bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and functional analysis of two di-domain aromatase/cyclases from type II polyketide synthases
Authors: Caldara-Festin Grace , Jackson David R. , Barajas Jesus F. , Valentic Timothy R. , Patel Avinash B. , Aguilar Stephanie , Nguyen MyChi , Vo Michael , Khanna Avinash , Sasaki Eita , Liu Hung-wen , Tsai Shiou-Chuan 
Published: December 2015

Significance
Polyketides are a class of diverse natural products with well-documented bioactivity and medicinal importance. Enzymes known as aromatase/cyclases (ARO/CYCs) catalyze regiospecific cyclization and aromatization during type II polyketide biosynthesis. Understanding how ARO/CYCs catalyze cyclization and aromatization is critical for developing strategies for engineering biosynthetic pathways. This is the first study, to our knowledge, to use X-ray crystallography, bioinformatic and structural analysis, and in vitro functional assays to critically compare a reducing di-domain ARO/CYC (BexL) and a nonreducing di-domain ARO/CYC (StfQ). Together, these results fill in a missing link in the structural enzymology of polyketide biosynthesis and will have a direct effect on future biosynthetic engineering efforts and bioinformatic analysis of type II PKS gene clusters.
Ground-Based Thermal Imaging of Stream Surface Temperatures: Technique and Evaluation
Authors: Bonar Scott A. , Petre Sally J. 
Published: December 2015

Abstract
We evaluated a ground-based handheld thermal imaging system for measuring water temperatures using data from eight southwestern USA streams and rivers. We found handheld thermal imagers could provide considerably more spatial information on water temperature (for our unit one image = 19,600 individual temperature measurements) than traditional methods could supply without a prohibitive amount of effort. Furthermore, they could provide measurements of stream surface temperature almost instantaneously compared with most traditional handheld thermometers (e.g., &gt;20 s/reading). Spatial temperature analysis is important for measurement of subtle temperature differences across waterways, and identification of warm and cold groundwater inputs. Handheld thermal imaging is less expensive and equipment intensive than airborne thermal imaging methods and is useful under riparian canopies. Disadvantages of handheld thermal imagers include their current higher expense than thermometers, their susceptibility to interference when used incorrectly, and their slightly lower accuracy than traditional temperature measurement methods. Thermal imagers can only measure surface temperature, but this usually corresponds to subsurface temperatures in well-mixed streams and rivers. Using thermal imaging in select applications, such as where spatial investigations of water temperature are needed, or in conjunction with stationary temperature data loggers or handheld electronic or liquid-in-glass thermometers to characterize stream temperatures by both time and space, could provide valuable information on stream temperature dynamics. These tools will become increasingly important to fisheries biologists as costs continue to decline.
Received October 3, 2014; accepted September 3, 2015
System-Specific Variability in Murray Cod and Golden Perch Maturation and Growth Influences Fisheries Management Options
Authors: Forbes Jamin P. , Watts Robyn J. , Robinson Wayne A. , Baumgartner Lee J. , Allen Micheal S. , McGuffie Prue , Cameron Leo M. , Crook David A. 
Published: December 2015

Abstract
The Murray Cod Maccullochella peelii and Golden Perch Macquaria ambigua are important recreational species in Australia's Murray–Darling Basin (MDB); both species have declined substantially, but recovery is evident in some areas. Minimum length limits (MLLs)—implemented to ensure fish could spawn at least once prior to harvest eligibility—have increased three times in the past decade. We quantified variation in length at 50% maturity (LM50), age at 50% maturity (AM50), and von Bertalanffy growth parameters (k = Brody growth coefficient; L∞ = asymptotic length; t0 = theoretical age at zero length) of these species within two rivers and two reservoirs of the MDB; to investigate whether fish length is a suitable surrogate for AM50 in setting MLLs. Between 2006 and 2013, we collected 1,118 Murray Cod and 1,742 Golden Perch by electrofishing and gillnetting. Values of k and L∞ were greater for reservoir fish than for riverine fish. For both species, AM50 was generally greater in rivers than in reservoirs; for Murray Cod, LM50 was greater in reservoirs than in rivers. A yield-per-recruit model demonstrated that smaller Murray Cod MLLs would be required for rivers and that an MLL at or below 600 mm (the existing MLL) across all populations could lead to overfishing in some systems. The differences in growth rate and the onset of reproductive maturation between riverine and reservoir populations suggest that system-specific regulations would be more effective at reducing the overfishing risk and meeting fishing quality objectives.
Received August 18, 2014; accepted September 10, 2015
Effects of Antimycin and its Neutralizing Agent, Potassium Permanganate, on Aquatic Macroinvertebrates in a Great Smoky Mountains National Park Watershed
Authors: Gibbs W. Keith , Kulp Matt A. , Moore Steve E. , Cook S. Bradford 
Published: December 2015

Abstract
We assessed the effects of antimycin (Fintrol) on benthic macroinvertebrates during a large Brook Trout Salvelinus fontinalis restoration project in the southeastern United States. Control and treatment sites were established in first- through fourth-order streams throughout the watershed and below the fish passage barrier where a neutralizing agent (potassium permanganate [KMnO4]) was administered. Hess samples were collected before and after chemical application (short term: 1 and 2 months after; long term: 9 and 12 months after). Analysis of similarity, nonmetric multidimensional scaling, and repeated-measures ANOVA were used to determine differences in assemblage metrics among control, treatment, and neutralization sites over time. Macroinvertebrate communities and their responses to antimycin were different at downstream (third- and fourth-order) sites relative to headwater (first- and second-order) sites. Overall, abundances (especially stonefly and caddisfly abundances) increased after antimycin application, reflecting a positive response within the macroinvertebrate assemblage. Several variables, including mayfly and stonefly abundances, were significantly different among control, concentrated-KMnO4, and dilute-KMnO4 sites; however, differences were undetectable after 9 months. Many taxa were substantially more abundant several months after treatment, indicating a thriving macroinvertebrate assemblage throughout the watershed. Future studies yielding similar results would suggest that native fish stocking efforts can commence shortly after chemical degradation.
Received May 2, 2014; accepted September 10, 2015
Genetic Stock Structure of Terapon jarbua in Taiwanese Waters
Authors: Liu Shang-Yin Vanson , Huang I-Hsiang , Liu Min-Yun , Lin Hung-Du , Wang Feng-Yu , Liao Te-Yu 
Published: December 2015

Abstract
Over the past century, stock identification, which is crucial for fisheries stock assessments, has relied heavily on intraspecies variations to differentiate management units. In recent years, however, DNA approaches have shed additional light on some aspects of the natural history and ecology of species and stocks. The Crescent Grunter Terapon jarbua is widely distributed across the Indo-Pacific region. It inhabits coastal waters with sandy substrates and tends to aggregate in estuaries. In the present study, we collected 96 individuals of T. jarbua from 10 locations around the shoreline of Taiwan as well as near Guangdong, China. A concatenated sequence (1,753 bp) of mtDNA (cytochrome c oxidase I and cytochrome b) was obtained from all individuals. We discovered two genetically distinct clades (lineages A and B) with different historical demographies occurring sympatrically except at the Yilan collection site, which was dominated by lineage A haplotypes. Connectivity within this region is high according to FST and AMOVA tests. The genetic variation between the two clades is far below the interspecies threshold for the genus Terapon (0.007 versus 0.3156). Therefore, we suggest that they be considered different genetic stocks from a fisheries management point of view and that future stock reassessment should be conducted based on the genetic information provided in this study. Further large-scale sampling is needed to understand the mechanisms that drive genetic partitioning on regional (Northwest Pacific) and global (Indo-Pacific) scales.
Received February 9, 2015; accepted July 9, 2015
Functional Status, Quality of Life, and Costs Associated With Fibromyalgia Subgroups
Authors: Luciano Juan V. , Forero Carlos G. , Cerdà-Lafont Marta , Peñarrubia-María María Teresa , Fernández-Vergel Rita , Cuesta-Vargas Antonio I. , Ruíz José M. , Rozadilla-Sacanell Antoni , Sirvent-Alierta Elena , Santo-Panero Pilar , García-Campayo Javier , Serrano-Blanco Antoni , Pérez-Aranda Adrián , Rubio-Valera María 
Published: December 2015

Objectives:
Although fibromyalgia syndrome (FM) is considered a heterogeneous condition, there is no generally accepted subgroup typology. We used hierarchical cluster analysis and latent profile analysis to replicate Giesecke’s classification in Spanish FM patients. The second aim was to examine whether the subgroups differed in sociodemographic characteristics, functional status, quality of life, and in direct and indirect costs.

Materials and Methods:
A total of 160 FM patients completed the following measures for cluster derivation: the Center for Epidemiological Studies-Depression Scale, the Trait Anxiety Inventory, the Pain Catastrophizing Scale, and the Control over Pain subscale. Pain threshold was measured with a sphygmomanometer. In addition, the Fibromyalgia Impact Questionnaire-Revised, the EuroQoL-5D-3L, and the Client Service Receipt Inventory were administered for cluster validation.

Results:
Two distinct clusters were identified using hierarchical cluster analysis (“hypersensitive” group, 69.8% and “functional” group, 30.2%). In contrast, the latent profile analysis goodness-of-fit indices supported the existence of 3 FM patient profiles: (1) a “functional” profile (28.1%) defined as moderate tenderness, distress, and pain catastrophizing; (2) a “dysfunctional” profile (45.6%) defined by elevated tenderness, distress, and pain catastrophizing; and (3) a “highly dysfunctional and distressed” profile (26.3%) characterized by elevated tenderness and extremely high distress and catastrophizing. We did not find significant differences in sociodemographic characteristics between the 2 clusters or among the 3 profiles. The functional profile was associated with less impairment, greater quality of life, and lower health care costs.

Discussion:
We identified 3 distinct profiles which accounted for the heterogeneity of FM patients. Our findings might help to design tailored interventions for FM patients.
Pediatric Traumatic Amputations in the United States: A 5-Year Review
Authors: Borne Allen , Porter Austin , Recicar John , Maxson Todd , Montgomery Corey 
Published: December 2015

Background:
Pediatric traumatic amputations are devastating injuries capable of causing permanent physical and psychological sequelae. Few epidemiologic reports exist for guidance of prevention strategies. The objective of this study is to review the recent trends in pediatric traumatic amputations using a national databank.

Methods:
A review of all pediatric (age, 0 to 17 y) amputee patients was performed using the National Trauma Data Bank from 2007 to 2011. Data including demographics, location of amputation, and mechanism of injury were analyzed.

Results:
In the analysis 2238 patients were identified. The majority of amputations occurred in the youngest (0 to 5 y) and oldest (15 to 17 y) age groups with a 3:1 male to female ratio. The most common amputation locations were finger (54%) and toe (20%). A caught between mechanism (16.3%) was most common overall followed by machinery, powered lawn mowers, motor vehicle collisions, firearms, and off-road vehicles. Males were statistically more likely to have an amputation and lawnmower injuries were statistically associated with lower extremity amputations in children 5 years old and below. Motor vehicle injuries were the most common cause of adolescent amputations. Firearm-related amputations occurred predominantly in adolescents, whereas off-road vehicle amputations occurred in all ages.

Conclusions:
Common trends in pediatric amputations are relatively unchanged over the last decade. Young children sustain more finger amputations from a caught between objects mechanism, whereas adolescents sustain serious amputations from higher energy mechanisms such as firearms-related and motor vehicle–related injuries. Lawnmower-related amputations continue to most significantly affect younger children despite increased public awareness. Improved prevention strategies targeting age and mechanism-related trends are necessary to prevent these costly and debilitating injuries.

Level of Evidence:
Level IV.
Relationships Between 3 Classification Systems in Brachial Plexus Birth Palsy
Authors: Greenhill Dustin A. , Lukavsky Robert , Tomlinson-Hansen Sandra , Kozin Scott H. , Zlotolow Dan A. 
Published: December 2015

Background:
The Mallet scale, Active Movement Scale (AMS), and Toronto Test are validated for use in children with brachial plexus birth palsy (BPBP). However, the inability to compare these evaluation systems has led to difficulty gauging treatment efficacy and interpreting available literature in which multiple scoring systems are reported. Given the critical importance of physical examination, we compared 3 scoring systems to clarify statistical relationships between current validated evaluation methods.

Methods:
The medical records of children with BPBP treated at a single institution over a 14-year period were retrospectively reviewed. Modified Mallet, AMS, and Toronto scores were recorded throughout the entire period. Data were included if at least 2 complete scoring systems were documented during the same examination session. Spearman correlation coefficients were calculated for all composite and subscore combinations. A concordance table was constructed for select variables found to be highly correlated.

Results:
Total single-session score combinations were as follows: 157 Mallet and AMS, 325 AMS and Toronto, and 143 Mallet and Toronto. Composite AMS and Toronto scores were found to have a strong correlation (r=0.928, P<0.001). A concordance table comparing these variables revealed that a Toronto score of 3.5 is concordant to an AMS score of 45. Modified Mallet scores had only a moderate correlation with composite AMS (r=0.512, P<0.001) and Toronto (r=0.458, P<0.001) scores. Specifically regarding the modified Mallet score, maneuvers requiring external rotation had stronger correlations with the composite modified Mallet score than maneuvers highlighting internal rotation.

Conclusions:
Modified Mallet scores do not correlate well with AMS or Toronto scores and should be utilized separately when managing children with BPBP. Similarly, AMS and Toronto scores are inadequate to guide clinical decisions for which the literature cites Mallet scores as outcome measures, and vice versa. Lastly, Mallet scores should incorporate an isolated internal rotation component to adequately assess midline function.

Level of Evidence:
Diagnostic level III.
A Population-based Investigation of Circadian Rhythm of Intraocular Pressure in Habitual Position Among Healthy Subjects: The Handan Eye Study
Authors: Wang Ning Li , Hao Jie , Zhen Yi , Liu John H.K. , Li Si Zhen , Wang Hao , Chen Hui , Peng Xiao Xia , Han Wei , Fan Su Jie , Weinreb Robert N. 
Published: December 2015

Purpose:
(1) To investigate the reference value of peak-trough difference in circadian rhythm of intraocular pressure (IOP) in habitual position and (2) to compare the IOP parameters among 3 age groups.

Materials and Methods:
Habitual IOP of healthy subjects sampled from the population in the Handan Eye Study was measured every 2 hours in the seated position during light-wake period (7:30 am, 9:30 AM, 11:30 AM, 1:30 PM, 3:30 PM, 5:30 PM, 7:30 PM, 9:30 PM) and in the supine position during dark-sleep period (11:30 PM, 1:30 AM, 3:30 AM, 5:30 AM). Blood pressure and heart rate were obtained subsequently at each IOP measurement.

Results:
Two hundred six healthy subjects were included in the final analyses (n=20, 30 to 39 y old; n=95, 40 to 49 y old; n=91, 50 to 59 y old). For peak-trough difference (7.2±2.3 mm Hg; 6.8 to 7.5 mm Hg, 95% confidence interval) in habitual position, the reference value was described as median 7.0 mm Hg, 25th percentile 5.5 mm Hg, and 95th percentile 11.5 mm Hg. No significant differences in peak-trough difference, acrophase (cosine-fit analysis derived peak timing) and amplitude (half distance between the cosine-fit maximum and minimum) were found among the 3 age groups. In the cosine model, the nocturnal acrophase (3:49±0.53 AM; 3:42 to 3:55 AM, 95% confidence interval) was detected for the entire group. Furthermore, 106 subjects (52%) had a nocturnal peak pattern, 36 subjects (17%) had a diurnal peak pattern, and 64 subjects (31%) had no evident pattern.

Conclusions:
In habitual position, 75% of healthy subjects from a population-based investigation had IOP variation >5.5 mm Hg and 95% subjects had <11.5 mm Hg variation. Aging may not influence the circadian habitual IOP rhythm.
nihexporter: an R package for NIH funding data
Authors: Hesselberth Jay , Baschal Erin , Ellinwood Nick , Pacheco Ashley , Peach Sally , Sweet Mary , Wang Yuying 
Published: December 2015

1Abstract1.1MotivationThe National Institutes of Health (NIH) is the major source of federal funding for biomedical research in the United States. Analysis of past and current NIH funding can illustrate funding trends and identify productive research topics, but these analyses are conductedad hocby the institutes themselves and only provide a small glimpse of the available data. The NIH provides free access to funding data via NIH EXPORTER, but no tools have been developed to enable analysis of this data.1.2ResultsWe developed thenihexporter Rpackage, which provides access to NIH EXPORTER data. We used the package to develop several analysis vignettes that show funding trends across NIH institutes over 15 years and highlight differences in how institutes change their funding profiles. Investigators and institutions can use the package to perform self-studies of their own NIH funding.1.3AvailabilityThenihexporter Rpackage can be installed via github.1.4ImplementationThenihexporterpackage is implemented in the R Statistical Computing Environment.1.5ContactJay Hesselberthjay.hesselberth@gmail.com, University of Colorado School of Medicine
Male sex pheromone components inHeliconiusbutterflies released by the androconia affect female choice
Authors: Darragh Kathy , Vanjari Sohini , Mann Florian , Gonzalez-R Maria F , Morrison Colin R , Salazar Camilo , Pardo-Diaz Carolina , Merrill Richard M , McMillan W Owen , Schulz Stefan , Jiggins Chris D. 
Published: December 2015

AbstractSex specific pheromones are known to play an important role in butterfly courtship, and may influence both individual reproductive success and reproductive isolation between species. Extensive ecological, behavioural and genetic studies ofHeliconiusbutterflies have made a substantial contribution to our understanding of speciation. Male pheromones, although long suspected to play an important role, have received relatively little attention in this genus. Here, we combine morphological, chemical, and behavioural analyses of male pheromones in the Neotropical butterflyHeliconius melpomene.First, we identify putative androconia that are specialized brush-like scales that lie within the shiny grey region of the male hindwing. We then describe putative male sex pheromone compounds, which are largely confined to the androconial region of the hindwing of mature males, but are absent in immature males and females. Finally, behavioural choice experiments reveal that females ofH. melpomene,H. eratoandH. timaretastrongly discriminate against conspecific males which have their androconial region experimentally blocked. As well as demonstrating the importance of chemical signalling for female mate choice inHeliconiusbutterflies, the results describe structures involved in release of the pheromone and a list of potential male sex pheromone compounds.
Reticulate evolution is favored in influenza niche switching
Authors: Ma Eric J. , Hill Nichola J. , Zabilansky Justin , Yuan Kyle , Runstadler Jonathan A. 
Published: December 2015

AbstractReticulate evolution is thought to accelerate the process of evolution beyond simple genetic drift and selection, helping to rapidly generate novel hybrids with combinations of adaptive traits. However, the long-standing dogma that reticulate evolutionary processes are likewise advantageous for switching ecological niches, as in microbial pathogen host switch events, has not been explicitly tested. We use data from the influenza genome sequencing project and a phylogenetic heuristic approach to show that reassortment, a reticulate evolutionary mechanism, predominates over mutational drift in transmission between different host species. Moreover, as host evolutionary distance increases, reassortment is increasingly favored. We conclude that the greater the quantitative difference between ecological niches, the greater the importance of reticulate evolutionary processes in overcoming niche barriers.Significance StatementAre the processes that result in the exchange of genes between microbes quantitatively advantageous for those microbes when switching between ecological niches? To address this question, we consider the influenza A virus as a model microbe, with its ability to infect multiple host species (ecological niches) and undergo reassortment (exchange genes) with one another. Through our analysis of sequence data from the Influenza Research Database and the Barcode of Life Database, we find that the greater the quantitative difference between influenza hosts, the greater the proportion of reassortment events were found. More broadly, for microbes, we infer that reticulate evolutionary processes should be quantitatively favoured when switching between ecological niches.