bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Structure of Steelhead in Coastal California
Authors: Garza John Carlos , Gilbert‐Horvath Elizabeth A. , Spence Brian C. , Williams Thomas H. , Fish Heidi , Gough Stephen A. , Anderson Joseph H. , Hamm David , Anderson Eric C. 
Published: January 2014

AbstractSteelhead Oncorhynchus mykiss are the most widespread of the Pacific salmonids Oncorhynchus spp. and are found in nearly all basins within their native range around the northern Pacific Rim. Here, we elucidate genetic population structure of steelhead in coastal basins from most of their coastal‐California range using variation at 15 microsatellite loci. Juvenile fish from 60 streams in 40 river basins were sampled in a single year from a single cohort. As samples of juvenile salmonids often contain sibling groups, a method was implemented to identify and eliminate all but one member of larger sibships. This, in conjunction with a rigorous sampling protocol and hierarchical sampling design, provided substantially improved resolution for understanding patterns of migration and demography. A pattern of isolation by distance was evident, as indicated by both phylograms that were largely concordant with geography and a significant regression of genetic distance on geographic distance, indicating that population structure is largely determined by migration that is dependent upon geographic distance. Within‐basin genetic distances tended to be smaller than those between basins, although there was substantial overlap between them. Using a Bayesian clustering method to evaluate signals of population structure above the level of a river basin, four geographic sites were identified where genetic composition shifted abruptly. These areas largely correspond to major geographic features of the coastline: San Francisco and Humboldt bays and two extended sections of coast (the so‐called Lost Coast and Russian Gulch areas) with no streams reaching inland more than several kilometers. Only one of these boundaries is concordant with the current delineation of steelhead Distinct Population Segments designated under the U.S. Endangered Species Act. Finally, there was a strong correlation between latitude and genetic variation, with fewer alleles present in the south, a pattern consistent with generally smaller population sizes in the south.
Barriers Impede Upstream Spawning Migration of Flathead Chub
Authors: Walters David M. , Zuellig Robert E. , Crockett Harry J. , Bruce James F. , Lukacs Paul M. , Fitzpatrick Ryan M. 
Published: January 2014

AbstractMany native cyprinids are declining throughout the North American Great Plains. Some of these species require long reaches of contiguous, flowing riverine habitat for drifting eggs or larvae to develop, and their declining populations have been attributed to habitat fragmentation or barriers (e.g., dams, dewatered channels, and reservoirs) that restrict fish movement. Upstream dispersal is also needed to maintain populations of species with passively drifting eggs or larvae, and prior researchers have suggested that these fishes migrate upstream to spawn. To test this hypothesis, we conducted a mark–recapture study of Flathead Chub Platygobio gracilis within a 91‐km reach of continuous riverine habitat in Fountain Creek, Colorado. We measured CPUE, spawning readiness (percent of Flathead Chub expressing milt), and fish movement relative to a channel‐spanning dam. Multiple lines of evidence indicate that Flathead Chub migrate upstream to spawn during summer. The CPUE was much higher at the base of the dam than at downstream sites; the seasonal increases in CPUE at the dam closely tracked seasonal increases in spawning readiness, and marked fish moved upstream as far as 33 km during the spawning run. The upstream migration was effectively blocked by the dam. The CPUE of Flathead Chub was much lower upstream of the OHDD than at downstream sites, and <0.2% of fish marked at the dam were recaptured upstream. This study provides the first direct evidence of spawning migration for Flathead Chub and supports the general hypothesis that barriers limit adult dispersal of these and other plains fishes.
Evaluating the Barrier Assessment Technique Derived from FishXing Software and the Upstream Movement of Brook Trout through Road Culverts
Authors: Mahlum Shad , Cote David , Wiersma Yolanda F. , Kehler Dan , Clarke Keith D. 
Published: January 2014

AbstractAnthropogenic barriers to fish passage, such as culverts and dams, are major factors impeding the persistence and recovery of aquatic species. Considerable work has focused on mitigating these impacts; however, activities associated with measuring and restoring connectivity of aquatic ecosystems often face challenges in determining the passability of barriers by aquatic species. Hydrological modeling software that incorporates biological aspects of a focal species is often used as a relatively inexpensive method for assessing barrier passability for restoration decisions. However, the biological relevance of these approaches remains to be rigorously tested. We assessed passage rates of PIT‐tagged Brook Trout Salvelinus fontinalis through four road culverts and adjacent reference sites (unaltered areas of the streams) on the island of Newfoundland to determine whether upstream passage through road culverts was more restrictive than unaltered reference areas of the stream. Next, we examined the usefulness of barrier passability predictions derived from FishXing software by comparing them with in situ movement data for this species. Brook Trout passage for three of the four reference sites had a significantly higher range of passable stream flows compared with that for culverts, indicating the presence of velocity barriers in culverts. However, FishXing predictions of suitable fish passage discharges were conservative, and tagged fish successfully navigated partial barriers that were at least 2–3 times the upper limits of stream flow predicted to allow successful passage. The results of our study show a clear need for an improved understanding of fish movement through these structures so that barrier assessment techniques can be refined. The implications of not doing so may lead to restoration actions that result in limited biological benefit.
Use of a Molecular Assay to Detect Predation on an Endangered Fish Species
Authors: Ley Guillermo , Saltzgiver Melody J. , Dowling Thomas E. , Karam Abraham P. , Kesner Brian R. , Marsh Paul C. 
Published: January 2014

AbstractMastication, digestion, and rapid evacuation rates make visual identification of larval fish remains in the digestive tracts of predatory fishes problematic. Recent advances in molecular technology, however, have increased the likelihood of identifying remnants of partially digested larval prey, thereby enabling assessment of predator impacts on local populations. Conducting controlled laboratory experiments, we evaluated the utility of quantitative polymerase chain reaction (qPCR) for identification of Razorback Sucker Xyrauchen texanus larvae in the digestive tracts of Green Sunfish Lepomis cyanellus and Western Mosquitofish Gambusia affinis. Primers and a probe were developed to amplify a fragment from Razorback Sucker mtDNA. Tests using a suite of potential predators and prey indicated that these primers and probes amplified only mtDNA from Razorback Sucker and Flannelmouth Sucker Catostomus latipinnis, an allopatric and allochronic species in the lower Colorado River. Amplification with primers for Razorback Sucker‐specific DNA fragments identified Razorback Sucker DNA in the digestive tracts of 87.5% of Green Sunfish and Western Mosquitofish at 2 h postfeeding. After 12 h, DNA fragments were identified in 75.0% of Green Sunfish but in only 28.6% of Western Mosquitofish. No Razorback Sucker DNA was found in 24‐h postfeeding samples, though it was detected in 12.5% of both Western Mosquitofish and Green Sunfish at 48 h postingestion. The sensitivity of qPCR provides a useful tool for extending the time period in which Razorback Sucker larvae can be identified beyond that of traditional visual analyses of stomach contents.
Habitat Use and Selection by Adult Pallid Sturgeon in the Lower Mississippi River
Authors: Herrala Jason R. , Kroboth Patrick T. , Kuntz Nathan M. , Schramm Harold L. 
Published: January 2014

AbstractThe Pallid Sturgeon Scaphirhynchus albus is an endangered riverine sturgeon with historical distribution restricted to the Yellowstone, Missouri, Mississippi, and Atchafalaya rivers. Although not abundant, Pallid Sturgeon in the lower Mississippi River appear to be naturally recruiting, and information about habitat use is important to conserve this species. Thirty‐four adult Pallid Sturgeon (612–1,013‐mm FL) were tagged with acoustic transmitters and relocated a total of 272 times in a 40‐km reach of the lower Mississippi River from April 2009 through December 2012. Pallid Sturgeon strongly selected island tip and natural bank habitats, and, to a lesser degree, revetted bank habitat. Although frequently used, Pallid Sturgeon exhibited negative selection for the expansive main channel habitat. Secondary channel habitat was seasonally available and excluded from habitat selection analysis, but this habitat was frequently used in the spring when available. Fifty percent of Pallid Sturgeon detections were in relatively narrow ranges of depths (6.2–13.6 m) and surface current velocities (0.64–1.05 m/s). Use of different habitats was related to river stage and water temperature, suggesting use of some habitats was seasonal. Results suggest that maintaining natural bank habitat and secondary channel–island complexes will benefit conservation of this endangered species in the lower Mississippi River.
White Perch in Small North Carolina Reservoirs: What Explains Variation in Population Structure?
Authors: Bethke Bethany J. , Rice James A. , Aday D. Derek 
Published: January 2014

AbstractWhite Perch Morone americana have been introduced into many inland systems throughout the United States. To determine factors affecting White Perch abundance and size structure, we compared White Perch growth, timing of maturity, and trophic level; the abundance of a predator (Largemouth Bass Micropterus salmoides); the abundance of an ecologically significant mid‐level omnivore (Gizzard Shad Dorosoma cepedianum); prey availability (chironomid and zooplankton abundances); and environmental variables (specific conductivity, Secchi depth, dissolved oxygen concentration, and temperature) among four reservoirs (two with high White Perch abundance and two with low abundance). White Perch size structure was closely tied to abundance, with truncated size structure as abundance increased. Among the other variables we tested, only Largemouth Bass abundance had a significant (negative) relationship with White Perch abundance. White Perch size structure appeared to be highly density dependent, and variables that commonly explain variation in abundance of introduced fishes did not explain differences in the four White Perch populations we studied. Further study of the competitive and predatory interactions of White Perch and Largemouth Bass over ontogeny could shed light on the mechanism(s) potentially shaping population structure of the two species where they coexist.
Geographic Variability in Elevation and Topographic Constraints on the Distribution of Native and Nonnative Trout in the Great Basin
Authors: Warren Dana R. , Dunham Jason B. , Hockman‐Wert David 
Published: January 2014

AbstractUnderstanding local and geographic factors influencing species distributions is a prerequisite for conservation planning. Our objective in this study was to model local and geographic variability in elevations occupied by native and nonnative trout in the northwestern Great Basin, USA. To this end, we analyzed a large existing data set of trout presence (5,156 observations) to evaluate two fundamental factors influencing occupied elevations: climate‐related gradients in geography and local constraints imposed by topography. We applied quantile regression to model upstream and downstream distribution elevation limits for each trout species commonly found in the region (two native and two nonnative species). With these models in hand, we simulated an upstream shift in elevation limits of trout distributions to evaluate potential consequences of habitat loss. Downstream elevation limits were inversely associated with latitude, reflecting regional gradients in temperature. Upstream limits were positively related to maximum stream elevation as expected. Downstream elevation limits were constrained topographically by valley bottom elevations in northern streams but not in southern streams, where limits began well above valley bottoms. Elevation limits were similar among species. Upstream shifts in elevation limits for trout would lead to more habitat loss in the north than in the south, a result attributable to differences in topography. Because downstream distributions of trout in the north extend into valley bottoms with reduced topographic relief, trout in more northerly latitudes are more likely to experience habitat loss associated with an upstream shift in lower elevation limits. By applying quantile regression to relatively simple information (species presence, elevation, geography, topography), we were able to identify elevation limits for trout in the Great Basin and explore the effects of potential shifts in these limits that could occur in response to changing climate conditions that alter streams directly (e.g., through changes in temperature and precipitation) or indirectly (e.g., through changing water use).
Coastwide Stock Structure of Winter Flounder Using Nuclear DNA Analyses
Authors: Wirgin Isaac , Maceda Lorraine , Grunwald Cheryl , Roy Nirmal K. , Waldman John R. 
Published: January 2014

AbstractMany Winter Flounder Pseudopleuronectes americanus populations have declined dramatically. In U.S. waters, Winter Flounder are managed as three stocks: Gulf of Maine, southern New England–Mid‐Atlantic Bight, and Georges Bank. Historically, it was believed that the spawning of inshore stocks occurs exclusively within natal estuaries. Based on the supposition of estuary‐specific spawning, we hypothesized that Winter Flounder exhibit greater stock structure than predicted by the three‐stock model and, in fact, that they exhibit genetic differentiation at the level of individual estuaries. We tested this hypothesis by conducting microsatellite DNA analysis at 12 loci and single‐nucleotide polymorphism analysis at 4 loci on young‐of‐the year and adult Winter Flounder collected from 27 estuaries from Newfoundland to Delaware as well as from Georges Bank. We found highly significant coastwide genetic stock structure among Winter Flounder; however, there was little evidence of estuary‐specific structure. Pooled collections from north and south of Cape Cod were genetically distinct, as were many individual collections compared between these two regions. However, there was little genetic heterogeneity among estuarine collections within either of these major geographic regions. The two Canadian collections from the Miramichi River and Newfoundland were genetically distinct from those in the Gulf of Maine. Our collection from Georges Bank was marginally distinct from the inshore collections from north and south of Cape Cod. Overall, our genetic results support the three‐stock model used to manage Winter Flounder in U.S. waters and indicate the presence of at least two genetic stocks in Canadian waters (the Miramichi River in the Gulf of St. Lawrence and Passamaquoddy Bay in the Bay of Fundy). Furthermore, our data suggest that the spawning of Winter Flounder in nearshore coastal waters is more extensive than previously thought or that homing is weaker, contributing to the absence of genetic differentiation among populations from proximal estuaries.
Early Ocean Dispersal Patterns of Columbia River Chinook and Coho Salmon
Authors: Fisher J. P. , Weitkamp L. A. , Teel D. J. , Hinton S. A. , Orsi J. A. , Farley E. V. , Morris J. F. T. , Thiess M. E. , Sweeting R. M. , Trudel M. 
Published: January 2014

AbstractSeveral evolutionarily significant units (ESUs) of Columbia River asin Chinook SalmonOncorhynchus tshawytschaand Coho SalmonO. kisutchare listed as threatened or endangered under the U.S. Endangered Species Act. Yet little is known about the spatial and temporal distributions of these ESUs immediately following ocean entry, when year‐class success may be determined. We documented differences in dispersal patterns during the early ocean period among groups defined by ESU, adult run timing, and smolt age. Between 1995 and 2006, 1,896 coded‐wire‐tagged juvenile fish from the Columbia River basin were recovered during 6,142 research trawl events along the West Coast of North America. Three distinct ocean dispersal patterns were observed: (1) age‐1 (yearling) mid and upper Columbia River spring‐run and Snake River spring–summer‐run Chinook Salmon migrated rapidly northward and by late summer were not found south of Vancouver Island; (2) age‐0 (subyearling) lower Columbia River fall, upper Columbia River summer, upper Columbia River fall, and Snake River fall Chinook Salmon dispersed slowly, remaining mainly south of Vancouver Island through autumn; and (3) age‐1 lower Columbia River spring, upper Columbia River summer, and upper Willamette River spring Chinook Salmon and Coho Salmon were widespread along the coast from summer through fall, indicating a diversity of dispersal rates. Generally, the ocean dispersal of age‐1 fish was faster and more extensive than that of age‐0 fish, with some age‐1 fish migrating as fast as 10–40 km/d (0.5–3.0 body lengths/s). Within groups, interannual variation in dispersal was moderate. Identification of the distinct temporal and spatial ocean distribution patterns of juvenile salmon from Columbia River basin ESUs is important in order to evaluate the potential influence of changing ocean conditions on the survival and long term sustainability of these fish populations.
The open conformation of WASP regulates its nuclear localization and gene transcription in myeloid cells
Authors: Looi Chung Yeng , Sasahara Yoji , Watanabe Yuko , Satoh Miki , Hakozaki Ikuko , Uchiyama Meri , Wong Won Fen , Du Wei , Uchiyama Toru , Kumaki Satoru , Tsuchiya Shigeru , Kure Shigeo 
Published: January 2014

Abstract
Mutations in the gene encoding the Wiskott–Aldrich syndrome protein (WASP) are responsible for Wiskott–Aldrich syndrome and WASP is a major actin regulator in the cytoplasm. Although rare gain-of-function mutations in the WASP gene are known to result in X-linked neutropenia (XLN), the molecular pathogenesis of XLN is not fully understood. In this study, we showed that all reported constitutively activating mutants (L270P, S272P and I294T) of WASP were hyperphosphorylated by Src family tyrosine kinases and demonstrated higher actin polymerization activities compared with wild-type (WT) WASP. Further analysis showed a tendency of activating WASP mutants to localize in the nucleus compared with WT or the Y291F mutant of WASP. In addition, we found that WASP could form a complex with nuclear RNA-binding protein, 54kDa (p54nrb) and RNA polymerase II (RNAP II). ChIP assays revealed that WASP associated with DNA, although the affinity was relatively weaker than RNAP II. To determine whether gene transcription was affected by WASP mutation in myeloid cells, we performed microarray analysis and found different expression profiles between WT and L270P WASP-transfected K562 cells. Among the genes affected, granulocyte colony-stimulating factor receptor, Runx1, and protein tyrosine phosphatase receptor c were included. ChIP on chip analysis of genomic DNA showed WT and L270P WASP had a highly similar DNA-binding pattern but differed in binding affinity at the same locus. Therefore, our results suggest that the open conformation of WASP regulates its nuclear localization and plays requisite roles in regulating gene transcription that would contribute to the outcome in the nucleus of myeloid cells.
1910s' brains revisited. Cortical complexity in early 20th century patients with intellectual disability or with dementia praecox
Authors: Sandu A.‐L. , Paillère Martinot M.‐L. , Artiges E. , Martinot J.‐L. 
Published: January 2014

ObjectiveThe idea of cortical surface anomalies in subjects with intellectual disability (mental retardation) and schizophrenia can be traced back to early 20th century qualitative observations. Since it is unknown whether modern quantitative measures of cortical complexity and folding would retrieve those early empirical observations, we measured fractal dimension and sulcal span index in photographs of human brains taken in the 1910's.MethodBrain photographs were compared between 36 patients with mental retardation and 21 patients with dementia praecox for the fractal dimension and sulcal span index. Also, a mental retardation subgroup with no‐or‐non‐understandable speech (n = 12) was compared with a subgroup with comprehensible speech (n = 23).ResultsMental retardation group had a lower whole‐brain fractal dimension than dementia praecox, and a higher sulcal span index in left posterior cortex. The mental retardation subgroup with comprehensible speech had a lower fractal dimension in left hemisphere than the subgroup with no‐or‐non‐understandable speech and a lower sulcal index in left posterior cortex.ConclusionMeasures of cortical complexity and folding suggest differences between mental retardation and dementia praecox, and regional variations according to language abilities in mental retardation. The findings provide a unique picture of cortical surface changes in their original untreated form, one century ago.
Evaluation of the medium‐term outcomes and impact of the Rowan Nicks Scholarship Programme
Authors: Masterton John P. , Moss Daliah , Korin Stephanie J. , Watters David A. K. 
Published: January 2014

AbstractBackgroundRowan Nicks was a cardiothoracic surgeon in Sydney. He endowed the Rowan Nicks Scholarship Programme of the Royal Australasian College of Surgeons, which was initiated in 1991 to provide opportunities for clinicians from developing countries so that they return to their countries as leaders and teachers. This paper's objective was to evaluate the outcomes and impact of the scholarship on individuals and their communities.MethodsA survey was undertaken of 34 eligible scholars of whom 29 participated. It was directed at whether objectives were achieved in technical skills, patient management and in competency in research and leadership.ResultsNinety‐eight per cent of scholars returned to work in their home country. Twenty‐eight of 29 were working in their chosen specialty and had returned to their former positions. The clinical/operative skills obtained were regarded as useful by 86%, and 22/29 (76%) scholars reported they had gained worthwhile leadership and administrative skills. Improved clinical outcomes for patients were achieved as evidenced by reduced mortality and less disability. There was also a positive impact on health systems. The best documented of these were improved trauma management, development of paediatric surgery in rural Bangladesh, a new cardiac unit in Myanmar, organ transplantation and better injury outcomes in Papua New Guinea.ConclusionThe programme has resulted in potential and actual leaders returning to their home countries where they positively impacted on health and surgical services. This has resulted in a reduced burden of surgical disease in the scholars' countries as measured by less death, disability and deformity.