bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relationship between patient and practitioner expectations and preferences and clinical outcomes in a trial of exercise and acupuncture for knee osteoarthritis
Authors: Foster Nadine E. , Thomas Elaine , Hill Jonathan C. , Hay Elaine M. 
Published: August 2009

ABSTRACTWe investigated the relationship between patient and therapist preferences and expectations and clinical outcomes in a trial of exercise and acupuncture for clinical knee osteoarthritis.352 Patients were randomised to advice and exercise or advice and exercise plus true or non‐penetrating acupuncture. Before randomisation, patients recorded their general outcome expectations, treatment‐specific preferences and expectations. Clinical outcome was (a) change scores on the Western Ontario and McMaster Osteoarthritis Index (WOMAC) and (b) treatment response according to the OMERACT‐OARSI criteria. Physiotherapists recorded their treatment expectations and preferences for each patient following an assessment prior to randomisation. We investigated the relationship between (a) patient, (b) therapist and (c) matched patient–therapist preferences and expectations on clinical outcomes using univariate and multivariate analyses.There was no significant relationship between patients’ treatment preferences and clinical outcomes at 6 or 12months nor between patients’ expectations and pain (WOMAC) at 6 or 12months. Using our secondary outcome (OMERART‐OARSI), those who received the treatment for which they had high expectations of benefit were almost twice as likely to be classified as a treatment responder at 6months (odds ratio (OR) 1.7 (95% Confidence Interval 1.06, 2.79)) and 12months (OR) 1.9 (1.13, 3.13). Therapists’ preferences and expectations for individual patients did not add further explanation of outcomes.There was no evidence of a relationship between patients’ treatment preferences or expectations and pain reduction. We found weak evidence, from secondary outcomes, that patients’ expectations, both general and treatment‐specific, are related to clinical outcome from exercise and acupuncture.
Restricted growth and insulin‐like growth factor‐1 deficiency in mice lacking presenilin‐1 in the neural crest cell lineage
Authors: Nakajima Mitsunari , Watanabe Sono , Okuyama Satoshi , Shen Jie , Furukawa Yoshiko 
Published: August 2009

AbstractPresenilin‐1 (PS1) is a transmembrane protein that is in many cases responsible for the development of early‐onset familial Alzheimer's disease. PS1 is essential for neurogenesis, somitogenesis, angiogenesis, and cardiac morphogenesis. We report here that PS1 is also required for maturation and/or maintenance of the pituitary gland. We generated PS1‐conditional knockout (PS1‐cKO) mice by crossing floxed PS1 and Wnt1‐cre mice, in which PS1 was lacking in the neural crest‐derived cell lineage. Although the PS1‐cKO mice exhibited no obvious phenotypic abnormalities for several days after birth, reduced body weight in the mutant was evident by the age of 3–5 weeks. Pituitary weight and serum insulin‐like growth factor (IGF)‐1 level were also reduced in the mutant. Histologic analysis revealed severe atrophy of the cytosol in the anterior and intermediate pituitary lobes of the mutant. Immunohistochemistry did not reveal clear differences in the expression levels of thyroid‐stimulating hormone, adrenocorticotropic hormone, or prolactin in the mutant pituitary. In contrast, growth hormone expression levels were reduced in the anterior lobe of the mutant. PS1 was defective in the posterior lobe, but not the anterior or intermediate lobes, in the mutant pituitary. These findings suggest that PS1 indirectly mediates the development and/or maintenance of the anterior and intermediate lobes in the pituitary gland via actions in other regions, such as the posterior lobe.
Assessment of obstruction level and selection of patients for obstructive sleep apnoea surgery: an evidence-based approach
Authors: Georgalas C , Garas G , Hadjihannas E , Oostra A 
Published: August 2009

AbstractIntroduction:Obstructive sleep apnoea has long been recognised as a clinical syndrome; however, high quality evidence on the effects of surgery for this condition is still missing. Despite this, a consensus seems to be evolving, albeit based on limited evidence, that surgery should be offered as a second line treatment to suitable patients with obstructive sleep apnoea.Aims:This article aims to assess the different methods of investigating upper airway obstruction in patients with obstructive sleep apnoea, in respect to these methods' relevance to surgical treatment, via a systematic review of the literature.Methods:The Cochrane Controlled Trials Register, Medline and EMBASE were searched from 1966 onwards. The search was performed in August 2008. A total of 2001 citations were retrieved.Results and conclusion:There is not yet a generally accepted way to assess surgical candidacy based on the level of obstruction. Better organised clinical studies with well defined endpoints are needed. In the meanwhile, it appears that sleep nasendoscopy, acoustic reflectometry and pressure catheters can all provide useful information, and their use may be decided upon based on the experience and resources available in individual departments.
Echinococcus species in African wildlife
Authors: HÜTTNER M. , ROMIG T. 
Published: August 2009

SUMMARYCystic echinococcosis, caused by different species of the Echinococcus granulosus complex, is an important zoonotic disease with a particular impact on pastoralist societies. In addition to the widespread taxa with synanthropic transmission, a number of Echinococcus species were described from African wild carnivores early in the 20th century. For lack of study material, most of these were later tentatively synonymized with E. granulosus. Early infection experiments with wildlife isolates gave ambiguous results due to the use of unspecified parasite material, and only recently molecular methods provided the opportunity to shed light on the confusing scenery e.g. by characterizing E. felidis from the African lion. Here we will summarize the convoluted history of Echinococcus research in sub-Saharan Africa and highlight the necessity of molecular surveys to establish the life cycles and estimate the zoonotic potential of these parasites.
Convergence analysis for the uncalibrated robotic hand–eye coordination based on the unmodeled dynamics observer
Authors: Su Jianbo 
Published: August 2009

SUMMARYThe uncalibrated robotic hand–eye coordination problem is firstly modeled by a dynamic system, where the unknown hand–eye relationship is regarded as the system's unmodeled dynamics. A state observer is then designed to estimate impacts of this modeling error together with the system's external disturbances. With the estimation results as the compensation, the system control is thus accomplished based on a nonlinear combination of the system state errors. Convergence analysis of the whole system under the proposed control scheme is emphasized. Simulations and experiment results are presented to verify the performance of the proposed approach.
A biologically inspired method for robot navigation in a cluttered environment
Authors: Teimoori Hamid , Savkin Andrey V. 
Published: August 2009

SUMMARYThe problem of wheeled mobile robot (WMR) navigation toward an unknown target in a cluttered environment has been considered. The biologically inspired navigation algorithm is the equiangular navigation guidance (ENG) law combined with a local obstacle avoidance technique. The collision avoidance technique uses a system of active sensors which provides the necessary information about obstacles in the vicinity of the robot. In order for the robot to avoid collision and bypass the enroute obstacles, the angle between the instantaneous moving direction of the robot and a reference point on the surface of the obstacle is kept constant. The performance of the navigation strategy is confirmed with computer simulations and experiments with ActivMedia Pioneer 3-DX wheeled robot.
Dynamic modeling of planar parallel robots considering passive joint sensor data
Authors: Zubizarreta Asier , Cabanes Itziar , Marcos Marga , Pinto Charles 
Published: August 2009

SUMMARYModel-based advanced control approaches are needed to achieve high speed and acceleration and precision in robotic operations. These control schemes need a proper dynamic model. Many approaches have been proposed by different authors in order to obtain the dynamic model of these structures. However, most of them do not consider the possibility to introduce redundant sensor data. In this paper, a methodology for obtaining a compact dynamic model considering passive joint sensor data is proposed. The dynamic model is defined in compact and structured form, which makes it appropriate to be used in advanced control techniques.
Landmark detection and localization for mobile robot applications: a multisensor approach
Authors: Amarasinghe Dilan , Mann George K. I. , Gosine Raymond G. 
Published: August 2009

SUMMARYThis paper describes a landmark detection and localization using an integrated laser-camera sensor. Laser range finder can be used to detect landmarks that are direction invariant in the laser data such as protruding edges in walls, edges of tables, and chairs. When such features are unavailable, the dependant processes will fail to function. However, in many instances, larger number of landmarks can be detected using computer vision. In the proposed method, camera is used to detect landmarks while the location of the landmark is measured by the laser range finder using laser-camera calibration information. Thus, the proposed method exploits the beneficial aspects of each sensor to overcome the disadvantages of the other sensor. While highlighting the drawbacks and limitations of single sensor based methods, an experimental results and important statistics are provided for the verification of the affectiveness sensor fusion method using Extended Kalman Filter (EKF) based simultaneous localization and mapping (SLAM) as an example application.
Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication
Authors: Kim Youngchul , Bekiranov Stefan , Lee Jae K. , Park Taesung 
Published: August 2009

Abstract
Motivation: ChIP–chip has been widely used for various genome-wide biological investigations. Given the small number of replicates (typically two to three) per biological sample, methods of analysis that control the variance are desirable but in short supply. We propose a double error shrinkage (DES) method by using moving average statistics based on local-pooled error estimates which effectively control both heterogeneous error variances and correlation structures of an extremely large number of individual probes on tiling arrays.
Results: Applying DES to ChIP–chip tiling array study for discovering genome-wide protein-binding sites, we identified 8400 target regions that include highly likely TFIID binding sites. About 33% of these were well matched with the known transcription starting sites on the DBTSS library, while many other newly identified sites have a high chance to be real binding sites based on a high positive predictive value of DES. We also showed the superior performance of DES compared with other commonly used methods for detecting actual protein binding sites.
Contact: tspark@snu.ac.kr; jaeklee@virginia.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments
Authors: Chi Pin-Hao , Pang Bin , Korkin Dmitry , Shyu Chi-Ren 
Published: August 2009

Abstract
Motivation: To investigate structure–function relationships, life sciences researchers usually retrieve and classify proteins with similar substructures into the same fold. A manually constructed database, SCOP, is believed to be highly accurate; however, it is labor intensive. Another known method, DALI, is also precise but computationally expensive. We have developed an efficient algorithm, namely, index-based protein substructure alignment (IPSA), for protein-fold classification. IPSA constructs a two-layer indexing tree to quickly retrieve similar substructures in proteins and suggests possible folds by aligning these substructures.
Results: Compared with known algorithms, such as DALI, CE, MultiProt and MAMMOTH, on a sample dataset of non-redundant proteins from SCOP v1.73, IPSA exhibits an efficiency improvement of 53.10, 16.87, 3.60 and 1.64 times speedup, respectively. Evaluated on three different datasets of non-redundant proteins from SCOP, average accuracy of IPSA is approximately equal to DALI and better than CE, MAMMOTH, MultiProt and SSM. With reliable accuracy and efficiency, this work will benefit the study of high-throughput protein structure–function relationships.
Availability: IPSA is publicly accessible at http://ProteinDBS.rnet.missouri.edu/IPSA.php
Contact: ShyuC@missouri.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
PineSAP—sequence alignment and SNP identification pipeline
Authors: Wegrzyn Jill L. , Lee Jennifer M. , Liechty John , Neale David B. 
Published: August 2009

Abstract
Summary: The Pine Alignment and SNP Identification Pipeline (PineSAP) provides a high-throughput solution to single nucleotide polymorphism (SNP) prediction using multiple sequence alignments from re-sequencing data. This pipeline integrates a hybrid of customized scripting, existing utilities and machine learning in order to increase the speed and accuracy of SNP calls. The implementation of this pipeline results in significantly improved multiple sequence alignments and SNP identifications when compared with existing solutions. The use of machine learning in the SNP identifications extends the pipeline's application to any eukaryotic species where full genome sequence information is unavailable.
Availability: All code used for this pipeline is freely available at the Dendrome project website (http://dendrome.ucdavis.edu/adept2/resequencing.html)
Contact: jlwegrzyn@ucdavis.edu
Knowledge-guided inference of domain–domain interactions from incomplete protein–protein interaction networks
Authors: Liu Mei , Chen Xue-wen , Jothi Raja 
Published: August 2009

Abstract
Motivation: Protein-protein interactions (PPIs), though extremely valuable towards a better understanding of protein functions and cellular processes, do not provide any direct information about the regions/domains within the proteins that mediate the interaction. Most often, it is only a fraction of a protein that directly interacts with its biological partners. Thus, understanding interaction at the domain level is a critical step towards (i) thorough understanding of PPI networks; (ii) precise identification of binding sites; (iii) acquisition of insights into the causes of deleterious mutations at interaction sites; and (iv) most importantly, development of drugs to inhibit pathological protein interactions. In addition, knowledge derived from known domain–domain interactions (DDIs) can be used to understand binding interfaces, which in turn can help discover unknown PPIs.
Results: Here, we describe a novel method called K-GIDDI (knowledge-guided inference of DDIs) to narrow down the PPI sites to smaller regions/domains. K-GIDDI constructs an initial DDI network from cross-species PPI networks, and then expands the DDI network by inferring additional DDIs using a divide-and-conquer biclustering algorithm guided by Gene Ontology (GO) information, which identifies partial-complete bipartite sub-networks in the DDI network and makes them complete bipartite sub-networks by adding edges. Our results indicate that K-GIDDI can reliably predict DDIs. Most importantly, K-GIDDI's novel network expansion procedure allows prediction of DDIs that are otherwise not identifiable by methods that rely only on PPI data.
Contact: xwchen@ku.edu
Availability: http://www.ittc.ku.edu/∼xwchen/domainNetwork/ddinet.html
Supplementary information: Supplementary data are available at Bioinformatics online.
Ectopic 5′ Splice Sites Inhibit Gene Expression by Engaging RNA Surveillance and Silencing Pathways in Plants
Authors: Wypijewski Krzysztof , Hornyik Csaba , Shaw Jane A. , Stephens Jennifer , Goraczniak Rafal , Gunderson Samuel I. , Lacomme Christophe 
Published: August 2009

Abstract
The quality control of mRNA maturation is a highly regulated process that surveys pre-mRNA integrity and eliminates improperly matured pre-mRNAs. In nature, certain viruses regulate the expression of their genes by hijacking the endogenous RNA quality control machinery. We demonstrate that the inclusion of 5′ splice sites within the 3′-untranslated region of a reporter gene in plants alters the pre-mRNA cleavage and polyadenylation process, resulting in pre-mRNA degradation, exemplifying a regulatory mechanism conserved between kingdoms. Altered pre-mRNA processing was associated with an inhibition of homologous gene expression in trans and the preferential accumulation of 24-nucleotide (nt) short-interfering RNAs (siRNAs) as opposed to 21-nt siRNA subspecies, suggesting that degradation of the aberrant pre-mRNA involves the silencing machinery. However, gene expression was not restored by coexpression of a silencing suppressor or in an RNA-dependent RNA polymerase (RDR6)-deficient background despite reduced 24-nt siRNA accumulation. Our data highlight a complex cross talk between the quality control RNA machinery, 3′-end pre-mRNA maturation, and RNA-silencing pathways capable of discriminating among different types of aberrant RNAs.
Increased frequencies of T helper type 17 cells in the peripheral blood of patients with acute myeloid leukaemia
Authors: Wu C , Wang S , Wang F , Chen Q , Peng S , Zhang Y , Qian J , Jin J , Xu H 
Published: August 2009

Summary
T helper type 17 (Th17) cells, which represent a novel subset of CD4+ T cells, play an active role in inflammatory and autoimmune diseases. Recent studies have also suggested that they have an impact on solid tumours. However, the nature of Th17 cells in haematological malignancies remains unknown. In this study, we investigated Th17 cell frequency and secretion of related cytokines in patients with acute myeloid leukaemia (AML). First, we found that Th17 cell frequencies were increased significantly in peripheral blood samples from untreated patients with AML, compared with those from healthy volunteers. Moreover, increased interleukin (IL)-17 concentrations accompanied the increased Th17 cell frequencies in these patients. These results suggest that Th17 cells may play a role in the pathogenesis of AML. Secondly, we found that the increased Th17 cell frequencies were reduced when patients achieved complete remission after chemotherapy, suggesting that measurement of Th17 cell frequencies may have clinical value in the evaluation of therapeutic effect. In addition, we found that IL-6 and transforming growth factor (TGF)-β1 concentrations increased in the untreated patients and that IL-6 concentrations showed a positive correlation with the frequencies of Th17 cells, suggesting that IL-6 may play an important role in Th17 cell differentiation in patients with AML.
Contribution of fungal biomass to the growth of the shredder, Pycnopsyche gentilis (Trichoptera: Limnephilidae)
Authors: CHUNG NAMIL , SUBERKROPP KELLER 
Published: August 2009

Summary1. 1. It has been accepted that aquatic hyphomycetes colonising submerged leaves increase the nutritional value of leaf detritus and suggested that fungal biomass plays a greater role in the growth of shredders than leaf tissue itself. However, it is not clear what proportion of the nutritional needs of shredders is met by fungal biomass.2. We fed Pycnopsyche gentilis larvae with tulip poplar (Liriodendron tulipifera) leaf discs colonised by the aquatic hyphomycete, Anguillospora filiformis, which had been radiolabelled to quantify the contribution of fungal carbon to the growth of the shredder at different larval developmental stages. Instantaneous growth rates of larvae on this diet were also estimated.3. When provided with fungal‐colonised leaves (14–16% fungal biomass), the third and the fifth instar larvae of P. gentilis grew at the rates of 0.061 and 0.034 day−1, respectively, but on a diet of sterile leaves, both larval instars lost weight. The incorporation rates of fungal carbon were 31.6 μg C mg−1 AFDM day−1, accounting for 100% of the daily growth rate of the third instar larvae and 8.6 μg C mg−1 AFDM day−1, accounting for 50% of the daily growth rate of the fifth instar larvae.4. These results suggest that leaf material colonised by A. filiformis is a high quality food resource for P. gentilis larvae, and that fungal biomass can contribute significantly to the growth of these larvae. Differences in feeding behaviour and digestive physiology may explain the significantly greater assimilation of fungal biomass by the earlier instar than the final instar. To satisfy their nutritional needs the fifth instar larvae would have to assimilate detrital mass that may have been modified by fungal exoenzymes.
Effect of non‐random dispersal strategies on spatial coexistence mechanisms
Authors: Amarasekare Priyanga 
Published: August 2009

Summary 1.  Random dispersal leads to spatial coexistence via two mechanisms (emigration‐mediated and source–sink), both of which involve the movement of organisms from areas of higher to lower fitness. What is not known is whether such coexistence would occur if organisms dispersed non‐randomly, using cues such as density and habitat quality to gauge fitness differences between habitats. Here, I conduct a comparative analysis of random and non‐random dispersal strategies in a foodweb with a basal resource, top predator, and two intermediate consumers that exhibit a trade‐off between competitive ability and predator susceptibility. 2.  I find a striking contrast between density‐ and habitat‐dependent dispersal in their effects on spatial coexistence. Dispersal in response to competitor and predator density facilitates coexistence while dispersal in response to habitat quality (resource productivity and predator pressure) inhibits it. Moreover, density‐dependent dispersal changes species’ distribution patterns from interspecific segregation to interspecific aggregation, while habitat‐dependent dispersal preserves the interspecific segregation observed in the absence of dispersal. Under density‐dependent dispersal, widespread spatial coexistence results in an overall decline in the abundance of the inferior competitor that is less susceptible to predation and an overall increase in the abundance of the superior competitor that is more susceptible to predation. Under habitat‐dependent dispersal, restricted spatial coexistence results in species’ abundances being essentially unchanged from those observed in the absence of dispersal. 3.  A key outcome is that when the superior competitor moves in the direction of increasing fitness but the inferior competitor does not, spatial coexistence is possible in both resource‐poor and resource‐rich habitats. However, when the inferior competitor moves in the direction of increasing fitness but the superior competitor does not, spatial coexistence is precluded in resource‐poor habitats and greatly reduced in resource‐rich habitats. This suggests that species‐specific differences may play an important role in driving spatial coexistence patterns. 4.  The comparative framework yields predictions that can be tested with experiments that manipulate the relative mobilities of interacting species, or observational data on relative abundances and distribution patterns.