bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new single‐nucleotide deletion of PMP22 in an HNPP family without recurrent palsies
Authors: Luigetti Marco , Conte Amelia , Madia Francesca , Mereu Maria Lucia , Zollino Marcella , Marangi Giuseppe , Pomponi Maria Grazia , Liberatore Giuseppe , Tonali Pietro Altilio , Sabatelli Mario 
Published: July 2008

AbstractIn this study we describe four patients from the same kindred who were affected by an autosomal‐dominantly inherited peripheral neuropathy. They presented an unusual combination of clinical, electrophysiological, and pathological findings in association with a new mutation of the PMP22 gene. Clinically, three patients had carpal tunnel syndrome symptoms and one patient had late‐onset peroneal atrophy. Motor and sensory nerve conduction velocities were reduced without focal slowing at entrapment sites. Nerve biopsy disclosed diffuse hypomyelination with focal thickening of the myelin sheath in some fibers. Sequence analysis of the PMP22 gene showed a single‐nucleotide deletion (227delG) in the affected patients. This mutation, which has not been reported previously, leads to an open reading frame shift and probably to a truncated and unstable PMP22 protein. We conclude that this novel 227delG mutation of PMP22 gives a mild form of hereditary neuropathy with liability to pressure palsy with atypical clinical and electrophysiological findings. Muscle Nerve, 2008
The influence of substrate peptide length on human β‐tryptase specificity
Authors: Spichalska Bożena , Lesner Adam , Wysocka Magdalena , Śledź Marcin , Łȩgowska Anna , Jaśkiewicz Anna , Miecznikowska Hanna , Rolka Krzysztof 
Published: July 2008

AbstractCombinatorial chemistry approach was applied to design chromogenic substrates of human β‐tryptase. The most active substrate, Ala‐Ala‐Pro‐Ile‐Arg‐Asn‐Lys‐ANB‐NH2, was selected from among over 9 million heptapeptides. The amide of 5‐amino‐2‐nitrobenzoic acid (ANB‐NH2) attached at the C‐terminus served as a chromophore. In order to determine the optimal length of the tryptase substrate, a series of N‐terminally truncated fragments of this substrate was synthesized. Pro‐Ile‐Arg‐Asn‐Lys‐ANB‐NH2, with the determined value of the specificity constant (kcat/KM) above 9 × 106 M−1 s−1, appeared to be the most specific substrate of tryptase. This substrate was twice as active as the parent heptapeptide substrate. We postulate that the optimal size of the pentapeptide substrate for the interaction with human β‐tryptase is associated with the unique structure of this proteinase, comprising four almost identical monomer subunits arranged in a square flat ring with its substrate pockets faced inside, forming a tetramer with a central pore that can be penetrated by this short peptide. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Augmented Three‐mode MIA‐QSAR Modeling for a Series of Anti‐HIV‐1 Compounds
Authors: Goodarzi Mohammad , Freitas Matheus P. 
Published: July 2008

AbstractThe bioactivities of a series of 2‐amino‐6‐arylsulfonylbenzonitriles and their thio‐ and sulfinyl congeners have been previously modeled by using the MIA‐QSAR approach and the PLS regression method [10]. The present work reports the significant improvement in the prediction ability of the Multivariate Image Analysis applied to Quantitative Structure–Activity Relationship (MIA–QSAR) model by applying Parallel Factor Analysis (PARAFAC) and Artificial Neural Network (ANN) directly to the three‐way array built. This perspective represents an important advance for the accurate prediction of potential drug candidates.
Pathobiology of the human prostate
Authors: Maitland Norman J. 
Published: July 2008

AbstractMost disorders of the prostate are a result of a loss of essential growth control. The three main pathologies associated with this multifunctional but non‐essential gland – prostatitis, benign prostatic hyperplasia and adenocarcinoma – are thought to originate in the central, transitional and peripheral zones, respectively. Professor Maitland outlines factors that affect the development of prostate cancer and discusses the stem cell hypothesis, which provides explanations for the relative resistance of the tumours to most types of conventional therapy, and for the presence of residual disease after androgen therapy. Copyright © 2008 Wiley Interface Ltd
Cervical schistosomiasis infection in a woman with an abnormal smear
Authors: Okunoye Gbemisola O. , Beattie Gerry J. , AL Nafussi Awatif , Jones Michael 
Published: July 2008

AbstractThe authors present a case history of a Caucasian woman who was found to have cervical schistosomiasis on histology following investigations for an abnormal cervical smear. This case highlights the importance of taking a history of foreign travel, particularly as travel to endemic areas is becoming increasingly common. Copyright © 2008 Wiley Interface Ltd
Age‐ and region‐dependent patterns of Ca2+ accumulations following status epilepticus
Authors: Friedman Linda K. , Saghyan Aleksandr , Peinado Alex , Keesey Robert 
Published: July 2008

AbstractElevated Ca2+ concentrations have been implicated in cell death mechanisms following seizures, however, the age and brain region of intracellular Ca2+ accumulations [Ca2+]i, may influence whether or not they are toxic. Therefore, we examined regional accumulations of 45Ca2+ by autoradiography from rats of several developmental stages (P14, P21, P30 and P60) at 5, 14, and 24 h after status epilepticus. To determine whether the uptake was intracellular, Ca2+ was also assessed in hippocampal slices with the dye indicator, Fura 2AM at P14. Control animals accumulated low homogeneous levels of 45Ca2+; however, highly specific and age‐dependent patterns of 45Ca2+ uptake were observed at 5 h. 45Ca2+ accumulations were predominant in dorsal hippocampal regions, CA1/CA2/CA3a, in P14 and P21 rats and in CA3a and CA3c neurons of P30 and P60 rats. Selective midline and amygdala nuclei were marked at P14 but not at P21 and limbic accumulations recurred with maturation that were extensive at P30 and even more so at P60. At 14 h, P14 and P21 rats had no persistent accumulations whereas P30 and P60 rats showed persistent uptake patterns within selective amygdala, thalamic and hypothalamic nuclei, and other limbic cortical regions that continued to differ at these ages. For example, piriform cortex accumulation was highest at P60. Fura 2AM imaging at P14 confirmed that Ca2+ rises were intracellular and occurred in both vulnerable and invulnerable regions of the hippocampus, such as CA2 pyramidal and dentate granule cells. Silver impregnation showed predominant CA1 injury at P20 and P30 but CA3 injury at P60 whereas little or no injury was found in extrahippocampal structures at P14 and P20 but was modest at P30 and maximal at P60. Thus, at young ages there was an apparent dissociation between high 45Ca2+ accumulations and neurotoxicity whereas in adults a closer relationship was observed, particularly in the extrahippocampal structures.
Distribution of local earthquakes in the crust beneath central Lake Baikal
Authors: Suvorov V.D. , Tubanov Ts.A. 
Published: July 2008

Abstract
We have located earthquake hypocenters in the area of central Lake Baikal using the Hypoellipse inversion of direct P traveltimes collected by a local seismological network of seven stations in 2001 through 2005. The location accuracy depends on the agreement between the reference velocity model and the real subsurface. Traveltime residuals have no bearing on the accuracy of depth estimates due to origin time errors.
Hypocenter location with reference to a DSS-derived layered velocity model predicts that the crust is seismogenic between 10 and 22 km. The hypocenters cluster densely in belts trending in NE and SE directions along and across Lake Baikal. Earthquakes become deeper from 10 to 22 km toward the Selenga basin.
Analysis of experimental data on the diffusion coefficients of Fe, Mn, Mg, and Ca in garnets
Authors: Korolyuk V.N. , Lepezin G.G. 
Published: July 2008

Abstract
Experimental data on the diffusion coefficients of Fe, Mn, Mg, and Ca in garnets are generalized. Frequency factors (cm2/s), activation energies (cal/mole), and activation volumes (cm3/mole) are optimized. Based on the compensation law, the dependences of diffusion coefficients on pressure (kbar) and temperature (K) have been derived:
“Area by Area the Machine Unfolds”: The Improvisational Performance Practice of the Art Ensemble of Chicago
Authors: STEINBECK PAUL 
Published: July 2008

AbstractSince their emergence from the Association for the Advancement of Creative Musicians (AACM) in the 1960s, the members of the Art Ensemble of Chicago have created a distinctive multi-disciplinary performance practice centered on collective improvisation. In this article, I conceptualize Art Ensemble improvisations as networks of group interactions, and I analyze an excerpt from a 1972 Art Ensemble concert recording using a phenomenological perspective informed by my conversations with the group about the performance and by my own experience as an improvised-music practitioner. The analysis focuses on the integration of composed material into the improvisatory process, the functions of stylistic diversity and multi-instrumentalism in Art Ensemble performance practice, and the interactive roles played by Lester Bowie, Roscoe Mitchell, Joseph Jarman, Malachi Favors, and Don Moye.
Tyrosine modification enhances metal-ion binding
Authors: Baldwin Graham S. , Bailey Michael F. , Shehan B. Philip , Sims Ioulia , Norton Raymond S. 
Published: July 2008

Tyrosine sulfation is a common modification of many proteins, and the ability to phosphorylate tyrosine residues is an intrinsic property of many growth-factor receptors. In the present study, we have utilized the peptide hormone CCK8 (cholecystokinin), which occurs naturally in both sulfated and unsulfated forms, as a model to investigate the effect of tyrosine modification on metal-ion binding. The changes in absorbance and fluorescence emission on Fe3+ binding indicated that tyrosine sulfation or phosphorylation increased the stoichiometry from 1 to 2, without greatly affecting the affinity (0.6–2.8 μM at pH 6.5). Measurement of Ca2+ binding with a Ca2+-selective electrode revealed that phosphorylated CCK8 bound two Ca2+ ions. CCK8 and sulfated CCK8 each bound only one Ca2+ ion with lower affinity. Binding of Ca2+, Zn2+ or Bi3+ to phosphorylated CCK8 did not cause any change in absorbance, but substantially increased the change in absorbance on subsequent addition of Fe3+. The results of the present study demonstrate that tyrosine modification may increase the affinity of metal-ion binding to peptides, and imply that metal ions may directly regulate many signalling pathways.
Considering dependence among genes and markers for false discovery control in eQTL mapping
Authors: Chen Liang , Tong Tiejun , Zhao Hongyu 
Published: July 2008

AbstractMotivation: Multiple comparison adjustment is a significant and challenging statistical issue in large-scale biological studies. In previous studies, dependence among genes is largely ignored. However, such dependence may be strong for some genomic-scale studies such as genetical genomics [also called expression quantitative trait loci (eQTL) mapping] in which thousands of genes are treated as quantitative traits and mapped to different genetical markers. Besides the dependence among markers, the dependence among the expression levels of genes can also have a significant impact on data analysis and interpretation.Results: In this article, we propose to consider both the mean as well as the variance of false discovery number for multiple comparison adjustment to handle dependence among hypotheses. This is achieved by developing a variance estimator for false discovery number, and using the upper bound of false discovery proportion (uFDP) for false discovery control. More importantly, we introduce a weighted version of uFDP (wuFDP) control to improve the statistical power of eQTL identification. In addition, the wuFDP approach can better control false positives than false discovery rate (FDR) and uFDP approaches when markers are in linkage disequilibrium. The relative performance of uFDP control and wuFDP control is illustrated through simulation studies and real data analysis.Contacts: liang.chen@usc.edu; hongyu.zhao@yale.eduSupplementary information: Supplementary figures, tables and appendices are available at Bioinformatics online.
A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?
Authors: Haibe-Kains B. , Desmedt C. , Sotiriou C. , Bontempi G. 
Published: July 2008

AbstractMotivation: Survival prediction of breast cancer (BC) patients independently of treatment, also known as prognostication, is a complex task since clinically similar breast tumors, in addition to be molecularly heterogeneous, may exhibit different clinical outcomes. In recent years, the analysis of gene expression profiles by means of sophisticated data mining tools emerged as a promising technology to bring additional insights into BC biology and to improve the quality of prognostication. The aim of this work is to assess quantitatively the accuracy of prediction obtained with state-of-the-art data analysis techniques for BC microarray data through an independent and thorough framework.Results: Due to the large number of variables, the reduced amount of samples and the high degree of noise, complex prediction methods are highly exposed to performance degradation despite the use of cross-validation techniques. Our analysis shows that the most complex methods are not significantly better than the simplest one, a univariate model relying on a single proliferation gene. This result suggests that proliferation might be the most relevant biological process for BC prognostication and that the loss of interpretability deriving from the use of overcomplex methods may be not sufficiently counterbalanced by an improvement of the quality of prediction.Availability: The comparison study is implemented in an R package called survcomp and is available from http://www.ulb.ac.be/di/map/bhaibeka/software/survcomp/.Contact: bhaibeka@ulb.ac.beSupplementary information: Supplementary data are available at Bioinformatics online.
Landscape scale effects of disturbance on riparian vegetation
Authors: RENÖFÄLT BIRGITTA MALM , NILSSON CHRISTER 
Published: July 2008

Summary1. Differing responses in riparian species richness and composition to disturbance have been reported as a possible explanation for the differences along and between rivers. This paper explores the role of physical disturbance in shaping landscape‐scale patterns of species distribution in riparian vegetation along a free‐flowing river in northern Sweden.2. To test whether sensitivity to disturbance varies across large landscapes, we experimentally disturbed riparian vegetation along an entire, free‐flowing river by scouring the soil and the vegetation turf, cutting vegetation, applying waterborne plant litter, and after a period of recovery we measured vegetation responses. The experiment was repeated for two consecutive years.3. We found no significant effect of disturbance on species composition, but all three forms of disturbance significantly reduced species richness. There was no downstream variation in community responses to disturbance but morphological groups of species responded differently to different kinds of disturbance. Graminoids were most resistant, suppressed only by litter burial. All forms of disturbance except cutting reduced the density of herbaceous species, and species density of trees + shrubs and dwarf shrubs was negatively affected by both scouring and cutting. We also evaluated the effects of disturbance in relation to varying levels of species richness. In nearly all cases, responses were significantly negatively correlated with control plot species richness, and relative responses indicated that species‐rich plots were less resistant to scouring and cutting.4. Our results suggest that although all disturbance treatments had an effect on species richness, variation in sensitivity to disturbance is not the most important factor shaping landscape‐scale patterns of riparian plant species richness along rivers.
To what extent do microsatellite markers reflect genome‐wide genetic diversity in natural populations?
Authors: VÄLI ÜLO , EINARSSON ANNIKA , WAITS LISETTE , ELLEGREN HANS 
Published: July 2008

AbstractMicrosatellite variability is widely used to infer levels of genetic diversity in natural populations. However, the ascertainment bias caused by typically selecting only the most polymorphic markers in the genome may lead to reduced sensitivity for judging genome‐wide levels of genetic diversity. To test this potential limitation of microsatellite‐based approaches, we assessed the degree of nucleotide diversity in noncoding regions of eight different carnivore populations, including inbred as well as outbred populations, by sequencing 10 introns (5.4–5.7 kb) in 20 individuals of each population (wolves, coyotes, wolverines and lynxes). Estimates of nucleotide diversity varied 30‐fold (7.1 × 10−5 –2.1 × 10−3), with densities of one single nucleotide polymorphism every 112–5446 bp. Microsatellite genotyping (10–27 markers) of the same animals revealed mean multilocus heterozygosities of 0.54–0.78, a 1.4‐fold difference among populations. There was a positive yet not perfect (r2 = 0.70) correlation between microsatellite marker heterozygosity and nucleotide diversity at the population level. For example, point estimates of nucleotide diversity varied in some cases with an order of magnitude despite very similar levels of microsatellite marker heterozygosity. Moreover, at the individual level, no significant correlation was found. Our results imply that variability at microsatellite marker sets typically used in population studies may not accurately reflect the underlying genomic diversity. This suggests that researchers should consider using resequencing‐based approaches for assessing genetic diversity when accurate inference is critical, as in many conservation and management contexts.
Characterization of the porcine Kisspeptins receptor gene and evaluation as candidate for timing of puberty in sows
Authors: Li S. , Ren J. , Yang G. , Guo Y. , Huang L. 
Published: July 2008

SummaryKisspeptins receptor (KISS1R), also called GPR54, is a key regulator of puberty in many species. KISS1R and its genetics in pigs remain unexplored. The objective of this study was to characterize the porcine KISS1R gene and evaluate the association of KISS1R mutations with age at puberty in sows. KISS1R was assigned to pig chromosome 2q21‐24 by radiation hybrid mapping. It has a 1438 bp full‐length cDNA and spans 3349 bp genomic sequence consisting of five exons and four introns. Semi‐quantitative RT‐PCR showed that KISS1R transcripts was particularly abundant in the adrenal, prostate, testis, thymus, pituary and hypothalamus. KISS1R mRNA content in the hypothalamus was determined by real‐time quantitative RT‐PCR, and it fluctuated during the oestrous cycle with the highest level in the luteal phase. Anoestrus sows had markedly lower hypothalamic KISS1R mRNA content than cyclic animals. Seven KISS1R SNPs were identified in the founder animals of a White Duroc × Erhualian intercross. One missense mutation (T/C245) showed quite different allele distribution in Chinese and Western breeds. All F0, F1 animals and 367 detailed phenotyped cyclic F2 sows in the White Duroc × Erhualian intercross were genotyped for three KISS1R polymorphisms. No significant association of KISS1R haplotypes and haplotype pairs with age at puberty was observed in the resource population, indicating that mutations in KISS1R are not responsible for divergent age at puberty in White Duroc and Erhualian pigs.
Iron availability affects mcyD expression and microcystin‐LR synthesis in Microcystis aeruginosa PCC7806
Authors: Sevilla Emma , Martin‐Luna Beatriz , Vela Laura , Bes M. Teresa , Fillat Maria F. , Peleato M. Luisa 
Published: July 2008

SummaryMicrocystins are toxins produced by cyanobacteria that entail serious health and environmental problems. They are cyclic heptapeptides synthesized via a mixed polyketide synthase/non‐ribosomal peptide synthetase system called microcystin synthetase. Environmental and nutritional factors that trigger microcystin synthesis are still debated and this work deals with the study of the influence of iron nutritional status on the microcystin synthesis. The results indicate that iron deficiency could be one of the inducing factors of the microcystin synthesis. For the first time, increased transcription of an essential mcy gene and correlative microcystin synthesis has been established. Real‐time PCR analysis of mcyD, and microcystin‐LR synthesis were studied on Microcystis aeruginosa PCC7806 grown in iron‐replete and iron‐deplete media. Iron starvation causes an increase of mcyD transcription, correlative to the increase of microcystin‐LR levels. Four transcription start points were identified for mcyD and two for mcyA, and they are not changed as a consequence of iron deficiency.
Use of guilds for modelling avian responses to vegetation in the Intermountain West (USA)
Authors: Mac Nally Ralph , Fleishman Erica , Thomson James R. , Dobkin David S. 
Published: July 2008

ABSTRACTAim Individually focused conservation management of many species is expensive and logistically impractical. Mesofilter conservation methods may facilitate the simultaneous management of multiple species. We used data on distributions of two sets of avian guilds, based on dependence on riparian vegetation and on nest location, to relate occurrence rates to environmental variables. Variables were selected by expert opinion and are likely to be affected by changes in climate and land use.Location Data were collected from 2001–06 in four adjacent mountain ranges in the central Great Basin (Lander, Nye and Eureka counties, Nevada, USA): the Shoshone Mountains and the Toiyabe, Toquima and Monitor ranges.Methods Data on occurrence of birds, vegetation composition and vegetation structure were obtained in the field. Geographical coordinates and the normalized difference vegetation index were derived from a digital elevation model and a satellite image. To construct a general model for guilds as a whole, while allowing flexibility for variation in the functional responses of individual species, we applied multivariate adaptive regression splines.Results The predictive capacity of expert knowledge of relationships between birds and vegetation was inconsistent. Latitude, longitude and elevation may constrain the response of some guilds to changes in vegetation structure and composition. Guild‐based models were useful for modelling species with sparse distributions, which are difficult to model individually. In essence, this method supplements models for the individual species with patterns for the guild to which they belong.Main conclusions Guilds of birds appeared to have predictable associations with selected attributes of vegetation structure and composition. The criteria by which species are grouped into guilds may affect the success of predictions and management interventions. Our derived models offer the potential to predict effects on the avifauna of management or climate‐driven change in vegetation.