bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methods for Detection ofAlternaria padwickiiin Rice Seeds
Authors: Gutiérrez Susana Alejandra , Carmona Marcelo Anibal , Reis Erlei Melo 
Published: December 2009

AbstractThe fungusAlternaria padwickiihas been frequently detected in seed tests of rice collected from commercial crops in Corrientes Province, Argentina. This pathogen causes germination inhibition, seedling death or spotted grains and is the causal agent ofAlternarialeaf spot. The pathogen survives as mycelia and sclerotia on seeds, plant debris and soil. Four detection methods were compared in laboratory tests, to select the best for a quick identification of the fungus in seeds. The methods were (i) Blotter Test (ii) Potato glucose agar, (iii) Bean agar (BA) and (iv) Malt extract agar. Twenty seed samples of different varieties of rice collected from Empedrado, Goya, Itá Ibaté, La Cruz, Mercedes, Paso de los Libres and Perugorría localities (Corrientes, Argentina), were analyzed in the assays. Theanovatest and the Tukey multiple range test were applied on the data to compare theA. padwickiiincidence among the varieties and detection methods. BA method was found more sensitive than other methods forA. padwickii. The incidence values ranged from 3.6 to 76%. The statistical analysis demonstrated that the BA method was the most efficient for the detection of seed pathogens, and it could be useful in studies of transmission and chemical control.
Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogenous 2000 km2 area
Authors: Jezberová Jitka , Jezbera Jan , Brandt Ulrike , Lindström Eva S. , Langenheder Silke , Hahn Martin W. 
Published: December 2009

SummaryWe present a survey on the distribution and habitat range of Polynucleobacter necessarius ssp. asymbioticus (PnecC), a numerically and functionally important taxon in the plankton of freshwater systems. We systematically sampled stagnant freshwater habitats in a heterogeneous 2000 km2 area, together with ecologically different habitats outside this area. In total, 137 lakes, ponds and puddles were investigated, which represent an enormous diversity of habitats differing, e.g. in depth (< 10 cm – 171 m) and pH (3.9–8.5). PnecC bacteria were detected by cultivation‐independent methods in all investigated habitats, and their presence was confirmed by cultivation of strains from selected habitats representing the whole studied ecological range. The determined relative abundance of the subspecies ranged from values close to the detection limit of FISH (0.2%) to 67% (average 14.5%), and the highest observed absolute abundance was 5.3 × 106 cells ml−1. Statistical analyses revealed that the abundance of PnecC bacteria was partially controlled by factors linked to concentrations of humic substances, which support the hypothesis that these bacteria utilize photodegradation products of humic substances. Based on the revealed statistical relationships, an average relative abundance of this subspecies of 20% in global freshwater habitats was extrapolated. Our study provides important implications for the current debate on ubiquity and biogeography in microorganisms.
Minimal anatomical disruption in stoma formation: the lateral rectus abdominis positioned stoma (LRAPS)
Authors: Stephenson B. M. , Evans M. D. , Hilton J. , McKain E. S. , Williams G. L. 
Published: December 2009

AbstractAim  Parastomal hernias are difficult to manage and recent attention has focused on their prevention including the use of prophylactic mesh at the time of initial surgery.Method  A novel ‘anatomical’ approach to stoma formation, the lateral rectus abdominis positioned stoma (LRAPS), involving minimal anterior abdominal wall disruption is described.Results  LRAPS was carried out electively (n = 25) or as an emergency (n = 4) for benign or malignant pathology. Twenty‐two had a midline laparotomy and all types of stomas were fashioned. There were two early and three later deaths from advanced malignancy. No parastomal hernias have been detected at a mean follow‐up of 13 (range 7–18) months and none detected by CT scanning in 20 of 24 patients with colorectal cancer at a mean follow‐up of 14 (range 10–18) months.Conclusion  LRAPS reduces the incidence of early stomal herniation.
Skin peptide defences of New Zealand frogs against chytridiomycosis
Authors: Melzer S. , Bishop P. J. 
Published: December 2009

AbstractOver the past few decades, amphibian populations have undergone drastic declines on a global scale. Declines in many anuran populations have been linked to the emergent skin‐invasive amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). Antimicrobial peptides in the skin are thought to act as important components of the innate immune system that may protect some species from infectious diseases. The four archaic species of Leiopelma in New Zealand are of great conservation concern and a severe population crash of Leiopelma archeyi between 1996 and 2001 has been tentatively linked with the outbreak of Bd. Here, we investigated the in vitro activity of skin secretions of six frog species in New Zealand against Bd zoospore growth. The activity of skin secretions produced by frogs in the wild varied significantly between species, with those of Le. archeyi being the most active. The skin secretions of native Leiopelmatid species showed greater Bd zoospore inhibition (31.0–71.9%) than the naturalized Litoria species (17.4–18.2%). Leiopelma archeyi has the most active peptides, even though it is the only native species with known susceptibility to Bd infections.
Prevalence of interictal psychiatric disorders in patients with refractory temporal and extratemporal lobe epilepsy in Spain. A comparative study
Authors: Sanchez‐Gistau Vanessa , Pintor Luis , Sugranyes Gisela , Baillés Eva , Carreño Mar , Donaire Antonio , Boget Teresa , Setoain Xavier , Bargalló Nuria , Rumia Jordi 
Published: December 2009

SummaryWe aim to investigate whether temporal origin of epilepsy increases the risk of developing a psychiatric disorder and more specifically a major depressive disorder. The lack of standardized diagnostic instruments and the methodologic differences between studies highlight the fact that this issue warrants further, systematic, study. Three‐hundred eight patients with complex partial seizures were classified according to temporal or extratemporal origin, following the Commission on Classification and Terminology of the International League Against Epilepsy (ILAE), 1989 localization‐related concept. All patients were assessed using the Structured Interview for DSM‐IV axis I psychiatric disorders (SCID‐I). Lifetime and previous‐year prevalence of psychiatric disorders were compared in temporal and extratemporal subgroups, using multivariate analysis. Previous‐year major depression was significantly associated with temporal lobe origin. Our results do not support the hypothesis that patients with temporal lobe epilepsy (TLE) have more psychiatric illness in general, although they do suggest a specific connection between TLE and major depression.
Cortical Thinning in Vascular Mild Cognitive Impairment and Vascular Dementia of Subcortical Type
Authors: Seo Sang Won , Ahn Jaewon , Yoon Uicheul , Im Kiho , Lee Jong‐Min , Tae Kim Sung , Ahn Hyun‐Jung , Chin Juhee , Jeong Yong , Na Duk L. 
Published: December 2009

ABSTRACTBACKGROUND AND PURPOSE Amnestic mild cognitive impairment (MCI) is known to be a preclinical stage of Alzheimer's disease (AD). Similarly, MCI associated with small‐vessel disease (svMCI), might be a forme froste of subcortical vascular dementia (SVaD). Patterns of cortical thinning in addition to the ischemia rating on MRI may further elucidate the clinical characteristics and pathogenesis of SVaD and svMCI. We tried to determine if svMCI differs from SVaD in the distribution of cortical atrophy, which may help understand the hierarchy between svMCI and SVaD and possibly also how svMCI evolves into SVaD. METHODS Twenty patients with SVaD, 34 patients with svMCI, 115 patients with AD, and 96 individuals with normal‐cognition (NC) were imaged with magnetic resonance imaging (MRI) including 3‐dimensional volumetric images for cortical thickness analysis across the entire brain. RESULTS Compared to NC, svMCI patients showed cortical thinning in inferior frontal and orbitofrontal gyri, anterior cingulate, insula, superior temporal gyrus, and lingual gyrus, while cortical thinning in SVaD patients involved all these areas plus dorsolateral prefrontal and temporal cortices. CONCLUSION Our findings suggest the presence of hierarchy between svMCI and SVaD, and that the cognitive decline from svMCI to SVaD is associated with lesions in dorsolateral prefrontal and temporal cortices.
Correlation between Cognitive Deficits and Glucose Hypometabolism in Mild Cognitive Impairment
Authors: Nishi Hiroko , Sawamoto Nobukatsu , Namiki Chihiro , Yoshida Hidefumi , Thuy Dinh Ha Duy , Ishizu Koichi , Hashikawa Kazuo , Fukuyama Hidenao 
Published: December 2009

ABSTRACTBACKGROUND In patients with mild cognitive impairment (MCI), poor performances on delayed recall and executive function are risk factors of progression to dementia. The aim of the present study was to clarify neural correlates of these neuropsychological deficits. METHODS Thirty patients with amnestic MCI and 15 control subjects underwent neuropsychological tests including three‐word delayed recall, visual delayed recall of Rey complex figure (RCF), and two‐relational reasoning of Raven's colored progressive matrices (RCPM) with a 18F‐fluorodeoxyglucose (FDG)‐position emission tomography (PET) measurement of resting state. We evaluated a relationship between performance of neuropsychological tests and regional cerebral glucose metabolism using voxel‐based analysis. RESULTS Poor performance in three‐word delayed recall was related to glucose hypometabolism in the right medial temporal, right prefrontal, and left superior parietal cortices. The deficit in visual delayed recall of RCF correlated positively with hypometabolism in the bilateral posterior cingulate. The impairment in two‐relational reasoning was associated with hypometabolism in the right prefrontal cortex. CONCLUSIONS The present findings suggest that hypometabolism in the right medial temporal cortex, right prefrontal cortex, left superior parietal cortex, and bilateral posterior cingulate reflects impairments in delayed recall while hypometabolism in the right prefrontal cortex mirrors deficits in executive function in MCI. J Neuroimaging 2010;20:29‐36.
New chloroplast primers for intraspecific variation in Dicranum scoparium Hedw. (Dicranaceae) and amplification success in other bryophyte species
Authors: LANG A. , NACIRI Y. 
Published: December 2009

AbstractPrimers for four loci that amplify cpDNA regions have been designed for population genetic analyses in Dicranum scoparium Hedw. and compared with trnL(UAA)5′exon‐trnF. All loci showed intraspecific variation with a number of haplotypes ranging between two and six. trnH‐psbADic showed an intercontinental disjunction, but no variability within the four Swiss populations surveyed, whereas the three remaining loci displayed intrapopulation variability in at least one population (rps19‐rpl2, rpoB, trnT‐rps4). These primers were additionally tested on 22 bryophytes and three fern species. The primers amplified mostly in mosses and liverworts, but less well in ferns, pointing to their evolutionary distance from the bryophytes.
fHANT‐AC genes of the ectomycorrhizal fungus Laccaria bicolor are not repressed by l‐glutamine allowing simultaneous utilization of nitrate and organic nitrogen sources
Authors: Kemppainen Minna J. , Alvarez Crespo Maria C. , Pardo Alejandro G. 
Published: December 2009

SummaryIn boreal and temperate forest ectomycorrhizal fungi play a crucial role in nitrogen cycling by assimilating nitrogenous compounds from soil and transferring them to tree hosts. The expression profile of fHANT‐AC genes, nitrate transporter (Lbnrt), nitrate reductase (Lbnr) and nitrite reductase (Lbnir), responsible for nitrate utilization in the ectomycorrhizal fungus Laccaria bicolor, was studied on variable N regimens. The three genes were shown to be under a common regulation: repressed in the presence of ammonium while growth on nitrate resulted in high transcripts accumulation. The presence of nitrate was shown not to be indispensable for activation of Laccaria fHANT‐AC as also N starvation and growth on urea and l‐asparagine resulted in high transcript levels. Equally high expression of Laccaria fHANT‐AC genes was detected in mycelia grown on variable concentrations of l‐glutamine. This finding shows that in L. bicolor N metabolite repression of fHANT‐AC is not signalled via l‐glutamine like described in ascomycetes. The expression patterns of Lbnrt and Lbnir were also studied in an Lbnr RNA‐silenced Laccaria strain. No differences were observed on the N source regulation or the degree of transcript accumulation of these genes, indicating that the presence of high nitrate reductase activity is not a core regulator of L. bicolor fHANT‐AC expression. The simultaneous utilization of nitrate and organic N sources, already suggested by high transcript levels of Laccaria fHANT‐AC genes on organic N, was supported by the increase of culture medium pH as a result of nitrate transporter activity. The possible ecological and evolutionary significance of the herein reported high regulatory flexibility of Laccaria nitrate utilization pathway for ectomycorrizal fungi and the ectomycorrhizal symbiosis is discussed.
Mitochondrial KATPopening confers protection against lethal myocardial injury and ischaemia-induced arrhythmias in the rat heart via PI3K/Akt-dependent and -independent mechanismsThis article is one of a selection of papers published in a special issue on Advances in Cardiovascular Research.
Authors: Matejíková Jana , Ravingerová Táňa , Pancza Dezider , Čarnická Slávka , Kolář František 
Published: December 2009

Opening of mitochondrial KATPchannels (mitoKATP) has been reported to underlie protection against ischaemia–reperfusion injury induced by ischaemic preconditioning (I-PC); however, the molecular mechanisms of its antiarrhythmic effect have not been fully elucidated. We explored the involvement of phosphatidylinositol 3-kinase (PI3K)/Akt in the PC-like effect of mitoKATPopener diazoxide with particular regard to its role in protection against ischaemia-induced arrhythmias. Langendorff-perfused rat hearts were subjected to 30 min LAD occlusion with or without a prior 15 min of perfusion with diazoxide (50 µmol/L) given either alone (D-PC) or in combination with the PI3K/Akt inhibitor wortmannin (100 nmol/L). In an additional protocol, ischaemia was followed by 2 h reperfusion for infarct size (IS) determination (tetrazolium staining). The total number of premature ventricular complexes over the whole period of ischaemia, episodes of ventricular tachycardia and its duration were significantly lower in the D-PC group than in the non-preconditioned controls (158 ± 20, 2 ± 0.6 and 4.6 ± 1.8 s vs. 551 ± 61, 11 ± 2 and 42 ± 8 s, respectively; p < 0.05), concomitant with a 62% reduction in the size of infarction. Wortmannin modified neither arrhythmogenesis nor IS in the non-preconditioned hearts. Bracketing of diazoxide with wortmannin did not reverse the antiarrhythmic protection, whereas the IS-limiting effect was blunted. The results indicate that in contrast with the positive role of PI3K/Akt in protection against lethal myocardial injury, its activity is not involved in suppression of ischaemia-induced arrhythmias conferred by mitoKATPopening in the rat heart.
A new measurement of sequence conservation
Authors: Cai Xiaohui , Hu Haiyan , Li Xiaoman 
Published: December 2009

Abstract

Background
Understanding sequence conservation is important for the study of sequence evolution and for the identification of functional regions of the genome. Current studies often measure sequence conservation based on every position in contiguous regions. Therefore, a large number of functional regions that contain conserved segments separated by relatively long divergent segments are ignored. Our goal in this paper is to define a new measurement of sequence conservation such that both contiguously conserved regions and discontiguously conserved regions can be detected based on this new measurement. Here and in the following, conserved regions are those regions that share similarity higher than a pre-specified similarity threshold with their homologous regions in other species. That is, conserved regions are good candidates of functional regions and may not be always functional. Moreover, conserved regions may contain long and divergent segments.

Results
To identify both discontiguously and contiguously conserved regions, we proposed a new measurement of sequence conservation, which measures sequence similarity based only on the conserved segments within the regions. By defining conserved segments using the local alignment tool CHAOS, under the new measurement, we analyzed the conservation of 1642 experimentally verified human functional non-coding regions in the mouse genome. We found that the conservation in at least 11% of these functional regions could be missed by the current conservation analysis methods. We also found that 72% of the mouse homologous regions identified based on the new measurement are more similar to the human functional sequences than the aligned mouse sequences from the UCSC genome browser. We further compared BLAST and discontiguous MegaBLAST with our method. We found that our method picks up many more conserved segments than BLAST and discontiguous MegaBLAST in these regions.

Conclusions
It is critical to have a new measurement of sequence conservation that is based only on the conserved segments in one region. Such a new measurement can aid the identification of better local "orthologous" regions. It will also shed light on the identification of new types of conserved functional regions in vertebrate genomes [1].
Survival of cancer patients treated with mistletoe extract (Iscador): a systematic literature review
Authors: Ostermann Thomas , Raak Christa , Büssing Arndt 
Published: December 2009

Abstract

Background
In Europe, extracts from Viscum album (VA-E), the European white-berry mistletoe, are widely used to treat patients with cancer.

Methods
We searched several databases such as Cochrane, EMBASE, NCCAM, NLM, DIMDI, CAMbase, and Medline. Inclusion criteria were controlled clinical studies on parameters associated with survival in cancer patients treated with Iscador. Outcome data were extracted as they were given in the publication, and expressed as hazard ratios (HR), their logarithm, and the respective standard errors using standard formulas.

Results
We found 49 publications on the clinical effects of Iscador usage on survival of cancer patients which met our criteria. Among them, 41 studies and strata provided enough data to extract hazard ratios (HR) and their standard errors (Iscador versus no extra treatment). The majority of studies reported positive effects in favour of the Iscador application. Heterogeneity of study results was moderate (I2 = 38.3%, p < 0.0001). The funnel plots were considerably skewed, indicating a publication bias, a notion which is corroborated by statistical means (AC = -1.3, CI: -1.9 to -0.6, p <= 0.0001). A random effect meta-analysis estimated the overall hazard ratio at HR = 0.59 (CI: 0.53 to 0.66, p < 0.0001). Randomized studies showed less effects than non-randomized studies (ratio of HRs: 1.24, CI: 0.79 to 1.92, p = 0.35), and matched-pair studies gave significantly better results than others (ratio of HRs: 0.33; CI: 0.17 to 0.65, p = 0.0012).

Conclusions
Pooled analysis of clinical studies suggests that adjuvant treatment of cancer patients with the mistletoe extract Iscador is associated with a better survival. Despite obvious limitations, and strong hints for a publication bias which limits the evidence found in this meta-analysis, one can not ignore the fact that studies with positive effects of VA-E on survival of cancer patients are accumulating. Future studies evaluating the effects of Iscador should focus on a transparent design and description of endpoints in order to provide greater insight into a treatment often being depreciated as ineffective, but highly valued by cancer patients.
Depot-specific differences in perilipin and hormone-sensitive lipase expression in lean and obese
Authors: Ray Hind , Pinteur Claudie , Frering Vincent , Beylot Michel , Large Valérie 
Published: December 2009

Abstract

Background
Mainly dependent on hormone-sensitive lipase, lipolysis is differently impaired between fat depots in human obesity. Perilipin A expression is a critical element in adipocyte lipolysis. The present study aimed at comparing expression and subcellular distribution of perilipin and hormone-sensitive lipase in two abdominal adipose tissues of lean and obese women. We examined whether regional differences in perilipin expression contribute to impaired lipolytic rates.

Methods
Abdominal subcutaneous and omental adipose tissues were obtained from six lean and ten obese women. We measured total protein content and relative distribution of hormone-sensitive lipase and perilipin proteins between lipid and non-lipid fractions in tissue homogenates. Hormone-sensitive lipase and perilipin mRNA levels, adipocyte size, basal (non-stimulated) and noradrenaline-stimulated lipolysis in isolated adipocytes were determined.

Results
Adipocytes were significantly larger in the obese versus the lean women and in subcutaneous versus omental fat. Expressed as a function of cell number, basal lipolysis and noradrenaline responsiveness were higher in subcutaneous versus omental adipocytes from the obese women (P < 0.05). Despite higher or identical mRNA levels in the lean and the obese subjects and in subcutaneous and omental tissues, perilipin protein expression was lower in both depots in the obese versus the lean women, and in subcutaneous versus omental in both lean and obese women (P < 0.05). Perilipin was mostly (above 80%) present in the lipid fraction in both depots from the obese patients and the value decreased to 60% in the lean subjects (P < 0.05). Perilipin protein expression was inversely correlated to adipocyte size and basal lipolysis in both depots. Despite higher mRNA levels, hormone-sensitive lipase protein expression decreased in both depots of the obese women. Regional difference for hormone-sensitive lipase was reported in lipid fraction of subcutaneous fat of the obese subjects: hormone-sensitive lipase content was twice as low as in omental adipose tissue.

Conclusion
In both fat depots, a reduced perilipin protein expression was observed in women obesity. Perilipin protein level may contribute to differences in basal lipolysis and in adipocyte size between fat depots and may regulate lipid accumulation in adipocytes. Differences in hormone-sensitive lipase subcellular distribution were reported between fat depots in the obese women.