bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene copy number variation and common human disease
Authors: Fanciulli M , Petretto E , Aitman TJ 
Published: December 2009

Fanciulli M, Petretto E, Aitman TJ. Gene copy number variation and common human disease.Variation in gene copy number is increasingly recognized as a common, heritable source of inter‐individual differences in genomic sequence. The role of copy number variation is well established in the pathogenesis of rare genomic disorders. More recently, germline and somatic copy number variation have been shown to be important pathogenic factors in a range of common diseases, including infectious, autoimmune and neuropsychiatric diseases and cancer. In this review, we describe the range of methods available for measuring copy number variants (CNVs) in individuals and populations, including the limitations of presently available assays, and highlight some key examples of common diseases in which CNVs have been shown clearly to have a pathogenic role. Although there has been major progress in this field in the last 5 years, understanding the full contribution of CNVs to the genetic basis of common diseases will require further studies, with more accurate CNV assays and larger cohorts than have presently been completed.
Factors influencing infection of Acacia mearnsii by the wilt pathogen Ceratocystis albifundus in South Africa
Authors: Heath R. N. , Van Der Linde M. , Groeneveld H. , Wingfield B. D. , Wingfield M. J. , Roux J. 
Published: December 2009

SummaryIt is well known that species of Ceratocystis, which cause canker and wilt diseases on trees, require wounds for infection. In this regard, a number of physical and environmental factors influence the success of wound colonization by these fungi. The aim of this study was to consider the influence of wound age, stem diameter and colonization of wounds by Ophiostoma quercus on the success of infection by Ceratocystis albifundus, an important wilt pathogen of Acacia mearnsii in southern and eastern Africa, under field conditions. This was performed by doing controlled inoculations on Acacia mearnsii trees, of different diameters, with C. albifundus at different time intervals after wounding and after pre‐inoculation of wounds with O. quercus at the time of wounding. The success of infection by C. albifundus decreased significantly from 8 h after wounding and was higher on stems of greater diameter. Pre‐infection of wounds by O. quercus reduced the infection success of C. albifundus. The overall results showed that managing wounds created during forestry operations by treating wounds with naturally occurring, non‐virulent fungi, such as O. quercus, could reduce the prevalence of infections by C. albifundus.
Phenotypic differences among three clonal lineages of Phytophthora ramorum
Authors: Elliott M. , Sumampong G. , Varga A. , Shamoun S. F. , James D. , Masri S. , Grünwald N. J. 
Published: December 2009

SummaryThere are three major clonal lineages of Phytophthora ramorum present in North America and Europe named NA1, NA2, and EU1. Twenty‐three isolates representing all three lineages were evaluated for phenotype including (i) aggressiveness on detached Rhododendron leaves and (ii) growth rate at minimum, optimum, and maximum temperatures. Closely related species P. foliorum and P. hibernalis were included in phenotypic tests since these species are encountered in nursery surveys for P. ramorum. Isolates from the NA2 and EU1 lineages were the most aggressive and isolates from the NA1 group were the least aggressive. The NA1 lineage of P. ramorum was the most variable in aggressiveness and growth rate. The variability in the NA1 lineage was due to the presence of non‐wild type (nwt) isolates. There was no significant difference in growth rate among NA1 wild type (wt), NA2, and EU1 lineages at any temperature tested. The difference between wt and nwt P. ramorum isolates is discussed.
Phytotoxins produced by the oak pathogen Discula quercina
Authors: Maddau L. , Perrone C. , Andolfi A. , Spanu E. , Linaldeddu B. T. , Evidente A. 
Published: December 2009

SummaryTwo phytotoxic metabolites, p‐hydroxybenzaldehyde and indol‐3‐aldehyde, were isolated and identified by spectroscopic methods from solid cultures of Discula quercina, an endophytic fungal pathogen frequently associated with oak decline in Italy. In addition, the fungus produced an unusual acyclic keto acid as a major metabolite, which was identified by spectroscopic and chemical methods as 5‐oxo‐6E,8E‐octadecadienoic acid. In leaf puncture assays on Quercus suber and Q. ilex leaves, indol‐3‐aldehyde proved to be more toxic than p‐hydroxybenzaldehyde, while 5‐oxo‐6E,8E‐octadecadienoic acid was inactive even at the highest concentration used (1 mg ml−1). Although indol‐3‐aldehyde is a known microbial metabolite, its phytotoxic activity has hitherto not been reported. This report is the first to describe the production of phytotoxic compounds by D. quercina.
High gene flow promotes the genetic homogeneity of the fish goby Pomatoschistus marmoratus (Risso, 1810) from Mar Menor coastal lagoon and adjacent marine waters (Spain)
Authors: Vergara‐Chen Carlos , González‐Wangüemert Mercedes , Marcos Concepción , Pérez‐Ruzafa Ángel 
Published: December 2009

AbstractThe extreme environmental variability of coastal lagoons suggests that physical and ecological factors could contribute to the genetic divergence among populations occurring in lagoon and open‐coast environments. In this study we analysed the genetic variability of lagoon and marine samples of the sand goby, Pomatoschistus marmoratus (Risso, 1810) (Pisces: Gobiidae), on the SW Spain coast. A fragment of mitochondrial DNA control region (570 bp) was sequenced for 196 individuals collected in five localities: Lo Pagan, Los Urrutias and Playa Honda (Mar Menor coastal lagoon), and Veneziola and Mazarrón (Mediterranean Sea). The total haplotype diversity was h = 0.9424 ± 0.0229, and the total nucleotide diversity was π = 0.0108 ± 0.0058. Among‐sample genetic differentiation was not significant and small‐scale patterns in the distribution of haplotypes were not apparent. Gene flow and dispersal‐related life history traits may account for low genetic structure at a small spatial scale. The high genetic diversity found in P. marmoratus increases its potential to adapt to changing conditions of the Mar Menor coastal lagoon.
Misalignments of rest–activity rhythms in inpatients with schizophrenia
Authors: Kodaka Manami , Tanaka Satoshi , Takahara Madoka , Inamoto Atsuko , Shirakawa Shuichiro , Inagaki Masatoshi , Kato Nobumasa , Yamada Mitsuhiko 
Published: December 2009

Aims:  Rest–activity rhythms of human beings generally synchronize to a 24‐h time cue. Very few detailed research studies have examined rest–activity rhythms in patients with schizophrenia. The present study aimed to explore (i) rest–activity rhythms in patients with schizophrenia, and (ii) factors relevant to their rhythm characteristics.Methods:  We selected only inpatients for this research, because the time cue for inpatients was considered more standardized than that of outpatients. Sixteen inpatients with schizophrenia wore an ActiTrac accelerometer‐based activity monitor (IM Systems Inc., Baltimore, USA) for eight consecutive days to measure their activity. We used a χ2 periodogram to compute rest–activity rhythms from the activity data, whereby the χ2 value amplitude was regarded as an index of regularity. We conducted non‐parametric tests to identify factors relevant to rhythm cycles and patterns.Results:  Half of the participants exhibited prolonged rest–activity cycles, and 25% also had irregular rest–activity patterns defined by insufficient χ2 value amplitude, even though they were clearly under a 24‐h time cue. Participants with misaligned rest–activity rhythms had attended daytime non‐medical treatment programs less frequently, and had received more anti‐anxiety/hypnotic medications than those with proper rhythms.Conclusion:  Changes in rest–activity rhythms by optimizing pharmacological and non‐pharmacological treatment could improve social adjustment or quality of life in patients with schizophrenia.
Spinal needle design and size affect the incidence of postdural puncture headache in children
Authors: APILIOGULLARI SEZA , DUMAN ATES , GOK FUNDA , AKILLIOGLU ISAK 
Published: December 2009

SummaryBackground:  In adults, pencil point spinal needles are known to be less traumatic and hence to be superior compared with cutting point needles in respect of postpuncture complications. In children, only a few trials have evaluated the difference in the incidence of postdural puncture headache (PDPH) using spinal needles with different tip designs. The aim of this study was to evaluate the success rate and the incidence of PDPH and backache following spinal anesthesia (SA) with the two types of needles currently in use for children.Methods:  This is a retrospective study of prospectively collected data. The success rate and postpuncture complications of 26G cutting point (Atraucan®) spinal needle were compared with 27G pencil point (Pencan®) spinal needle in 414 children aged 2–17 years undergoing surgery with SA.Results:  Both needles had similar first‐attempt success rates: 87% in the cutting point group and 91% in the pencil point group (P = 0.16). Pencil point needles caused less PDPH compared to cutting point needles; 0.4% vs 4.5%, respectively (P = 0.005). Both needles caused similar backache (P = 0.08). No severe neurologic symptom was reported for both needles.Conclusion:  The data suggest that 27G pencil point spinal needles lead to less PDPH compared to 26G cutting point spinal needles in children.
Extraordinarily widespread and fantastically complex: comparative biology of endosymbiotic bacterial and fungal mutualists of insects
Authors: Gibson Cara M. , Hunter Martha S. 
Published: December 2009

Ecology Letters(2010) 13: 223–234AbstractEndosymbiosis is a pervasive, powerful force in arthropod evolution. In the recent literature, bacterial symbionts of insects have been shown to function as reproductive manipulators, nutritional mutualists and as defenders of their hosts. Fungi, like bacteria, are also frequently associated with insects. Initial estimates suggest that insect–fungal endosymbionts are hyperdiverse, yet there has been comparatively little research investigating the roles that fungi play in their insect hosts. In many systems in which the bacterial symbionts are well‐characterized, the possible presence of fungi has been routinely ignored. Why has there been so little research on this important group of symbionts? Here, we explore the differences between fungal and bacterial endosymbiotic insect mutualists. We make predictions about why a bacterium or fungus might be found associated with an insect host given particular ecological, physiological, or evolutionary conditions. We also touch on the various hurdles for studying fungal vs. bacterial endosymbionts and potential future research directions.
Ability of stress‐related volatiles to attract and induce attacks by Xylosandrus germanus and other ambrosia beetles
Authors: Ranger Christopher M. , Reding Michael E. , Persad Anand B. , Herms Daniel A. 
Published: December 2009

Xylosandrus germanus typically colonizes physiologically‐stressed deciduous hosts but it is increasingly being recognized as a key pest of ornamental nursery stock. We tested the attractiveness of common plant stress‐related volatiles to ambrosia beetles occupying the nursery agroecosystem, as well as their ability to induce attacks on selected trees. Experiments were conducted in Ohio, U.S.A.
Stress volatile attractiveness was first assessed by positioning traps baited with acetaldehyde, acetone, ethanol and methanol in ornamental nurseries. Cumulative trap counts confirmed that ethanol was the most attractive stress‐related volatile to X. germanus. Methanol‐baited traps were slightly attractive to X. germanus, whereas traps baited with acetaldehyde and acetone were not attractive to any ambrosia beetle.
A series of tree injection experiments were also conducted to determine the ability of these volatiles to induce attacks by ambrosia beetles under field conditions. Injection of ethanol into Magnolia virginiana induced the largest number of attacks, whereas injection of acetaldehyde induced more attacks than methanol or acetone. Xylosandrus germanus was the most predominant species emerging from M. virginiana injected with each of the stress‐related volatiles. No attacks by wood‐boring beetles were observed on water injected or uninjected control trees.
Solid‐phase microextraction–gas chromatography–mass spectrometry confirmed the emission of acetaldehyde, acetone, ethanol and methanol after their injection into M. virginiana.
Xylosandrus germanus has an efficient olfactory‐based mechanism for differentiating among host volatile cues. Injecting select trees with stress‐related volatiles, particularly ethanol, shows promise as a trap tree strategy for X. germanus and other ambrosia beetles.
Syndecan‐1 expression in prostate cancer and its value as biomarker for disease progression
Authors: Brimo Fadi , Vollmer Robin T. , Friszt Matthew , Corcos Jacques , Bismar Tarek A. 
Published: December 2009

OBJECTIVETo evaluate the association between syndecan‐1 (CD138) expression and prostate cancer.PATIENTS AND METHODSWe evaluated syndecan‐1 expression using a recently constructed tissue microarray of prostatic samples taken from 243 patients, corresponding to 1400 cores, with 69.8%, 5.6%, 17.6% and 7% of the cores representing localized prostate cancer, high‐grade prostatic intraepithelial neoplasia, benign prostate tissue and hormone refractory/metastatic disease, respectively.RESULTSMetastatic cases had the highest frequency and membranous staining intensity for syndecan‐1 overexpression, followed by hormone refractory and localized disease (83.3% vs 34.8% and 25.7%, respectively). There was no significant difference in the frequency of membranous syndecan‐1 expression between localized prostate cancer and benign glands (25.7% vs 24.7% of cases, respectively). However, benign glands showed significantly higher intensity staining than localized prostate cancer. We found no significant association between syndecan‐1 expression and any of the following: Gleason score, pathological stage, surgical margin status and biochemical recurrence.CONCLUSIONThe current available evidence, from the present and previous studies, show that syndecan‐1 is not an independent predictor of recurrence or tumour‐specific survival, diminishing its significance as a clinical marker.
Extraprostatic extension of prostatic adenocarcinoma on needle core biopsy: report of 72 cases with clinical follow‐up
Authors: Miller Jeremy S. , Chen YingBei , Ye HuiHui , Robinson Brian D. , Brimo Fadi , Epstein Jonathan I. 
Published: December 2009

Study Type – Prognosis (case series) Level of Evidence 4OBJECTIVETo describe the histological findings and prognosis that are associated with extraprostatic extension (EPE) on needle core biopsy of prostatic adenocarcinoma.PATIENTS AND METHODSWe retrieved 99 cases of prostatic adenocarcinoma with EPE at initial diagnosis on biopsy from the consultation files of one of the authors between 1997 and 2009. The 72 cases that had available clinical follow‐up data formed the basis of this study.RESULTSThe mean (range) age of the patients was 64 (48–87) years, the median (mean, range) serum prostatic specific antigen level was 7.8 (64.8, 0.3–1505) ng/mL, and 60 of the patients (83%) had abnormalities on a digital rectal examination. The mean (range) number of malignant cores was 7.7 (1–23); the mean percentage of carcinoma in each core was 69.6%, and that in the core(s) with EPE was 76.8%. The mean Gleason score in the core(s) with EPE was 8, with a mean highest Gleason score per case of 8.4. Perineural invasion was detected in 54 cases (75%). Ten of 11 patients treated surgically had EPE on the radical prostatectomy (RP) specimen; also six had positive resection margins, five showed invasion into the seminal vesicles and one had lymph node metastasis. The Gleason scores in nine of the RP specimens did not differ from the highest grade found in the associated biopsies (score 9 in three, 8 in two, 7 in four); in one case it increased (from score 6 to 8) and in one it decreased (from score 9 to 8). Patients were followed for a mean (median, range) of 2.9 (2, 0.1–9) years, with metastases identified in 29 (40%); 10 (14%) died from the disease.CONCLUSIONEPE on needle core biopsy of the prostate is strongly associated with extensive, high‐grade prostatic adenocarcinoma, such that its usefulness as an isolated prognostic factor is relatively limited.
Narrow‐band imaging cystoscopy to evaluate bladder tumours – individual surgeon variability
Authors: Herr Harry , Donat Machele , Dalbagni Guido , Taylor Jennifer 
Published: December 2009

Study Type – Diagnosis (exploratory cohort) Level of Evidence 2bOBJECTIVETo assess individual urologist variability using narrow‐band imaging (NBI) cystoscopy to evaluate bladder tumours.PATIENTS AND METHODSIn all, 50 patients underwent white‐light and NBI cystoscopy to evaluate for recurrent bladder tumours. Endoscopic images in each patient were independently viewed by four urologists assessing presence or absence of tumour. Their findings were correlated with biopsy results.RESULTSIn all, 26 patients had recurrent tumour and 24 had benign histology. There were no significant differences among urologists detecting recurrent tumour or in determining final pathology.CONCLUSIONSThere does not appear to be a ‘learning curve’ for adapting to NBI‐surveillance cystoscopy in patients with bladder cancer.
Long‐term data on the survival of patients with prostate cancer treated with radical prostatectomy in the prostate‐specific antigen era
Authors: Isbarn Hendrik , Wanner Manuela , Salomon Georg , Steuber Thomas , Schlomm Thorsten , Köllermann Jens , Sauter Guido , Haese Alexander , Heinzer Hans , Huland Hartwig , Graefen Markus 
Published: December 2009

Study Type – Therapy (case series) Level of Evidence 4OBJECTIVETo examine the long‐term rates of biochemical recurrence (BCR)‐free survival, cancer‐specific mortality (CSM)‐free survival, and overall survival (OS) in patients with prostate cancer treated with open radical prostatectomy (RP) in the prostate‐specific antigen (PSA) era.PATIENTS AND METHODSThe study comprised 436 patients who were treated with RP between 1992 and 1997 at our institution. None received adjuvant/salvage therapy in the absence of BCR. The BCR‐free, CSM‐free and OS rateswere defined using the Kaplan‐Meier method. Multivariable Cox‐regression models were used to test the effect of age, preoperative PSA level, neoadjuvant hormonal therapy, pT stage, lymph node status, RP Gleason sum and surgical margin status on BCR.RESULTSThe median follow‐up of censored patients was 122, 128, and 132 months for, respectively, BCR‐free, CSM‐free and OS estimates. The 10‐year event‐free survival rates for the same endpoints were 60%, 94% and 86%, respectively. Preoperative PSA level, RP Gleason sum, pT stage, lymph node status, and surgical margin status were independent predictors of BCR (all adjusted P < 0.05).CONCLUSIONSThis study is the first to evaluate the long‐term cancer control outcomes after RP from a European country in the PSA era. Our data indicate that RP provides excellent long‐term survival rates in patients with clinically localized prostate cancer. Although ≈40% of patients have BCR after 10 years of follow‐up, the CSM rate after 10 years is as low as 6%.
Patterns and controls of the variability of radiation use efficiency and primary productivity across terrestrial ecosystems
Authors: Garbulsky Martín F. , Peñuelas Josep , Papale Dario , Ardö Jonas , Goulden Michael L. , Kiely Gerard , Richardson Andrew D. , Rotenberg Eyal , Veenendaal Elmar M. , Filella Iolanda 
Published: December 2009

ABSTRACTAim  The controls of gross radiation use efficiency (RUE), the ratio between gross primary productivity (GPP) and the radiation intercepted by terrestrial vegetation, and its spatial and temporal variation are not yet fully understood. Our objectives were to analyse and synthesize the spatial variability of GPP and the spatial and temporal variability of RUE and its climatic controls for a wide range of vegetation types.Location  A global range of sites from tundra to rain forest.Methods  We analysed a global dataset on photosynthetic uptake and climatic variables from 35 eddy covariance (EC) flux sites spanning between 100 and 2200 mm mean annual rainfall and between −13 and 26°C mean annual temperature. RUE was calculated from the data provided by EC flux sites and remote sensing (MODIS).Results  Rainfall and actual evapotranspiration (AET) positively influenced the spatial variation of annual GPP, whereas temperature only influenced the GPP of forests. Annual and maximum RUE were also positively controlled primarily by annual rainfall. The main control parameters of the growth season variation of gross RUE varied for each ecosystem type. Overall, the ratio between actual and potential evapotranspiration and a surrogate for the energy balance explained a greater proportion of the seasonal variation of RUE than the vapour pressure deficit (VPD), AET and precipitation. Temperature was important for determining the intra‐annual variability of the RUE at the coldest energy‐limited sites.Main conclusions  Our analysis supports the idea that the annual functioning of vegetation that is adapted to its local environment is more constrained by water availability than by temperature. The spatial variability of annual and maximum RUE can be largely explained by annual precipitation, more than by vegetation type. The intra‐annual variation of RUE was mainly linked to the energy balance and water availability along the climatic gradient. Furthermore, we showed that intra‐annual variation of gross RUE is only weakly influenced by VPD and temperature, contrary to what is frequently assumed. Our results provide a better understanding of the spatial and temporal controls of the RUE and thus could lead to a better estimation of ecosystem carbon fixation and better modelling.
Scandalous Scarcities: Black Slave Women, Plantation Domesticity, and Travel Writing in Nineteenth‐Century Cuba
Authors: FINCH AISHA K. 
Published: December 2009

AbstractThis article draws on the writing of North American and European travelers to illustrate the ways in which enslaved black women became central to Cuba's visions of colonial prosperity in the mid‐nineteenth century. Such literature highlights the anxieties that plagued Cuban colonial elites as the slave trade consistently brought fewer African women than men to the island. As mothers, wives, and caretakers of domestic space, black and African women became critical to planters' dreams of continued wealth and stability. To further encourage this idealized culture of respectable domesticity, white Cuban elites erected slave cabins and barracks whose physical arrangements could increase slaves' compulsion to marry, and enhance managers' ability to survey and oversee the enslaved populations. Thus white Cuban elites hoped that enslaved women – and the ideas about marriage, home, and family such women were thought to inspire – would help to produce plantation regimes as orderly and disciplined as they were prosperous.