bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rational constructivism, statistical inference, and core cognition
Authors: Xu Fei 
Published: May 2011

AbstractI make two points in this commentary on Carey (2009). First, it may be too soon to conclude that core cognition is innate. Recent advances in computational cognitive science and developmental psychology suggest possible mechanisms for developing inductive biases. Second, there is another possible answer to Fodor's challenge – if concepts are merely mental tokens, then cognitive scientists should spend their time on developing a theory of belief fixation instead.
Language and analogy in conceptual change
Authors: Gentner Dedre , Simms Nina 
Published: May 2011

AbstractCarey proposes that the acquisition of the natural numbers relies on the interaction between language and analogical processes: specifically, on an analogical mapping from ordinal linguistic structure to ordinal conceptual structure. We suggest that this analogy in fact requires several steps. Further, we propose that additional analogical processes enter into the acquisition of number.
Definitions as a window to the acquisition of relative clauses
Authors: FRIEDMANN NAAMA , ARAM DORIT , NOVOGRODSKY RAMA 
Published: May 2011

ABSTRACTDefinitions that children provide can be a valuable measure of their syntax, and specifically, of their ability to produce relative clauses. This research explored the acquisition of subject, object, and indirect object relative clauses in 121 Hebrew-speaking children aged 3 years, 5 months to 8 years, 6 months (3;5–8;6). The children were asked to define 14 nouns, and their responses were collected and analyzed for various syntactic aspects. The main results were that children started using relative clauses in their definitions at age 3;8, and their use of relative clause increased consistently until they were 6 years old. Retesting 38 of the 6-year-olds at age 8;6 indicated no differences in several syntactic measures between their production of relative clauses at age 6 and 8;6, suggesting that the ability to produce relative clauses stabilizes around age 6. The participants made almost no grammatical errors at any of the ages, probably because they avoided the use of relative clauses when they had not mastered them yet. In the early stages participants produced mainly headless relatives, and with age the use of a relative head increased. The acquisition of relative clauses was not related to the ability to embed or to the ability to use pronouns: these abilities existed already in the youngest age group and remained constant throughout the age groups.
Modeling and experiment of a planar 3-DOF parallel micromanipulator
Authors: Yue Yi , Gao Feng , Jin Zhenlin , Zhao Xianchao 
Published: May 2011

SUMMARYIn this paper, a planar 3-DOF XYγ parallel micromanipulator with monolithic structure is presented. The micromanipulator is driven by three piezoelectric (PZT) actuators. To achieve highly accurate control, a new approach investigating the relationship among input-force, payload, stiffness, and displacement (IPSD model) of the XYγ micromanipulator is proposed in analytical style, and the analytical expression of the relationship between driving voltages of PZT actuators and outputs of end-effector is deduced based on the IPSD model. Finally, in order to verify the IPSD model, the simulations by finite element method and experiment are performed. The micromanipulator can be used to do microtasks that need the manipulator perform only planar motion, such as microoperation and microassembly, and the proposed IPSD model is useful for both digital control and design of the XYγ micromanipulator.
Optimal motion planning by reinforcement learning in autonomous mobile vehicles
Authors: Gómez M. , González R. V. , Martínez-Marín T. , Meziat D. , Sánchez S. 
Published: May 2011

SUMMARYThe aim of this work has been the implementation and testing in real conditions of a new algorithm based on the cell-mapping techniques and reinforcement learning methods to obtain the optimal motion planning of a vehicle considering kinematics, dynamics and obstacle constraints. The algorithm is an extension of the control adjoining cell mapping technique for learning the dynamics of the vehicle instead of using its analytical state equations. It uses a transformation of cell-to-cell mapping in order to reduce the time spent during the learning stage. Real experimental results are reported to show the satisfactory performance of the algorithm.
Porcine bocaviruses: genetic analysis and prevalence in Chinese swine population
Authors: ZHANG H. B. , HUANG L. , LIU Y. J. , LIN T. , SUN C. Q. , DENG Y. , WEI Z. Z. , CHEUNG A. K , LONG J. X. , YUAN S. S. 
Published: May 2011

SUMMARYIn members of theBocavirusgenus, that contain three open reading frames (ORFs) of the Parvovirinae subfamily, porcine bocaviruses (PoBoVs) exhibit the most genetic diversity. Based on the ORF2-encoded viral protein (VP1) classification, the six reported porcine bocaviruses were grouped into four species: PoBoV1 (porcine boca-like virus or PBoLV), PoBoV2 (porcine parvovirus 4 or PPV4), PoBoV3 (PBoV1/PBoV2) and PoBoV4 (6V/7V), with PoBoV3 and PoBoV4 each having two genotype viruses. All four PoBoV species were detected in the 166 samples collected in 2010 from swine herds located in ten provinces of China. The detection rates for PoBoV1-4 were 28·9%, 6·6%, 19·3% and 39·7%, respectively. The co-infection combinations involving these six porcine bocaviruses in the collected samples were very complex. Furthermore, mixed infections with viruses from other families (porcine reproductive and respiratory syndrome virus, classic swine fever virus and porcine circovirus type 2) were also detected.
Transmission of Streptococcus pneumoniae in adults may occur through saliva
Authors: LEVINE H. , ZARKA S. , DAGAN R. , SELA T. , ROZHAVSKI V. , COHEN D. I. , BALICER R. D. 
Published: May 2011

SUMMARYOf 742 army recruits tested for pneumococcal nasopharyngeal/oropharyngeal carriage, 6·6% were positive. Frequent sharing of a drinking glass/bottle was a common, strong and independent risk factor for pneumococcal carriage. Our findings strongly suggest, for the first time, that in young adults, transmission of pneumococci may occur via saliva and this should be considered when conducting an outbreak investigation and carriage studies.
Danon disease: characteristic late gadolinium enhancement pattern on cardiac magnetic resonance imaging
Authors: Dara Bharat S. , Rusconi Paolo G. , Fishman Joel E. 
Published: May 2011

AbstractDanon disease is a rare entity associated with the clinical triad of mental retardation, skeletal myopathy, and severe hypertrophic cardiomyopathy. We report two cases of Danon disease and describe the results of the cardiac magnetic resonance imaging studies that were conducted to assess the pattern of cardiac hypertrophy.
Comparison of right ventricular deformation and dyssynchrony in patients with different subtypes of hypoplastic left heart syndrome after Fontan surgery using two-dimensional speckle tracking
Authors: Petko Colin , Voges Inga , Schlangen Jana , Scheewe Jens , Kramer Hans-Heiner , Uebing Anselm S. 
Published: May 2011

AbstractBackgroundThe left ventricle in patients with hypoplastic left heart syndrome may influence right ventricular function and outcome. We aimed to investigate differences in right ventricular deformation and intraventricular dyssynchrony between hypoplastic left heart syndrome patients with different anatomical subtypes and left ventricle sizes after Fontan surgery using two-dimensional speckle tracking.Patients and methodsWe examined 29 hypoplastic left heart syndrome patients aged 5.4 plus or minus 2.8 years after Fontan surgery and compared 15 patients with mitral and aortic atresia with the remaining 14 patients with other anatomic subtypes. We used two-dimensional speckle tracking to measure the global and regional systolic longitudinal strain and strain rate as well as intraventricular dyssynchrony.ResultsGlobal strain (−19.5, 2.8% versus −17.4, 3.9%) and global strain rate (−1.0, 0.2 per second versus −0.9, 0.3 per second) were not different between groups. The mitral and aortic atresia group had higher strain in the basal septal (−13.0, 5.0% versus −3.9, 9.3%, p = 0.003) and mid-septal (−19.4, 4.7% versus −13.2, 6.5%, p = 0.009) segments, and higher strain rates in the mid-septal segment (−1.14, 0.3 per second versus −0.95, 0.4 per second, p = 0.047), smaller left ventricle area (0.18, 0.41 square centimetre versus 2.83, 2.07 square centimetre, p = 0.0001), and shorter wall-to-wall delay (38, 29 milliseconds versus 81, 57 milliseconds, p = 0.02).ConclusionSignificant differences in regional deformation and intraventricular dyssynchrony exist between the mitral and aortic atresia subtype with small left ventricles and the other anatomic subtypes with larger left ventricles after Fontan surgery.
Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone
Authors: Pitcher Angela , Villanueva Laura , Hopmans Ellen C , Schouten Stefan , Reichart Gert-Jan , Sinninghe Damsté Jaap S 
Published: May 2011

Abstract
Ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria have emerged as significant factors in the marine nitrogen cycle and are responsible for the oxidation of ammonium to nitrite and dinitrogen gas, respectively. Potential for an interaction between these groups exists; however, their distributions are rarely determined in tandem. Here we have examined the vertical distribution of AOA and anammox bacteria through the Arabian Sea oxygen minimum zone (OMZ), one of the most intense and vertically exaggerated OMZs in the global ocean, using a unique combination of intact polar lipid (IPL) and gene-based analyses, at both DNA and RNA levels. To screen for AOA-specific IPLs, we developed a high-performance liquid chromatography/mass spectrometry/mass spectrometry method targeting hexose-phosphohexose (HPH) crenarchaeol, a common IPL of cultivated AOA. HPH-crenarchaeol showed highest abundances in the upper OMZ transition zone at oxygen concentrations of ca. 5 μm, coincident with peaks in both thaumarchaeotal 16S rDNA and amoA gene abundances and gene expression. In contrast, concentrations of anammox-specific IPLs peaked within the core of the OMZ at 600 m, where oxygen reached the lowest concentrations, and coincided with peak anammox 16S rDNA and the hydrazine oxidoreductase (hzo) gene abundances and their expression. Taken together, the data reveal a unique depth distribution of abundant AOA and anammox bacteria and the segregation of their respective niches by &gt;400 m, suggesting no direct coupling of their metabolisms at the time and site of sampling in the Arabian Sea OMZ.
Ligand-gated diffusion across the bacterial outer membrane
Authors: Lepore Bryan W. , Indic Mridhu , Pham Hannah , Hearn Elizabeth M. , Patel Dimki R. , van den Berg Bert 
Published: May 2011

Ligand-gated channels, in which a substrate transport pathway is formed as a result of the binding of a small-molecule chemical messenger, constitute a diverse class of membrane proteins with important functions in prokaryotic and eukaryotic organisms. Despite their widespread nature, no ligand-gated channels have yet been found within the outer membrane (OM) of Gram-negative bacteria. Here we show, using in vivo transport assays, intrinsic tryptophan fluorescence and X-ray crystallography, that high-affinity (submicromolar) substrate binding to the OM long-chain fatty acid transporter FadL from
Escherichia coli
causes conformational changes in the N terminus that open up a channel for substrate diffusion. The OM long-chain fatty acid transporter FadL from
E. coli
is a unique paradigm for OM diffusion-driven transport, in which ligand gating within a β-barrel membrane protein is a prerequisite for channel formation.
Fast accessibility-based prediction of RNA–RNA interactions
Authors: Tafer Hakim , Amman Fabian , Eggenhofer Florian , Stadler Peter F. , Hofacker Ivo L. 
Published: May 2011

Abstract
Motivation: Currently, the best RNA–RNA interaction prediction tools are based on approaches that consider both the inter- and intramolecular interactions of hybridizing RNAs. While accurate, these methods are too slow and memory-hungry to be employed in genome-wide RNA target scans. Alternative methods neglecting intramolecular structures are fast enough for genome-wide applications, but are too inaccurate to be of much practical use.
Results: A new approach for RNA–RNA interaction was developed, with a prediction accuracy that is similar to that of algorithms that explicitly consider intramolecular structures, but running at least three orders of magnitude faster than RNAup. This is achieved by using a combination of precomputed accessibility profiles with an approximate energy model. This approach is implemented in the new version of RNAplex. The software also provides a variant using multiple sequences alignments as input, resulting in a further increase in specificity.
Availability: RNAplex is available at www.bioinf.uni-leipzig.de/Software/RNAplex.
Contact: htafer@bioinf.uni-leipzig.de; ivo@tbi.univie.ac.at
Supplementary information: Supplementary data are available at Bioinformatics Online.
Evaluation of drug–human serum albumin binding interactions with support vector machine aided online automated docking
Authors: Zsila Ferenc , Bikadi Zsolt , Malik David , Hari Peter , Pechan Imre , Berces Attila , Hazai Eszter 
Published: May 2011

AbstractMotivation: Human serum albumin (HSA), the most abundant plasma protein is well known for its extraordinary binding capacity for both endogenous and exogenous substances, including a wide range of drugs. Interaction with the two principal binding sites of HSA in subdomain IIA (site 1) and in subdomain IIIA (site 2) controls the free, active concentration of a drug, provides a reservoir for a long duration of action and ultimately affects the ADME (absorption, distribution, metabolism, and excretion) profile. Due to the continuous demand to investigate HSA binding properties of novel drugs, drug candidates and drug-like compounds, a support vector machine (SVM) model was developed that efficiently predicts albumin binding. Our SVM model was integrated to a free, web-based prediction platform (http://albumin.althotas.com). Automated molecular docking calculations for prediction of complex geometry are also integrated into the web service. The platform enables the users (i) to predict if albumin binds the query ligand, (ii) to determine the probable ligand binding site (site 1 or site 2), (iii) to select the albumin X-ray structure which is complexed with the most similar ligand and (iv) to calculate complex geometry using molecular docking calculations. Our SVM model and the potential offered by the combined use of in silico calculation methods and experimental binding data is illustrated.Contact: eszter.hazai@virtuadrug.comSupplementary information: Supplementary data are available at Bioinformatics online.
Java bioinformatics analysis web services for multiple sequence alignment—JABAWS:MSA
Authors: Troshin Peter V. , Procter James B. , Barton Geoffrey J. 
Published: May 2011

Abstract
Summary: JABAWS is a web services framework that simplifies the deployment of web services for bioinformatics. JABAWS:MSA provides services for five multiple sequence alignment (MSA) methods (Probcons, T-coffee, Muscle, Mafft and ClustalW), and is the system employed by the Jalview multiple sequence analysis workbench since version 2.6. A fully functional, easy to set up server is provided as a Virtual Appliance (VA), which can be run on most operating systems that support a virtualization environment such as VMware or Oracle VirtualBox. JABAWS is also distributed as a Web Application aRchive (WAR) and can be configured to run on a single computer and/or a cluster managed by Grid Engine, LSF or other queuing systems that support DRMAA. JABAWS:MSA provides clients full access to each application's parameters, allows administrators to specify named parameter preset combinations and execution limits for each application through simple configuration files. The JABAWS command-line client allows integration of JABAWS services into conventional scripts.
Availability and Implementation: JABAWS is made freely available under the Apache 2 license and can be obtained from: http://www.compbio.dundee.ac.uk/jabaws.
Contact: g.j.barton@dundee.ac.uk
An ensemble biclustering approach for querying gene expression compendia with experimental lists
Authors: De Smet Riet , Marchal Kathleen 
Published: May 2011

Abstract
Motivation: Query-based biclustering techniques allow interrogating a gene expression compendium with a given gene or gene list. They do so by searching for genes in the compendium that have a profile close to the average expression profile of the genes in this query-list. As it can often not be guaranteed that the genes in a long query-list will all be mutually coexpressed, it is advisable to use each gene separately as a query. This approach, however, leaves the user with a tedious post-processing of partially redundant biclustering results. The fact that for each query-gene multiple parameter settings need to be tested in order to detect the ‘most optimal bicluster size’ adds to the redundancy problem.
Results: To aid with this post-processing, we developed an ensemble approach to be used in combination with query-based biclustering. The method relies on a specifically designed consensus matrix in which the biclustering outcomes for multiple query-genes and for different possible parameter settings are merged in a statistically robust way. Clustering of this matrix results in distinct, non-redundant consensus biclusters that maximally reflect the information contained within the original query-based biclustering results. The usefulness of the developed approach is illustrated on a biological case study in Escherichia coli.
Availability and implementation: Compiled Matlab code is available from http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Information_DeSmet_2011/.
Contact: kathleen.marchal@biw.kuleuven.be
Supplementary information:Supplementary data are available at Bioinformatics online.
Carbon storage, structure and composition of miombo woodlands in Tanzania’s Eastern Arc Mountains
Authors: Shirima Deo D. , Munishi Pantaleo K. T. , Lewis Simon L. , Burgess Neil D. , Marshall Andrew R. , Balmford Andrew , Swetnam Ruth D. , Zahabu Eliakimu Mnkondo 
Published: May 2011

AbstractWe determine the aboveground biomass and carbon storage (ABGC) of trees and the herbaceous layer in miombo woodland in the Eastern Arc Mountains (EAM) of Tanzania. In four 1‐ha sample plots in Nyanganje and Kitonga Forests, we measured all trees ≥10 cm diameter alongside height and wood mass density. The plots contained an average of 20 tree species ha−1 (range 11–29) and 344 stems ha−1 (range 281–382) with Shannon diversity values of 1.05 and 1.25, respectively. We weighted nine previously published woody savannah allometric models based on whether: (i) the model was derived from the same geographical region; (ii) the model included tree height/wood mass density in addition to stem diameter; and (iii) sample size was used to fit the model. The weighted mean ABGC storage from the nine models range from 13.5 ± 2 to 29.8 ± 5 Mg ha−1. Measured ABGC storage in the herbaceous layer, using the wet combustion method, adds 0.55 ± 0.02 Mg C ha−1. Estimates suggest that EAM miombo woodlands store a range of 13–30 Mg ha−1 of carbon. Although the estimates suggest that miombo woodlands store significant quantities of carbon, caution is required as this is the first estimate based on in situ data.
Paracetamol prescribing in primary care: too little and too much?
Authors: Kazouini Ammar , Mohammed Baba S. , Simpson Colin R. , Helms Peter J. , McLay James S. 
Published: May 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Paracetamol is the most frequently prescribed analgesic and antipyretic in children.• The adherence to paracetamol dosage recommendation in children is poor, with paracetamol prescriptions alone accounting for 30% of off label prescribing as a result of dose violation. WHAT THIS STUDY ADDS • Our study has identified that approximately a fifth of paracetamol prescriptions issued to children by their GP are off label, with the most common reason being either too small or too high a dose.• Both overdosing in young children and underdosing in older children together with their associated risks of toxicity or under treatment occur relatively frequently.AIMS To assess the level of paracetamol off label prescribing in the community and the potential for paracetamol under or overdosing.METHODS The Scottish Practice Team Information (PTI) database containing prescribing data for approximately 35 839 children aged (0–12 years) was analysed for paracetamol prescriptions for the year 2006. Off label prescribing was defined as prescribing outside the BNFc age and dose recommendations.RESULTS Two thousand seven hundred and sixty‐one children aged 0–12 years were issued with 4423 prescriptions for paracetamol. (1446 males). Children 1–5 years (1329, 42.2%) accounted for 48.9% (2164) of all paracetamol prescriptions. Eighteen per cent (793) of individual prescriptions were off label and after accounting for repeat prescriptions 625 (22.75%) individuals were exposed to off label prescriptions. A further 15% (668) of prescriptions contained insufficient dosage data to determine their status, 13.3% (368) being underdosed and 4.4% (121) overdosed at least once during the study year. In total 11.3% (502) of all prescriptions were classified as underdose, 2.9% (127) as overdose and 15% (667) had no dosage instructions. Age was significantly related to non recommended dosage (χ2 test, P < 0.001). Children 1–3 months old were at highest risk of being overdosed; 27% of prescriptions recommended actual or potential overdosage and 25% (354) of children aged 6–12 years were prescribed an actual or potential underdose. Overall 57.2% of all prescriptions failed to comply with current BNFc recommendations.CONCLUSION Paracetamol off label prescribing is common in primary care, with relatively high levels of potential overdosing in the youngest children and potential underdosing in the oldest children.