bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk of bleeding after thyroid surgery: matched pairs analysis
Authors: Morton R P , Mak V , Moss D , Ahmad Z , Sevao J
Published: July 2011

Objective:

To identify those patients most at risk of developing a compressive post-operative haematoma following thyroid surgery.

Method:

Retrospective analysis of patients undergoing thyroid surgery. Factors associated with the group of patients who developed a post-operative haematoma were examined using a matched pairs, case–control design.

Results:

Following 355 thyroid operations, seven patients developed a post-operative haematoma requiring return to the operating theatre for bleeding control. A post-operative systolic blood pressure of greater than 150 mmHg, in the post-anaesthetic care unit, was the major significant factor identified by regression analysis (p = 0.002). Current smoking status was also a significant factor (p = 0.04).

Conclusion:

In our facility, a post-anaesthetic systolic blood pressure in excess of 150 mmHg was associated with an increased risk of haemorrhage following thyroid surgery.
Continuum simulations of biomembrane dynamics and the importance of hydrodynamic effects
Authors: Brown Frank L. H.
Published: July 2011

Traditional particle-based simulation strategies are impractical for the study of lipid bilayers and biological membranes over the longest length and time scales (microns, seconds and longer) relevant to cellular biology. Continuum-based models developed within the frameworks of elasticity theory, fluid dynamics and statistical mechanics provide a framework for studying membrane biophysics over a range of mesoscopic to macroscopic length and time regimes, but the application of such ideas to simulation studies has occurred only relatively recently. We review some of our efforts in this direction with emphasis on the dynamics in model membrane systems. Several examples are presented that highlight the prominent role of hydrodynamics in membrane dynamics and we argue that careful consideration of fluid dynamics is key to understanding membrane biophysics at the cellular scale.
The Value and Valuation of Maritime Cultural Heritage
Authors: Claesson Stefan
Published: July 2011

Maritime cultural heritage is made up of finite and nonrenewable cultural resources including coastal or submerged prehistoric and indigenous archaeological sites and landscapes, historic waterfront structures, the remnants of seagoing vessels, and the maritime traditions and lifeways of the past and present. To date, evaluative tools used to assess the social and economic “value” of this heritage are extremely limited, the lack of which often results in the loss of maritime cultural resources and unrealized socioeconomic opportunities. Market and nonmarket valuations, derived from ecological economics and ecosystem assessments, are viable techniques that may be integrated into existing U.S. environmental and historic preservation regulatory procedures to support resource significance determinations. In doing so, decision-making regarding maritime cultural heritage can include assessments of the short- and long-term trade-offs of human actions, and can examine the socioeconomic costs and benefits of heritage conservation projects.
Formal proofs for theoretical properties of Newton's method
Authors: PAŞCA IOANA
Published: July 2011

We discuss a formal development for the certification of Newton's method. We address several issues encountered in the formal study of numerical algorithms: developing the necessary libraries for our proofs, adapting paper proofs to suit the features of a proof assistant and designing new proofs based on the existing ones to deal with optimisations of the method. We start from Kantorovitch's Theorem, which gives the convergence of Newton's method in the case of a system of equations. To formalise this proof inside the proof assistant Coq, we first need to code the necessary concepts from multivariate analysis. We also prove that rounding at each step in Newton's method still yields a convergent process with an accurate correlation between the precision of the input and that of the result. This proof is based on Kantorovitch's Theorem, but is an original result. An algorithm including rounding is a more accurate model for computations with Newton's method in practice.
Anatomic biventricular repair by intraatrial and intraventricular re-routing in patients with left isomerism
Authors: Uemura Hideki , Yagihara Toshikatsu , Kawahira Youichi , Yoshikawa Yoshiro
Published: July 2011

Objective: To determine the efficacy of anatomic biventricular repair by a combination of intraatrial and intraventricular re-routing in patients with isomerism of the left atrial appendages.Methods: Anatomic biventricular repair by means of combined intraratrial and intraventricular re-routing was achieved in 5 of the 63 patients with left isomerism in whom we attempted a definitive surgical procedure. The inferior caval vein was interrupted in 3. The Mustard procedure was chosen for intraatrial redirection of blood in 4, and the Senning procedure in the other. Intraventricular re-routing was carried out via a right ventriculotomy in all patients, using an external conduit to reconstruct the morphologically right ventricular outflow tract.Results: One patient died one month after the procedure because of low cardiac output and bronchial bleeding. Obstruction across the superior caval venous channel occurred after the Senning procedure in this particular patient, related to the interrupted inferior caval vein draining via the azygous vein. The other 4 patients are currently doing well. Postoperative catheterization showed excellent cardiac performance, with no obstruction across the venous channels or the ventricular outflow tracts in these 4. No episode of significant archythmia has been noted, all patients having a regular atrial rhythm, although the P wave vector was unusual in each patient. Reoperation has been needed thus far in one patient, 128 months after the initial repair, because of obstruction of the external conduit.Conclusion: With precise recognition of the morphologic features, a combination of intraatrial and intraventricular re-routing can successfully be established in patients with isomeric left atrial appendages, with functional results in the intermediate term being reasonable.
Long-term assessment and serial evaluation of cardiorespiratory exercise performance and cardiac function in patients with atrial switch operation for complete transposition
Authors: Reybrouck Tony , Mertens Luc , Brown Steven , Eyskens Benedicte , Daenen Willem , Gewillig Marc
Published: July 2011

Background: At present, a considerable number of patients survive who underwent an atrial switch operation for correction of complete transposition. Our study aimed to assess their long-term exercise performance and the serial evolution of cardiac function.Methods: We studied 22 patients 5 to 17 years after an atrial switch operation, and followed them serially for 3.5 ± 2 years after the first evaluation. Cardiorespiratory exercise function was assessed by analysis of gas exhange and by determination of the ventilatory anaerobic threshold. Echocardiography was performed on all evaluations.Results: All patients were in Class I of the classification of the New York Heart Association at all assessments. Ventilatory anaerobic threshold, however, was significantly lower than normal. It averaged 77.9% ± 13.7 of the normal mean value at the initial evaluation, and remained stable when re-evaluated later (76.2 ± 13.7%). At the initial study, the increase in oxygen uptake during graded exercise was below the 95% confidence limit in 6 of the patients, and was below this level in 10 patients at re-assessment. The subnormal values for oxygen uptake during submaximal exercise were associated with moderate to severe haemodynamic dysfunction. At echocardiography, 15 of 17 patients studied twice had mild to moderate right ventricular dilation and tricuspidregurgiation, which remained virtually the same at reasssesment. A stable sinus rhythm was initially present in 17 patients, and persisted in 15 patients during follow-up.Conclusion: At medium term follow-up, cardiorespiratory exercise performance remains stable in patients after atrial switch repair. Serial exercise testing appears useful, because in individual patients in the present study, a decreasing exercise tolerance correlated with development of haemodynamic sequels.
Outcomes of transcatheter balloon angioplasty of obstruction in the neo-aortic arch after the Norwood operation
Authors: Soongswang Jarupim , McCrindle Brian W. , Jones Thomas K. , Vincent Robert N. , Hsu Daphne T. , Kuhn Michael A. , Moskowitz William B. , Cheatham John R. , Kholwadwala Dipak H. , Benson Lee N. , Nykanen David G.
Published: July 2011

Obstruction of the reconstructed aortic arch, or the neoaortic arch, is now known to be an important factor increasing mortality after the Norwood operation for hypoplastic left heart syndrome. Transcatheter balloon angioplasty has been shown to provide effective relief of both native aortic coarctation and obstructions of the aortic arch occurring subsequent to therapeutic intervention. We sought to determine the outcomes of balloon angioplasty used as an initial treatment for obstruction of the neoaortic arch occurring after the Norwood operation. We gathered the characteristics of 58 patients with such obstruction from 8 institutions, noting procedural factors and outcomes of initial balloon dilation. Obstruction occurred at a median interval of 4 months, with a range from 1.5 months to 6.3 years, after a Norwood operation. Ventricular dysfunction was present before dilation in 13 patients. Mean peak to peak systolic pressure gradients were acutely reduced from 31±20 mm Hg to 6±9 mmHg (p<0.001), with outcome subjectively judged to be successful in 89%- Three patients with pre-existing ventricular dysfunction died within 48 hours of dilation. There were 10 additional deaths during the period of followup, with Kaplan Meier estimates of survival after intervention of 87% at 1 month, 77% at 12 months, and 72% after 15 months. In addition, 9 patients required re-intervention during the period of follow-up, with Kaplan Meier estimates of freedom from re-intervention after dilation of 87% at 6 months, 78% at 12 months and 74% after 18 months. Although transcatheter dilation of neoaortic arch obstructions after Norwood operation is successful, there is a high risk of re-intervention and ongoing mortality in this subgroup of patients. Close follow-up is recommended.
The spectrum of fetal cardiac malformations
Authors: Cook Andrew C.
Published: July 2011

Increasingly, paediatric cardiologists are called upon to diagnose cardiac malformations prenatally. In the main, the types of malformation seen during fetal life will be similar to those documented postnatally, but the frequency with which they are encountered, as well as the views that can be used for diagnosis, will be different. This review aims to describe the anatomic spectrum of malformations seen in 917 fetal hearts examined consecutively following prenatal diagnosis. The distribution of anomalies is illustrated in terms of a simple sweep through the fetal thorax passing from the four-chamber plane to the outflow tracts, and then to more cranial views of the mediastinum. Two-thirds of the anomalies described would have been detectable in the four-chamber plane. Some, such as tricuspid valvar abnormalities, will alter the normal appearances of the four-chambers dramatically. In terms of the overall spectrum, however, such obvious abnormalities only form a minor part of the total number. Others, such as atrioventricular septal defect, will often require closer inspection of intracardiac anatomy, but will make up a large proportion of the entire cohort. Up to one third of the anomalies in the series would have required views more cranial to the four-chamber plane of section. In these, it would have been necessary to examine the nature of the left ventricular outflow tract, the crossing of the two outflows, or else the arterial arches in order to secure detection. In the fetus, these and other planes must be considered by the echocardiographer in order completely to detect and document the entire spectrum of cardiac abnormalities likely to be encountered.
The left-sided aortic arch in humans, viewed as the end-result of natural selection during vertebrate evolution
Authors: Muster Alexander J. , Idriss Rachid F. , Backer Carl L.
Published: July 2011

At some point during vertebrate evolution from species dwelling in water to living on land, the ancestral double or right aortic arches became single and left-sided in mammals, including humans, as the result of synchronous developments in cardiovascular and respiratory embryogenesis. Since left-sided aortic arches are unique to mammals, hemodynamics related to the placenta, specifically the requirement for a large arterial duct connecting to the descending aorta, may have led to switching from the right-sided to the left-sided arch. Additionally, development of a trilobar right lung and its bronchial tree, also unique to mammalian evolution, restricted the space above the high eparterial bronchus to a single large vessel. Consequently, mammals that mutated to the left-sided aortic arch avoided respiratory, digestive or circulatory problems that are often associated with an isolated right-sided aortic arch – something which could be considered a successful mistake. Due to natural selection, and survival of the fittest, the left-sided arch became the norm in mammals.

In congenital cardiac malformations where a large arterial duct is not mandatory in fetal life, as in Fallot's tetralogy or common arterial trunk, a right-sided aortic arch continues to occur, perhaps as an atavistic reversion to the anatomy seen in ancestral vertebrates.
Exploring the potential for sustainable weed control with integrated rice−fish culture for smallholder irrigated rice agriculture in the Maranhão Lowlands of Amazonia
Authors: de Sousa Aurea Maria Barbosa , Santos Raimundo Reginaldo Soares , Moraes Flávio Henrique Reis , Gehring Christoph
Published: July 2011

Combining existing traditions of rice and of fish in an integrated rice−fish (IRF) culture is a promising strategy for sustainably increasing land productivity and diminishing the need for external inputs in smallholder agriculture of Amazonia. This study evaluates the potential of IRF for weed control in irrigated rice production. It was conducted from August 18 to December 5, 2008 in the Maranhão lowlands in the eastern periphery of Amazonia. We compared weed communities in four 3-year-old IRF and four adjacent ‘conventional’ irrigated rice (CIR) fields at 20 and 40 days after transplanting (DAT), at the mid-vegetative stage and at the onset of flowering, which served as an indicator of potential grain yield. Rice–fish fields contained differing mixtures of herbivore and omnivore fish species totaling 4000 fish per ha or 1.7 fish per m3. Total weed density was reduced in the IRF system, particularly early in the season, the most critical stage for rice development. The integration of fish into irrigated rice cultivation affected weed species composition, with fish-weeding preferentially reducing monocotyledonous Cyperaceae, one of the more aggressive and problematic weed families in this region. Monocot weed density was negatively correlated with rice aboveground biomass at 40 DAT rice. Although floristic similarity between IRF and CIR fields was low, the impacts of IRF on weed species diversity and weed species richness were not significant. Thus, IRF was not associated with a simplification of the weed community. We conclude that fish-weeding may substitute for manual or chemical weeding in irrigated rice agriculture, an important consideration for resource-poor smallholder agriculture in environmentally sensitive riverine or delta areas of eastern Amazonia.
Earth and space science funding at risk
Authors: Buhrman Joan
Published: July 2011

With debt ceiling deadlines quickly approaching, U.S. lawmakers are still markedly divided over how to address the nation's economic and budgetary troubles. AGU is closely monitoring these debates and any cuts directed at funding for scientific research and development. Cuts beyond the already reduced levels from the current fiscal year 2011 continuing resolution have the potential to be devastating not only for the scientific community but also for the health, safety, and welfare of the public and America's economic competitiveness. It is not clear how the current proposals would apply to cutting scientific research and development, but it is very likely that federal funding levels for fiscal year 2012 will be even lower than those seen in 2011, a trend that could continue for a number of years. The Obama administration and congressional leadership are reported to be negotiating up to $4 trillion in reduced expenditures, with cuts of at least $1.1 trillion being made in discretionary appropriations over the next 10 years, starting in fiscal year 2012. While it is possible that a smaller, interim deal could pass, which would bring another debt ceiling vote before November 2012, there is significant opposition to such a stopgap measure.
Dufek and Rust receive 2010 Hisashi Kuno Award: Response
Authors: Dufek Josef
Published: July 2011

Josef Dufek and Alison Rust each received the Hisashi Kuno Award at the 2010 AGU Fall Meeting, held 13–17 December in San Francisco, Calif. The award recognizes “accomplishments of junior scientists who make outstanding contributions to the fields of volcanology, geochemistry, and petrology.”
Dufek and Rust receive 2010 Hisashi Kuno Award: Citation
Authors: Manga Michael
Published: July 2011

Josef Dufek and Alison Rust each received the Hisashi Kuno Award at the 2010 AGU Fall Meeting, held 13–17 December in San Francisco, Calif. The award recognizes “accomplishments of junior scientists who make outstanding contributions to the fields of volcanology, geochemistry, and petrology.”
Dufek and Rust receive 2010 Hisashi Kuno Award: Response
Authors: Rust Alison
Published: July 2011

Josef Dufek and Alison Rust each received the Hisashi Kuno Award at the 2010 AGU Fall Meeting, held 13–17 December in San Francisco, Calif. The award recognizes “accomplishments of junior scientists who make outstanding contributions to the fields of volcanology, geochemistry, and petrology.”
Mapping the magnetic mayhem in the heliosheath
Authors: Schultz Colin
Published: July 2011

When Voyager 1 passed into the heliosheath in 2004, it became the first human‐made object to explore the remote edge of the Sun's magnetic influence. The heliosheath, between 1.5 and 15 billion kilometers thick and starting roughly 14 billion kilometers from the Sun, is where the outgoing flows of solar wind start to be pushed back by interstellar particles and magnetic fields that are heading toward the solar system. While passing through the heliosheath, Voyager 1 experienced many sudden and drastic changes in the surrounding magnetic field driven by structures called current sheets. Using Voyager 1's ongoing measurements of the magnetic field, Burlaga and Ness identified three distinct types of current sheets. The structures, appearing as proton boundary layers (PBLs), magnetic holes or humps, or sector boundaries, were identified by characteristic fluctuations in either magnetic field strength or direction as the spacecraft crossed nearly 500 million kilometers of heliosheath in 2009. PBLs are defined by a rapid jump in magnetic field strength, with one observed event resulting in a doubling of the field strength in just half an hour. Passing through a sector boundary led to a sudden change in direction of the magnetic field. Magnetic holes saw the field strength drop to near zero before returning to the original background strength. Magnetic humps consisted of a sudden spike in strength and then a return to initial levels. (Journal of Geophysical Research‐Space Physics, doi:10.1029/2010JA016309, 2011)
Input variable selection for median flood regionalization
Authors: Wan Jaafar W. Z. , Liu J. , Han D.
Published: July 2011

Flood estimation for ungauged catchments is a challenging task for hydrologists. A modern geographical information system is able to extract a large number of catchment characteristics as input variables for regionalization analysis. Effective and efficient selection of the best input variables is urgently needed in this field. This paper explores a new methodology for selecting the best input variable combination on the basis of the gamma test and leave‐one‐out cross validation (LOOCV) to estimate the median annual maximum flow (as an index flood). Since the gamma test is capable of efficiently calculating the output variance on the basis of the input without the need to select a model structure type, more effective regionalization models could be developed because there is no need to define an a priori model structure. A case study from 20 catchments in southwest England has been used to illustrate and validate the proposed scheme. It has been found that the gamma test is able to narrow down the search options to be further explored by the LOOCV. The best formula from this approach outperforms the conventional approaches based on cross validation, data filtering with Spearman's rank correlation matrix, and corrected Akaike information criterion. In addition, the developed formula is significantly more accurate than the existing equation used in the Flood Estimation Handbook.
Metaclocks
Authors: Reddy Akhilesh B , O'Neill John S
Published: July 2011

The transcription‐translation model of circadian clocks has served scientists well for the past 20 years. Yet, gaps in our knowledge have remained. New evidence suggests that the cellular clock might keep time using rhythms of metabolism.
Reaching a Milestone: 25 Years of the Native American Caucus
Authors: Long Edgarita , Drevniak Alyssa
Published: July 2011

For the past 25 years, the Native American Caucus has brought together speech-language pathologists and audiologists dedicated to improving speech, language, and hearing service delivery for Indigenous communities. This article briefly describes the history and goals of the Caucus along with some of the related actions that have been undertaken to achieve the goals. The information provided, literature cited, and a selected resource list can serve as resources for professionals who serve Indigenous populations.
A Language and Literacy Program for Indigenous Kindergartners: Preliminary Findings
Authors: Loeb Diane Frome , Redbird Katherine , McConnell Grace E.
Published: July 2011

Nine Indigenous kindergarteners displayed gains in targeted expressive vocabulary, narrative comprehension, alphabet identification, phonological awareness, and comprehension of passage reading following a 6-week shared reading program using storybooks about Indigenous children and their adventures. Cultural values and beliefs guided the selection of the storybooks and the content of the supplemental language and literacy activities. This classroom program may be a viable way to provide culturally relevant Response to Intervention (RTI) for Indigenous children who are at risk for language and reading difficulties.
From Theme Park to Resort: Customer Information Management at Port Aventura
Authors: Hervás Mariano A , Rodon Joan , Planell Marc , Sala Xavier
Published: July 2011

After Port Aventura's launch as a theme park in 1995, it continued to invest heavily in new shows, rides, hotels, golf courses, a convention center, and a shopping mall, all with the aim of adjusting to seasonal adjusted demand. This transformation from a theme park to a resort posed new challenges for Port Aventura's executive team. In particular, as a theme park, the analysis of its commercial activity focused on aggregated statistical information about groups of customers. By contrast, as a resort, management now needed to know and target individual customers. Yet, the company's existing information management processes and systems were not ready to support such a one-to-one marketing approach. This case is situated in mid-2009 when the general manager asked the chief financial officer and the director of information systems to find a solution to address the marketing needs of the resort. The case discussion encourages students to identify and assess the business problems and relate them to the existing information management processes and systems. Students will also have to present a proposal that addresses this one-to-one marketing strategy.
Neoclassical physics in full distribution function gyrokinetics
Authors: Dif-Pradalier G. , Diamond P. H. , Grandgirard V. , Sarazin Y. , Abiteboul J. , Garbet X. , Ghendrih Ph. , Latu G. , Strugarek A. , Ku S. , Chang C. S.
Published: July 2011

Treatment of binary Coulomb collisions when the full gyrokinetic distribution function is evolved is discussed here. A spectrum of different collision operators is presented, differing through both the physics that can be addressed and the numerics they are based on. Eulerian-like (semi-Lagrangian) and particle in cell (PIC) (Monte-Carlo) schemes are successfully cross-compared, and a detailed confrontation to neoclassical theory is shown.
The double electrostatic ion ring experiment: A unique cryogenic electrostatic storage ring for merged ion-beams studies
Authors: Thomas R. D. , Schmidt H. T. , Andler G. , Björkhage M. , Blom M. , Brännholm L. , Bäckström E. , Danared H. , Das S. , Haag N. , Halldén P. , Hellberg F. , Holm A. I. S. , Johansson H. A. B. , Källberg A. , Källersjö G. , Larsson M. , Leontein S. , Liljeby L. , Löfgren P. , Malm B. , Mannervik S. , Masuda M. , Misra D. , Orbán A. , Paál A. , Reinhed P. , Rensfelt K.-G. , Rosén S. , Schmidt K. , Seitz F. , Simonsson A. , Weimer J. , Zettergren H. , Cederquist H.
Published: July 2011

We describe the design of a novel type of storage device currently under construction at Stockholm University, Sweden, using purely electrostatic focussing and deflection elements, in which ion beams of opposite charges are confined under extreme high vacuum cryogenic conditions in separate “rings” and merged over a common straight section. The construction of this double electrostatic ion ring experiment uniquely allows for studies of interactions between cations and anions at low and well-defined internal temperatures and centre-of-mass collision energies down to about 10 K and 10 meV, respectively. Position sensitive multi-hit detector systems have been extensively tested and proven to work in cryogenic environments and these will be used to measure correlations between reaction products in, for example, electron-transfer processes. The technical advantages of using purely electrostatic ion storage devices over magnetic ones are many, but the most relevant are: electrostatic elements which are more compact and easier to construct; remanent fields, hysteresis, and eddy-currents, which are of concern in magnetic devices, are no longer relevant; and electrical fields required to control the orbit of the ions are not only much easier to create and control than the corresponding magnetic fields, they also set no upper mass limit on the ions that can be stored. These technical differences are a boon to new areas of fundamental experimental research, not only in atomic and molecular physics but also in the boundaries of these fields with chemistry and biology. For examples, studies of interactions with internally cold molecular ions will be particular useful for applications in astrophysics, while studies of solvated ionic clusters will be of relevance to aeronomy and biology.
Spectral collocation methods for polymer brushes
Authors: Chantawansri Tanya L. , Hur Su-Mi , García-Cervera Carlos J. , Ceniceros Hector D. , Fredrickson Glenn H.
Published: July 2011

We provide an in-depth study of pseudo-spectral numerical methods associated with modeling the self-assembly of molten mixed polymer brushes in the framework of self-consistent field theory (SCFT). SCFT of molten polymer brushes has proved numerically challenging in the past because of sharp features that arise in the self-consistent pressure field at the grafting surface due to the chain end tethering constraint. We show that this pressure anomaly can be reduced by smearing the grafting points over a narrow zone normal to the surface in an incompressible model, and/or by switching to a compressible model for the molten brush. In both cases, we use results obtained from a source (delta function) distribution of grafting points as a reference. At the grafting surface, we consider both Neumann and Dirichlet conditions, where the latter is paired with a masking method to mimic a confining surface. When only the density profiles and relative free energies of two comparison phases are of interest, either source or smeared distributions of grafting points can be used, but a smeared distribution of grafting points exhibits faster convergence with respect to the number of chain contour steps. Absolute free energies converge only within the smeared model. In addition, when a sine basis is used with the masking method and a smeared distribution, fewer iterations are necessary to converge the SCFT fields for the compressible model. The numerical methods described here and investigated in one-dimension will provide an enabling platform for computationally more demanding three-dimensional SCFT studies of a broad range of mixed polymer brush systems.
Kinetic models of the interference of gene transcription to ncRNA and mRNA
Authors: Zhdanov Vladimir P.
Published: July 2011

The experiments indicate that the transcription of genes into ncRNA can positively or negatively interfere with transcription into mRNA. We propose two kinetic models describing this effect. The first model is focused on the ncRNA-induced chromatin modification facilitating the transcription of the downstream gene into mRNA. The second model includes the competition between the transcription into ncRNA and the binding of activator to a regulatory site of the downstream gene transcribed into mRNA. Our analysis based on the mean-field kinetic equations and Monte Carlo simulations shows the likely dependences of the transcription rate on RNA polymerase concentration in situations with different rate-limiting steps. Our models can also be used to scrutinize the dependence of the transcription rate on other kinetic parameters. Our kinetic Monte Carlo simulations show that the first model predicts stochastic bursts in the mRNA formation provided that the transcription into ncRNA is slow, while the second model predicts in addition anti-phase stochastic bursts in the mRNA and ncRNA formation provided that that the protein attachment to and detachment from a regulatory site is slow.
Spatial control of cell fate using synthetic surfaces to potentiate TGF-β signaling
Authors: Li Lingyin , Klim Joseph R. , Derda Ratmir , Courtney Adam H. , Kiessling Laura L.
Published: July 2011

In organisms, cell-fate decisions result from external cues presented by the extracellular microenvironment or the niche. In principle, synthetic niches can be engineered to give rise to patterned cell signaling, an advance that would transform the fields of tissue engineering and regenerative medicine. Biomaterials that display adhesive motifs are critical steps in this direction, but promoting localized signaling remains a major obstacle. We sought to exert precise spatial control over activation of TGF-β signaling. TGF-β signaling, which plays fundamental roles in development, tissue homeostasis, and cancer, is initiated by receptor oligomerization. We therefore hypothesized that preorganizing the transmembrane receptors would potentiate local TGF-β signaling. To generate surfaces that would nucleate the signaling complex, we employed defined self-assembled monolayers that present peptide ligands to TGF-β receptors. These displays of nondiffusible ligands do not compete with the growth factor but rather sensitize bound cells to subpicomolar concentrations of endogenous TGF-β. Cells adhering to the surfaces undergo TGF-β-mediated growth arrest and the epithelial to mesenchymal transition. Gene expression profiles reveal that the surfaces selectively regulate TGF-β responsive genes. This strategy provides access to tailored surfaces that can deliver signals with spatial control.
The Scavenger Hunt: Getting to Know Your Psychology Department
Authors: Segrist Dan J. , Nordstrom Cynthia R.
Published: July 2011

One hundred and forty-four undergraduates enrolled in a careers in psychology course participated in a group-oriented scavenger hunt activity. The purpose of this activity was to increase students' awareness of the types of resources, available to them within the psychology department and within the larger campus community, related to psychology as a major and a career. Pre–post data indicated that the activity significantly increased students' self-reported knowledge of the resources available to them. Evaluation ratings also indicated that students found the activity both helpful and enjoyable.
Still Crazy about Teaching after All These Years: An Interview with Dick Gorman
Authors: Burke Brian L.
Published: July 2011

Richard Gorman received his BA in philosophy from the University of Notre Dame and his PhD in educational psychology from Fordham University. Over the years, he has taught at several colleges and universities—both in the east and west—and is currently a member of the Psychology Department at Central New Mexico Community College. He has taught courses in developmental, educational, and cognitive psychology, but is currently concentrating on the introductory psychology course. His publications include a text in the psychology of classroom learning, an introduction to Piaget's theory for teachers, and, more recently, an introductory psychology text. He has given presentations and workshops on discovery learning to various audiences including the National Institute on the Teaching of Psychology (NITOP).

Brian L. Burke is an Assistant Professor of Psychology at Fort Lewis College, a public liberal arts college in Durango, Colorado. He is a licensed clinical psychologist whose principal academic interests include motivational interviewing and college teaching. He regularly attends teaching conferences, twice winning the Doug Bernstein Award for innovative teaching ideas (NITOP 2004, 2005). He also won the New Faculty Teaching Award at Fort Lewis College in 2005. He teaches a wide variety of courses, including introductory psychology, personality, abnormal, counseling, research methods, history of psychology (via a European trip), and forensic psychology. Brian hails originally from Montreal, Canada, and received his PhD from the University of Arizona in 2003.
The F-box protein Ppa is a common regulator of core EMT factors Twist, Snail, Slug, and Sip1
Authors: Lander Rachel , Nordin Kara , LaBonne Carole
Published: July 2011

A small group of core transcription factors, including Twist, Snail, Slug, and Sip1, control epithelial–mesenchymal transitions (EMTs) during both embryonic development and tumor metastasis. However, little is known about how these factors are coordinately regulated to mediate the requisite behavioral and fate changes. It was recently shown that a key mechanism for regulating Snail proteins is by modulating their stability. In this paper, we report that the stability of Twist is also regulated by the ubiquitin–proteasome system. We found that the same E3 ubiquitin ligase known to regulate Snail family proteins, Partner of paired (Ppa), also controlled Twist stability and did so in a manner dependent on the Twist WR-rich domain. Surprisingly, Ppa could also target the third core EMT regulatory factor Sip1 for proteasomal degradation. Together, these results indicate that despite the structural diversity of the core transcriptional regulatory factors implicated in EMT, a common mechanism has evolved for controlling their stability and therefore their function.
Transient binding of an activator BH3 domain to the Bak BH3-binding groove initiates Bak oligomerization
Authors: Dai Haiming , Smith Alyson , Meng X. Wei , Schneider Paula A. , Pang Yuan-Ping , Kaufmann Scott H.
Published: July 2011

The mechanism by which the proapoptotic Bcl-2 family members Bax and Bak release cytochrome c from mitochondria is incompletely understood. In this paper, we show that activator BH3-only proteins bind tightly but transiently to the Bak hydrophobic BH3-binding groove to induce Bak oligomerization, liposome permeabilization, mitochondrial cytochrome c release, and cell death. Analysis by surface plasmon resonance indicated that the initial binding of BH3-only proteins to Bak occurred with similar kinetics with or without detergent or mitochondrial lipids, but these reagents increase the strength of the Bak–BH3-only protein interaction. Point mutations in Bak and reciprocal mutations in the BH3-only proteins not only confirmed the identity of the interacting residues at the Bak–BH3-only protein interface but also demonstrated specificity of complex formation in vitro and in a cellular context. These observations indicate that transient protein–protein interactions involving the Bak BH3-binding groove initiate Bak oligomerization and activation.
Gain-of-function human STAT1 mutations impair IL-17 immunity and underlie chronic mucocutaneous candidiasis
Authors: Liu Luyan , Okada Satoshi , Kong Xiao-Fei , Kreins Alexandra Y. , Cypowyj Sophie , Abhyankar Avinash , Toubiana Julie , Itan Yuval , Audry Magali , Nitschke Patrick , Masson Cécile , Toth Beata , Flatot Jérome , Migaud Mélanie , Chrabieh Maya , Kochetkov Tatiana , Bolze Alexandre , Borghesi Alessandro , Toulon Antoine , Hiller Julia , Eyerich Stefanie , Eyerich Kilian , Gulácsy Vera , Chernyshova Ludmyla , Chernyshov Viktor , Bondarenko Anastasia , María Cortés Grimaldo Rosa , Blancas-Galicia Lizbeth , Madrigal Beas Ileana Maria , Roesler Joachim , Magdorf Klaus , Engelhard Dan , Thumerelle Caroline , Burgel Pierre-Régis , Hoernes Miriam , Drexel Barbara , Seger Reinhard , Kusuma Theresia , Jansson Annette F. , Sawalle-Belohradsky Julie , Belohradsky Bernd , Jouanguy Emmanuelle , Bustamante Jacinta , Bué Mélanie , Karin Nathan , Wildbaum Gizi , Bodemer Christine , Lortholary Olivier , Fischer Alain , Blanche Stéphane , Al-Muhsen Saleh , Reichenbach Janine , Kobayashi Masao , Rosales Francisco Espinosa , Lozano Carlos Torres , Kilic Sara Sebnem , Oleastro Matias , Etzioni Amos , Traidl-Hoffmann Claudia , Renner Ellen D. , Abel Laurent , Picard Capucine , Maródi László , Boisson-Dupuis Stéphanie , Puel Anne , Casanova Jean-Laurent
Published: July 2011

Chronic mucocutaneous candidiasis disease (CMCD) may be caused by autosomal dominant (AD) IL-17F deficiency or autosomal recessive (AR) IL-17RA deficiency. Here, using whole-exome sequencing, we identified heterozygous germline mutations in STAT1 in 47 patients from 20 kindreds with AD CMCD. Previously described heterozygous STAT1 mutant alleles are loss-of-function and cause AD predisposition to mycobacterial disease caused by impaired STAT1-dependent cellular responses to IFN-γ. Other loss-of-function STAT1 alleles cause AR predisposition to intracellular bacterial and viral diseases, caused by impaired STAT1-dependent responses to IFN-α/β, IFN-γ, IFN-λ, and IL-27. In contrast, the 12 AD CMCD-inducing STAT1 mutant alleles described here are gain-of-function and increase STAT1-dependent cellular responses to these cytokines, and to cytokines that predominantly activate STAT3, such as IL-6 and IL-21. All of these mutations affect the coiled-coil domain and impair the nuclear dephosphorylation of activated STAT1, accounting for their gain-of-function and dominance. Stronger cellular responses to the STAT1-dependent IL-17 inhibitors IFN-α/β, IFN-γ, and IL-27, and stronger STAT1 activation in response to the STAT3-dependent IL-17 inducers IL-6 and IL-21, hinder the development of T cells producing IL-17A, IL-17F, and IL-22. Gain-of-function STAT1 alleles therefore cause AD CMCD by impairing IL-17 immunity.
Single panel liquid crystal device switchable between reflective and transmissive modes
Authors: Kim Ki-Han , Song Dong Han , Jin Hye-Jung , Yoon Tae-Hoon
Published: July 2011

We propose a single panel liquid crystal (LC) device that is switchable between reflective and transmissive modes. Operation in the reflective mode can be achieved by applying a vertical field to a dye-doped LC device, whereas the device can be in-plane switched for operation in the transmissive mode. Image inversion that was inevitable in a single panel device using a reflective polarizer is effectively eliminated through the absorption of ambient light by the dye-doped LCs. We believe that the proposed device can be applied to various display systems for outdoor mobile use.
Investigating the influence of the operating frequency on the gas phase emitter effect of dysprosium in ceramic metal halide lamps
Authors: Reinelt J , Westermeier M , Ruhrmann C , Bergner A , Luijks G M J F , Awakowicz P , Mentel J
Published: July 2011

On page 4 in the second paragraph, the first sentence should read:

The delay time of the current source, which is realized by an electronic device, varies so much in dependence on the operating parameters that the 'sync' output of the signal generator, by which the current source is controlled, is unsuitable to provide an appropriate trigger pulse.
Stanley depth and size of a monomial ideal
Authors: Herzog Jürgen , Popescu Dorin , Vladoiu Marius
Published: July 2011

Lyubeznik introduced the concept of size of a monomial ideal and showed that the size of a monomial ideal increased by

1
1

is a lower bound for its depth. We show that the size increased by

1
1

is also a lower bound for its Stanley depth. Applying Alexander duality we obtain upper bounds for the regularity and Stanley regularity of squarefree monomial ideals.
A statistical framework for biomarker discovery in metabolomic time course data
Authors: Berk Maurice , Ebbels Timothy , Montana Giovanni
Published: July 2011

Motivation: Metabolomics is the study of the complement of small molecule metabolites in cells, biofluids and tissues. Many metabolomic experiments are designed to compare changes observed over time under two experimental conditions or groups (e.g. a control and drug-treated group) with the goal of identifying discriminatory metabolites or biomarkers that characterize each condition. A common study design consists of repeated measurements taken on each experimental unit thus producing time courses of all metabolites. We describe a statistical framework for estimating time-varying metabolic profiles and their within-group variability and for detecting between-group differences. Specifically, we propose (i) a smoothing splines mixed effects (SME) model that treats each longitudinal measurement as a smooth function of time and (ii) an associated functional test statistic. Statistical significance is assessed by a non-parametric bootstrap procedure.

Results: The methodology has been extensively evaluated using simulated data and has been applied to real nuclear magnetic resonance spectroscopy data collected in a preclinical toxicology study as part of a larger project lead by the COMET (Consortium for Metabonomic Toxicology). Our findings are compatible with the previously published studies.

Availability: An R script is freely available for download at http://www2.imperial.ac.uk/~gmontana/sme.htm.

Contact:  g.montana@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Carbon-Consuming Home: Residential Markets and Energy Transitions
Authors: Jones Christopher
Published: July 2011

Home heating and lighting markets have played crucial and underappreciated roles in driving energy transitions. When historians have studied the adoption of fossil fuels, they have often privileged industrial actors, markets, and technologies. My analysis of the factors that stimulated the adoption of anthracite coal and petroleum during the nineteenth century reveals that homes shaped how, when, and why Americans began to use fossil fuel energy. Moreover, a brief survey of other fossil fuel transitions shows that heating and lighting markets have been critical drivers in other times and places. Reassessing the historical patterns of energy transitions offers a revised understanding of the past for historians and suggests a new set of options for policymakers seeking to encourage the use of renewable energy in the future.
PBP5, PBP6 and DacD play different roles in intrinsic β-lactam resistance of Escherichia coli
Authors: Sarkar Sujoy Kumar , Dutta Mouparna , Chowdhury Chiranjit , Kumar Akash , Ghosh Anindya S.
Published: July 2011

Escherichia coli PBP5, PBP6 and DacD, encoded by dacA, dacC and dacD, respectively, share substantial amino acid identity and together constitute ~50 % of the total penicillin-binding proteins of E. coli. PBP5 helps maintain intrinsic β-lactam resistance within the cell. To test if PBP6 and DacD play simlar roles, we deleted dacC and dacD individually, and dacC in combination with dacA, from E. coli 2443 and compared β-lactam sensitivity of the mutants and the parent strain. β-Lactam resistance was complemented by wild-type, but not dd-carboxypeptidase-deficient PBP5, confirming that enzymic activity of PBP5 is essential for β-lactam resistance. Deletion of dacC and expression of PBP6 during exponential or stationary phase did not alter β-lactam resistance of a dacA mutant. Expression of DacD during mid-exponential phase partially restored β-lactam resistance of the dacA mutant. Therefore, PBP5 dd-carboxypeptidase activity is essential for intrinsic β-lactam resistance of E. coli and DacD can partially compensate for PBP5 in this capacity, whereas PBP6 cannot.
Extensive relationship between antisense transcription and alternative splicing in the human genome
Authors: Morrissy A. Sorana , Griffith Malachi , Marra Marco A.
Published: July 2011

To analyze the relationship between antisense transcription and alternative splicing, we developed a computational approach for the detection of antisense-correlated exon splicing events using Affymetrix exon array data. Our analysis of expression data from 176 lymphoblastoid cell lines revealed that the majority of expressed sense–antisense genes exhibited alternative splicing events that were correlated to the expression of the antisense gene. Most of these events occurred in areas of sense–antisense (SAS) gene overlap, which were significantly enriched in both exons and nucleosome occupancy levels relative to nonoverlapping regions of the same genes. Nucleosome occupancy was highly correlated with Pol II abundance across overlapping regions and with concomitant increases in local alternative exon usage. These results are consistent with an antisense transcription-mediated mechanism of splicing regulation in normal human cells. A comparison of the prevalence of antisense-correlated splicing events between individuals of Mormon versus African descent revealed population-specific events that may indicate the continued evolution of new SAS loci. Furthermore, the presence of antisense transcription was correlated to alternative splicing across multiple metazoan species, suggesting that it may be a conserved mechanism contributing to splicing regulation.