bluuebunny/crossref_metadata_2025_split huggingface dataset:
Confirmation bias: why psychiatrists stick to wrong preliminary diagnoses
Authors: Mendel R. , Traut-Mattausch E. , Jonas E. , Leucht S. , Kane J. M. , Maino K. , Kissling W. , Hamann J. 
Published: May 2011

BackgroundDiagnostic errors can have tremendous consequences because they can result in a fatal chain of wrong decisions. Experts assume that physicians' desire to confirm a preliminary diagnosis while failing to seek contradictory evidence is an important reason for wrong diagnoses. This tendency is called ‘confirmation bias’.MethodTo study whether psychiatrists and medical students are prone to confirmation bias and whether confirmation bias leads to poor diagnostic accuracy in psychiatry, we presented an experimental decision task to 75 psychiatrists and 75 medical students.ResultsA total of 13% of psychiatrists and 25% of students showed confirmation bias when searching for new information after having made a preliminary diagnosis. Participants conducting a confirmatory information search were significantly less likely to make the correct diagnosis compared to participants searching in a disconfirmatory or balanced way [multiple logistic regression: odds ratio (OR) 7.3, 95% confidence interval (CI) 2.53–21.22, p<0.001; OR 3.2, 95% CI 1.23–8.56, p=0.02]. Psychiatrists conducting a confirmatory search made a wrong diagnosis in 70% of the cases compared to 27% or 47% for a disconfirmatory or balanced information search (students: 63, 26 and 27%). Participants choosing the wrong diagnosis also prescribed different treatment options compared with participants choosing the correct diagnosis.ConclusionsConfirmatory information search harbors the risk of wrong diagnostic decisions. Psychiatrists should be aware of confirmation bias and instructed in techniques to reduce bias.
Prevalence of psychiatric diagnoses in preterm and full-term children, adolescents and young adults: a meta-analysis
Authors: Burnett A. C. , Anderson P. J. , Cheong J. , Doyle L. W. , Davey C. G. , Wood S. J. 
Published: May 2011

BackgroundPreterm (PT) birth and low birth weight (LBW) are high-prevalence events that are associated with adverse outcomes in the longer term, with vulnerability increasing as maturity at birth decreases. Psychiatric symptomatology appears heightened in PT/LBW survivors, though there are some discordant findings from studies using questionnaire measures, particularly with respect to anxiety and depressive symptoms.MethodThis article synthesises findings from research using clinical psychiatric diagnostic criteria in PT/LBW individuals aged 10–25 years compared with term-born peers. Key outcomes of interest were the rates of individuals receiving any psychiatric diagnosis and the number of diagnoses of anxiety or depressive disorders.ResultsA literature search for studies reporting prevalence of ‘any diagnosis’ yielded five studies that met inclusion criteria, with a total of 565 PT/LBW and 533 control individuals. Also, five studies were found that reported rates of anxiety/depression (692 PT/LBW and 605 control individuals). The risk of these outcomes was increased for PT/LBW individuals compared with controls [any diagnosis: odds ratio (OR) 3.66, 95% confidence interval (CI) 2.57–5.21; anxiety or depressive disorder: OR 2.86, 95% CI 1.73–4.73].ConclusionsThe studies reviewed here indicate that, in addition to monitoring and management of medical and cognitive sequelae, the psychological well-being of PT/LBW individuals should be a key part of ongoing care.
New concepts of molecular communication among neurons
Authors: Dismukes R. Key 
Published: May 2011

AbstractRecently a number of complex electrophysiological responses to neurotransmitters have been observed that cannot be described as simple excitation or inhibition. These responses are often characterized as modulatory, although there is no consensus on what defines modulation. Morphological studies reveal certain neurotransmitters stored in what might be release sites without synaptic contact. There is no direct evidence for nonsynaptic release from CNS sites, although such release does occur in the periphery and in invertebrates. Nonsynaptic release might provide a basis for diffuse one-cell-to-many communication, but it might also simply be a means of sending the transmitter to a broader area of a single neuron than occurs in typical synapses. Several kinds of macromolecules have been found to be transported in a retrograde direction – and in some cases transsynaptically. There have been suggestions that some neurons may release more than one type of transmitter. Particularly intriguing is the possibility of release of substances that modulate actions of a primary transmitter. Taken together this range of evidence suggests that neurons may use a variety of forms of molecular communication in addition to traditionally described synaptic transmission.Several authors have suggested modes of communication distinct from classical synaptic transmission and have classified released substances using terms such as neurohumor, neurohormone, neuroregulator, and modulator. These suggestions have the heuristic value of drawing together diverse kinds of data, but it remains to be established that the pieces fit together in that fashion – for example, that complex electrophysiological effects are associated with substances released nonsynaptically. In order to reduce confusion, a flexible, generic approach to nomenclature for substances released from neurons and for hypothetical modes of communication is recommended. Some behavioral implications of nonconventional transmission are considered.
Analyzing vision at the complexity level
Authors: Tsotsos John K. 
Published: May 2011

AbstractThe general problem of visual search can be shown to be computationally intractable in a formal, complexity-theoretic sense, yet visual search is extensively involved in everyday perception, and biological systems manage to perform it remarkably well. Complexity level analysis may resolve this contradiction. Visual search can be reshaped into tractability through approximations and by optimizing the resources devoted to visual processing. Architectural constraints can be derived using the minimum cost principle to rule out a large class of potential solutions. The evidence speaks strongly against bottom-up approaches to vision. In particular, the constraints suggest an attentional mechanism that exploits knowledge of the specific problem being solved. This analysis of visual search performance in terms of attentional influences on visual information processing and complexity satisfaction allows a large body of neurophysiological and psychological evidence to be tied together.
The potential role of small fish species in improving micronutrient deficiencies in developing countries: building evidence
Authors: Kawarazuka Nozomi , Béné Christophe 
Published: May 2011

AbstractObjectiveTo build a comprehensive overview of the potential role of fish in improving nutrition with respect to certain micronutrient deficiencies in developing countries.DesignA comprehensive literature review was completed. For this the electronic library databases ASFA, CABD and Scopus were systematically searched and relevant references cited in these sources were carefully analysed. The search terms used were ‘fish’, ‘small fish species’, ‘micronutrients’, ‘food-based strategies’, ‘fish consumption’ and ‘developing countries’. The quality of data on nutritional analyses was carefully reviewed and data that lacked proper information on methods, units and samples were excluded.ResultsThe evidence collected confirmed the high levels of vitamin A, Fe and Zn in some of the small fish species in developing countries. These small fish are reported to be more affordable and accessible than the larger fish and other usual animal-source foods and vegetables. Evidence suggests that these locally available small fish have considerable potential as cost-effective food-based strategies to enhance micronutrient intakes or as a complementary food for undernourished children. However, the present review shows that only a few studies have been able to rigorously assess the impact of fish consumption on improved nutritional status in developing countries.ConclusionsFurther research is required in areas such as determination of fish consumption patterns of poor households, the nutritional value of local fish and other aquatic animals and the impact of fish intake on improved nutritional status in developing countries where undernutrition is a major public health problem.
Mutually agreed solutions under the WTO Dispute Settlement Understanding: An Analytical Framework after theSoftwood LumberArbitration
Authors: ALVAREZ-JIMÉNEZ ALBERTO 
Published: May 2011

AbstractThe unprecedented enforcement of the mutually agreed solution (MAS) in the WTOSoftwood Lumberdisputes – but outside the WTO dispute settlement system – and the recent use of MAS to resolve important trade disputes should trigger a hard look at these dispute settlement instruments provided for by the DSU. This article seeks to provide a detailed framework of analysis of MAS under the DSU that allows the WTO dispute settlement system to adjudicate MAS-related disputes. WTO Members should not go outside the system to enforce MAS. The article illustrates that MAS can create binding obligations and that MAS are WTO law, given the explicit reference to them in the DSU, their intimate relation with the WTO-covered agreements and the requirement for compliance with these agreements. In addition, the article offers an interpretation of the DSU that allows panels and the Appellate Body to regard MAS as applicable law. This interpretation is offered in the view that there is no policy reason to sustain that these controversies – always fully related to WTO rights and obligations and framed under the corners of the covered agreements – have to be resolved by an adjudication system other than that of the WTO.
Controlled studies further the development of practical guidelines to manage dodder (Cuscuta gronovii) in cranberry production with short-term flooding
Authors: O'Connell James M. , Sandler Hilary A. , Adler Lynn S. , Caruso Frank L. 
Published: May 2011

AbstractFlooding is an inexpensive cultural practice used for pest management in Massachusetts cranberry (Vaccinium macrocarponAit.) production. This project examined the use of short-term floods (<72 h) for dodder (Cuscuta gronoviiWilld.) management under controlled conditions. Using incubators, seed was submerged in water for 0, 24 and 48 h at 10, 15 and 20°C (simulating spring water temperatures) and 0, 12, 24, 36 and 48 h at 15, 20 and 25°C (simulating summer water temperatures). Two 1-year controlled studies (field and greenhouse) evaluated three flood durations (0, 24 and 48 h) and four flood initiations (1, 2, 3 and 4 weeks after early seedling emergence (AEE)). Treated seeds were planted to cranberry vines and to Petri dishes; percent germination, degree of dodder attachment and dodder biomass data were collected. Treatments had limited effect on seed germination. Flooding 4 weeks AEE resulted in the lowest mean attachment ratings and dodder stem biomass on cranberry. This preliminary work provides evidence that flooding may retard dodder stem growth rather than reducing seed germination and that floods initiated after some time has elapsed after early emergence may be more effective than those initiated closer to the time of seedling emergence. More information is needed to thoroughly understand the processes involved; however, small projects such as this can provide interim guidelines that growers can immediately consider when deciding on a dodder management program.
Lipid models for united-atom molecular dynamics simulations of protein
Authors: Kukol Andreas 
Published: May 2011

AbstractMolecular dynamics (MD) simulations of biomolecules are performed at various levels of atomic detail from all-atom models to coarse grained models. United-atom models are at an intermediate level, in which non-polar hydrogen atoms are subsumed into their adjacent carbon-atom reducing the number of particles for a DPPC lipid molecule by 60%. United-atom models of the lipids DPPC, DMPC, POPC and POPG in the GROMOS96 53a6 force field were developed, that reproduced experimental properties of lipid bilayers without assumption of a constant surface area or inclusion of surface pressure. In the absence of experimental data a	surface	per lipid area for the negatively charged POPG of 0.700±0.007 nm2 was obtained	that is higher than 0.53 to 0.56 nm2 reported in previous simulation studies in the literature. It is argued that MD simulations of anionic bilayers may have underestimated the steric requirements of sodium counter ions	entering the head group	region in order	to compensate the negative charge. The use of the DMPC GROMOS96 53a6 model was evaluated in an MD simulation of the ErbB2 transmembrane peptide and showed closer agreement with the NMR-derived structure than the GROMOS87 force field that was most commonly used for membrane protein simulations previously. Lipid topologies and coordinates are available via LipidBook (http://lipidbook.bioch.ox.ac.uk/).
Influence of different breathing patterns on heart rate variability indices and reproducibility during experimental endotoxaemia in human subjects
Authors: Kox Matthijs , Pompe Jan C. , van der Hoeven Johannes G. , Hoedemaekers Cornelia W. , Pickkers Peter 
Published: May 2011

HRV (heart rate variability) analysis is a widely employed method to assess cardiac autonomic nervous system activity. Accurate HRV measurement is critical to its value as a diagnostic and prognostic tool. Different breathing patterns may affect HRV, but results obtained under static conditions are conflicting. HRV indices decrease considerably during systemic inflammation evoked by experimental endotoxaemia, enabling the determination of the effects of different breathing patterns on HRV in a dynamic setting. We investigated the impact of different breathing patterns on short-term HRV measurements during experimental endotoxaemia. Furthermore, we assessed whether paced breathing improved HRV reproducibility. Twelve healthy male volunteers received an intravenous bolus (2 ng/kg of body weight) of endotoxin [LPS (lipopolysaccharide), derived from Escherichia coli O:113] on two occasions with an interval of 2 weeks. Five-minute HRV recordings were performed just prior to LPS administration and hourly thereafter until 8 h post-LPS. Three breathing protocols were employed every hour: (i) spontaneous breathing, (ii) metronome-guided breathing at the subject's normal respiratory rate (‘paced’) and (iii) metronome-guided breathing at 150% of the subject's normal respiratory rate (‘mild hyperventilation’). LPS administration resulted in a sharp decrease in all of the HRV indices measured, which was similar during both LPS administrations. Neither paced breathing nor mild hyperventilation influenced HRV indices compared with spontaneous breathing. Paced breathing did not improve reproducibility as it did not exert a significant effect on intra-subject coefficients of variation and intra-class correlation coefficients (calculated between both visits). In conclusion, over a wide range of HRV magnitudes during experimental endotoxaemia, neither paced breathing nor mild hyperventilation affected HRV indices. Moreover, paced breathing did not result in a significant improvement in reproducibility. Therefore employing a paced breathing protocol is not required to obtain valid HRV data during endotoxaemia.
Calculating solvation energies by means of a fluctuating charge model combined with continuum solvent model
Authors: Zhao Dong-Xia , Yu Ling , Gong Li-Dong , Liu Cui , Yang Zhong-Zhi 
Published: May 2011

Continuum solvent models have shown to be very efficient for calculating solvation energy of biomolecules in solution. However, in order to produce accurate results, besides atomic radii or volumes, an appropriate set of partial charges of the molecule is needed. Here, a set of partial charges produced by a fluctuating charge model—the atom-bond electronegativity equalization method model (ABEEMσπ) fused into molecular mechanics is used to fit for the analytical continuum electrostatics model of generalized-Born calculations. Because the partial atomic charges provided by the ABEEMσπ model can well reflect the polarization effect of the solute induced by the continuum solvent in solution, accurate and rapid calculations of the solvation energies have been performed for series of compounds involving 105 small neutral molecules, twenty kinds of dipeptides and several protein fragments. The solvation energies of small neutral molecules computed with the combination of the GB model with the fluctuating charge protocol (ABEEMσπ/GB) show remarkable agreement with the experimental results, with a correlation coefficient of 0.97, a slope of 0.95, and a bias of 0.34 kcal/mol. Furthermore, for twenty kinds of dipeptides and several protein fragments, the results obtained from the analytical ABEEMσπ/GB model calculations correlate well with those from ab initio and Poisson-Boltzmann calculations. The remarkable agreement between the solvation energies computed with the ABEEMσπ/GB model and PB model provides strong motivation for the use of ABEEMσπ/GB solvent model in the simulation of biochemical systems.
Phonons of the anomalous element cerium
Authors: Krisch Michael , Farber D. L. , Xu R. , Antonangeli Daniele , Aracne C. M. , Beraud Alexandre , Chiang Tai-Chang , Zarestky J. , Kim Duck Young , Isaev Eyvaz I. , Ahuja Rajeev , Johansson Börje 
Published: May 2011

Many physical and chemical properties of the light rare-earths and actinides are governed by the active role of
f
electrons, and despite intensive efforts the details of the mechanisms of phase stability and transformation are not fully understood. A prominent example which has attracted a lot of interest, both experimentally and theoretically over the years is the isostructural
γ
-
α
transition in cerium. We have determined by inelastic X-ray scattering, the complete phonon dispersion scheme of elemental cerium across the
γ
→
α
transition, and compared it with theoretical results using
ab initio
lattice dynamics. Several phonon branches show strong changes in the dispersion shape, indicating large modifications in the interactions between phonons and conduction electrons. This is reflected as well by the lattice Grüneisen parameters, particularly around the X point. We derive a vibrational entropy change

, illustrating the importance of the lattice contribution to the transition. Additionally, we compare first principles calculations with the experiments to shed light on the mechanism underlying the isostructural volume collapse in cerium under pressure.
THE SOLAR ORIGIN OF SMALL INTERPLANETARY TRANSIENTS
Authors: Rouillard A. P. , Sheeley N. R. , Cooper T. J. , Davies J. A. , Lavraud B. , Kilpua E. K. J. , Skoug R. M. , Steinberg J. T. , Szabo A. , Opitz A. , Sauvaud J.-A. 
Published: May 2011

ABSTRACT
In this paper, we present evidence for magnetic transients with small radial extents ranging from 0.025 to 0.118 AU measured in situ by the Solar-Terrestrial Relations Observatory (STEREO) and the near-Earth Advanced Composition Explorer (ACE) and Wind spacecraft. The transients considered in this study are much smaller (<0.12 AU) than the typical sizes of magnetic clouds measured near 1 AU (∼0.23 AU). They are marked by low plasma beta values, generally lower magnetic field variance, short timescale magnetic field rotations, and are all entrained by high-speed streams by the time they reach 1 AU. We use this entrainment to trace the origin of these small interplanetary transients in coronagraph images. We demonstrate that these magnetic field structures originate as either small or large mass ejecta. The small mass ejecta often appear from the tip of helmet streamers as arch-like structures and other poorly defined white-light features (the so-called blobs). However, we have found a case of a small magnetic transient tracing back to a small and narrow mass ejection erupting from below helmet streamers. Surprisingly, one of the small magnetic structures traces back to a large mass ejection; in this case, we show that the central axis of the coronal mass ejection is along a different latitude and longitude to that of the in situ spacecraft. The small size of the transient is related to the in situ measurements being taken on the edges or periphery of a larger magnetic structure. In the last part of the paper, an ejection with an arch-like aspect is tracked continuously to 1 AU in the STEREO images. The associated in situ signature is not that of a magnetic field rotation but rather of a temporary reversal of the magnetic field direction. Due to its “open-field topology,” we speculate that this structure is partly formed near helmet streamers due to reconnection between closed and open magnetic field lines. The implications of these observations for our understanding of the variability of the slow solar wind are discussed.
Bioinformatics challenges for personalized medicine
Authors: Fernald Guy Haskin , Capriotti Emidio , Daneshjou Roxana , Karczewski Konrad J. , Altman Russ B. 
Published: May 2011

Abstract
Motivation: Widespread availability of low-cost, full genome sequencing will introduce new challenges for bioinformatics.
Results: This review outlines recent developments in sequencing technologies and genome analysis methods for application in personalized medicine. New methods are needed in four areas to realize the potential of personalized medicine: (i) processing large-scale robust genomic data; (ii) interpreting the functional effect and the impact of genomic variation; (iii) integrating systems data to relate complex genetic interactions with phenotypes; and (iv) translating these discoveries into medical practice.
Contact: russ.altman@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
GenPlay, a multipurpose genome analyzer and browser
Authors: Lajugie Julien , Bouhassira Eric E. 
Published: May 2011

Abstract
Motivation: Rapidly decreasing sequencing cost due to the emergence and improvement of massively parallel sequencing technologies has resulted in a dramatic increase in the quantity of data that needs to be analyzed. Therefore, software tools to process, visualize, analyze and integrate data produced on multiple platforms and using multiple methods are needed.
Results: GenPlay is a fast, easy to use and stable tool for rapid analysis and data processing. It is written in Java and runs on all major operating systems. GenPlay recognizes a wide variety of common genomic data formats from microarray- or sequencing-based platforms and offers a library of operations (normalization, binning, smoothing) to process raw data into visualizable tracks. GenPlay displays tracks adapted to summarize gene structure, gene expression, repeat families, CPG islands, etc. as well as custom tracks to show the results of RNA-Seq, ChIP-Seq, TimEX-Seq and single nucleotide polymorphism (SNP) analysis. GenPlay can generate statistics (minimum, maximum, SD, correlation, etc.). The tools provided include Gaussian filter, peak finders, signal saturation, island finders. The software also offers graphical features such as scatter plots and bar charts to depict signal repartition. The library of operations is continuously growing based on the emerging needs.
Availability: GenPlay is an open-source project available from http://www.genplay.net. The code source of the software is available at https://genplay.einstein.yu.edu/svn/GenPlay.
Contact: eric.bouhassira@einstein.yu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.