bluuebunny/crossref_metadata_2025_split huggingface dataset:
PFP 1: A Large Planetary Nebula Caught in the First Stages of ISM Interaction
Authors: Pierce Mark J. , Frew David J. , Parker Quentin A. , Köppen Joachim 
Published: September 2004

AbstractThis paper presents (Hα + [Nii]) imaging and spectroscopy of a previously unknown, highly evolved planetary nebula of low excitation which is in the first stages of an interaction with the interstellar medium (ISM). It was discovered serendipitously from AAO/UKST Hα Survey images as part of a project to exploit the survey data and has evaded detection by previous surveys due to its very low surface brightness. It is a remarkable hollow-sphere planetary nebula, some 19´ across, making it one of the largest examples of its type. We estimate a radius of 1.5 pc and a distance of 550 pc as derived from a new Hα surface brightness–radius relation. PFP 1 has near-perfect circular symmetry, broken only at the north-western edge which is coupled with significantly increased (Hα + [Nii]) intensity, both of which provide evidence for an interaction with the ISM. We find a near solar composition for this object with possibly enhanced He and N abundances. A blue central star candidate has been identified from the SuperCosmos Sky Survey data.
The open access scientific journal: an empirical study
Authors: Hedlund Turid , Gustafsson Tomas , Björk Bo‐Christer 
Published: September 2004

ABSTRACTThe open access (OA) model for journals is compared to the open source principle for computer software. Since the early 1990s nearly 1,000 OA scientific journals have emerged – mostly as voluntary community efforts, although recently some professionally operating publishers have used author charges or institutional membership. This study of OA journals without author charges shows that their impact is still relatively small, but awareness of it is increasing. The average number of research articles per year is lower than for major scientific journals but the publication times are shorter.
The demand side of STM publishing: understanding value creation in new market units
Authors: Akie Ronald , Baron Joel , Berkooz Gahl 
Published: September 2004

ABSTRACTFive factors are shaping the STM publishing industry: the shift from a supply‐driven to a user‐driven industry; conversion of paper‐based products to an all electronic environment; commoditization of online publishing technology; consolidation; and saturation of the traditional buyer market. Opportunities exist for publishers who can leverage their traditional content assets into new products that help specifically defined user‐groups accelerate and enhance the value creation process in vertical industry sectors. Research conducted with one group of researchers within one group of functions in one given industry describes the results of such an approach.
CrossRef and the research experience
Authors: Brand Amy 
Published: September 2004

ABSTRACTCrossRef is an independent membership association for building collaborative publishing technologies. Its mission is to provide services that enable the scholar to reach source material easily; it focuses on methods that are best achieved through collective agreement among publishers. The CrossRef network now covers millions of journal articles and other content items from hundreds of publishers. This article looks at CrossRef's significance for the online research experience, four years after the launch of the CrossRef initiative.
Research practices and scholarly communication in the digital environment
Authors: Houghton John W. , Steele Colin , Henty Margaret 
Published: September 2004

ABSTRACTThis paper examines changing research practices in the digital environment. A review of the literature and our own field research in Australia suggest that there is a new mode of knowledge production emerging, changing research practices and bringing new information access and dissemination needs. Adjustments will be required to accommodate these changes, but new opportunities are emerging for more cost‐effective and sustainable information access and dissemination. It will be necessary, however, to take an holistic approach and treat the creation, production and distribution of scholarly information, the management of information rights and access, systems of review and evaluation and the underlying infrastructure as parts of a single research information and scholarly communication system.
ProViz: protein interaction visualization and exploration
Authors: Iragne Florian , Nikolski Macha , Mathieu Bertrand , Auber David , Sherman David 
Published: September 2004

AbstractSummary: ProViz is a tool for the visualization of protein–protein interaction networks, developed by the IntAct European project. It provides facilities for navigating in large graphs and exploring biologically relevant features, and adopts emerging standards such as GO and PSI-MI.Availability: ProViz is available under the GPL and may be freely downloaded. Source code and binaries are available at http://cbi.labri.fr/eng/proviz.htmContact: david.sherman@labri.fr
SNPbox: a modular software package for large-scale primer design
Authors: Weckx Stefan , De Rijk Peter , Van Broeckhoven Christine , Del-Favero Jurgen 
Published: September 2004

Abstract
Summary: We developed a modular software package SNPbox that automates and standardizes the generation of PCR primers and is used in the strategy for constructing single nucleotide polymorphisms (SNPs) maps. In this strategy, the focus of primer design can be either on the validation of annotated public SNPs or on the SNP discovery in exon regions or extended genomic regions, both by resequencing. SNPbox relies on Primer3 for the primer design and combines this program with other publicly available software tools such as BLAST, Spidey and RepeatMasker, and newly developed algorithms. Primer conditions were chosen such that PCR amplifications are uniform for each PCR amplicon facilitating the use of high-throughput genetic platforms. SNPbox can also be used for the design of primer sets for mutation analysis, STR marker genotyping and microarray oligo design. Of the 2500 primer sets designed by SNPbox, 95% successfully amplified genomic DNA under uniform PCR conditions.
Availability: The software is available from the authors upon request.
Contact: jurgen.delfavero@ua.ac.be
Supplementary information: SNPbox_supplement.
Detecting overlapping coding sequences with pairwise alignments
Authors: Firth Andrew E. , Brown Chris M. 
Published: September 2004

Abstract
Motivation: Overlapping gene coding sequences (CDSs) are particularly common in viruses but also occur in more complex genomes. Detecting such genes with conventional gene-finding algorithms can be difficult for several reasons. If an overlapping CDS is on the same read-strand as a known CDS, then there may not be a distinct promoter or mRNA. Furthermore, the constraints imposed by double-coding can result in atypical codon biases. However, these same constraints lead to particular mutation patterns that may be detectable in sequence alignments.
Results: In this paper, we investigate several statistics for detecting double-coding sequences with pairwise alignments—including a new maximum-likelihood method. We also develop a model for double-coding sequence evolution. Using simulated sequences generated with the model, we characterize the distribution of each statistic as a function of sequence composition, length, divergence time and double-coding frame. Using these results, we develop several algorithms for detecting overlapping CDSs.
The algorithms were tested on known overlapping CDSs and other overlapping open reading frames (ORFs) in the hepatitis B virus (HBV), Escherichia coli and Salmonella typhimurium genomes. The algorithms should prove useful for detecting novel overlapping genes—especially short coding ORFs in viruses.
Availability: Programs may be obtained from the authors.
Contact: chris.brown@otago.ac.nz
Supplementary information: http://biochem.otago.ac.nz/double.html
Evaluating putative chimeric sequences from PCR-amplified products
Authors: Gonzalez Juan M. , Zimmermann Johannes , Saiz-Jimenez Cesareo 
Published: September 2004

AbstractMotivation: PCR amplification of highly homologous genes from complex DNA mixtures is known to generate a significant proportion of chimeric sequences. Ribosomal RNA genes are used for microbial species detection and identification in natural environments, and current assessments of microbial diversity are based on these sequences. Thus, chimeric sequences could lead to the discovery of non-existent microbial species and false diversity estimates.Methods: In essence, our only source of information to decide if a sequence is chimeric or not is to compare it with known, non-chimeric sequences. Putative chimeric sequences were analyzed from sequence fragments of selected length (referred to as words) by comparing nucleotides at corresponding positions. Distances for each word between reference sequences (closely related to the tested sequence) were compared to the differences introduced by the tested sequence. The proposed strategy considers the actual variability existing in different regions throughout the analyzed sequences. The result is an efficient strategy for the evaluation of putative chimeric sequences.Availability: A program computing the above procedure, Chimera and Cross-Over Detection and Evaluation (Ccode), is available at http://www.irnase.csic.es/users/jmgrau/index.html and http://www.rtphc.csic.es/download.htmlContact: jmgrau@irnase.csic.es
The SSEA server for protein secondary structure alignment
Authors: Fontana Paolo , Bindewald Eckart , Toppo Stefano , Velasco Riccardo , Valle Giorgio , Tosatto Silvio C. E. 
Published: September 2004

Abstract
Summary: We present a web server that computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a library of domain folds. It can calculate global and local secondary structure element alignments. A combination of local and global alignment steps can be used to search for domains inside the query sequence or help in the discrimination of novel folds. Both the SCOP and PDB fold libraries, clustered at 95 and 40% sequence identity, are available for alignment.
Availability: The web server interface is freely accessible to academic users at http://protein.cribi.unipd.it/ssea/. The executable version and benchmarking data are available from the same web page.
Contact: silvio@cribi.unipd.it
Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
Authors: Haft Daniel H. , Selengut Jeremy D. , Brinkac Lauren M. , Zafar Nikhat , White Owen 
Published: September 2004

AbstractMotivation: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable. Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics.Results: We have created a Genome Properties system to present key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties.Availability: Genome Properties can be found at http://www.tigr.org/Genome_PropertiesContact: selengut@tigr.orgSupplementary information: http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl
Layered Lithospheric Mantle Beneath the Ontong Java Plateau: Implications from Xenoliths in Alnöite, Malaita, Solomon Islands
Authors: ISHIKAWA AKIRA , MARUYAMA SHIGENORI , KOMIYA TSUYOSHI 
Published: September 2004

Abstract
A varied suite of mantle xenoliths from Malaita, Solomon Islands, was investigated to constrain the evolution of the mantle beneath the Ontong Java Plateau. Comprehensive petrological and thermobarometric studies make it possible to identify the dominant processes that produced the compositional diversity and to reconstruct the lithospheric stratigraphy in the context of a paleogeotherm. P–T estimates show that both peridotites and pyroxenites can be assigned to a shallower or deeper origin, separated by a garnet-poor zone of 10 km between 90 and 100 km. This zone is dominated by refractory spinel harzburgites (Fo91–92), indicating the occurrence of an intra-lithospheric depleted zone. Shallower mantle (∼Moho to 95 km) is composed of variably metasomatized peridotite with subordinate pyroxenite derived from metacumulates. Deeper mantle (∼95–120 km) is represented by pyroxenite and variably depleted peridotites that are unevenly distributed; the least-depleted garnet lherzolite (Fo90–91) lies just below the garnet-poor depleted zone (∼100–110 km), whereas the presence of pyroxenite is restricted to the deepest region (∼110–120 km), together with relatively Fe-enriched garnet lherzolite (Fo87–88). This depth-related variation (including the depleted zone) can be explained by assuming that the degree of melting for a basalt–peridotite hybrid source was systematically different at each level of arrival depth within a single adiabatically ascending mantle plume: (1) the depleted zone at the top of the mantle plume, where garnet was totally consumed in the residual solid; (2) an intermediate part of the plume dominated by the least-depleted garnet lherzolite just above the depth of the peridotite solidus; (3) the deepest pyroxenite-rich zone, whose petrochemical variation is best explained by the interaction between peridotite and normative quartz-rich basaltic melt, below the solidus of peridotite and liquidus of basalt. We explain the obvious lack of pyroxenites at shallower depths as the effective extraction of hybrid melt from completely molten basalt through the partially molten ambient peridotite, which caused the voluminous eruption of the Ontong Java Plateau basalts. From these interpretations, we conclude that the lithosphere forms a genetically unrelated two-layered structure, comprising shallower oceanic lithosphere and deeper impinged plume material, which involved a recycled basaltic component, now present as a pyroxenitic heterogeneity. This interpretation for the present lithospheric structure may explain the seismically anomalous root beneath the Ontong Java Plateau.
Management of Severe Burn Injuries in Neonates
Authors: Sun Bing-Wei , Zhou Xiao-Qin , Xia Chen-Lin , Chen Yu-Lin 
Published: September 2004

Abstract
Although rare, burns suffered by neonates can be fatal. Many complex difficulties are faced during the management of burns in neonates because of the neonate's complex physiological and pathological changes. We compiled a retrospective review from the treatment of four burned neonates (including a premature neonate). All four neonates suffered bath-related burns in the hospital as a result of careless nursing when being bathed. The total body surface area burned ranged from 1 to 60% in these patients, and all survived the burn injury. All the patients were treated in the Burn Intensive Care Unit with close co-operation of burn surgeons and neonatologists. Based on our experience as well as a review of literature, management recommendations are proposed as the following: 1) prompt and aggressive fluid resuscitation, 2) early administration of oxygen and keeping the patient warm, 3) application of specific biological dressing and recombinant human growth hormone if necessary, 4) establishment of a multidisciplinary team, and 5) removal of necrosis tissue early and aggressively. Furthermore, a very important issue is also discussed, which is about the prevention of newborn burns in the neonate unit in developing countries.
Intravenous Immunoglobulin Does Not Improve Outcome in Toxic Epidermal Necrolysis
Authors: Shortt Rodger , Gomez Manuel , Mittman Nicole , Cartotto Robert 
Published: September 2004

Abstract
Intravenous Immunoglobulin (IVIG) has been proposed as a beneficial therapy for toxic epidermal necrolysis (TEN). However, this has been based on a limited amount of Class 5 evidence. To compare outcomes in TEN patients treated in our burn unit since 1999, when we began to use IVIG (IG group), with TEN patients treated between 1995 and 1999 who did not receive IVIG (control group). Retrospective cohort review of the records of all TEN patients admitted between April 5, 1995 and December 4, 2002. There were 16 patients in the IG group (age 53 ± 21 years, with initial rash involving 65 ± 29% TBSA) and 16 patients in the control group (age 52 ± 20 years, with initial rash involving 65 ± 27% TBSA). The IG group received 0.7 ± 0.2 g/kg/day of IVIG for 4 ± 1 days. There were no significant differences between the groups with respect to the length of stay, duration of mechanical ventilation, severity of systemic inflammatory response syndrome and multiple organ dysfunction syndrome, or the incidence of sepsis. Significant progression of the wound occurred in 13% of the IG patients and in 27% of control patients, whereas no wound progression was observed in 47% of the IG patients and in 18% of the control patients (P = .299). The time to healing did not differ between IG and control groups (11.2 ± 3.6 vs 11.4 ± 2.6 days, respectively). There was no significant difference in the mortality rate between the IG group (25%) and the control group (38%). There were no complications from IVIG aside from one case of hyponatremia from the hypotonic IVIG solution. Although there may have been a trend towards less severe wound progression in patients who received IVIG, this was not associated with any substantial improvement in outcome in our TEN patients. A prospective randomized study with a larger sample size is needed to confirm our findings.
Quantification and Risk Analysis of Occupational Burns: Oregon Workers' Compensation Claims, 1990 to 1997
Authors: Horwitz Irwin B. , McCall Brian P. 
Published: September 2004

Abstract
This study examined all accepted Oregon workers' compensation claims for occupational burn injuries during the period of 1990 to 1997 (N = 3,158). The Current Population Survey was used to derive employee population baselines for establishing rate estimates. It was estimated that the average occupational burn claim rate was 2.89 per 10,000 workers (95% confidence interval [CI] 2.76, 3.02). The majority of claimants (71.7%) were males, the largest proportion (32.6%) was aged 25 years or less, and almost half (48.7%) had less than 1 year of job tenure. The most frequent burn type cited was heat/scald burns (78.9%) followed by chemical burns (19.3%). Costs averaged over $1.6 million annually. The average indemnity period was 16 days. Higher relative risks were found for evening workers (2.97, 95% CI 2.96, 2.98) and night workers (2.13, 95% CI 2.12, 2.13) compared with dayshift workers. Kitchen workers had the highest burn rate of all occupations, with 62.5 claims per 10,000 workers.
Burn Education Awareness Recognition and Support (BEARS): A Community-Based Juvenile Firesetters Assessment and Treatment Program
Authors: Bennett B. K. , Gamelli R. L. , Duchene R. C. , Atkocaitis D. , Plunkett J. A. 
Published: September 2004

Abstract
In response to the continued staggering statistics of fires set by juveniles and the devastating personal and property costs that are associated with these fires, the Burn and Shock Trauma Institute of Loyola University Medical Center, in collaboration with the State Fire Marshal's Office; the Illinois Fire Safety Alliance; and representatives from the firefighting community, law enforcement, emergency medicine and mental health, came together to create the Burn Education Awareness Recognition and Support Program. Through financial grant support from the International Association of Firefighters, the Illinois Fire Safety Alliance, and other private donations, the Burn Education Awareness Recognition and Support Program is able to provide a free resource to anyone who is concerned about a child playing with fire. Specially trained firefighters assess each child using the tool developed by the Federal Emergency Management Agency. In 2002, we assessed 42 children; 29 of those children were referred through the courts. So far, none of the children treated in our program have returned to fire-setting behaviors.
A Review of Keratinocyte Delivery to the Wound Bed
Authors: Chester D. L. , Balderson D. S. , Papini R. P. G. 
Published: September 2004

Abstract
Over the last 20 years, confluent sheets of cultured epithelial autograft have been used for patients with major burns. Problems with the lack of “take” and long-term durability, as well as the time delay to produce such grafts, have led to the development of delivery systems to transfer keratinocytes to the wound bed. This review article describes the problems of using cultured epithelial autograft and the advantages of using preconfluent keratinocytes. Despite the numerous delivery systems that have been reported, most studies are limited to animal wound bed models. There are a few small clinical studies that have demonstrated enhanced healing using mainly subjective methods. There is a need for controlled, randomized clinical trials to prove the efficacy of keratinocyte delivery systems. Proposals for the use of this technology are made.
Serum Levels of Prolactin, Growth Hormone, and Cortisol in Burn Patients: Correlations with Severity of Burn, Serum Cytokine Levels, and Fatality
Authors: Dugan A. L. , Malarkey W. B. , Schwemberger S. , Jauch E. C. , Ogle C. K. , Horseman N. D. 
Published: September 2004

AbstractIn this study, we measured serum prolactin (PRL), cortisol, growth hormone, interleukin (IL)-1β, IL-6, IL-8, IL-10, IL-12, and tumor necrosis factor-α in patients admitted with small-to-moderate burn injuries. Serum samples were obtained at the time of admission from 49 adult male burn patients with ages ranging from 18 to 91 years and TBSA ranging from 0.001 to 60%. The levels of serum PRL, IL-8, IL-6, and IL-1β correlated positively with the TBSA, whereas only serum IL-8 levels correlated positively with fatality. Each of these factors were increased at least 2-fold at the higher burn severity. Not surprisingly, there was a large degree of variability in the hormone and cytokine levels in this patient population, which presumably reflects individual levels of stress, as well as other physiological variables. We also studied relationships between serum hormone levels and serum cytokine levels in this context. Linear regression analysis revealed a significant positive correlation between the serum PRL level and the levels of IL-10, IL-6, and IL-8. These results indicate that PRL responds to burn injury at early time points and that a subset of cytokines are involved in the early response to burn injury.