bluuebunny/crossref_metadata_2025 huggingface dataset:
Voltage- and calcium-dependent gating of TMEM16A/Ano1 chloride channels are physically coupled by the first intracellular loop
Authors: Xiao Qinghuan , Yu Kuai , Perez-Cornejo Patricia , Cui Yuanyuan , Arreola Jorge , Hartzell H. Criss
Published: May 2011

Ca
2+
-activated Cl
−
channels (CaCCs) are exceptionally well adapted to subserve diverse physiological roles, from epithelial fluid transport to sensory transduction, because their gating is cooperatively controlled by the interplay between ionotropic and metabotropic signals. A molecular understanding of the dual regulation of CaCCs by voltage and Ca
2+
has recently become possible with the discovery that Ano1 (TMEM16a) is an essential subunit of CaCCs. Ano1 can be gated by Ca
2+
or by voltage in the absence of Ca
2+
, but Ca
2+
- and voltage-dependent gating are very closely coupled. Here we identify a region in the first intracellular loop that is crucial for both Ca
2+
and voltage sensing. Deleting
448
EAVK in the first intracellular loop dramatically decreases apparent Ca
2+
affinity. In contrast, mutating the adjacent amino acids
444
EEEE abolishes intrinsic voltage dependence without altering the apparent Ca
2+
affinity. Voltage-dependent gating of Ano1 measured in the presence of intracellular Ca
2+
was facilitated by anions with high permeability or by an increase in [Cl
−
]
e
. Our data show that the transition between closed and open states is governed by Ca
2+
in a voltage-dependent manner and suggest that anions allosterically modulate Ca
2+
-binding affinity. This mechanism provides a unified explanation of CaCC channel gating by voltage and ligand that has long been enigmatic.
Herpesviral replication compartments move and coalesce at nuclear speckles to enhance export of viral late mRNA
Authors: Chang Lynne , Godinez William J. , Kim Il-Han , Tektonidis Marco , de Lanerolle Primal , Eils Roland , Rohr Karl , Knipe David M.
Published: May 2011

The role of the intranuclear movement of chromatin in gene expression is not well-understood. Herpes simplex virus forms replication compartments (RCs) in infected cell nuclei as sites of viral DNA replication and late gene transcription. These structures develop from small compartments that grow in size, move, and coalesce. Quantitative analysis of RC trajectories, derived from 4D images, shows that most RCs move by directed motion. Directed movement is impaired in the presence of actin and myosin inhibitors as well as a transcription inhibitor. In addition, RCs coalesce at and reorganize nuclear speckles. Lastly, distinct effects of actin and myosin inhibitors on viral gene expression suggest that RC movement is not required for transcription, but rather, movement results in the bridging of transcriptionally active RCs with nuclear speckles to form structures that enhance export of viral late mRNAs.
RAS-converting enzyme 1-mediated endoproteolysis is required for trafficking of rod phosphodiesterase 6 to photoreceptor outer segments
Authors: Christiansen Jeffrey R. , Kolandaivelu Saravanan , Bergo Martin O. , Ramamurthy Visvanathan
Published: May 2011

Prenylation is the posttranslational modification of a carboxyl-terminal cysteine residue of proteins that terminate with a CAAX motif. Following prenylation, the last three amino acids are cleaved off by the endoprotease, RAS-converting enzyme 1 (RCE1), and the prenylcysteine residue is methylated. Although it is clear that prenylation increases membrane affinity of CAAX proteins, less is known about the importance of the postprenylation processing steps. RCE1 function has been studied in a variety of tissues but not in neuronal cells. To approach this issue, we generated mice lacking
Rce1
in the retina. Retinal development proceeded normally in the absence of
Rce1
, but photoreceptor cells failed to respond to light and subsequently degenerated in a rapid fashion. In contrast, the inner nuclear and ganglion cell layers were unaffected. We found that the multimeric rod phosphodiesterase 6 (PDE6), a prenylated protein and RCE1 substrate, was unable to be transported to the outer segments in
Rce1
-deficient photoreceptor cells. PDE6 present in the inner segment of
Rce1
-deficient photoreceptor cells was assembled and functional. Synthesis and transport of transducin, and rhodopsin kinase 1 (GRK1), also prenylated substrates of RCE1, was unaffected by
Rce1
deficiency. We conclude that RCE1 is essential for the intracellular trafficking of PDE6 and survival of photoreceptor cells.
Dual and opposing roles of the unfolded protein response regulated by IRE1α and XBP1 in proinsulin processing and insulin secretion
Authors: Lee Ann-Hwee , Heidtman Keely , Hotamisligil Gökhan S. , Glimcher Laurie H.
Published: May 2011

As a key regulator of the unfolded protein response, the transcription factor XBP1 activates genes in protein secretory pathways and is required for the development of certain secretory cells. To elucidate the function of XBP1 in pancreatic β-cells, we generated β-cell-specific XBP1 mutant mice. Xbp1
f/f
;RIP-cre mice displayed modest hyperglycemia and glucose intolerance resulting from decreased insulin secretion from β-cells. Ablation of XBP1 markedly decreased the number of insulin granules in β-cells, impaired proinsulin processing, increased the serum proinsulin:insulin ratio, blunted glucose-stimulated insulin secretion, and inhibited cell proliferation. Notably, XBP1 deficiency not only compromised the endoplasmic reticulum stress response in β-cells but also caused constitutive hyperactivation of its upstream activator, IRE1α, which could degrade a subset of mRNAs encoding proinsulin-processing enzymes. Hence, the combined effects of XBP1 deficiency on the canonical unfolded protein response and its negative feedback activation of IRE1α caused β-cell dysfunction in XBP1 mutant mice. These results demonstrate that IRE1α has dual and opposing roles in β-cells, and that a precisely regulated feedback circuit involving IRE1α and its product XBP1s is required to achieve optimal insulin secretion and glucose control.
Dual-mode of insulin action controls GLUT4 vesicle exocytosis
Authors: Xu Yingke , Rubin Bradley R. , Orme Charisse M. , Karpikov Alexander , Yu Chenfei , Bogan Jonathan S. , Toomre Derek K.
Published: May 2011

Insulin stimulates translocation of GLUT4 storage vesicles (GSVs) to the surface of adipocytes, but precisely where insulin acts is controversial. Here we quantify the size, dynamics, and frequency of single vesicle exocytosis in 3T3-L1 adipocytes. We use a new GSV reporter, VAMP2-pHluorin, and bypass insulin signaling by disrupting the GLUT4-retention protein TUG. Remarkably, in unstimulated TUG-depleted cells, the exocytic rate is similar to that in insulin-stimulated control cells. In TUG-depleted cells, insulin triggers a transient, twofold burst of exocytosis. Surprisingly, insulin promotes fusion pore expansion, blocked by acute perturbation of phospholipase D, which reflects both properties intrinsic to the mobilized vesicles and a novel regulatory site at the fusion pore itself. Prolonged stimulation causes cargo to switch from ∼60 nm GSVs to larger exocytic vesicles characteristic of endosomes. Our results support a model whereby insulin promotes exocytic flux primarily by releasing an intracellular brake, but also by accelerating plasma membrane fusion and switching vesicle traffic between two distinct circuits.
Asymmetric properties of the Chlamydomonas reinhardtii cytoskeleton direct rhodopsin photoreceptor localization
Authors: Mittelmeier Telsa M. , Boyd Joseph S. , Lamb Mary Rose , Dieckmann Carol L.
Published: May 2011

The eyespot of the unicellular green alga Chlamydomonas reinhardtii is a photoreceptive organelle required for phototaxis. Relative to the anterior flagella, the eyespot is asymmetrically positioned adjacent to the daughter four-membered rootlet (D4), a unique bundle of acetylated microtubules extending from the daughter basal body toward the posterior of the cell. Here, we detail the relationship between the rhodopsin eyespot photoreceptor Channelrhodopsin 1 (ChR1) and acetylated microtubules. In wild-type cells, ChR1 was observed in an equatorial patch adjacent to D4 near the end of the acetylated microtubules and along the D4 rootlet. In cells with cytoskeletal protein mutations, supernumerary ChR1 patches remained adjacent to acetylated microtubules. In mlt1 (multieyed) mutant cells, supernumerary photoreceptor patches were not restricted to the D4 rootlet, and more anterior eyespots correlated with shorter acetylated microtubule rootlets. The data suggest a model in which photoreceptor localization is dependent on microtubule-based trafficking selective for the D4 rootlet, which is perturbed in mlt1 mutant cells.
Sharps Injuries among Employees of Acute Care Hospitals in Massachusetts, 2002–2007
Authors: Laramie Angela K. , Pun Vivian C. , Fang Shona C. , Kriebel David , Davis Letitia
Published: May 2011

Objective.

Sharps with engineered sharps injury protections (SESIPs) have been found to reduce risk of sharps injuries (Sis). We examined trends in SI rates among employees of acute care hospitals in Massachusetts, including the impact of SESIPs on SI trends during 2002-2007.

Design.

Prospective surveillance.

Setting.

Seventy-six acute care hospitals licensed by the Massachusetts Department of Public Health.

Participants.

Employees of acute care hospitals who reported Sis to their employers.

Methods.

Data on Sis in acute care hospitals collected by the Massachusetts Sharps Injury Surveillance System were used to examine trends in SI rates over time by occupation, hospital size, and device. Negative binomial regression was used to assess trends.

Results.

During 2002-2007, 16,158 Sis among employees of 76 acute care hospitals were reported to the surveillance system. The annual SI rate decreased by 22%, with an annual decline of 4.7% (P< .001). Rates declined significantly among nurses (—7.2% per year;P< .001) but not among physicians (—0.9% per year;P= .553). SI rates associated with winged steel needles and hypodermic needles and syringes also declined significantly as the proportion of injuries involving devices with sharps injury prevention features increased during the same time period.

Conclusion.

SI rates involving devices for which SESIPs are widely available and appear to be increasingly used have declined. The continued use of devices lacking SI protections for which SESIPs are available needs to be addressed. The extent to which injuries involving SESIPs are due to flaws in design or lack of experience and training must be examined.
Epidemiological Model forClostridium difficileTransmission in Healthcare Settings
Authors: Lanzas C. , Dubberke E. R. , Lu Z. , Reske K. A. , Gröhn Y. T.
Published: May 2011

Objective.

Recent outbreaks ofClostridium difficileinfection (CDI) have been difficult to control, and data indicate that the importance of different sources of transmission may have changed. Our objectives were to evaluate the contributions of asymptomatic and symptomatic C.difficilecarriers to new colonizations and to determine the most important epidemiological factors influencing C.difficiletransmission.

Design, Setting, and Patients.

Retrospective cohort study of all patients admitted to medical wards at a large tertiary care hospital in the United States in the calendar year 2008.

Methods.

Data from six medical wards and published literature were used to develop a compartmental model of C.difficiletransmission. Patients could be in one of five transition states in the model: resistant to colonization (R), susceptible to colonization (S), asymptomatically colonized without protection against CDI (C-), asymptomatically colonized with protection against CDI (C+), and diseased (ie, with CDI; D).

Results.

The contributions of C-, C+, and D patients to new colonizations were similar. The simulated basic reproduction number ranged from 0.55 to 1.99, with a median of 1.04. These values suggest that transmission within the ward alone from patients with CDI cannot sustain new C.difficilecolonizations and therefore that the admission of colonized patients plays an important role in sustaining transmission in the ward. The epidemiological parameters that ranked as the most influential were the proportion of admitted C-patients and the transmission coefficient for asymptomatic carriers.

Conclusion.

Our study underscores the need to further evaluate the role of asymptomatically colonized patients in C.difficiletransmission in healthcare settings.
Hospital Staff Perceptions of a Legislative Mandate for Methicillin-Resistant Staphylococcus aureus Screening
Authors: Wise Matthew E. , Weber Stephen G. , Schneider Amy , Stojcevski Meg , France Anne Marie , Schaefer Melissa K. , Lin Michael Y. , Kallen Alexander J. , Cochran Ronda L.
Published: May 2011

Objective.

In August 2007, Illinois passed legislation mandating methicillin-resistant Staphylococcus aureus (MRSA) admission screening for intensive care unit patients. We assessed hospital staff perceptions of the implementation of this law.

Design.

Mixed-methods evaluation using structured focus groups and questionnaires.

Setting.

Eight Chicago-area hospitals.

Participants.

Three strata of staff (leadership, midlevel, and frontline) at each hospital.

Methods.

All participants completed a questionnaire and participated in a focus group. Focus group transcripts were thematically coded and analyzed. The proportion of staff agreeing with statements about MRSA and the legislation was compared across staff types.

Results.

Overall, 126 hospital staff participated in 23 focus groups. Fifty-six percent of participants agreed that the legislation had a positive effect at their facility; frontline staff were more likely to agree than midlevel and leadership staff (P < .01). Perceived benefits of the legislation included increased awareness of MRSA among staff and better knowledge of the epidemiology of MRSA colonization. Perceived negative consequences included the psychosocial effect of screening and contact precautions on patients and increased use of resources. Most participants (59%) would choose to continue the activities associated with the legislation but advised facilities in states considering similar legislation to educate staff and patients about MRSA screening and to draft clear implementation plans.

Conclusion.

Staff from Chicago-area hospitals perceived that mandatory MRSA screening legislation resulted in some benefits but highlighted implementation challenges. States considering similar initiatives might minimize these challenges by optimizing messaging to patients and healthcare staff, drafting implementation plans, and developing program evaluation strategies.
Effect of Oral Hygiene with 0.12% Chlorhexidine Gluconate on the Incidence of Nosocomial Pneumonia in Children Undergoing Cardiac Surgery
Authors: Jácomo Andréa D. N. , Carmona Fabio , Matsuno Alessandra K. , Manso Paulo H. , Carlotti Ana P. C. P.
Published: May 2011

Objective.

To evaluate the effect of oral hygiene with 0.12% Chlorhexidine gluconate on the incidence of nosocomial pneumonia and ventilator-associated pneumonia (VAP) in children undergoing cardiac surgery.

Design.

Prospective, randomized, double-blind, placebo-controlled trial.

Setting.

Pediatric intensive care unit (PICU) at a tertiary care hospital.

Patients.

One hundred sixty children undergoing surgery for congenital heart disease, randomized into 2 groups: Chlorhexidine (n= 87) and control (n= 73).

Interventions.

Oral hygiene with 0.12% Chlorhexidine gluconate or placebo preoperatively and twice a day postoperatively until PICU discharge or death.

Results.

Patients in experimental and control groups had similar ages (median, 12.2 vs 10.8 months;P= .72) and risk adjustment for congenital heart surgery 1 score distribution (66% in category 1 or 2 in both groups;P= .17). The incidence of nosocomial pneumonia was 29.8% versus 24.6% (P= .46) and the incidence of VAP was 18.3% versus 15% (P = .57) in the Chlorhexidine and the control group, respectively. There was no difference in intubation time (P= .34), need for reintubation (P= .37), time interval between hospitalization and nosocomial pneumonia diagnosis (P= .63), time interval between surgery and nosocomial pneumonia diagnosis (P= .10), and time on antibiotics (P= .77) and vasoactive drugs (P= .16) between groups. Median length of PICU stay (3 vs 4 days;P= .53), median length of hospital stay (12 vs 11 days;P= .67), and 28-day mortality (5.7% vs 6.8%;P= .77) were also similar in the Chlorhexidine and the control group.

Conclusions.

Oral hygiene with 0.12% Chlorhexidine gluconate did not reduce the incidence of nosocomial pneumonia and VAP in children undergoing cardiac surgery.

Trial Registration.

ClinicalTrials.gov identifier: NCT00829842.
Clinical Vignettes Provide an Understanding of Antibiotic Prescribing Practices in Neonatal Intensive Care Units
Authors: Patel Sameer , Landers Timothy , Larson Elaine , Zaoutis Theoklis , Delamora Patricia , Paul David A. , Wong-McLoughlin Jennifer , Ferng Yu-hui , Saiman Lisa
Published: May 2011

Objective.

To use clinical vignettes to understand antimicrobial prescribing practices in neonatal intensive care units (NICUs).

Design.

Vignette-based survey.

Setting.

Four tertiary care NICUs.

Participants.

Antibiotic prescribers in NICUs.

Methods.

Clinicians from 4 tertiary care NICUs completed an anonymous survey containing 12 vignettes that described empiric, targeted, or prophylactic antibiotic use. Responses were compared with Centers for Disease Control and Prevention guidelines for appropriate use.

Results.

Overall, 161 (59% of 271 eligible respondents) completed the survey, 37% of whom had worked in NICUs for 7 or more years. Respondents were more likely to appropriately identify use of targeted therapy for methicillin-susceptible Staphylococcus aureus, that is, use of oxacillin rather than vancomycin, than for Escherichia coli, that is, use of first-generation rather than third-generation cephalosporin, (P < .01). Increased experience significantly predicted appropriate prescribing (P = .02 ). The proportion of respondents choosing appropriate duration of postsurgical prophylaxis (P < .01) and treatment for necrotizing enterocolitis differed by study site (P = .03).

Conclusions.

The survey provides insight into antibiotic prescribing practices and informs the development of future antibiotic stewardship interventions for NICUs.
Modulation of surface-enhanced Raman spectra by depth selective excitation of embedded indium tin oxide nanoisland arrays
Authors: Yang Yimin , Qiu Teng , Ou Huiling , Lang Xianzhong , Xu Qingyu , Kong Fan , Zhang Wenjun , Chu Paul K
Published: May 2011

Embedded transparent conducting indium tin oxide (ITO) nanoisland arrays were prepared by pulsed laser deposition of ITO films on roughened Si templates and post-annealing to investigate the surface-enhanced Raman scattering activities. Considerable Raman enhancement of a rhodamine 6G probe during Ar+ laser excitation was observed and modulated by the thickness of the ITO film due to the exponentially decaying field of the localized surface plasmon polaritons at the interface. Because the Raman-enhancing functional layer is protected at the ITO/Si interface, this system is reusable and also believed to be immune to contamination and other surface activities.
The study of electron scattering mechanisms in single crystal oxide nanowires
Authors: Berengue Olivia M , Simon Ricardo A , Leite Edson R , Chiquito Adenilson J
Published: May 2011

We report on transport measurements of individual Sn doped In2O3 nanowires. From these measurements we point out that spin–orbit and boundary scattering mechanisms seem to give a negligible contribution to the transport of electrons in these nanowires. In fact, these results can be extended to other oxide systems: the presence of a weak disorder arising from the random potential at the boundaries screen electrons away from the surface into the nanowire. Electrons travelling through the nanowire in inner conducting channels are not directly influenced by the surfaces and the boundary scattering is decreased. These findings were also supported by calculations of the electron distribution in the cross-section of the nanowires when some disorder is taken into account.
Why does the lumen maintenance of sodium–scandium metal halide lamps improve by VHF operation?
Authors: van Erk W , Luijks G M J F , Hitchcock W
Published: May 2011

Lifetime experiments show that sodium–scandium metal halide lamps perform better on very high frequency (VHF) drivers than on low frequency (LF) constant wattage autotransformer (CWA) ballasts. The question why, will be addressed with focus on arc tube aspects. It is argued that at high frequency operation sodium loss is less, and that the absence of thermal fluctuations in the electrode tip causes less damage and cracking to this part of the electrode. Sudden lm W−1drops, observed with CWA-operated lamps, most probably occur when the arc attaches on such a corroded and cracked surface.

Thorium is effective as an emitter both in the CWA and the VHF operation mode, despite the absence of cataphoretic transport to the cathode in the VHF case.
Ac breakdown in near-atmospheric pressure noble gases: I. Experiment
Authors: Sobota A , Kanters J H M , Manders F , Gendre M F , Hendriks J , van Veldhuizen E M , Haverlag M
Published: May 2011

Ac-driven breakdown processes have been explored much less than the pulsed or dc breakdown, even though they have possible applications in industry. This paper focuses on the frequency range between 60 kHz and 1 MHz, at a pin–pin electrode geometry and gap lengths of 4 or 7 mm. The breakdown process was examined in argon and xenon at 0.3 and 0.7 bar. We used electrical and optical measurements to characterize the breakdown process, to observe the influence of frequency change and the effect of ignition enhancers—UV irradiation and radioactive material.
Mercury-free high pressure discharge lamps dominated by molecular radiation
Authors: Käning M , Hitzschke L , Schalk B , Berger M , Franke St , Methling R
Published: May 2011

High intensity discharge (HID) lamps dominated by molecular radiation offer a very promising alternative for use in future light sources. They are able to deliver competitive efficacies of about 110 lm W−1 and higher, excellent colour rendering index above 90 and a correlated colour temperature in the 3000–4000 K region at the operating point near the Planckian locus. Moreover, these lamps are opening up the possibility of dimming. Due to the fact that they are able to omit mercury they are environmentally friendly.

The emission spectra generated by these HID lamps differ significantly from those of conventional lamps. The reason for this is the dominance of molecular radiation processes. In comparison with conventional HID lamps atomic contributions are usually rather small. In the present case they amount to less than about 10% of the total intensity in the visible range.
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: May 2011

The dependence of the gas phase emitter effect of Dy on a variation of the operating frequency between a few Hz and 2 kHz is investigated in a high intensity discharge lamp. The buffer gas of the lamp consisting of Ar, Kr and predominantly Hg is seeded with DyI3, its burner vessel is formed from transparent yttrium–alumina–garnet material. Phase and spatial resolved emission spectroscopy in front of the lamp electrode and pyrometric temperature measurements along the tungsten electrode are performed with a spectroscopic setup. Dy atom and ion densities in front of the electrode are deduced from absolute intensities of optically thin Dy lines and a plasma temperature, derived from the absolute intensity of mercury lines. Phase resolved values of the electrode tip temperature T
tip and input power P
in are obtained from temperature distributions along the electrode. Distinctly higher Dy ion and atom densities are measured in front of the electrode within the cathodic phase. With increasing operating frequency a reduction in both atoms and ions is observed in front of the cathode. In contrast, an increase in the ion density in front of the anode is seen. Moreover, the Dy ion density is drastically reduced by an additional seeding of the lamp with TlI. It is found that an up rating of the Dy ion density is correlated with a decline of T
tip and P
in. At higher frequencies this effect takes place not only within the cathodic phase but also within the anodic phase. The reduction of the average electrode tip temperature of the order of several hundred kelvin compared with a YAG lamp with a pure mercury filling is explained by a Dy monolayer on the electrode surface which is sustained by a Dy ion current.
Dust in magnetic fusion devices
Authors: Krasheninnikov S I , Smirnov R D , Rudakov D L
Published: May 2011

This paper reviews recent results of the study of dust in magnetic fusion devices. Assessment of the role of dust in current fusion devices and ITER is presented. Dust diagnostics, main experimental results, different theoretical aspects of dust in fusion plasmas, as well as the comparison of theoretical estimates and numerical simulations with available experimental data are discussed. Some limitations of current theoretical models of dust–plasma interactions and the gaps in current experimental and theoretical approaches to dust study in fusion devices are considered. Possible directions for further advancements are suggested.
On the “main conjecture” of equivariant Iwasawa theory
Authors: Ritter Jürgen , Weiss Alfred
Published: May 2011

We prove the “main conjecture” of equivariant Iwasawa theory whenμ=0\mu =0.
Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method
Authors: Jia Gengjie , Stephanopoulos Gregory N. , Gunawan Rudiyanto
Published: May 2011

Motivation: Time-series measurements of metabolite concentration have become increasingly more common, providing data for building kinetic models of metabolic networks using ordinary differential equations (ODEs). In practice, however, such time-course data are usually incomplete and noisy, and the estimation of kinetic parameters from these data is challenging. Practical limitations due to data and computational aspects, such as solving stiff ODEs and finding global optimal solution to the estimation problem, give motivations to develop a new estimation procedure that can circumvent some of these constraints.

Results: In this work, an incremental and iterative parameter estimation method is proposed that combines and iterates between two estimation phases. One phase involves a decoupling method, in which a subset of model parameters that are associated with measured metabolites, are estimated using the minimization of slope errors. Another phase follows, in which the ODE model is solved one equation at a time and the remaining model parameters are obtained by minimizing concentration errors. The performance of this two-phase method was tested on a generic branched metabolic pathway and the glycolytic pathway of Lactococcus lactis. The results showed that the method is efficient in getting accurate parameter estimates, even when some information is missing.

Contact:  rudi.gunawan@chem.ethz.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Reconciling single-species TACs in the North Sea demersal fisheries using the Fcube mixed-fisheries advice framework
Authors: Ulrich Clara , Reeves Stuart A. , Vermard Youen , Holmes Steven J. , Vanhee Willy
Published: May 2011

Ulrich, C., Reeves, S. A., Vermard, Y., Holmes, S. J., and Vanhee, W. 2011. Reconciling single-species TACs in the North Sea demersal fisheries using the Fcube mixed-fisheries advice framework. – ICES Journal of Marine Science, 68: 1535–1547. Single-species management is a cause of discarding in mixed fisheries, because individual management objectives may not be consistent with each other and the species are caught simultaneously in relatively unselective fishing operations. As such, the total allowable catch (TAC) of one species may be exhausted before the TAC of another, leading to catches of valuable fish that cannot be landed legally. This important issue is, however, usually not quantified and not accounted for in traditional management advice. A simple approach using traditional catch and effort information was developed, estimating catch potentials for distinct fleets (groups of vessels) and métiers (type of activity), and hence quantifying the risks of over- and underquota utilization for the various stocks. This method, named Fcube (Fleet and Fisheries Forecast), was applied successfully to international demersal fisheries in the North Sea and shaped into the advice framework. The substantial overquota catches of North Sea cod likely under the current fisheries regimes are quantified, and it is estimated that the single-species management targets for North Sea cod cannot be achieved unless substantial reductions in TACs of all other stocks and corresponding effort reductions are applied.
Fixed Effects Vector Decomposition: A Magical Solution to the Problem of Time-Invariant Variables in Fixed Effects Models?
Authors: Greene William
Published: May 2011

Plümper and Troeger (2007) propose a three-step procedure for the estimation of a fixed effects (FE) model that, it is claimed, “provides the most reliable estimates under a wide variety of specifications common to real world data.” Their fixed effects vector decomposition (FEVD) estimator is startlingly simple, involving three simple steps, each requiring nothing more than ordinary least squares (OLS). Large gains in efficiency are claimed for cases of time-invariant and slowly time-varying regressors. A subsequent literature has compared the estimator to other estimators of FE models, including the estimator of Hausman and Taylor (1981) also (apparently) with impressive gains in efficiency. The article also claims to provide an efficient estimator for parameters on time-invariant variables (TIVs) in the FE model. None of the claims are correct. The FEVD estimator simply reproduces (identically) the linear FE (dummy variable) estimator then substitutes an inappropriate covariance matrix for the correct one. The consistency result follows from the fact that OLS in the FE model is consistent. The “efficiency” gains are illusory. The claim that the estimator provides an estimator for the coefficients on TIVs in an FE model is also incorrect. That part of the parameter vector remains unidentified. The “estimator” relies upon a strong assumption that turns the FE model into a type of random effects model.
Fixed-Effects Vector Decomposition: Properties, Reliability, and Instruments
Authors: Plümper Thomas , Troeger Vera E.
Published: May 2011

This article reinforces our 2007 Political Analysis publication in demonstrating that the fixed-effects vector decomposition (FEVD) procedure outperforms any other estimator in estimating models that suffer from the simultaneous presence of time-varying variables correlated with unobserved unit effects and time-invariant variables. We compare the finite-sample properties of FEVD not only to the Hausman-Taylor estimator but also to the pretest estimator and the shrinkage estimator suggested by Breusch, Ward, Nguyen and Kompas (BWNK), and Greene in this symposium. Moreover, we correct the discussion of Greene and BWNK of FEVD's asymptotic and finite-sample properties.
Of Fixed-Effects and Time-Invariant Variables
Authors: Beck Nathaniel
Published: May 2011

What follows is a longish controversy (two critiques, a reply and two rejoinders) over the quality of the estimates and associated SEs provided by Plümper and Troeger's (2007) “fixed-effect vector decomposition” (FEVD) procedure; Plümper and Troeger (PT) will refer to that article and not any persons. My role is to lay out some issues that separate the authors rather than to adjudicate between them. As with many controversies, a bit of heat is generated along with some light. Readers care a bit less than the authors about what was said when, but they do care a lot about what appropriate method to use when a panel data model has both unit-specific intercepts and variables that are invariant over a unit. Thus, I also take it upon myself to discuss some things that I gleaned from this controversy; this discussion has a bit less heat than what follows, but of course readers should judge the evidence for themselves.
FEVD: Just IV or Just Mistaken?
Authors: Breusch Trevor , Ward Michael B. , Nguyen Hoa Thi Minh , Kompas Tom
Published: May 2011

Fixed effects vector decomposition (FEVD) is simply an instrumental variables (IV) estimator with a particular choice of instruments and a special case of the well-known Hausman-Taylor IV procedure. Plümper and Troeger (PT) now acknowledge this point and disown the three-stage procedure that previously defined FEVD. Their old recipe for SEs, which has regrettably been used in dozens of published research papers, produces dramatic overconfidence in the estimates. Again PT concede the point and now adopt the standard IV formula for SEs. Knowing that FEVD is an application of IV also has the benefit of focusing attention on the choice of instruments. Now it seems PT claim that the FEVD instruments are always the best choice, on the grounds that one cannot know whether any potential instrument is correlated with the unit effect. One could just as readily make the same specious claim about other estimators, such as ordinary least squares, and support it with similar Monte Carlo assumptions and evidence.
First Report of Phytophthora infestans Genotype US23 Causing Late Blight in Canada
Authors: Kawchuk L. M. , Howard R. J. , Peters R. D. , Al-Mughrabi K. I.
Published: May 2011

Late blight is caused by the oomycete Phytophthora infestans (Mont.) de Bary and is one of the most devastating diseases of potato and tomato. Late blight occurs in all major potato- and tomato-growing regions of Canada. Its incidence in North America increased during 2009 and 2010 (2). Foliar disease symptoms appeared earlier than usual (June rather than July) and coincided with the identification of several new P. infestans genotypes in the United States, each with unique characteristics. Prior to 2007, isolates collected from potato and tomato crops were mainly US8 or US11 genotypes (1). However, P. infestans populations in the United States have recently experienced a major genetic evolution, producing isolates with unique genotypes and epidemiological characteristics in Florida and throughout the northeastern states (2). Recent discoveries of tomato transplants with late blight for sale at Canadian retail outlets prompted an examination of the genotypes inadvertently being distributed and causing disease in commercial production areas in Canada. Analysis of isolates of P. infestans from across Canada in 2010 identified the US23 genotype for the first time from each of the four western provinces (Manitoba, Saskatchewan, Alberta, and British Columbia) but not from eastern Canada. Allozyme banding patterns at the glucose phosphate isomerase (Gpi) locus indicated a 100/100 profile consistent with US6 and US23 genotypes (4). Mating type assays confirmed the isolates to be A1 and in vivo metalaxyl sensitivity was observed. Restriction fragment length polymorphic analysis of 50 isolates from western Canada with the multilocus RG57 sequence and EcoRI produced the DNA pattern 1, 2, 5, 6, 10, 13, 14, 17, 20, 21, 24, 24a, 25 that was indicative of US23 (3). The recently described P. infestans genotype US23 appears to be more aggressive on tomato, and although isolates were recovered from both tomato and potato, disease symptoms were often more severe on tomato. Results indicate that movement and evolution of new P. infestans genotypes have contributed to the increased incidence of late blight and that movement of the pathogen on retail plantlets nationally and internationally may provide an additional early season source of inoculum. A major concern is that the introduced new A1 populations in western Canada have established a dichotomy with the endogenous A2 populations in eastern Canada, increasing the potential for sexual recombination producing oospores and additional genotypes should these populations merge.

References: (1) Q. Chen et al. Am. J. Potato Res. 80:9, 2003. (2) K. Deahl. (Abstr.) Phytopathology 100(suppl.):S161, 2010. (3) S. B. Goodwin et al. Curr. Genet. 22:107, 1992. (4) S. B. Goodwin et al. Phytopathology 88:939, 2004.
Suppression of Common Scab of Potato Caused by Streptomyces turgidiscabies Using Lopsided Oat Green Manure
Authors: Sakuma F. , Maeda M. , Takahashi M. , Hashizume K. , Kondo N.
Published: May 2011

Field experiments were conducted to determine the effect of green manure as fallow on common scab of potato caused by Streptomyces turgidiscabies. Significantly fewer diseased tubers were harvested from soil incorporated with lopsided oat or woolly pod vetch compared with those from oat and continuous potato cultivation in a planter experiment. Each field experiment consisted of lopsided oat cultivated during the spring and summer prior to the potato planting. Comparisons were also made with several other treatments, including cultivation of woolly pod vetch, oat, soybean, sugar beet, and potato (‘Yukirasya’, which is resistant to potato common potato scab) and soil application of Ferosand (Fe, mainly FeSO4, to decrease the soil pH). In field experiments conducted during 1999–2000, treatment with lopsided oat followed by lopsided oat or woolly pod vetch was significantly more effective at suppressing the disease severity than oat and continuous potato cultivation (P < 0.001). An increase in the marketable tuber ratio was also more significant than for oat and continuous potato cultivation (P < 0.001). In field experiments conducted during 2000–01, lopsided oat cultivation alone and with the application of Ferosand (1.8 t/ha) or resistant potato cultivar treatment were significantly more effective at suppressing the disease severity and incidence than sugar beet cultivation (P < 0.001), even under high disease intensity in the field. However, potato yield had a tendency to reduce after lopsided oat treatment with an application of Ferosand (1.8 t/ha) compared with lopsided oat alone or the application of Ferosand at 600 kg/ha, due to low pH conditions. In field experiments conducted during 2001–02, the lowest severity and incidence of common scab of potato were observed in soil treated with lopsided oat than with other treatments (P < 0.05 and P < 0.001, respectively). These findings suggest that lopsided oat used as fallow green manure can reduce the severity of common scab and increase potato yield.
Sublethal Doses of Mefenoxam Enhance Pythium Damping-off of Geranium
Authors: Garzón Carla D. , Molineros Julio E. , Yánez Jennifer M. , Flores Francisco J. , del Mar Jiménez-Gasco María , Moorman Gary W.
Published: May 2011

The effect of sublethal doses of fungicides on fungicide-resistant Pythium isolates is unknown but potentially relevant to disease management. Occasional grower reports of Pythium disease increases after fungicide applications and our observations of greater radial growth in vitro on fungicide-amended media than on nonamended media suggests that Pythium isolates may be stimulated by sublethal doses of fungicides. The objectives of this study were to determine whether Pythium isolates were stimulated by sublethal doses of mefenoxam in vitro and whether this stimulation had any influence on Pythium damping-off of geranium seedlings. A mefenoxam-resistant isolate of Pythium aphanidermatum displayed 10% mean radial growth increase in vitro with mefenoxam at 1 × 10–10 μg/ml compared with growth on nonamended agar (nonsignificant). Geranium seedlings treated with one of eight mefenoxam concentrations were inoculated with 5-mm-diameter colonized agar plugs and evaluated for disease severity every 24 h. The area under the disease progress curve and the survival curve were estimated for each treatment and compared. Significant increases in damping-off were observed with mefenoxam at 1 × 10–6 and 1 × 10–10 μg/ml. Our data indicate that a Pythium isolate with resistance to mefenoxam can be stimulated by sublethal doses of the fungicide, and that this stimulation can result in significantly higher rates of Pythium damping-off of geranium seedlings.
Advances in Plant Virus Evolution: Translating Evolutionary Insights into Better Disease Management
Authors: Acosta-Leal R. , Duffy S. , Xiong Z. , Hammond R. W. , Elena S. F.
Published: May 2011

Recent studies in plant virus evolution are revealing that genetic structure and behavior of virus and viroid populations can explain important pathogenic properties of these agents, such as host resistance breakdown, disease severity, and host shifting, among others. Genetic variation is essential for the survival of organisms. The exploration of how these subcellular parasites generate and maintain a certain frequency of mutations at the intra- and inter-host levels is revealing novel molecular virus–plant interactions. They emphasize the role of host environment in the dynamic genetic composition of virus populations. Functional genomics has identified host factors that are transcriptionally altered after virus infections. The analyses of these data by means of systems biology approaches are uncovering critical plant genes specifically targeted by viruses during host adaptation. Also, a next-generation resequencing approach of a whole virus genome is opening new avenues to study virus recombination and the relationships between intra-host virus composition and pathogenesis. Altogether, the analyzed data indicate that systematic disruption of some specific parameters of evolving virus populations could lead to more efficient ways of disease prevention, eradication, or tolerable virus–plant coexistence.
Treatment with Epinephrine (Adrenaline) in Suspected Anaphylaxis during Anesthesia in Denmark
Authors: Garvey Lene H. , Belhage Bo , Krøigaard Mogens , Husum Bent , Malling Hans-Jørgen , Mosbech Holger
Published: May 2011

Background

Literature on the use of epinephrine in the treatment of anaphylaxis during anesthesia is very limited. The objective of this study was to investigate how often epinephrine is used in the treatment of suspected anaphylaxis during anesthesia in Denmark and whether timing of treatment is important.

Methods

A retrospective study of 270 patients investigated at the Danish Anaesthesia Allergy Centre after referral due to suspected anaphylaxis during anesthesia was performed. Reactions had been graded by severity: C1, mild reactions; C2, moderate reactions; C3, anaphylactic shock with circulatory instability; C4, cardiac arrest. Use of epinephrine, dosage, route of administration, and time between onset of circulatory instability and epinephrine administration were noted.

Results

A total of 122 (45.2%) of referred patients had C3 or C4 reactions; of those, 101 (82.8%) received epinephrine. Route of administration was intravenous in 95 (94%) patients. Median time from onset of reported hypotension to treatment with epinephrine was 10 min (range, 1-70 min). Defining epinephrine treatment less than or equal to 10 min after onset of hypotension as early, and more than 10 min as late, infusion was needed in 12 of 60 patients (20%) treated early versus 12 of 35 patients (34%) treated late (odds ratio, 2.09) (95% confidence interval, 0.81-5.35).

Conclusion

Anaphylaxis may be difficult to diagnose during anesthesia, and treatment with epinephrine can be delayed as a consequence. Anaphylaxis should be considered and treated in patients with circulatory instability during anesthesia of no apparent cause who do not respond to the usual treatments.
Ultrasound Imaging Facilitates Spinal Anesthesia in Adults with Difficult Surface Anatomic Landmarks
Authors: Chin Ki Jinn , Perlas Anahi , Chan Vincent , Brown-Shreves Danielle , Koshkin Arkadiy , Vaishnav Vandana
Published: May 2011

Background

Poor surface anatomic landmarks are highly predictive of technical difficulty in neuraxial blockade. The authors examined the use of ultrasound imaging to reduce this difficulty.

Methods

The authors recruited 120 orthopedic patients with one of the following: body mass index more than 35 kg/m² and poorly palpable spinous processes; moderate to severe lumbar scoliosis; or previous lumbar spine surgery. Patients were randomized to receive spinal anesthetic by the conventional surface landmark-guided technique (group LM) or by an ultrasound-guided technique (group US). Patients in group US had a preprocedural ultrasound scan to locate and mark a suitable needle insertion point. The primary outcome was the rate of successful dural puncture on the first needle insertion attempt. Normally distributed data were summarized as mean ± SD and nonnormally distributed data were summarized as median [interquartile range].

Results

The first-attempt success rate was twice as high in group US than in group LM (65% vs. 32%; P < 0.001). There was a twofold difference between groups in the number of needle insertion attempts (group US, 1 [1-2] vs. group LM, 2 [1-4]; P < 0.001) and number of needle passes (group US, 6 [1-10] vs. group LM, 13 [5-21]; P = 0.003). More time was required to establish landmarks in group US (6.7 ± 3.1; group LM, 0.6 ± 0.5 min; P < 0.001), but this was partially offset by a shorter spinal anesthesia performance time (group US, 5.0 ± 4.9 vs. group LM, 7.3 ± 7.6 min; P = 0.038). Similar results were seen in subgroup analyses of patients with body mass index more than 35 kg/m and patients with poorly palpable landmarks.

Conclusion

Preprocedural ultrasound imaging facilitates the performance of spinal anesthesia in the nonobstetric patient population with difficult anatomic landmarks.
Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition
Authors: Aanes Håvard , Winata Cecilia L. , Lin Chi Ho , Chen Jieqi P. , Srinivasan Kandhadayar G. , Lee Serene G.P. , Lim Adrian Y.M. , Hajan Hajira Shreen , Collas Philippe , Bourque Guillaume , Gong Zhiyuan , Korzh Vladimir , Aleström Peter , Mathavan Sinnakaruppan
Published: May 2011

Maternally deposited mRNAs direct early development before the initiation of zygotic transcription during mid-blastula transition (MBT). To study mechanisms regulating this developmental event in zebrafish, we applied mRNA deep sequencing technology and generated comprehensive information and valuable resources on transcriptome dynamics during early embryonic (egg to early gastrulation) stages. Genome-wide transcriptome analysis documented at least 8000 maternal genes and identified the earliest cohort of zygotic transcripts. We determined expression levels of maternal and zygotic transcripts with the highest resolution possible using mRNA-seq and clustered them based on their expression pattern. We unravel delayed polyadenylation in a large cohort of maternal transcripts prior to the MBT for the first time in zebrafish. Blocking polyadenylation of these transcripts confirms their role in regulating development from the MBT onward. Our study also identified a large number of novel transcribed regions in annotated and unannotated regions of the genome, which will facilitate reannotation of the zebrafish genome. We also identified splice variants with an estimated frequency of 50%–60%. Taken together, our data constitute a useful genomic information and valuable transcriptome resource for gene discovery and for understanding the mechanisms of early embryogenesis in zebrafish.