bluuebunny/crossref_metadata_2025 huggingface dataset:
Lymphovascular invasion is a pathological feature related to aggressive cancer behavior and predicts early recurrence in prostate cancer
Authors: Luo Hao Lun , Chiang Po Hui , Chen Yen Ta , Cheng Yuan Tso
Published: April 2012

In order to determine the prognostic impact of lymphovascular invasion (LVI) in patients after radical prostatectomy, the retrospective data from our institution has been analyzed. From 1998 to 2010, 117 patients underwent radical prostatectomy. A total of 87 patients were included in this retrospective study. The relationship between LVI and advanced prostate cancer characteristics was evaluated by χ2 test. The Kaplan‐Meier method and meta‐analysis were used to describe the impact of LVI invasion upon early biochemical failure after radical prostatectomy. LVI was observed in patients with clinically or pathologically aggressive prostate cancer including patients of higher preoperative risk group, higher preoperative PSA, advanced Gleason grade, and pathological T3 disease. LVI is also associated with early biochemical failure rate both in our report and in the literature. Therefore, LVI is a pathological feature which indicates prognosis correlates with aggressive prostate cancer behavior and results in early biochemical failure after radical prostatectomy.
Fluconazole exposure rather than clonal spreading is correlated with the emergence of Candida glabrata with cross‐resistance to triazole antifungal agents
Authors: Chen Tun‐Chieh , Chen Yen‐Hsu , Chen Yee‐Chun , Lu Po‐Liang
Published: April 2012

The emergence of antifungal resistance in Candida species has raised concern in recent years, especially resistance toward triazole. Several newer triazole antifungal agents have been introduced which have a broader spectrum for fungal infections, such as voriconazole. However, cross‐resistance among triazoles is a major concern with regard to their clinical application. Antifungal susceptibility was performed using E‐test for 166 clinical isolates (29 blood and 137 nonblood isolates) in 2003 and 2004. We applied pulsed‐field gel electrophoresis for genotyping. Ninety isolates of C. albicans, 47 isolates of C. tropicalis, 27 isolates of C. glabrata, and two isolates of C. krusei were included. All isolates were susceptible to amphotericin B. Eleven (40.7%) of the 27 C. glabrata had intermediate resistance to caspofungin. Forty‐seven (28.3%) of the 166 isolates were not susceptible to fluconazole, including two C. albicans, 16 C. tropicalis, 27 C. glabrata, and two C. krusei isolates. All except seven of the C. glabrata isolates were susceptible to voriconazole. All the triazole drugs had a positive correlation among their minimum inhibitory concentrations (MICs). Fluconazole MIC was a good predictor for susceptibility to voriconazole, as determined using a receiver operating characteristic curve. Furthermore, a high diversity of pulsotypes for the 27 clinical isolates of C. glabrata was observed. Previous fluconazole exposure within 3 months was associated with reduced triazole susceptibility for C. glabrata. We demonstrated a significant positive correlation of MIC values among the four tested triazole drugs. No amphotericin B and caspofungin resistant isolates were found in this study. The cross‐resistance to triazole among C. glabrata isolates was associated with previous fluconazole exposure as opposed to clonal spreading. Selection pressure due to fluconazole use may play a major role in triazole cross‐resistance.
The alteration of plasma TGF‐β1 levels in patients with brain tumors after tumor removal
Authors: Loh Joon‐Khim , Lieu Ann‐Shung , Su Yu‐Feng , Cheng Chi‐Yun , Tsai Tai‐Hsin , Lin Chih‐Lung , Lee Kung‐Shing , Hwang Shiuh‐Lin , Kwan Aij‐Lie , Wang Chih‐Jen , Hong Yi‐Ren , Howng Shen‐Long , Chio Chung‐Ching
Published: April 2012

Transforming growth factor (TGF) β1 may be a candidate for a serologic tumor marker. In this study, the plasma levels of TGF‐β1 in patients with brain tumors were measured using enzyme‐linked immunosorbent assay before and after tumor removal. Patients were divided into four groups, the control group and the benign, malignant, and metastatic brain tumor groups. All brain tumor groups showed significant increases in the levels of TGF‐β1 before tumor removal (6.36 ± 3.94, 17.0 ± 9.7, and 12.2 ± 10.3 ng/ml for the benign, malignant, and metastatic groups, respectively). When compared with the results obtained in the control group (1.12 ± 0.74 ng/ml), significant decreases in TGF‐β1 concentrations after total tumor removal were found in both the benign and malignant brain tumor groups (2.55 ± 2.00 and 8.93 ± 5.73 ng/ml, respectively; p = 0.0001 and p = 0.003, respectively). On the other hand, plasma TGF‐β1 levels in the metastatic brain tumor group showed a slight but significant increase (14.7 ± 9.3 ng/ml, p = 0.035) after tumor removal. In a case of low‐grade astrocytoma, plasma levels of TGF‐β1 were found to be 3.6 and 1.1 ng/ml before and after tumor removal, respectively. However, recurrent tumor was noted in this patient 7 months later, and the levels of TGF‐β1 were 26.2 and 8.4 ng/ml before and after the second operation, respectively. The data show that plasma TGF‐β1 was elevated in the circulation of patients with brain tumors and that significant decreases in TGF‐β1 levels were observed after the removal of benign and malignant tumors. The results also suggest that TGF‐β1 may be a useful serologic marker for brain tumors.
EMPIRICAL TESTS OF INTEREST-RELATIVE INVARIANTISM
Authors: Sripada Chandra Sekhar , Stanley Jason
Published: April 2012

According to Interest-Relative Invariantism, whether an agent knows that p, or possesses other sorts of epistemic properties or relations, is in part determined by the practical costs of being wrong about p. Recent studies in experimental philosophy have tested the claims of IRI. After critically discussing prior studies, we present the results of our own experiments that provide strong support for IRI. We discuss our results in light of complementary findings by other theorists, and address the challenge posed by a leading intellectualist alternative to our view.
Power (Empowerment) through the Body, Self, and Black Male Identity in Contemporary Theatrical Modern Dance
Authors: Paris Carl
Published: April 2012

Postmodern articulations in contemporary theatrical modern dance have produced new black male expressions–straight and gay–that disrupt rigid and reductive representations of identity and masculinity and also open up pluralistic and libratory possibilities through the black male dancing body. I use this context to examine power (and empowerment) in the work of choreographers Bill T. Jones, Ronald K. Brown, Reggie Wilson, Nicholas Leichter, Helanius Wilkins, and Kyle Abraham, who approach the particularity of black male identity from postmodern perspectives. My idea of power, here, is inspired by Ralph Ellison's nameless black protagonist inInvisible Manwhose search for self-understanding and identity stands as both a literal and allegorical struggle for the power over one's “visibility” and agency as a black man. Through identifying key philosophical, stylistic, and thematic representations across the choreographers, I explore how power negotiates and is negotiated around issues of self, sexuality, and identity in the black male dancing body.
Price of Gold and Light: Power and Politics in Hey Ananta Punya
Authors: Rahman Munjulika
Published: April 2012

Hey Ananta Punya, a dance-drama adapted and choreographed by the Bangladeshi choreographer Warda Rihab was performed in Kolkata, India, in December 2009. Rihab plays the main character Srimoti, a dancer at the court of King Ajatashatru. Srimoti embraces Buddhism but is not allowed to practice since Ajatashatru decrees Hinduism to be the state religion. In the narrative, Hinduism, the predominant religion of India, represses Buddhism, which is a minority religion in the subcontinent. Even though on the surface the dance-drama deals with Hinduism and Buddhism, the performance is complicated by the knowledge that the choreographer and most of the performers are Bangladeshi Muslims. In the context of Hindu-Muslim conflicts and India's political and economic hegemony in South Asia, the performance can be considered as a critique of India's policies. In considering the choreographer's background and the dance-drama's narrative, aesthetics, and location of performance, I analyze the various structures of power that a Bangladeshi female choreographer operates within during her training and performance in India. Hey Ananta Punya is significant because it points to the complex web of issues involving politics, history, and religion that have been a part of dance in Bangladesh for the past few decades because of India's influence in the field, particularly through Indian-government scholarships for advanced dance training. In the paper, I use Michel Foucault's theory of power as systems of interrelated networks and knowledge as a system of power to show how dance as a form of embodied knowledge can function as a tool in shaping, disseminating, and expressing ideology.
United States – Certain Measures Affecting Imports of Poultry from China: the fascinating case that wasn't
Authors: REGAN DONALD H.
Published: April 2012

US–Poultry (China) was the first Panel decision dealing with an origin-specific SPS measure, or with what the United States referred to as an ‘equivalence regime’. More specifically, it was the first instance in which the basis for the challenged measure was the claimed inability of the complainant country to enforce its own food-safety rules. Unfortunately, as the litigation developed, the very interesting novel issues raised by such a measure were not discussed. This essay discusses those novel issues – in particular, what sort of scientific justification or risk assessment should be required for a measure like this, and what SPS Article 4 says about equivalence regimes. The essay also criticizes the Panel's analysis of some of the issues the Panel does discuss, such as the meaning of the ‘appropriate level of protection’ in SPS 5.5 and 5.6, and the relationship between the SPS and GATT XX(b).
United States – Anti-Dumping Measures on Polyethylene Retail Carrier Bags from Thailand: a cat in the bag
Authors: PRUSA THOMAS J. , VERMULST EDWIN
Published: April 2012

This paper analyzes the dispute between Thailand and the United States regarding the method of calculating the anti-dumping duty on polyethylene retail carrier bags from Thailand. In December 2006, after a series of WTO Appellate Body reports, the United States ceased zeroing in original investigations. The United States implemented the policy change prospectively, that is only for future cases. Consequently, the margins in this case remained unchanged because they had been calculated in 2004. Thailand challenged the United States' use of zeroing in the final determination. The US did not contest the claim. The Panel confirmed that zeroing was used and, following the long line of Appellate Body rulings, found the United States' practice inconsistent with Article 2.4.2 of the Anti-Dumping Agreement. After the Panel Report was adopted, the United States retroactively applied the policy change to the facts of this case and recalculated the margins without zeroing. The relative simplicity of the panel proceeding and the United States' willingness to amend the calculations following the adoption of the Panel Report may invite other WTO members to pursue a similar course of action in instances where their exporters have been subjected to US zeroing.
Supporting the Interests of Intercountry Adoptees beyond Childhood: Access to Adoption Information and Identity
Authors: Walton Jessica
Published: April 2012

Drawing on select examples of adoption policy, this article considers key assumptions in discourse about ‘the best interests of the child’. The central argument is that the life-long impact of adoption needs to be recognised so that the long-term interests of adoptees are met, and not only when they are children. Based on doctoral research into the experiences of adult Korean adoptees in the United States and Australia, this article argues that currently post-adoption services are geared to adoptive parents and the adoptee-as-child and do not adequately address the needs of adoptees beyond childhood. Accurate and accessible information is important for adoptees as they try to understand their past and make sense of their identities.
Geoeffectiveness and efficiency of CIR, sheath, and ICME in generation of magnetic storms
Authors: Yermolaev Y. I. , Nikolaeva N. S. , Lodkina I. G. , Yermolaev M. Y.
Published: April 2012

We investigate the relative role of various types of solar wind streams in generation of magnetic storms. On the basis of the OMNI data of interplanetary measurements for the period of 1976–2000, we analyze 798 geomagnetic storms with Dst ≤ −50 nT and five various types of solar wind streams as their interplanetary sources: corotating interaction regions (CIR), interplanetary coronal mass ejection (ICME) including magnetic clouds (MC) and ejecta, and a compression region sheath before both types of ICME (SHEMC and SHEEj, respectively). For various types of the solar wind we study the following relative characteristics: occurrence rate; mass, momentum, energy and magnetic fluxes; probability of generation of a magnetic storm (geoeffectiveness); efficiency of the process of this generation; and solar cycle variation of some of these parameters. Obtained results show that in spite of the fact that magnetic clouds have lower occurrence rates and lower efficiency than CIR and sheath, they play an essential role in generation of magnetic storms due to higher geoeffectiveness of storm generation (i.e., higher probability to contain large and long‐term southward IMF Bz component). Geoeffectiveness for all drives has the smallest value during a solar cycle minimum and increases at other phases of the cycle.
Fast cloud adjustment to increasing CO2 in a superparameterized climate model
Authors: Wyant Matthew C. , Bretherton Christopher S. , Blossey Peter N. , Khairoutdinov Marat
Published: April 2012

Two‐year simulation experiments with a superparameterized climate model, SP‐CAM, are performed to understand the fast tropical (30S‐30N) cloud response to an instantaneous quadrupling of CO2 concentration with SST held fixed at present‐day values. The greenhouse effect of the CO2 perturbation quickly warms the tropical land surfaces by an average of 0.5 K. This shifts rising motion, surface precipitation, and cloud cover at all levels from the ocean to the land, with only small net tropical‐mean cloud changes. There is a widespread average reduction of about 80 m in the depth of the trade inversion capping the marine boundary layer (MBL) over the cooler subtropical oceans. One apparent contributing factor is CO2‐enhanced downwelling longwave radiation, which reduces boundary‐layer radiative cooling, a primary driver of turbulent entrainment through the trade inversion. A second contributor is a slight CO2‐induced heating of the free troposphere above the MBL, which strengthens the trade inversion and also inhibits entrainment. There is a corresponding downward displacement of MBL clouds with a very slight decrease in mean cloud cover and albedo. Two‐dimensional cloud‐resolving model (CRM) simulations of this MBL response are run to steady state using composite SP‐CAM simulated thermodynamic and wind profiles from a representative cool subtropical ocean regime, for the control and 4xCO2 cases. Simulations with a CRM grid resolution equal to that of SP‐CAM are compared with much finer resolution simulations. The coarse‐resolution simulations maintain a cloud fraction and albedo comparable to SP‐CAM, but the fine‐resolution simulations have a much smaller cloud fraction. Nevertheless, both CRM configurations simulate a reduction in inversion height comparable to SP‐CAM. The changes in low cloud cover and albedo in the CRM simulations are small, but both simulations predict a slight reduction in low cloud albedo as in SP‐CAM.
The faint young Sun problem
Authors: Feulner Georg
Published: April 2012

For more than four decades, scientists have been trying to find an answer to one of the most fundamental questions in paleoclimatology, the “faint young Sun problem.” For the early Earth, models of stellar evolution predict a solar energy input to the climate system that is about 25% lower than today. This would result in a completely frozen world over the first 2 billion years in the history of our planet if all other parameters controlling Earth's climate had been the same. Yet there is ample evidence for the presence of liquid surface water and even life in the Archean (3.8 to 2.5 billion years before present), so some effect (or effects) must have been compensating for the faint young Sun. A wide range of possible solutions have been suggested and explored during the last four decades, with most studies focusing on higher concentrations of atmospheric greenhouse gases like carbon dioxide, methane, or ammonia. All of these solutions present considerable difficulties, however, so the faint young Sun problem cannot be regarded as solved. Here I review research on the subject, including the latest suggestions for solutions of the faint young Sun problem and recent geochemical constraints on the composition of Earth's early atmosphere. Furthermore, I will outline the most promising directions for future research. In particular I would argue that both improved geochemical constraints on the state of the Archean climate system and numerical experiments with state‐of‐the‐art climate models are required to finally assess what kept the oceans on the Archean Earth from freezing over completely.
Morphology, propagation dynamics and scaling characteristics of drying fronts in porous media
Authors: Shokri N. , Sahimi Muhammad , Or D.
Published: April 2012

Effects of surface wettability on the dynamics and morphology of evaporation‐induced drying fronts (DF) receding into hydrophilic (HI) or hydrophobic (HO) sands were studied using highly‐resolved neutron radiography. A more pronounced pinning‐depinning motion (larger steps and longer waiting times) was observed for the DF in HI sand relative to HO, due to weaker capillary pinning forces in the latter. For length scalesl smaller than a correlation length ξ, quenched disorder dominates DF roughness expressed by a roughness exponent α = 0.77, whereas for l > ξ the fluctuations induced by the DF motion annealed the disorder and result in α= 0.44. Although wettability suppressed evaporation rates in HO relative to HI sand, differences in the evaporation dynamics and pinning behavior did not alter the DF morphology indicators‐the fractal dimension and roughness exponent‐which remained similar for the HI and HO sands.
Neuroglobin Regulates Hypoxic Response of Neuronal Cells through Hif-1α- and Nrf2-mediated Mechanism
Authors: Hota Kalpana B , Hota Sunil K , Srivastava Ravi B , Singh Shashi B
Published: April 2012

Oxygen sensing in hypoxic neurons has been classically attributed to cytochrome c oxidase and prolyl-4-hydroxylases and involves stabilization of transcription factors, hypoxia-inducible factor-1 α (Hif-1 α) and nuclear factor erythroid 2-related factor 2 (Nrf2) that mediate survival responses. On the contrary, release of cytochrome c into the cytosol during hypoxic stress triggers apoptosis in neuronal cells. We, here advocate that the redox state of neuroglobin (Ngb) could regulate both Hif-1 α and Nrf2 stabilization and cytochrome c release during hypoxia. The hippocampal regions showing higher expression of Ngb were less susceptible to global hypoxia-mediated neurodegeneration. During normoxia, Ngb maintained cytochrome c in the reduced state and prevented its release from mitochondria by using cellular antioxidants. Greater turnover of oxidized cytochrome c and increased utilization of cellular antioxidants during acute hypoxia altered cellular redox status and stabilized Hif-1 α and Nrf2 through Ngb-mediated mechanism. Chronic hypoxia, however, resulted in oxidation and degradation of Ngb, accumulation of ferric ions and release of cytochrome c that triggered apoptosis. Administration of N-acetyl-cysteine during hypoxic conditions improved neuronal survival by preventing Ngb oxidation and degradation. Taken together, these results establish a role for Ngb in regulating both the survival and apoptotic mechanisms associated with hypoxia.
Genome Replikin Count Predicts Increased Infectivity/Lethality of Viruses
Authors: Bogoch Samuel , Bogoch Elenore
Published: April 2012

The genomes of all groups of viruses whose sequences are listed on Pubmed, specimens since 1918, analyzed by a software from Bioradar UK Ltd., contain Replikins which range in concentration from a Replikin Count (number of Replikins per 100 amino acids) of less than 1 to 30 (see accompanying communications for higher Counts in tuberculosis, malaria, and cancer, associated with higher lethality). Counts of less than 4.0 were found in ‘resting’ virus states; Counts greater than 4.0, found to be associated with rapid replication, were found invariably to accompany or to predict virus outbreaks, by as much as two years, in viral hosts examined from salmon, to birds, to livestock, to humans. X-ray diffraction showed Replikins to be on the surface of the hemagglutinin gene of influenza and to spread as the Count increased from 3.2 to 10.1, prior to, then during, the 2009 H1N1 influenza pandemic. The degree of lethality of these outbreaks was found to be a function of the statistically significant increase in Replikin Count, particularly in the influenza polymerase gene p B1 or its equivalent in other viruses. Prediction up to two years in advance of the outbreak, and the geographic location of the outbreak, now done in 7/7 trials (see Bogoch, Nature Precedings), has permitted the solid phase synthesis of Replikin vaccines in 7 days, with time to permit manufacture, adequate testing for safety and efficacy, and distribution freeze-dried to all populations. These completely synthetic Replikins vaccines so far have been shown to be effective against Taura Syndrome virus in shrimp, and H5N1 in chickens. Thus for the first time this new technology provides the practical possibility to prevent pandemics rather than just to react to them.
Word-Finding Intervention for Children With Specific Language Impairment: A Multiple Single-Case Study
Authors: Bragard Anne , Schelstraete Marie-Anne , Snyers Perrine , James Deborah G. H.
Published: April 2012

Purpose

This study examined the effectiveness of a combined phonological and semantic intervention for children with specific language impairment who had word-finding difficulties (WFDs).

Method

To evaluate the intervention, a multiple single-case design was implemented with 4 children, ages 9;6 (years;months) to 13;9, who had WFDs. Some items were trained using a phonological intervention; others were trained using a semantic one. Lexical access outcomes were measured using a picture-naming test at pre- and posttesting.

Results

Three children exhibited a significant reduction in WFDs on the intervention words after 6 sessions. These effects were present at posttest and 6 months later for the treated words only and not the control words. Each child responded differently to the intervention, and these response patterns seemed to be related to each child’s linguistic profile.

Conclusion

This intervention seemed to achieve long-lasting reductions in children’s WFDs. The differential responses to phonological and semantic intervention imply the need to tailor intervention for differing children by matching it to their linguistic profile.
A new device for performing reference point indentation without a reference probe
Authors: Bridges Daniel , Randall Connor , Hansma Paul K.
Published: April 2012

Here we describe a novel, hand-held reference point indentation (RPI), instrument that is designed for clinical measurements of bone material properties in living patients. This instrument differs from previous RPI instruments in that it requires neither a reference probe nor removal of the periosteum that covers the bone, thus significantly simplifying its use in patient testing. After describing the instrument, we discuss five guidelines for optimal and reproducible results. These are: (1) the angle between the normal to the surface and the axis of the instrument should be less than 10°, (2) the compression of the main spring to trigger the device must be performed slowly (>1 s), (3) the probe tip should be sharper than 10 μm; however, a normalized parameter with a calibration phantom can correct for dull tips up to a 100 μm radius, (4) the ambient room temperature should be between 4 °C and 37 °C, and (5) the effective mass of the bone or material under test must exceed 1 kg, or if under 1 kg, the specimen should be securely anchored in a fixation device with sufficient mass (which is not a requirement of previous RPI instruments). Our experience is that a person can be trained with these guidelines in about 5 min and thereafter obtain accurate and reproducible results. The portability, ease of use, and minimal training make this instrument suitable to measure bone material properties in a clinical setting.
Travelling waves in a cylindrical magnetohydrodynamically forced flow
Authors: Boisson J. , Klochko A. , Daviaud F. , Padilla V. , Aumaître S.
Published: April 2012

We present an experimental study of a liquid metal flow electromagnetically forced in a large aspect ratio coaxial cylindrical geometry. An azimuthal Lorentz force is applied on the liquid metal gap, through a radial current and an axial magnetic field. Using ultrasonic velocity measurements, we focus on the effect of these two parameters on the flow properties. We show that, depending on the strength of the magnetic field and not only on the applied Lorentz force, different dynamical states exist. We first observe a stationary structure at low forcing. Then, two other regimes of different travelling waves are exhibited at higher forcing. We characterize them by their different frequencies and speeds. Higher magnetic fields clearly promote the faster waves. Connections with other magnetohydrodynamics instabilities are discussed.
High passive-stability diode-laser design for use in atomic-physics experiments
Authors: Cook Eryn C. , Martin Paul J. , Brown-Heft Tobias L. , Garman Jeffrey C. , Steck Daniel A.
Published: April 2012

We present the design and performance characterization of an external-cavity diode-laser system optimized for high stability, low passive spectral linewidth, low cost, and ease of in-house assembly. The main cavity body is machined from a single aluminum block for robustness to temperature changes and mechanical vibrations, and features a stiff and light diffraction-grating arm to suppress low-frequency mechanical resonances. The cavity is vacuum sealed, and a custom-molded silicone external housing further isolates the system from acoustic noise and temperature fluctuations. Beam shaping, optical isolation, and fiber coupling are integrated, and the design is easily adapted to many commonly used wavelengths. Resonance data, passive-linewidth data, and passive stability characterization of the new design demonstrate that its performance exceeds published specifications for commercial precision diode-laser systems. The design is fully documented and freely available.
Particle-in-cell simulation of collisionless undriven reconnection with open boundaries
Authors: Klimas Alex , Hesse Michael , Zenitani Seiji
Published: April 2012

The results are discussed of a 2½ dimensional, undriven, fully open-boundary particle-in-cell simulation of symmetric, anti-parallel reconnection. It is shown that the reconnection rate as measured by the strength of the out-of-plane electric field component at the dominant x-line is fast and unrelated to the emergence of magnetic islands. In contrast, it is shown that this reconnection rate normalized by the inflowing VAlf,inBin at the x-line does show a striking relationship to island emergence in a majority of cases. A detailed study of an outflow jet is discussed. It is shown that for this example the concept of an outer electron diffusion region is a misnomer. In this jet, the electrons are tied to the magnetic field motion in the local Hall plane. The extended electron diffusion region (E2DR) surrounding a reconnection site, where the out-of-plane non-ideal electric field is greater than zero, is discussed. The width d of this region is shown to remain between the ion and electron bounce length scales, in contrast, to the behavior in driven reconnection simulations in which d evolves from the electron bounce width to the ion bounce width, where it remains. The boundaries of the E2DR in the outflow directions are shown to mark the positions at which the electrons are magnetized and begin their drift with the field in the local Hall plane. It is shown that the aspect ratio d/L, in which L is the length of the E2DR, yields an excellent approximation to the normalized reconnection rate while the expression Ti/L, in which Ti is the ion temperature at the x-line, yields an excellent approximation to the un-normalized rate. It is concluded that the dynamics of the electrons in the E2DR is intimately related to the reconnection rate and it is suggested that in two dimensional, anti parallel, symmetric simulations, this region is the correct choice for the controversial electron diffusion region.
Experimental study of a photoelectron sheath
Authors: Dove Adrienne , Horanyi Mihaly , Wang Xu , Piquette Marcus , Poppe Andrew R. , Robertson Scott
Published: April 2012

We describe a set of laboratory experiments to reproduce and investigate the photoelectron layer that occurs above UV-illuminated surfaces in space. The experiments are done in vacuum with UV illumination at 172 nm that is sufficiently intense for the creation of a photoelectron layer above a large, planar metal surface with a Debye shielding distance of ∼7 centimeters, small in comparison with the scale of the experiment. The emitting surface electrically floats to a potential approximately 1.5 V more positive than a nearby equipotential surface. Retarding potential analysis of the energy distribution of the electrons emitted from the electrically floating surface, as well as Langmuir probe data, show an effective electron temperature of 1.4 (±0.3) eV and a density of 4×1010 m−3. Langmuir probe measurements are taken throughout the photoelectron sheath to determine the electron density, which show good agreement with results from a 1-D particle-in-cell simulation. These experiments enable the better understanding of the plasma environment of spacecraft, the moon, and other airless bodies in the solar system, and the processes that might be responsible for the charging, mobilization, and transport of dust particles on their surfaces.
Weighted Shapes for Embedding Perceived Wholes
Authors: Keles Hacer Yalim , Özkar Mine , Tari Sibel
Published: April 2012

Embedding parts is a key problem in computing when dealing with continuous matter such as shapes rather than discrete matter such as symbols. For computing part relations such as embedding, a technical framework that uses weighted shapes is introduced and implemented. In the proposed framework, for any given two-dimensional shape, the entire canvas is defined as a weighted shape and serves as a registration mark in detecting embedded parts. The approach treats shapes as perceived wholes rather than composed and eliminates the technical distinction between shape categories such as line, curve, or plane. The implementation is shown for two-dimensional shapes but is extendable to three dimensions. As demonstrated on a Seljuk geometric pattern, the framework allows for embedding multiple and various perceived wholes, thus exploring emerging shapes and shape relations to be used for analysis and synthesis in design.
Network Effects in Schelling's Model of Segregation: New Evidence from Agent-Based Simulation
Authors: Banos Amaud
Published: April 2012

According to two recent studies, Thomas Schelling's model of segregation is only weakly affected by the underlying spatial structure whatever its complexity. Such a conclusion is important from an urban planning perspective as it suggests that only a very restricted range of possible actions, if any, would be able to contribute to limiting social segregation, unless individual preferences are significantly modified. My own simulations show that, using appropriate graph-based spatial structures, one can reveal significant spatial effects and thus provide alternative planning insights. Cliques in networks indeed play a significant role, reinforcing segregation effects in Schelling's model. Introducing a small amount of noise into the model permits us to reveal this effect more precisely, without modifying the global behavior of the initial model. Furthermore, I show how a logistic model describes in a concise but precise way this global behavior at an aggregated level.
A Positive Theory of Network Connectivity
Authors: Levinson David , Huang Arthur
Published: April 2012

In this paper we develop a positive theory of network connectivity, seeking to provide the microfoundations of alternative network topologies as the result of self-interested actors. By building roads, landowners hope to increase their parcels' accessibility and economic value. A simulation model is performed on a grid-like land-use layer with a downtown in the center. The degree to which the networks are tree-like is evaluated. This research posits that road networks experience an evolutionary process where a tree-like structure first emerges around the centered parcel before the network pushes outward to the periphery. Road network topology becomes increasingly connected as the accessibility value of reaching other parcels increases. The results demonstrate that, even without a centralized authority, road networks can display the property of self-organization and evolution, and that, in the absence of intervention, the degree to which a network structure is tree-like or web-like results from the underlying economies.
Use of a Structured Panel Process to Define Quality Metrics for Antimicrobial Stewardship Programs
Authors: Morris Andrew M. , Brener Stacey , Dresser Linda , Daneman Nick , Dellit Timothy H. , Avdic Edina , Bell Chaim M.
Published: April 2012

Introduction.

Antimicrobial stewardship programs are being implemented in health care to reduce inappropriate antimicrobial use, adverse events, Clostridium difficile infection, and antimicrobial resistance. There is no standardized approach to evaluate the impact of these programs.

Objective.

To use a structured panel process to define quality improvement metrics for evaluating antimicrobial stewardship programs in hospital settings that also have the potential to be used as part of public reporting efforts.

Design.

A multiphase modified Delphi technique.

Setting.

Paper-based survey supplemented with a 1-day consensus meeting.

Participants.

A 10-member expert panel from Canada and the United States was assembled to evaluate indicators for relevance, effectiveness, and the potential to aid quality improvement efforts.

Results.

There were a total of 5 final metrics selected by the panel: (1) days of therapy per 1000 patient-days; (2) number of patients with specific organisms that are drug resistant; (3) mortality related to antimicrobial-resistant organisms; (4) conservable days of therapy among patients with community-acquired pneumonia (CAP), skin and soft-tissue infections (SSTI), or sepsis and bloodstream infections (BSI); and (5) unplanned hospital readmission within 30 days after discharge from the hospital in which the most responsible diagnosis was one of CAP, SSTI, sepsis or BSI. The first and second indicators were also identified as useful for accountability purposes, such as public reporting.

Conclusion.

We have successfully identified 2 measures for public reporting purposes and 5 measures that can be used internally in healthcare settings as quality indicators. These indicators can be implemented across diverse healthcare systems to enable ongoing evaluation of antimicrobial stewardship programs and complement efforts for improved patient safety.
CONTRA: copy number analysis for targeted resequencing
Authors: Li Jason , Lupat Richard , Amarasinghe Kaushalya C. , Thompson Ella R. , Doyle Maria A. , Ryland Georgina L. , Tothill Richard W. , Halgamuge Saman K. , Campbell Ian G. , Gorringe Kylie L.
Published: April 2012

Motivation: In light of the increasing adoption of targeted resequencing (TR) as a cost-effective strategy to identify disease-causing variants, a robust method for copy number variation (CNV) analysis is needed to maximize the value of this promising technology.

Results: We present a method for CNV detection for TR data, including whole-exome capture data. Our method calls copy number gains and losses for each target region based on normalized depth of coverage. Our key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. Our methods are made available via CONTRA (COpy Number Targeted Resequencing Analysis), a software package that takes standard alignment formats (BAM/SAM) and outputs in variant call format (VCF4.0), for easy integration with other next-generation sequencing analysis packages. We assessed our methods using samples from seven different target enrichment assays, and evaluated our results using simulated data and real germline data with known CNV genotypes.

Availability and implementation: Source code and sample data are freely available under GNU license (GPLv3) at http://contra-cnv.sourceforge.net/

Contact:  Jason.Li@petermac.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Evaluation of Fungicides for the Management of Botryosphaeria Canker of Grapevines
Authors: Pitt Wayne M. , Sosnowski Mark R. , Huang Rujuan , Qiu Yu , Steel Christopher C. , Savocchia Sandra
Published: April 2012

The family Botryosphaeriaceae comprises a number of species that are associated with the dieback disease of grapevine (Vitis vinifera), referred to as Botryosphaeria canker. To date, there are few effective agents available for the management of this disease. In this study, fungicides were evaluated for controlling the disease using a combination of in vitro tests and field trials. Twenty fungicides registered for use on other diseases in Australian viticulture were tested in vitro for their effect on mycelial growth of four species within the Botryosphaeriaceae. The concentrations of fungicide at which 50% of mycelial growth is inhibited (EC50values) were significantly affected both by fungicide and isolate (P < 0.001). Differences in sensitivities of the four species to the fungicides were negligible (0.41 to 0.59 mg/liter). The most effective fungicides were fludioxonil, carbendazim, fluazinam, tebuconazole, flusilazole, penconazole, procymidone, iprodione, myclobutanil, and pyraclostrobin, for which EC50values were <1.0 mg/liter. These fungicides were evaluated under field conditions, in addition to the pruning wound protectants Bacseal Super, Garrison, and ATCS tree wound dressing, as well as the biological control agent Vinevax. In field trials, carbendazim (Bavistin), fluazinam (Shirlan), tebuconazole (Folicur), Garrison, and ATCS tree wound dressing applied to freshly cut pruning wounds were the most effective and reduced infection by Diplodia seriata and D. mutila by 41 to 65%. These results suggest that the occurrence of Botryosphaeria canker on grapevines may be reduced via treatment of pruning wounds with selected fungicides as soon as possible after pruning.
A test of the oxidative damage hypothesis for discontinuous gas exchange in the locust
Locusta migratoria
Authors: Matthews Philip G. D. , Snelling Edward P. , Seymour Roger S. , White Craig R.
Published: April 2012

The discontinuous gas exchange cycle (DGC) is a breathing pattern displayed by many insects, characterized by periodic breath-holding and intermittently low tracheal O
2
levels. It has been hypothesized that the adaptive value of DGCs is to reduce oxidative damage, with low tracheal O
2
partial pressures (
P
O
2
∼2–5 kPa) occurring to reduce the production of oxygen free radicals. If this is so, insects displaying DGCs should continue to actively defend a low tracheal
P
O
2
even when breathing higher than atmospheric levels of oxygen (hyperoxia). This behaviour has been observed in moth pupae exposed to ambient
P
O
2
up to 50 kPa. To test this observation in adult insects, we implanted fibre-optic oxygen optodes within the tracheal systems of adult migratory locusts
Locusta migratoria
exposed to normoxia, hypoxia and hyperoxia. In normoxic and hypoxic atmospheres, the minimum tracheal
P
O
2
that occurred during DGCs varied between 3.4 and 1.2 kPa. In hyperoxia up to 40.5 kPa, the minimum tracheal
P
O
2
achieved during a DGC exceeded 30 kPa, increasing with ambient levels. These results are consistent with a respiratory control mechanism that functions to satisfy O
2
requirements by maintaining
P
O
2
above a critical level, not defend against high levels of O
2
.
Identification of intermittent control in man and machine
Authors: Loram Ian D. , van de Kamp Cornelis , Gollee Henrik , Gawthrop Peter J.
Published: April 2012

Regulation by negative feedback is fundamental to engineering and biological processes. Biological regulation is usually explained using continuous feedback models from both classical and modern control theory. An alternative control paradigm, intermittent control, has also been suggested as a model for biological control systems, particularly those involving the central nervous system. However, at present, there is no identification method explicitly formulated to distinguish intermittent from continuous control; here, we present such a method. The identification experiment uses a special paired-step set-point sequence. The corresponding data analysis use a conventional ARMA model to relate a theoretically derived equivalent set-point to control signal; the novelty lies in sequentially and iteratively adjusting the timing of the steps of this equivalent set-point to optimize the linear time-invariant fit. The method was verified using realistic simulation data and was found to robustly distinguish not only between continuous and intermittent control but also between event-driven intermittent and clock-driven intermittent control. When applied to human pursuit tracking, event-driven intermittent control was identified, with an intermittent interval of 260–310 ms (
n
= 6,
p
< 0.05). This new identification method is applicable for machine and biological applications.
Polyploidy in fungi: evolution after whole-genome duplication
Authors: Albertin Warren , Marullo Philippe
Published: April 2012

Polyploidy is a major evolutionary process in eukaryotes—particularly in plants and, to a less extent, in animals, wherein several past and recent whole-genome duplication events have been described. Surprisingly, the incidence of polyploidy in other eukaryote kingdoms, particularly within fungi, remained largely disregarded by the scientific community working on the evolutionary consequences of polyploidy. Recent studies have significantly increased our knowledge of the occurrence and evolutionary significance of fungal polyploidy. The ecological, structural and functional consequences of polyploidy in fungi are reviewed here and compared with the knowledge acquired with conventional plant and animal models. In particular, the genusSaccharomycesemerges as a relevant model for polyploid studies, in addition to plant and animal models.
The Helicase and RNaseIIIa Domains of Arabidopsis Dicer-Like1 Modulate Catalytic Parameters during MicroRNA Biogenesis
Authors: Liu Chenggang , Axtell Michael J. , Fedoroff Nina V.
Published: April 2012

Dicer-Like1 (DCL1), an RNaseIII endonuclease, and Hyponastic Leaves1 (HYL1), a double-stranded RNA-binding protein, are core components of the plant microRNA (miRNA) biogenesis machinery. hyl1 null mutants accumulate low levels of miRNAs and display pleiotropic developmental phenotypes. We report the identification of five new hyl1 suppressor mutants, all of which are alleles of DCL1. These new alleles affect either the helicase or the RNaseIIIa domains of DCL1, highlighting the critical functions of these domains. Biochemical analysis of the DCL1 suppressor variants reveals that they process the primary transcript (pri-miRNA) more efficiently than wild-type DCL1, with both higher K  cat and lower K  m values. The DCL1 variants largely rescue wild-type miRNA accumulation levels in vivo, but do not rescue the MIRNA processing precision defects of the hyl1 null mutant. In vitro, the helicase domain confers ATP dependence on DCL1-catalyzed MIRNA processing, attenuates DCL1 cleavage activity, and is required for precise MIRNA processing of some substrates.
Chiral crystals from an achiral molecule: 4,6-di-O-benzyl-1,3-O-benzylidene-2-O-(4-methoxybenzyl)-myo-5-inosose
Authors: Gurale Bharat P. , Gonnade Rajesh G. , Shashidhar Mysore S.
Published: April 2012

The title achiral compound, C35H34O7, crystallizes in the chiral monoclinic space groupP21. The molecules are densely packed to form a helical assembly along the crystallographic twofold screw axisviaC—H...O and C—H...π interactions. Interestingly, the unit-translated helical chains are loosely connectedviaa rather uncommon edge-to-edge Ph—H...H—Ph short contact (H...H = 2.33 Å).
Naltrexone in the treatment of opioid‐dependent pregnant women: the case for a considered and measured approach to research
Authors: Jones Hendrée E. , Chisolm Margaret S. , Jansson Lauren M. , Terplan Mishka
Published: April 2012

The present paper considers naltrexone to treat opioid dependence during pregnancy. The public health problem of opioid dependence and its treatment during pregnancy is reviewed first. Next, the naltrexone and opioid dependence treatment literature is summarized, with overviews of the pre‐clinical and clinical research on prenatal naltrexone exposure. Finally, considerations and recommendations for future medication research for the treatment of opioid dependence in pregnant women are provided. The efficacy of long‐acting injectable naltrexone relative to placebo, its blockade of opioid agonist euphoric effects, its lack of abuse and tolerance development and its modest adverse effect profile make it a potential medication for opioid‐dependent pregnant women. However, it is not without seriously concerning potential drawbacks, including the difficulty surrounding medication induction that may lead to vulnerability with regard to relapse, physical dependence re‐establishment, increased risk behaviors, treatment dropout and resulting opioid overdose. Before embarking on future research with this medication, the benefits and risks for the mother–embryo/fetus/child dyad should be weighed carefully. Should future research be conducted, a multi‐level commitment to proactive ethical research is needed to reach the ultimate goal of improving the lives of women and children affected by opioid dependence.