bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do Anglers Know What They Catch? Identification Accuracy and Its Effect on Angler Survey-Derived Catch Estimates
Authors: Page Kevin S. , Zweifel Richard D. , Carter George , Radabaugh Nick , Wilkerson Michael , Wolfe Matthew , Greenlee Michael , Brown Kipp 
Published: October 2012

Abstract
Angler surveys are reliant on the ability of anglers to accurately report various aspects of their fishing trips. Misidentification of sport fishes has been postulated as a source of error among angler surveys but has received little attention. We evaluated the overall ability of anglers to identify sport fishes common to Ohio and the potential impacts on catch estimates derived from angler surveys. During angler surveys conducted on lakes and reservoirs (2007, n = 34) and Ohio River tailwaters (2010, n = 3), anglers were presented with artist-rendered images of 18 different sport fishes common to these waters. Anglers (lake and reservoir, n = 2,442; Ohio River, n = 458) were asked to identify sport fish by their common name. On average, anglers correctly identified sport fishes 42% of the time, but accuracy varied widely among species (lake and reservoir, range = 4.4–85.1%; Ohio River, range = 9.4–71.8%), with greater accuracy exhibited for the most common species (e.g., largemouth bass Micropterus salmoides). However, by grouping angler responses into species groups (e.g., black bass Micropterus spp., sunfish Lepomis spp.) angler identification of sport fishes was more reliable (lake and reservoir, mean = 83.4%; Ohio River, mean = 83.8%). Using these estimates of angler accuracy, we simulated the potential error in sport fish catch estimates using data from an angler survey conducted at one Ohio reservoir. These results suggested that misidentification error may result in a substantial error in catch estimates. A survey of North American fisheries management agencies regarding angler surveys and angler sport fish identification revealed that the majority of agencies group similar species for analysis and cited species misidentification by anglers as the primary reason for doing so.
Received April 19, 2012; accepted August 17, 2012
Effects of van der Waals interactions on the nonlinear vibration of multi-layered graphene sheets
Authors: Arghavan S , Singh A V 
Published: October 2012

Abstract
This paper is concerned with the forced nonlinear vibration of multi-layered graphene sheets modelled at the atomic level by the lattice structure approach. In this, the covalent bond between two carbon atoms is assumed as a structural member with prescribed physical and material properties. An atom is treated as a nodal point with its own mass and six degrees of freedom. The highly nonlinear van der Waals interaction between adjacent graphene layers is fully incorporated in the model by placing it in the force vector. This adjustment significantly reduces the computational hardships due to nonlinearity and increases the efficiency of the method. Newmark's direct integration method is modified to address the nonlinearity in the load vector and used for the solution of the matrix equation governing the motion of the multi-layered graphene sheet. Double-layered square graphene with simply supported and clamped boundary conditions is analysed to examine the out-of-plane and in-plane vibrational characteristics. Also, in order to illustrate the applicability of the numerical method, analyses are carried out with the first- and second-order Taylor series approximations of the van der Waals interactions, influence of which is found to be quite significant in the bending modes of vibration, but it essentially does not have a role in the in-plane modes. The numerical method developed herein is quite appropriate with reference to the structural formation at the atomic scale and also more efficient than previous computational approaches by others.
Human protein–protein interaction prediction by a novel sequence-based co-evolution method: co-evolutionary divergence
Authors: Hsin Liu Chia , Li Ker-Chau , Yuan Shinsheng 
Published: October 2012

Abstract
Motivation: Protein–protein interaction (PPI) plays an important role in understanding gene functions, and many computational PPI prediction methods have been proposed in recent years. Despite the extensive efforts, PPI prediction still has much room to improve. Sequence-based co-evolution methods include the substitution rate method and the mirror tree method, which compare sequence substitution rates and topological similarity of phylogenetic trees, respectively. Although they have been used to predict PPI in species with small genomes like Escherichia coli, such methods have not been tested in large scale proteome like Homo sapiens.
Result: In this study, we propose a novel sequence-based co-evolution method, co-evolutionary divergence (CD), for human PPI prediction. Built on the basic assumption that protein pairs with similar substitution rates are likely to interact with each other, the CD method converts the evolutionary information from 14 species of vertebrates into likelihood ratios and combined them together to infer PPI. We showed that the CD method outperformed the mirror tree method in three independent human PPI datasets by a large margin. With the arrival of more species genome information generated by next generation sequencing, the performance of the CD method can be further improved.
Availability: Source code and support are available at http://mib.stat.sinica.edu.tw/LAP/tmp/CD.rar.
Contact: syuan@stat.sinica.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
Discriminative modelling of context-specific amino acid substitution probabilities
Authors: Angermüller Christof , Biegert Andreas , Söding Johannes 
Published: October 2012

Abstract
Motivation: Protein sequence searching and alignment are fundamental tools of modern biology. Alignments are assessed using their similarity scores, essentially the sum of substitution matrix scores over all pairs of aligned amino acids. We previously proposed a generative probabilistic method that yields scores that take the sequence context around each aligned residue into account. This method showed drastically improved sensitivity and alignment quality compared with standard substitution matrix-based alignment.
Results: Here, we develop an alternative discriminative approach to predict sequence context-specific substitution scores. We applied our approach to compute context-specific sequence profiles for Basic Local Alignment Search Tool (BLAST) and compared the new tool (CS-BLASTdis) to BLAST and the previous context-specific version (CS-BLASTgen). On a dataset filtered to 20% maximum sequence identity, CS-BLASTdisis was 51% more sensitive than BLAST and 17% more sensitive than CS-BLASTgenin, detecting remote homologues at 10% false discovery rate. At 30% maximum sequence identity, its alignments contain 21 and 12% more correct residue pairs than those of BLAST and CS-BLASTgen, respectively. Clear improvements are also seen when the approach is combined with PSI-BLAST and HHblits. We believe the context-specific approach should replace substitution matrices wherever sensitivity and alignment quality are critical.
Availability: Source code (GNU General Public License, version 3) and benchmark data are available at ftp://toolkit.genzentrum.lmu.de/pub/csblast/.
Contact: soeding@genzentrum.lmu.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Stock identification of wahoo (Acanthocybium solandri) in the Pacific and Indian Oceans using morphometrics and parasites
Authors: Zischke Mitchell T. , Griffiths Shane P. , Tibbetts Ian R. , Lester Robert J. G. 
Published: October 2012

Abstract
Zischke, M. T., Griffiths, S. P., Tibbetts, I. R., and Lester, R. J. G. 2013. Stock identification of wahoo (Acanthocybium solandri) in the Pacific and Indian Oceans using morphometrics and parasites. – ICES Journal of Marine Science, 70:164–172. The wahoo (Acanthocybium solandri) is an increasingly important by-product species of tropical pelagic fisheries worldwide. However, specific management of the species is currently hindered by a dearth of information on basic biology and stock structure. This study examined the stock structure of wahoo using morphometric characters and parasite fauna from fish collected in three regions of the western Pacific, and one region in each of the eastern Pacific and eastern Indian Oceans. Similar morphometric measurements and parasite abundance of wahoo collected off eastern Australia suggest they may form part of a single phenotypic stock in the western Pacific Ocean. Morphometric measurements and parasite fauna were significantly different among wahoo from the western Pacific and eastern Pacific Oceans, suggesting multiple discrete phenotypic stocks despite genetic homogeneity. Assessing fish from a range of regions throughout the Pacific Ocean may help discriminate stock boundaries in this region. Future research using complementary techniques, such as otolith microchemistry and genetic microsatellites, may improve our understanding of the global stock structure of wahoo to suitably inform regional fishery management organizations.
Patient-specific reconstructed anatomies and computer simulations are fundamental for selecting medical device treatment: application to a new percutaneous pulmonary valve
Authors: Capelli Claudio , Taylor Andrew M. , Migliavacca Francesco , Bonhoeffer Philipp , Schievano Silvia 
Published: October 2012

Nowadays, percutaneous pulmonary valve implantation is a successful alternative to surgery for patients requiring treatment of pulmonary valve dysfunction. However, owing to the wide variety of implantation site morphology, size and dynamics, only about 15 per cent of cases are suitable for current devices. In order to increase the number of patients who could benefit from minimally invasive procedures, a new valved stent graft for percutaneous implantation has been designed recently. In this study, patient-specific computational analyses have been applied to investigate the suitability of new device designs, using real data from 62 patients who had undergone surgical pulmonary valve replacement. Magnetic resonance images of these patients before surgery were elaborated using imaging post-processing software to reconstruct the three-dimensional volume of each patient's implantation site. Three stent designs were created and tested in these patient outflow tracts using finite-element simulations: stent graft SG1 resembles the first device tested in animals; stent graft SG2 is a custom device tailored for a specific patient morphology; and stent graft SG3 represents a hypothetical larger device. The three devices showed an implantation success rate of 37 per cent, 42 per cent and 63 per cent, respectively. Using patient-specific simulations, we have shown that a percutaneous approach with these new devices may be possible for many patients who are currently referred for surgery. Furthermore, when the new devices become available, the methodologies described may help clinicians in the decision-making process, by enabling virtual implantation prior to the actual procedure.
Growth of Transplastomic Cells Expressing d-Amino Acid Oxidase in Chloroplasts Is Tolerant to d-Alanine and Inhibited by d-Valine
Authors: Gisby Martin F. , Mudd Elisabeth A. , Day Anil 
Published: October 2012

Abstract
Dual-conditional positive/negative selection markers are versatile genetic tools for manipulating genomes. Plastid genomes are relatively small and conserved DNA molecules that can be manipulated precisely by homologous recombination. High-yield expression of recombinant products and maternal inheritance of plastid-encoded traits make plastids attractive sites for modification. Here, we describe the cloning and expression of a dao gene encoding d-amino acid oxidase from Schizosaccharomyces pombe in tobacco (Nicotiana tabacum) plastids. The results provide genetic evidence for the uptake of d-amino acids into plastids, which contain a target that is inhibited by d-alanine. Importantly, this nonantibiotic-based selection system allows the use of cheap and widely available d-amino acids, which are relatively nontoxic to animals and microbes, to either select against (d-valine) or for (d-alanine) cells containing transgenic plastids. Positive/negative selection with d-amino acids was effective in vitro and against transplastomic seedlings grown in soil. The dual functionality of dao is highly suited to the polyploid plastid compartment, where it can be used to provide tolerance against potential d-alanine-based herbicides, control the timing of recombination events such as marker excision, influence the segregation of transgenic plastid genomes, identify loci affecting dao function in mutant screens, and develop d-valine-based methods to manage the spread of transgenic plastids tagged with dao.
The AINTEGUMENTA LIKE1 Homeotic Transcription Factor PtAIL1 Controls the Formation of Adventitious Root Primordia in Poplar
Authors: Rigal Adeline , Yordanov Yordan S. , Perrone Irene , Karlberg Anna , Tisserant Emilie , Bellini Catherine , Busov Victor B. , Martin Francis , Kohler Annegret , Bhalerao Rishi , Legué Valérie 
Published: October 2012

Abstract
Adventitious rooting is an essential but sometimes rate-limiting step in the clonal multiplication of elite tree germplasm, because the ability to form roots declines rapidly with age in mature adult plant tissues. In spite of the importance of adventitious rooting, the mechanism behind this developmental process remains poorly understood. We have described the transcriptional profiles that are associated with the developmental stages of adventitious root formation in the model tree poplar (Populus trichocarpa). Transcriptome analyses indicate a highly specific temporal induction of the AINTEGUMENTA LIKE1 (PtAIL1) transcription factor of the AP2 family during adventitious root formation. Transgenic poplar samples that overexpressed PtAIL1 were able to grow an increased number of adventitious roots, whereas RNA interference mediated the down-expression of PtAIL1 expression, which led to a delay in adventitious root formation. Microarray analysis showed that the expression of 15 genes, including the transcription factors AGAMOUS-Like6 and MYB36, was overexpressed in the stem tissues that generated root primordia in PtAIL1-overexpressing plants, whereas their expression was reduced in the RNA interference lines. These results demonstrate that PtAIL1 is a positive regulator of poplar rooting that acts early in the development of adventitious roots.
A Drug Fatality Involving Kratom
Authors: Neerman Michael F. , Frost Randall E. , Deking Janine 
Published: October 2012

AbstractA 17‐year‐old white man who showed no obvious signs of trauma was found unresponsive in bed and was pronounced dead at the scene. The decedent had a documented history of heroin abuse and chronic back pain and reportedly self‐medicated with Kratom (mitragynine). The autopsy was remarkable only for pulmonary congestion and edema and a distended bladder, both of which are consistent with, though not diagnostic of, opiate use. A laboratory work‐up revealed therapeutic levels of over‐the‐counter cold medications and benzodiazepines. However, of interest was a level of mitragynine at 0.60 mg/L. Given the facts of the case, the Medical Examiner certified the cause of death as “possible Kratom toxicity” and the manner of death was classified as “accident.”
The Evaluation of Fatty Acid Ratios in Latent Fingermarks by Gas Chromatography/Mass Spectrometry (GC/MS) Analysis
Authors: Michalski Seth , Shaler Robert , Dorman Frank L. 
Published: October 2012

AbstractDespite advances in DNA, fingermarks remain one the best forms of evidence available. While fingermarks are routinely analyzed in terms of their patterns, it may be possible to obtain additional information in terms of their chemical composition. If successful, a chemical analysis of the constituents of a fingermark may give scientists additional information that may help in the identification of a person. The results presented herein describe the initial investigation into the analytical determination of some of these compounds, specifically the fatty acids. This study was specifically aimed at identifying possible fatty acids, which could aid in profiling or perhaps uniquely identifying an individual. Preliminary data obtained in this study suggests that this may in fact be possible, though additional research is certainly necessary. Utilizing gas chromatography–mass spectrometry, significant differences in the ratios of several fatty acid methyl esters were found when comparing individuals of varying race and gender. In addition, large intervariability and intravariability was discovered for some compounds, suggesting the possibility of being able to individualize based on chemical profile. Follow‐up investigations will continue to determine whether this continues to be the case as greater numbers of individuals are sampled and more extensive control and information on the subjects is obtained.
Belimumab: targeted therapy for lupus
Authors: Chugh Preeta K. , Kalra Bhupinder S. 
Published: October 2012

AbstractSystemic lupus erythematosus (SLE), a complex autoimmune disease with multisystem involvement, is characterised by recurring flares and remissions throughout the course of illness. The agents currently being used for management include corticosteroids, antimalarials and various immunosuppressants. Belimumab, a B lymphocyte stimulator (BLyS) inhibitor has been recently approved for the treatment of SLE. This review aims to discuss the role of belimumab in the treatment of SLE and the trials leading to its FDA approval. Belimumab demonstrated high degree of activity in patients with autoantibody‐positive active SLE disease on a stable treatment regimen. There was a significantly greater response compared to placebo as assessed with the SLE Responder Index (SRI) in two randomized, double‐blind, phase III trials (BLISS‐52 and BLISS‐76). The treatment was well tolerated. Additional studies are required to evaluate belimumab in special populations and assess its long‐term safety. This therapy could change the focus of management from symptomatic treatment to targeting an important step in the disease pathogenesis. It could enable development of treatment which could halt long‐term progression, minimize target organ damage and thus provide a better quality of life for these patients.
Cardiovascular morbidity in rheumatoid arthritis patients in North Canterbury, New Zealand 1999–2008
Authors: Khan Emon A. R. , Stamp Lisa K. , O'Donnell John L. , Chapman Peter T. 
Published: October 2012

AbstractAimCardiovascular disease is a substantial contributor to increased morbidity and mortality in rheumatoid arthritis (RA). The aim of this audit was to determine the rate of cardiovascular events in a cohort of newly diagnosed RA patients.MethodThe inpatient clinical database from Christchurch Hospital, Christchurch, New Zealand, was searched using the International Classification of Diseases 9th Revision (ICD9) and 10 codes representing RA and cardiovascular disease between 1 January 1999 and 31 December 2008. Notes were reviewed with additional demographic and medication data sought. Outpatient data for RA patients was collated from the Rheumatology Department's letter database.ResultsFour hundred and six patients were identified with combined ICD9 or 10 codes for RA and ischemic heart disease, of whom 194 had a confirmed myocardial event. Of these, 34 were diagnosed with RA between January 1999 and December 2008 prior to their myocardial event. Kaplan–Meier analysis showed risk of a cardiovascular event at 1 and 10 years was 0.64% and 9.4%, respectively. There were 26 confirmed deaths in the study period. The risk of death at 1 and 10 years was 0.48% and 8.16%, respectively.ConclusionWe have shown a relatively low prevalence of cardiovascular events in this RA population diagnosed within a 10 year period. This is consistent with other reports and likely reflects the short follow‐up period. Prospective longer‐term studies will be required to further investigate the relative contribution of disease activity and other parameters to cardiovascular events in patients with early RA.
Oral health in Australian HIV patients since the advent of combination antiretroviral therapy
Authors: Freeman AD , Liberali SA , Coates EA , Logan RM 
Published: October 2012

AbstractBackground:  The introduction of combination antiretroviral therapy (cART) for the treatment of human immunodeficiency virus (HIV) has resulted in changes to the oral health of infected individuals. Little data are available describing prevalence and severity of oral manifestations in a post cART cohort of HIV positive patients.Methods:  A retrospective case note analysis was performed at the Special Needs Unit (SNU), Adelaide Dental Hospital with emphasis on identifying the prevalence of HIV related oral manifestations (OM). A total of 498 (474 males: 24 females) HIV positive individuals were identified who had attended SNU for dental care between 2001 and 2008.Results:  There were significant differences observed in the prevalence of oral manifestations between cART and non‐cART groups, and also in comparison to a previous pilot study. Individuals taking cART therapy tended to present with more evidence of linear gingival erythema, angular cheilitis, human papilloma virus associated squamous papillomas and xerostomia.Conclusions:  The widespread adoption of cART in the treatment of HIV has altered the oral health profile of these individuals. These findings provide information on the incidence of oral conditions and demonstrate the need to identify and address oral health needs for people living with HIV.