bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coral microbial communities, zooxanthellae and mucus along gradients of seawater depth and coastal pollution
Authors: Klaus James S. , Janse Ingmar , Heikoop Jeffrey M. , Sanford Robert A. , Fouke Bruce W. 
Published: February 2007

SummaryThe high incidence of coral disease in shallow coastal marine environments suggests seawater depth and coastal pollution have an impact on the microbial communities inhabiting healthy coral tissues. A study was undertaken to determine how bacterial communities inhabiting tissues of the coral Montastraea annularis change at 5 m, 10 m and 20 m water depth in varying proximity to the urban centre and seaport of Willemstad, Curaçao, Netherlands Antilles. Analyses of terminal restriction fragment length polymorphisms (TRFLP) of 16S rRNA gene sequences show significant differences in bacterial communities of polluted and control localities only at the shallowest seawater depth. Furthermore, distinct differences in bacterial communities were found with increasing water depth. Comparisons of TRFLP peaks with sequenced clone libraries indicate the black band disease cyanobacterium clone CD1C11 is common and most abundant on healthy corals in less than 10 m water depth. Similarly, sequences belonging to a previously unrecognized group of likely phototrophic bacteria, herein referred to as CAB‐I, were also more common in shallow water. To assess the influence of environmental and physiologic factors on bacterial community structure, canonical correspondence analysis was performed using explanatory variables associated with: (i) light availability; (ii) seawater pollution; (iii) coral mucus composition; (iv) the community structure of symbiotic algae; and (v) the photosynthetic activity of symbiotic algae. Eleven per cent of the variation in bacterial communities was accounted for by covariation with these variables; the most important being photosynthetically active radiation (sunlight) and the coral uptake of sewage‐derived compounds as recorded by the δ15N of coral tissue.
Functionally distinct communities of ammonia‐oxidizing bacteria along an estuarine salinity gradient
Authors: Bernhard Anne E. , Tucker Jane , Giblin Anne E. , Stahl David A. 
Published: February 2007

SummaryThe relationship between ammonia‐oxidizing bacteria (AOB) and potential nitrification rates was examined along a salinity gradient in a New England estuary in spring and late summer over 3 years. Ammonia‐oxidizing bacteria abundance was estimated by measuring gene copies of the ammonia monooxygenase catalytic subunit (amoA) using real‐time polymerase chain reaction. Ammonia‐oxidizing bacteria abundance ranged from below detection to 6.0 × 107amoA copies (gdw sediment)−1. Mean potential nitrification rates ranged from 0.5 to 186.5 nmol N (gdw sediment)−1 day−1. Both AOB abundance and potential rates were significantly higher in spring than late summer. Correlations between rates and abundance varied significantly among sites, but showed site‐specific ammonia oxidation kinetics related to AOB community structure. The effect of salinity on potential nitrification rates was evaluated by incubating sediment from each site under four salinity conditions (0, 5, 10 and 30 psu). At all sites, rates were generally highest in the intermediate salinity treatments, but rates at the upstream site were inhibited at high salinity, while rates at the two downstream sites were inhibited at the lowest salinity. Although salinity appears to be an important factor in determining AOB distribution, it may not be the primary factor as AOB exhibited a broad range of salinity tolerance in our experiments. Our results indicate that there are significant differences in abundance and community composition of AOB along the salinity gradient, and the differences are reflected in community function.
Dual‐head lithotripsy in synchronous mode: acute effect on renal function and morphology in the pig
Authors: Handa Rajash K. , McAteer James A. , Willis Lynn R. , Pishchalnikov Yuri A. , Connors Bret A. , Ying Jun , Lingeman James E. , Evan Andrew P. 
Published: February 2007

OBJECTIVETo assess the effect of dual‐head lithotripsy on renal function and morphology in a pig model of shockwave (SW) injury, as lithotripters with two shock heads are now available for treating patients, but little information is available with which to judge the safety of treatment with dual pulses.MATERIALS AND METHODSA dual‐head electrohydraulic lithotripter (Duet, Direx Corp., Natick, MA, USA) was used to treat the lower renal pole of anaesthetized pigs with a clinical dose of SWs (2400 dual SWs; 10 kidneys) delivered in synchronous mode, i.e. both heads fired simultaneously. For comparison, pigs were treated with either 2400 SWs (12 kidneys) or 4800 SWs (eight) with a conventional electrohydraulic lithotripter (HM3, Dornier, Wessling, Germany).RESULTSDual‐pulse SW treatment with the Duet lithotripter caused a decline in the mean (sd) glomerular filtration rate (GFR) of 4.1 (1.9) mL/min, with a trend for the effective renal plasma flow (RPF), at 31 (19) mL/min, to also decrease. These changes in renal haemodynamics were similar to the decreases in GFR and RPF in response to treatment with the HM3 lithotripter with 2400 SWs, at 4.8 (0.8) and 32 (10) mL/min, respectively, or 4800 SWs, at 5.4 (1.0) and 68 (14) mL/min, respectively. Linear association analysis showed that the functional response to dual‐pulse SWs was more variable than with conventional SWs. Morphological quantification of kidney damage (expressed as a percentage of functional renal volume, FRV) showed that tissue injury with 2400 paired SWs with the Duet, at 0.96 (0.39)% FRV, was similar to injury produced by either 2400 single SWs, at 1.08 (0.38)% FRV, or 4800 single SWs, at 2.71 (1.02)% FRV, with the HM3. However, morphological damage was less consistent with the Duet (measurable in only five of eight kidneys) than that with the HM3 (measurable in all 12 kidneys). Acoustic output and the timing of dual SWs in synchronous mode increased in variability as the electrodes aged, affecting the amplitude and targeting of focal pressures.CONCLUSIONWith the caveat that variability in the timing of dual SWs will unpredictably alter the distribution of SW energy within the kidney, this study shows that a clinical dose of dual‐head SWs delivered in synchronous mode elicits a renal response similar to, but more variable than, that with a clinical dose of SWs from a conventional electrohydraulic lithotripter.
An electron microscopic examination of the intravesical ureter in children with primary vesico‐ureteric reflux
Authors: Sofikerim Mustafa , Sargon Mustafa , Oruc Ozgur , Dogan Hasan S. , Tekgul Serdar 
Published: February 2007

OBJECTIVETo determine the structure of the intravesical distal ureteric wall of patients with primary vesico‐ureteric reflux (VUR), and to compare the findings with previous reports.MATERIALS AND METHODSSpecimens of the distal intravesical ureteric segments were taken surgically from children undergoing ureteric reimplantation surgery for primary VUR. There were 24 distal intravesical ureteric specimens from 15 children (nine female and six male). Ultra‐thin sections were cut from the specimens and examined with a transmission electron microscope.RESULTSThe appearance of the muscular layers of the specimens of different grades differed markedly. There were intercellular oedematous areas in the muscular layer in specimens from patients with grade 2 and 3 VUR. In specimens from grade 4 VUR there were also intracytoplasmic vacuoles in the smooth muscle cells. The most marked and striking changes were in the specimens from children with grade 5 VUR, in which there were large intercellular oedematous areas and prominent large intracytoplasmic vacuoles.CONCLUSIONRefluxing ureters differ from normal ureters in having disorganized smooth muscle fibres and altered smooth muscle cell structure, leading to incompetence of the valve mechanism. Although we cannot confirm that these pathological changes in the smooth muscle layer of the intravesical ureteric wall are caused by VUR we conclude that, with increasing degrees of reflux, the degree of smooth muscle damage increases, and that the rate of spontaneous resolution decreases.
Partial nephrectomy and autotransplantation with pyelovesicostomy for renal urothelial carcinoma in solitary kidneys: a clinical update
Authors: Steffens Joachim , Humke Ulrich , Alloussi Schahnaz , Ziegler Manfred , Siemer Stefan 
Published: February 2007

OBJECTIVETo evaluate the indications and outcomes after partial nephrectomy and renal autotransplantation for urothelial cancer in solitary kidneys, with special attention to the ease of endoscopic tumour control after pyelovesicostomy.PATIENTS AND METHODSIn all, 978 records of three institutions were reviewed for patients undergoing partial nephrectomy between January 1990 and December 2000. Ex vivo organ‐preserving surgery was used in selected patients with a solitary kidney and localized pelvic or calyceal tumour. Autotransplantation was established using a pyelovesicostomy. The follow‐up included ultrasonography, pelvi‐cystoscopy, urine cytology, computed tomography, renal functional evaluation and video‐urodynamics. The study included four patients aged 52–56 years, with a follow‐up of 6–14 years.RESULTSThe histopathological status was pT1G2R0 in two and pT1G1R0 in the other two patients. One of them had an additional papilloma in the upper ureter. All patients entered a protocol of mitomycin/bacille Calmette‐Guérin instillation therapy after surgery. The patients are currently alive with no recurrences. There is stable kidney function despite vesico‐renal reflux, and normal bladder function with no subvesical obstruction.CONCLUSIONSPartial nephrectomy and renal autotransplantation for renal urothelial cancer in solitary kidneys is feasible, but should only be used in the rarest cases, and for the most selective indications. Dialysis and renal replacement can be avoided. Pyelovesicostomy allows effective chemotherapy instillation therapy, and easy and secure urothelial cancer control of the upper urinary tract.
Minimally invasive percutaneous nephrolithotomy for upper urinary tract calculi in transplanted kidneys
Authors: He Zhaohui , Li Xun , Chen Lizhong , Zeng Guohua , Yuan Jian 
Published: February 2007

Authors from China describe their experience with percutaneous nephrolithotomy for upper urinary tract calculi in transplanted kidneys. They confirm that it is a suitable way to treat such stones, and suggest it as initial therapy for stones other than those in the middle or lower calyx, particularly if they are small stones.OBJECTIVETo report our experience with minimally invasive percutaneous nephrolithotomy (mPCNL) for upper urinary tract (UUT) calculi in transplanted kidneys.PATIENTS AND METHODSBetween August 2002 and June 2006, seven patients (mean age 40.7 years) with UUT stones in transplanted kidneys (including one staghorn, two pelvic and four ureteric stones) were treated by mPCNL. A 16 F peel‐away sheath was placed as the percutaneous access port and a 8.5/11.5 F nephroscope or a 8/9.8 F ureteroscope was used for manipulation. Every 2–3 months during the follow‐up, patients had their serum urea, creatinine and uric acid measured, with urine culture and ultrasonography.RESULTSAll patients were rendered stone‐free at one mPCNL procedure, with no complications during or after surgery. The mean (range) operative duration was 53 (20–100) min and the mean haemoglobin decrease was 0.55 (0.2–1.2) g/dL. At a mean (range) follow‐up of 23 (3–48) months renal allograft function was stable in all patients and no recurrence of stone was detected.CONCLUSIONSmPCNL is safe and effective for managing calculi in transplanted kidneys, and it can be the initial therapy for most cases of UUT stones in transplanted kidneys, except for simple and small stones in the middle or lower calyx.
Non‐random patterns in the Yellowstone ecosystem: inferences from mammalian body size, order and biogeographical affinity
Authors: Bruzgul Judsen E. , Hadly Elizabeth A. 
Published: February 2007

ABSTRACTAim  Our aim was to investigate how the environment, species characteristics and historical factors at the subcontinental scale affect patterns of diversity. We used the assembly of the Yellowstone biota over the past 10,000 years as a natural experiment for investigating the processes that generate a modern non‐volant mammal species pool.Location  The data represent species from throughout North America with special attention to the non‐volant mammals of Yellowstone National Park, USA.Methods  We used digitized range maps to determine biogeographical affinity for all non‐volant mammals in the Rocky Mountains, Deserts and Great Plains biogeographical regions of North America. This biogeographical affinity, along with taxonomic order and body size class, was used to test whether non‐random patterns exist in the assemblage of Yellowstone non‐volant mammals. These characteristics were also used to investigate the strength of non‐random processes, such as habitat or taxon filtering, on particular groups of species or individual species.Results  Our results indicated that the Yellowstone fauna is composed of a non‐random subset of mammals from specific body size classes and with particular biogeographical affinities. Analyses by taxonomic order found significantly more Carnivora from the Rocky Mountains region and significantly fewer Rodentia from the Deserts region than expected from random assembly. Analyses using body size classes revealed deviations from expectations, including several significant differences between the frequency distribution of regional body sizes and the distribution of those species found within Yellowstone.Main conclusions  Our novel approach explores processes affecting species pool assembly in the Yellowstone region and elsewhere, and particularly identifies unique properties of species that may contribute to non‐random assembly. Focusing on the mechanisms generating diversity, not just current diversity patterns, will assist the design of conservation strategies given future environmental change scenarios.
Parasite species richness in carnivores: effects of host body mass, latitude, geographical range and population density
Authors: Lindenfors Patrik , Nunn Charles L. , Jones Kate E. , Cunningham Andrew A. , Sechrest Wes , Gittleman John L. 
Published: February 2007

ABSTRACTAim Comparative studies have revealed strong links between ecological factors and the number of parasite species harboured by different hosts, but studies of different taxonomic host groups have produced inconsistent results. As a step towards understanding the general patterns of parasite species richness, we present results from a new comprehensive data base of over 7000 host–parasite combinations representing 146 species of carnivores (Mammalia: Carnivora) and 980 species of parasites.Methods We used both phylogenetic and non‐phylogenetic comparative methods while controlling for unequal sampling effort within a multivariate framework to ascertain the main determinants of parasite species richness in carnivores.Results We found that body mass, population density, geographical range size and distance from the equator are correlated with overall parasite species richness in fissiped carnivores. When parasites are classified by transmission mode, body mass and home range area are the main determinants of the richness of parasites spread by close contact between hosts, and population density, geographical range size and distance from the equator account for the diversity of parasites that are not dependent on close contact. For generalist parasites, population density, geographical range size and latitude are the primary predictors of parasite species richness. We found no significant ecological correlates for the richness of specialist or vector‐borne parasites.Main conclusions Although we found that parasite species richness increases instead of decreases with distance from the equator, other comparative patterns in carnivores support previous findings in primates, suggesting that similar ecological factors operate in both these independent evolutionary lineages.
Niche properties of Central European spiders: shading, moisture and the evolution of the habitat niche
Authors: Entling Wiebke , Schmidt Martin H. , Bacher Sven , Brandl Roland , Nentwig Wolfgang 
Published: February 2007

ABSTRACTAim  Niche theory emphasizes the importance of environmental conditions for the distribution and abundance of species. Using a macroecological approach our study aimed at identifying the important environmental gradients for spiders. We generated numerical values of niche position and niche width. We also investigated relationships between these niche properties as well as the degree of phylogenetic conservatism in order to draw conclusions about the evolution of the habitat niche.Location  Central Europe: lowlands of Austria, Belgium, Germany, Luxembourg, the Netherlands and Switzerland.Methods  We analysed 244 published spider communities from 70 habitat types by correspondence analysis. The resulting community scores were used to test for correlations with habitat characteristics. Species scores were used to derive niche position (mean scores) and niche width (standard deviation of scores). To test for niche conservatism we estimated variance components across the taxonomic hierarchy.Results  The first two axes of the correspondence analysis were correlated with shading and moisture, respectively. Niche width had a hump‐shaped relationship to both environmental gradients. β‐diversity was strikingly higher in open habitats than in forests. Habitat niche conservatism was lower than phylogenetic conservatism in body size.Main conclusions  Environmental factors are important drivers for the β‐diversity of spiders, especially across open habitats. This underlines the importance of preserving the whole range of moisture conditions in open habitats. Narrow niches of species occurring at the ends of both environmental gradients indicate that adaptations to extreme habitats lead to constraints in ecological flexibility. Nevertheless, the habitat niche of species seems to evolve much faster than morphological or physiological traits.
Small mammal (rodents and lagomorphs) European biogeography from the Late Oligocene to the mid Pliocene
Authors: Maridet Olivier , Escarguel Gilles , Costeur Loïc , Mein Pierre , Hugueney Marguerite , Legendre Serge 
Published: February 2007

ABSTRACTAim  To analyse the fossil species assemblages of rodents and lagomorphs from the European Neogene in order to assess what factors control small mammal biogeography at a deep‐time evolutionary time‐scale.Location  Western Europe: 626 fossil‐bearing localities located within 31 regions and distributed among 18 successive biochronological units ranging from c. 27 Ma (million years ago; Late Oligocene) to c. 3 Ma (mid Pliocene).Methods  Taxonomically homogenized pooled regional assemblages are compared using the Raup and Crick index of faunal similarity; then, the inferred similarity matrices are visualized as neighbour‐joining trees and by projecting the statistically significant interregional similarities and dissimilarities onto palaeogeographical maps. The inferred biogeographical patterns are analysed and discussed in the light of known palaeogeographical and palaeoclimatic events.Results  Successive time intervals with distinct biogeographical contexts are identified. Prior to c. 18 Ma (Late Oligocene and Early Miocene), a relative faunal homogeneity (high interregional connectivity) is observed all over Europe, a time when major geographical barriers and a weak climatic gradient are known. Then, from the beginning of the Middle Miocene onwards, the biogeography is marked by a significant decrease in interregional faunal affinities which matches a drastic global climatic degradation and leads, in the Late Miocene (c. 11 Ma), to a marked latitudinal pattern of small mammal distribution. In spite of a short rehomogenization around the Miocene/Pliocene boundary (6–4 Ma), the biogeography of small mammals in the mid Pliocene (c. 3 Ma) finally closely reflects the extant situation.Main conclusions  The resulting biogeographical evolutionary scheme indicates that the extant endemic situation has deep historical roots corresponding to global tectonic and climatic events acting as primary drivers of long‐term changes. The correlation of biogeographical events with climatic changes emphasizes the prevalent role of the climate over geography in generating heterogeneous biogeographical patterns at the continental scale.
The effect of climatic gradients, topographic variation and species traits on the beta diversity of rain forest trees
Authors: Davidar Priya , Rajagopal B. , Mohandass D. , Puyravaud Jean‐Philippe , Condit Richard , Wright S. J. , Leigh E. G. 
Published: February 2007

ABSTRACTAim We assessed the rates of turnover of tree species with distance (beta diversity) in wet forests of the Western Ghats (WG) complex of India to see whether climate, topographic variation or species traits influence beta diversity.Location The Western Ghats is a chain of mountains about 1600 km in length, running parallel to the western coast of the Indian Peninsula from above 8° N to almost 21° N latitude.Methods We used data from 60 small plot inventories concentrated in three regions: the southernmost part of the Western Ghats (SWG) (8°24′ to 9°37′ N), the Nilgiri Hills (11°12′ to 11°14′ N), and the central Western Ghats (CWG) (12°32′ to 14°51′ N). We used Sorensen's index (SI) to estimate the similarity in species composition between two plots and regressed SI against the logarithm of the distance between plots to assess beta diversity. A bootstrapping procedure provided confidence intervals for regression coefficients. To test for the effects of climate, we regressed seasonality differences between plots against SI for low‐elevation (< 800 m) plots along the north–south axis, and all plots in the SWG. We assessed the impact of the rainfall gradient in the Kogar region.Results Among all three regions, beta diversity was highest along the latitudinal axis, and along the rainfall gradient in the Kogar region. Differences in seasonality between sites were strongly related to beta diversity along the north–south seasonality gradient and within the SWG. Within the three regions, beta diversity was highest in the region with the strongest rainfall gradient and lowest for the topographically heterogeneous SWG. Beta diversity did not differ between forest strata and dispersal modes.Main conclusions We conclude that climate, particularly seasonality, is probably the primary driver of beta diversity among rain forest trees of the Western Ghats complex.
Plant peptide deformylase: a novel selectable marker and herbicide target based on essential cotranslational chloroplast protein processing
Authors: Hou Cai‐Xia , Dirk Lynnette M. A. , Pattanaik Sitakanta , Das Narayan C. , Maiti Indu B. , Houtz Robert L. , Williams Mark A. 
Published: February 2007

SummaryTransgenic tobacco plants expressing three different forms of Arabidopsis plant peptide deformylase (AtDEF1.1, AtDEF1.2 and AtDEF2; EC 3.5.1.88) were evaluated for resistance to actinonin, a naturally occurring peptide deformylase inhibitor. Over‐expression of either AtDEF1.2 or AtDEF2 resulted in resistance to actinonin, but over‐expression of AtDEF1.1 did not. Immunological analyses demonstrated that AtDEF1.2 and AtDEF2 enzymes were present in both stromal and thylakoid fractions in chloroplasts, but AtDEF1.1 was localized to mitochondria. The highest enzyme activity was associated with stromal AtDEF2, which was approximately 180‐fold greater than the level of endogenous activity in the host plant. Resistance to actinonin cosegregated with kanamycin resistance in Atdef1.2‐D and Atdef2‐D transgenic plants. Here, we demonstrate that the combination of plant peptide deformylase and peptide deformylase inhibitors may represent a native gene selectable marker system for chloroplast and nuclear transformation vectors, and also suggest plant peptide deformylase as a potential broad‐spectrum herbicide target.