bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perforation predicts poor prognosis in patients with primary intestinal diffuse large B‐cell lymphoma
Authors: Chuang S‐S , Ye H , Yang S‐F , Huang W‐T , Chen H‐K , Hsieh P‐P , Hwang W‐S , Chang K‐Y , Lu C‐L , Du M‐Q 
Published: September 2008

Aims: To elucidate the clinicopathological features and prognostic factors of primary intestinal diffuse large B‐cell lymphoma (PI‐DLBL).Methods and results: Archival tissues from 30 tumours were used for tissue microarray construction, immunohistochemistry and interphase fluorescence in situ hybridization for chromosomal translocation. The M:F ratio was 1.7:1, with a median age of 60 years. The ileum and ileocaecum were most frequently involved (40% each). Fourteen (47%) were at stage IE disease, 15 (50%) at stage IIE. Five (17%) tumours were perforated at presentation. The tumours expressed Bcl‐6 (73%), MUM1 (70%), Bcl‐2 (67%) and CD10 (23%). Nine (30%) were classified as germinal centre B‐cell (GCB) phenotype and 21 non‐GCB. Eight of 30 (27%), 7/30 (23%) and 2/29 (7%) cases were positive for rearrangements involving IGH, BCL6, and C‐MYC loci, respectively, whereas all cases were negative for BCL2 and CCND1 translocation. Perforation was a poor prognostic indicator, with a hazard ratio of tumour‐related death at 8.75 (P = 0.001). The differentiation antigens, GCB versus non‐GCB phenotype, or lymphoma‐associated translocations were of no prognostic significance.Conclusions: We found a higher rate of perforation and lower frequency of GCB phenotype in PI‐DLBL in Taiwan compared with other geographical areas; perforation is a poor prognostic indicator.
Influence of organizational characteristics and caring attributes of managers on nurses’ job enjoyment
Authors: Wade Gail H. , Osgood Bonnie , Avino Karen , Bucher Gale , Bucher Linda , Foraker Theresa , French Denise , Sirkowski Carol 
Published: September 2008

AbstractTitle.  Influence of organizational characteristics and caring attributes of managers on nurses' job enjoyment Aim.  This paper is a report of a study to investigate the effect of organizational characteristics and perceived caring attributes of managers on nurses’ job enjoyment.Background.  Job satisfaction was the outcome of several studies about organizational or professional practice environments. Study variables predicted 30–60% of the variance in job satisfaction. Job enjoyment, the affective dimension of job satisfaction and manager caring were not variables in previous studies.Methods.  We recruited a convenience sample of Registered Nurses (n = 731) employed by a large healthcare system in the mid‐Atlantic region of the United States of America. Participants were primarily staff nurses, female, white, full‐time employees and 41 years of age or older. Most had a baccalaureate degree in nursing and 4·5% had an advanced practice license. Participants were surveyed in 2005 using Lake’s Practice Environment Scale of the Nursing Work Index, Nyberg’s Caring Assessment Scale, the Job Enjoyment Subscale of the Atwood and Hinshaw Job Satisfaction Scale and a demographic data form. Descriptive statistics were used to explore the study variables. Data were analysed using multiple regression.Results.  Nursing foundations for quality of care, nurse manager ability, leadership and support of nurses, staffing and resource adequacy and collegial nurse–physician relations explained 30·6% of the variance in job enjoyment. Age, area of practice and job type explained an additional 5·4%.Conclusion.  Quantitative measures did not identify a majority of the variables associated with job enjoyment. Research using a qualitative and quantitative methodology with different practice samples may reveal other variables that influence job enjoyment.
Resource selection by sympatric wild equids in the Mongolian Gobi
Authors: Kaczensky P. , Ganbaatar O. , Von Wehrden H. , Walzer C. 
Published: September 2008

Summary

Historically, the overlap zones of wild equids were small in Africa but extensive for Przewalski's horses Equus ferus przewalskii and Asiatic wild asses Equus hemionus in Asia. Currently, the Great Gobi B Strictly Protected Area in south‐western Mongolia is the only place where sympatric, free‐ranging populations of these equids occur. This provides a unique opportunity to test the hypothesis that Przewalski's horses are primarily adapted to mesic steppes and Asiatic wild asses to arid desert steppes and semi‐deserts. Understanding the spatial needs and habitat requirements of these little‐studied species is a pre‐requisite for setting aside and managing protected areas and planning future re‐introductions.
From 2001 to 2005, we followed nine Przewalski's horses and seven Asiatic wild asses using satellite telemetry and direct observations to assess differences in their resource selection strategies and social organization.
Przewalski's horses had non‐exclusive home ranges of 152–826 km2, selected for the most productive plant communities and formed stable harems groups.
Asiatic wild asses had non‐exclusive home ranges of 4449–6835 km2, showed little preferences for any plant community and seemed to live in fission–fusion groups.
Synthesis and applications. Our results provide evidence for different resource selection strategies in two sympatric equid species. Our findings indicate that the Gobi areas provide an edge, rather than an optimal habitat for Przewalski's horses. Consequently, only small and isolated pockets of suitable habitat remain for future re‐introductions. Asiatic wild asses, on the other hand, need access to large tracts of land to cope with the unpredictable resource distribution of the Gobi. Managers should be aware that protecting habitat where Asiatic wild asses occur does not necessarily benefit Przewalski's horse restoration, whereas setting aside habitat for the conservation of Przewalski's horses will only locally benefit Asiatic wild asses.
Synergistic, antagonistic and additive effects of multiple stressors: predation threat, parasitism and pesticide exposure in Daphnia magna
Authors: Coors Anja , De Meester Luc 
Published: September 2008

Summary

Predation and parasitism are important factors in the ecology and evolution of natural populations and may, along with other environmental factors, interact with the impact of anthropogenic pollutants.
Our study aimed at identifying potential interactions between three stressors (predation threat, parasitism and pesticide exposure) and at exploring the predictability of their joint effects by using the model of independent action. We assessed in a full‐factorial design the impacts of these stressors on key life‐history traits and population growth rate of the water flea Daphnia magna.
When applied as single stressors, predation threat and parasite challenge induced varying stressor‐specific adaptive responses. The pesticide carbaryl was applied at a generally sublethal concentration, which caused low mortality only in first‐brood offspring.
Pesticide exposure interacted synergistically with parasite challenge regarding survival, which suggests immunomodulatory activity of the pesticide. Predation threat by phantom midge larvae showed antagonistic interactions for amount of first‐brood offspring with both parasite challenge and carbaryl exposure. All stressors additively affected age and size at maturity, which added up to a considerable delay in the onset of reproduction in the three‐stressor combination. The intrinsic rate of natural increase, r, reflected the non‐additive and additive effects on single endpoints and showed significant synergistic interactions for all two‐stressor combinations. The combination of all stressors resulted in a dramatic reduction of r compared to the stressor‐free control.
The model of independent action proved useful in quantitatively predicting effects of additively acting stressors, and in visualizing the occurrence and magnitude of non‐additive effects in accordance with results of analysis of variances.
Synthesis and applications. Cumulative additive effects and non‐additive interactions of natural antagonists and pollutants are shown to result in considerable impacts on ecologically relevant parameters. As a starting point for an environmentally more realistic risk assessment of chemicals, it may be a valuable strategy to screen for non‐additive effects among many stress factors simultaneously in simplified experimental designs by using the model of independent action.
Assessing sleepiness in the rat: a multiple sleep latencies test compared to polysomnographic measures of sleepiness
Authors: MCKENNA JAMES T. , CORDEIRA JOSHUA W. , CHRISTIE MICHAEL A. , TARTAR JAIME L. , MCCOY JOHN G. , LEE EUNHO , MCCARLEY ROBERT W. , STRECKER ROBERT E. 
Published: September 2008

SummarySleepiness following 6 h of sleep deprivation (SD) was evaluated with a rat multiple sleep latencies test (rMSLT), and the findings were compared to conventional polysomnographic measures of sleepiness. The 6 h of SD was produced by automated activity wheels, and was terminated at either the end of the light period or at the beginning of the dark period. The rMSLT consisted of 5 min wakefulness induced by sensory stimulation followed by 25 min of freedom to sleep. This procedure was repeated every 30 min for 3 h and was designed to minimize the amount of sleep lost due to the testing procedure. In separate rats, 6 h SD was followed by undisturbed recovery, allowing evaluation of conventional polysomnographic measures of sleepiness. Sleep onset latencies were reduced following SD, with recovery in the light (baseline = 8 min, 3 s versus post‐SD = 1 min, 17 s) and dark period (baseline = 14 min, 17 s versus 7 min, 7 s). Sleep onset latencies were not altered by varying the duration criterion for the first sleep bout (i.e., sleep bout length criteria of 10, 20, 30, or 60 s were compared). Polysomnographic variables (non‐rapid eye movement sleep episode duration, delta power, and number of awakenings) also provided reliable indirect measures of sleepiness, regardless of whether the recovery sleep occurred in the light or dark period. Evaluation of effect size indicated that the rMSLT was a strong measure of sleepiness, and was influenced by homeostatic, circadian, and illumination factors. The rMSLT provided a simple, objective, robust and direct measure of sleepiness that was as effective as conventional polysomnographic measures of sleepiness.
Mitochondrial DNA reveals a strong phylogeographic structure in the badger across Eurasia
Authors: MARMI J. , LÓPEZ‐GIRÁLDEZ F. , MACDONALD D. W. , CALAFELL F. , ZHOLNEROVSKAYA E. , DOMINGO‐ROURA X. 
Published: September 2008

AbstractThe badger,Meles meles, is a widely distributed mustelid in Eurasia and shows large geographic variability in morphological characters whose evolutionary significance is unclear and needs to be contrasted with molecular data. We sequenced 512 bp of the mitochondrial DNA control region in 115 Eurasian badgers from 21 countries in order to test for the existence of structuring in their phylogeography, to describe the genetic relationships among their populations across its widespread geographic range, and to infer demographic and biogeographic processes. We found that the Eurasian badger is divided into four groups regarding their mitochondrial DNA: Europe, Southwest Asia, North and East Asia, and Japan. This result suggests that the separation of badgers into phylogeographic groups was influenced by cold Pleistocene glacial stages and permafrost boundaries in Eurasia, and by geographic barriers, such as mountains and deserts. Genetic variation within phylogeographic groups based on distances assuming the Tamura–Nei model with rate heterogeneity and invariable sites (dT‐Nrange: 3.3–4.2) was much lower than among them (dT‐Nrange: 10.7–38.0), and 80% of the variation could be attributed to differences among regions. Spatial analysis of molecular variance (samova), median‐joining network, and Mantel test did not detect genetic structuring within any of the phylogeographic groups with the exception of Europe, where 50% of variation was explained by differences among groups of populations. Our data suggest that the European, Southwest Asian, and North and East Asian badgers evolved separately since the end of Pliocene, at the beginnings of glacial ages, whereas Japanese badgers separated from continental Asian badgers during the middle Pleistocene. Endangered badgers from Crete Island, classified asMeles meles arcalussubspecies, were closely related to badgers from Southwest Asia. We also detected sudden demographic growth in European and Southwest Asian badgers that occurred during the Middle Pleistocene.
Phylogeography and systematics of zebra mussels and related species
Authors: GELEMBIUK GREGORY W. , MAY GEMMA E. , LEE CAROL EUNMI 
Published: September 2008

AbstractThe genus Dreissena includes two widespread and aggressive aquatic invaders, the zebra mussel, Dreissena polymorpha, and the quagga mussel, Dreissena bugensis. This genus evolved in the Ponto‐Caspian Sea basin, characterized by dynamic instability over multiple timescales and a unique evolutionary environment that may predispose to invasiveness. The objectives of this study were to gain insights into the demographic history of Dreissena species in their endemic range, to reconstruct intraspecific phylogeographic relationships among populations, and to clarify systematics of the genus, using DNA sequences from the mitochondrial cytochrome oxidase I (COI) gene. We found four deeply diverged clades within this genus, with a basal split that approximately coincided with the Cretaceous–Tertiary boundary. Divergence events within the four base clades were much more recent, corresponding to geographically disjunct sets of populations, which might represent species complexes. Across all taxa, populations of Dreissena shared a common pattern of genetic signatures indicating historical population bottlenecks and expansions. Haplotype diversity was relatively low in Ponto‐Caspian drainages relative to more stable tectonic lakes in Greece, Macedonia, and Turkey. The phylogeographic and demographic patterns in the endemic range of Dreissena might have resulted from vicariance events, habitat instability, and the high fecundity and passive dispersal of these organisms.
A comparison of variability and population structure for major histocompatibility complex and microsatellite loci in California coastal steelhead (Oncorhynchus mykissWalbaum)
Authors: AGUILAR ANDRES , GARZA JOHN CARLOS 
Published: September 2008

AbstractThe major histocompatibility complex (MHC) contains genes integral to immune response in vertebrates. MHC genes have been shown to be under selection in a number of vertebrate taxa, making them intriguing for population genetic studies. We have conducted a survey of genetic variation in an MHC class II gene for steelhead trout from 24 sites in coastal California and compared this variation to that observed at 16 presumably neutral microsatellite loci. A high amount of allelic variation was observed at the MHC when compared to previously published studies on other Pacific salmonids. Elevated nonsynonymous substitutions, relative to synonymous substitutions, were detected at the MHC gene, indicating the signature of historical balancing selection. The MHC data were tested for correlations to and deviations from the patterns found with the microsatellite data. Estimates of allelic richness for the MHC gene and for the microsatellites were positively correlated, as were estimates of population differentiation (FST). An analysis forFSToutliers indicates that the MHC locus has an elevatedFSTrelative to the neutral expectation, although a significant result was found for only one particular geographical subgroup. Relatively uniform allele frequency distributions were detected in four populations, although this finding may be partially due to recent population bottlenecks. These results indicate that, at the scale studied here, drift and migration play a major role in the observed geographical variability of MHC genes in steelhead, and that contemporary selection is relatively weak and difficult to detect.
Estimating population structure under nonequilibrium conditions in a conservation context: continent‐wide population genetics of the giant Amazon river turtle,Podocnemis expansa(Chelonia; Podocnemididae)
Authors: PEARSE DEVON E. , ARNDT ALLAN D. , VALENZUELA NICOLE , MILLER BECKY A. , CANTARELLI VITOR , SITES JACK W. 
Published: September 2008

AbstractGiant Amazon river turtles,Podocnemis expansa,are indigenous to the Amazon, Orinoco, and Essequibo River basins, and are distributed across nearly the entire width of the South American continent. Although once common, their large size, high fecundity, and gregarious nesting, madeP. expansaespecially vulnerable to over‐harvesting for eggs and meat. Populations have been severely reduced or extirpated in many areas throughout its range, and the species is now regulated under Appendix II of the Convention on International Trade in Endangered Species. Here, we analyse data from mitochondrial DNA sequence and multiple nuclear microsatellite markers with an array of complementary analytical methods. Results show that concordance from multiple data sets and analyses can provide a strong signal of population genetic structure that can be used to guide management. The general lack of phylogeographic structure but large differences in allele and haplotype frequencies among river basins is consistent with fragmented populations and female natal‐river homing. Overall, the DNA data show thatP. expansapopulations lack a long history of genetic differentiation, but that each major tributary currently forms a semi‐isolated reproductive population and should be managed accordingly.
The genetic mosaic suggests a new role for hitchhiking in ecological speciation
Authors: VIA SARA , WEST JOAN 
Published: September 2008

AbstractEarly in ecological speciation, the genomically localized effects of divergent selection cause heterogeneity among loci in divergence between incipient species. We call this pattern of genomic variability in divergence the ‘genetic mosaic of speciation’. Previous studies have usedFSToutliers as a way to identify divergently selected genomic regions, but the nature of the relationship between outlier loci and quantitative trait loci (QTL) involved in reproductive isolation has not yet been quantified. Here, we show thatFSToutliers between a pair of incipient species are significantly clustered around QTL for traits that cause ecologically based reproductive isolation. Around these key QTL, extensive ‘divergence hitchhiking’ occurs because reduced inter‐race mating and negative selection decrease the opportunity for recombination between chromosomes bearing different locally adapted QTL alleles. Divergence hitchhiking is likely to greatly increase the opportunity for speciation in populations that are sympatric, regardless of whether initial divergence was sympatric or allopatric. Early in ecological speciation, analyses of population structure, gene flow or phylogeography based on different random or arbitrarily chosen neutral markers should be expected to conflict — only markers in divergently selected genomic regions will reveal the evolutionary history of adaptive divergence and ecologically based reproductive isolation. Species retain mosaic genomes for a very long time, and gene exchange in hybrid zones can vary dramatically among loci. However, in hybridizing species, the genomic regions that affect ecologically based reproductive isolation are difficult to distinguish from regions that have diverged for other reasons.
Mesozoic transpression, transtension, subduction and metallogenesis in northern and central California
Authors: Ernst W. G. , Snow Cameron A. , Scherer Hannah H. 
Published: September 2008

AbstractMiddle Paleozoic to Middle Jurassic terrane assemblies in the Klamaths and Sierran Foothills consist of mafic–ultramafic complexes + fine‐grained terrigenous strata derived from previously accreted continental‐margin belts. Sutured oceanic terranes reflectc.230 Myr of margin‐parallel slip involving chiefly transtension and transpression. Quartzofeldspathic clastic rocks and blueschists ± eclogites are very rare. Little devolatilization occurred at magmagenic depths; hence, coeval hydrothermal ore deposits and granitoids are uncommon. In contrast, nearly head‐on Cretaceous subduction of the Farallon plate generated the massive Klamath–Sierra Nevada volcanic–plutonic arc, reflecting dewatering of the eastward descending oceanic lithosphere in the magmagenic zone. Immature Great Valley forearc and Franciscan trench deposits shed from the arc recordc.70 Myr. of rapid crustal growth. Au‐bearing solutions rising from magmagenic depths, exsolved from plutons, and expelled from heated wall rocks were mobilized attending arc construction. Precipitation of gold‐bearing quartz veins occurred where H2O + CO2‐bearing fluids encountered major geochemical discontinuities in the wall rocks.
Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine
Authors: Baubec Tuncay , Pecinka Ales , Rozhon Wilfried , Mittelsten Scheid Ortrun 
Published: September 2008

SummaryCovalent modification by methylation of cytosine residues represents an important epigenetic hallmark. While sequence analysis after bisulphite conversion allows correlative analyses with single‐base resolution, functional analysis by interference with DNA methylation is less precise, due to the complexity of methylation enzymes and their targets. A cytidine analogue, 5‐azacytidine, is frequently used as an inhibitor of DNA methyltransferases, but its rapid degradation in aqueous solution is problematic for culture periods of longer than a few hours. Application of zebularine, a more stable cytidine analogue with a similar mode of action that is successfully used as a methylation inhibitor in Neurospora and mammalian tumour cell lines, can significantly reduce DNA methylation in plants in a dose‐dependent and transient manner independent of sequence context. Demethylation is connected with transcriptional reactivation and partial decondensation of heterochromatin. Zebularine represents a promising new and versatile tool for investigating the role of DNA methylation in plants with regard to transcriptional control, maintenance and formation of (hetero‐) chromatin.
Sarcoids in two captive tapirs (Tapirus bairdii): clinical, pathological and molecular study
Authors: Kidney Beverly A. , Berrocal Alexis 
Published: September 2008

AbstractThis case report describes for the first time sarcoids in tapirs (Tapirus bairdii), namely, a 2‐year‐old male and a 3.6‐year‐old female born and housed at the same facility. The male presented with a 3‐cm nodular, red, pedunculated, hairless, ulcerated mass on the inner surface of the left pinna. No recurrence or additional growths were present during the 3 years following surgical excision of the mass. The female presented with a similar 2‐cm mass on the inner surface of the right pinna, which recurred 2 months following surgical excision, but was subsequently successfully treated locally with liquid nitrogen with no further recurrence during a 2‐year follow‐up period. Histologically, these two masses closely resembled equine sarcoids. Similarly, an association with bovine papillomavirus 1 was demonstrated using polymerase chain reaction and in situ hybridization.