bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity, aggressiveness and metalaxyl sensitivity of Pythium aphanidermatum populations infecting cucumber in Oman
Authors: Al‐Sa'di A. M. , Drenth A. , Deadman M. L. , Aitken E. A. B. 
Published: September 2007

Seventy three isolates of Pythium aphanidermatum obtained from cucumber from four different regions of Oman and 16 isolates of muskmelon from the Batinah region in Oman were characterized for aggressiveness, sensitivity to metalaxyl and genetic diversity using AFLP fingerprinting. Twenty isolates of P. aphanidermatum from diverse hosts from different countries were also included in the study. Most isolates from Oman were found to be aggressive on cucumber seedlings and all were highly sensitive to metalaxyl (EC50 < 0·80 µg mL−1). Isolates from cucumber and muskmelon were as aggressive as each other on both hosts (P > 0·05), which implies a lack of host specialization in P. aphanidermatum on these two hosts in Oman. AFLP analysis of all isolates using four primer–pair combinations resolved 152 bands, of which 61 (~40%) were polymorphic. Isolates of P. aphanidermatum from Oman and other countries exhibited high genetic similarity (mean = 94·1%) and produced 59 different AFLP profiles. Analysis of molecular variance indicated that most AFLP variation among populations of P. aphanidermatum in Oman was associated with geographical regions (FST = 0·118; P < 0·0001), not hosts (FST = –0·004; P = 0·4323). These data were supported by the high rate of recovery (24%) of identical phenotypes between cucumber and muskmelon fields in the same region as compared to the low recovery (10%) across regions in Oman, which suggests more frequent movement of Pythium inoculum among muskmelon and cucumber fields in the same region compared to movement across geographically separated regions. However, recovering clones among regions and different countries may imply circulation of Pythium inoculum via common sources in Oman and also intercontinental spread of isolates.
Reanalysis of sequence‐based HLA‐A, ‐B and ‐Cw typings: how ambiguous is today’s SBT typing tomorrow
Authors: Voorter C. E. M. , Mulkers E. , Liebelt P. , Sleyster E. , Van Den Berg‐Loonen E. M. 
Published: September 2007

AbstractThe permanently increasing number of human leukocyte antigen (HLA)‐alleles and the growing list of ambiguities require continuous updating of high‐resolution HLA typing results. Two different kinds of ambiguities exist: the first, when two or more allele combinations have identical heterozygous sequences, and the second, when differences are located outside the analyzed region. The number of HLA‐A, B and C alleles recognized in 1999 was almost tripled in 2006. Two hundred individuals, sequence‐based typing (SBT) typed in the period from 1999 to 2002, were reanalyzed using the 2006 database. A final allele typing result of at least four digits was obtained for HLA‐A, ‐B and ‐C by heterozygous sequencing of exons 2 and 3 and, if necessary, additional exons and/or allele‐specific sequencing. Storage of the individual sequences in a specially developed database enabled reanalysis with all present and future HLA releases. In the 5‐year period HLA‐A, ‐B and ‐C typing results became ambiguous in 37%, 46% and 41% of the cases. Most were because of differences outside the analyzed region; ambiguities because of different allele combinations with identical heterozygous sequences were present in 7%, 8% and 13% of the HLA‐A, ‐B and ‐C typings. These results indicate that within 5 years, approximately half of the HLA SBT typings become ambiguous.
Plasma adiponectin is associated with ankle‐brachial index in patients on haemodialysis
Authors: LIM PAIK‐SEONG , HU CHUEN‐YUH , WU MING‐YING , WU TSAI‐KUN , CHANG HUI‐CHEN 
Published: September 2007

SUMMARY:Background:  Peripheral arterial disease (PAD) is a leading cause of morbidity in haemodialysis (HD) patients. Recent evidence suggests that adiponectin, an adipose‐derived cytokine, may play a role in atherosclerosis. However, the association between plasma levels of the adiponectin and the ankle‐brachial index (ABI), an indicator of the presence and severity of PAD, has not been thoroughly studied in HD patients.Methods:  The present cross‐sectional study attempted to examine the relationship between plasma adiponectin and PAD in a cohort of 136 chronic HD patients. The ABI was used as an estimate of the presence of PAD. Plasma adiponectin, high‐sensitivity C‐reactive protein (hsCRP), tumour necrosis factor‐α and lipid profiles were measured. Logistic regression was used to estimate the association between presence of PAD and adiponectin as well as other potential risk factors.Results:  Plasma levels of adiponectin were significantly lower among patients with evidence of PAD than among those without (8.51 ± 5.75 vs 17.15 ± 11.53; P < 0.001). Univariate analysis showed a positive correlation between ABI values and plasma adiponectin levels (r = 0.369, P < 0.001), high‐density lipoprotein cholesterol levels, diastolic blood pressure, Kt/V and serum phosphate. On the other hand, negative correlations between ABI and log‐transformed triglyceride, hsCRP, fasting blood sugar, girth circumference and white blood cell counts were noted. Using logistic regression, plasma adiponectin was found to be associated with PAD independently of classical risk factors for atherosclerosis. In addition, models that incorporated plasma adiponectin were significantly better at predicting PAD than models limited to classical confounding factors.Conclusion:  We conclude that there was a significant inverse correlation between plasma adiponectin levels and the presence of PAD in dialysis patients. This suggests that plasma adiponectin level may have a role in the atherosclerotic process of PAD.
Increased levels of serum matrix metalloproteinase‐3 in haemodialysis patients with dialysis‐related amyloidosis
Authors: NAGANUMA TOSHIHIDE , SUGIMURA KAZUNOBU , UCHIDA JUNJI , TASHIRO KOICHIRO , YOSHIMURA RIKIO , TAKEMOTO YOSHIAKI , NAKATANI TATSUYA 
Published: September 2007

SUMMARY:Background:  It is recognized that matrix metalloproteinase‐3 (MMP‐3) is abundantly expressed in active rheumatoid synovium, and that serum level of MMP‐3 is a useful marker for diagnosis of rheumatoid arthritis and for evaluation of prognosis in joint destruction. Little is known about serum MMP‐3 levels in haemodialysis (HD) patients, and thus, the association between serum MMP‐3 and dialysis‐related amyloidosis (DRA) has yet to be elucidated.Methods:  Serum levels of MMP‐3 were measured by enzyme immunoassay in 150 HD patients, 90 without DRA and 60 with DRA, before HD. Simple regression analysis was performed to investigate the relationship between serum level of MMP‐3 and clinical parameters, including age, HD duration, C‐reactive protein and β2 microglobulin (BMG).Results:  Serum levels of MMP‐3 were significantly higher in HD patients with DRA than in HD patients without DRA (258.2 ± 118.1 vs 201.5 ± 98.4 pg/mL, P = 0.0017), and both levels were significantly higher than those of healthy subjects (45.6 ± 13.4 pg/mL, P < 0.0001). Serum MMP‐3 levels significantly correlated with serum levels of BMG (r = 0.197, P = 0.0164) and HD duration (r = 0.168, P = 0.0427). Moreover, serum MMP‐3 levels significantly correlated with serum BMG levels in HD patients without DRA (r = 0.341, P = 0.0012), but not in HD patients with DRA.Conclusion:  Our results suggest that matrix metalloproteinase activity increases in HD patients, which may be associated with BMG and DRA.
Disturbance of lymph circulation develops renal fibrosis in rats with or without contralateral nephrectomy
Authors: ZHANG TAOYAN , GUAN GUANGJU , LIU GANG , SUN JINGCANG , CHEN BIN , LI XUEGANG , HOU XIANGHUA , WANG HAIPING 
Published: September 2007

SUMMARY:Background:  The knowledge on renal lymphatics is very limited and their importance is often neglected in kidney transplantation surgery practice. Early papers demonstrated that acute ligation of hilar lymphatic ducts has a significant effect on sodium excretion and urine volume. However, the long‐term effects of hilar lymphatic ducts ligation on renal function and histology were not mentioned. Here we show the time course of renal lesions caused by long‐term ligation of renal hilar lymphatic vessels in rats with or without contralateral nephrectomy.Methods:  Animals were divided into three groups: rats with bilateral renal lymphatic ducts ligation (2KL); rats with one renal ligation and another nephrectomy (1KL); sham‐operated rats (Sham). Proteinuria, serum creatinine value and creatinine clearance were monitored. Renal histology was examed by light microscopy. Further biochemical analysis was provided using real‐time polymerase chain reaction, immunostaining and western blot techniques.Results:  From week 1 after ligation, both 1KL and 2KL rats developed severe proteinuria, whereas elevated serum creatinine and reduced creatinine clearance were observed from week 2. Histomorphological changes appeared in ligated kidneys at week 2, characterized by tubular damage, tubulointerstitial fibrosis and expansion of the mesangium. Overexpression of transforming growth factor‐β1 (TGF‐β1), Smad2/3, COL I genes and proteins were detected in 1KL and 2KL rats. Compared with 2KL rats, the changes in renal function and histology were more pronounced in 1KL rats.Conclusion:  Disturbance of lymph circulation induced chronic renal failure and renal fibrosis, which were aggravated by lymphatic vessels ligation combined with contralateral nephrectomy. The effect of lymphatic ducts ligation on renal lesions may be explained by enhanced activation of the TGF‐β1/Smad signalling.
High prevalence of ascorbate deficiency in an Australian peritoneal dialysis population
Authors: SINGER RICHARD , RHODES HELEN C , CHIN GEORGE , KULKARNI HEMANT , FERRARI PAOLO 
Published: September 2007

SUMMARY:Background:  An adequate total body pool of ascorbate is essential for optimum health in humans. Requirements for ascorbate are increased in peritoneal dialysis (PD) patients most likely due to a combination of poor nutrition and increased dialysate losses.Methods:  We measured serum ascorbate levels in 45 clinically stable PD patients to assess the prevalence of ascorbate insufficiency (level between 2 and 4 mg/L) and deficiency (level <2 mg/L). We also assessed the efficacy of subsequent supplementation and patients' adherence to the prescribed supplementation. All patients were advised on commencement of dialysis to take a multivitamin tablet containing 100–120 mg ascorbate.Results:  Eighteen (41%) PD patients were regularly taking ascorbate‐containing multivitamins, while 27 (59%) patients did not take ascorbate supplements. Serum ascorbate levels ranged from <0.2 to 41 mg/L, with wide variations in serum ascorbate at any given intake level. Ascorbate deficiency was present in 1/3 of the current PD population (44% of patients not taking supplements and in 16% of those on supplements), although none of the patients demonstrated clinical manifestations of scurvy. Targeted supplementation of ascorbate insufficient patients increased the median serum ascorbate level from 1.7 mg/L (IQR 1.2–2.2) to 22.5 mg/L (IQR 16.7–32.9).Conclusion:  Our results show that, in PD patients, ascorbate deficiency is common and can readily be identified with serum ascorbate measurements. Oral supplements in the form of inexpensive multivitamin preparations restore adequate serum ascorbate levels in the majority of these patients. We therefore suggest measurement of ascorbate levels in all PD patients at the commencement of dialysis with a target level in the normal range (4–14 mg/L).
Association of cytokine polymorphisms with subclinical progressive chronic allograft nephropathy in Japanese renal transplant recipients: Preliminary study
Authors: Satoh Shigeru , Saito Mitsuru , Inoue Kazuyuki , Miura Masatomo , Komatsuda Atsushi , Habuchi Tomonori 
Published: September 2007

Background:  The present study calculated the risk of developing subclinical progressive chronic/sclerosing allograft nephropathy (CAN) under tacrolimus‐based immunosuppression according to genetic polymorphisms of cytokines and growth factors, and clinical events including delayed graft function (DGF), acute rejection (AR) and cytomegalovirus (CMV) infection.Methods:  The subjects were 50 recipients with stable graft function more than one year after renal transplantation. The criteria for subclinical progressive CAN were CAN grade 2 or 3 changes on Banff classification and stable serum creatinine (SCr) levels. Ten genetic polymorphisms were assessed.Results:  Eleven patients (22.0%) developed progressive CAN. The mean ages and SCr levels of recipients with and without progressive CAN were 41.2 and 47.1 years, and 1.46 and 1.22 mg/dL, respectively. There were no significant differences in donor age, number of HLA mismatches, DGF or CMV infection. Although the rate of AR episode seemed to be greater in patients with subclinical progressive CAN, the difference did not reach significance (P = 0.093). The frequencies of the interleukin (IL)‐2 T‐330G TT genotype (P = 0.046) and IL‐4 C‐590T C allele (P = 0.092) were higher in patients with progressive CAN. In univariate analysis, the presence of IL‐2 T‐330G TT (OR 4.57, P = 0.044) was associated with CAN development.Conclusion:  The presence of IL‐2 T‐330G TT genotype may be a risk factor for CAN. Further studies with a large number of subjects and analyses of many cytokine polymorphisms would contribute to the ability to make prognostic determinations or tailor immunomodulatory regimens after renal transplantation.
Biomarkers at the microscopic range: ToF‐SIMS molecular imaging of Archaea‐derived lipids in a microbial mat
Authors: THIEL V. , HEIM C. , ARP G. , HAHMANN U. , SJÖVALL P. , LAUSMAA J. 
Published: September 2007

ABSTRACTTime‐of‐Flight Secondary Ion Mass Spectrometry (ToF‐SIMS) with a bismuth cluster primary ion source was used for analysing microbial lipid biomarkers in 10‐µm‐thick microscopic cryosections of methanotrophic microbial mats from the Black Sea. Without further sample preparation, archaeal isopranyl glycerol di‐ and tetraether core lipids, together with their intact diglycoside (gentiobiosyl‐) derivatives, were simultaneously identified by exact mass determination. Utilizing the imaging capability of ToF‐SIMS, the spatial distributions of these biomarkers were mapped at a lateral resolution of < 5 µm in 500 × 500 µm2 areas on the mat sections. Using cluster projectiles in the burst alignment mode, it was possible to reach a lateral resolution of 1 µm on an area of 233 × 233 µm, thus approaching the typical size of microbial cells. The mappings showed different ‘provenances’ within the sections that are distinguished by individual lipid fingerprints, namely (A) the diethers archaeol and hydroxyarchaeol co‐occurring with glycerol dialkyl glycerol tetraethers (GDGT), (B) hydroxyarchaeol and dihydroxyarchaeol, and (C) GDGT and gentiobiosyl‐GDGT. Because ToF‐SIMS is a virtually nondestructive technique affecting only the outermost layers of the sample surface (typically 10–100 nm), it was possible to further examine the studied areas using conventional microscopy, and associate the individual lipid patterns with specific morphological traits. This showed that provenance (B) was frequently associated with irregular, methane‐derived CaCO3 crystallites, whereas provenance (C) revealed a population of fluorescent, filamentous microorganisms showing the morphology of known methanotrophic ANME‐1 archaea. The direct coupling of imaging mass spectrometry with microscopic techniques reveals interesting perspectives for the in‐situ study of lipids in geobiology, microbial ecology, and organic geochemistry. After further developing protocols for handling different kinds of environmental samples, ToF‐SIMS could be used as a tool to attack many challenging problems in these fields, such as the attribution of biological source(s) to particular biomarkers in question, or the high‐resolution tracking of biogeochemical processes in modern and ancient natural environments.
Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan
Authors: SHIMIZU S. , AKIYAMA M. , NAGANUMA T. , FUJIOKA M. , NAKO M. , ISHIJIMA Y. 
Published: September 2007

ABSTRACTWe investigated microbial methanogenesis and community structure based on 16S rRNA gene sequences from a coal seam aquifer located 843–907 m below ground level in northern Japan; additionally, we studied the δ13C and δ2H (δD) of coal‐bed gases and other physicochemical parameters. Although isotopic analysis suggested a thermocatalytic origin for the gases, the microbial activity and community structure strongly implied the existence of methanogenic microbial communities in situ. Methane was generated in the enrichment cultures of the hydrogenotrophic and methylotrophic microorganisms obtained from coal seam groundwater. Methanogen clones dominated the archaeal 16S rRNA gene libraries and were mostly related to the hydrogenotrophic genus Methanoculleus and the methylotrophic genus Methanolobus. Bacterial 16S rRNA gene libraries were dominated by the clones related to the genera Acetobacterium and Syntrophus which have a symbiotic association with methanogens. LIBSHUFF analysis revealed that N2 gas injected into the coal seam (for enhanced methane production) does not affect the coverage of archaeal and bacterial populations. However, amova analysis does provide evidence for a change in the genetic diversity of archaeal populations that are dominated by methanogens. Therefore, N2 injection into the coal seam might affect the cycling of matter by methanogens in situ.
Early colonization of thermal niches in a silica‐depositing hot spring in central Tibet
Authors: LAU C. Y. , AITCHISON J. C. , POINTING S. B. 
Published: September 2007

ABSTRACTThermophilic microbial mats dominated by the anoxygenic phototroph Roseiflexus castenholzii commonly develop around sinter‐depositing geysers in the Daggyai Tso geothermal field of central Tibet. In this study we used morphological and molecular genetic techniques to reveal a diverse pioneer biofilm community including both archaea and bacteria involved in early colonization of such thermal niches at temperatures ranging from 46 to 77 °C. Sinter precipitation and biomineralization were evident at all locations, but the latter was selective between taxa and most evident on filamentous cells. Evidence for possible indirect biosignatures from biofilms overwhelmed by sinter deposition was found. Succession to a mature community appeared to relate to the growth rate for key taxa outpacing that of silicification within an optimum temperature range of 54–61 °C. The thin surface layer of silicification‐resistant cyanobacteria that developed on the surface of mature mats may play a role in preventing biomineralization of the susceptible R. castenholzii beneath within these communities.
The Precambrian emergence of animal life: a geobiological perspective
Authors: GAIDOS E. , DUBUC T. , DUNFORD M. , MCANDREW P. , PADILLA‐GAMIÑO J. , STUDER B. , WEERSING K. , STANLEY S. 
Published: September 2007

ABSTRACTThe earliest record of animals (Metazoa) consists of trace and body fossils restricted to the last 35 Myr of the Precambrian. It has been proposed that animals arose much earlier and underwent significant evolution as a cryptic fauna; however, the need for any unrecorded prelude of significant duration has been disputed. In this context, we consider recent published research on the nature and chronology of the earliest fossil record of metazoans and on the molecular‐based analysis that yielded older dates for the appearance of major animal groups. We review recent work on the climatic, geochemical, and ecological events that preceded animal fossils and consider their portent for metazoan evolution. We also discuss inferences about the physiology and gene content of the last common ancestor of animals and their closest unicellular relatives. We propose that the recorded Precambrian evolution of animals includes three intervals of advancement that begin with sponge‐grade organisms, and that any preceding cryptic fauna would be no more complex than sponges. The molecular data do not require that more complex animals appeared well before the recognized fossil record; nor, however, do they rule the possibility out, particularly if the interval of simpler metazoan ancestors lasted no more than about 100 or 200 Myr. The geological record of abrupt changes in climate, biogeochemistry, and phytoplankton diversity can be taken to be the result of changes in the carbon cycle triggered by the appearance and diversification of metazoans in an organic carbon‐rich ocean, but as yet no compelling evidence exists for this interpretation. By the end of this cryptic period, animals would already have possessed sophisticated systems of cell–cell signalling, adhesion, apoptosis, and segregated germ cells, possibly with a rudimentary body plan based on anterior–posterior organization. The controls on the timing and tempo of the earliest steps in metazoan evolution are unknown, but it seems likely that oxygen was a key factor in later diversification and increase in body size. We consider several recent scenarios describing how oxygen increased near the end of the Precambrian and propose that grazing and filter‐feeding animals depleted a marine reservoir of suspended organic matter, releasing a microbial ‘clamp’ on atmospheric oxygen.
Conceptual and Design Essentials for Evaluating Mechanisms of Change
Authors: Nock Matthew K. 
Published: September 2007

Background:  Considerable progress has been made toward the development of evidence‐based treatments for a wide range of psychological disorders; however, little is known about the mechanisms through which these treatments actually lead to clinical change. Although the use of traditional randomized controlled treatment designs and tests of statistical mediation have significantly advanced understanding of psychological treatments, they are insufficient to test mechanisms of change.Method:  This article outlines the conceptual and methodological requirements for evaluating mechanisms of change, highlights the importance of such a focus, and offers specific recommendations for research aimed at elucidating change mechanisms.Results and Conclusions:  Conceptualizing and conducting studies that test mechanisms of change requires substantial modifications to traditional research designs, but doing so will significantly enhance scientific understanding as well as the efficiency and effectiveness of clinical interventions.
The Search for Mechanisms of Change in Behavioral Treatments for Alcohol Use Disorders: A Commentary
Authors: Longabaugh Richard 
Published: September 2007

Background:  Definitive results from efforts to identify mechanisms of change in behavioral treatments for alcohol use disorders have been elusive. The working hypothesis guiding this paper is that one of the reasons for this elusiveness is that the models we hypothesize to account for treatments effectiveness are unnecessarily restricted and too simple.Methods:  This paper aims to accomplish 3 things. First, a typography for locating potential mediators of change will be presented. In the course of doing so, a nomenclature will be proposed with the hope that this will facilitate communications among alcohol treatment researchers studying mechanisms of change. Second, alternatives to the classic test of mediation of alcohol treatment effects will be considered and one such alternative described. Third, alternative ways of conceptualizing, constructing and analyzing variables to measure mediators will be suggested.Results:  It is hoped that this commentary will facilitate research on mechanisms of change in behavioral treatments for alcohol use disorders.Conclusions:  Behavioral change is a complex process, and the models that we develop to account for this process need to reflect this complexity. Advances in statistical approaches for testing mediation, along with a better understanding as to how to use these tools should help in moving toward this goal.