bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparison of the HCR-20V3 Among Male and Female Insanity Acquittees: A Retrospective File Study
Authors: Green Debbie , Schneider Melanie , Griswold Hali , Belfi Brian , Herrera Michelle , DeBlasi Ashley 
Published: March 2016

The current retrospective risk assessment study evaluated the use of the Historical-Clinical-Risk Management-20 Version 3 (HCR-20V3) in a sample of 100 male and 24 female insanity acquittees, comparing the presence of risk factors and its validity in assessing violence in a state forensic hospital across males and females. Over an average of 15.5 months, 44.4% of the total sample engaged in any act of violence within the institution, highlighting the need for effective risk assessment and management tools. An equivalent proportion of males and females engaged in violence (42.0% of males and 54.2% of females). Results indicated higher interrater reliability on scoring risk factors among males as compared to females, calling for future research into the role of item indicators across genders and possible differences in interpretations of scoring guidelines. Results indicated that females exhibited similar numerical ratings of presence risk factors as males, although they were rated higher on Past Problems in Relationships and Traumatic Experiences. The relationships between scale scores and violence were higher among males than females. However, gender was not a significant moderator in logistic regression analyses predicting likelihood of violence. Additional research is necessary to evaluate how ratings of risk factors are translated into summary risk estimates, opinions about dangerousness, and treatment interventions, with a particular focus on how such decision-making is influenced by the gender of examinees.
Survival of Hatchery Raised Red Drum Exposed to Abrupt Salinity Increases—Simulating Bay Stockings
Authors: McDonald Dusty L , Cason Paul D , Bumguardner Britt W , Tomasso Joseph R 
Published: March 2016

Abstract
As part of a stock enhancement program in Texas, Red Drum Sciaenops ocellatus are subject to a standard salinity acclimation protocol between the hauling trailer and stock site of 1 h per 10‰ salinity difference. In certain circumstances (hypersaline sites or drought) salinity differences can exceed 20‰ between hauling trailer and stock site. Information is needed on whether the current protocol is sufficient to investigate whether extending the acclimation time can improve survival. We conducted nine trials, each exposing pond-cultured Red Drum fingerlings to salinity increases of 10‰ (over 1, 2, and 3 h), 20‰ (over 2, 4, and 6 h), and no salinity change (control). Survival at 96 h following a change in salinity of either 10‰ or 20‰ was independent of the rate of increase in salinity. However, survival was lower among Red Drum subjected to an increase of 20‰ (survival, 61%) than to 10‰ (82%). Fish condition, length and weight of fish examined here had no significant effect on survival, across trials. Results suggest that hatchery personnel should select stocking sites within 10‰ salinity of the production pond and hauling trailer.
Quantifying the Trophic Importance of Gulf Menhaden within the Northern Gulf of Mexico Ecosystem
Authors: Sagarese Skyler R. , Nuttall Matthew A. , Geers Tess M. , Lauretta Matthew V. , Walter John F. , Serafy Joseph E. 
Published: March 2016

Abstract
The Gulf Menhaden Brevoortia patronus is frequently cited as playing a predominant role in the trophic structure and function of the northern Gulf of Mexico (GOM) marine ecosystem, yet much work remains in quantifying its ecological importance. We performed a meta-analysis of diet studies to quantify the trophic role of Gulf Menhaden within this ecosystem. Of the 568 references consulted, 136 identified predator–prey interactions involving Gulf Menhaden, menhaden Brevoortia spp., or unidentified clupeid prey items. Overall, 79 species were reported to consume menhaden, and no significant difference was detected between the Atlantic Ocean and the GOM in the mean occurrence of Brevoortia spp. in predator stomachs. We employed a probabilistic approach using maximum likelihood estimation to quantify trophic interactions within the northern GOM, with a focus on the trophic role of Gulf Menhaden. The estimated contribution of identifiable menhaden to the diets of all predators generally ranged between 2% and 3%; the largest dietary contribution was identified for Blacktip Sharks Carcharhinus limbatus (8%), and lower estimates (&lt;2%) were obtained for oceanic species, including sharks, billfishes, and tunas. When diet compositions were adjusted for unidentified prey by using the proportion of fish species biomass in the ecosystem, five predator groups showed a relatively large dependence on menhaden prey: juvenile King Mackerel Scomberomorus cavalla, juvenile Spanish Mackerel Scomberomorus maculatus, adult Spanish Mackerel, Red Drum Sciaenops ocellatus, and Blacktip Sharks. The quantification of trophic linkages and key predators identified herein will be fundamental to future modeling efforts focused on the northern GOM ecosystem.
Received March 24, 2015; accepted September 3, 2015
Trophic Ecology of a Predatory Community in a Shallow-Water, High-Salinity Estuary Assessed by Stable Isotope Analysis
Authors: Shaw Ashley L. , Frazier Bryan S. , Kucklick John R. , Sancho Gorka 
Published: March 2016

Abstract
Estuaries serve as habitats and nurseries for many recreationally and commercially important fishes, often contributing recruits to adult populations that remain in close proximity to estuarine environments. Upper-level predatory fish species are among the most sought after by fisheries; thus, an understanding of the trophic dynamics of the community can assist ecological fisheries management of these highly productive ecosystems. Dietary niche overlap within the predatory fish community of Bulls Bay, a subtropical estuary in South Carolina, was assessed by using stable isotope analyses (δ13C and δ15N) to compare seven elasmobranch species and three teleost species. Cownose Rays Rhinoptera bonasus and Finetooth Sharks Carcharhinus isodon had no isotopic overlap with other species and therefore exhibited unique isotopic niche spaces that were indicative of potential resource partitioning. The teleosts and remaining elasmobranchs had varying degrees of overlap, implying shared resources; a high degree of dietary niche overlap was observed among Spotted Seatrout Cynoscion nebulosus, Sandbar Sharks Carcharhinus plumbeus, and Atlantic Sharpnose Sharks Rhizoprionodon terraenovae. Although most pairs of species showed some isotopic overlap, there were also interspecific differences in niche overlap, signifying that this predatory fish community has a widely varied prey base overall. Bulls Bay is an important nursery habitat with a balanced predator community, as illustrated by a combination of unique dietary niches and varying degrees of dietary niche overlap.
Received August 31, 2015; accepted November 9, 2015
Impact of an invasive nitrogen-fixing tree on arbuscular mycorrhizal fungi and the development of native species
Authors: Guisande-Collazo Alejandra , González Luís , Souza-Alonso Pablo 
Published: March 2016

Abstract
Arbuscular mycorrhizal fungi (AMF) are obligate soil biotrophs that establish intimate relationships with 80 % of terrestrial plant families. Arbuscular mycorrhizal fungi obtain carbon from host plants and contribute to the acquisition of mineral nutrients, mainly phosphorus. The presence of invasive plants has been identified as a soil disturbance factor, often conditioning the structure and function of soil microorganisms. Despite the investigation of many aspects related to the invasion of Acacia dealbata , the effect produced on the structure of AMF communities has never been assessed. We hypothesize that A. dealbata modifies the structure of AMF community, influencing the establishment and growth of plants that are dependent on these mutualisms. To validate our hypothesis, we carried out denaturing gradient gel electrophoresis (DGGE) analysis and also grew plants of Plantago lanceolata in pots using roots of native shrublands or from A. dealbata , as inoculum of AMF. Cluster analyses from DGGE indicated an alteration in the structure of AMF communities in invaded soils. After 15 weeks, we found that plants grown in pots containing native roots presented higher stem and root growth and also produced higher biomass in comparison with plants grown with A. dealbata inoculum. Furthermore, plants that presented the highest biomass and growth exhibited the maximum mycorrhizal colonization and phosphorus content. Moreover, fluorescence measurements indicated that plants grown with A. dealbata inoculum even presented higher photosynthetic damage. Our results indicate that the presence of the invader A. dealbata modify the composition of the arbuscular fungal community, conditioning the establishment of native plants.
Integrating fishers’ knowledge research in science and management
Authors: Stephenson Robert L. , Paul Stacey , Pastoors Martin A. , Kraan Marloes , Holm Petter , Wiber Melanie , Mackinson Steven , Dankel Dorothy J. , Brooks Kate , Benson Ashleen 
Published: March 2016

AbstractFishers' knowledge research (FKR) aims to enhance the use of experiential knowledge of fish harvesters in fisheries research, assessment, and management. Fishery participants are able to provide unique knowledge, and that knowledge forms an important part of “best available information” for fisheries science and management. Fishers' knowledge includes, but is much greater than, basic biological fishery information. It includes ecological, economic, social, and institutional knowledge, as well as experience and critical analysis of experiential knowledge. We suggest that FKR, which may in the past have been defined quite narrowly, be defined more broadly to include both fishery observations and fishers “experiential knowledge” provided across a spectrum of arrangements of fisher participation. FKR is part of the new and different information required in evolving “ecosystem-based” and “integrated” management approaches. FKR is a necessary element in the integration of ecological, economic, social, and institutional considerations of future management. Fishers' knowledge may be added to traditional assessment with appropriate analysis and explicit recognition of the intended use of the information, but fishers' knowledge is best implemented in a participatory process designed to receive and use it. Co-generation of knowledge in appropriately designed processes facilitates development and use of fishers' knowledge and facilitates the participation of fishers in assessment and management, and is suggested as best practice in improved fisheries governance.
Actinobacillus hominis osteomyelitis: First reported case in the English language medical literature
Authors: O’Neill Gavin , Ker Andrew , Mohammed Aslam , Karcher Anne Marie 
Published: March 2016

Introduction:

Actinobacillus hominis is currently a rarely reported pathogen. It has previously been associated with respiratory tract infections and bacteraemia in debilitated patients. However, under-reporting may occur due to misidentification by commonly used laboratory bacterial identification systems. This case is, to the best of our knowledge, the first reported case of A. hominis osteomyelitis in the English language medical literature.

Case presentation:
A 37-year-old male presented with a painful foot. He had no previous foot problems, history of injury or animal contact. Osteomyelitis was confirmed by magnetic resonance imaging (MRI), and blood cultures were positive for Gram-variable bacilli. The organism was identified initially as Pasteurella pneumotropica by the local routine diagnostic laboratory and as a Pasteurella species by the UK National Reference Laboratory (Colindale, London, UK), using standard operating procedures at the time. It was finally identified as an A. hominis using 16S rRNA gene sequence analysis. Difficulties in the accurate identification of this organism remain current, as other biochemical identification systems have also resulted in misidentifications. The patient refused admission and intravenous antibiotics. He was successfully treated using an 8-week course of oral ciprofloxacin and amoxicillin based on antibiotic disc susceptibility testing resulting in clinical, serological and radiological resolution.

Conclusion:
Laboratories should maintain a high index of suspicion for A. hominis as several commonly used bacterial identification systems may not accurately identify the organism. Colonial morphology and absence of animal contact should prompt consideration of this organism in appropriate clinical situations. Oral ciprofloxacin and amoxicillin treatment was successful in this case.
A statistical framework for neuroimaging data analysis based on mutual information estimated via a Gaussian copula
Authors: Ince Robin A. A. , Giordano Bruno L. , Kayser Christoph , Rousselet Guillaume A. , Gross Joachim , Schyns Philippe G. 
Published: March 2016

AbstractWe begin by reviewing the statistical framework of information theory as applicable to neuroimaging data analysis. A major factor hindering wider adoption of this framework in neuroimaging is the difficulty of estimating information theoretic quantities in practice. We present a novel estimation technique that combines the statistical theory of copulas with the closed form solution for the entropy of Gaussian variables. This results in a general, computationally efficient, flexible, and robust multivariate statistical framework that provides effect sizes on a common meaningful scale, allows for unified treatment of discrete, continuous, uni-and multi-dimensional variables, and enables direct comparisons of representations from behavioral and brain responses across any recording modality. We validate the use of this estimate as a statistical test within a neuroimaging context, considering both discrete stimulus classes and continuous stimulus features. We also present examples of analyses facilitated by these developments, including application of multivariate analyses to MEG planar magnetic field gradients, and pairwise temporal interactions in evoked EEG responses. We show the benefit of considering the instantaneous temporal derivative together with the raw values of M/EEG signals as a multivariate response, how we can separately quantify modulations of amplitude and direction for vector quantities, and how we can measure the emergence of novel information over time in evoked responses. Open-source Matlab and Python code implementing the new methods accompanies this article.HighlightsNovel estimator for mutual information and other information theoretic quantitiesProvides general, efficient, flexible and robust multivariate statistical frameworkValidated statistical performance on EEG and MEG dataApplications to spectral power and phase, 2D magnetic field gradients, temporal derivativesInteraction information relates information content in different responses
Strawberry: fast and accurate genome-guided transcript reconstruction and quantification from RNA-seq
Authors: Liu Ruolin , Dickerson Julie A. 
Published: March 2016

AbstractWe propose a novel method and computational tool, Strawberry, for transcript reconstruction and quantification from paired-end RNA-seq data under the guidance of genome alignment and independent of gene annotation. Strawberry achieves this through disentangling assembly and quantification in a sequential manner. The application of a fast flow network algorithm for assembly speeds up the construction of a parsimonious set of transcripts. The resulting reduced data representation improves the efficiency of expression-level quantification. Strawberry leverages the speed and accuracy of transcript assembly and quantification in such a way that processing 10 million simulated reads (after alignment) requires only 90 seconds using a single thread while achieving over 92% correlation with the ground truth, making it the state-of-the-art method. Strawberry outperforms Cufflinks and StringTie, the two other leading methods, in many aspects, including the number of corrected assembled transcripts and the correlation with the ground truth of simulated RNA-seq data.Availability:Strawberry is written in C++11, and is available as open source software athttps://github.com/ruolin/Strawberryunder the GPLv3 license.
Transcriptome remodeling contributes to epidemic disease caused by the human pathogenStreptococcus pyogenes
Authors: Beres Stephen B. , Kachroo Priyanka , Nasser Waleed , Olsen Randall J. , Zhu Luchang , Flores Anthony R. , de la Riva Ivan , Paez-Mayorga Jesus , Jimenez Francisco E. , Cantu Concepcion , Vuopio Jaana , Jalava Jari , Kristinsson Karl G. , Gottfredsson Magnus , Corander Jukka , Fittipaldi Nahuel , Di Luca Maria Chiara , Petrelli Dezemona , Vitali Luca A. , Raiford Annessa , Jenkins Leslie , Musser James M. 
Published: March 2016

AbstractFor over a century, a fundamental objective in infection biology research has been to understand the molecular processes contributing to the origin and perpetuation of epidemics. Divergent hypotheses have emerged concerning the extent to which environmental events or pathogen evolution dominates in these processes. Remarkably few studies bear on this important issue. Based on population pathogenomic analysis of 1200Streptococcus pyogenestypeemm89 infection isolates, we report that a series of horizontal gene transfer events produced a new pathogenic genotype with increased ability to cause infection, leading to an epidemic wave of disease on at least two continents. In the aggregate, these and other genetic changes substantially remodeled the transcriptomes of the evolved progeny, causing extensive differential expression of virulence genes and altered pathogen - host interaction, including enhanced immune evasion. Our findings delineate the precise molecular genetic changes that occurred and enhance our understanding of the evolutionary processes that contribute to the emergence and persistence of epidemically successful pathogen clones. The data have significant implications for understanding bacterial epidemics and translational research efforts to blunt their detrimental effects.ImportanceThe confluence of studies of molecular events underlying pathogen strain emergence, evolutionary genetic processes mediating altered virulence, and epidemics is in its infancy. Although understanding these events is necessary to develop new or improved strategies to protect health, surprisingly few studies have addressed this issue, in particular at the comprehensive population genomic level. Herein we establish that substantial remodeling of the transcriptome of the human-specific pathogenStreptococcus pyogenesby horizontal gene flow and other evolutionary genetic changes is a central factor in precipitating and perpetuating epidemic disease. The data unambiguously show that the key outcome of these molecular events is evolution of a new, more virulent pathogenic genotype. Our findings provide new understanding of epidemic disease.
Climatic warming strengthens a positive feedback between alpine shrubs and fire
Authors: Camac James S , Williams Richard J , Wahren Carl-Henrik , Hoffmann Ary A , Vesk Peter A 
Published: March 2016

AbstractClimate change is expected to increase fire activity and woody plant encroachment in arctic and alpine landscapes. However, the extent to which these increases interact to affect the structure, function and composition of alpine ecosystems is largely unknown. Here we use field surveys and experimental manipulations to examine how warming and fire affect recruitment, seedling growth and seedling survival in four dominant Australian alpine shrubs. We found that fire increased establishment of shrub seedlings by as much as 33–fold. Experimental warming also doubled growth rates of tall shrub seedlings and could potentially increase their survival. By contrast, warming had no effect on shrub recruitment, post-fire tussock regeneration, or how tussock grass affected shrub seedling growth and survival. These findings indicate that warming, coupled with more frequent or severe fires, will likely result in an increase in the cover and abundance of evergreen shrubs. Given shrubs are one of the most flammable components in alpine and tundra environments, warming is likely to strengthen an existing feedback between woody species abundance and fire in these ecosystems.
The aptabot: an inducibly affinity-switching, minimally invasivein vivocontrast agent
Authors: Webster Heffern Elleard Felix , Fuller Jason , Hanson Russell W. 
Published: March 2016

AbstractThe ambitions of current neuroscience—understanding neurological disease progression and mapping the connectome—demonstrate a need for safein vivotools for creating intricate maps of brain circuitry. Presentin vivocontrast agents are often limited by their specificity, uptake, resolvability, and/or clearance.We describe an aptamer-functionalized sensor for high-resolution imaging that can switch imaging targets by an induced multi-stage aptamer reaction. Included are synthetic methods as well as calculations of sensor efficacy based on known kinetics. Calculations show that 10 distinct targets may be imaged in a living brain at the submicron scale within 42 hours.
The role of transposable elements for gene expression inCapsellahybrids and allopolyploids
Authors: Steige Kim A. , Reimegård Johan , Rebernig Carolin A. , Köhler Claudia , Scofield Douglas G. , Slotte Tanja 
Published: March 2016

AbstractThe formation of an allopolyploid species involves the merger of two genomes with separate evolutionary histories. In allopolyploids, genes derived from one progenitor species are often expressed at higher levels than those from the other progenitor. It has been suggested that this could be due to differences in transposable element (TE) content among progenitors, as silencing of TEs can affect expression of nearby genes. Here, we examine the role of TEs for expression biases in the widespread allotetraploidCapsella bursa-pastorisand in diploid F1 hybrids generated by crossingCapsella orientalisandCapsella rubella, two close relatives of the progenitors ofC. bursa-pastoris. AsC. rubellaharbors more TEs thanC. orientalis, we expectC. orientalisalleles to be expressed at higher levels if TE content is key for expression biases. To test this hypothesis, we quantified expression biases at approximately 5800 genes in flower buds and leaves, while correcting for read mapping biases using genomic data. While three of fourC. bursa-pastorisaccessions exhibited a shift toward higher relative expression ofC. orientalisalleles, the fourthC. bursa-pastorisaccession had the opposite direction of expression bias, as did diploid F1 hybrids. Associations between TE polymorphism and expression bias were weak, and the effect of TEs on expression bias was small. These results suggest that differences in TE content alone cannot fully explain expression biases in these species. Future studies should investigate the role of differences in TE silencing efficacy, as well as a broader set of other factors. Our results are important for a more general understanding of the role of TEs for cis-regulatory evolution in plants.