bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short-Term Effectiveness of Constructed Barriers at Protecting Apache Trout
Authors: Avenetti Lorraine D. , Robinson Anthony T. , Cantrell Christopher J. 
Published: February 2006

Abstract
Placement of fish migration barriers (primarily of gabion construction) on select streams is one of the major recovery actions used to isolate and protect upstream populations of Apache trout Oncorhynchus gilae apache from downstream populations of nonnative salmonids. However, the effectiveness of the recovery action has not been evaluated. We evaluated the success of constructed barriers at preventing upstream movement of nonnative salmonids into areas occupied by native Apache trout. We collected and marked salmonids downstream of six barriers on six streams in the White Mountains of east-central Arizona and subsequently electrofished upstream of the barriers to determine whether marked fish had moved past them. Only 1 of 1,436 marked salmonids was collected upstream of one of the six barriers evaluated over a 3-year period. Our results showed that the barriers evaluated in our study are effective for a short term; however, long-term evaluation is needed, as these failure rates represent minimum failure rates and they could increase as the number of years since barrier construction increases.
Utility and Validation of Day and Night Snorkel Counts for Estimating Bull Trout Abundance in First- to Third-Order Streams
Authors: Thurow Russell F. , Peterson James T. , Guzevich John W. 
Published: February 2006

Abstract
Despite the widespread use of underwater observation to census stream-dwelling fishes, the accuracy of snorkeling methods has rarely been validated. We evaluated the efficiency of day and night snorkel counts for estimating the abundance of bull trout Salvelinus confluentus in 215 sites within first- to third-order streams. We used a dual-gear approach that applied multiple-pass electrofishing catch data adjusted for capture efficiency to estimate true or baseline fish abundance. Our multiple-pass electrofishing capture efficiency models were based on a prior study and used recapture data for known numbers of individually marked fish. Snorkeling efficiency was estimated by comparing day and night snorkel counts with the baseline. We also evaluated the influence of fish size and stream habitat features on snorkeling efficiency. Bull trout snorkeling efficiency was higher at night (mean = 33.2%) than during the day (mean = 12.5%). Beta-binomial regression indicated that bull trout day and night snorkeling efficiencies were positively related to fish size and negatively related to stream width and habitat characteristics. Day snorkeling efficiency also was positively influenced by water temperature and nonlinearly related to underwater visibility, whereas night snorkeling efficiency was nonlinearly related to water temperature and pool abundance. Although bull trout were our target species, day and night snorkeling efficiencies combined for rainbow trout Oncorhynchus mykiss and subspecies of cutthroat trout O. clarkii averaged 32.3% and 18.0%, respectively. Our ability to detect and accurately count fish underwater was influenced by fish size, species, time of day, and stream habitat characteristics. Although snorkeling is versatile and has many advantages over other sampling methods, the use of raw snorkel counts unadjusted for the effects of these biases will result in biased conclusions. We recommend that biologists adjust underwater count data to minimize the effect of such biases. We illustrate how to apply sampling efficiency models to validate snorkel counts.
Abundance Trends and Status of the Little Colorado River Population of Humpback Chub
Authors: Coggins Lewis G. , Pine William E. , Walters Carl J. , Van Haverbeke David R. , Ward David , Johnstone Helene C. 
Published: February 2006

Abstract
The abundance of the Little Colorado River population of federally listed humpback chub Gila cypha in Grand Canyon has been monitored since the late 1980s by means of catch rate indices and capture–recapture-based abundance estimators. Analyses of data from all sources using various methods are consistent and indicate that the adult population has declined since monitoring began. Intensive tagging led to a high proportion (&gt;80%) of the adult population being marked by the mid-1990s. Analysis of these data using both closed and open abundance estimation models yields results that agree with catch rate indices about the extent of the decline. Survival rates for age-2 and older fish are age dependent but apparently not time dependent. Back-calculation of recruitment using the apparent 1990s population age structure implies periods of higher recruitment in the late 1970s to early 1980s than is now the case. Our analyses indicate that the U.S. Fish and Wildlife Service recovery criterion of stable abundance is not being met for this population. Also, there is a critical need to develop new abundance indexing and tagging methods so that early, reliable, and rapid estimates of humpback chub recruitment can be obtained to evaluate population responses to management actions designed to facilitate the restoration of Colorado River native fish communities.
Estimates of Tackle Loss for Five Minnesota Walleye Fisheries
Authors: Radomski Paul , Heinrich Tom , Jones Thomas S. , Rivers Pat , Talmage Phil 
Published: February 2006

Abstract
Lead poisoning in waterbirds from ingestion of lead fishing items may be a growing problem. There are few studies that quantify tackle loss for recreational fisheries. Tackle loss from large recreational lake fisheries in Minnesota is unknown. The objectives of this study were to determine tackle loss for five large lake fisheries targeting walleye Sander vitreus in Minnesota by means of creel surveys and to estimate recent cumulative losses. Mean rates of tackle loss were low: 0.0127/h for lures, 0.0081/h for large sinkers, 0.0057/h for small sinkers, 0.0247/h for jigs, and 0.0257/h for hooks. Many anglers lost no fishing tackle on a fishing trip. The estimated total loss of tackle for the five water bodies in the summer of 2004 was 214,811 items. Over 100,000 lead-based items were estimated to have been lost, representing about 1 metric ton of lead. Assuming 2004 lead tackle loss rates, estimates of cumulative lead item loss for Lake of the Woods and Mille Lacs and Rainy lakes from 1983 to 2004 were 285,000 (SE = 8,800), 1,033,000 (SE = 39,700), and 211,000 (SE = 8,400) items, respectively. In critical wildlife areas with high angling effort or high tackle loss rates, determining the impacts of lead tackle on wildlife would be prudent, and prohibiting the use of lead tackle may be necessary.
Age-Structured Mark–Recapture Analysis: A Virtual-Population-Analysis-Based Model for Analyzing Age-Structured Capture–Recapture Data
Authors: Coggins Lewis G. , Pine William E. , Walters Carl J. , Martell Steven J. D. 
Published: February 2006

Abstract
We present a new model to estimate capture probabilities, survival, abundance, and recruitment using traditional Jolly–Seber capture–recapture methods within a standard fisheries virtual population analysis framework. This approach compares the numbers of marked and unmarked fish at age captured in each year of sampling with predictions based on estimated vulnerabilities and abundance in a likelihood function. Recruitment to the earliest age at which fish can be tagged is estimated by using a virtual population analysis method to back-calculate the expected numbers of unmarked fish at risk of capture. By using information from both marked and unmarked animals in a standard fisheries age structure framework, this approach is well suited to the sparse data situations common in long-term capture–recapture programs with variable sampling effort.
Evaluation of Oral Health Knowledge and Oral Health Status in Mothers and Their Children with Cleft Lip and Palate
Authors: deCastilho Aline Rogéria Freire , das Neves Lucimara Teixeira , de Carvalho Carrara Cleide Felício 
Published: February 2006

Objective: To assess the oral health knowledge of mothers of children with cleft lip and/or palate, analyzing the practical application of this information on the basis of the oral hygiene of the children and caries prevalence of mothers and children. Design: Cross-sectional. Setting: Pediatric Dentistry sector of the Hospital for Rehabilitation of Craniofacial Anomalies. Patients: Mothers (n = 300) and their children with cleft lip and/or palate, ages 3 years to 5 years 6 months. Materials and Methods: An interview with questions related to dietary habits and oral health knowledge and habits was conducted. Children and their mothers also were evaluated by intraoral clinical examination. Results: Of the mothers, 47.3% displayed poor oral health status (Group A) and 52.7% had a satisfactory oral health status (Group B). Children in Group A presented a mean dmft of 6.0, whereas children in Group B had a mean dmft of 5.6. No significant differences were observed between groups. Mothers demonstrated a reasonable knowledge on prevention of dental caries and oral hygiene. Conclusion: Even though the mothers interviewed had some knowledge on the causes and prevention of dental caries, other factors should be regarded as relevant in the caries process.
Struggling Reader to Struggling Reader: High School Students' Responses to a Cross‐Age Tutoring Program
Authors: Paterson Patricia O. , Elliott Lori N. 
Published: February 2006

This qualitative study examines the perceptions and responses of struggling ninth‐grade readers who are teaching reading to struggling second‐ and third‐grade students in a cross‐age tutoring program. The program was designed to overcome the entrenched, negative affective barriers that older students often bring to the required reading class by placing them in a leadership role. It also intended simultaneously to improve their vocabulary, fluency, and comprehension.Results indicate that the older students developed strong mirroring relationships with their younger counterparts based on shared community strengths and norms, shifted their perspective to see themselves as increasingly competent role models, and applied their developing reading abilities as they selected and modified strategies based on the needs of their younger students. Important implications for literacy teachers include a clearer understanding of the powerful, positive attitudinal effects of a well‐planned, low‐cost tutoring program that provides authentic opportunities for literacy learning for all students involved.
“Real‐World Cognition Doesn't End When the Bell Rings”: Literacy Instruction Strategies Derived From Situated Cognition Research
Authors: Darvin Jacqueline 
Published: February 2006

This article discusses situated cognition research and its impact on literacy studies concepts and instruction. It provides a brief historical comparison of cognitive psychology and situated cognition and emphasizes the importance of understanding the complex relationships that exist between learners, the settings in which they engage in cognitive activities, and the reconceptualization of time and its usage. Two classroom strategies derived from the work of Jean Lave and Sylvia Scribner are discussed in depth, as are the lives of students who benefited from these approaches.The author emphasizes the need for cognitive activities that begin in the classroom to continue after the class has ended and encourages educators and researchers to further examine the nature of adaptive thinking and working intelligence. Instead of teacher training courses placing emphasis on teachers' mastery of “closure” of the 40‐minute lesson, courses should encourage teachers to allow their students to engage in problem‐solving opportunities that will persist after instruction has ended. Finally, the article asserts that processes of deriving meaning from reading and writing require components of positive affect in order to be successful and that further studies are needed to explore the nature of adaptive thinking and working intelligence.
Mesenchymal Stem Cells and Adipogenesis in Hemangioma Involution
Authors: Yu Ying , Fuhr Jasmin , Boye Eileen , Gyorffy Steve , Soker Shay , Atala Anthony , Mulliken John B. , Bischoff Joyce 
Published: February 2006

Abstract
Hemangioma is a benign tumor of infancy whose hallmark is rapid growth during the first year of life followed by slow regression during early childhood. The proliferating phase is characterized by abundant immature endothelial cells, the involuting phase by prominent endothelial-lined vascular channels and endothelial apoptosis, and the involuted phase by few remaining capillary-like vessels surrounded by loose fibrofatty tissue. Nothing is known about the mechanisms that contribute to the adipogenesis during this spontaneous regression. We postulated that mesenchymal stem cells (MSCs) reside in the tumor and preferentially differentiate into adipocytes. To test this hypothesis, we isolated MSCs from 14 proliferating and five involuting hemangiomas by taking advantage of the well known selective adhesion of MSCs to bacteriologic dishes. These hemangioma-derived MSCs (Hem-MSCs) are similar to MSCs obtained from human bone marrow, expressing the cell surface markers SH2 (CD105), SH3, SH4, CD90, CD29, smooth muscle α-actin, and CD133 but not the hematopoietic markers CD45 and CD14 or the hematopoietic/endothelial markers CD34, CD31, and kinase insert domain receptor (KDR). Hem-MSCs exhibited multilineage differentiation with robust adipogenic potential that correlated with the proliferating phase. The numbers of adipogenic Hem-MSCs were higher in proliferating-phase than in involuting-phase tumors and higher than in normal infantile skin. Furthermore, Hem-MSCs exhibited a random pattern of X-chromosomal inactivation, indicating that these cells are not clonally derived. In summary, we have identified MSCs as a novel cellular constituent in infantile hemangioma. These MSCs may contribute to the adipogenesis during hemangioma involution.
Reverse Serial Analysis of Gene Expression (SAGE) Characterization of Orphan SAGE Tags from Human Embryonic Stem Cells Identifies the Presence of Novel Transcripts and Antisense Transcription of Key Pluripotency Genes
Authors: Richards Mark , Tan Siew-Peng , Chan Woon-Khiong , Bongso Ariff 
Published: February 2006

Abstract
Serial analysis of gene expression (SAGE) is a powerful technique for the analysis of gene expression. A significant portion of SAGE tags, designated as orphan tags, however, cannot be reliably assigned to known transcripts. We used an improved reverse SAGE (rSAGE) strategy to convert human embryonic stem cell (hESC)-specific orphan SAGE tags into longer 3′ cDNAs. We show that the systematic analysis of these 3′ cDNAs permitted the discovery of hESC-specific novel transcripts and cis-natural antisense transcripts (cis-NATs) and improved the assignment of SAGE tags that resulted from splice variants, insertion/deletion, and single-nucleotide polymorphisms. More importantly, this is the first description of cis-NATs for several key pluripotency markers in hESCs and mouse embryonic stem cells, suggesting that the formation of short interfering RNA could be an important regulatory mechanism. A systematic large-scale analysis of the remaining orphan SAGE tags in the hESC SAGE libraries by rSAGE or other 3′ cDNA extension strategies should unravel additional novel transcripts and cis-NATs that are specifically expressed in hESCs. Besides contributing to the complete catalog of human transcripts, many of them should prove to be a valuable resource for the elucidation of the molecular pathways involved in the self-renewal and lineage commitment of hESCs.
Embryonic Stem Cell-Derived Neuronally Committed Precursor Cells with Reduced Teratoma Formation After Transplantation into the Lesioned Adult Mouse Brain
Authors: Dihné Marcel , Bernreuther Christian , Hagel Christian , Wesche Kai O. , Schachner Melitta 
Published: February 2006

Abstract
The therapeutic potential of embryonic stem (ES) cells in neurodegenerative disorders has been widely recognized, and methods are being developed to optimize culture conditions for enriching the cells of interest and to improve graft stability and safety after transplantation. Whereas teratoma formation rarely occurs in xenogeneic transplantation paradigms of ES cell-derived neural progeny, more than 70% of mice that received murine ES cell-derived neural precursor cells develop teratomas, thus posing a major safety problem for allogeneic and syngeneic transplantation paradigms. Here we introduce a new differentiation protocol based on the generation of substrate-adherent ES cell-derived neural aggregates (SENAs) that consist predominantly of neuronally committed precursor cells. Purified SENAs that were differentiated into immature but postmitotic neurons did not form tumors up to four months after syngeneic transplantation into the acutely degenerated striatum and showed robust survival.
Differentiation of Mouse Embryonic Stem Cells after RNA Interference-Mediated Silencing of OCT4 and Nanog
Authors: Hough Shelley R. , Clements Ian , Welch Peter J. , Wiederholt Kristin A. 
Published: February 2006

Abstract
RNA interference (RNAi) holds great promise as a tool to study the basic biology of stem cells or to direct differentiation in a specific manner. Barriers to achieving efficient and specific gene silencing in RNAi experiments include limitations in transfection efficiency and in the efficacy and specificity of RNAi silencing effectors. Here, we combine methods of efficient lipid-mediated delivery with chemically modified RNAi compounds to silence genes related to pluripotency, in order to direct differentiation of mouse embryonic stem cells. After transfection of embryonic stem cells with OCT4- or Nanog-targeted RNAi compounds, levels of OCT4 or Nanog transcript and protein were reduced accordingly. Reduction in OCT4 expression correlated with induction of trophectoderm genes Cdx2, Hand1, and PL-1, with formation of cells with trophoblast giant cell phenotype after 6 days. Reduction in Nanog expression correlated with induction of extraembryonic endoderm genes GATA4, GATA6, and laminin B1, with subsequent generation of groups of cells with parietal endoderm phenotype. Our results indicate that transient inhibition of OCT4 or Nanog by RNAi compounds is sufficient to induce differentiation toward extraembryonic lineages, which supports the model that these transcription factors function in a dose-dependent manner to influence cell fate.
Effects of Aging and Niche Microenvironment on Spermatogonial Stem Cell Self-Renewal
Authors: Ryu Buom-Yong , Orwig Kyle E. , Oatley Jon M. , Avarbock Mary R. , Brinster Ralph L. 
Published: February 2006

Abstract
Aging is evident in most tissues and organ systems, but the mechanisms of aging are difficult to identify and poorly understood. Here, we test the hypothesis that aging results in uncorrected defects in stem cell and/or niche function, which lead to system failure. We used the spermatogonial stem cell (SSC) transplantation assay to determine the effect of aging on testis stem cell/niche function in mice. Between 12 and 24 months of age, male mice experienced a declining level of fertility associated with decreased testis weight, level of spermatogenesis, and total stem cell content. However, when stem cells were consecutively passaged at 3-month intervals to testes of young males, these stem cells continued to produce spermatogenesis for more than 3 years. Thus, SSC self-renewal continues long past the normal life span of the animal when the stem cell is continually maintained in a young niche/microenvironment. Moreover, these data suggest that infertility in old males results from deterioration of the SSC niche and failure to support an appropriate balance between stem cell self-renewal and differentiation.
Soil Acidity and Manganese in Declining and Nondeclining Sugar Maple Stands in Pennsylvania
Authors: Kogelmann Wilhelm J. , Sharpe William E. 
Published: February 2006

ABSTRACTFor decades, the hardwood forests of northern Pennsylvania have been subjected to chronic atmospheric loading of acidifying agents. On marginal, high‐elevation, unglaciated sites, sugar maples (Acer saccharum Marsh.) have experienced severe decline symptoms and mortality. Accelerated soil acidification, base cation leaching, and increased availability of toxic metals have been suggested as predisposing factors contributing to this decline. Manganese, an essential micronutrient, is also a potentially phytotoxic metal that may be a factor associated with poor sugar maple health on soils vulnerable to acidification from anthropogenic sources. We measured Mn levels in four compartments of the soil–tree system (soil, foliage, xylem wood, and sap) on three sugar maple stands in northern Pennsylvania. Two stands were classified as declining and one was in good health. Negative correlations were found between soil pH and Mn levels in the soil, foliage, sap, and xylem wood. Levels of Mn in these pools were consistently higher on declining sites, which correspondingly exhibited lower levels of Ca and Mg. Species differences between red maple (Acer rubrum L.) and sugar maple at the two declining sites suggested different tolerances to excessive Mn. Molar ratios of Mg/Mn and Ca/Mn were different among sites and showed potential as indicators of soil acidification. Significant correlations among soil, sap, foliage, and xylem wood Mn were also noted. These results show clear Mn differences among sites and, when viewed with recent Mn toxicity experiments and other observational studies, suggest that excessive Mn may play a role in the observed decline and mortality of sugar maple.
A Method for Measuring Low‐Weight Carboxylic Acids from Biosolid Compost
Authors: Himanen Marina , Latva‐Kala Kyösti , Itävaara Merja , Hänninen Kari 
Published: February 2006

ABSTRACTConcentration of low‐weight carboxylic acids (LWCA) is one of the important parameters that should be taken into consideration when compost is applied as soil improver for plant cultivation, because high amounts of LWCA can be toxic to plants. The present work describes a method for analysis of LWCA in compost as a useful tool for monitoring compost quality and safety. The method was tested on compost samples of two different ages: 3 (immature) and 6 (mature) months old. Acids from compost samples were extracted at high pH, filtered, and freeze‐dried. The dried sodium salts were derivatized with a sulfuric acid–methanol mixture and concentrations of 11 low‐weight fatty acids (C1–C10) were analyzed using headspace gas chromatography. The material was analyzed with two analytical techniques: the external calibration method (tested on 11 LWCA) and the standard addition method (tested only on formic, acetic, propionic, butyric, and iso‐butyric acids). The two techniques were compared for efficiency of acids quantification. The method allowed good separation and quantification of a wide range of individual acids with high sensitivity at low concentrations. Detection limit for propionic, butyric, caproic, caprylic, and capric acids was 1 mg kg−1 compost; for formic, acetic, valeric, enanthoic and pelargonic acids it was 5 mg kg−1 compost; and for iso‐butyric acid it was 10 mg kg−1 compost. Recovery rates of LWCA were higher in 3‐mo‐old compost (57–99%) than in 6‐mo‐old compost (29–45%). In comparison with the external calibration technique the standard addition technique proved to be three to four times more precise for older compost and two times for younger compost. Disadvantages of the standard addition technique are that it is more time demanding and laborious.