bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproducibility of energy intake, gastric emptying, blood glucose, plasma insulin and cholecystokinin responses in healthy young males
Authors: Nair Nivasinee S. , Brennan Ixchel M. , Little Tanya J. , Gentilcore Diana , Hausken Trygve , Jones Karen L. , Wishart Judith M. , Horowitz Michael , Feinle-Bisset Christine 
Published: August 2008

Gastric emptying, as well as intragastric meal distribution, and gastrointestinal hormones, including cholecystokinin (CCK), play an important role in appetite regulation. The evaluation of gastrointestinal factors regulating food intake is commonly performed in healthy, lean, young male participants. It has, however, been suggested that there is a marked interindividual variability in the effects of nutrient ‘preloads’ on energy intake in this group. Whether there is significant intraindividual variation in acute energy intake after a nutrient preload, and, if so, how this relates to day-to-day differences in gastric emptying and gastrointestinal hormone release, is unclear. The purpose of the present paper is to evaluate the hypothesis that energy intake after a nutrient preload would be reproducible and associated with reproducible patterns of gastric emptying, intragastric distribution and gastrointestinal hormone release. Fifteen healthy men (age 25 (sem5) years) consumed a glucose preload (50 g glucose in 300 ml water; 815 kJ) on three occasions. Gastric emptying and intragastric meal distribution (using three-dimensional ultrasound), blood glucose, plasma insulin and CCK concentrations and appetite perceptions were evaluated over 90 min, and energy intake from a cold buffet-style meal was then quantified. Energy intake was highly reproducible within individuals between visits (intraclass correlation coefficient,ri = 0·9). Gastric emptying, intragastric meal distribution, blood glucose, plasma insulin and CCK concentrations and appetite perceptions did not differ between visits (ri>0·7 for all). In healthy males, energy intake is highly reproducible, at least in the short term, and is associated with reproducible patterns of gastric emptying, glycaemia, insulinaemia and CCK release.
Powerful fusion: PSI-BLAST and consensus sequences
Authors: Przybylski Dariusz , Rost Burkhard 
Published: August 2008

Abstract
Motivation: A typical PSI-BLAST search consists of iterative scanning and alignment of a large sequence database during which a scoring profile is progressively built and refined. Such a profile can also be stored and used to search against a different database of sequences. Using it to search against a database of consensus rather than native sequences is a simple add-on that boosts performance surprisingly well. The improvement comes at a price: we hypothesized that random alignment score statistics would differ between native and consensus sequences. Thus PSI-BLAST-based profile searches against consensus sequences might incorrectly estimate statistical significance of alignment scores. In addition, iterative searches against consensus databases may fail. Here, we addressed these challenges in an attempt to harness the full power of the combination of PSI-BLAST and consensus sequences.
Results: We studied alignment score statistics for various types of consensus sequences. In general, the score distribution parameters of profile-based consensus sequence alignments differed significantly from those derived for the native sequences. PSI-BLAST partially compensated for the parameter variation. We have identified a protocol for building specialized consensus sequences that significantly improved search sensitivity and preserved score distribution parameters. As a result, PSI-BLAST profiles can be used to search specialized consensus sequences without sacrificing estimates of statistical significance. We also provided results indicating that iterative PSI-BLAST searches against consensus sequences could work very well. Overall, we showed how a very popular and effective method could be used to identify significantly more relevant similarities among protein sequences.
Availability: http://www.rostlab.org/services/consensus/
Contact: dariusz@mit.edu
Model-based prediction of sequence alignment quality
Authors: Ahola Virpi , Aittokallio Tero , Vihinen Mauno , Uusipaikka Esa 
Published: August 2008

AbstractMotivation: Multiple sequence alignment (MSA) is an essential prerequisite for many sequence analysis methods and valuable tool itself for describing relationships between protein sequences. Since the success of the sequence analysis is highly dependent on the reliability of alignments, measures for assessing the quality of alignments are highly requisite.Results: We present a statistical model-based alignment quality score. Unlike other quality scores, it does not require several parallel alignments for the same set of sequences or additional structural information. Our quality score is based on measuring the conservation level of reference alignments in Homstrad. Reference sequences were realigned with the Mafft, Muscle and Probcons alignment programs, and a sum-of-pairs (SP) score was used to measure the quality of the realignments. Statistical modelling of the SP score as a function of conservation level and other alignment characteristics makes it possible to predict the SP score for any global MSA. The predicted SP scores are highly correlated with the correct SP scores, when tested on the Homstrad and SABmark databases. The results are comparable to that of multiple overlap score (MOS) and better than those of normalized mean distance (NorMD) and normalized iRMSD (NiRMSD) alignment quality criteria. Furthermore, the predicted SP score is able to detect alignments with badly aligned or unrelated sequences.Availability: The method is freely available at http://www.mtt.fi/AlignmentQuality/Contact: virpi.ahola@mtt.fiSupplementary information: Supplementary data are available at Bioinformatics online.
The influence of protected area management on the status of coral reefs at Misali Island, Tanzania following the 1998 bleaching event in the western Indian Ocean
Authors: Poonian C. N. S. 
Published: August 2008

AbstractThe reefs of Misali Island, Tanzania suffered serious coral mortality as a result of the 1998 coral bleaching event in the western Indian Ocean. Four years after this event, Frontier‐Tanzania assessed reef substrate in Misali Island Marine Conservation Area (MIMCA) using scuba surveys. Substrate cover was compared between sites within and outside the nonextraction zone (NEZ) of MIMCA and recovery rates were estimated through reference to previous studies. Coral recovery at Misali Island following the bleaching event has generally been slow, but nonextractive management of MIMCA has enhanced coral recovery within the NEZ. The absence of fishing activities in the NEZ has sustained herbivorous fish populations and thus reduced algal overgrowth; however, outside the NEZ, diving and anchoring activities have caused further coral damage and led to increased levels of debris. Awareness‐raising programmes could lessen these problems and the NEZ appeared to be well‐placed to capitalize on nonmanageable factors that are thought to mitigate the effects of coral bleaching. In addition, the implementation of flexible zoning schemes could improve recovery rates after future bleaching events.
Shading delays bud break in Brachsyegia spiciformis
Authors: Richer R. A. 
Published: August 2008

AbstractWhole tree manipulation experiments were performed in the common southern African tree species, Brachystegia spiciformis to test a novel hypothesis that decreasing Total nonstructural carbohydrates (TNC) in the stem could cause bud break in Brachystegia spiciformis. The experimental treatments included fertilization, canopy defoliation, shading and stem heating to decrease stem carbohydrates. None of the treatments significantly decreased mean stem TNC. Likewise the heating, fertilization and defoliation treatments did not significantly affect the date of bud break. However, shading significantly delayed bud break. This delay in bud break could not be attributed to changes in leaf level photosynthetic traits, stem water content, leaf predawn water potential or delayed leaf fall. These results question widely accepted hypotheses about the mechanisms controlling bud break and suggest a carbohydrate homeostatic mechanism.
Effect of shade and shading history on species abundances and ecosystem processes in temporary ponds
Authors: MOKANY A. , WOOD J. T. , CUNNINGHAM S. A. 
Published: August 2008

Summary1. The amount of sunlight that an ecosystem receives is an important determinant of primary productivity, which in turn can influence species diversity and nutrient cycling. Here, we examine the effects of shading and shading history on ecosystem processes, macroinvertebrate diversity and development of dominant ecosystem states in field‐based aquatic mesocosms.2. We found that there were large effects of the level of shade, but few effects of shading history. Increasing light increased the biomass of filamentous algae (metaphyton) which increased the overall productivity of the ecosystem, and shifted the invertebrate community from one with more mosquitoes (filter feeders) to one with more anuran tadpoles (algal grazers).3. There was also an effect of shading history, where increased shade led to changes in the macroinvertebrate communities that were maintained after shade was reduced in the later part of the experiment.4. Finally, our results indicated that correlations between ecosystem processes, specific key macrofauna and the development of pond ecosystem states were greater than correlations of these factors to shading treatments. These results suggest that the history of community assembly can have a greater impact on the development of ecosystem processes than diminishing light by as much as 50%. However, light may have a potentially strong indirect effect and may impact the communities through altered bottom‐up structuring forces.
Periphyton as alternative food source for the filter‐feeding cladoceran Daphnia magna
Authors: SIEHOFF SILVANA , HAMMERS‐WIRTZ MONIKA , STRAUSS TIDO , RATTE HANS TONI 
Published: August 2008

Summary1.  Daphnia magna, a well‐studied primary consumer, is mainly known as a filter feeder. In this study, we investigated the ability of D. magna to use periphyton as an alternative food source to phytoplankton. We examined the development of laboratory populations fed with different food sources (Desmodesmus subspicatus and/or periphyton or neither) over a period of 42 days, and observed the behaviour of the daphnids.2. The addition of periphyton to phytoplankton food led to an increase of daphnid population biomass. When fed with periphyton as the only food source, a small but stable D. magna population developed.3. The behaviour of daphnids fed with both food sources revealed a preference for feeding on D. subspicatus. Only below a concentration of D. subspicatus of approximately 0.05 mg C L−1 (0.4 × 107 cells L−1) did D. magna use periphyton as an alternative food source.4. Periphyton showed distinct reactions to grazing by D. magna. The thickness of the periphyton layer was reduced from about 4 to 1 mm and we observed a change in species composition due to grazing.5. The ability of D. magna to graze on periphyton could serve to stabilize its population density and reinforce its competitive advantage over other cladocerans. By switching between food sources, D. magna can act as a coupler between pelagic and benthic habitats and food webs.
Ancient DNA applications for wildlife conservation
Authors: LEONARD JENNIFER A 
Published: August 2008

AbstractAncient DNA analyses of historical, archaeological and paleontological remains can contribute important information for the conservation of populations and species that cannot be obtained any other way. In addition to ancient DNA analyses involving a single or few individuals, population level studies are now possible. Biases inherent in estimating population parameters and history from modern genetic diversity are exaggerated when populations are small or have been heavily impacted by recent events, as is common for many endangered species. Going directly back in time to study past populations removes many of the assumptions that undermine conclusions based only on recent populations. Accurate characterization of historic population size, levels of gene flow and relationships with other populations are fundamental to developing appropriate conservation and management plans. The incorporation of ancient DNA into conservation genetics holds a lot of potential, if it is employed responsibly.
Internal coordination between hydraulics and stomatal control in leaves
Authors: BRODRIBB TIM J. , JORDAN GREGORY J. 
Published: August 2008

ABSTRACTThe stomatal response to changing leaf‐atmospheric vapour pressure gradient (Dl) is a crucial yet enigmatic process that defines the daily course of leaf gas exchange. Changes in the hydration of epidermal cells are thought to drive this response, mediated by the transpiration rate and hydraulic conductance of the leaf. Here, we examine whether species‐specific variation in the sensitivity of leaves to perturbation of Dl is related to the efficiency of water transport in the leaf (leaf hydraulic conductivity, Kleaf). We found good correlation between maximum liquid (Kleaf) and gas phase conductances (gmax) in leaves, but there was no direct correlation between normalized Dl sensitivity and Kleaf. The impact of Kleaf on Dl sensitivity in our diverse sample of eight species was important only after accounting for the strong relationship between Kleaf and gmax. Thus, the ratio of gmax/Kleaf was strongly correlated with stomatal sensitivity to Dl. This ratio is an index of the degree of hydraulic buffering of the stomata against changes in Dl, and species with high gmax relative to Kleaf were the most sensitive to Dl perturbation. Despite the potentially high adaptive significance of this phenomenon, we found no significant phylogenetic or ecological trend in our species.
Structural and functional patterns of bacterial communities in response to protist predation along an experimental productivity gradient
Authors: Corno Gianluca , Jürgens Klaus 
Published: August 2008

SummarySubstrate supply and protist grazing are two of the most important forces that determine the composition and properties of bacterial assemblages. General ecological theory predicts that the relative importance of these factors is changing with the environmental productivity. In the present study, the interplay between bottom‐up and top‐down control was studied in a productivity gradient simulated in one‐stage chemostats containing natural assemblages of freshwater bacteria and heterotrophic nanoflagellates. Bacterial assemblages in the chemostats differed strongly with respect to their morphological, physiological and compositional properties in the presence versus the absence of predators. However, theses differences were modified by the productivity gradient. Whereas in predator‐free chemostats the mean abundance and biomass of bacteria increased proportionally with increasing substrate supply, in treatments that included flagellates bacterial production was largely channelled into predator biomass. The bacterial morphological diversity increased along the productivity gradient with increasing substrate input but even more so with predators. Proportional to the increasing substrate supply, predation shifted the remaining bacteria towards morphologically inedible forms. Predation also caused shifts in bacterial substrate‐utilization profiles, and in bacterial community composition, as analysed by terminal restriction fragment length polymorphism of PCR‐amplified 16S‐rRNA genes. Without predators, bacterial richness increased along the productivity gradient whereas with predators bacterial richness was higher at intermediate substrate levels. In accordance with ecological theory, these results demonstrated that predators influence all of the major characteristics of bacterial assemblages but the magnitude of this effect is modulated by the productivity of the system.
Erectile haemodynamic status after radical prostatectomy correlates with erectile functional outcome
Authors: Ohebshalom Michael , Parker Marilyn , Waters Bedford , Flanagan Robert , Mulhall John P. 
Published: August 2008

OBJECTIVETo define haemodynamic changes after radical retropubic prostatectomy (RP) and the predictive value of these for the outcome of erectile function (EF), as although there are predictors of the recovery of EF, penile vascular changes might also affect the recovery of EF.PATIENTS AND METHODSProspective data were analysed from men who had RP followed by duplex penile Doppler ultrasonography (DUS) within 6 months of RP. All men had functional erections before RP, based on self‐report and partner corroboration, and all completed the International Index of Erectile Function (IIEF) questionnaire serially after RP. The EF, based on IIEF scores, was then correlated with the penile DUS results.RESULTSIn all, the study included 111 patients; 32 (29%) had normal erectile haemodynamics after RP, while 79 (71%) had abnormal haemodynamics. Twelve patients (11%) had a venous leak. There were no differences in mean patient age or comorbidity profile between those with and without haemodynamic changes. Comparing those with normal and abnormal haemodynamics, the mean IIEF EF domain scores were 25 and 17 (P = 0.025), the percentages of erectile rigidity at 18 months was 66% vs 35% (P = 0.013), the percentage of patients with normal EF domain scores was 28% vs 6% (P < 0.01), the percentage of patients with functional erections permitting sexual intercourse unassisted by pharmacological agents was 47% vs 22% (P = 0.018), and the percentage of patients responding to sildenafil citrate, as defined by vaginal penetration, was 72% vs 43% (P = 0.03), respectively.CONCLUSIONSThe results of this prospective study indicate that a patient’s penile vascular status is correlated with their EF after RP.
Laser robotically assisted nerve‐sparing radical prostatectomy: a pilot study of technical feasibility in the canine model
Authors: Gianduzzo Troy , Colombo Jose R. , Haber Georges‐Pascal , Hafron Jason , Magi‐Galluzzi Cristina , Aron Monish , Gill Inderbir S. , Kaouk Jihad H. 
Published: August 2008

OBJECTIVESTo examine the feasibility of using laser energy during nerve‐sparing robotically assisted radical prostatectomy (RARP), as the energy sources currently used for haemostasis in RARP adversely affect cavernous nerve function, while clips require application by a skilled assistant, but laser energy potentially allows precise dissection with minimal collateral tissue injury.MATERIALS AND METHODSWe used laser‐based RARP in 10 dogs, using the da Vinci S system (Intuitive Surgical, Sunnyvale, CA, USA) and a prototype robotic laser instrument. The potassium‐titanyl‐phosphate laser was used for dissection at 2–6 W, with intermittent use of the neodymium‐doped yttrium‐aluminium‐garnet laser at 5 W for coagulating larger vessels. The peak intracavernosal pressure response to nerve stimulation was recorded as a percentage of mean arterial pressure (ICP%MAP) before and after RARP. Five dogs were killed immediately after RARP and five were maintained alive for 72 h; the haemoglobin and haematocrit levels were measured before and after RARP in the latter five dogs.RESULTSAll 10 procedures were performed solely using laser energy and no additional haemostatic manoeuvres. The median prostate excision time was 65 min. The ICP%MAP before and after RARP (median 98.5% and 77.0%, P = 0.12) were not significantly different; similarly, the respective haemoglobin (median 14.4 vs 12.6 g/dL, P = 0.06) and haematocrit levels (45.1% vs 40.2%, P = 0.06) were not significantly different. Two dogs had catheter‐related complications and one had an anastomotic leak. There were no laser‐related complications or postoperative haemorrhage.CONCLUSIONSLaser RARP is feasible in dogs and further assessment is warranted.
Evaluation of a novel precision template‐guided biopsy system for detecting prostate cancer
Authors: Megwalu Ifeanyichukwu I. , Ferguson Genoa G. , Wei John T. , Mouraviev Vladimir , Polascik Thomas J. , Taneja Samir , Black Linda , Andriole Gerald L. , Kibel Adam S. 
Published: August 2008

OBJECTIVETo explore the ability of a novel transrectal ultrasonography (TRUS) device (TargetScanTM, Envisioneering Medical Technologies, St. Louis MO) that creates a three‐dimensional map of the prostate and calculates an optimal biopsy scheme, to accurately sample the prostate and define the true extent of disease, as standard TRUS‐guided prostate biopsy relies on the operator to distribute the biopsy sites, often resulting in under‐ and oversampling regions of the gland.PATIENTS AND METHODSIn a multicentre retrospective chart review evaluating patients who had a TargetScan prostate biopsy between January 2006 and June 2007, we determined the overall cancer detection rate in all patients and in subgroups based on prostate specific antigen level, digital rectal examination, and indication for biopsy. We assessed the pathological significance of cancer detected, defined as a Gleason score of ≥7, positive margins, extracapsular disease or >20% tumour volume in the prostatectomy specimen. We also evaluated the concordance in Gleason score between the biopsy and prostatectomy specimen.RESULTSCancer was detected in 50 (35.7%) of the 140 patients biopsied, including 39 (47.6%) with no previous biopsies. Of 23 prostatectomy specimens, 20 (87%) had pathologically significant disease. The biopsy predicted the prostatectomy Gleason score in 12 patients (52%), overestimated in two (9%), underestimated in eight (35%), and biopsy Gleason score could not be assigned in one (4%).CONCLUSIONSTemplate‐guided biopsy potentially produces a higher cancer detection rate and more accurate assessment of grade. Prostatectomy specimens did not have a high rate of pathologically insignificant disease.
IN DEFENCE OF METAPHYSICAL ANALYTICITY
Authors: Hofmann Frank , Horvath Joachim 
Published: August 2008

AbstractAccording to the so‐called metaphysical conception of analyticity, analytic truths are true in virtue of meaning (or content) alone and independently of (extralinguistic) facts. Quine and Boghossian have tried to present a conclusive argument against the metaphysical conception of analyticity. In effect, they tried to show that the metaphysical conception inevitably leads into a highly implausible view about the truthmakers of analytic truths. We would like to show that their argument fails, since it relies on an ambiguity of the notion of ‘independence of (extralinguistic) facts’. If one distinguishes between variation independence and existence independence, the unwelcome view about the truthmakers of analytic truths no longer follows. Thus, there is at best a challenge, but no conclusive argument. The door to the metaphysical conception of analyticity is still open.1
Deep Brain Stimulation Devices: A Brief Technical History and Review
Authors: Coffey Robert J. 
Published: August 2008

AbstractDeep brain stimulation (DBS)—a broadly accepted therapeutic modality with tens of thousands of patients currently implanted—is the application of implantable electrical stimulation devices to treat neurological disorders. Approved indications include involuntary movement disorders; investigational applications include epilepsy, selected psychiatric disorders, and other conditions. DBS differs fundamentally from functional electrical stimulation and sensory prosthetics in that DBS therapies do not substitute for or replace injured tissues, organs, or body functions. DBS—targeted to particular brain nuclei or pathways that are specific for the disorder under treatment—influences brain function and behavioral output in ways that can relieve symptoms and improve the overall functioning of the patient. We will briefly review the history and present status of DBS from a technical and device‐oriented perspective, with an eye toward future advances.