bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in the population density of pelagic salmonids in relation to changes in lake enrichment in Windermere (northwest England)
Authors: Elliott J. M. , Fletcher J. M. , Elliott J. A. , Cubby P. R. , Baroudy E. 
Published: July 2006

AbstractFrom July 1989 to December 1994, an echo sounder provided monthly estimates, usually for both day and night, of pelagic salmonid densities in the North and South Basins of Windermere, the largest natural lake in England. Sampling was along contiguous transects, three in the North Basin and five in the South Basin. Records for Arctic charr (Salvelinus alpinus) could not be separated from those for brown trout (Salmo trutta), but previous sampling by gill‐nets and anglers showed that charr formed over 90% of this mixed population in the North Basin and about 60–75% in the South Basin. Associated with the increasing eutrophication of the lake, there has been a decline in anglers' catches of charr and, since 1984, an increase in brown trout taken in the pelagic zone of the South Basin. The echo‐sounder data showed that pelagic salmonid density in the North Basin was about two to five times that in the more eutrophic South Basin in 1989, 1990 and 1991. Since the start, in April 1992, of the reduction of phosphorus discharged from sewage works, this ratio has decreased, especially at night when the highest densities were recorded. This improvement was chiefly due to a significant (P<0.001) increase in the density of small fish (length <20 cm), in both the upper (depth <20 m) and deeper (depth >20 m) water layers. Although a similar improvement has still to be shown in the upper water layer by larger fish above the size limit for removal by angling (20 cm), there has been a significant increase (P<0.01) in the density of these fish in the deeper water layer of the South Basin. The increased density of small fish suggests that the stock available to charr anglers (fish >20 cm at water depths <20 m) should increase in the next few years, especially in the South Basin. It is therefore important to continue the monitoring program and thus ensure that there is advance warning of any marked changes in charr stocks.
Observations on the natural history of the Gulf of Mexico sturgeon (Acipenser oxyrinchus de sotoi Vladykov 1955) in the Suwannee River, southeastern United States
Authors: Carr S. H. , Tatman F. , Chapman F. A. 
Published: July 2006

AbstractFrom 1986 to 1994, we collected 3,098 Gulf of Mexico sturgeon (Acipenser oxyrinchus de sotoi) during their spring migration from the Gulf of Mexico to the Suwannee River, Florida. We estimated population size and described migratory and seasonal growth patterns of sturgeon in the Suwannee River, using data from tag returns, movement of ultrasonic‐lagged fish and weight records. Population size estimates for 3.0‐ to 81.0‐kg Gulf of Mexico sturgeon in the Suwannee River ranged from 1,504 to 3,066 fish. Sturgeon migrated from the Gulf of Mexico into the Suwannee River from mid‐February to early May. Fish moved upstream and remained within a 2‐km upstreamdownstream “home” area. These sites were closely associated with undenvater springs that discharge into the river. Sturgeon migrated downstream and into the Gulf of Mexico in October and November. In the Gulf of Mexico, ultrasonic‐tagged fish were located in the Suwannee Sound area just north of Cedar Key, Florida. On an annual basis, fish gained an average of 20% of their body weight while in the Gulf of Mexico and lost about 12% of their weight during their stay in the Suwannee River. We observed movement of tagged sturgeon between the Suwannee and Apalachicola Rivers.
Distribution of and reproductive isolation among color morphs of a rock‐dwelling Lake Victoria cichlid (Haplochromis nyererei)
Authors: Seehausen O. 
Published: July 2006

AbstractGeographical, macro‐ and microhabitat distribution of and mate recognition among color morphs of a complex of Lake Victoria cichlids was studied. The distribution of most morphs was mutually exclusive but two morphs overlapped extensively and differed only in microhabitat requirements. Coloration differences between them were inherited, and wild fishes were homozygous in this respect. Positive morph assortative female mate choice was demonstrated. Over the largest part of their common geographical range intermediate phenotypes are absent and the two morphs are to be considered two biological species. However, in populations at one end of the range intermediate phenotypes with continuously varying male coloration make up the majority of the individuals. It is suggested that the status of color morphs as phenotypes of one species or as separate biological species is a function of environmental conditions that vary considerably between the localities. The data support the hypothesis that polymorphisms can be a step preceding speciation in cichlid fish.
Effect of water temperature and growth variation on the sex ratio of experimentally reared eels
Authors: Holmgren K. 
Published: July 2006

AbstractIn a controlled experiment, elvers (Anguilla anguillaL.) were reared for 137 weeks at 17, 20 and 26°C. Most eels with macroscopically sexable gonads were males. The proportions of females were 14% of sexable individuals at 26°C and 7–8% at 17 and 20°C. During the first 15 weeks, 20–50% of initial numbers were lost, but this early mortality was not significantly size selective. In spite of a long term experiment, a significant number of the survivors never attained a sexable size. Nongrowers (7–9 cm) were still alive nearly three years after being caught as glass eels. Among the earliest fast growers, 5% females, or less, were found. The proportion of females increased in later grading groups, but the pattern of increase did not indicate that males and females have separated mean ranks in a fixed growth hierarchy. Water temperature influenced observed sex ratios, but probably not through direct influence on the sex differentiation. Some alternative hypotheses, dealing with population density and individual growth status, are discussed.
Possible increase in catch of Atlantic elver Anguilla anguilla in 1993 and 1994
Authors: Moriarty C. , Tesch F.‐W. 
Published: July 2006

AbstractData on catches of O+ elvers from nine countries in Europe and of juvenile eels ascending the St. Lawrence River in Canada are presented and compared with previous records. Consideration of a parallel decline in recruitment in Canada supports the theory that oceanic conditions are responsible for the observed fall in catches. A substantial increase in the Loire, to 95 tons in 1994, may indicate an overall improvement in stocks.
Cathodic Electrodeposition of Ordered Porous Titania Films by Polystyrene Colloidal Crystal Templating
Authors: Yan Hongwei , Yang Yingling , Fu Zhengping , Yang Beifang , Xia Linsheng , Xu Yuandong , Fu Shengquan , Li Fanqing 
Published: July 2006

Abstract
The fabrication of ordered porous titania films using polystyrene colloidal crystal templates by cathodic electrodeposition is reported. A new strategy using Ti(SO4)2 as Ti source for the potentiostatic electrodeposition of titania has been developed. An improved post-treatment of the electrodeposited samples was executed to obtain long-range ordered porous films.
No Accelerated Rate of Protein Evolution in Male-Biased Drosophila pseudoobscura Genes
Authors: Metta Muralidhar , Gudavalli Rambabu , Gibert Jean-Michel , Schlötterer Christian 
Published: July 2006

Abstract
Sexually dimorphic traits are often subject to diversifying selection. Genes with a male-biased gene expression also are probably affected by sexual selection and have a high rate of protein evolution. We used SAGE to measure sex-biased gene expression in Drosophila pseudoobscura. Consistent with previous results from D. melanogaster, a larger number of genes were male biased (402 genes) than female biased (138 genes). About 34% of the genes changed the sex-related expression pattern between D. melanogaster and D. pseudoobscura. Combining gene expression with protein divergence between both species, we observed a striking difference in the rate of evolution for genes with a male-biased gene expression in one species only. Contrary to expectations, D. pseudoobscura genes in this category showed no accelerated rate of protein evolution, while D. melanogaster genes did. If sexual selection is driving molecular evolution of male-biased genes, our data imply a radically different selection regime in D. pseudoobscura.
Introns Regulate RNA and Protein Abundance in Yeast
Authors: Juneau Kara , Miranda Molly , Hillenmeyer Maureen E , Nislow Corey , Davis Ronald W 
Published: July 2006

AbstractThe purpose of introns in the architecturally simple genome of Saccharomyces cerevisiae is not well understood. To assay the functional relevance of introns, a series of computational analyses and several detailed deletion studies were completed on the intronic genes of S. cerevisiae. Mining existing data from genomewide studies on yeast revealed that intron-containing genes produce more RNA and more protein and are more likely to be haplo-insufficient than nonintronic genes. These observations for all intronic genes held true for distinct subsets of genes including ribosomal, nonribosomal, duplicated, and nonduplicated. Corroborating the result of computational analyses, deletion of introns from three essential genes decreased cellular RNA levels and caused measurable growth defects. These data provide evidence that introns improve transcriptional and translational yield and are required for competitive growth of yeast.
Accumulation of Recessive Lethal Mutations in Saccharomyces cerevisiae mlh1 Mismatch Repair Mutants Is Not Associated With Gross Chromosomal Rearrangements
Authors: Heck Julie Akiko , Gresham David , Botstein David , Alani Eric 
Published: July 2006

Abstract
We examined mismatch repair (MMR)-defective diploid strains of budding yeast grown for ∼160 generations to determine whether decreases in spore viability due to the uncovering of recessive lethal mutations correlated with an increase in gross chromosomal rearrangements (GCRs). No GCRs were detected despite dramatic decreases in spore viability, suggesting that frameshift and/or other unrepaired DNA replication lesions play a greater role than chromosomal instability in decreasing viability in MMR-defective strains.
Novel Role for Checkpoint Rad53 Protein Kinase in the Initiation of Chromosomal DNA Replication inSaccharomyces cerevisiae
Authors: Dohrmann Paul R , Sclafani Robert A 
Published: July 2006

AbstractA novel role for Rad53 in the initiation of DNA replication that is independent of checkpoint or deoxynucleotide regulation is proposed. Rad53 kinase is part of a signal transduction pathway involved in the DNA damage and replication checkpoints, while Cdc7-Dbf4 kinase (DDK) is important for the initiation of DNA replication. In addition to the known cdc7-rad53 synthetic lethality, rad53 mutations suppress mcm5-bob1, a mutation in the replicative MCM helicase that bypasses DDK's essential role. Rad53 kinase activity but neither checkpoint FHA domain is required. Conversely, Rad53 kinase can be activated without DDK. Rad53's role in replication is independent of both DNA and mitotic checkpoints because mutations in other checkpoint genes that act upstream or downstream of RAD53 or in the mitotic checkpoint do not exhibit these phenotypes. Because Rad53 binds an origin of replication mainly through its kinase domain and rad53 null mutants display a minichromosome loss phenotype, Rad53 is important in the initiation of DNA replication, as are DDK and Mcm2–7 proteins. This unique requirement for Rad53 can be suppressed by the deletion of the major histone H3/H4 gene pair, indicating that Rad53 may be regulating initiation by controlling histone protein levels and/or by affecting origin chromatin structure.
Nonlinear Tests for Genomewide Association Studies
Authors: Zhao Jinying , Jin Li , Xiong Momiao 
Published: July 2006

AbstractAs millions of single-nucleotide polymorphisms (SNPs) have been identified and high-throughput genotyping technologies have been rapidly developed, large-scale genomewide association studies are soon within reach. However, since a genomewide association study involves a large number of SNPs it is therefore nearly impossible to ensure a genomewide significance level of 0.05 using the available statistics, although the multiple-test problems can be alleviated, but not sufficiently, by the use of tagging SNPs. One strategy to circumvent the multiple-test problem associated with genome-wide association tests is to develop novel test statistics with high power. In this report, we introduce several nonlinear tests, which are based on nonlinear transformation of allele or haplotype frequencies. We investigate the power of the nonlinear test statistics and demonstrate that under certain conditions, some nonlinear test statistics have much higher power than the standard $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{{\chi}}^{2}\) \end{document}$-test statistic. Type I error rates of the nonlinear tests are validated using simulation studies. We also show that a class of similarity measure-based test statistics is based on the quadratic function of allele or haplotype frequencies, and thus they belong to nonlinear tests. To evaluate their performance, the nonlinear test statistics are also applied to three real data sets. Our study shows that nonlinear test statistics have great potential in association studies of complex diseases.
A Genomewide Screen for Suppressors of par-2 Uncovers Potential Regulators of PAR Protein-Dependent Cell Polarity in Caenorhabditis elegans
Authors: Labbé Jean-Claude , Pacquelet Anne , Marty Thomas , Gotta Monica 
Published: July 2006

Abstract
The PAR proteins play an essential role in establishing and maintaining cell polarity. While their function is conserved across species, little is known about their regulators and effectors. Here we report the identification of 13 potential components of the C. elegans PAR polarity pathway, identified in an RNAi-based, systematic screen to find suppressors of par-2(it5ts) lethality. Most of these genes are conserved in other species. Phenotypic analysis of double-mutant animals revealed that some of the suppressors can suppress lethality associated with the strong loss-of-function allele par-2(lw32), indicating that they might impinge on the PAR pathway independently of the PAR-2 protein. One of these is the gene nos-3, which encodes a homolog of Drosophila Nanos. We find that nos-3 suppresses most of the phenotypes associated with loss of par-2 function, including early cell division defects and maternal-effect sterility. Strikingly, while PAR-1 activity was essential in nos-3; par-2 double mutants, its asymmetric localization at the posterior cortex was not restored, suggesting that the function of PAR-1 is independent of its cortical localization. Taken together, our results identify conserved components that regulate PAR protein function and also suggest a role for NOS-3 in PAR protein-dependent cell polarity.
Genomewide Evolutionary Rates in Laboratory and Wild Yeast
Authors: Ronald James , Tang Hua , Brem Rachel B 
Published: July 2006

Abstract
As wild organisms adapt to the laboratory environment, they become less relevant as biological models. It has been suggested that a commonly used S. cerevisiae strain has rapidly accumulated mutations in the lab. We report a low-to-intermediate rate of protein evolution in this strain relative to wild isolates.
Antagonism of Chk1 Signaling in the G2 DNA Damage Checkpoint by Dominant Alleles of Cdr1
Authors: Calonge Teresa M , O'Connell Matthew J 
Published: July 2006

Abstract
Activation of the Chk1 protein kinase by DNA damage enforces a checkpoint that maintains Cdc2 in its inactive, tyrosine-15 (Y15) phosphorylated state. Chk1 downregulates the Cdc25 phosphatases and concomitantly upregulates the Wee1 kinases that control the phosphorylation of Cdc2. Overproduction of Chk1 causes G2 arrest/delay independently of DNA damage and upstream checkpoint genes. We utilized this to screen fission yeast for mutations that alter sensitivity to Chk1 signaling. We describe three dominant-negative alleles of cdr1, which render cells supersensitive to Chk1 levels, and suppress the checkpoint defects of chk1Δ cells. Cdr1 encodes a protein kinase previously identified as a negative regulator of Wee1 activity in response to limited nutrition, but Cdr1 has not previously been linked to checkpoint signaling. Overproduction of Cdr1 promotes checkpoint defects and exacerbates the defective response to DNA damage of cells lacking Chk1. We conclude that regulation of Wee1 by Cdr1 and possibly by related kinases is an important antagonist of Chk1 signaling and represents a novel negative regulation of cell cycle arrest promoted by this checkpoint.
The Mechanism of Secondary Nondisjunction inDrosophila melanogasterFemales
Authors: Xiang Youbin , Hawley R Scott 
Published: July 2006

AbstractBridges (1916) observed that X chromosome nondisjunction was much more frequent in XXY females than it was in genetically normal XX females. In addition, virtually all cases of X nondisjunction in XXY females were due to XX ↔ Y segregational events in oocytes in which the two X chromosomes had failed to undergo crossing over. He referred to these XX ↔ Y segregation events as “secondary nondisjunction.” Cooper (1948) proposed that secondary nondisjunction results from the formation of an X-Y-X trivalent, such that the Y chromosome directs the segregation of two achiasmate X chromosomes to opposite poles on the first meiotic spindle. Using in situ hybridization to X and YL chromosomal satellite sequences, we demonstrate that XX ↔ Y segregations are indeed presaged by physical associations of the X and Y chromosomal heterochromatin. The physical colocalization of the three sex chromosomes is observed in virtually all oocytes in early prophase and maintained at high frequency until midprophase in all genotypes examined. Although these XXY associations are usually dissolved by late prophase in oocytes that undergo X chromosomal crossing over, they are maintained throughout prophase in oocytes with nonexchange X chromosomes. The persistence of such XXY associations in the absence of exchange presumably facilitates the segregation of the two X chromosomes and the Y chromosome to opposite poles on the developing meiotic spindle. Moreover, the observation that XXY pairings are dissolved at the end of pachytene in oocytes that do undergo X chromosomal crossing over demonstrates that exchanges can alter heterochromatic (and thus presumably centromeric) associations during meiotic prophase.
Ubiquitin-Like Protein 5 Positively Regulates Chaperone Gene Expression in the Mitochondrial Unfolded Protein Response
Authors: Benedetti Cristina , Haynes Cole M , Yang Yun , Harding Heather P , Ron David 
Published: July 2006

Abstract
Perturbation of the protein-folding environment in the mitochondrial matrix selectively upregulates the expression of nuclear genes encoding mitochondrial chaperones. To identify components of the signal transduction pathway(s) mediating this mitochondrial unfolded protein response (UPRmt), we first isolated a temperature-sensitive mutation (zc32) that conditionally activates the UPRmt in C. elegans and subsequently searched for suppressors by systematic inactivation of genes. RNAi of ubl-5, a gene encoding a ubiquitin-like protein, suppresses activation of the UPRmt markers hsp-60∷gfp and hsp-6∷gfp by the zc32 mutation and by other manipulations that promote mitochondrial protein misfolding. ubl-5 (RNAi) inhibits the induction of endogenous mitochondrial chaperone encoding genes hsp-60 and hsp-6 and compromises the ability of animals to cope with mitochondrial stress. Mitochondrial morphology and assembly of multi-subunit mitochondrial complexes of biotinylated proteins are also perturbed in ubl-5(RNAi) worms, indicating that UBL-5 also counteracts physiological levels of mitochondrial stress. Induction of mitochondrial stress promotes accumulation of GFP-tagged UBL-5 in nuclei of transgenic worms, suggesting that UBL-5 effects a nuclear step required for mounting a response to the threat of mitochondrial protein misfolding.
Symptoms of Cognitive Impairment Among Children With Atopic Dermatitis
Authors: Ma Emily Z. , Chang Hannah R. , Radtke Sarah , Wan Joy 
Published: March 2024

ImportancePrevious studies suggest that atopic dermatitis (AD) is associated with cognitive impairment in children, but these studies have relied primarily on neurodevelopmental diagnoses (rather than symptoms) as proxy measures of cognitive function. It remains unknown if certain subpopulations of children with AD are at greater risk of cognitive impairment.ObjectiveTo examine the association of AD with symptoms of cognitive impairment (difficulty in learning or memory) among US children and whether this association varies according to the presence or absence of neurodevelopmental comorbidities (attention-deficit/hyperactivity disorder [ADHD], developmental delay, or learning disability).Design, Setting, and ParticipantsThis cross-sectional study used 2021 data from the US National Health Interview Survey collected on children aged 17 years or younger without intellectual disability or autism. The presence of AD was based on a parent or adult caregiver’s report indicating either a current diagnosis of AD or a previous medical confirmation of AD by a health care professional.Main Outcomes and MeasuresDifficulty with learning or memory as reported by the child’s caregiver.ResultsAmong the weighted total of 69 732 807 participants, 9 223 013 (13.2%) had AD. Compared with children without AD, children with AD were more likely to experience difficulties with learning (10.8% [95% CI, 7.8%-15.8%] vs 5.9% [95% CI, 5.1%-6.9%]; P &amp;lt; .001) and difficulties with memory (11.1% [95% CI, 8.0%-15.9%] vs 5.8% [95% CI, 4.9%-6.9%]; P &amp;lt; .001). In multivariable logistic regression models adjusted for sociodemographic factors, asthma, food allergies, and seasonal allergies or hay fever, AD was associated with increased odds of difficulties in learning (adjusted odds ratio [AOR], 1.77; 95% CI, 1.28-2.45) and memory (AOR, 1.69; 95% CI, 1.19-2.41). In analyses stratified by neurodevelopmental comorbidities, AD was associated with 2- to 3-fold greater odds of memory difficulties among children with any neurodevelopmental disorder (AOR, 2.26; 95% CI, 1.43-3.57), including ADHD (AOR, 2.90; 95% CI, 1.60-5.24) or learning disabilities (AOR, 2.04; 95% CI, 1.04-4.00). However, AD was not associated with learning or memory difficulties among children without neurodevelopmental conditions.Conclusions and RelevanceResults of this cross-sectional study suggest that pediatric AD was generally associated with greater odds of reported difficulties in learning and memory. However, this association was primarily limited to children with neurodevelopmental comorbidities, such as ADHD or learning disabilities. These findings may improve the risk stratification of children with AD for cognitive impairments and suggest that evaluation for cognitive difficulties should be prioritized among children with AD and neurodevelopmental disorders.