most of the cases, knots cannot be loosened without breaking the strand where they are tightened, herein, attention is focused on slip or running knots, which on the contrary can be unfastened without compromising the structural integrity of their hosting material. Two different topologies are considered, involving opposite unfastening mechanisms, and their influence on the mechanical properties of natural fibers, as silkworm silk raw and degummed single fibers, is investigated and quantified. Slip knots with optimized shape and size result in a significant enhancement of fibers energy dissipation capability, up to 300-400%, without affecting their load bearing capacity.

  19. Folding of small knotted proteins: Insights from a mean field coarse-grained model

    NASA Astrophysics Data System (ADS)

    Najafi, Saeed; Potestio, Raffaello

    2015-12-01

    A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.

  20. Successful retrieval of a knotted pulmonary artery catheter trapped in the tricuspid valve apparatus.

    PubMed

    Ishaq, Muhammad; Alexander, Nicki; Scott, David H T

    2013-04-01

    We report the case of a 64-year-old patient in whom a pulmonary artery catheter formed a knot fixed within the right ventricle in the region of the tricuspid valve apparatus. Knot formation is a recognized complication associated with pulmonary artery catheters (PAC) insertion. This problem is usually dealt with by simply withdrawing the PAC until the knot impacts onto the introducer and after enlarging the puncture site by a small skin incision removing the introducer-PAC as one unit. However, we recently encountered a situation where the PAC was knotted around the tricuspid valve apparatus and could not be withdrawn. An interventional radiologist was able to unknot the catheter and release it from the tricuspid valve. We reviewed the literature related to this topic. We believe our experience could be of use to others.

  1. Folding of small knotted proteins: Insights from a mean field coarse-grained model

    SciTech Connect

    Najafi, Saeed; Potestio, Raffaello

    2015-12-28

    A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.

  2. Miniature fiber-optic temperature sensors based on silica/polymer microfiber knot resonators.

    PubMed

    Wu, Yu; Rao, Yun-Jiang; Chen, Yi-Huai; Gong, Yuan

    2009-09-28

    In this paper, we report two fiber-optic temperature sensors based on silica/polymer microfiber knot resonators (SMKR/PMKR). The structures of these sensors are composed of three layers, MgF(2) crystal plate is adopted as the substrate, and the sensing knots are covered by a thin MgF(2) slab to keep it steady and immunity to the environment fluctuations. Experimental results show that the temperature sensitivity of SMKR is approximately 52 pm/ degrees C within 30 degrees C approximately 700 degrees C, while the sensitivity of PMKR is approximately 266 pm/ degrees C within 20 degrees C approximately 80 degrees C. The temporal response of SMKR and PMKR sensors are less than 1 ms and 5 ms, respectively. These microfiber knot resonators can be used as miniature high temperature sensors with fast response. Higher resolution can be anticipated with further improvement of the Q factor of the microfiber knot resonators.

  3. Knotted solutions for linear and nonlinear theories: Electromagnetism and fluid dynamics

    NASA Astrophysics Data System (ADS)

    Alves, Daniel W. F.; Hoyos, Carlos; Nastase, Horatiu; Sonnenschein, Jacob

    2017-10-01

    We examine knotted solutions, the most simple of which is the ;Hopfion;, from the point of view of relations between electromagnetism and ideal fluid dynamics. A map between fluid dynamics and electromagnetism works for initial conditions or for linear perturbations, allowing us to find new knotted fluid solutions. Knotted solutions are also found to be solutions of nonlinear generalizations of electromagnetism, and of quantum-corrected actions for electromagnetism coupled to other modes. For null configurations, electromagnetism can be described as a null pressureless fluid, for which we can find solutions from the knotted solutions of electromagnetism. We also map them to solutions of Euler's equations, obtained from a type of nonrelativistic reduction of the relativistic fluid equations.

  4. Tightening slip knots in raw and degummed silk to increase toughness without losing strength.

    PubMed

    Pantano, Maria F; Berardo, Alice; Pugno, Nicola M

    2016-02-12

    Knots are fascinating topological elements, which can be found in both natural and artificial systems. While in most of the cases, knots cannot be loosened without breaking the strand where they are tightened, herein, attention is focused on slip or running knots, which on the contrary can be unfastened without compromising the structural integrity of their hosting material. Two different topologies are considered, involving opposite unfastening mechanisms, and their influence on the mechanical properties of natural fibers, as silkworm silk raw and degummed single fibers, is investigated and quantified. Slip knots with optimized shape and size result in a significant enhancement of fibers energy dissipation capability, up to 300-400%, without affecting their load bearing capacity.

  5. Spontaneous peritoneal catheter knot formation: A rare cause of ventriculoperitoneal shunt malfunction.

    PubMed

    Sher, Idrees; Gambhir, Shanu; Pinto, Sarah; Mujic, Asim; Peters-Willke, Jens; Hunn, Andrew

    2017-04-01

    Ventriculoperitoneal (VP) shunting remains invaluable in the management of hydrocephalus. It is a common procedure that can be complicated by shunt malfunction due to infection, blockage and disconnection. Spontaneous peritoneal catheter knot formation causing CSF flow obstruction is a rare phenomenon. We present a case of a 12years old boy with spontaneous knot formation in the peritoneal catheter causing VP shunt obstruction and hydrocephalus.

  6. Management of root-knot nematode (Meloidogyne incognita) in bottle gourd using different botanicals in pots.

    PubMed

    Singh, Tulika; Patel, B A

    2015-09-01

    A pot experiment was conducted to study the efficacy of different botanicals in varying doses for management of root-knot nematode, M. incognita in bottle gourd. The results exhibited that madar (Calotropis procera) and neem (Azadirachta indica) leaves application proved to be more effective in improving plant growth characters and reducing root-knot index and final nematode population. Among the doses tested, higher dose of 1.5 % (w/w) was more effective than lower ones.

  7. AN ASYMMETRICAL SYNCHROTRON MODEL FOR KNOTS IN THE 3C 273 JET

    SciTech Connect

    Liu, Wen-Po; Chen, Y. J.; Wang, Chun-Cheng

    2015-06-20

    To interpret the emission of knots in the 3C 273 jet from radio to X-rays, we propose a synchrotron model in which, owing to the shock compression effect, the injection spectra from a shock into the upstream and downstream emission regions are asymmetric. Our model could well explain the spectral energy distributions of knots in the 3C 273 jet, and predictions regarding the knots’ spectra could be tested by future observations.

  8. Characterization of the inner knot of the crab: The site of the gamma-ray flares?

    DOE PAGES

    Rudy, Alexander; Horns, Dieter; DeLuca, Andrea; ...

    2015-09-16

    A particularly intriguing recent result from γ-ray astronomy missions is the detection of powerful flares from the Crab Nebula, which challenges the current understanding of pulsar wind nebulae and acceleration mechanisms. In order to search for the production site(s) of these flares, we conducted a multi-wavelength observing campaign using Keck, the Hubble Space Telescope (HST), and the Chandra X-ray Observatory. As the short timescales of the γ-ray flares (more » $$\\lesssim 1$$ day) suggest a small emitting region, the Crab's inner knot (about 0.6 arcsec from the pulsar) is a candidate site for such flaring. Our paper describes observations of the inner knot, seeking to understand its nature and possible relationship with γ-ray flares. Using singular-value decomposition, analysis of the HST images yielded results consistent with traditional methods while substantially reducing some uncertainties. These analyses show that the knot's intrinsic properties (especially size and brightness) are correlated with its (projected) separation from the pulsar. This characterization of the inner knot helps in constraining standard shock model parameters, under the assumption that the knot lies near the shocked surface. While the standard shock model gives good agreement in several respects, two puzzles persist: (a) the observed angular size of the knot relative to the pulsar–knot separation is much smaller than expected; and (b) the variable high degree of polarization (reported by others) is difficult to reconcile with a highly relativistic downstream flow. But, the IR–optical flux of the inner knot is marginally consistent with the shock accelerating most of the Nebula's optical-emitting particles.« less

  9. Characterization of the inner knot of the crab: The site of the gamma-ray flares?

    SciTech Connect

    Rudy, Alexander; Horns, Dieter; DeLuca, Andrea; Kolodziejczak, Jeffery; Tennant, Allyn; Yuan, Yajie; Buehler, Rolf; Arons, Jonathon; Blandford, Roger; Caraveo, Patrizia; Costa, Enrico; Funk, Stephan; Hays, Elizabeth; Lobanov, Andrei; Max, Claire; Mayer, Michael; Mignani, Roberto; O’Dell, Stephen L.; Romani, Roger; Tavani, Marco; Weisskopf, Martin C.

    2015-09-16

    A particularly intriguing recent result from γ-ray astronomy missions is the detection of powerful flares from the Crab Nebula, which challenges the current understanding of pulsar wind nebulae and acceleration mechanisms. In order to search for the production site(s) of these flares, we conducted a multi-wavelength observing campaign using Keck, the Hubble Space Telescope (HST), and the Chandra X-ray Observatory. As the short timescales of the γ-ray flares ($\\lesssim 1$ day) suggest a small emitting region, the Crab's inner knot (about 0.6 arcsec from the pulsar) is a candidate site for such flaring. Our paper describes observations of the inner knot, seeking to understand its nature and possible relationship with γ-ray flares. Using singular-value decomposition, analysis of the HST images yielded results consistent with traditional methods while substantially reducing some uncertainties. These analyses show that the knot's intrinsic properties (especially size and brightness) are correlated with its (projected) separation from the pulsar. This characterization of the inner knot helps in constraining standard shock model parameters, under the assumption that the knot lies near the shocked surface. While the standard shock model gives good agreement in several respects, two puzzles persist: (a) the observed angular size of the knot relative to the pulsar–knot separation is much smaller than expected; and (b) the variable high degree of polarization (reported by others) is difficult to reconcile with a highly relativistic downstream flow. But, the IR–optical flux of the inner knot is marginally consistent with the shock accelerating most of the Nebula's optical-emitting particles.

  10. The energy landscape, folding pathways and the kinetics of a knotted protein.

    PubMed

    Prentiss, Michael C; Wales, David J; Wolynes, Peter G

    2010-07-01

    The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N or C terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N terminus portion of the knot and a rate-determining step where the C terminus is incorporated. The low-lying minima with the N terminus knotted and the C terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N and C termini into the knot occurs late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.

  11. Steric confinement and enhanced local flexibility assist knotting in simple models of protein folding.

    PubMed

    Soler, Miguel A; Rey, Antonio; Faísca, Patrícia F N

    2016-09-29

    The chaperonin complex GroEL-GroES is able to accelerate the folding process of knotted proteins considerably. However, the folding mechanism inside the chaperonin cage is elusive. Here we use a combination of lattice and off-lattice Monte Carlo simulations of simple Gō models to study the effect of physical confinement and local flexibility on the folding process of protein model systems embedding a trefoil knot in their native structure. This study predicts that steric confinement plays a specific role in the folding of knotted proteins by increasing the knotting probability for very high degrees of confinement. This effect is observed for protein MJ0366 even above the melting temperature for confinement sizes compatible with the size of the GroEL/GroES chaperonin cage. An enhanced local flexibility produces the same qualitative effects on the folding process. In particular, we observe that knotting probability increases up to 40% in the transition state of protein MJ0366 when flexibility is enhanced. This is underlined by a structural change in the transition state, which becomes devoid of helical content. No relation between the knotting mechanism and flexibility was found in the context of the off-lattice model adopted in this work.

  12. An eddy-current-based sensor for preventing knots in metallic wire drawing processes

    NASA Astrophysics Data System (ADS)

    Esteban, Bernat; Riba, Jordi-Roger; Baquero, Grau; Ferrater, Cèsar

    2011-06-01

    During metallic wire drawing processes, the presence of knots and the failure to detect them can lead to long production interruptions, significant economic losses and a lower quality of final product. Consequently, there is a pressing need to develop methods for real-time detection and prevention of this fault. In this paper, a sensor to prevent the formation of knots during the metallic wire drawing process is presented and evaluated by means of experimental data. This fast, inexpensive, non-contact sensor is based on electromagnetic principles such as eddy current induction, magnetic reluctance variations and magnetic coupling. The proposed sensor without direct contact can detect knots in a target metallic wire by measuring the impedance variations of a calibrated sensing coil caused by either a knot or an unwound loop rising from a wire rod. The incorporation of this type of sensor into a wire-drawing machine can avoid the tightening of the knot, thereby reducing downtime and increasing the security and reliability of the process. Experiments were conducted using a scale model of the above proposed system. This allowed highlighting the sensor's potential by carrying out an automatic, real-time knot detection during steel wire drawing.

  13. Knotted versus knotless suture bridge repair of the achilles tendon insertion: a biomechanical study.

    PubMed

    Cox, Joseph T; Shorten, Peter L; Gould, Gregory C; Markert, Ronald J; Barnett, Michael D; Laughlin, Richard T

    2014-11-01

    Surgical treatment of insertional Achilles tendinopathy often involves detachment and debridement of the Achilles tendon insertion. A recent study has shown that knotted suture bridge fixation of the Achilles to the calcaneus is biomechanically superior to single-row fixation, but there is an absence of literature on the use of different suture bridge constructs to repair the Achilles tendon. There will be no significant difference in the load to failure, mode of failure, tendon strain, tendon stiffness, repair site gapping, or footprint size when comparing knotted suture bridge repair to knotless suture bridge repair of the Achilles tendon after detachment for insertional Achilles tendinopathy. Controlled laboratory study. A single specimen from each pair of 10 cadaveric Achilles tendons was randomized to 1 of 2 Achilles insertion repair groups: knotted (n = 10) or knotless (n = 10) suture bridge repair. Repaired footprint size was measured, and then cyclic testing from 10 to 100 N for 2000 cycles was performed. This was followed by measurement of tendon strain, repair site displacement, load to failure, and tendon stiffness. The knotted suture bridge repair had a significantly higher load to failure compared with the knotless suture bridge (mean ± SD, 317.8 ± 93.6 N vs 196.1 ± 12.1 N, respectively; P = .001). All constructs failed at the tendon-suture interface. Tendon strain after cyclic testing was significantly greater in the knotless (1.20 ± 1.05) compared with the knotted (0.39 ± 0.4) suture repair groups (P = .011). There was no significant difference in footprint size between the knotted (230.3 ± 63.3 mm(2)) and knotless (248.5 ± 48.8 mm(2)) groups (P = .40). There was also no significant difference in stiffness (knotted = 76.4 ± 8.0 N/mm; knotless = 69.6 ± 10.9 N/mm; P = .17) and repair site displacement after cyclic testing (knotted = 2.8 ± 1.2 mm; knotless = 3.6 ± 1.1 mm; P = .17). During suture bridge repair of the Achilles tendon after

  14. Evaluation of the effect of 4 types of knots on the mechanical properties of 4 types of suture material used in small animal practice.

    PubMed

    Avoine, Xytilis; Lussier, Bertrand; Brailovski, Vladimir; Inaekyan, Karine; Beauchamp, Guy

    2016-04-01

    The influence of the type of material used, knot configuration, and use of an additional throw on the tensile force at failure, the elongation, and the mode of failure of different configurations of linear sutures and knotted suture loops was evaluated in this in-vitro mechanical study. We hypothesized that all types of knots would significantly influence the initial force and elongation of suture materials and would influence the force and elongation at which the knotted loops break, but not their mode of failure. A total of 432 samples of 4 types of size 3-0 suture material (polydioxanone, polyglecaprone 25, polyglactin 910, and nylon), representing 9 configurations, were tested in a tensiometer. The configurations were 1 linear suture without a knot and the following loops: square (SQ) knot; surgeon's (SU) knot; granny (GR) knot; and sliding half-hitch (SHH) knot using either 4 and 5 or 3 and 4 throws, depending on the material. For polydioxanone, SQ and SU knots did not decrease the initial force at failure of the suture. Granny (GR) and SHH knots decreased the tensile force at failure and elongation by premature failure of the loop. For polyglecaprone 25, all knots decreased the initial force at failure of the suture, with SHH being weaker than the other knots. For coated polyglactin 910, all knots decreased the initial force at failure of the suture and slippage increased significantly compared with the other 3 sutures. The use of SQ knots with 3 throws did not result in a safe knot. For nylon, knots did not alter the original mechanics of the suture. In conclusion, all knots and types of suture material do not necessarily have the same effect on the initial tensile force at failure of suture materials.

  15. Evaluation of the effect of 4 types of knots on the mechanical properties of 4 types of suture material used in small animal practice

    PubMed Central

    Avoine, Xytilis; Lussier, Bertrand; Brailovski, Vladimir; Inaekyan, Karine; Beauchamp, Guy

    2016-01-01

    The influence of the type of material used, knot configuration, and use of an additional throw on the tensile force at failure, the elongation, and the mode of failure of different configurations of linear sutures and knotted suture loops was evaluated in this in-vitro mechanical study. We hypothesized that all types of knots would significantly influence the initial force and elongation of suture materials and would influence the force and elongation at which the knotted loops break, but not their mode of failure. A total of 432 samples of 4 types of size 3-0 suture material (polydioxanone, polyglecaprone 25, polyglactin 910, and nylon), representing 9 configurations, were tested in a tensiometer. The configurations were 1 linear suture without a knot and the following loops: square (SQ) knot; surgeon’s (SU) knot; granny (GR) knot; and sliding half-hitch (SHH) knot using either 4 and 5 or 3 and 4 throws, depending on the material. For polydioxanone, SQ and SU knots did not decrease the initial force at failure of the suture. Granny (GR) and SHH knots decreased the tensile force at failure and elongation by premature failure of the loop. For polyglecaprone 25, all knots decreased the initial force at failure of the suture, with SHH being weaker than the other knots. For coated polyglactin 910, all knots decreased the initial force at failure of the suture and slippage increased significantly compared with the other 3 sutures. The use of SQ knots with 3 throws did not result in a safe knot. For nylon, knots did not alter the original mechanics of the suture. In conclusion, all knots and types of suture material do not necessarily have the same effect on the initial tensile force at failure of suture materials. PMID:27127344

  16. CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Structural statistical properties of knotted proteins

    NASA Astrophysics Data System (ADS)

    Wang, Xiang-Hong; Shen, Yu; Zhang, Lin-Xi

    2009-04-01

    The composition and residue-residue interactions of knotted proteins, compared with those of other proteins, can provide considerable insight into the driver of the knots in proteins. In this paper, we calculate the probabilities of 20 amino acids in 273 knotted entries from the Protein Data Bank (PDB). The collection of 273 entries contains all knotted structures in the PDB, and it is not a subset. With an appropriate value of Rc, the numbers of all residue-residue contacts are counted in all 273 knotted structures. To make an accurate comparison, we count up to 9000 other entries from the PDB as well, and these entries spread over all sorts. In knotted structures, Leu occupies a maximal proportion of 9.62% among all 20 amino acids, and Leu, Phe, Trp, Gly, His, Gln, Asp, Lys and Pro may all play a more important role. Also, we analyse the effects of amino acid residues on the long-range contacts. We observe a larger average number of long-range contacts in the knotted structures than that in other ones, implying their important role in achieving the knots. Accordingly, the average number of short-range contacts becomes small when the structure becomes knotted because it depends mainly on the short-haul sequence of amino acids to form the short-range contact. In addition, the shape distribution of knotted proteins and the contrast with the other proteins are also presented. A comparison shows that the knots may make structures more globular because the average shape factor is 0.059 for the knotted proteins, which is only about 1/3 of the average shape factor for the other proteins.

  17. Temperature Sensing in Seawater Based on Microfiber Knot Resonator

    PubMed Central

    Yang, Hongjuan; Wang, Shanshan; Wang, Xin; Liao, Yipeng; Wang, Jing

    2014-01-01

    Ocean internal-wave phenomena occur with the variation in seawater vertical temperature, and most internal-wave detections are dependent on the measurement of seawater vertical temperature. A seawater temperature sensor based on a microfiber knot resonator (MKR) is designed theoretically and demonstrated experimentally in this paper. Especially, the dependences of sensing sensitivity on fiber diameter and probing wavelength are studied. Calculated results show that sensing sensitivity increases with the increasing microfiber diameter with the range of 2.30–3.91 μm and increases with the increasing probing wavelength, which reach good agreement with results obtained by experiments. By choosing the appropriate parameters, the maximum sensitivity measured can reach to be 22.81 pm/°C. The seawater temperature sensor demonstrated here shows advantages of small size, high sensitivity, easy fabrication, and easy integration with fiber systems, which may offer a new optical method to detect temperature of seawater or ocean internal-wave phenomenon and offer valuable reference for assembling micro sensors used for other parameters related to seawater, such as salinity, refractive index, concentration of NO3− and so on. PMID:25299951

  18. Helicity, topology, and Kelvin waves in reconnecting quantum knots

    NASA Astrophysics Data System (ADS)

    Clark di Leoni, P.; Mininni, P. D.; Brachet, M. E.

    2016-10-01

    Helicity is a topological invariant that measures the linkage and knottedness of lines, tubes, and ribbons. As such, it has found myriads of applications in astrophysics, fluid dynamics, atmospheric sciences, and biology. In quantum flows, where topology-changing reconnection events are a staple, helicity appears as a key quantity to study. However, the usual definition of helicity is not well posed in quantum vortices, and its computation based on counting links and crossings of centerline vorticity can be downright impossible to apply in complex and turbulent scenarios. We present a definition of helicity which overcomes these problems and which gives the expected result in the large-scale limit. With it, we show that certain reconnection events can excite Kelvin waves and other complex motions of the centerline vorticity, which slowly deplete helicity as they interact nonlinearly, thus linking the theory of vortex knots with observations of quantum fluids. This process also results in the depletion of helicity in a fully turbulent quantum flow, in a way reminiscent of the decay of helicity in classical fluids.

  19. Optical vortex knots - one photon at a time.

    PubMed

    Tempone-Wiltshire, Sebastien J; Johnstone, Shaun P; Helmerson, Kristian

    2016-04-18

    Feynman described the double slit experiment as "a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics". The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot - one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing.

  20. Optical vortex knots - one photon at a time

    NASA Astrophysics Data System (ADS)

    Tempone-Wiltshire, Sebastien J.; Johnstone, Shaun P.; Helmerson, Kristian

    2016-04-01

    Feynman described the double slit experiment as “a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics”. The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot - one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing.

  1. Novel inhibitor cystine knot peptides from Momordica charantia.

    PubMed

    He, Wen-Jun; Chan, Lai Yue; Clark, Richard J; Tang, Jun; Zeng, Guang-Zhi; Franco, Octavio L; Cantacessi, Cinzia; Craik, David J; Daly, Norelle L; Tan, Ning-Hua

    2013-01-01

    Two new peptides, MCh-1 and MCh-2, along with three known trypsin inhibitors (MCTI-I, MCTI-II and MCTI-III), were isolated from the seeds of the tropical vine Momordica charantia. The sequences of the peptides were determined using mass spectrometry and NMR spectroscopy. Using a strategy involving partial reduction and stepwise alkylation of the peptides, followed by enzymatic digestion and tandem mass spectrometry sequencing, the disulfide connectivity of MCh-1 was elucidated to be CysI-CysIV, CysII-CysV and CysIII-CysVI. The three-dimensional structures of MCh-1 and MCh-2 were determined using NMR spectroscopy and found to contain the inhibitor cystine knot (ICK) motif. The sequences of the novel peptides differ significantly from peptides previously isolated from this plant. Therefore, this study expands the known peptide diversity in M. charantia and the range of sequences that can be accommodated by the ICK motif. Furthermore, we show that a stable two-disulfide intermediate is involved in the oxidative folding of MCh-1. This disulfide intermediate is structurally homologous to the proposed ancestral fold of ICK peptides, and provides a possible pathway for the evolution of this structural motif, which is highly prevalent in nature.

  2. Induction of Tolerance to Root-Knot Nematode by Oxycom

    PubMed Central

    Anwar, Safdar A.; McKenry, M. V.; Yang, Kwang-Yeol; Anderson, A. J.

    2003-01-01

    Oxycom applications increased plant growth and population levels of Meloidogyne incognita on susceptible tomato. A single Oxycom drench at 2,500 ppm applied 7 days prior to inoculation with M. incognita provided remediation of plant growth measured 63 days later. This occurred without reducing nematode population levels. Follow-up drenches at 2,500 ppm at 10-day intervals stunted shoots and roots (P = 0.05). The same application rates at 20-day intervals did not reduce plant growth. Plants receiving multiple drenches had more galls (P = 0.05), females, and second-stage juveniles (J2) per root system compared to plants receiving only the single treatment. Foliar mass and height of plants treated with a single pre-inoculation Oxycom drench were indistinguishable from plants without nematodes. Oxycom treatments activated signaling pathways for plant defense as confirmed by detection of elevated defense gene transcripts in root tissues. The finding of increased reproduction of root-knot nematode without loss of plant growth is consistent with the definition of induced tolerance. Frequency, rate, and timing of applications need further study with other nematodes and various field settings. PMID:19262766

  3. Root-Knot Nematode Parasitism Suppresses Host RNA Silencing.

    PubMed

    Walsh, E; Elmore, J M; Taylor, C G

    2017-04-12

    Root-knot nematodes damage crops around the world by developing complex feeding sites from normal root cells of their hosts. The ability to initiate and maintain this feeding site (composed of individual "giant cells") is essential to their parasitism process. RNA silencing pathways in plants serve a diverse set of functions, from directing growth and development to defending against invading pathogens. Influencing a host's RNA silencing pathways as a pathogenicity strategy has been well-documented for viral plant pathogens, but recently, it has become clear that silencing pathways also play an important role in other plant pathosystems. To determine if RNA silencing pathways play a role in nematode parasitism, we tested the susceptibility of plants that express a viral suppressor of RNA silencing. We observed an increase in susceptibility to nematode parasitism in plants expressing viral suppressors of RNA silencing. Results from studies utilizing a silenced reporter gene suggest that active suppression of RNA silencing pathways may be occurring during nematode parasitism. With these studies, we provide further evidence to the growing body of plant-biotic interaction research that suppression of RNA silencing is important in the successful interaction between a plant-parasitic animal and its host.

  4. Optical vortex knots – one photon at a time

    PubMed Central

    Tempone-Wiltshire, Sebastien J.; Johnstone, Shaun P.; Helmerson, Kristian

    2016-01-01

    Feynman described the double slit experiment as “a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics”. The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot – one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing. PMID:27087642

  5. Knotting of a Cervical Epidural Catheter in the Patient with Post-Herpetic Neuralgia: A Rare Complication

    PubMed Central

    Park, Jong Taek; Cho, Dong Woo; Lee, Young Bok

    2017-01-01

    Epidural block is achieved either by single injection of local anesthetic through an epidural needle or as a continuous block by infusion pump through an epidural catheter. Complications associated with epidural catheters include breakage, entrapment, and knotting. Knotting of epidural catheters is very rare, but knotting in lumbar epidural catheters has been reported in a number of studies, and most of these cases involved removal difficulty. We report a case in which we inserted a cervical epidural catheter in a patient who was experiencing severe post-herpetic neuralgia and then removed the knotted catheter without complications. PMID:28261560

  6. Bounds for the minimum step number of knots confined to slabs in the simple cubic lattice

    NASA Astrophysics Data System (ADS)

    Ishihara, K.; Scharein, R.; Diao, Y.; Arsuaga, J.; Vazquez, M.; Shimokawa, K.

    2012-02-01

    Volume confinement is a key determinant of the topology and geometry of a polymer. However, the direct relationship between the two is not fully understood. For instance, recent experimental studies have constructed P4 cosmids, i.e. P4 bacteriophages whose genome sequence and length have been artificially engineered and have shown that upon extraction their DNA knot distribution differs from that of wild-type bacteriophage P4. In particular, it was observed that the complexity of the knots decreases sharply with the length of the packed genome. This problem is the motivation of this paper. Here, a polymer is modeled as a self-avoiding polygon on the simple cubic lattice and the confining condition is such that the polygon is bounded between two parallel planes (i.e. bounded within a slab). We estimate the minimum length required for such a polygon to realize a knot type. Our numerical simulations show that in order to realize a prime knot (with up to ten crossings) in a 1-slab (i.e. a slab of height 1), one needs a polygon of length strictly longer than the minimum length needed to realize the same knot when there is no confining condition. In the case of the trefoil knot, we can in fact establish this result analytically by proving that the minimum length required to tie a trefoil in the 1-slab is 26, which is greater than 24, the known minimum length required to tie a trefoil without a confinement condition. Additionally, we find that in the 1-slab not all geometrical realizations of a given knot type are equivalent under BFACF moves. This suggests that in certain confined volumes, knowing the topology of a polymer is not enough to describe all its states.

  7. Evidence for Mass Outflow from the Nucleus of M101: Knots, Rings, and a Geyser

    NASA Astrophysics Data System (ADS)

    Moody, J. W.; Roming, P. W. A.; Joner, M. D.; Hintz, E. G.; Geisler, D.; Durrell, P. R.; Scowen, P. A.; Jee, R. O.

    1995-11-01

    Hα on-line and off-line CCD images of M101 obtained with the Canada-France-Hawaii 3.6 m telescope show the presence of two Hα bright, filled knots paired linearly across the nucleus in a north-south orientation. The knots are centered 2.4" (85 pc, assuming a distance to M101 of 7.4 Mpc) from the nucleus and lie roughly perpendicular to an east-west molecular bar. Each knot in turn is connected to an elongated, photoionized ring lying parallel along the bar. The eastern ring, connected to the southern knot, reaches outward in a well-defined 500 x 200 pc oval. The 700 x 300 pc western ring, connected to the northern knot, is more broken and dissipated in the middle. An arc containing blue stars and/or significant Hα absorption lies along the southern side of a dust lane extending from the nucleus westward along the bar. Hubble Space Telescope Planetary Camera image data show pockets of star-forming regions to the east and to the south of the nucleus which are associated with the knot and ring in that half. The imaging data, together with velocity data obtained with the Coude' feed spectrometer at Kitt Peak National Observatory show that the knots and rings are likely a bipolar outflow originating from a velocity <100 km s^-1^ "geyser" which has a period of approximately 22 million years and is located in the nucleus. The geyser may be caused by a mass < 10^6^ M_sun_ black hole orbiting within the nucleus, sweeping material from the molecular bar.

  8. DYNAMICS OF VERTICAL THREADS AND DESCENDING KNOTS IN A HEDGEROW PROMINENCE

    SciTech Connect

    Chae, Jongchul

    2010-05-01

    The existence and behavior of vertical fine structures of plasma-threads and knots-are a significant observational clue to understanding the magnetic structure and dynamics of quiescent prominences on the quiet Sun. Based on the equation of motion in ideal MHD, we reason that the non-hydrostatic support of plasma against gravity in general requires either the motion of plasma with a high value of downward acceleration (dynamical support) or the role of horizontal magnetic fields (magnetic support). By carefully tracking the motion of several bright threads seen in a hedgerow prominence observed by the Solar Optical Telescope aboard Hinode, we confirm that these threads are essentially static and stable, which negates the dynamic support. The application of the Kippenhahn-Schlueter solution suggests that they may be supported by sagged magnetic field lines with a sag angle of about 43{sup 0}. We also track several bright descending knots and find that their descending speeds range from 10 to 30 km s{sup -1}, with a mean value of 16 km s{sup -1}, and their vertical accelerations from -0.10 to 0.10 km s{sup -2}, with a mean of practically zero. This finding suggests that these knots are basically supported by horizontal magnetic fields against gravity even when they descend, and the complex variations of their descending speeds should be attributed to small imbalances between gravity and the force of magnetic tension. Furthermore, some knots are observed to impulsively get accelerated downward from time to time. We conjecture that these impulsive accelerations are a result of magnetic reconnection and the subsequent interchange of magnetic configuration between a knot and its surrounding structure. It is proposed that this process of reconnection and interchange not only initiates the descending motion of the knots, but also allows knots to keep falling long distance through the medium permeated by horizontal magnetic fields.

  9. A novel knot selection method for the error-bounded B-spline curve fitting of sampling points in the measuring process

    NASA Astrophysics Data System (ADS)

    Liang, Fusheng; Zhao, Ji; Ji, Shijun; Fan, Cheng; Zhang, Bing

    2017-06-01

    The B-spline curve has been widely used in the reconstruction of measurement data. The error-bounded sampling points reconstruction can be achieved by the knot addition method (KAM) based B-spline curve fitting. In KAM, the selection pattern of initial knot vector has been associated with the ultimate necessary number of knots. This paper provides a novel initial knots selection method to condense the knot vector required for the error-bounded B-spline curve fitting. The initial knots are determined by the distribution of features which include the chord length (arc length) and bending degree (curvature) contained in the discrete sampling points. Firstly, the sampling points are fitted into an approximate B-spline curve Gs with intensively uniform knot vector to substitute the description of the feature of the sampling points. The feature integral of Gs is built as a monotone increasing function in an analytic form. Then, the initial knots are selected according to the constant increment of the feature integral. After that, an iterative knot insertion (IKI) process starting from the initial knots is introduced to improve the fitting precision, and the ultimate knot vector for the error-bounded B-spline curve fitting is achieved. Lastly, two simulations and the measurement experiment are provided, and the results indicate that the proposed knot selection method can reduce the number of ultimate knots available.

  10. Arthroscopic Bankart repair using knot-tying versus knotless suture anchors: is there a difference?

    PubMed

    Ng, Dennis Zhaowen; Kumar, V Prem

    2014-04-01

    To compare the clinical outcome between the use of knotless sutures versus knot-tying sutures in arthroscopic Bankart repairs. Between January 2007 and January 2011, 87 patients who underwent arthroscopic Bankart repair with the use of knot-tying suture anchors or knotless suture anchors were evaluated, with 45 patients in the knot-tying suture group and 42 patients in the knotless group. Patients were assigned to either group, with odd-numbered patients going to the knot-tying suture arm and even-numbered patients assigned to the knotless arm. Outcomes included the Constant score, the visual analog scale (VAS) score, patient satisfaction score, and range of motion in forward flexion and external rotation with the arm in adduction. Redislocations or subluxations with the 2 techniques was also studied. Both groups showed a statistically significant improvement between the preoperative and postoperative VAS scores and Constant scores. In the knot-tying suture group, the VAS score improved from 2.5 ± 2.3 to 0.7 ± 0.5 (P < .05) and the Constant score improved from 64 ± 7 to 92 ± 10 (P < .05). In the knotless group, the VAS score improved from 2.8 ± 2.5 to 0.9 ± 0.6 (P < .05), and the Constant score improved from 62 ± 6 to 89 ± 9 (P < .05). The patient satisfaction scores were 6.9 and 7.1 for the knot tying and knotless groups, respectively. No statistically significant differences were found when comparing the outcomes between the 2 groups. The change in the range of forward flexion and external rotation was also similar in the 2 groups. There was also no difference in recurrence or redislocation rates. Both the knot-tying and knotless suture anchors groups showed statistically significant and similar improvement in VAS and Constant scores. Both anchors provided reasonable outcomes. The knotless suture anchor is a good alternative to knot-tying suture anchors so that arthroscopic Bankart repairs can be performed without knot tying. Level II, prospective

  11. Freely Expanding Knots of X-Ray-emitting Ejecta in Kepler’s Supernova Remnant

    NASA Astrophysics Data System (ADS)

    Sato, Toshiki; Hughes, John P.

    2017-08-01

    We report measurements of proper motion, radial velocity, and elemental composition for 14 compact X-ray-bright knots in Kepler’s supernova remnant (SNR) using archival Chandra data. The knots with the highest speed show both large proper motions (μ ˜ 0.″11-0.″14 yr-1) and high radial velocities (v ˜ 8700-10,020 km s-1). For these knots the estimated space velocities (9100 km s-1 ≲ v 3D ≲ 10,400 km s-1) are similar to the typical Si velocity seen in supernovae (SNe) Ia near maximum light. High-speed ejecta knots appear only in specific locations and are morphologically and kinematically distinct from the rest of the ejecta. The proper motions of five knots extrapolate back over the age of Kepler’s SNR to a consistent central position. This new kinematic center agrees well with previous determinations, but is less subject to systematic errors and denotes a location about which several prominent structures in the remnant display a high degree of symmetry. These five knots are expanding at close to the free expansion rate (expansion indices of 0.75 ≲ m ≲ 1.0), which we argue indicates either that they were formed in the explosion with a high density contrast (more than 100 times the ambient density) or that they have propagated through regions of relatively low density (n H < 0.1 cm-3) in the ambient medium. X-ray spectral analysis shows that the undecelerated knots have high Si and S abundances, a lower Fe abundance, and very low O abundance, pointing to an origin in the partial Si-burning zone, which occurs in the outer layer of the exploding white dwarf for models of SNe Ia. Other knots show lower speeds and expansion indices consistent with decelerated ejecta knots or features in the ambient medium overrun by the forward shock. Our new accurate location for the explosion site has well-defined positional uncertainties, allowing for a great reduction in the area to be searched for faint surviving donor stars under non-traditional single

  12. Long-slit spectrophotometry of the multiple knots of the polar ring galaxy IIZw71

    NASA Astrophysics Data System (ADS)

    Pérez-Montero, E.; García-Benito, R.; Díaz, A. I.; Pérez, E.; Kehrig, C.

    2009-04-01

    Aims: The blue compact dwarf galaxy IIZw71 is catalogued as a probable polar-ring galaxy, and along its long axis it has several very luminous knots showing recent episodes of star formation. Our main aim is to study the physical properties, the stellar content, and the kinematics in the brightest knots of the polar ring. Methods: We carried out long-slit spectroscopic observations of the polar ring in the spectral range 3500-10 000 Å taken with the William Herschel Telescope (WHT). The spectroscopic observations complemented by the available photometry of the galaxy in narrow Hα filters. Results: We measured the rotation curve of the ring, from which we infer a ratio M/LB ≈ 3.9 inside the star-forming ring. We measured the auroral [Oiii] line in the two brightest knots, allowing us to measure oxygen, sulphur, nitrogen, argon, and neon chemical abundances following the direct method. Different empirical calibrators were used to estimate the oxygen abundance in the two faintest knots where the temperature sensitive lines could not be measured. The metallicities obtained are very similar for all the knots, but lower than previously reported in the literature from integrated spectra. The N/O abundance, as derived from the N2O2 parameter (the ratio of the [Nii] and [Oii] intensities), is remarkably constant over the ring, indicating that local polution processes are not conspicuous. Using synthetic stellar populations (SSPs) calculated with the code STARLIGHT, we studied the age distribution of the stellar populations in each knot, finding that in all of them there is a combination of a very young population with less than 10 Myr, responsible for the ionisation of the gas, with other populations older than 100 Myr, probably responsible for the chemical evolution of the knots. The small differences in metallicity and the age distributions among the different knots are indicative of a common chemical evolution, probably related to the process of interaction with the

  13. Multispecies modeling for adaptive management of horseshoe crabs and red knots in the Delaware Bay

    USGS Publications Warehouse

    McGowan, Conor P.; Smith, David; Sweka, John A.; Martin, Julien; Nichols, James D.; Wong, Richard; Lyons, James E.; Niles, Lawrence J.; Kalasz, Kevin; Brust, Jeffrey; Klopfer, Michelle; Spear, Braddock

    2011-01-01

    Adaptive management requires that predictive models be explicit and transparent to improve decisions by comparing management actions, directing further research and monitoring, and facilitating learning. The rufa subspecies of red knots (Calidris canutus rufa), which has recently exhibited steep population declines, relies on horseshoe crab (Limulus polyphemus) eggs as their primary food source during stopover in Delaware Bay during spring migration. We present a model with two different parameterizations for use in the adaptive management of horseshoe crab harvests in the Delaware Bay that links red knot mass gain, annual survival, and fecundity to horseshoe crab dynamics. The models reflect prevailing hypotheses regarding ecological links between these two species. When reported crab harvest from 1998 to 2008 was applied, projections corresponded to the observed red knot population abundances depending on strengths of the demographic relationship between these species. We compared different simulated horseshoe crab harvest strategies to evaluate whether, given this model, horseshoe crab harvest management can affect red knot conservation and found that restricting harvest can benefit red knot populations. Our model is the first to explicitly and quantitatively link these two species and will be used within an adaptive management framework to manage the Delaware Bay system and learn more about the specific nature of the linkage between the two species.

  14. Prediction of the optimal set of contacts to fold the smallest knotted protein

    NASA Astrophysics Data System (ADS)

    Dabrowski-Tumanski, P.; Jarmolinska, A. I.; Sulkowska, J. I.

    2015-09-01

    Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map.

  15. Prediction of the optimal set of contacts to fold the smallest knotted protein.

    PubMed

    Dabrowski-Tumanski, P; Jarmolinska, A I; Sulkowska, J I

    2015-09-09

    Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map.

  16. Condensates and instanton - torus knot duality. Hidden Physics at UV scale

    NASA Astrophysics Data System (ADS)

    Gorsky, A.; Milekhin, A.

    2015-11-01

    We establish the duality between the torus knot superpolynomials or the Poincaré polynomials of the Khovanov homology and particular condensates in Ω-deformed 5D supersymmetric QED compactified on a circle with 5d Chern-Simons (CS) term. It is explicitly shown that n-instanton contribution to the condensate of the massless flavor in the background of four-observable exactly coincides with the superpolynomial of the T (n , nk + 1) torus knot where k is the level of CS term. In contrast to the previously known results, the particular torus knot corresponds not to the partition function of the gauge theory but to the particular instanton contribution and summation over the knots has to be performed in order to obtain the complete answer. The instantons are sitting almost at the top of each other and the physics of the "fat point" where the UV degrees of freedom are slaved with point-like instantons turns out to be quite rich. Also we see knot polynomials in the quantum mechanics on the instanton moduli space. We consider the different limits of this correspondence focusing at their physical interpretation and compare the algebraic structures at the both sides of the correspondence. Using the AGT correspondence, we establish a connection between superpolynomials for unknots and q-deformed DOZZ factors.

  17. Allotides: Proline-Rich Cystine Knot α-Amylase Inhibitors from Allamanda cathartica.

    PubMed

    Nguyen, Phuong Q T; Luu, Thuy T; Bai, Yang; Nguyen, Giang K T; Pervushin, Konstantin; Tam, James P

    2015-04-24

    Cystine knot α-amylase inhibitors belong to a knottin family of peptidyl inhibitors of 30-32 residues and contain two to four prolines. Thus far, only four members of the group of cystine knot α-amylase inhibitors have been characterized. Herein, the discovery and characterization of five cystine knot α-amylase inhibitors, allotides C1-C5 (Ac1-Ac5) (1-5), from the medicinal plant Allamanda cathartica are reported using both proteomic and genomic methods. Proteomic analysis showed that 1-5 are 30 amino acids in length with three or four proline residues. NMR determination of 4 revealed that it has two cis- and one trans-proline residues and adopts two equally populated conformations in solution. Determination of disulfide connectivity of 2 by differential S-reduction and S-alkylation provided clues of its unfolding process. Genomic analysis showed that allotide precursors contain a three-domain arrangement commonly found in plant cystine knot peptides with conserved residues flanking the processing sites of the mature allotide domain. This work expands the number of known cystine knot α-amylase inhibitors and furthers the understanding of both the structural and biological diversity of this type of knottin family.

  18. Synthesizing a Trefoil Knotted Block Copolymer via Ring-Expansion Strategy

    DOE PAGES

    Cao, Pengfei; Rong, Li-Han; Mangadlao, Joey; ...

    2017-02-07

    We synthesized a synthetic trefoil knotted poly(e-caprolatone) block-poly(L-lactide) (TK-PLA-b-PCL) via a ring expansion strategy from a trefoil knotted tin (Sn) initiator. Ring closing reaction between the bis-copper(I) templated phenanthro line complex and dibutyldimethoxytin results in a templated trefoil knotted initiator. Furthermore, the bis-copper(I) templated trefoil knotted poly(L-lactide) (TK-PLA) can be synthesized by ring-opening polymerization of L-lactide monomer, and decomplexation reaction of the templated TK-PLA will result in a geniune TK-PLA without constraint from the copper template. Subsequent insertion of e caprolactone in the bis-copper(I) templated TK-PLA forms the templated trefoil knotted block copolymer, i.e., TK-PLA-b-PCL, and the copper-free TK-PLA-b-PCL canmore » be obtained by decomplexation reaction. Finally, both TK-PLA and TK-PLA-b-PCL are analyzed by the 1 H NMR, FT-IR, UV-vis, DLS, and GPC.« less

  19. The effect of topological constraint on the theta temperature of a knotted polymer

    NASA Astrophysics Data System (ADS)

    Sheng, Yu-Jane; Liao, Chen-Shin

    2003-03-01

    Monte Carlo simulations were used to study the effect of topological constraints of knotted polymers on their theta temperatures. The theta temperatures were determined through two different definitions—the vanishing of the second virial coefficient A2=0, and the quasi-ideal behavior of the radius of gyration, ˜N. Prime knots with chain lengths from N=60 to 300 and with crossings from 31 to 91 were considered. For chains with finite lengths, it was found that the theta temperature determined from quasi-ideal condition of the knot increases, as the complexity of the knot increases. On the other hand, the topological complexity seemed to have no effect on the theta temperatures determined from the vanishing of the second virial coefficient. Also, our simulation results suggest that for chains with finite crossing numbers, as N→∞, theta temperatures for all knots obtained from two different approaches coincide and are equivalent to that of a linear polymer chain.

  20. Particle on a torus knot: Constrained dynamics and semi-classical quantization in a magnetic field

    NASA Astrophysics Data System (ADS)

    Das, Praloy; Pramanik, Souvik; Ghosh, Subir

    2016-11-01

    Kinematics and dynamics of a particle moving on a torus knot poses an interesting problem as a constrained system. In the first part of the paper we have derived the modified symplectic structure or Dirac brackets of the above model in Dirac's Hamiltonian framework, both in toroidal and Cartesian coordinate systems. This algebra has been used to study the dynamics, in particular small fluctuations in motion around a specific torus. The spatial symmetries of the system have also been studied. In the second part of the paper we have considered the quantum theory of a charge moving in a torus knot in the presence of a uniform magnetic field along the axis of the torus in a semiclassical quantization framework. We exploit the Einstein-Brillouin-Keller (EBK) scheme of quantization that is appropriate for multidimensional systems. Embedding of the knot on a specific torus is inherently two dimensional that gives rise to two quantization conditions. This shows that although the system, after imposing the knot condition reduces to a one dimensional system, even then it has manifested non-planar features which shows up again in the study of fractional angular momentum. Finally we compare the results obtained from EBK (multi-dimensional) and Bohr-Sommerfeld (single dimensional) schemes. The energy levels and fractional spin depend on the torus knot parameters that specifies its non-planar features. Interestingly, we show that there can be non-planar corrections to the planar anyon-like fractional spin.

  1. Hippo pathway/Yap regulates primary enamel knot and dental cusp patterning in tooth morphogenesis.

    PubMed

    Kwon, Hyuk-Jae Edward; Li, Liwen; Jung, Han-Sung

    2015-11-01

    The shape of an individual tooth crown is primarily determined by the number and arrangement of its cusps, i.e., cusp patterning. Enamel knots that appear in the enamel organ during tooth morphogenesis have been suggested to play important roles in cusp patterning. Animal model studies have shown that the Hippo pathway effector Yap has a critical function in tooth morphogenesis. However, the role of the Hippo pathway/Yap in cusp patterning has not been well documented and its specific roles in tooth morphogenesis remain unclear. Here, we provide evidence that Yap is a key mediator in tooth cusp patterning. We demonstrate a correlation between Yap localization and cell proliferation in developing tooth germs. We also show that, between the cap stage and bell stage, Yap is crucial for the suppression of the primary enamel knot and for the patterning of secondary enamel knots, which are the future cusp regions. When Yap expression is stage-specifically knocked down during the cap stage, the activity of the primary enamel knot persists into the bell-stage tooth germ, leading to ectopic cusp formation. Our data reveal the importance of the Hippo pathway/Yap in enamel knots and in the proper patterning of tooth cusps.

  2. The insecure airway: a comparison of knots and commercial devices for securing endotracheal tubes.

    PubMed

    Lovett, Paris B; Flaxman, Alexander; Stürmann, Kai M; Bijur, Polly

    2006-05-24

    Endotracheal Tubes (ETTs) are commonly secured using adhesive tape, cloth tape, or commercial devices. The objectives of the study were (1) To compare degrees of movement of ETTs secured with 6 different commercial devices and (2) To compare movement of ETTs secured with cloth tape tied with 3 different knots (hitches). A 17 cm diameter PVC tube with 14 mm "mouth" hole in the side served as a mannequin. ETTs were subjected to repeated jerks, using a cable and pulley system. (1) Total movement of ETTs relative to "mouth" (measure used for devices) (2) Slippage of ETT through securing knot (measure used for knots). Among commercial devices, the Dale showed less movement than other devices, although some differences between devices did not reach significance. Among knots, Magnus and Clove Hitches produced less slippage than the Cow Hitch, but these differences did not reach statistical significance. Among devices tested, the Dale was most secure. Within the scope offered by the small sample sizes, there were no statistically significant differences between the knots in this study.

  3. Knotting of linear DNA in nano-slits and nano-channels: a numerical study.

    PubMed

    Orlandini, Enzo; Micheletti, Cristian

    2013-03-01

    The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic devices and by the introduction of algorithms capable of detecting knots in open chains, we investigate numerically the entanglement of linear, open DNA chains confined inside nano-slits. The results regard the abundance, type, and length of occurring knots and are compared with recent findings for DNA inside nano-channels. In both cases, the width of the confining region, D, spans the 30 nm-1 μm range and the confined DNA chains are 1-4 μm long. It is found that the knotting probability is maximum for slit widths in the 70-100 nm range. However, over the considered DNA contour lengths, the maximum incidence of knots remains below 20%, while for channel confinement it tops 50%. Further differences of the entanglement are seen for the average contour length of the knotted region, which drops significantly below D ~100 nm for channel-confinement, while it stays approximately constant for slit-like confinement. These properties ought to reverberate in different kinetic properties of linear DNA depending on confinement and could be detectable experimentally or exploitable in nano-technological applications.

  4. Particle on a torus knot: Constrained dynamics and semi-classical quantization in a magnetic field

    SciTech Connect

    Das, Praloy Pramanik, Souvik Ghosh, Subir

    2016-11-15

    Kinematics and dynamics of a particle moving on a torus knot poses an interesting problem as a constrained system. In the first part of the paper we have derived the modified symplectic structure or Dirac brackets of the above model in Dirac’s Hamiltonian framework, both in toroidal and Cartesian coordinate systems. This algebra has been used to study the dynamics, in particular small fluctuations in motion around a specific torus. The spatial symmetries of the system have also been studied. In the second part of the paper we have considered the quantum theory of a charge moving in a torus knot in the presence of a uniform magnetic field along the axis of the torus in a semiclassical quantization framework. We exploit the Einstein–Brillouin–Keller (EBK) scheme of quantization that is appropriate for multidimensional systems. Embedding of the knot on a specific torus is inherently two dimensional that gives rise to two quantization conditions. This shows that although the system, after imposing the knot condition reduces to a one dimensional system, even then it has manifested non-planar features which shows up again in the study of fractional angular momentum. Finally we compare the results obtained from EBK (multi-dimensional) and Bohr–Sommerfeld (single dimensional) schemes. The energy levels and fractional spin depend on the torus knot parameters that specifies its non-planar features. Interestingly, we show that there can be non-planar corrections to the planar anyon-like fractional spin.

  5. Specific microbial attachment to root knot nematodes in suppressive soil.

    PubMed

    Adam, Mohamed; Westphal, Andreas; Hallmann, Johannes; Heuer, Holger

    2014-05-01

    Understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. Three arable soils were investigated for their suppressiveness against the root knot nematode Meloidogyne hapla. For all three soils, M. hapla developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. Egg numbers were reduced by up to 93%. This suggested suppression by soil microbial communities. The soils significantly differed in the composition of microbial communities and in the suppressiveness to M. hapla. To identify microorganisms interacting with M. hapla in soil, second-stage juveniles (J2) baited in the test soil were cultivation independently analyzed for attached microbes. PCR-denaturing gradient gel electrophoresis of fungal ITS or 16S rRNA genes of bacteria and bacterial groups from nematode and soil samples was performed, and DNA sequences from J2-associated bands were determined. The fingerprints showed many species that were abundant on J2 but not in the surrounding soil, especially in fungal profiles. Fungi associated with J2 from all three soils were related to the genera Davidiella and Rhizophydium, while the genera Eurotium, Ganoderma, and Cylindrocarpon were specific for the most suppressive soil. Among the 20 highly abundant operational taxonomic units of bacteria specific for J2 in suppressive soil, six were closely related to infectious species such as Shigella spp., whereas the most abundant were Malikia spinosa and Rothia amarae, as determined by 16S rRNA amplicon pyrosequencing. In conclusion, a diverse microflora specifically adhered to J2 of M. hapla in soil and presumably affected female fecundity.

  6. Specific Microbial Attachment to Root Knot Nematodes in Suppressive Soil

    PubMed Central

    Adam, Mohamed; Westphal, Andreas; Hallmann, Johannes

    2014-01-01

    Understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. Three arable soils were investigated for their suppressiveness against the root knot nematode Meloidogyne hapla. For all three soils, M. hapla developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. Egg numbers were reduced by up to 93%. This suggested suppression by soil microbial communities. The soils significantly differed in the composition of microbial communities and in the suppressiveness to M. hapla. To identify microorganisms interacting with M. hapla in soil, second-stage juveniles (J2) baited in the test soil were cultivation independently analyzed for attached microbes. PCR-denaturing gradient gel electrophoresis of fungal ITS or 16S rRNA genes of bacteria and bacterial groups from nematode and soil samples was performed, and DNA sequences from J2-associated bands were determined. The fingerprints showed many species that were abundant on J2 but not in the surrounding soil, especially in fungal profiles. Fungi associated with J2 from all three soils were related to the genera Davidiella and Rhizophydium, while the genera Eurotium, Ganoderma, and Cylindrocarpon were specific for the most suppressive soil. Among the 20 highly abundant operational taxonomic units of bacteria specific for J2 in suppressive soil, six were closely related to infectious species such as Shigella spp., whereas the most abundant were Malikia spinosa and Rothia amarae, as determined by 16S rRNA amplicon pyrosequencing. In conclusion, a diverse microflora specifically adhered to J2 of M. hapla in soil and presumably affected female fecundity. PMID:24532076

  7. Below-Ground Attack by the Root Knot Nematode Meloidogyne graminicola Predisposes Rice to Blast Disease.

    PubMed

    Kyndt, Tina; Zemene, Henok Yimer; Haeck, Ashley; Singh, Richard; De Vleesschauwer, David; Denil, Simon; De Meyer, Tim; Höfte, Monica; Demeestere, Kristof; Gheysen, Godelieve

    2017-03-01

    Magnaporthe oryzae (rice blast) and the root-knot nematode Meloidogyne graminicola are causing two of the most important pathogenic diseases jeopardizing rice production. Here, we show that root-knot nematode infestation on rice roots leads to important above-ground changes in plant immunity gene expression, which is correlated with significantly enhanced susceptibility to blast disease. A detailed metabolic analysis of oxidative stress responses and hormonal balances demonstrates that the above-ground tissues have a disturbed oxidative stress level, with accumulation of H2O2, as well as hormonal disturbances. Moreover, double infection experiments on an oxidative stress mutant and an auxin-deficient rice line indicate that the accumulation of auxin in the above-ground tissue is at least partly responsible for the blast-promoting effect of root-knot nematode infection.

  8. Self-assembling knots of controlled topology by designing the geometry of patchy templates

    NASA Astrophysics Data System (ADS)

    Polles, Guido; Marenduzzo, Davide; Orlandini, Enzo; Micheletti, Cristian

    2015-03-01

    The self-assembly of objects with a set of desired properties is a major goal of material science and physics. A particularly challenging problem is that of self-assembling structures with a target topology. Here we show by computer simulation that one may design the geometry of string-like rigid patchy templates to promote their efficient and reproducible self-assembly into a selected repertoire of non-planar closed folds including several knots. In particular, by controlling the template geometry, we can direct the assembly process so as to strongly favour the formation of constructs tied in trefoil or pentafoil, or even of more exotic torus knots. Polydisperse and racemic mixtures of helical fragments of variable composition add further tunability in the topological self-assembly we discovered. Our results should be relevant to the design of new ways to synthesize molecular knots, which may prove, for instance, to be efficient cargo-carriers due to their mechanical stability.

  9. Twists, knots, and rings in proteins. Structural definition of the cyclotide framework.

    PubMed

    Rosengren, K Johan; Daly, Norelle L; Plan, Manuel R; Waine, Clement; Craik, David J

    2003-03-07

    In recent years an increasing number of miniproteins containing an amide-cyclized backbone have been discovered. The cyclotide family is the largest group of such proteins and is characterized by a circular protein backbone and six conserved cysteine residues linked by disulfide bonds in a tight core of the molecule. These form a cystine knot in which an embedded ring formed by two of the disulfide bonds and the connecting backbone segment is threaded by a third disulfide bond. In the current study we have undertaken high resolution structural analysis of two prototypic cyclotides, kalata B1 and cycloviolacin O1, to define the role of the conserved residues in the sequence. We provide the first comprehensive analysis of the topological features in this unique family of proteins, namely rings (a circular backbone), twists (a cis-peptide bond in the Möbius cyclotides) and knots (a knotted arrangement of the disulfide bonds).

  10. Velocity dispersions of knots in the Cygnus Loop and IC 443

    NASA Technical Reports Server (NTRS)

    Shull, P., Jr.; Dufour, R. J.; Parker, R. A. R.; Gull, T. R.

    1982-01-01

    Very high resolution spectroscopy of optical emission lines indicates that the velocity dispersions of knots in Cygnus Loop and IC 443 filaments result primarily from turbulence within the emitting regions. Line-of-sight velocity dispersions (half-widths at half-maximum) for the observed knots are on the order of 10-30 km/s, including associated thermal velocity dispersions of roughly 15 km/s for hydrogen, 6 km/s for oxygen, and 4 km/s for nitrogen. The knots themselves move randomly relative to each other with speeds of 10-30 km/s. Occasionally, diffuse components of the filaments are observed. These diffuse components have velocity dispersions between 60 and 85 km/s, but the relative contributions of turbulent and thermal motion to the dispersions are unkown.

  11. Avian influenza virus antibodies in Pacific Coast Red Knots (Calidris canutus rufa)

    USGS Publications Warehouse

    Johnson, James A.; DeCicco, Lucas H.; Ruthrauff, Daniel R.; Krauss, Scott; Hall, Jeffrey S.

    2014-01-01

    Prevalence of avian influenza virus (AIV) antibodies in the western Atlantic subspecies of Red Knot (Calidris canutus rufa) is among the highest for any shorebird. To assess whether the frequency of detection of AIV antibodies is high for the species in general or restricted only to C. c. rufa, we sampled the northeastern Pacific Coast subspecies of Red Knot (Calidris canutus roselaari) breeding in northwestern Alaska. Antibodies were detected in 90% of adults and none of the chicks sampled. Viral shedding was not detected in adults or chicks. These results suggest a predisposition of Red Knots to AIV infection. High antibody titers to subtypes H3 and H4 were detected, whereas low to intermediate antibody levels were found for subtypes H10 and H11. These four subtypes have previously been detected in shorebirds at Delaware Bay (at the border of New Jersey and Delaware) and in waterfowl along the Pacific Coast of North America.

  12. New technique for iridodialysis correction: Single-knot sewing-machine suture.

    PubMed

    Silva, João Luis; Póvoa, João; Lobo, Conceição; Murta, Joaquim

    2016-04-01

    Iridodialysis is a common occurrence after trauma and can be the source of considerable morbidity for the patients. Several options to repair iridodialysis are described in the literature. We present a new technique-a single-thread single-knot suture. This simple approach does not require special material and uses a single thread and a single knot, avoiding the need for using multiple sutures or placing multiple knots. We used this technique in several patients, and it appears to be an effective alternative to iridodialysis repair. None of the authors has a financial or proprietary interest in any material or method mentioned. Copyright © 2016 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  13. Ventriculoperitoneal shunt blockage due to spontaneous knot formation in the peritoneal catheter. Case report.

    PubMed

    Eftekhar, Behzad; Hunn, Andrew

    2008-02-01

    The authors report the third case of ventriculoperitoneal shunt blockage due to spontaneous knot formation in the peritoneal catheter that had been placed in a 3.5-year-old boy 8 months earlier. On surgical exploration a double knot was found 10 cm from the distal end of the peritoneal catheter. Although the underlying mechanism remains unknown, the authors used the analogy of related physical studies and true knot formation in the umbilical cord and determined the possible causes as related to the catheter, volume and configuration of the abdomen, and kinetics of the catheter movements. If further study should reveal a significantly higher incidence of this complication, the authors suggest further in vitro studies, designed to investigate the optimal characteristics and safe range of length of peritoneal catheters in different situations.

  14. A cactus-derived toxin-like cystine knot Peptide with selective antimicrobial activity.

    PubMed

    Aboye, Teshome L; Strömstedt, Adam A; Gunasekera, Sunithi; Bruhn, Jan G; El-Seedi, Hesham; Rosengren, K Johan; Göransson, Ulf

    2015-05-04

    Naturally occurring cystine knot peptides show a wide range of biological activity, and as they have inherent stability they represent potential scaffolds for peptide-based drug design and biomolecular engineering. Here we report the discovery, sequencing, chemical synthesis, three-dimensional solution structure determination and bioactivity of the first cystine knot peptide from Cactaceae (cactus) family: Ep-AMP1 from Echinopsis pachanoi. The structure of Ep-AMP1 (35 amino acids) conforms to that of the inhibitor cystine knot (or knottin) family but represents a novel diverse sequence; its activity was more than 500 times higher against bacterial than against eukaryotic cells. Rapid bactericidal action and liposome leakage implicate membrane permeabilisation as the mechanism of action. Sequence homology places Ec-AMP1 in the plant C6-type of antimicrobial peptides, but the three dimensional structure is highly similar to that of a spider neurotoxin. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Physical experience leads to enhanced object perception in parietal cortex: insights from knot tying.

    PubMed

    Cross, Emily S; Cohen, Nichola Rice; Hamilton, Antonia F de C; Ramsey, Richard; Wolford, George; Grafton, Scott T

    2012-12-01

    What does it mean to "know" what an object is? Viewing objects from different categories (e.g., tools vs. animals) engages distinct brain regions, but it is unclear whether these differences reflect object categories themselves or the tendency to interact differently with objects from different categories (grasping tools, not animals). Here we test how the brain constructs representations of objects that one learns to name or physically manipulate. Participants learned to name or tie different knots and brain activity was measured whilst performing a perceptual discrimination task with these knots before and after training. Activation in anterior intraparietal sulcus, a region involved in object manipulation, was specifically engaged when participants viewed knots they learned to tie. This suggests that object knowledge is linked to sensorimotor experience and its associated neural systems for object manipulation. Findings are consistent with a theory of embodiment in which there can be clear overlap in brain systems that support conceptual knowledge and control of object manipulation.

  16. Topological Jamming of Spontaneously Knotted Polyelectrolyte Chains Driven Through a Nanopore

    NASA Astrophysics Data System (ADS)

    Rosa, A.; Di Ventra, M.; Micheletti, C.

    2012-09-01

    The advent of solid state nanodevices allows for interrogating the physicochemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been recently characterized by theoretical and computational studies of model polymer chains free from self-entanglement. However, sufficiently long equilibrated chains are necessarily knotted. The impact of such topological “defects” on the translocation process is largely unexplored, and is addressed in this Letter. By using Brownian dynamics simulations on a coarse-grained polyelectrolyte model we show that knots, despite being trapped at the pore entrance, do not per se cause the translocation process to jam. Rather, knots introduce an effective friction that increases with the applied force, and practically halts the translocation above a threshold force. The predicted dynamical crossover, which is experimentally verifiable, ought to be relevant in applicative contexts, such as DNA nanopore sequencing.

  17. Demographic consequences of migratory stopover: linking red knot survival to horseshoe crab spawning abundance

    USGS Publications Warehouse

    McGowan, Conor P.; Hines, James E.; Nichols, James D.; Lyons, James E.; Smith, David; Kalasz, Kevin S.; Niles, Lawrence J.; Dey, Amanda D.; Clark, Nigel A.; Atkinson, Philip W.; Minton, Clive D.T.; Kendall, William

    2011-01-01

    Understanding how events during one period of the annual cycle carry over to affect survival and other fitness components in other periods is essential to understanding migratory bird demography and conservation needs. Previous research has suggested that western Atlantic red knot (Calidris canutus rufa) populations are greatly affected by horseshoe crab (Limulus polyphemus) egg availability at Delaware Bay stopover sites during their spring northward migration. We present a mass-based multistate, capturerecapture/resighting model linking (1) red knot stopover mass gain to horseshoe crab spawning abundance and (2) subsequent apparent annual survival to mass state at the time of departure from the Delaware Bay stopover area. The model and analysis use capture-recapture/resighting data with over 16,000 individual captures and 13,000 resightings collected in Delaware Bay over a 12 year period from 1997–2008, and the results are used to evaluate the central management hypothesis that red knot populations can be influenced by horseshoe crab harvest regulations as part of a larger adaptive management effort. Model selection statistics showed support for a positive relationship between horseshoe crab spawning abundance during the stopover and the probability of red knots gaining mass (parameter coefficient from the top model b = 1.71, SE = 0.46). Our analyses also supported the link between red knot mass and apparent annual survival, although average estimates for the two mass classes differed only slightly. The addition of arctic snow depth as a covariate influencing apparent survival improved the fit of the data to the models (parameter coefficient from the top model b = 0.50, SE = 0.08). Our results indicate that managing horseshoe crab resources in the Delaware Bay has the potential to improve red knot population status.

  18. Characterization of the Inner Knot of the Crab: the Site of the Gamma-ray Flares?

    NASA Technical Reports Server (NTRS)

    Weisskopf, Martin C.

    2015-01-01

    One of the most intriguing recent discoveries has been the detection of powerful gamma-ray flares from the Crab Nebula. Such events, with a recurrence time of about once per year, can be so dramatic to make the system the brightest source in the gamma-ray sky as occurred, e.g. in April 2011. These flares challenge our understanding of how pulsar wind nebulae work and defy current astrophysical models for particle acceleration. We present here our study of the inner knot located within a fraction of an arcsecond from the pulsar with the aim of characterizing the feature and asking if this might be the site of the origin of the gamma-ray flares. We took data using Keck, HST, and Chandra obtained as part of our multi-wavelength campaign to identify the source of the enigmatic flares. We set an upper limit as to the gamma-ray flux from the knot. We also find that the dimensions, surface brightness, flux, etc. of the optical and infrared knot are all correlated with distance from the pulsar. This distance, in turn, varies with time. In addition to this most thorough characterization of the inner knot's properties, we examine the hypothesis that the knot may be the site of the flares by examining the knot separation versus the Fermi/LAT gamma-ray flux. Finally, as part of this research, we make use of a new approach employing singular value decomposition (SVD) for analyzing time series of images and compare the approach to more traditional methods. Our conclusions are only refined but not impacted by using the new approach.

  19. Characterization of the Inner Knot of the Crab: The Site of the Gamma-ray Flares?

    NASA Astrophysics Data System (ADS)

    Weisskopf, Martin C.; Chandra/HST/Keck gamma-ray flare Team

    2015-01-01

    One of the most intriguing recent discoveries has been the detection of powerful γ-ray flares from the Crab Nebula. Such events, with a recurrence time of about once per year, can be so dramatic to make the system the brightest source in the gamma-ray sky as occurred, e.g. in April 2011. These flares challenge our understanding of how pulsar wind nebulae work and defy current astrophysical models for particle acceleration. We present here our study of the inner knot located within a fraction of an arcsecond from the pulsar with the aim of characterizing the feature and asking if this might be the site of the origin of the γ-ray flares. We took data using Keck, HST, and Chandra obtained as part of our multi-wavelength campaign to identify the source of the enigmatic flares. We set an upper limit as to the x-ray flux from the knot. We also find that the dimensions, surface brightness, flux, etc. of the optical and infrared knot are all correlated with distance of from the pulsar. This distance, in turn, varies with time. In addition to this most thorough characterization of the inner knot's properties, we examine the hypothesis that the knot may be the site of the flares by examining the knot separation versus the Fermi/LAT γ-ray flux. Finally, as part of this research, we make use of a new approach employing singular value decomposition (SVD) for analyzing time series of images and compare the approach to more traditional methods. Our conclusions are only refined but not impacted by using the new approach.

  20. DIRECT DETECTION OF THE HELICAL MAGNETIC FIELD GEOMETRY FROM 3D RECONSTRUCTION OF PROMINENCE KNOT TRAJECTORIES

    SciTech Connect

    Zapiór, Maciej; Martinez-Gómez, David

    2016-02-01

    Based on the data collected by the Vacuum Tower Telescope located in the Teide Observatory in the Canary Islands, we analyzed the three-dimensional (3D) motion of so-called knots in a solar prominence of 2014 June 9. Trajectories of seven knots were reconstructed, giving information of the 3D geometry of the magnetic field. Helical motion was detected. From the equipartition principle, we estimated the lower limit of the magnetic field in the prominence to ≈1–3 G and from the Ampère’s law the lower limit of the electric current to ≈1.2 × 10{sup 9} A.

  1. Potential of tissue culture for breeding root-knot nematode resistance into vegetables.

    PubMed

    Fassuliotis, G; Bhatt, D P

    1982-01-01

    Plant protoplast technology is being investigated as a means of transferring root-knot nematode resistance factors from Solanum sisymbriifolium into the susceptible S. melongena. Solanum sisymbriifolium plants regenerated from callus lost resistance to Meloidogyne javanica but retained resistance to M. incognita. Tomato plants cloned from leaf discs of the root-knot nematode resistant 'Patriot' were completely susceptible to M. incognita, while sections of stems and leaves rooted in sand in the absence of growth hormones retained resistance. Changes in resistance persisted for three generations. It is postulated that the exogenous hormonal constituents of the culture medium are modifying the expression of genetic resistance.

  2. Design considerations for attaining 250-knot test velocities at the aircraft landing dynamics facility

    NASA Technical Reports Server (NTRS)

    Gray, C. E., Jr.; Snyder, R. E.; Taylor, J. T.; Cires, A.; Fitzgerald, A. L.; Armistead, M. F.

    1980-01-01

    Preliminary design studies are presented which consider the important parameters in providing 250 knot test velocities at the Aircraft Landing Dynamics Facility. Four major components of this facility are: the hydraulic jet catapult, the test carriage structure, the reaction turning bucket, and the wheels. Using the hydraulic-jet catapult characteristics, a target design point was selected and a carriage structure was sized to meet the required strength requirements. The preliminary design results indicate that to attain 250 knot test velocities for a given hydraulic jet catapult system, a carriage mass of 25,424 kg (56,000 lbm.) cannot be exceeded.

  3. Knotting probabilities after a local strand passage in unknotted self-avoiding polygons

    NASA Astrophysics Data System (ADS)

    Szafron, M. L.; Soteros, C. E.

    2011-06-01

    We investigate, both theoretically and numerically, the knotting probabilities after a local strand passage is performed in an unknotted self-avoiding polygon (SAP) on the simple cubic lattice. In the polygons studied, it is assumed that two polygon segments have already been brought close together for the purpose of performing a strand passage. This restricts the polygons considered to those that contain a specific pattern called Θ at a fixed location; an unknotted polygon containing Θ is called a Θ-SAP. It is proved that the number of n-edge Θ-SAPs grows exponentially (with n) at the same rate as the total number of n-edge unknotted SAPs (those with no prespecified strand passage structure). Furthermore, it is proved that the same holds for subsets of n-edge Θ-SAPs that yield a specific after-strand-passage knot-type. Thus, the probability of a given after-strand-passage knot-type does not grow (or decay) exponentially with n. Instead, it is conjectured that these after-strand-passage knot probabilities approach, as n goes to infinity, knot-type dependent amplitude ratios lying strictly between 0 and 1. This conjecture is supported by numerical evidence from Monte Carlo data generated using a composite (aka multiple) Markov chain Monte Carlo BFACF algorithm developed to study Θ-SAPs. A new maximum likelihood method is used to estimate the critical exponents relevant to this conjecture. We also obtain strong numerical evidence that the after-strand-passage knotting probability depends on the local structure around the strand-passage site. If the local structure and the crossing sign at the strand-passage site are considered, then we observe that the more 'compact' the local structure, the less likely the after-strand-passage polygon is to be knotted. This trend for compactness versus knotting probability is consistent with results obtained for other strand-passage models; however, we are the first to note the influence of the crossing-sign information. We

  4. RGS Spectroscopy of the Cygnus Loop XA Knot

    NASA Technical Reports Server (NTRS)

    Gaetz, Terrance J.; Mushotzky, Richard F. (Technical Monitor)

    2003-01-01

    The observations were performed at the end of April 2002, and the data were received in July 2002. Unfortunately, the observations were badly compromised by high levels of background radiation; one the three observations lost entirely. Two replacement observations were scheduled for November 2002, and were only made available in January of 2003. Consequently, we have had little time to grapple with the unusual data analysis challenges. The search for a postdoctoral fellow has been successfully concluded, and Manami Sasaki began working for us in January 2003. She will be supported in part by these funds, and will be working to help understand these data. Examination of the RGS 'Orders' images indicate the presence of broad emission lines (as expected for the diffuse XA knot). However, examination of the 'Spatial' dispersion/cross-dispersion images indicate that the emission is also broad in the cross-dispersion direction. (As a crosscheck, some of the 'Lockman Hole' datasets were also examined as representative 'sky background' datasets; in these, both types of images are relatively flat (outside the calibration source regions). The quicklook plots of the spectra show the expected O VII and O VIII lines, in addition to a complex around 35 Angstroms; the approx. 35 Angstrom line is likely the C V He-beta line at 34.97 Angstrom, but identifying the additional line(s) will require a more careful reduction of the data. Consequently, there is valuable information to be extracted from these data, but it is complicated by diffuse nature of the emission. Because the angular scale is large, we will have to make use of sky background datasets in order to do the background fitting. A color composite image of OM data in the three UV bands was presented at the 'How does the Galaxy Work?' meeting, and compared to optical and X-ray imaging data. Quantitative analysis will require obtaining the effective bandpasses of the UV filters so that the predominant line and continuum

  5. Design, pharmacology, and NMR structure of a minimized cystine knot with agouti-related protein activity.

    PubMed

    Jackson, Pilgrim J; McNulty, Joseph C; Yang, Ying-Kui; Thompson, Darren A; Chai, Biaoxin; Gantz, Ira; Barsh, Gregory S; Millhauser, Glenn L

    2002-06-18

    The agouti-related protein (AGRP) is an endogenous antagonist of the melanocortin receptors MC3R and MC4R found in the hypothalamus and exhibits potent orexigenic activity. The cysteine-rich C-terminal domain of this protein, corresponding to AGRP(87-132), exhibits receptor binding affinity and antagonism equivalent to that of the full-length protein. The NMR structure of this active domain was recently determined and suggested that melanocortin receptor contacts were made primarily by two loops presented by a well-structured cystine knot domain within AGRP(87-132) [McNulty et al. (2001) Biochemistry 40, 15520-15527]. This hypothesis is tested here with NMR structure and activity studies of a 34-residue AGRP analogue designed to contain only the cystine knot domain. The designed miniprotein folds to a homogeneous product, retains the desired cystine knot architecture, functions as an antagonist, and maintains the melanocortin receptor pharmacological profile of AGRP(87-132). The AGRP-like activity of this molecule supports the hypothesis that indeed the cystine knot region possesses the melanocortin receptor contact points. Moreover, this potent AGRP analogue is synthetically accessible, may serve in the development of therapeutics for the treatment of diseases related to energy balance. and may also find use as a new reagent for probing melanocortin receptor structure and function.

  6. Managing root-knot nematodes: A case for cover crops in establishing peach orchards

    USDA-ARS?s Scientific Manuscript database

    Root-knot nematodes (Meloidogyne spp.) are an important pathogen of peach in the United States. Several Meloidogyne spp. have been reported to cause damage to stone fruits, but M. incognita and M. javanica are the predominant species on peach. Preplant fumigant nematicides have traditionally been ...

  7. Rye residue levels affect suppression of the southern root-knot nematode in cotton

    USDA-ARS?s Scientific Manuscript database

    In the southeastern United States, rye (Secale cereale) is frequently planted as a winter cover crop in conservation tillage cotton. Although rye produces toxic benzoxazinoid compounds which may play a role in nematode suppression, it is also a host for the southern root-knot nematode Meloidogyne i...

  8. Evaluation of nematicides for southern root-knot nematode management in lima bean

    USDA-ARS?s Scientific Manuscript database

    Southern root-knot nematodes (Meloidogyne incognita; RKN) significantly reduce lima bean (Phaseolus lunatus) yields. Chemical control options for RKN are limited. We evaluated the efficacy of new nematicidal products on RKN in lima bean experiments conducted in greenhouse (GH) and microplot (MP) set...

  9. Wormholes in chemical space connecting torus knot and torus link pi-electron density topologies.

    PubMed

    Rzepa, Henry S

    2009-03-07

    Möbius aromaticities can be considered as deriving from cyclic delocalized pi-electron densities rho(r)(pi) which have the topological form of either a two-component torus link or a single-component torus knot. These two topological forms are distinguished by their (non-zero) linking number L(k), which describes how many times the two components of a torus link cross each other or the single component of a torus knot crosses with itself. The special case of Hückel or benzenoid aromaticity is associated with a pi-electron density that takes the form of a two-component torus link for which the linking number is zero. A class of molecule has been identified which here is termed a Janus aromatic, and which bears the characteristics of both a two-component torus link and a single-component torus knot in the topology of the pi-electron density. This is achieved by the formation of one (or more) wormholes or throats in the pi-electron density connecting the two torus forms, which can impart a Janus-like dual personality to the aromaticity of the system. The impact of such wormholes on the overall pi-delocalized aromaticity of such molecules is approximately estimated using a NICS(rcp) index, and subdivides into two types; those where the forms of aromaticity associated with a torus link and a torus knot cooperate and those where they oppose.

  10. New Discoveries in Resistances to Columbia Root-knot Nematode and Corky Ringspot Disease

    USDA-ARS?s Scientific Manuscript database

    The Columbia root-knot nematode CRKN (Meloidogyne chitwoodi) is a serious pest of potato in the Pacific Northwest. In the warmer zones, with longer growing seasons, this nematode builds up to high populations and damages the potato tubers by invading and causing discoloration and galling. It is pr...

  11. Evidence for a disease complex between Pythium aphanidermatum and root-knot nematodes in cucumber

    USDA-ARS?s Scientific Manuscript database

    A field trial in 2012 indicated a possible disease complex between Pythium aphanidermatum and the root-knot nematode (RKN) Meloidogyne incognita in cucumber. Two growth chamber trials were conducted to investigate this potential disease complex. Treatments included inoculating nine-day-old cucumbe...

  12. Ultrasonic detection of knots, cross grain and bark pockets in wooden pallet parts

    Treesearch

    Mohammed F. Kabir; Daniel L. Schmoldt; Mark E. Schafer

    2000-01-01

    This study investigates defect detection in wooden pallet parts using ultrasonic scanning. Yellow-poplar (Liriodendron tulipifera, L.) deckboards were scanned using two rolling transducers in a pitch-catch arrangement to detect unsound and sound knots, bark pockets and cross grain. Data were collected, stored, and processed using LabView? software. Six ultrasonic...

  13. A knotted1-like homeobox protein regulates abscission in tomato by modulating the auxin pathway

    USDA-ARS?s Scientific Manuscript database

    KD1, a gene encoding a KNOTTED1-LIKE HOMEOBOX transcription factor is known to be involved, in tomato, in ontogeny of the compound leaf. KD1 is also highly expressed in both leaf and flower abscission zones. Reducing abundance of transcripts of this gene in tomato, using both virus induced gene sile...

  14. T & I--Textiles, Weaver's Knot. Instructor's Manual [and] Student Activity Guide.

    ERIC Educational Resources Information Center

    Nicholson, W. H.

    An instructor's manual and student activity guide on the weaver's knot are provided in this set of prevocational education materials which focuses on the vocational area of trade and industry (textiles). (This set of materials is one of ninety-two prevocational education sets arranged around a cluster of seven vocational offerings: agriculture,…

  15. Knot Optimization for Biharmonic B-splines on Manifold Triangle Meshes.

    PubMed

    Hou, Fei; He, Ying; Qin, Hong; Hao, Aimin

    2017-09-01

    Biharmonic B-splines, proposed by Feng and Warren, are an elegant generalization of univariate B-splines to planar and curved domains with fully irregular knot configuration. Despite the theoretic breakthrough, certain technical difficulties are imperative, including the necessity of Voronoi tessellation, the lack of analytical formulation of bases on general manifolds, expensive basis re-computation during knot refinement/removal, being applicable for simple domains only (e.g., such as euclidean planes, spherical and cylindrical domains, and tori). To ameliorate, this paper articulates a new biharmonic B-spline computing paradigm with a simple formulation. We prove that biharmonic B-splines have an equivalent representation, which is solely based on a linear combination of Green's functions of the bi-Laplacian operator. Consequently, without explicitly computing their bases, biharmonic B-splines can bypass the Voronoi partitioning and the discretization of bi-Laplacian, enable the computational utilities on any compact 2-manifold. The new representation also facilitates optimization-driven knot selection for constructing biharmonic B-splines on manifold triangle meshes. We develop algorithms for spline evaluation, data interpolation and hierarchical data decomposition. Our results demonstrate that biharmonic B-splines, as a new type of spline functions with theoretic and application appeal, afford progressive update of fully irregular knots, free of singularity, without the need of explicit parameterization, making it ideal for a host of graphics tasks on manifolds.

  16. Nasogastric tube knotting: a rare and potentially overlooked complication among healthcare professionals.

    PubMed

    Chavda, Vijay; Alhammali, Tariq; Farrant, Joanna; Naidu, Leena; El-Rabaa, Saleem

    2017-09-07

    Nasogastric tube placement is a common procedure performed in surgical and medical specialities. The occurrence of knot formation is perhaps one of the least well-recognised complications associated with its usage. We present a case of nasogastric tube knotting to remind colleagues of this rare but important complication. A 75-year-old woman with adhesional bowel obstruction was admitted under the general surgery team. A wide bore nasogastric tube was inserted for drainage and decompression. Although placement of the tube was deemed to be successful, there was no drainage of gastric content evident. On removal of the 'non-functioning' tube a simple knot was seen at its proximal end. A further nasogastric tube was placed and the patient's symptoms resolved with conservative management. Nasogastric tube knotting is a rare and often overlooked complication with the potential to cause significant trauma on tube removal if unrecognised. © BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  17. Percutaneous Untying of a Knot in a Retained Swan-Ganz Catheter

    SciTech Connect

    Bhatti, Waqar A.; Sinha, Sankar; Rowlands, Peter

    2000-03-15

    A patient was referred to us with a tightly knotted Swan-Ganz catheter. The catheter could not be removed by conventional simple methods. We describe a minimally invasive means of removal of the catheter using an Amplatz gooseneck snare and an angioplasty balloon. This allowed the catheter to be removed without trauma.

  18. On the implications of recent observations of the inner knot in the Crab nebula

    NASA Astrophysics Data System (ADS)

    Yuan, Yajie; Blandford, Roger D.

    2015-12-01

    Recent observations of the Crab nebula (Rudy et al.) have maintained its reputation for high-energy astrophysical enlightenment and its use as a test-bed for theories of the behaviour of magnetized, relativistic plasma. In particular, new observations of the inner knot located 0.65 arcsec SE from the pulsar confirm that it is compact, elongated transversely to the symmetry axis and curved concave towards the pulsar. 60 per cent polarization has been measured along the symmetry axis (Moran et al.). The knot does not appear to be involved in the gamma-ray flares. The new observations both reinforce the interpretation of the knot as dissipation of the pulsar wind at a strong shock and challenge the details of existing models of this process. In particular, it is argued that the compactness, high polarization, and curvature are difficult to reconcile with simple relativistic shock models. Alternative possibilities include deflection of the outflow ahead of the shock and spatial variation in which the knot is interpreted as a caustic. Some future observations are proposed and new theoretical investigations are suggested.

  19. Managing Root-knot on Tobacco in the Southeastern United States

    PubMed Central

    Johnson, Charles S.

    1989-01-01

    Root-knot nematodes suppress yields of flue-cured tobacco an estimated 0.1 to 4.8% annually in the southeastern United States, even though nematode management practices have been widely adopted. Although Meloidogyne incognita races 1 and 3 have predominated, M. arenaria, M. javanica, and M. incognita races 2 and 4 are increasingly important. Seventy-five percent of the flue-cured tobacco hectarage in North Carolina and Virginia is rotated on 2-year or 3-year intervals. Over half of the hectarage in the southeastern United States was planted with tobacco cultivars resistant to M. incognita races 1 and 3 in 1986. Resistance to other species or races of root-knot nematodes is not available in commercially available flue-cured tobacco cultivars. Most producers plow and (or) disc-out flue-cured tobacco roots and stalks after harvest. Nematicide use ranges from virtually 100% in Florida and Georgia to 60% in Virginia. Continued research is needed to develop management strategies for mixed populations of root-knot nematodes and to incorporate resistance to more root-knot nematode species and races into tobacco cultivars. Nematode advisory programs that allow producers to optimize nematicide use from an economical and ecological point of view are also needed. PMID:19287655

  20. Transcriptome analysis of resistant and susceptible alfalfa cultivars infected with root-knot nematode Meloidogyne incognita

    USDA-ARS?s Scientific Manuscript database

    Nematodes are one of the major limiting factors in alfalfa production. Root knot nematodes (RKN, Meloidogyne spp.) are widely distributed and economically important sedentary endoparasites of agricultural crops (Castagnone-Sereno et al. 2013) and they may inflict significant damage to alfalfa fields...

  1. Black knot [Apiosporina morbosa (Schw.)] resistance in imported and domestic Prunus domestica L. germplasm and cultivars

    USDA-ARS?s Scientific Manuscript database

    Black knot (BK) Apisporina morbosa (Schw.) is an important fungal disease of Prunus domestica and other Prunus species in North America. BK causes economic losses in the plum growing regions of northern and eastern U.S. and eastern Canada. Relatively few P. domestica commercial cultivars are resis...

  2. Is Grafting Useful for Managing Root-Knot Nematodes in Watermelon?

    USDA-ARS?s Scientific Manuscript database

    Five Citrullus lanatus var. citroides germplasm lines, four Lagenaria siceraria cultivars, one Cucurbita moschata x C. maxima hybrid, and one commercial wild watermelon (Citrullus lanatus spp.) cultivar were evaluated as rootstocks for watermelon in a field infested with the southern root-knot nemat...

  3. Mustard seed meal for management of root-knot nematode and weeds in tomato production

    USDA-ARS?s Scientific Manuscript database

    Mustard seed meals of indian mustard [InM (Brassica juncea)] and yellow mustard [YeM (Sinapis alba)], alone and combined, were tested for effects on tomato (Solanum lycopersicum) plants and for suppression of southern root-knot nematode [RKN (Meloidogyne incognita)] and weed populations. In the gree...

  4. A new class of magnetic confinement device in the shape of a knot

    SciTech Connect

    Hudson, S. R. Startsev, E.; Feibush, E.

    2014-01-15

    We describe a new class of magnetic confinement device, with the magnetic axis in the shape of a knot. We call such devices “knotatrons.” An example is given that has a large volume filled with magnetic surfaces, with significant rotational-transform, and with the magnetic field produced entirely by external circular coils.

  5. Automated image analysis of placental villi and syncytial knots in histological sections.

    PubMed

    Kidron, Debora; Vainer, Ifat; Fisher, Yael; Sharony, Reuven

    2017-05-01

    Delayed villous maturation and accelerated villous maturation diagnosed in histologic sections are morphologic manifestations of pathophysiological conditions. The inter-observer agreement among pathologists in assessing these conditions is moderate at best. We investigated whether automated image analysis of placental villi and syncytial knots could improve standardization in diagnosing these conditions. Placentas of antepartum fetal death at or near term were diagnosed as normal, delayed or accelerated villous maturation. Histologic sections of 5 cases per group were photographed at ×10 magnification. Automated image analysis of villi and syncytial knots was performed, using ImageJ public domain software. Analysis of hundreds of histologic images was carried out within minutes on a personal computer, using macro commands. Compared to normal placentas, villi from delayed maturation were larger and fewer, with fewer and smaller syncytial knots. Villi from accelerated maturation were smaller. The data were further analyzed according to horizontal placental zones and groups of villous size. Normal placentas can be discriminated from placentas of delayed or accelerated villous maturation using automated image analysis. Automated image analysis of villi and syncytial knots is not equivalent to interpretation by the human eye. Each method has advantages and disadvantages in assessing the 2-dimensional histologic sections representing the complex, 3-dimensional villous tree. Image analysis of placentas provides quantitative data that might help in standardizing and grading of placentas for diagnostic and research purposes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. RKVL-318, a root-knot nematode resistant rootstock line for grafted watermelon

    USDA-ARS?s Scientific Manuscript database

    The Agriculture Research Service, U.S. Department of Agriculture, announces the release of ‘RKVL-318’, a novel germplasm line useful as a rootstock and as a genetic resource for enhancing resistance to root-knot nematodes (RKN) in watermelon cultivars. ‘RKVL-318’ is derived from the wild-type water...

  7. Evaluation of edible ginger and turmeric cultivars for root-knot nematode resistance

    USDA-ARS?s Scientific Manuscript database

    Edible ginger and turmeric roots are important agricultural commodities for the State of Hawaii. Bacterial wilt, Ralstonia solanacearum, and root-knot nematodes, Meloidogyne spp. are major factors hindering optimum production. An evaluation of tolerance and resistance to M. incognita was undertake...

  8. Resistant Citrullus lanatus var. citroides Rootstocks for Managing Root-knot Nematodes in Grafted Watermelon

    USDA-ARS?s Scientific Manuscript database

    Southern root-knot nematode (RKN), Meloidogyne incognita, is an important re-emerging pest of watermelon. Several factors have contributed to re-emergence of RKN including: 1) ban of methyl bromide for soil fumigation; 2) reduced land area for crop rotation; and 3) continuous cropping of cucurbits u...

  9. Tm1: A Mutator/Foldback Transposable Element Family in Root-Knot Nematodes

    PubMed Central

    Gross, Stephen M.; Williamson, Valerie M.

    2011-01-01

    Three closely related parthenogenetic species of root-knot nematodes, collectively termed the Meloidogyne incognita-group, are economically significant pathogens of diverse crop species. Remarkably, these asexual root-knot nematodes are capable of acquiring heritable changes in virulence even though they lack sexual reproduction and meiotic recombination. Characterization of a near isogenic pair of M. javanica strains differing in response to tomato with the nematode resistance gene Mi-1 showed that the virulent strain carried a deletion spanning a gene called Cg-1. Herein, we present evidence that the Cg-1 gene lies within a member of a novel transposable element family (Tm1; Transposon in Meloidogyne-1). This element family is defined by composite terminal inverted repeats of variable lengths similar to those of Foldback (FB) transposable elements and by 9 bp target site duplications. In M. incognita, Tm1 elements can be classified into three general groups: 1) histone-hairpin motif elements; 2) MITE-like elements; 3) elements encoding a putative transposase. The predicted transposase shows highest similarity to gene products encoded by aphids and mosquitoes and resembles those of the Phantom subclass of the Mutator transposon superfamily. Interestingly, the meiotic, sexually-reproducing root-knot nematode species M. hapla has Tm1 elements with similar inverted repeat termini, but lacks elements with histone hairpin motifs and contains no elements encoding an intact transposase. These Tm1 elements may have impacts on root-knot nematode genomes and contribute to genetic diversity of the asexual species. PMID:21931741

  10. Phytotoxicity of Clove Oil to Vegetable Crop Seedlings and Nematotoxicity to Root-knot Nematodes

    USDA-ARS?s Scientific Manuscript database

    Clove oil derived from the plant Syzygium aromaticum is active against various soilborne plant pathogens, and therefore has potential for use as a biobased pesticide. A clove oil formulation previously found to be toxic to the root-knot nematode Meloidogyne incognita in laboratory assays was invest...

  11. Molecular markers and mapping of root-knot nematode resistance in cotton.

    USDA-ARS?s Scientific Manuscript database

    Host-plant resistance is economic and highly effective for root-knot nematode (RKN) Meloidogyne incognita control in cotton Gossypium hirsutum. Recently, nematode R gene mapping in cotton has revealed relationships between resistance sources and linked molecular markers. Markers are important for th...

  12. Response of root-knot nematodes and Palmer amaranth to tillage and rye green manure

    USDA-ARS?s Scientific Manuscript database

    Rye (Secale cereale L.), which produces bioactive benzoxazinoid compounds, is a frequently used winter cover crop in many agronomic production systems in the USA. Our objective was to determine whether incorporating rye into soil while still green results in greater suppression of root-knot nematod...

  13. Root knot nematode effects on metabolic profiles of susceptible and resistant grapevine rootstocks

    USDA-ARS?s Scientific Manuscript database

    Root knot nematodes (Meloidogyne spp.) can negatively impact newly planted and stressed vineyards. Nematode infestations also may increase grapevine susceptibility to other stresses such as water deficit or various diseases. However, little is known about direct or indirect effects of nematode feedi...

  14. Tm1: a mutator/foldback transposable element family in root-knot nematodes.

    PubMed

    Gross, Stephen M; Williamson, Valerie M

    2011-01-01

    Three closely related parthenogenetic species of root-knot nematodes, collectively termed the Meloidogyne incognita-group, are economically significant pathogens of diverse crop species. Remarkably, these asexual root-knot nematodes are capable of acquiring heritable changes in virulence even though they lack sexual reproduction and meiotic recombination. Characterization of a near isogenic pair of M. javanica strains differing in response to tomato with the nematode resistance gene Mi-1 showed that the virulent strain carried a deletion spanning a gene called Cg-1. Herein, we present evidence that the Cg-1 gene lies within a member of a novel transposable element family (Tm1; Transposon in Meloidogyne-1). This element family is defined by composite terminal inverted repeats of variable lengths similar to those of Foldback (FB) transposable elements and by 9 bp target site duplications. In M. incognita, Tm1 elements can be classified into three general groups: 1) histone-hairpin motif elements; 2) MITE-like elements; 3) elements encoding a putative transposase. The predicted transposase shows highest similarity to gene products encoded by aphids and mosquitoes and resembles those of the Phantom subclass of the Mutator transposon superfamily. Interestingly, the meiotic, sexually-reproducing root-knot nematode species M. hapla has Tm1 elements with similar inverted repeat termini, but lacks elements with histone hairpin motifs and contains no elements encoding an intact transposase. These Tm1 elements may have impacts on root-knot nematode genomes and contribute to genetic diversity of the asexual species.

  15. Technique for retrieval of a knotted and entrapped guide wire after central venous catheterization.

    PubMed

    Yong, Yao Pey; Abisi, Said; Whitaker, Simon; Braithwaite, Bruce

    2013-04-01

    Central venous catheterization is a common procedure performed in the critically ill patient. The complication associated with this invasive procedure is well established. However, complication related to the guide wire is rare. We present a case of knotted and entrapped guide wire following central venous catheterization using the Seldinger method and technique to retrieve it nonoperatively.

  16. Tomato susceptibility to root-knot nematodes requires an intact jasmonic Acid signaling pathway

    USDA-ARS?s Scientific Manuscript database

    Response of tomato (Solanum lycopersicum) to root-knot nematode (RKN; Meloidogyne spp.) infection was monitored using TOM1 cDNA microarray with resistant (‘Motelle’; Mi-1) and susceptible (‘Moneymaker’; mi) tomato at 24 h after RKN infection. The array analysis identified 1497 genes and 750 genes d...

  17. Tolerance of a knotted near infrared fluorescent protein to random circular permutation

    PubMed Central

    Pandey, Naresh; Kuypers, Brianna E.; Nassif, Barbara; Thomas, Emily E.; Alnahhas, Razan N.; Segatori, Laura; Silberg, Jonathan J.

    2016-01-01

    Bacteriophytochrome photoreceptors (BphP) are knotted proteins that have been developed as near-infrared fluorescent protein (iRFP) reporters of gene expression. To explore how rearrangements in the peptides that interlace into the knot within the BphP photosensory core affect folding, we subjected iRFP to random circular permutation using an improved transposase mutagenesis strategy and screened for variants that fluoresce. We identified twenty seven circularly permuted iRFP that display biliverdin-dependent fluorescence in Escherichia coli. The variants with the brightest whole cell fluorescence initiated translation at residues near the domain linker and knot tails, although fluorescent variants were discovered that initiated translation within the PAS and GAF domains. Circularly permuted iRFP retained sufficient cofactor affinity to fluoresce in tissue culture without the addition of biliverdin, and one variant displayed enhanced fluorescence when expressed in bacteria and tissue culture. This variant displayed a similar quantum yield as iRFP, but exhibited increased resistance to chemical denaturation, suggesting that the observed signal increase arose from more efficient protein maturation. These results show how the contact order of a knotted BphP can be altered without disrupting chromophore binding and fluorescence, an important step towards the creation of near-infrared biosensors with expanded chemical-sensing functions for in vivo imaging. PMID:27304983

  18. Post-transcriptional gene silencing of root knot-nematode in transformed soybean roots

    USDA-ARS?s Scientific Manuscript database

    Plant-parasitic nematodes cause about $100 billion in crop losses annually. Root-knot nematodes (RKN; Meloidogyne spp.) are sedentary endoparasites, and the genus has been found on more than 3000 host plant species. In this study four different gene constructs were designed to produce RNA interferen...

  19. Spline curve matching with sparse knot sets: applications to deformable shape detection and recognition

    Treesearch

    Sang-Mook Lee; A. Lynn. Abbott; Neil A. Clark; Philip A. Araman

    2003-01-01

    Splines can be used to approximate noisy data with a few control points. This paper presents a new curve matching method for deformable shapes using two-dimensional splines. In contrast to the residual error criterion, which is based on relative locations of corresponding knot points such that is reliable primarily for dense point sets, we use deformation energy of...

  20. Resistance in peanut cultivars and breeding lines to three root-knot nematode species

    USDA-ARS?s Scientific Manuscript database

    Three major species of root-knot nematode infect peanut: Meloidogyne arenaria race 1 (Ma), M. hapla (Mh), and M. javanica race 3 (Mj). Sources of resistance to all three nematodes are needed for developing novel peanut cultivars with broad resistance to Meloidogyne spp. Cultivars and breeding lines ...

  1. The mutual attraction of magnetic knots. [solar hydromagnetic instability in sunspot regions

    NASA Technical Reports Server (NTRS)

    Parker, E. N.

    1978-01-01

    It is observed that the magnetic knots associated with active regions on the sun have an attraction for each other during the formative period of the active regions, when new magnetic flux is coming to the surface. The attraction disappears when new flux ceases to rise through the surface. Then the magnetic spots and knots tend to come apart, leading to disintegration of the sunspots previously formed. The dissolution of the fields is to be expected, as a consequence of the magnetic repulsion of knots of like polarity and as a consequence of the hydromagnetic exchange instability. The purpose of this paper is to show that the mutual attraction of knots during the formative stages of a sunspot region may be understood as the mutual hydrodynamic attraction of the rising flux tubes. Two rising tubes attract each other, as a consequence of the wake of the leading tube when one is moving behind the other, and as a consequence of the Bernoulli effect when rising side by side.

  2. Field level risk assessment for root-knot nematodes in lima beans

    USDA-ARS?s Scientific Manuscript database

    Southern Root-Knot Nematode (RKN), Meloidogyne incognita, is a major yield limiting pest in lima beans (Phaseolus lunatus). RKN are not evenly distributed through fields and population dynamics are fluid making whole field management challenging. The objectives of this research were to characterize ...

  3. Rootstock assessment for root-knot nematode management in grafted honeydew melon

    USDA-ARS?s Scientific Manuscript database

    Root-knot nematodes (RKN) are one of the most damaging soilborne pathogens of honeydew melon (Cucumis melo var. inodorus). Currently their management is dependent on soil fumigation. Vegetable grafting with resistant rootstocks may be an effective approach for RKN management in the sustainable produ...

  4. Transgressive segregation of root-knot nematode resistance in cotton determined by QTL analysis

    USDA-ARS?s Scientific Manuscript database

    Transgressive resistance to root-knot nematode, Meloidogyne incognita, was found in intraspecific (Gossypium hirsutum; resistant Acala NemX x susceptible Acala SJ-2) and interspecific (G. barbadense susceptible Pima-S7 x Acala NemX) cotton recombinant inbred line (RIL) populations. Similar contribut...

  5. Toward sequencing regions responsible for root-knot nematode resistance in cotton on chromosome 11.

    USDA-ARS?s Scientific Manuscript database

    In several described sources of genetic resistance to root-knot nematode (RKN), Meloidogyne incognita including ‘Acala NemX’ and Auburn 623, interaction of at least two genes and transgressive segregation occur, and resistance to RKN in cotton may involve the interaction of several genes. The concen...

  6. Edar/Eda interactions regulate enamel knot formation in tooth morphogenesis.

    PubMed

    Tucker, A S; Headon, D J; Schneider, P; Ferguson, B M; Overbeek, P; Tschopp, J; Sharpe, P T

    2000-11-01

    tabby and downless mutant mice have apparently identical defects in teeth, hair and sweat glands. Recently, genes responsible for these spontaneous mutations have been identified. downless (Dl) encodes Edar, a novel member of the tumour necrosis factor (TNF) receptor family, containing the characteristic extracellular cysteine rich fold, a single transmembrane region and a death homology domain close to the C terminus. tabby (Ta) encodes ectodysplasin-A (Eda) a type II membrane protein of the TNF ligand family containing an internal collagen-like domain. As predicted by the similarity in adult mutant phenotype and the structure of the proteins, we demonstrate that Eda and Edar specifically interact in vitro. We have compared the expression pattern of Dl and Ta in mouse development, taking the tooth as our model system, and find that they are not expressed in adjacent cells as would have been expected. Teeth develop by a well recorded series of epithelial-mesenchymal interactions, similar to those in hair follicle and sweat gland development, the structures found to be defective in tabby and downless mice. We have analysed the downless mutant teeth in detail, and have traced the defect in cusp morphology back to initial defects in the structure of the tooth enamel knot at E13. Significantly, the defect is distinct from that of the tabby mutant. In the tabby mutant, there is a recognisable but small enamel knot, whereas in the downless mutant the knot is absent, but enamel knot cells are organised into a different shape, the enamel rope, showing altered expression of signalling factors (Shh, Fgf4, Bmp4 and Wnt10b). By adding a soluble form of Edar to tooth germs, we were able to mimic the tabby enamel knot phenotype, demonstrating the involvement of endogenous Eda in tooth development. We could not, however, reproduce the downless phenotype, suggesting the existence of yet another ligand or receptor, or of ligand-independent activation mechanisms for Edar. Changes in

  7. Pierced Lasso Bundles are a new class of knot-like motifs.

    PubMed

    Haglund, Ellinor; Sulkowska, Joanna I; Noel, Jeffrey K; Lammert, Heiko; Onuchic, José N; Jennings, Patricia A

    2014-06-01

    A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins). We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB) and the knot-like threaded structural motif a Pierced Lasso (PL). In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso) in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets.

  8. Pierced Lasso Bundles Are a New Class of Knot-like Motifs

    PubMed Central

    Haglund, Ellinor; Sulkowska, Joanna I.; Noel, Jeffrey K.; Lammert, Heiko; Onuchic, José N.; Jennings, Patricia A.

    2014-01-01

    A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins). We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB) and the knot-like threaded structural motif a Pierced Lasso (PL). In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso) in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets. PMID:24945798

  9. Generation of radiative knots in a randomly pulsed protostellar jet. I. Dynamics and energetics

    NASA Astrophysics Data System (ADS)

    Bonito, R.; Orlando, S.; Peres, G.; Eislöffel, J.; Miceli, M.; Favata, F.

    2010-02-01

    Context. Herbig-Haro objects are characterized by a complex knotty morphology detected mainly along the axis of protostellar jets in a wide range of bands: from radio to IR to optical bands, with X-rays knots also detected in the past few years. Evidence of interactions between knots formed in different epochs have been found, suggesting that jets may result from the ejection of plasma blobs from the stellar source. Aims: We aim at investigating the physical mechanism leading to the irregular knotty structure observed in protostellar jets in different wavelength bands and the complex interactions occurring among blobs of plasma ejected from the stellar source. Methods: We performed 2D axisymmetric hydrodynamic numerical simulations of a randomly ejected pulsed jet. The jet consists of a train of blobs that ram with supersonic speed into the ambient medium. The initial random velocity of each blob follows an exponential distribution. We explored the ejection rate parameter to derive constraints on the physical properties of protostellar jets by comparing model results with observations. Our model takes the effects of radiative losses and thermal conduction into account. Results: We find that the mutual interactions of blobs ejected at different epochs and with different speeds lead to a variety of plasma components not described by current models of jets. The main features characterizing the randomly pulsed jet scenario are: single high-speed knots, showing a measurable proper motion in nice agreement with optical and X-rays observations; irregular chains of knots aligned along the jet axis and possibly interacting with each other; reverse shocks interacting with outgoing knots; oblique shock patterns produced by the reflection of shocks at the cocoon surrounding the jet. All these structures work together to help determining the morphology of the jet in different wavelength bands. We also find that the thermal conduction plays a crucial role in damping out

  10. Knot a Bad Idea: Testing BLISS Mapping for Spitzer Space Telescope Photometry

    NASA Astrophysics Data System (ADS)

    Schwartz, J. C.; Cowan, N. B.

    2017-01-01

    Much of transiting exoplanet science relies on high-precision photometry. The current generation of instruments can exhibit sensitivity variations greater than the astrophysical signals. For the InfraRed Array Camera (IRAC) on the Spitzer Space Telescope, a popular way to handle this is BiLinearly-Interpolated Subpixel Sensitivity (BLISS) mapping. As part of a Markov Chain Monte Carlo (MCMC), BLISS mapping estimates the sensitivity at many locations (knots) on the pixel, then interpolates to the target star’s centroids. We show that such embedded optimization schemes can misfit or bias parameters. Thus, we construct a model of Spitzer eclipse light curves to test the accuracy and precision of BLISS mapping. We compare standard BLISS mapping to a variant where the knots are fit during the MCMC, as well as to a polynomial model. Both types of BLISS mapping give similar eclipse depths, and we find that standard knots behave like real parameters. Standard BLISS mapping is therefore a reasonable shortcut to fitting for knots in an MCMC. BLISS maps become inaccurate when the photon noise is low, but typically approximate the real sensitivity well. We also find there is no perfect method for choosing the ideal number of BLISS knots to use on given data. BLISS mapping gives fits that are usually more accurate than precise (i.e., they are overly conservative), and the routine is more precise than polynomial models for significant eclipses or pixels with more varied sensitivities. BLISS mapping has better predictive power for most of these particular synthetic data, depending on how one treats time-correlated residuals. Overall, we conclude that BLISS mapping can be a reasonable sensitivity model for IRAC photometry.

  11. X-Wing RSRA - 80 Knot Taxi Test

    NASA Technical Reports Server (NTRS)

    1987-01-01

    The Rotor Systems Research Aircraft/X-Wing, a vehicle that was used to demonstrate an advanced rotor/fixed wing concept called X-Wing, is shown here during high-speed taxi tests at NASA's Ames-Dryden Flight Research Facility (later redesignated Dryden Flight Research Center), Edwards, California, on 4 November 1987. During these tests, the vehicle made three taxi tests at speeds of up to 138 knots. On the third run, the RSRA/X-Wing lifted off the runway to a 25-foot height for about 16 seconds. This liftoff maneuver was pre-planned as an aid to evaluations for first flight. At the controls were NASA pilot G. Warren Hall and Sikorsky pilot W. Faull. The unusual aircraft that resulted from the Ames Research Center/Army X-Wing Project was flown at the Ames-Dryden Flight Research Facility (now Dryden Flight Research Center), Edwards, California, beginning in the spring of 1984, with a follow-on program beginning in 1986. The program, was conceived to provide an efficient combination of the vertical lift characteristic of conventional helicopters and the high cruise speed of fixed-wing aircraft. It consisted of a hybrid vehicle called the NASA/Army Rotor Systems Research Aircraft (RSRA), which was equipped with advanced X-wing rotor systems. The program began in the early 1970s to investigate ways to increase the speed of rotor aircraft, as well as their performance, reliability, and safety . It also sought to reduce the noise, vibration, and maintenance costs of helicopters. Sikorsky Aircraft Division of United Technologies Laboratories built two RSRA aircraft. NASA's Langley Research Center, Hampton, Virginia, did some initial testing and transferred the program to Ames Research Center, Mountain View, California, for an extensive flight research program conducted by Ames and the Army. The purpose of the 1984 tests was to demonstrate the fixed-wing capability of the helicopter/airplane hybrid research vehicle and explore its flight envelope and flying qualities. These

  12. 78 FR 60023 - Endangered and Threatened Wildlife and Plants; Proposed Threatened Status for the Rufa Red Knot...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-30

    ...). Important fall stopover sites include southwest Hudson Bay (including the Nelson River delta), James Bay... knots typically make a short stop at James Bay in Canada, but may also stop briefly along the Great...

  13. Accomplishments of a 10-year initiative to develop host plant resistance to root-knot and reniform nematodes in cotton

    USDA-ARS?s Scientific Manuscript database

    In 2003 Cotton Incorporated initiated a Beltwide research program to develop host plant resistance against root-knot (Meloidogyne incognita) and reniform (Rotylenchulus reniformis) nematodes. Objectives formulated at a coordinating meeting in 2003 that included participants from public institutions...

  14. [Double umbilical cord knot in mono-amniotic twin pregnancy as the cause of intrauterine fetal death of both twins].

    PubMed

    Krüssel, J S; von Eckardstein, S; Schwenzer, T

    1994-01-01

    In cases of rare monoamniotic-monochronic geminie pregnancies there is a high risk of complications by real umbilical cord knots, including the cords of both gemini. In these cases fetal mortality is very high. Modern examination techniques (Colour doppler sonography) are able to detect such cord knots in monoamniotic twins. Therefore it is necessary in all twin pregnancies, especially following fertility treatment, to examine precisely by a routine examinator the question of mono - or diamniotic pregnancy. In monoamniotic pregnancy there should be a look for real knots of umbilical cord in regular intervals. In such a case, if a knot is present, the pregnant woman had to be supervised by CTG, to react immediately at first signs of hypoxia.

  15. Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi.

    PubMed

    Passos da Silva, Daniel; Devescovi, Giulia; Paszkiewicz, Konrad; Moretti, Chiaraluce; Buonaurio, Roberto; Studholme, David J; Venturi, Vittorio

    2013-05-09

    Erwinia toletana was first reported in 2004 as a bacterial species isolated from olive knots caused by the plant bacterium Pseudomonas savastanoi pv. savastanoi. Recent studies have shown that the presence of this bacterium in the olive knot environment increases the virulence of the disease, indicating possible interspecies interactions with P. savastanoi pv. savastanoi. Here, we report the first draft genome sequence of an E. toletana strain.

  16. Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi

    PubMed Central

    Passos da Silva, Daniel; Devescovi, Giulia; Paszkiewicz, Konrad; Moretti, Chiaraluce; Buonaurio, Roberto; Studholme, David J.

    2013-01-01

    Erwinia toletana was first reported in 2004 as a bacterial species isolated from olive knots caused by the plant bacterium Pseudomonas savastanoi pv. savastanoi. Recent studies have shown that the presence of this bacterium in the olive knot environment increases the virulence of the disease, indicating possible interspecies interactions with P. savastanoi pv. savastanoi. Here, we report the first draft genome sequence of an E. toletana strain. PMID:23661482

  17. An Expanding Plasma Model for the X-ray/radio knots in KPC-scale Jets of Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Sahayanathan, S.; Misra, R.; Kembhavi, A. K.; Kaul, C. L.

    2003-03-01

    We model the observed X-ray/radio knots in Active Galactic Nuclei (AGN) as isotropically expanding spherical plasma clouds fed continously by non-thermal electrons. The time-dependent electron distribution and the emitted photon spectrum are computed using the standard kinetic equation considering synchrotron, adiabatic and inverse Compton cooling processes. We use this model to study the knots of 1136 - 135 and 1150 + 497, recenly observed by Chandra. 29

  18. Highly sensitive refractive index sensor based on cascaded microfiber knots with Vernier effect.

    PubMed

    Xu, Zhilin; Sun, Qizhen; Li, Borui; Luo, Yiyang; Lu, Wengao; Liu, Deming; Shum, Perry Ping; Zhang, Lin

    2015-03-09

    We propose and experimentally demonstrate a refractive index (RI) sensor based on cascaded microfiber knot resonators (CMKRs) with Vernier effect. Deriving from high proportional evanescent field of microfiber and spectrum magnification function of Vernier effect, the RI sensor shows high sensitivity as well as high detection resolution. By using the method named "Drawing-Knotting-Assembling (DKA)", a compact CMKRs is fabricated for experimental demonstration. With the assistance of Lorentz fitting algorithm on the transmission spectrum, sensitivity of 6523nm/RIU and detection resolution up to 1.533 × 10(-7)RIU are obtained in the experiment which show good agreement with the numerical simulation. The proposed all-fiber RI sensor with high sensitivity, compact size and low cost can be widely used for chemical and biological detection, as well as the electronic/magnetic field measurement.

  19. Teaching students with autism to tie a shoelace knot using video prompting and backward chaining.

    PubMed

    Rayner, Christopher

    2011-01-01

    To evaluate the effects of video prompting and backward chaining for teaching students with autism to tie a shoelace knot. Videos featuring an adult and a peer or sibling model were used as part of the video prompting procedures to teach three boys with autism to tie a shoelace knot. A backward chaining procedure involving live modelling and verbal instruction was introduced following the video prompting phases. Although the video prompting interventions increased the number of steps in the shoelace tying task completed by each of the participants, the backward chaining procedure was more effective, enabling one participant to reach mastery and a second participant to approach mastery. Practitioners should consider the pre-requisite skills of the participants and the nature of the target behaviour when selecting an intervention to teach daily living skills to individuals with autism.

  20. Sensitivity of Bedding Plants to Southern Root-knot Nematode, Meloidogyne incognita Race 3.

    PubMed

    Walker, J T; Melin, J B; Davis, J

    1994-12-01

    Thirty-two cultivars of 10 commonly-grown bedding plants, representing eight families, were evaluated for their response to infection by the root-knot nematode, Meloidogyne incognita race 3, under greenhouse conditions. Four ageratum cultivars, two marigold, and two salvia cultivars were rated resistant after exposure for 8 weeks. Four begonia, four celosia, one dianthus, one verbena, one vinca, and three pansy cultivars were susceptible. Three salvia, one begonia, one gerber, one verbena, and three vinca cultivars were slightly susceptible with an average of knot nematode.

  1. Sensitivity of Bedding Plants to Southern Root-knot Nematode, Meloidogyne incognita Race 3

    PubMed Central

    Walker, J. T.; Melin, J. B.; Davis, J.

    1994-01-01

    Thirty-two cultivars of 10 commonly-grown bedding plants, representing eight families, were evaluated for their response to infection by the root-knot nematode, Meloidogyne incognita race 3, under greenhouse conditions. Four ageratum cultivars, two marigold, and two salvia cultivars were rated resistant after exposure for 8 weeks. Four begonia, four celosia, one dianthus, one verbena, one vinca, and three pansy cultivars were susceptible. Three salvia, one begonia, one gerber, one verbena, and three vinca cultivars were slightly susceptible with an average of ≤ 1 gall per plant. Nematodes, at two initial population densities, affected the dry weights of only a few cultivars. The diversity of annual bedding plant germplasm available may provide adequate sources of resistance to this race of root-knot nematode. PMID:19279964

  2. Oxidative folding of peptides with cystine-knot architectures: kinetic studies and optimization of folding conditions.

    PubMed

    Reinwarth, Michael; Glotzbach, Bernhard; Tomaszowski, Michael; Fabritz, Sebastian; Avrutina, Olga; Kolmar, Harald

    2013-01-02

    Bioactive peptides often contain several disulfide bonds that provide the main contribution to conformational rigidity and structural, thermal, or biological stability. Among them, cystine-knot peptides-commonly named "knottins"-make up a subclass with several thousand natural members. Hence, they are considered promising frameworks for peptide-based pharmaceuticals. Although cystine-knot peptides are available through chemical and recombinant synthetic routes, oxidative folding to afford the bioactive isomers still remains a crucial step. We therefore investigated the oxidative folding of ten protease-inhibiting peptides from two knottin families, as well as that of an HIV entry inhibitor and of aprotinin, under two conventional sets of folding conditions and by a newly developed procedure. Kinetic studies identified folding conditions that resulted in correctly folded miniproteins with high rates of conversion even for highly hydrophobic and aggregation-prone peptides in concentrated solutions.

  3. Superpolynomials for torus knots from evolution induced by cut-and-join operators

    NASA Astrophysics Data System (ADS)

    Dunin-Barkowski, P.; Mironov, A.; Morozov, A.; Sleptsov, A.; Smirnov, A.

    2013-03-01

    The colored HOMFLY polynomials, which describe Wilson loop averages in Chern-Simons theory, possess an especially simple representation for torus knots, which begins from quantum R-matrix and ends up with a trivially-looking split W representation familiar from character calculus applications to matrix models and Hurwitz theory. Substitution of MacDonald polynomials for characters in these formulas provides a very simple description of "superpolynomials", much simpler than the recently studied alternative which deforms relation to the WZNW theory and explicitly involves the Littlewood-Richardson coefficients. A lot of explicit expressions are presented for different representations (Young diagrams), many of them new. In particular, we provide the superpolynomial {P}_{{[ 1 ]}}^{{[ {m,km± 1} ]}} for arbitrary m and k. The procedure is not restricted to the fundamental (all antisymmetric) representations and the torus knots.

  4. Root-knot nematodes in golf course greens of the western United States

    USDA-ARS?s Scientific Manuscript database

    A survey of 238 golf courses in ten of the Western U.S. found root-knot nematodes (Meloidogyne spp.) in 60 % of the putting greens sampled. Sequence and phylogenetic analyses of 18S rRNA, D2-D3 of 28S rRNA, ITS-rRNA and mtDNA gene sequences were used to identify specimens from 110 golf courses. The...

  5. Exposure of red knots (Calidris canutus rufa) to select avian pathogens; Patagonia, Argentina.

    PubMed

    D'Amico, Veronica L; Bertellotti, Marcelo; Baker, Allan J; Diaz, Luis A

    2007-10-01

    As part of the shorebird surveillance, Red Knots (Calidris canutus rufa) were sampled in two Patagonian sites in Argentina, Río Grande and San Antonio Oeste, during 2005-2006. Cloacal swabs and serum samples were collected from 156 birds and tested by virus isolation (Newcastle disease virus), polymerase chain reaction (PCR; avian influenza virus and Plasmodium/Hemoproteus), and for antibodies to St. Louis encephalitis virus. All test results were negative.

  6. Determination of volatile organic compounds in water using headspace knotted hollow fiber microextraction.

    PubMed

    Chen, Pai-Shan; Tseng, Yu-Hsiang; Chuang, Yuh-Lin; Chen, Jung-Hsuan

    2015-05-22

    An efficient and effective headspace microextraction technique named static headspace knotted hollow fiber microextraction (HS-K-HFME) has been developed for the determination of volatile organic compounds (VOCs) in water samples. The knot-shaped hollow fiber is filled with 25μL of the extraction solvent. The excess solvent forms a large droplet (13μL) and is held in the center of the knot. Even after 20min of extraction time at high temperature (95°C) without cooling, there was still enough volume of extraction solvent for gas chromatography-mass spectrometry (GC-MS) analysis, which extends the choice of solvents for headspace LPME. Moreover, the knot-shaped fiber has a larger extraction contact interface, which increases the rate of mass transfer between the headspace and extraction solvent film attached to the fiber, thus improving the extraction efficiency. The effects of extraction solvent, temperature, stirring rate, salt concentration and extraction time on extraction performance were optimized. The calibration curves exhibited coefficients of determination (R(2)) ranging from 0.9957 to 0.9999 and the limit of detection (LOD) ranged from 0.2 to 10μgL(-1). Relative standard deviations (RSDs) ranged from 4.5% to 11.6% for intraday measurements (n=5). Interday (n=15) values were between 2.2% and 12.9%. The relative recoveries (RRs) ranged from 90.3% to 106.0% for river water and 95.9% to 103.6% for wastewater.

  7. Automated knot detection with visual post-processing of Douglas-fir veneer images

    Treesearch

    C.L. Todoroki; Eini C. Lowell; Dennis Dykstra

    2010-01-01

    Knots on digital images of 51 full veneer sheets, obtained from nine peeler blocks crosscut from two 35-foot (10.7 m) long logs and one 18-foot (5.5 m) log from a single Douglas-fir tree, were detected using a two-phase algorithm. The algorithm was developed using one image, the Development Sheet, refined on five other images, the Training Sheets, and then applied to...

  8. Application of lariat lock catch knot suture in the achilles tendon rupture

    PubMed Central

    Wang, Baocang; Feng, Xiaona; Yan, Ming; Wang, Hui; Li, Yong

    2015-01-01

    The aim of this study was to summarize the clinical experience of repairing the Achilles tendon rupture by lariat lock catch knot suture. Between January 2011 and February, 2014, 32 cases of the Achilles tendon rupture were treated by lariat lock catch knot suture. There were 26 males and 6 females, with the average age of 39 years (range 17-53 years), including 13 left knees and 19 right knees. 29 wounds healed by first intention, and 3 cases who were performed local flap transfer due to necrosis of skin were healed by second intention. Thirty-two cases were followed up 10-25 months (13 months on average). No re-rupture of Achilles tendon or deep infection occurred during follow-up period. According to Arner-Lindholm assessment standard, the results were excellent in 19 cases and good in 13 cases, the excellent and good rate was 100%. Lariat lock catch knot suture is a safe and effective method for repairing Achilles tendon. PMID:26770612

  9. The Origin of the Iron-Rich Knot in Tycho's Supernova Remnant

    NASA Technical Reports Server (NTRS)

    Yamaguchi, Hiroya; Hughes, John P.; Badenes, Carles; Bravo, Eduardo; Seitenzahl, Ivo R.; Martinez-Rodriguez, Hector; Park, Sangwook; Petre, Robert

    2017-01-01

    X-ray observations of supernova remnants (SNRs) allow us to investigate the chemical inhomogeneity of ejecta, offering unique insight into the nucleosynthesis in supernova explosions. Here we present detailed imaging and spectroscopic studies of the Fe knot located along the eastern rim of the Type Ia SNR Tycho ( SN 1572) using Suzaku and Chandra long-exposure data. Surprisingly, the Suzaku spectrum of this knot shows no emission from Cr, Mn, or Ni, which is unusual for the Fe-rich regions in this SNR. Within the framework of the canonical delayed-detonation models for SN Ia, the observed mass ratios M(sub Cr)/M(sub Fe) is less than 0.023, M(sub Mn)/M(sub Fe) is less than 0.012, and M(sub Ni)/M(sub Fe) is less than 0.029 (at 90% confidence) can only be achieved for a peak temperature of (5.3 - 5.7) x 10(exp. 9) K and a neutron excess of approximately less than 2.0 x 10(exp. -3). These constraints rule out the deep, dense core of a Chandrasekhar-mass white dwarf as the origin of the Fe knot and favor either incomplete Si burning or an Alpha-rich freeze-out regime, probably close to the boundary. An explosive He burning regime is a possible alternative, although this hypothesis is in conflict with the main properties of this SNR.

  10. Folding analysis of the most complex Stevedore’s protein knot

    PubMed Central

    Wang, Iren; Chen, Szu-Yu; Hsu, Shang-Te Danny

    2016-01-01

    DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore’s protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I’. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I’ to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures. PMID:27527519

  11. The properties of conformal blocks, the AGT hypothesis, and knot polynomials

    NASA Astrophysics Data System (ADS)

    Morozov, A. A.

    2016-09-01

    Various properties of correlators of the two-dimensional conformal field theory are discussed. Specifically, their relation to the partition function of the four-dimensional supersymmetric theory is analyzed. In addition to being of interest in its own right, this relation is of practical importance. For example, it is much easier to calculate the known expressions for the partition function of supersymmetric theory than to calculate directly the expressions for correlators in conformal theory. The examined representation of conformal theory correlators as a matrix model serves the same purpose. The integral form of these correlators allows one to generalize the obtained results for the Virasoro algebra to more complicated cases of the W algebra or the quantum Virasoro algebra. This provides an opportunity to examine more complex configurations in conformal field theory. The three-dimensional Chern-Simons theory is discussed in the second part of the present review. The current interest in this theory stems largely from its relation to the mathematical knot theory (a rather well-developed area of mathematics known since the 17th century). The primary objective of this theory is to develop an algorithm that allows one to distinguish different knots (closed loops in three-dimensional space). The basic way to do this is by constructing the so-called knot invariants.

  12. DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model.

    PubMed

    Sperschneider, Jana; Datta, Amitava

    2010-04-01

    RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accuracy for longer sequences. A heuristic approach is to search for promising pseudoknot candidates in a sequence and verify those. Afterwards, the detected pseudoknots can be further analysed using bioinformatics or laboratory techniques. We present a novel pseudoknot detection method called DotKnot that extracts stem regions from the secondary structure probability dot plot and assembles pseudoknot candidates in a constructive fashion. We evaluate pseudoknot free energies using novel parameters, which have recently become available. We show that the conventional probability dot plot makes a wide class of pseudoknots including those with bulged stems manageable in an explicit fashion. The energy parameters now become the limiting factor in pseudoknot prediction. DotKnot is an efficient method for long sequences, which finds pseudoknots with higher accuracy compared to other known prediction algorithms. DotKnot is accessible as a web server at http://dotknot.csse.uwa.edu.au.

  13. Characterization of a Root-Knot Nematode Population of Meloidogyne arenaria from Tupungato (Mendoza, Argentina)

    PubMed Central

    Evangelina García, Laura; Sánchez-Puerta, María Virginia

    2012-01-01

    Root-knot nematodes (Meloidogyne spp.) are polyphagous plant parasites of global importance. Successful host infection depends on the particular interaction between a specific nematode species and race and a specific plant species and cultivar. Accurate diagnosis of nematode species is relevant to effective agricultural management; and benefits further from understanding the variability within a single nematode species. Here, we described a population of M. arenaria race 2 from Mendoza (Argentina). This study represents the first morphometric, morphological, biochemical, reproductive, molecular, and host range characterization of a root-knot nematode species from Argentina. Even after gathering morphological and morphometric data of this population and partially sequencing its rRNA, an unequivocal taxonomic assignment could not be achieved. The most decisive data was provided by esterase phenotyping and molecular methods using SCARs. These results highlight the importance of taking a multidimensional approach for Meloidogyne spp. diagnosis. This study contributes to the understanding of the variability of morphological, reproductive and molecular traits of M. arenaria, and provides data on the identification of root-knot nematodes on tomato cultivars from Argentina. PMID:23481918

  14. [Controlling effect of antagonist bioorganic fertilizer on tomato root-knot nematode].

    PubMed

    Zhu, Zhen; Chen, Fang; Xiao, Tong-jian; Wang, Xiao-hui; Ran, Wei; Yang, Xing-ming; Shen, Qi-rong

    2011-04-01

    Indoor in vitro culture experiment and greenhouse pot experiment were conducted to evaluate the capabilities of three bacterial strains XZ-173 (Bacillus amyloliquefaciens), SL-25 (B. gibsonii), and KS-62 (Paenibacillus polymyxa) that can hydrolyze collagen protein in controlling tomato root-knot nematode. In the in vitro culture experiment, suspensions of XZ-173, SL-25, and KS-62 induced a mortality rate of 75.9%, 66.7%, and 50.0% to the second-stage junior nematode within 24 h, and decreased the egg hatching rate to 17.8%, 28.9% and 37.6% after 7-day incubation, respectively, in contrast to the 17.4% mortality rate and 53.6% egg hatching rate in the control (sterilized water). In the greenhouse pot experiment, the bioorganic fertilizer mixed with equal parts of fermented XZ-173, SL-25, and KS-62 gained the best result, with the root-knot nematode population in rhizosphere soil decreased by 84.0% as compared with the control. The bioorganic fertilizer also decreased the numbers of galls and eggs on tomato roots significantly, and increased the underground and aboveground biomass of tomato. Therefore, antagonist bioorganic fertilizer has promising potential in controlling root-knot nematode.

  15. Hair-on-hair static friction coefficient can be determined by tying a knot.

    PubMed

    Chevalier, Nicolas R

    2017-09-04

    Characterizing the tribological properties of the hair-hair interface is important to quantify the manageability of hair and to assess the performance of hair care products. Audoly et al. (Phys. Rev. Lett. 99, 164301, 2007) derived an equation relating the self-friction coefficient of an elastic fiber to the dimensions of a simple, relaxed overhand knot made from this fiber. I experimentally tested and validated their equation using nylon thread and an independent measurement of its self-friction coefficient. I show that this methodology can be applied to provide high-throughput data on the static self-friction coefficient of single hair fibers in various conditions and to quantitatively assess how hair care treatments (conditioner, relaxant) alter frictional properties. I find that treatment of hair with 1M sodium hydroxide leads to a quick, irreversible self-friction coefficient increase; the resulting fine frictional fibers can be used to form very small knots for microsurgical vessel and organ ligature in medicine or embryology. The relaxed overhand knot method can more generally be used to measure the self-friction coefficients of a wide range of elastic fibers from the nano- (e.g. proteins, nanotubes) to the macro-scale (e.g. textile fiber, fiberglass). Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Diversity of Knot Solitons in Liquid Crystals Manifested by Linking of Preimages in Torons and Hopfions

    NASA Astrophysics Data System (ADS)

    Ackerman, Paul J.; Smalyukh, Ivan I.

    2017-01-01

    Topological solitons are knots in continuous physical fields classified by nonzero Hopf index values. Despite arising in theories that span many branches of physics, from elementary particles to condensed matter and cosmology, they remain experimentally elusive and poorly understood. We introduce a method of experimental and numerical analysis of such localized structures in liquid crystals that, similar to the mathematical Hopf maps, relates all points of the medium's order parameter space to their closed-loop preimages within the three-dimensional solitons. We uncover a surprisingly large diversity of naturally occurring and laser-generated topologically nontrivial solitons with differently knotted nematic fields, which previously have not been realized in theories and experiments alike. We discuss the implications of the liquid crystal's nonpolar nature on the knot soliton topology and how the medium's chirality, confinement, and elastic anisotropy help to overcome the constraints of the Hobart-Derrick theorem, yielding static three-dimensional solitons without or with additional defects. Our findings will establish chiral nematics as a model system for experimental exploration of topological solitons and may impinge on understanding of such nonsingular field configurations in other branches of physics, as well as may lead to technological applications.

  17. Exponents of intrachain correlation for self-avoiding walks and knotted self-avoiding polygons

    NASA Astrophysics Data System (ADS)

    Uehara, Erica; Deguchi, Tetsuo

    2013-08-01

    We show numerically that critical exponents for two-point intrachain correlation of an infinite chain characterize those of finite chains in self-avoiding walk (SAW) and self-avoiding polygon (SAP) under a topological constraint. We evaluate short-distance exponents θ(i, j) through the probability distribution functions of the distance between the ith and jth vertices of N-step SAW (or SAP with a knot) for all pairs (1 ⩽ i, j ⩽ N). We construct the contour plot of θ(i, j), and express it as a function of i and j. We suggest that it has quite a simple structure. Here exponents θ(i, j) generalize des Cloizeaux’s three critical exponents for short-distance intrachain correlation of SAW, and we show the crossover among them. We also evaluate the diffusion coefficient of knotted SAP for a few knot types, which can be calculated with the probability distribution functions of the distance between two nodes.

  18. Digestive capacity and toxicity cause mixed diets in red knots that maximize energy intake rate.

    PubMed

    Oudman, Thomas; Onrust, Jeroen; de Fouw, Jimmy; Spaans, Bernard; Piersma, Theunis; van Gils, Jan A

    2014-05-01

    Among energy-maximizing animals, preferences for different prey can be explained by ranking the prey according to their energetic content. However, diet choice also depends on characteristics of the predator, such as the need to ingest necessary nutrients and the constraints imposed by digestion and toxins in food. In combination, these factors can lead to mixed diets in which the energetically most profitable food is not eaten exclusively even when it is abundant. We studied diet choice in red knots (Calidris canutus canutus) feeding on mollusks at a West African wintering site. At this site, the birds fed primarily on two species of bivalves, a thick-shelled one (Dosinia isocardia) that imposed a digestive constraint and a thin-shelled one (Loripes lucinalis) that imposed a toxin constraint. The latter species is toxic due to its symbiotic association with sulfide-oxidizing bacteria. We estimated experimentally the parameters of a linear programming model that includes both digestive and toxin constraints, leading to the prediction that red knots should eat a mixture of both mollusk species to maximize energy intake. The model correctly predicted the preferences of the captive birds, which depended on the digestive quality and toxicity of their previous diet. At our study site, energy-maximizing red knots appear to select a mixed diet as a result of the simultaneous effects of digestive and toxin constraints.

  19. Combinatorial Optimization of Cystine-Knot Peptides towards High-Affinity Inhibitors of Human Matriptase-1

    PubMed Central

    Weber, Niklas; Fabritz, Sebastian; Tomaszowski, Michael; Fittler, Heiko; Christmann, Andreas; Avrutina, Olga; Kolmar, Harald

    2013-01-01

    Cystine-knot miniproteins define a class of bioactive molecules with several thousand natural members. Their eponymous motif comprises a rigid structured core formed by six disulfide-connected cysteine residues, which accounts for its exceptional stability towards thermic or proteolytic degradation. Since they display a remarkable sequence tolerance within their disulfide-connected loops, these molecules are considered promising frameworks for peptide-based pharmaceuticals. Natural open-chain cystine-knot trypsin inhibitors of the MCoTI (Momordica cochinchinensis trypsin inhibitor) and SOTI (Spinacia oleracea trypsin inhibitor) families served as starting points for the generation of inhibitors of matriptase-1, a type II transmembrane serine protease with possible clinical relevance in cancer and arthritic therapy. Yeast surface-displayed libraries of miniproteins were used to select unique and potent matriptase-1 inhibitors. To this end, a knowledge-based library design was applied that makes use of detailed information on binding and folding behavior of cystine-knot peptides. Five inhibitor variants, four of the MCoTI family and one of the SOTI family, were identified, chemically synthesized and oxidatively folded towards the bioactive conformation. Enzyme assays revealed inhibition constants in the low nanomolar range for all candidates. One subnanomolar binder (Ki = 0.83 nM) with an inverted selectivity towards trypsin and matriptase-1 was identified. PMID:24146945

  20. Linked and knotted beams of light, conservation of helicity and the flow of null electromagnetic fields

    NASA Astrophysics Data System (ADS)

    Irvine, William T. M.

    2010-09-01

    Maxwell's equations allow for some remarkable solutions consisting of pulsed beams of light which have linked and knotted field lines. The preservation of the topological structure of the field lines in these solutions has previously been ascribed to the fact that the electric and magnetic helicities, a measure of the degree of linking and knotting between field lines, are conserved. Here we show that the elegant evolution of the field is due to the stricter condition that the electric and magnetic fields be everywhere orthogonal. The field lines then satisfy a 'frozen field' condition and evolve as if they were unbreakable filaments embedded in a fluid. The preservation of the orthogonality of the electric and magnetic field lines is guaranteed for null, shear-free fields such as the ones considered here by a theorem of Robinson. We calculate the flow field of a particular solution and find it to have the form of a Hopf fibration moving at the speed of light in a direction opposite to the propagation of the pulsed light beam, a familiar structure in this type of solution. The difference between smooth evolution of individual field lines and conservation of electric and magnetic helicities is illustrated by considering a further example in which the helicities are conserved, but the field lines are not everywhere orthogonal. The field line configuration at time t = 0 corresponds to a nested family of torus knots but unravels upon evolution.

  1. Cellular uptake of a cystine-knot peptide and modulation of its intracellular trafficking

    PubMed Central

    Gao, Xinxin; Stanger, Karen; Kaluarachchi, Harini; Maurer, Till; Ciepla, Paulina; Chalouni, Cecile; Franke, Yvonne; Hannoush, Rami N.

    2016-01-01

    Cyclotides or cyclic cystine-knot peptides have emerged as a promising class of pharmacological ligands that modulate protein function. Interestingly, very few cyclotides have been shown to enter into cells. Yet, it remains unknown whether backbone cyclization is required for their cellular internalization. In this report, we studied the cellular behavior of EETI-II, a model acyclic cystine-knot peptide. Even though synthetic methods have been used to generate EETI-II, recombinant methods that allow efficient large scale biosynthesis of EETI-II have been lagging. Here, we describe a novel protocol for recombinant generation of folded EETI-II in high yields and to near homogeneity. We also uncover that EETI-II is efficiently uptaken via an active endocytic pathway to early endosomes in mammalian cells, eventually accumulating in late endosomes and lysosomes. Notably, co-incubation with a cell-penetrating peptide enhanced the cellular uptake and altered the trafficking of EETI-II, leading to its evasion of lysosomes. Our results demonstrate the feasibility of modulating the subcellular distribution and intracellular targeting of cystine-knot peptides, and hence enable future exploration of their utility in drug discovery and delivery. PMID:27734922

  2. Knot invariants and M-theory: Hitchin equations, Chern-Simons actions, and surface operators

    NASA Astrophysics Data System (ADS)

    Dasgupta, Keshav; Errasti Díez, Verónica; Ramadevi, P.; Tatar, Radu

    2017-01-01

    Recently Witten introduced a type IIB brane construction with certain boundary conditions to study knot invariants and Khovanov homology. The essential ingredients used in his work are the topologically twisted N =4 Yang-Mills theory, localization equations and surface operators. In this paper we extend his construction in two possible ways. On one hand we show that a slight modification of Witten's brane construction could lead, using certain well-defined duality transformations, to the model used by Ooguri-Vafa to study knot invariants using gravity duals. On the other hand, we argue that both these constructions, of Witten and of Ooguri-Vafa, lead to two different seven-dimensional manifolds in M-theory from where the topological theories may appear from certain twisting of the G-flux action. The non-Abelian nature of the topological action may also be studied if we take the wrapped M2-brane states in the theory. We discuss explicit constructions of the seven-dimensional manifolds in M-theory, and show that both the localization equations and surface operators appear naturally from the Hamiltonian formalism of the theories. Knots and link invariants are then constructed using M2-brane states in both the models.

  3. The chemical abundances of the Cassiopeia A fast-moving knots - Explosive nucleosynthesis on a minicomputer

    NASA Technical Reports Server (NTRS)

    Johnston, M. D.; Joss, P. C.

    1980-01-01

    A simplified nuclear reaction network for explosive nucleosynthesis calculations is described in which only the most abundant nuclear species and the most important reactions linking these species are considered. This scheme permits the exploration of many cases without excessive computational effort. Good agreement with previous calculations employing more complex reaction networks is obtained. This scheme is applied to the observed chemical abundances of the fast-moving knots in the supernova remnant Cassiopeia A and it is found that a wide range of initial conditions could yield the observed abundances. The abundances of four of the knots with significant and different amounts of elements heavier than oxygen are consistent with an origin in material of the same initial composition but processed at different peak temperatures and densities. Despite the observed high oxygen abundances and low abundances of light elements in the knots, they did not necessarily undergo incomplete oxygen burning; in fact, it is not even necessary that oxygen have been present in the initial composition. The agreement between the calculated and observed chemical abundances in Cas A and similar supernova remnants depends primarily upon the relevant nuclear physics and does not provide strong evidence in favor of any particular model of the supernova event.

  4. High and Low Throughput Screens with Root-knot Nematodes Meloidogyne spp.

    PubMed Central

    Atamian, Hagop S.; Roberts, Philip A.; Kaloshian, Isgouhi

    2012-01-01

    Root-knot nematodes (genus Meloidogyne) are obligate plant parasites. They are extremely polyphagous and considered one of the most economically important plant parasitic nematodes. The microscopic second-stage juvenile (J2), molted once in the egg, is the infective stage. The J2s hatch from the eggs, move freely in the soil within a film of water, and locate root tips of suitable plant species. After penetrating the plant root, they migrate towards the vascular cylinder where they establish a feeding site and initiate feeding using their stylets. The multicellular feeding site is comprised of several enlarged multinuclear cells called 'giant cells' which are formed from cells that underwent karyokinesis (repeated mitosis) without cytokinesis. Neighboring pericycle cells divide and enlarge in size giving rise to a typical gall or root knot, the characteristic symptom of root-knot nematode infection. Once feeding is initiated, J2s become sedentary and undergo three additional molts to become adults. The adult female lays 150-250 eggs in a gelatinous matrix on or below the surface of the root. From the eggs new infective J2s hatch and start a new cycle. The root-knot nematode life cycle is completed in 4-6 weeks at 26-28°C. Here we present the traditional protocol to infect plants, grown in pots, with root-knot nematodes and two methods for high-throughput assays. The first high-throughput method is used for plants with small seeds such as tomato while the second is for plants with large seeds such as cowpea and common bean. Large seeds support extended seedling growth with minimal nutrient supplement. The first high throughput assay utilizes seedlings grown in sand in trays while in the second assay plants are grown in pouches in the absence of soil. The seedling growth pouch is made of a 15.5 x 12.5cm paper wick, folded at the top to form a 2-cm-deep trough in which the seed or seedling is placed. The paper wick is contained inside a transparent plastic pouch

  5. High and low throughput screens with root-knot nematodes Meloidogyne spp.

    PubMed

    Atamian, Hagop S; Roberts, Philip A; Kaloshian, Isgouhi

    2012-03-12

    Root-knot nematodes (genus Meloidogyne) are obligate plant parasites. They are extremely polyphagous and considered one of the most economically important plant parasitic nematodes. The microscopic second-stage juvenile (J2), molted once in the egg, is the infective stage. The J2s hatch from the eggs, move freely in the soil within a film of water, and locate root tips of suitable plant species. After penetrating the plant root, they migrate towards the vascular cylinder where they establish a feeding site and initiate feeding using their stylets. The multicellular feeding site is comprised of several enlarged multinuclear cells called 'giant cells' which are formed from cells that underwent karyokinesis (repeated mitosis) without cytokinesis. Neighboring pericycle cells divide and enlarge in size giving rise to a typical gall or root knot, the characteristic symptom of root-knot nematode infection. Once feeding is initiated, J2s become sedentary and undergo three additional molts to become adults. The adult female lays 150-250 eggs in a gelatinous matrix on or below the surface of the root. From the eggs new infective J2s hatch and start a new cycle. The root-knot nematode life cycle is completed in 4-6 weeks at 26-28°C. Here we present the traditional protocol to infect plants, grown in pots, with root-knot nematodes and two methods for high-throughput assays. The first high-throughput method is used for plants with small seeds such as tomato while the second is for plants with large seeds such as cowpea and common bean. Large seeds support extended seedling growth with minimal nutrient supplement. The first high throughput assay utilizes seedlings grown in sand in trays while in the second assay plants are grown in pouches in the absence of soil. The seedling growth pouch is made of a 15.5 x 12.5cm paper wick, folded at the top to form a 2-cm-deep trough in which the seed or seedling is placed. The paper wick is contained inside a transparent plastic pouch

  6. Transfer validity of laparoscopic knot-tying training on a VR simulator to a realistic environment: a randomized controlled trial.

    PubMed

    Verdaasdonk, E G G; Dankelman, J; Lange, J F; Stassen, L P S

    2008-07-01

    Laparoscopic suturing is one of the most difficult tasks in endoscopic surgery, requiring extensive training. The aim of this study was to determine the transfer validity of knot-tying training on a virtual-reality (VR) simulator to a realistic laparoscopic environment. Twenty surgical trainees underwent basic eye-hand coordination training on a VR simulator (SIMENDO, DelltaTech, Delft, The Netherlands) until predefined performance criteria were met. Then, they were randomized into two groups. Group A (the experimental group) received additional training with the knot-tying module on the simulator, during which they had to tie a double laparoscopic knot ten times. Group B (controls) did not receive additional manual training. Within a week the participants tied a double knot in the abdominal cavity of an anaesthetized porcine model. Their performance was captured on digital video and coded. Objective analysis parameters were: time taken to tie the knot and number of predefined errors made. Subjective assessments were also made by two laparoscopic surgeons using a global rating list with a five-point Likert scale. Trainees in group A (n = 9) were significantly faster than the controls (n = 10), with a median of 262 versus 374 seconds (p = 0.034). Group A made a significantly lower number of errors than the controls (median of 24 versus 36 errors, p = 0.030). Subjective assessments by the laparoscopic experts did not show any significant differences in economy of movement and erroneous behavior between the two groups. Surgical trainees who received knot-tying training on the VR simulator were faster and made fewer errors than the controls. The VR module is a useful tool to train laparoscopic knot-tying. Opportunities arose to improve simulator-based instruction that might enhance future training.

  7. Benefits of foraging in small groups: An experimental study on public information use in red knots Calidris canutus.

    PubMed

    Bijleveld, Allert I; van Gils, Jan A; Jouta, Jeltje; Piersma, Theunis

    2015-08-01

    Social foraging is common and may provide benefits of safety and public information. Public information permits faster and more accurate estimates of patch resource densities, thus allowing more effective foraging. In this paper we report on two experiments with red knots Calidris canutus, socially foraging shorebirds that eat bivalves on intertidal mudflats. The first experiment was designed to show that red knots are capable of using public information, and whether dominance status or sex affected its use. We showed that knots can detect the foraging success of conspecifics and choose a patch accordingly. Neither dominance status nor sex influenced public information use. In the second experiment, by manipulating group size, we investigated whether public information use affected food-patch discovery rates and patch residence times. We showed that the time needed before locating a food patch decreased in proportion to group size. Also, an individual's number of patch visits before locating the food declined with group size, and, to our surprise, their average patch residence time did as well. Moreover, knots differed in their search strategy in that some birds consistently exploited the searching efforts of others. We conclude that socially foraging knots have the potential to greatly increase their food-finding rate by using public information. This article is part of a Special Issue entitled: In Honor of Jerry Hogan.

  8. Robust in vitro assay system for quantitative analysis of parasitic root-knot nematode infestation using Lotus japonicus.

    PubMed

    Amin, Arshana N N; Hayashi, Shuhei; Bartlem, Derek G

    2014-08-01

    Root-knot nematodes are sedentary endoparasites that induce permanent infestation sites inside the roots of a broad range of crop plants. The development of effective control strategies require understanding the root-knot nematode parasitic process, however, the key molecular determinants for host manipulation during infestation remain elusive. One limiting factor has been the lack of a standardized conventional method for quantitative measurement of host parasitism by root-knot nematodes, particularly one that enables efficient downstream analyses and is free from other biological sources of variability. We report here a robust, highly reproducible system for quantitative analysis of all stages of root-knot nematode infestation using the legume Lotus japonicus as the plant host. This system provides a high quality nematode inoculum that maintains consistency in juvenile age and viability even between independently prepared populations. An optimized root transformation protocol was also developed for L. japonicus to facilitate downstream molecular studies in conjunction with the quantitative assay. Hairy root transformation efficiencies up to 91% were achieved. Root-knot nematodes formed egg masses at the root surface of both intact plants and transgenic hairy root cultures within eight weeks, confirming the assay conditions support an efficient completion of the infestation cycle. The in vitro assay system described here is compatible with other plant hosts and will benefit agricultural biotechnology research as it now enables specific high-throughput screening of nematode resistance traits together with subsequent mechanistic elucidation of the causative factors.

  9. EXPANSION OF HYDROGEN-POOR KNOTS IN THE BORN-AGAIN PLANETARY NEBULAE A30 AND A78

    SciTech Connect

    Fang, X.; Guerrero, M. A.; Marquez-Lugo, R. A.; Toalá, J. A.; Chu, Y.-H.; Gruendl, R. A.; Blair, W. P.; Hamann, W.-R.; Oskinova, L. M.; Todt, H.

    2014-12-20

    We analyze the expansion of hydrogen-poor knots and filaments in the born-again planetary nebulae A30 and A78 based on Hubble Space Telescope (HST) images obtained almost 20 yr apart. The proper motion of these features generally increases with distance to the central star, but the fractional expansion decreases, i.e., the expansion is not homologous. As a result, there is not a unique expansion age, which is estimated to be 610-950 yr for A30 and 600-1140 yr for A78. The knots and filaments have experienced complex dynamical processes: the current fast stellar wind is mass loaded by the material ablated from the inner knots; the ablated material is then swept up until it shocks the inner edges of the outer, hydrogen-rich nebula. The angular expansion of the outer filaments shows a clear dependence on position angle, indicating that the interaction of the stellar wind with the innermost knots channels the wind along preferred directions. The apparent angular expansion of the innermost knots seems to be dominated by the rocket effect of evaporating gas and by the propagation of the ionization front inside them. Radiation-hydrodynamical simulations show that a single ejection of material followed by a rapid onset of the stellar wind and ionizing flux can reproduce the variety of clumps and filaments at different distances from the central star found in A30 and A78.

  10. A knot in the protein structure: probing the near-infrared fluorescent protein iRFP designed from bacterial phytochrome

    PubMed Central

    Stepanenko, Olesya V.; Bublikov, Gregory S.; Stepanenko, Olga V.; Shcherbakova, Daria M.; Verkhusha, Vladislav V.; Turoverov, Konstantin K.; Kuznetsova, Irina M.

    2014-01-01

    Substantial interest to a family of the bacterial phytochrome photoreceptors (BphPs) is caused by development of near-infrared fluorescent proteins and biosensors, molecularly engineered from BphPs. The near-infrared fluorescent proteins have allowed bioimaging of deep tissues and whole organs noninvasively in living animals. BphPs and derived near-infrared fluorescent proteins contain a structural element, called knot, in their polypeptide chains. Formation of knot structures in proteins was denied for a long time. Here, we studied denaturation and renaturation processes of the near-infrared fluorescent probe, iRFP engineered from RpBphP2, which utilizes a heme-derived tetrapyrrole compound biliverdin as a chromophore. iRFP contains a unique figure-of-eight knot. The denaturation and renaturation curves of the iRFP apoform coincided well, suggesting its efficient refolding. However, the iRFP holoform exhibited the irreversible unfolding and aggregation, associated with the bound chromophore. The knot structure in the apoform did not prevent its subsequent binding of biliverdin, resulting in the functional iRFP holoform. We suggest that the irreversibility of protein unfolding is caused by posttranslational protein modifications, such as chromophore binding, rather than the presence of the knot. These results are important for future design of BphP-based near-infrared probes and add important features to the fundamental problem of protein folding. PMID:24628916

  11. Habitat use by Red Knots (Calidris canutus rufa): Experiments with oyster racks and reefs on the beach and intertidal of Delaware Bay, New Jersey

    NASA Astrophysics Data System (ADS)

    Burger, Joanna; Niles, Lawrence J.

    2017-07-01

    Sea level rise and increasing human activities have decreased intertidal habitat in many places in the world. The expansion of aquaculture in intertidal areas may impact birds and other organisms using these habitats, leading to questions of sustainability of both aquaculture and functioning estuarine ecosystems. Understanding the effect of oyster culture on shorebird activity, particularly on Red Knots (Calidris canutus rufa), a species on the U.S. Threatened List, is important for adaptive management and the expansion of oyster culture. In May 2013 we experimentally compared Red Knot and shorebird use of a beach section with racks and a control, and in 2016 we compared the use of sections with artificial reefs, oyster racks, and control on Delaware Bay, New Jersey (USA). The data included only times when no workers or other people were present. Censuses, conducted every 30 min throughout the day (279 censuses in 2013, 231 censuses in 2016), included the number of Red Knots and other shorebirds in each treatment section. In 2013, the total number of shorebirds was significantly higher in the rack section than in the control section, except for Red Knots and Ruddy Turnstones (Arenaria interpres) that occurred in higher numbers in the control than in the rack section. In 2016 Red Knot numbers were also significantly lower in the rack section. In 2013, the mean number of Red Knots/census was 13 for racks vs 59 for the control (P < 0.0002). In 2016, the mean number of Red Knots/census was 13 for racks and over 68 for other treatments (P < 0.0001). Treatment, date, and number of non-Knot shorebirds explained 60% (2013) and 69% (2016) of the variation in Red Knot numbers. Red Knots avoided the sections with racks while both foraging and roosting, suggesting that caution should be used before placing oyster racks in areas used for foraging by Red Knots.

  12. Changing Conceptions of Reading: Literacy Learning Instruction. Seventh Yearbook of the American Reading Forum.

    ERIC Educational Resources Information Center

    Lumpkin, Donavon, Ed.; And Others

    Articles in this yearbook contribute to a broad perspective of changing concepts of reading, each focusing attention on an area of major factors exercising current impact on reading and on the education of reading teachers. The articles and their authors are as follows: "Learning from Text" (T. Estes); "Untying the Gordian Knot" (W. Blanton and G.…

  13. SLA and the Literature Classroom: Fostering Dialogues. Issues in Language Program Direction: A Series of Annual Volumes.

    ERIC Educational Resources Information Center

    Scott, Virginia M., Ed.; Tucker, Holly, Ed.

    This monograph offers eight papers in four sections. Section 1, "Renewed Debates," includes "The Gordian Knot: Language, Literature, and Critical Thinking" (Jean Marie Schultz). Section 2, "Colleagues in Dialogue," includes "Developing Literacy and Literary Competence: Challenges for Foreign Language Departments" (Heidi Byrnes and Susanne Kord)…

  14. Changing Conceptions of Reading: Literacy Learning Instruction. Seventh Yearbook of the American Reading Forum.

    ERIC Educational Resources Information Center

    Lumpkin, Donavon, Ed.; And Others

    Articles in this yearbook contribute to a broad perspective of changing concepts of reading, each focusing attention on an area of major factors exercising current impact on reading and on the education of reading teachers. The articles and their authors are as follows: "Learning from Text" (T. Estes); "Untying the Gordian Knot" (W. Blanton and G.…

  15. Integrated management of root-knot nematode, Meloidogyne incognita infestation in tomato and grapevine.

    PubMed

    Kumari, N Swarna; Sivakumar, C V

    2005-01-01

    An integrated approach with the obligate bacterial parasite, Pasteuria penetrans and nematicides was assessed for the management of the root-knot nematode, Meloidogyne incognita infestation in tomato and grapevine. Seedlings of tomato cv. Co3 were transplanted into pots filled with sterilized soil and inoculated with nematodes (5000 juveniles/pot). The root powder of P. penetrans at 10 mg/pot was applied alone and in combination with carbofuran at 6 mg/pot. Application of P. penetrans along with carbofuran recorded lowest nematode infestation (107 nematodes/200 g soil) compared to control (325 nematodes/200 g soil). The rate of parasitization was 83.1% in the carbofuran and P. penetrans combination treatment as against 61.0% in the P. penetrans treatment only. The plant growth was also higher in the combination treatment compared to all other treatments. A field trial was carried out to assess the efficacy of P. penetrans and nematicides viz., carbofuran and phorate in the management of root-knot nematode, M. incognita infestation of grapevine cv. Muscat Hamburg. A nematode and P. penetrans infested grapevine field was selected and treatments either with carbofuran or phorate at 1 g a.i/vine was given. The observations were recorded at monthly interval. The results showed that the soil nematode population was reduced in nematicide treated plots. Suppression of nematodes was higher under phorate (117 nematodes/200 g soil) than under carbofuran (126.7 nematodes/200 g soil) treatment. The number of juveniles parasitized was also influenced by nematicides and spore load carried/juvenile with phorate being superior and the increase being 17.0 and 29.0% respectively over the control. The results of these experiment confirmed the compatibility of P. penetrans with nematicides and its biological control potential against the root-knot nematode.

  16. Meloidogyne aberrans sp. nov. (Nematoda: Meloidogynidae), a new root-knot nematode parasitizing kiwifruit in China.

    PubMed

    Tao, Ye; Xu, Chunling; Yuan, Chunfen; Wang, Honghong; Lin, Borong; Zhuo, Kan; Liao, Jinling

    2017-01-01

    High infection rates of roots of wild kiwifruit (Actinidia chinensis Planch) and soil infestation by a root-knot nematode were found in Anshun, GuiZhou Province, China. Morphology, esterase phenotype and molecular analyses confirmed that this nematode was different from previously described root-knot nematodes. In this report, the species is described, illustrated and named Meloidogyne aberrans sp. nov. The new species has a unique combination of characters. A prominent posterior protuberance, round and faint perineal pattern and a medium-length stylet (13.6-15.5 μm) characterized the females. Second-stage juveniles (J2) were characterized by a smooth lip region with distinctly protruded medial lips and a depression in outline at the oral aperture, a relatively long stylet (15.9-16.8 μm), four incisures in the lateral field and a very short, even poorly defined, hyaline tail terminus (2.2-5.5 μm). More incisures (11-15) existed in the lateral field of males, and the stylet and spicules of males were 18.2-19.6 μm and 22.7-36.8 μm long respectively. Egg masses were typically produced within the roots of kiwifruit. The new species had a rare Est phenotype, S2. Phylogenetic trees inferred from SSU, LSU D2D3, ITS, and partial coxII-16S rRNA revealed that M. aberrans sp. nov. was within the Meloidogyne clade and was distinguished from all described root-knot nematodes. Moreover, from histopathological observations, M. aberrans sp. nov. induced the formation of multinucleate giant cells.

  17. Nematicidal Effects of Silver Nanoparticles on Root-knot Nematode in Bermudagrass

    PubMed Central

    Cromwell, W. A.; Yang, Joopil; Starr, J. L.; Jo, Young-Ki

    2014-01-01

    Certain nematodes are common soilborne organisms found in turfgrass in the United States that cause significant economic damage to golf course turf. One of the most prevalent plant-parasitic nematodes infesting turfgrass are root-knot nematodes (Meloidogyne spp.). Chemical treatment options for root-knot nematodes in turfgrass are limited, and there is a need for new nematicidal active ingredients to address this problem. In this study, we evaluated the use of silver nanoparticles (AgNP) as a potential nematicide in laboratory and field experiments. AgNP was synthesized by a redox reaction of silver nitrate with sodium borohydride using 0.2% starch as a stabilizer. When J2 of M. incognita were exposed to AgNP in water at 30 to 150 μg/ml, >99% nematodes became inactive in 6 hr. When turfgrass and soil composite samples infested with M. graminis were treated with 150 μg/ml AgNP, J2 were reduced in the soil samples by 92% and 82% after 4- and 2-d exposures, respectively, in the treated compared to the nontreated soil samples. Field trials evaluating AgNP were conducted on a bermudagrass (Cynodon dactylon × C. transvaalensis) putting green infested with M. graminis. Biweekly application of 90.4 mg/m2 of AgNP improved turfgrass quality in one year and reduced gall formation in the roots in two years without phytotoxicity. The AgNP application did not significantly reduce the number of M. graminis J2 in plots during the growing season. The laboratory assays attested to the nematicidal effect of AgNP, and the field evaluation demonstrated its benefits for mitigating damage caused by root-knot nematode in bermudagrass. PMID:25275999

  18. Nematicidal Effects of Silver Nanoparticles on Root-knot Nematode in Bermudagrass.

    PubMed

    Cromwell, W A; Yang, Joopil; Starr, J L; Jo, Young-Ki

    2014-09-01

    Certain nematodes are common soilborne organisms found in turfgrass in the United States that cause significant economic damage to golf course turf. One of the most prevalent plant-parasitic nematodes infesting turfgrass are root-knot nematodes (Meloidogyne spp.). Chemical treatment options for root-knot nematodes in turfgrass are limited, and there is a need for new nematicidal active ingredients to address this problem. In this study, we evaluated the use of silver nanoparticles (AgNP) as a potential nematicide in laboratory and field experiments. AgNP was synthesized by a redox reaction of silver nitrate with sodium borohydride using 0.2% starch as a stabilizer. When J2 of M. incognita were exposed to AgNP in water at 30 to 150 μg/ml, >99% nematodes became inactive in 6 hr. When turfgrass and soil composite samples infested with M. graminis were treated with 150 μg/ml AgNP, J2 were reduced in the soil samples by 92% and 82% after 4- and 2-d exposures, respectively, in the treated compared to the nontreated soil samples. Field trials evaluating AgNP were conducted on a bermudagrass (Cynodon dactylon × C. transvaalensis) putting green infested with M. graminis. Biweekly application of 90.4 mg/m(2) of AgNP improved turfgrass quality in one year and reduced gall formation in the roots in two years without phytotoxicity. The AgNP application did not significantly reduce the number of M. graminis J2 in plots during the growing season. The laboratory assays attested to the nematicidal effect of AgNP, and the field evaluation demonstrated its benefits for mitigating damage caused by root-knot nematode in bermudagrass.

  19. Interaction between the GROWTH-REGULATING FACTOR and KNOTTED1-LIKE HOMEOBOX families of transcription factors.

    PubMed

    Kuijt, Suzanne J H; Greco, Raffaella; Agalou, Adamantia; Shao, Jingxia; 't Hoen, Corine C J; Overnäs, Elin; Osnato, Michela; Curiale, Serena; Meynard, Donaldo; van Gulik, Robert; de Faria Maraschin, Simone; Atallah, Mirna; de Kam, Rolf J; Lamers, Gerda E M; Guiderdoni, Emmanuel; Rossini, Laura; Meijer, Annemarie H; Ouwerkerk, Pieter B F

    2014-04-01

    KNOTTED1-LIKE HOMEOBOX (KNOX) genes are important regulators of meristem function, and a complex network of transcription factors ensures tight control of their expression. Here, we show that members of the GROWTH-REGULATING FACTOR (GRF) family act as players in this network. A yeast (Saccharomyces cerevisiae) one-hybrid screen with the upstream sequence of the KNOX gene Oskn2 from rice (Oryza sativa) resulted in isolation of OsGRF3 and OsGRF10. Specific binding to a region in the untranslated leader sequence of Oskn2 was confirmed by yeast and in vitro binding assays. ProOskn2:β-glucuronidase reporter expression was down-regulated by OsGRF3 and OsGRF10 in vivo, suggesting that these proteins function as transcriptional repressors. Likewise, we found that the GRF protein BGRF1 from barley (Hordeum vulgare) could act as a repressor on an intron sequence in the KNOX gene Hooded/Barley Knotted3 (Bkn3) and that AtGRF4, AtGRF5, and AtGRF6 from Arabidopsis (Arabidopsis thaliana) could repress KNOTTED-LIKE FROM ARABIDOPSIS THALIANA2 (KNAT2) promoter activity. OsGRF overexpression phenotypes in rice were consistent with aberrant meristematic activity, showing reduced formation of tillers and internodes and extensive adventitious root/shoot formation on nodes. These effects were associated with down-regulation of endogenous Oskn2 expression by OsGRF3. Conversely, RNA interference silencing of OsGRF3, OsGRF4, and OsGRF5 resulted in dwarfism, delayed growth and inflorescence formation, and up-regulation of Oskn2. These data demonstrate conserved interactions between the GRF and KNOX families of transcription factors in both monocot and dicot plants.

  20. Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways

    PubMed Central

    Mohazab, Ali R.; Plotkin, Steven S.

    2013-01-01

    We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the minimal uncrossing cost that would have been required to avoid such events. A depth-first tree search algorithm is applied to find minimal transformations to fold , , , and knotted proteins. In all cases, the extra uncrossing/non-crossing distance is a small fraction of the total distance travelled by a ghost chain. Different structural classes may be distinguished by the amount of extra uncrossing distance, and the effectiveness of such discrimination is compared with other order parameters. It was seen that non-crossing distance over chain length provided the best discrimination between structural and kinetic classes. The scaling of non-crossing distance with chain length implies an inevitable crossover to entanglement-dominated folding mechanisms for sufficiently long chains. We further quantify the minimal folding pathways by collecting the sequence of uncrossing moves, which generally involve leg, loop, and elbow-like uncrossing moves, and rendering the collection of these moves over the unfolded ensemble as a multiple-transformation “alignment”. The consensus minimal pathway is constructed and shown schematically for representative cases of an , , and knotted protein. An overlap parameter is defined between pathways; we find that proteins have minimal overlap indicating diverse folding pathways, knotted proteins are highly constrained to follow a dominant pathway, and proteins are somewhere in between. Thus we have shown how topological chain constraints can induce dominant pathway mechanisms in protein folding. PMID:23365638

  1. Management of root-knot nematode in tomato Lycopersicon esculentum, Mill, with biogas slurry.

    PubMed

    Jothi, G; Pugalendhi, S; Poornima, K; Rajendran, G

    2003-09-01

    The effect of biogas slurry application on the severity of root-knot nematode, Meloidogyne incognita, attack on tomato cv. Co-1, was tested in the green house with two levels of biogas slurry: 5% and 10% (w/w) added to soil. Both the number (3 fruits/plant) and fruit yield (35.2 g/plant) of tomato increased significantly with 10% (w/w) biogas slurry. The plants amended with biogas slurry put up more vegetative growth and tended to flower and fruit much earlier than did those of the control. The nematode population in the soil decreased thus decreasing the severity of nematode attack.

  2. Dynamic Patterns and Self-Knotting of a Driven Hanging Chain

    NASA Astrophysics Data System (ADS)

    Belmonte, Andrew; Shelley, Michael J.; Eldakar, Shaden T.; Wiggins, Chris H.

    2001-09-01

    When shaken vertically, a hanging chain displays a startling variety of distinct behaviors. We find experimentally that instabilities occur in tonguelike bands of parameter space, to swinging or rotating pendular motion, or to chaotic states. Mathematically, the dynamics are described by a nonlinear wave equation. A linear stability analysis predicts instabilities within the well-known resonance tongues; their boundaries agree very well with experiment. Full simulations of the 3D dynamics reproduce and elucidate many aspects of the experiment. The chain is also observed to tie knots in itself, some quite complex. This is beyond the reach of the current analysis and simulations.

  3. All-fiber magnetic-field sensor based on microfiber knot resonator and magnetic fluid.

    PubMed

    Li, Xianli; Ding, Hui

    2012-12-15

    All-fiber magnetic-field sensor based on a device consisting of a microfiber knot resonator and magnetic fluid is proposed for the first time in this Letter. Sensor principles and package technology are introduced in detail. Experimental results show that the resonance wavelength of the proposed sensor regularly varies with changes to the applied magnetic field. When the magnetic field is increased to 600 Oe, the wavelength shift reaches nearly 100 pm. Moreover, the sensor responding to the 50 Hz alternating magnetic field is also experimentally investigated, and a minimal detectable magnetic-field strength of 10 Oe is successfully achieved.

  4. A sequential method for spline approximation with variable knots. [recursive piecewise polynomial signal processing

    NASA Technical Reports Server (NTRS)

    Mier Muth, A. M.; Willsky, A. S.

    1978-01-01

    In this paper we describe a method for approximating a waveform by a spline. The method is quite efficient, as the data are processed sequentially. The basis of the approach is to view the approximation problem as a question of estimation of a polynomial in noise, with the possibility of abrupt changes in the highest derivative. This allows us to bring several powerful statistical signal processing tools into play. We also present some initial results on the application of our technique to the processing of electrocardiograms, where the knot locations themselves may be some of the most important pieces of diagnostic information.

  5. Effect of tea dust residues to control root-knot nematode of tomato.

    PubMed

    Fathi, G H; Eshtiaghi, H; Kheiri, A; Okhovat, M

    2004-01-01

    In this research, control of tomato root- knot nematode (Meloidogyne incognita) was conducted using tea dust residues at different rates. First, the species and race of nematode were identified by employing diagnostic keys. Then, with 5 replications in complete randomized design. Tea dust residues were used at 9 treatments (0, 5, 10, 15, 20, 25, 30, 35 and 40 g/kg of soil). Statistical analysis on mean treatments rates showed that treatment with 25 g/kg soil economically was effective in growth rates and reduction in gall index.

  6. The classical and quantum mechanics of a particle on a knot

    SciTech Connect

    Sreedhar, V.V.

    2015-08-15

    A free particle is constrained to move on a knot obtained by winding around a putative torus. The classical equations of motion for this system are solved in a closed form. The exact energy eigenspectrum, in the thin torus limit, is obtained by mapping the time-independent Schrödinger equation to the Mathieu equation. In the general case, the eigenvalue problem is described by the Hill equation. Finite-thickness corrections are incorporated perturbatively by truncating the Hill equation. Comparisons and contrasts between this problem and the well-studied problem of a particle on a circle (planar rigid rotor) are performed throughout.

  7. Video self-assessment of basic suturing and knot tying skills by novice trainees.

    PubMed

    Hu, Yinin; Tiemann, Debbie; Michael Brunt, L

    2013-01-01

    Self-assessment is important to learning but few studies have utilized video self-assessment of basic surgical skills. We compared a video self-assessment of suturing and knot tying skills by novice trainees to the assessment by a senior attending surgeon. Sixteen senior medical students and 7 beginner surgical interns were video-recorded while performing five suturing and knot tying tasks. All videos were analyzed using an objective structured assessment of technical skills (OSATS) metrics (1-5 scale; 1 = novice, 5 = expert). Video self-assessment was carried out within 4 weeks of an instructional session and subsequently by one senior surgery instructor (blinded to the individual). Both a Global score and total combined OSATS scores were analyzed. Total possible OSATS scores were: interrupted suture-30, subcuticular closure-30, one and two-handed knot tying-25 each, tying in a restricted space 20; maximum combined score-130 points). Confidence levels in performing the tasks pre-test and the value of video self-assessment were rated on a 1-5 Likert scale (1 = low and 5 = high). Data are mean±SD and statistical significance was evaluated using Friedman's test. Self-assessment scoring was significantly higher than the assessment by a senior instructor for three tasks by global score and all five tasks by combined OSATS score (self-assessment 71.8±16.7 vs attending assessment 56.7±11.0, p = 0.007). Mean self-assessment Global scores ranged from 2.5 to 2.8 for all tasks performed compared to 1.8-2.3 for attending surgeon assessment (p<0.05). Confidence levels demonstrated no correlation to performance speed or proficiency. The video self-assessment was rated as a highly valuable (mean 4.3±0.8) component to skills training. Novice trainees over-estimate their basic technical skills performance compared to the assessment by a senior surgeon. Video self-assessment may be a valuable addition to a pre-residency and surgical internship preparatory curriculum in basic

  8. Spectral characteristics of the microfiber MZ interferometer with a knot resonator

    NASA Astrophysics Data System (ADS)

    Liao, Yipeng; Wang, Jing; Wang, Shanshan; Yang, Hongjuan; Wang, Xin

    2017-04-01

    This paper investigates the transmission spectral characteristics of microfiber MZ interferometer with a knot resonator (MZIKR). The MZIKR exhibits a combined effect of resonance and interference in its transmission spectra. By adjusting the coupling coefficients to convert the relative strength of resonance and interference, the transmission spectra show various shapes, mainly reflected in the direction of fringes. The obtained upward fringe exhibits an extinction ratio of 17 dB and a FWHM of 0.3 nm. The tunable transmission spectrum demonstrated here may have great potential for narrow-band filtering, and the coexisting resonance and interference effect also allows the MZIKR to perform dual-parameters sensing.

  9. Understanding the light curves of the HST-1 knot in M87 with internal relativistic shock waves along its jet

    NASA Astrophysics Data System (ADS)

    Coronado, Y.; López-Corona, O.; Mendoza, S.

    2016-10-01

    Knots or blobs observed in astrophysical jets are commonly interpreted as shock waves moving along them. Long-time observations of the HST-1 knot inside the jet of the galaxy M87 have produced detailed multiwavelength light curves. In this paper, we model these light curves using the semi-analytical approach developed by Mendoza et al. This model was developed to account for the light curves produced by working surfaces (blobs) moving along relativistic jets. These working surfaces are generated by periodic oscillations of the injected flow velocity and mass ejection rates at the base of the jet. Using genetic algorithms to fit the parameters of the model, we are able to explain the outbursts observed in the light curves of the HST-1 knot with an accuracy greater than a 2σ statistical confidence level.

  10. 14 CFR 61.327 - How do I obtain privileges to operate a light-sport aircraft that has a VH greater than 87 knots...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... light-sport aircraft that has a VH greater than 87 knots CAS? 61.327 Section 61.327 Aeronautics and...: PILOTS, FLIGHT INSTRUCTORS, AND GROUND INSTRUCTORS Sport Pilots § 61.327 How do I obtain privileges to operate a light-sport aircraft that has a VH greater than 87 knots CAS? If you hold a sport pilot...

  11. Comparison of Veterinary Student Ability to Learn 1-Handed and 2-Handed Techniques for Surgical Knot Tying.

    PubMed

    Thomas, Angharad C J; Hayes, Graham M; Demetriou, Jackie L

    2015-08-01

    To determine which type of surgical hand-tie trainee surgeons learn most readily in a laboratory setting, using a combination of audiovisual demonstration and one-on-one teaching. Randomized controlled learning trial. Year 4 veterinary students in their 1st year of clinical training (n = 58). Veterinary students entering clinical rotations were randomly allocated to 2 learning groups: 1-handed (28 students) or 2-handed (30 students) surgical ties. Knot tying technique was taught followed by three 15-minute practice sessions with student progress recorded by filming each student tying a square knot (2 throws). All 3 knot tying attempts were scored for technique and knot formation. Data on potential confounding factors between groups, including age and gender, were recorded. There were no significant differences between group scores for each attempt (1st attempt P = .5; 2nd P = .2; 3rd P = .19). Initially, scores indicated more rapid learning in the 1-handed group but fewer individuals achieved a perfect technique and knot after 60 minutes of learning (29/30 for 2-handed; 24/28 for 1-handed group). The 1-handed group was the most error-prone (after 45 minutes P < .01; after 60 min P < .01). Over 95% of students in the 2-handed group performed the technique and knot perfectly after 60 minutes learning time; were significantly less error-prone and fewer students continued to make corrected errors after 60 minutes. This evidence indicates that the 2-handed technique allows students to achieve success in a manageable teaching time. © Copyright 2015 by The American College of Veterinary Surgeons.

  12. Novel single-loop and double-loop knot stitch in comparison with the modified Mason-Allen stitch for rotator cuff repair.

    PubMed

    Frosch, Stephan; Buchhorn, Gottfried; Hoffmann, Anja; Balcarek, Peter; Schüttrumpf, Jan Philipp; August, Florian; Stürmer, Klaus Michael; Walde, Hans Joachim; Walde, Tim Alexander

    2015-05-01

    In rotator cuff repair, strong and long-lasting suturing techniques that do not require additional implants are needed. This study examines the ultimate load to failure and the Young's modulus at the suture-tendon interface for a novel single-loop knot stitch and double-loop knot stitch. These values are compared to those of the modified Mason-Allen stitch. Twenty-four infraspinatus muscles with tendons were dissected from porcine shoulders (twelve Goettingen minipigs). The preparations were randomly allocated to three groups of eight samples. Load-to-failure testing of the single-loop knot stitch, the double-loop knot stitch and the mMAS were performed using a Zwick 1446 universal testing machine (Zwick-Roell AG, Ulm, Germany). The highest ultimate load to failure for the three techniques occurred with the double-loop knot stitch with a median value of 382.2 N (range 291.8-454.2 N). These values were significantly higher than those of the single-loop knot stitch, which had a median value of 259.5 N (range 139.6-366.3 N) and the modified Mason-Allen stitch, which had a median value of 309.3 N (range 84.55-382.9 N). The values of the single-loop knot stitch and the modified Mason-Allen stitch did not differ significantly. Regarding the Young's modulus, no significant differences were found between the double-loop knot stitch with a median value of 496.02 N/mm² (range 400.4-572.6 N/mm²) and the modified Mason-Allen stitch with 498.5 N/mm² (range 375.5-749.2 N/mm²) with respect to the stiffness of the suture-tendon complex. The median value for the Young's modulus of the single-loop knot stitch of 392.1 N/mm² (range 285.7-510.6 N/mm²) was significantly lower than those of the double-loop knot stitch and modified Mason-Allen stitch. This in vitro animal study demonstrated that both the single-loop knot stitch and the double-loop knot stitch have excellent ultimate load-to-failure properties when used for rotator cuff repair. The introduced single-loop knot stitch

  13. Knotting of percutaneous endoscopic jejunostomy feeding tubes in two patients with Parkinson's disease and continuous Duodopa® treatment.

    PubMed

    Krones, E; Zollner, G; Petritsch, W

    2012-02-01

    Continuous intraduodenal infusion of levodopa/carbidopa (Duodopa®) via PEJ tubes is increasingly used in patients with advanced stages of Parkinson's disease. Tube-related complications such as kinking or coiling have been frequently reported. We herein describe two cases of tube dysfunction in patients with Parkinson's disease and continuous Duodopa® treatment due to knotting of the distal end of the tube. The mechanisms of knotting are unclear although a causative role of impaired gastrointestinal motility either by Parkinson's disease itself or Duodopa® treatment might be suspected.

  14. Ethylene signaling pathway modulates attractiveness of host roots to the root-knot nematode Meloidogyne hapla.

    PubMed

    Fudali, Sylwia L; Wang, Congli; Williamson, Valerie M

    2013-01-01

    Infective juveniles of the root-knot nematode Meloidogyne hapla are attracted to the zone of elongation of roots where they invade the host but little is known about what directs the nematode to this region of the root. We found that Arabidopsis roots exposed to an ethylene (ET)-synthesis inhibitor attracted significantly more nematodes than control roots and that ET-overproducing mutants were less attractive. Arabidopsis seedlings with ET-insensitive mutations were generally more attractive whereas mutations resulting in constitutive signaling were less attractive. Roots of the ET-insensitive tomato mutant Never ripe (Nr) were also more attractive, indicating that ET signaling also modulated attraction of root-knot nematodes to this host. ET-insensitive mutants have longer roots due to reduced basipetal auxin transport. However, assessments of Arabidopsis mutants that differ in various aspects of the ET response suggest that components of the ET-signaling pathway directly affecting root length are not responsible for modulating root attractiveness and that other components of downstream signaling result in changes in levels of attractants or repellents for M. hapla. These signals may aid in directing this pathogen to an appropriate host and invasion site for completing its life cycle.

  15. Transcriptional reprogramming by root knot and migratory nematode infection in rice.

    PubMed

    Kyndt, Tina; Denil, Simon; Haegeman, Annelies; Trooskens, Geert; Bauters, Lander; Van Criekinge, Wim; De Meyer, Tim; Gheysen, Godelieve

    2012-11-01

    Rice is one of the most important staple crops worldwide, but its yield is compromised by different pathogens, including plant-parasitic nematodes. In this study we have characterized specific and general responses of rice (Oryza sativa) roots challenged with two endoparasitic nematodes with very different modes of action. Local transcriptional changes in rice roots upon root knot (Meloidogyne graminicola) and root rot nematode (RRN, Hirschmanniella oryzae) infection were studied at two time points (3 and 7 d after infection, dai), using mRNA-seq. Our results confirm that root knot nematodes (RKNs), which feed as sedentary endoparasites, stimulate metabolic pathways in the root, and enhance nutrient transport towards the induced root gall. The migratory RRNs, on the other hand, induce programmed cell death and oxidative stress, and obstruct the normal metabolic activity of the root. While RRN infection causes up-regulation of biotic stress-related genes early in the infection, the sedentary RKNs suppress the local defense pathways (e.g. salicylic acid and ethylene pathways). Interestingly, hormone pathways mainly involved in plant development were strongly induced (gibberellin) or repressed (cytokinin) at 3 dai. These results uncover previously unrecognized nematode-induced expression profiles related to their specific infection strategy.

  16. The Origin of the Iron-rich Knot in Tycho’s Supernova Remnant

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Hiroya; Hughes, John P.; Badenes, Carles; Bravo, Eduardo; Seitenzahl, Ivo R.; Martínez-Rodríguez, Héctor; Park, Sangwook; Petre, Robert

    2017-01-01

    X-ray observations of supernova remnants (SNRs) allow us to investigate the chemical inhomogeneity of ejecta, offering unique insight into the nucleosynthesis in supernova explosions. Here we present detailed imaging and spectroscopic studies of the “Fe knot” located along the eastern rim of the Type Ia SNR Tycho (SN 1572) using Suzaku and Chandra long-exposure data. Surprisingly, the Suzaku spectrum of this knot shows no emission from Cr, Mn, or Ni, which is unusual for the Fe-rich regions in this SNR. Within the framework of the canonical delayed-detonation models for SN Ia, the observed mass ratios {M}{Cr}/{M}{Fe}< 0.023, {M}{Mn}/{M}{Fe}< 0.012, and {M}{Ni}/{M}{Fe}< 0.029 (at 90% confidence) can only be achieved for a peak temperature of (5.3–5.7) × {10}9 K and a neutron excess of ≲ 2.0× {10}-3. These constraints rule out the deep, dense core of a Chandrasekhar-mass white dwarf as the origin of the Fe knot and favor either incomplete Si burning or an α-rich freeze-out regime, probably close to the boundary. An explosive He burning regime is a possible alternative, although this hypothesis is in conflict with the main properties of this SNR.

  17. Effect of Mulch Surface Color on Root-knot of Tomato Grown in Simulated Planting Beds.

    PubMed

    Fortnum, B A; Kasperbauer, M J; Decoteau, D R

    2000-03-01

    The effect of different-colored polyethylene mulches on quantity and spectra of reflected light, plant morphology, and root-knot disease was studied in tomato (Lycopersicon esculentum) grown in simulated planting beds. Tomato plants were inoculated with Meloidogyne incognita at initial populations (Pi) of 0, 1,000, 10,000, or 50,000 eggs/plant, and grown in a greenhouse for 50 days over white, red, or black mulch. Soil temperature was kept constant among the mulch treatments by placing an insulation barrier between the colored mulch and the soil surface. Soil temperature varied less than 0.5 degrees C between soil chambers at solar noon. Tomatoes grown over white mulch received more reflected photosynthetic light and had greater shoot weights (27%), root weights (32%), and leaf area (20%) than plants grown over black mulch. Plants grown over red mulch received a higher far-red-to-red ratio in the reflected light. Mulch color altered the plant's response to root-knot nematode infection by changing the distribution of mass in axillary shoots. At high Pi, axillary leaf area and leaf weight were greater in tomato grown over white mulch than when grown over red mulch. The root-gall index was lower for plants grown over white mulch than similar plants grown over red mulch.

  18. Effect of Mulch Surface Color on Root-knot of Tomato Grown in Simulated Planting Beds

    PubMed Central

    Fortnum, B. A.; Kasperbauer, M. J.; Decoteau, D. R.

    2000-01-01

    The effect of different-colored polyethylene mulches on quantity and spectra of reflected light, plant morphology, and root-knot disease was studied in tomato (Lycopersicon esculentum) grown in simulated planting beds. Tomato plants were inoculated with Meloidogyne incognita at initial populations (Pi) of 0, 1,000, 10,000, or 50,000 eggs/plant, and grown in a greenhouse for 50 days over white, red, or black mulch. Soil temperature was kept constant among the mulch treatments by placing an insulation barrier between the colored mulch and the soil surface. Soil temperature varied less than 0.5 °C between soil chambers at solar noon. Tomatoes grown over white mulch received more reflected photosynthetic light and had greater shoot weights (27%), root weights (32%), and leaf area (20%) than plants grown over black mulch. Plants grown over red mulch received a higher far-red-to-red ratio in the reflected light. Mulch color altered the plant's response to root-knot nematode infection by changing the distribution of mass in axillary shoots. At high Pi, axillary leaf area and leaf weight were greater in tomato grown over white mulch than when grown over red mulch. The root-gall index was lower for plants grown over white mulch than similar plants grown over red mulch. PMID:19270954

  19. Spherical DCB-spline surfaces with hierarchical and adaptive knot insertion.

    PubMed

    Cao, Juan; Li, Xin; Chen, Zhonggui; Qin, Hong

    2012-08-01

    This paper develops a novel surface fitting scheme for automatically reconstructing a genus-0 object into a continuous parametric spline surface. A key contribution for making such a fitting method both practical and accurate is our spherical generalization of the Delaunay configuration B-spline (DCB-spline), a new non-tensor-product spline. In this framework, we efficiently compute Delaunay configurations on sphere by the union of two planar Delaunay configurations. Also, we develop a hierarchical and adaptive method that progressively improves the fitting quality by new knot-insertion strategies guided by surface geometry and fitting error. Within our framework, a genus-0 model can be converted to a single spherical spline representation whose root mean square error is tightly bounded within a user-specified tolerance. The reconstructed continuous representation has many attractive properties such as global smoothness and no auxiliary knots. We conduct several experiments to demonstrate the efficacy of our new approach for reverse engineering and shape modeling.

  20. Helicity conservation by flow across scales in reconnecting vortex links and knots

    PubMed Central

    Scheeler, Martin W.; Kleckner, Dustin; Kindlmann, Gordon L.; Irvine, William T. M.

    2014-01-01

    The conjecture that helicity (or knottedness) is a fundamental conserved quantity has a rich history in fluid mechanics, but the nature of this conservation in the presence of dissipation has proven difficult to resolve. Making use of recent advances, we create vortex knots and links in viscous fluids and simulated superfluids and track their geometry through topology-changing reconnections. We find that the reassociation of vortex lines through a reconnection enables the transfer of helicity from links and knots to helical coils. This process is remarkably efficient, owing to the antiparallel orientation spontaneously adopted by the reconnecting vortices. Using a new method for quantifying the spatial helicity spectrum, we find that the reconnection process can be viewed as transferring helicity between scales, rather than dissipating it. We also infer the presence of geometric deformations that convert helical coils into even smaller scale twist, where it may ultimately be dissipated. Our results suggest that helicity conservation plays an important role in fluids and related fields, even in the presence of dissipation. PMID:25326419