bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation status of the San Christóbal pupfish Profundulus hildebrandi Miller (Teleostei: Profundulidae) in the face of urban growth in Chiapas, Mexico
Authors: Velázquez‐Velázquez Ernesto , Schmitter‐Soto Juan J. 
Published: February 2004

Abstract1. Profundulus hildebrandi, the San Cristóbal pupfish, is a small cyprinodontiform fish endemic to the closed basin of San Cristóbal de Las Casas, a fast‐growing city in highland Chiapas, Mexico. This study constitutes the first population study of this endangered taxon.2. In order to judge its conservation status, its distribution and habitat were described, and its population size was estimated through a capture–recapture technique. To the extent possible, present conditions of its habitat were compared with historic information, mainly old city maps and photographs.3. Introduction of largemouth bass (Micropterus salmoides) coincided with local extirpation of P. hildebrandi. Other risk factors related to urban growth include pollution of streams, as well as habitat destruction, fragmentation, and modification; about 60% of the original pupfish habitat is heavily polluted by sewage.4. Although its population size is apparently large (probably more than 8000), its very restricted distribution, its shrinking habitat and the increasing risk factors provide justification to consider P. hildebrandi as an endangered fish, according to the Mexican Official Norm and the Red Book of the IUCN. Copyright © 2004 John Wiley & Sons, Ltd.
Familial aggregation of genetically heterogeneous hypertrophic cardiomyopathy: A boy with LEOPARD syndrome due to PTPN11 mutation and his nonsyndromic father lacking PTPN11 mutations
Authors: Digilio M. Cristina , Pacileo Giuseppe , Sarkozy Anna , Limongelli Giuseppe , Conti Emanuela , Cerrato Fabiana , Marino Bruno , Pizzuti Antonio , Calabrò Raffaele , Dallapiccola Bruno 
Published: February 2004

AbstractBACKGROUNDNonsyndromic hypertrophic cardiomyopathy (HCM) is a primary cardiac disease transmitted as an autosomal dominant trait. Multiple chromosomal loci have been found to be involved in the etiology of this defect. LEOPARD syndrome is a genetic condition characteristically associated with HCM. Additional features of the syndrome include multiple lentigines, facial anomalies, sensorineural deafness, and growth retardation. Mutations in PTPN11, a gene encoding the protein tyrosine phosphatase SHP‐2 located at chromosome 12q24, have been identified in patients with LEOPARD syndrome.CASESWe report here on a patient with HCM presenting with classic clinical features of LEOPARD syndrome, whose father also has HCM, but lacks phenotypic anomalies of the syndrome. Molecular analysis searching for PTPN11 mutations was performed in this family. A missense mutation (836A→G; Tyr279Cys) in exon 7 of PTPN11 gene was identified in the patient with LEOPARD syndrome, whereas no mutation in PTPN11 gene was detected in the father or in additional family members.CONCLUSIONSAggregation of syndromic and nonsyndromic HCM in the same family is an unusual pattern of recurrence. Although genetic heterogeneity of LEOPARD and nonsyndromic HCM is not disputed, the existence of peculiar interactions linking genes causing nonsyndromic HCM and HCM in LEOPARD syndrome can be hypothesized. Different genes can work together, and a more severe cardiac phenotype can be due to additive effects. The involvement of familial susceptibility to specific cardiac malformations based on the presence of common predisposing factors can also be considered. Further molecular studies may shed light on these observations. Birth Defects Research (Part A), 2003. © 2004 Wiley‐Liss, Inc.
Secular decreasing trend of the frequency of hypospadias among newborn male infants in Spain
Authors: Martínez‐Frías María Luisa , Prieto David , Prieto Luis , Bermejo Eva , Rodríguez‐Pinilla Elvira , Cuevas Lourdes 
Published: February 2004

AbstractBACKGROUNDThe frequency of hypospadias is not uniform worldwide. Several countries have reported an increase in its frequency at birth. Although a better ascertainment of the minor forms has been considered as an explanation, the potential effect of environmental endocrine disrupters has also been proposed. We studied the secular trend of hypospadias in Spain over the past 22 years, separating the minor and major forms.METHODSWe used data from the Spanish Collaborative Study of Congenital Malformations (ECEMC) registry, analyzing the frequency in two different periods: from 1978 to 1995, and from 1996 to 2002. To evaluate the “step” of the frequency between the two periods, we applied a parametric Student's t‐test, and the nonparametric Mann‐Whitney rank test.RESULTSThe birth frequency of isolated and total hypospadias was quite stable between 1978 and 1995. In 1996, it decreased dramatically in a step, essentially due to isolated cases with minor forms of hypospadias. Study of the geographical distribution by the 17 Spanish regions showed that the frequency step occurred in nearly all of them.CONCLUSIONSIt is difficult to consider that the observed decrease of the frequency of minor forms of hypospadias could be due to less accurate reporting of these minor forms in all 87 hospitals in the same year without any previous physician agreement. This decrease rather suggests a change in some product or exposure affecting the whole country. We think that the observed change in the frequency cannot be attributable to a lower exposure to endocrine disrupters or the voluntary interruption of gestation. Birth Defects Research (Part A) 67:000–000, 2003. © 2004 Wiley‐Liss, Inc.
Application of kinetic polymerase chain reaction and molecular beacon assays to pooled analyses and high‐throughput genotyping for candidate genes
Authors: Shi Min , Caprau Diana , Dagle John , Christiansen Lene , Christensen Kaare , Murray Jeffrey C. 
Published: February 2004

AbstractBACKGROUNDThe addition of DNA analysis to epidemiologic studies that have traditionally incorporated demographic and interview data can provide additional power and open new avenues for investigation. DNA can be obtained from a variety of tissues, but each has attendant variation in sample quantity, quality, and cost of acquisition. Analytic approaches for DNA genotyping are under constant development, but current applications allow small amounts (less than 2 ng per assay) of DNA to be used for genotyping.METHODSIn this report, we designed effective assays for a spectrum of genes using either kinetic polymerase chain reaction (PCR) or molecular beacon applications. We also investigated the extent to which DNA use and reagent cost could be minimized. Kinetic PCR assays were also applied to investigate the potential of pooled sample analysis.RESULTSOur results show that small amounts of DNA can be successfully amplified in a high‐throughput fashion using both kinetic PCR and molecular beacon methods. Greater than 97% of the genotype results from these two methods are consistent. In addition, error rates in allele frequency measurements using DNA pools of 100 or more samples were often less than 1% and usually less than 3%, which provides another option for substantially minimizing the costs of genotyping in studies involving large numbers of individuals.CONCLUSIONSEffective assays have been designed for a spectrum of genes widely studied in birth defects, including: MTHFR, NAT1, TGFA, RFC1, PAX9, EPHX1, and SKI. An efficient assay has been designed for the detection of the presence of X and Y chromosomes, which can be applied to the studies of sex chromosome abnormalities or sample quality control. Birth Defects Research (Part A), 2004. © 2004 Wiley‐Liss, Inc.
Chemically induced supernumerary lumbar ribs in CD‐1 mice: Size distribution and dose response
Authors: Rogers John M. , Setzer R. Woodrow , Branch Stacy , Chernoff Neil 
Published: February 2004

AbstractSupernumerary ribs (SNR) of differing sizes are commonly observed in rodent developmental toxicity studies, and the significance of treatment‐related increases in SNR in standard studies has been contentious. We induced dose‐related increases in SNR in fetal CD‐1 mice by treating on gestation days 7–8 with benomyl (BEN; 0, 75, 150 mg/kg/d), dinoseb (DIN; 0, 30, 50 mg/kg/d); 2‐methoxyethanol (2‐ME; 0, 75, 150 mg/kg/d), or valproic acid (VPA; 0, 125, 250 mg/kg/d). Incidences of SNR were 9.3–27.6% in controls and 19.3–84.4% in the high dosage groups. SNR length showed a bimodal distribution with peaks at 0.3–0.4 mm and 0.9–1.1 mm in both treated and control groups. Based on length distributions, we used an actual length of 0.6 mm to separate short (rudimentary) from long (extra) SNR. DIN, 2‐ME, and VPA induced a dose‐related increase of extra ribs, while the incidence of rudimentary ribs remained at control levels. There was no apparent correlation of the presence of either type of SNR in a fetus and the occurrence of other anomalies. These data support the idea that extra and rudimentary SNR may reflect separate developmental phenomena, and should be considered and reported separately in developmental toxicity studies for risk assessment.Birth Defects Res B 71:17–25, 2004. Published 2004 Wiley‐Liss, Inc.
Photosynthetic evolution in parasitic plants: insight from the chloroplast genome
Authors: Bungard Ralph A. 
Published: February 2004

AbstractDespite the enormous diversity in plant form, structure and growth environment across the seed‐bearing plants (angiosperms and gymnosperms), the chloroplast genome has, with few exceptions, remained remarkably conserved. This conservation suggests the existence of universal evolutionary selection pressures associated with photosynthesis—the primary function of chloroplasts. The stark exceptions to this conservation occur in parasitic angiosperms, which have escaped the dominant model by evolving the capacity to obtain some or all of their carbon (and nutrients) from their plant hosts. The consequence of this evolution to parasitism is a relaxation of the evolutionary constraints associated with the need to maintain photosynthetic function, the very function that drove early stages of the ancient symbiotic relationship that produced the contemporary chloroplast. Extreme examples of reductionism among parasitic angiosperms reveals major alterations in chloroplast function with the loss of photosynthetic capacity and, with that, massive alterations in chloroplast genome content. This review highlights emerging patterns in reported gene loss and gene retention in the chloroplast genomes of parasitic plants. Some gene losses appear to occur in the early stages of parasitic evolution, even before the loss of photosynthetic capacity, like the chlororespiratory (ndh) genes. This contrasts with unexpected gene retentions, like that of the rbcL gene responsible for photosynthetic carbon dioxide fixation, and belies current understanding of gene function. The review relates gene retention to current knowledge of protein function and gene processing that has implications to broader aspects of genome conservation in organelles. BioEssays 26:235–247, 2004. Wiley Periodicals, Inc.
Notch function in the vasculature: insights from zebrafish, mouse and man
Authors: Shawber Carrie J. , Kitajewski Jan 
Published: February 2004

AbstractVascular development entails multiple cell‐fate decisions to specify a diverse array of vascular structures. Notch proteins are signaling receptors that regulate cell‐fate determination in a variety of cell types. The finding that Notch genes are robustly expressed in the vasculature suggests roles for Notch in guiding endothelial and associated mural cells through the myriad of cell‐fate decisions needed to form the vasculature. In fact, mice with defects in genes encoding Notch, Notch ligands, and components of the Notch signaling cascade invariably display vascular defects. Human Notch genes are linked to Alagille's Syndrome, a developmental disorder with vascular defects, and CADASIL, a cerebral arteriopathy. Studies in zebrafish, mice and humans indicate that Notch works in conjunction with other angiogenic pathways to pattern and stabilize the vasculature. Here, we will focus on established functions for Notch in vascular remodeling and arterial/venous specification and more speculative roles in vascular homeostasis and organ‐specific angiogenesis. BioEssays 26:225–234, 2004. © 2004 Wiley Periodicals, Inc.
Nonlinear Response Surface and Mixture Experiment Methodologies Applied to the Study of Synergism
Authors: White Donald B. , Faessel Hélène M. , Slocum Harry K. , Khinkis Leonid , Greco William R. 
Published: February 2004

AbstractA new paradigm for the study of the joint action (synergism, additivity and antagonism) of different agents that combines nonlinear response surface modeling with mixture experiment methodologies is described. We achieve a global nonlinear response surface model using raw data modeling and hierarchical parameter modeling along with numerical and graphical evaluations. The method is applied to a very large previously‐published (Faesselet al., 1998)in vitrostudy of the combined effect of Trimetrexate (TMQ) and AG2034 on inhibition of cancer cell growth. The modulator Folic acid (Folate) concentration is also included as a continuous process variable. The mixture portion of the analysis is best identified as an “NLMAZ‐PV” experiment, incorporating a nonlinear mixture‐amount model with zero amounts (control observations) and the process variable. The underlying nonlinear structural model, describing the relationship between the mixture amount and the observed effect, is the four parameter Hill (1910) equation. This model for studying synergism was developed as an improvement over the flagship synergy/antagonism model of Greco et al. (1995) and other response surface synergy models. This new modeling approach allows for irregularly‐shaped isobols, complex patterns of local synergism and antagonism, a modulating agent with no effect of its own, and extensions to three or more drugs (White et al., 2003). (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Composite Hazard Functions Reflecting Competing Latent Processes
Authors: Sæbø Solve , Almøy Trygve 
Published: February 2004

AbstractA method for fitting parametric models to apparently complex hazard rates in survival data is suggested. Hazard complexity may indicate competing causes of failure. A competing risks model is constructed on the assumption that a failure time can be considered as the first passage time of possibly several latent, stochastic processes competing in reaching a barrier. An additional assumption of independence between the hidden processes leads directly to a composite hazard function as the sum of the cause specific hazards. We show how this composite hazard model based on Wiener processes can serve as a flexible tool for modelling complex hazards by varying the number of processes and their starting conditions. An example with real data is presented. Parameter estimation and model assessment are based on Markov Chain Monte Carlo methods. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optional Randomized Response Techniques for Complex Survey Designs
Authors: Arnab Raghunath 
Published: February 2004

AbstractGupta, Gupta and Singh (2002) proposed an optional randomized response (ORR) technique based on SRSWR sampling using an unrealistic assumption that the probability of providing the true/randomized response for all the individuals in a population is the same. In this paper an alternative ORR has been proposed for an arbitrary sampling design. Expressions for the estimators of the population mean, variance and unbiased estimator for the variance have been provided. It is shown that the estimator, based on an ORR, is more efficient than an estimator derived from a non‐ORR technique. Sufficient conditions for the superiority of the proposed estimator over the existing estimator provided by Gupta et al.'s (2002) have also been established. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Inference for the Ratio of Two Normal Means with Unspecified Variances
Authors: Díaz‐Francés Eloísa , Sprott David A. 
Published: February 2004

AbstractMendoza and Gutiérrez‐Peña (1999) presented a Bayesian analysis of the ratio of two normal means when the ratio of the means determines the ratio of the variances, X ∼ N(βμ, β2σ2), Y ∼ N(μ, σ2). They claimed the superiority of the Bayesian analysis, based on the whole likelihood function with non‐informative priors, by comparing it with a non‐Bayesian analysis based only on the Fieller pivotal. The purpose here is to show that the Fieller pivotal constitutes only part of the likelihood function of β in this model, so that any analysis, including Bayesian, based solely on the Fieller pivotal is highly inefficient, possibly to the extent of discarding most of the information in the sample. A non‐Bayesian analysis based on the structure of the whole likelihood function exhibits this and rectifies such an oversight. The role of the variance ratio is discussed and exemplified. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Adjusting for Ordinal Covariates by Inducing a Partial Ordering
Authors: Berger Vance W. , Zhou YanYan , Ivanova Anastasia , Tremmel Lothar 
Published: February 2004

AbstractIn the context of randomized clinical trials, multiplicity arises in many forms. One prominent example is when a key endpoint is measured and analyzed both at baseline and after treatment. It is common to analyze each separately, but more efficient to adjust the post‐treatment comparisons for the baseline values. Adjustment techniques generally treat the covariate (baseline value, in this case) as either nominal or continuous. Either is problematic when applied to an ordinal covariate, the former because it fails to exploit the natural ordering and the latter because it relies on an artifical notion of linear prediction and differences between values. We propose new methods for adjusting for ordinal covariates without having to treat them as nominal or continuous. Specifically, the information‐preserving composite endpoint consists of the pair of values for each patient, one at baseline and one after treatment. Some of these patterns will indicate more improvement than others, yet some pairs of patterns are not comparable. Hence, the ordering is only partial. We develop an approach to testing and deriving estimators of magnitudes of the treatment effect based on comparing each observation in one group to each observation in the other group to which it is comparable. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structural analysis of biological aliphatic compounds using surface‐enhanced Fourier transform Raman spectroscopy
Authors: Hasegawa Takeshi 
Published: February 2004

AbstractThe surface‐enhanced Raman scattering (SERS) technique for Fourier transform Raman spectrometry is employed to reveal the chemical structure of biological aliphatic compounds consisting of folded, long aliphatic chains. The structural analysis is performed via the measurements of the accordion‐vibration modes generated in the ordered, long aliphatic chain. The SERS spectra after subtraction of a background spectrum give segment lengths that are almost perfectly consistent with the chemical structures studied by mass spectrometry. The agreement of the SERS results with those of mass spectrometry suggests the positions of kinks in the long hydrocarbon chain. The combination technique of SERS and mass spectrometry is useful to discuss the structure of folded, long biological lipids. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Effects of organic and inorganic polyamine cations on the structure of human serum albumin
Authors: Ouameur A. Ahmed , Mangier E. , Diamantoglou S. , Rouillon R. , Carpentier R. , Tajmir‐Riahi H. A. 
Published: February 2004

AbstractThe presence of several high affinity binding sites on human serum albumin (HSA) makes it a possible target for many organic and inorganic molecules. Organic polyamines are widely distributed in living cells and their biological roles have been associated with their physical and chemical interactions with proteins, nucleic acids, and lipids. This study is designed to examine the effects of spermine, spermidine, putrescine, and cobalt [Co(III)]–hexamine cations on the solution structure of HSA using Fourier transform IR, UV–visible, and circular dichroism (CD) spectroscopic methods. The spectroscopic results show that polyamine cations are located along the polypeptide chains with no specific interaction. The order of perturbations is associated with the number of positive charges of the polyamine cation: spermine > Co(III)–hexamine > spermidine > putrescine. The overall binding constants are 1.7 × 104, 1.1 × 104, 5.4 × 103, and 3.9 × 103M−1, respectively. The protein conformation is altered (IR and CD data) with reductions of α helices from 60 to 55% for free HSA to 50–40% and with increases of β structures from 22 to 15% for free HSA to 33–23% in the presence of polyamine cations. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Incorporation of anthraquinonyl group into λ‐Cro repressor protein for strand‐ and position‐specific photocleavage of double‐stranded DNA
Authors: Sasaki Hiroshi , Ikeda Kazumasa , Suzuki Maya , Ninomiya Keiko , Sisido Masahiko 
Published: February 2004

Abstractλ‐Cro repressor protein incorporated with a 2‐anthraquinonylalanine (anqAla) at the 64th position was chemically synthesized by solid‐phase method. The 64th position was selected according to previous information on various mutants of Cro incorporated with a single anqAla unit, that were synthesized through an Escherichia coli in vitro protein‐synthesizing system. The 64anqAla mutant bound to a dsDNA of consensus operator sequence and underwent strand‐ and position‐specific photocleavage of the dsDNA at the GG sequence after treatment with piperidine. The mutant also underwent position‐specific self‐photoscission. The self‐photoscission was retarded in the presence of the dsDNA. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci) , 2004
Multifunctional peptide fibrils for biomedical materials
Authors: Kasai Shingo , Ohga Yukiko , Mochizuki Mayumi , Nishi Norio , Kadoya Yuichi , Nomizu Motoyoshi 
Published: February 2004

AbstractThe Ile‐Lys‐Val‐Ala‐Val (IKVAV) containing peptide, A208 (AASIKVAVSADR, mouse laminin α1 chain 2097–2108), was recently found to form amyloid‐like fibrils. Fibril formation is critical for its biological activities, including promotion of cell adhesion and neurite outgrowth. In the present study, we designed multifunctional peptide fibrils using the A208 peptide and an Arg‐Gly‐Asp (RGD)‐containing fibronectin active sequence for biomedical applications. The fibronectin active sequence GRGDS (FN) or a scrambled sequence RSGGD (SC) were conjugated to either A208 or to A208S (AASVVIAKSADR), a scrambled peptide of A208, with a glycine as a spacer. The FN‐A208 and SC‐A208 peptides formed a gel and were stained with Congo red similar to that of A208, but FN‐A208S and SC‐A208S did not form a gel. These results indicate that FN‐A208 and SC‐A208 form amyloid‐like fibrils similar to A208. A208 and SC‐A208 promoted cell attachment with filopodia formation, and this adhesion was inhibited by the IKVAV‐containing peptide, but not by EDTA or a GRGDS peptide. FN‐A208 promoted cell attachment with well‐organized actin stress fibers, and this adhesion was partially inhibited by either EDTA, GRGDS, or IKVAV. These data suggest that A208 binds to only IKVAV receptor(s) while the FN‐A208 interacts with both integrins and the IKVAV receptor(s). We conclude that multifunctional peptide fibrils can be designed by conjugation of active peptides on A208 and that this construct has potential to serve as a bioadhesive for tissue regeneration and engineering. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004