bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heart rate after trauma and the specificity of fear circuitry disorders
Authors: Bryant R. A. , Creamer M. , O'Donnell M. , Silove D. , McFarlane A. C. 
Published: June 2011

BackgroundFear circuitry disorders purportedly include post-traumatic stress disorder (PTSD), panic disorder, agoraphobia, social phobia and specific phobia. It is proposed that these disorders represent a cluster of anxiety disorders triggered by stressful events and lead to fear conditioning. Elevated heart rate (HR) at the time of an aversive event may reflect strength of the unconditioned response, which may contribute to fear circuitry disorders.MethodThis prospective cohort study assessed HR within 48 h of hospital admission in 602 traumatically injured patients, who were assessed during hospital admission and within 1 month of trauma exposure for lifetime psychiatric diagnosis. At 3 months after the initial assessment, 526 patients (87%) were reassessed for PTSD, major depressive disorder, panic disorder, agoraphobia, social phobia, obsessive compulsive disorder and generalized anxiety disorder.ResultsAt the 3-month assessment there were 77 (15%) new cases of fear circuitry disorder and 87 new cases of non-fear circuitry disorder (17%). After controlling for gender, age, type of injury and injury severity, patients with elevated HR (defined as ⩾96 beats per min) at the time of injury were more likely to develop PTSD [odds ratio (OR) 5.78, 95% confidence interval (CI) 2.32–14.43], panic disorder (OR 3.46, 95% CI 1.16–10.34), agoraphobia (OR 3.90, 95% CI 1.76–8.61) and social phobia (OR 3.98, 95% CI 1.42–11.14). Elevated HR also predicted new fear circuitry disorders that were not co-morbid with a non-fear circuitry disorder (OR 7.28, 95% CI 2.14–24.79).ConclusionsThese data provide tentative evidence of a common mechanism underpinning the onset of fear circuitry disorders.
Falerii Novi: further survey of the northern extramural area
Authors: Hay Sophie , Johnson Paul , Keay Simon , Millett Martin 
Published: June 2011

Sommarii:L'articolo presenta i risultati di nuove ricognizioni geofisiche nell'area esterna, immediatamente a nord del circuito murario di Falerii Novi. I risultati, integrati con recenti pubblicazioni su evidenze da fotografia aerea, chiariscono ulteriormente la sequenza dello sviluppo della città dalla sua fondazione nel 241 a.C. al periodo imperiale. Essi rivelano nuovi dettagli delle necropoli e deH'anfiteatro, e pongono importanti questioni circa l'assegnazione dei terreni nelle vicinanze della città.
Cooking pots and cooking practice: an African bain-marie?
Authors: Fentress Elizabeth 
Published: June 2011

Sommarii:L'articolo prende in considerazione tre particolari forme di ceramica da cucina: l'Hayes 23B, 196 e 197. Realizzati nella Tunisia settentrionale fin dal periodo flavio, esse rappresentano le forme più comuni tra i rinvenimenti africani nei siti del Mediterraneo occidentale. Comunque, ci sono problemi nell'interpretare i modi in cui erano usati. In questa sede suggerisco che le tre forme costituissero un set per la cottura a bagnomaria (con il recipiente più basso che andava riempito per metà d'acqua; uno superiore in cui veniva immesso il cibo; e un coperchio soprastante). Vengono discusse le origini di simili vasi e il loro ruolo nella cottura.
Warmundus of Ivrea and episcopal attitudes to death, martyrdom and the millennium
Authors: Mackie Gillian 
Published: June 2011

Sommarii:Warmundo, vescovo di Ivrea nella seconda metà del X secolo, è conosciuto per i suoi ampi successi come patrono dell'architettura e del volume illustrato. Fu anche poeta. Questo articolo si focalizza sull'ultimo periodo della vita di Warmundo, quando ha fornito nuovi libri liturgici per la sua cattedrale. Le illustrazioni che scelse per il suo Sacramentario rivelano che in vecchiaia la sua attenzione era rivolta alia morte, sia del semplice Cristiano sia dei martiri della fede. Due serie di miniature dal Sacramentario sono senza un confronto tra i manoscritti del suo tempo sopravvissuti. Un gruppo di dieci miniature illustra, in sequenza, le preghiere liturgiche da usare nella malattia e nella morte, mentre un'unica serie di tre miniature a piena pagina accompagna il testo per il giorno di Tutti i Santi e dipinge la sofferenza dei martiri con dettaglio grafico. lo esamino le possibili fonti per queste immagini nei manoscritti e nell'arte monumentale, e anche nella lerteratura, in particolare nelLiber Peristephanondi Prudentio. Possibili influenze sulla scelta dell'immaginario di Warmundo comprendono la sua età avanzata, il clima politico scombussolato e pericoloso dei suoi giorni e l'approccio al regno millenario, con associate le sue paure che la fine del mondo fosse vicina. Tutti questi fattori sono esaminati nel contesto delle illustrazioni che egli sceglie per i suoi manoscritti. I suoi interessi, come dimostrato in queste illustrazioni, possono ben essere stati condivisi con altri vescovi della sua era meno ben documentati, il cui lavoro non è sopravvissuto.
Effect of porcine circovirus type 2 (PCV2) infection on reproduction: disease, vertical transmission, diagnostics and vaccination
Authors: Madson D. M. , Opriessnig T. 
Published: June 2011

AbstractPorcine circovirus type 2 (PCV2) causes great economic losses in growing pigs and there are several reviews on disease manifestations and lesions associated with PCV2 in growing pigs. Reproductive failure in breeding herds, predominately associated with increased numbers of mummies and non-viable piglets at parturition, is one of the disease manifestations of PCV2 infection. Boars shed low amounts of infectious PCV2 in semen for extended time periods, and vertical transmission of PCV2 to fetuses during PCV2 viremia of the dam has been experimentally confirmed. However, intrauterine-infected piglets often are clinically normal. Nevertheless, pigs infected with PCV2 by the intrauterine route can be born viremic, possibly contributing to horizontal spread of PCV2 within the breeding herd and into the nursery. Shedding of PCV2 in semen and prevalence of intrauterine-infected piglets can both be greatly reduced by PCV2 vaccination well ahead of expected PCV2 exposure. This review is a discussion on current knowledge on the effects of PCV2 infection in the dam and inin uterofetuses, including clinical signs, lesions, diagnosis and prevention through vaccination. Infection of boars with PCV2, the potential for PCV2 transmission via semen and prevention of PCV2 shedding are also discussed.
Nutritional and physiological role of medium-chain triglycerides and medium-chain fatty acids in piglets
Authors: Zentek J. , Buchheit-Renko S. , Ferrara F. , Vahjen W. , Van Kessel A. G. , Pieper R. 
Published: June 2011

AbstractMedium-chain fatty acids (MCFAs) are found at higher levels in milk lipids of many animal species and in the oil fraction of several plants, including coconuts, palm kernels and certainCupheaspecies. Medium-chain triglycerides (MCTs) and fatty acids are efficiently absorbed and metabolized and are therefore used for piglet nutrition. They may provide instant energy and also have physiological benefits beyond their energetic value contributing to several findings of improved performance in piglet-feeding trials. MCTs are effectively hydrolyzed by gastric and pancreatic lipases in the newborn and suckling young, allowing rapid provision of energy for both enterocytes and intermediary hepatic metabolism. MCFAs affect the composition of the intestinal microbiota and have inhibitory effects on bacterial concentrations in the digesta, mainly onSalmonellaand coliforms. However, most studies have been performedin vitroup to now andin vivodata in pigs are still scarce. Effects on the gut-associated and general immune function have been described in several animal species, but they have been less studied in pigs. The addition of up to 8% of a non-esterified MCFA mixture in feed has been described, but due to the sensory properties this can have a negative impact on feed intake. This may be overcome by using MCTs, allowing dietary inclusion rates up to 15%. Feeding sows with diets containing 15% MCTs resulted in a lower mortality of newborns and better development, particularly of underweight piglets. In conclusion, MCFAs and MCTs offer advantages for the improvement of energy supply and performance of piglets and may stabilize the intestinal microbiota, expanding the spectrum of feed additives supporting piglet health in the post-weaning period.
Mapping QTLs for yield components and chlorophyll a fluorescence parameters in wheat under three levels of water availability
Authors: Czyczyło-Mysza Ilona , Marcińska Izabela , Skrzypek Edyta , Chrupek Małgorzata , Grzesiak Stanisław , Hura Tomasz , Stojałowski Stefan , Myśków Beata , Milczarski Paweł , Quarrie Steve 
Published: June 2011

Drought is one of the major factors limiting wheat yield in many developing countries worldwide. Parameters of chlorophyll a fluorescence kinetics under drought stress conditions have been used to characterize dehydration tolerance in wheat. In the present study, a set of 94 doubled haploid lines obtained from Chinese Spring × SQ1 (CSDH), mapped with 450 markers, was evaluated for yield (grain dry weight/main stem ear), number of grains/main stem ear (NG) and chlorophyll a fluorescence parameters (FC) under moderate and severe drought stress, and compared with results for well-watered plants. quantitative trait loci (QTLs) were identified using Windows QTLCartographer version 2.5 software and the results were analysed using single-marker analysis (SMA) and composite interval mapping (CIM). Analysis using SMA and CIM showed mostly similar QTLs for all traits, though more QTLs were identified by SMA than by CIM. The genetic control of yield, NG and FC varied considerably between drought-stressed and non-stressed plants. Although no major QTL co-locations were found for yield and FC using CIM, the co-location of QTLs for NG, yield and Fv/Fm in drought-stressed plants was observed on chromosome 5A using SMA.
Moral Intuition and Media Entertainment
Authors: Tamborini Ron 
Published: June 2011

This paper applies the social intuitionist perspective of moral foundations theory (MFT) to the study of media entertainment. It begins by introducing the MFT’s conception of morality as an intuitive evaluative response governed by the association of moral codes organized in five mental modules. These include harm/care (concerned with suffering and empathy); fairness (related to reciprocity and justice); loyalty (dealing with common good and punitiveness toward outsiders); authority (negotiating dominance hierarchies); and purity (concerned with sanctity and contamination). After discussing initial tests examining MFT’s application to narrative appeal, and its potential broad application to entertainment theory, a model of intuitive morality and exemplars (MIME) is presented. The model describes long-term and short-term processes of reciprocal influence between media and moral intuition. In the long-term, the model predicts that repeated exposure to module-related content will lead to an individual and culturally-shared increase in the salience of specific modules and module exemplars. In the short-term, resulting patterns of module salience will affect the immediate appraisal of media content or, if content presents ambiguous or complex moral patterns, a delayed response though careful reappraisal. Patterns of positive or negative evaluative responses resulting from these appraisal processes are expected to shape individual and aggregate patterns of selective exposure to media, as well as the subsequent production of content within media systems driven by these exposure patterns. The paper concludes with an example of the model’s utility by showing how its short-term components can be applied to address conceptual difficulties in distinguishing enjoyment from appreciation.
The 15Πg state of C2
Authors: Schmidt Timothy W. , Bacskay George B. 
Published: June 2011

We report ab initio spectroscopic constants for the recently identified 15Πg state of C2 [P. Bornhauser, Y. Sych, G. Knopp, T. Gerber, and P. P. Radi, J. Chem. Phys. 134, 044302 (2011)]. The calculations are performed at the multi-reference configuration interaction level of theory with Davidson's correction using aug-cc-pV6Z basis sets and include core-valence correlation and relativistic corrections obtained with quadruple-zeta bases. Such treatment accurately reproduces the experimentally observed constants of the a3Πu and other states. Thus, we expect our calculated ωe value for the 15Πg state to be within a few cm−1, and rotational constants to be within 0.1% of experiment. Agreement with available spectroscopic data is excellent, with the calculations strongly suggesting that the 15Πg vibrational level observed by Bornhauser et al. is v = 0.
Parent-specific copy number in paired tumor–normal studies using circular binary segmentation
Authors: Olshen Adam B. , Bengtsson Henrik , Neuvial Pierre , Spellman Paul T. , Olshen Richard A. , Seshan Venkatraman E. 
Published: June 2011

Abstract
Motivation: High-throughput techniques facilitate the simultaneous measurement of DNA copy number at hundreds of thousands of sites on a genome. Older techniques allow measurement only of total copy number, the sum of the copy number contributions from the two parental chromosomes. Newer single nucleotide polymorphism (SNP) techniques can in addition enable quantifying parent-specific copy number (PSCN). The raw data from such experiments are two-dimensional, but are unphased. Consequently, inference based on them necessitates development of new analytic methods.
Methods: We have adapted and enhanced the circular binary segmentation (CBS) algorithm for this purpose with focus on paired test and reference samples. The essence of paired parent-specific CBS (Paired PSCBS) is to utilize the original CBS algorithm to identify regions of equal total copy number and then to further segment these regions where there have been changes in PSCN. For the final set of regions, calls are made of equal parental copy number and loss of heterozygosity (LOH). PSCN estimates are computed both before and after calling.
Results: The methodology is evaluated by simulation and on glioblastoma data. In the simulation, PSCBS compares favorably to established methods. On the glioblastoma data, PSCBS identifies interesting genomic regions, such as copy-neutral LOH.
Availability: The Paired PSCBS method is implemented in an open-source R package named PSCBS, available on CRAN (http://cran.r-project.org/).
Contact: olshena@biostat.ucsf.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Xwalk: computing and visualizing distances in cross-linking experiments
Authors: Kahraman Abdullah , Malmström Lars , Aebersold Ruedi 
Published: June 2011

Abstract
Motivation: Chemical cross-linking of proteins or protein complexes and the mass spectrometry-based localization of the cross-linked amino acids in peptide sequences is a powerful method for generating distance restraints on the substrate's topology.
Results: Here, we introduce the algorithm Xwalk for predicting and validating these cross-links on existing protein structures. Xwalk calculates and displays non-linear distances between chemically cross-linked amino acids on protein surfaces, while mimicking the flexibility and non-linearity of cross-linker molecules. It returns a ‘solvent accessible surface distance’, which corresponds to the length of the shortest path between two amino acids, where the path leads through solvent occupied space without penetrating the protein surface.
Availability: Xwalk is freely available as a web server or stand-alone JAVA application at http://www.xwalk.org.
Contact: abdullah@imsb.biol.ethz.ch; aebersold@imsb.biol.ethz.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Pathogen detection using short-RNA deep sequencing subtraction and assembly
Authors: Isakov Ofer , Modai Shira , Shomron Noam 
Published: June 2011

Abstract
Motivation: Early and accurate detection of human pathogen infection is critical for treatment and therapeutics. Here we describe pathogen identification using short RNA subtraction and assembly (SRSA), a detection method that overcomes the requirement of prior knowledge and culturing of pathogens, by using degraded small RNA and deep sequencing technology. We prove our approach's efficiency through identification of a combined viral and bacterial infection in human cells.
Contact: nshomron@post.tau.ac.il
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates
Authors: Yang Yuedong , Faraggi Eshel , Zhao Huiying , Zhou Yaoqi 
Published: June 2011

Abstract
Motivation: In recent years, development of a single-method fold-recognition server lags behind consensus and multiple template techniques. However, a good consensus prediction relies on the accuracy of individual methods. This article reports our efforts to further improve a single-method fold recognition technique called SPARKS by changing the alignment scoring function and incorporating the SPINE-X techniques that make improved prediction of secondary structure, backbone torsion angle and solvent accessible surface area.
Results: The new method called SPARKS-X was tested with the SALIGN benchmark for alignment accuracy, Lindahl and SCOP benchmarks for fold recognition, and CASP 9 blind test for structure prediction. The method is compared to several state-of-the-art techniques such as HHPRED and BoostThreader. Results show that SPARKS-X is one of the best single-method fold recognition techniques. We further note that incorporating multiple templates and refinement in model building will likely further improve SPARKS-X.
Availability: The method is available as a SPARKS-X server at http://sparks.informatics.iupui.edu/
Contact: yqzhou@iupui.edu
MGV: a generic graph viewer for comparative omics data
Authors: Symons Stephan , Nieselt Kay 
Published: June 2011

Abstract
Motivation: High-throughput transcriptomics, proteomics and metabolomics methods have revolutionized our knowledge of biological systems. To gain knowledge from comparative omics studies, strong data integration and visualization features are required. Knowledge gained from these studies is often available in the form of graphs, and their visualization is especially useful in a wide range of systems biology topics, including pathway analysis, interaction networks or gene models. Especially, it is necessary to compare biological models with measured data. This allows the identification of new models and new insights into existing ones.
Results: We present MGV, a versatile generic graph viewer for multiomics data. MGV is integrated into Mayday (Battke et al., 2010). It extends Mayday's visual analytics capabilities by integrating a wide range of biological models, high-throughput data and meta information to display enriched graphs that combine data and models. A wide range of tools is available for visualization of nodes, data-aware graph layout as well as automatic and manual aggregation and refinement of the data. We show the usefulness of MGV applied to several problems, including differential expression of alternative transcripts, transcription factor interaction, cross-study clustering comparison and integration of transcriptomics and metabolomics data for pathway analysis.
Availability: MGV is a open-source software implemented in Java and freely available as a part of Mayday at www.microarray-analysis.org/mayday.
Contact: symons@informatik.uni-tuebingen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Age, growth, and maturity of the whitebrow skate, Bathyraja minispinosa, from the eastern Bering Sea
Authors: Ainsley Shaara M. , Ebert David A. , Cailliet Gregor M. 
Published: June 2011

Abstract
Ainsley, S. M., Ebert, D. A., and Cailliet, G. M. 2011. Age, growth, and maturity of the whitebrow skate, Bathyraja minispinosa, from the eastern Bering Sea. – ICES Journal of Marine Science, 68: 1426–1434. Skates are a common bycatch in groundfish fisheries in the Bering Sea; however, their life-history characteristics are not well known. The study is the first to investigate the age, growth, and age at maturity of Bathyraja minispinosa. Ages were estimated using sectioned vertebrae and several growth models were compared. The Gompertz model was the best fit and no significant differences were detected between sexes for any model. The maximum age estimated was 37 years, and parameter estimates generated from the three-parameter von Bertalanffy model were k = 0.02 year−1 and L∞ = 146.9 cm total length (TL). Males reached their size at 50% maturity larger than females (70.1 and 67.4 cm, respectively), but no significant differences in the estimated size or age at maturity were found. Whereas B. minispinosa is smaller than many skate species in the eastern Bering Sea, it has a considerably longer estimated lifespan, indicating that size may not be a reliable method of estimating the vulnerability of a rajid species to population declines in the eastern North Pacific.
Misspent youth: does catching immature fish affect fisheries sustainability?
Authors: Vasilakopoulos Paraskevas , O'Neill Finbarr G. , Marshall C. Tara 
Published: June 2011

Abstract
Vasilakopoulos, P., O'Neill, F. G., and Marshall, C. T. 2011. Misspent youth: does catching immature fish affect fisheries sustainability? – ICES Journal of Marine Science, 68: 1525–1534. The “spawn-at-least-once” principle suggests that sustainability is secured if fish become vulnerable to commercial gears only after they have spawned. However, some studies suggest that protecting immature fish is not essential to sustainability because extrinsic factors determine both recruitment and stock status. A meta-analysis was conducted to quantify the independent effects of exploitation pattern and exploitation rate on current stock status. The analysis used empirical data for 38 fish stocks of 13 species in the NE Atlantic. Two metrics of exploitation pattern were used and their sensitivity was compared. As expected, exploitation rate had a significant negative effect on current stock status. Exploitation patterns associated with high proportional fishing mortality of immature fish also had a significant negative effect on current stock status, providing empirical support for the “spawn-at-least-once” principle. When the fishing mortality of immature fish exceeds half that of mature fish, stock status falls below precautionary limits. Our results suggest that a sensitive metric of exploitation pattern could provide useful information about an aspect of exploitation that is currently overlooked by fisheries management regimes that focus primarily on exploitation rate.