bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of a complex virtual reality simulation to train finger motion for persons with hemiparesis: a proof of concept study
Authors: Adamovich Sergei V , Fluet Gerard G , Mathai Abraham , Qiu Qinyin , Lewis Jeffrey , Merians Alma S 
Published: July 2009

Abstract

Background
Current neuroscience has identified rehabilitation approaches with the potential to stimulate adaptive changes in the brains of persons with hemiparesis. These approaches include, intensive task-oriented training, bimanual activities and balancing proximal and distal upper extremity interventions to reduce competition between these segments for neural territory.

Methods
This paper describes the design and feasibility testing of a robotic/virtual environment system designed to train the hand and arm of persons with hemiparesis. The system employs a simulated piano that presents visual, auditory and tactile feedback comparable to an actual piano. Arm tracking allows patients to train both the arm and hand as a coordinated unit, emphasizing the integration of both transport and manipulation phases. The piano trainer includes songs and scales that can be performed with one or both hands. Adaptable haptic assistance is available for more involved subjects. An algorithm adjusts task difficulty in proportion to subject performance. A proof of concept study was performed on four subjects with upper extremity hemiparesis secondary to chronic stroke to establish: a) the safety and feasibility of this system and b) the concurrent validity of robotically measured kinematic and performance measures to behavioral measures of upper extremity function.

Results
None of the subjects experienced adverse events or responses during or after training. As a group, the subjects improved in both performance time and key press accuracy. Three of the four subjects demonstrated improvements in fractionation, the ability to move each finger individually. Two subjects improved their aggregate time on the Jebsen Test of Hand Function and three of the four subjects improved in Wolf Motor Function Test aggregate time.

Conclusion
The system designed in this paper has proven to be safe and feasible for the training of hand function for persons with hemiparesis. It features a flexible design that allows for the use and further study of adjustments in point of view, bilateral and unimanual treatment modes, adaptive training algorithms and haptically rendered collisions in the context of rehabilitation of the hemiparetic hand.
BioGlue and Peri-strips in lung volume reduction surgery: pilot randomised controlled trial
Authors: Rathinam Sridhar , Naidu Babu V , Nanjaiah Prakash , Loubani Mahmoud , Kalkat Maninder S , Rajesh Pala B 
Published: July 2009

Abstract

Background
Both tissue sealants and buttressing have been advocated to reduce alveolar air leaks from staple lines following Lung Volume Reduction Surgery (LVRS). However, the long term detrimental effects of buttressing material are increasingly apparent. We performed a pilot prospective randomised self controlled trial in patients undergoing LVRS comparing BioGlue and Peri-strips as adjuncts in preventing alveolar air-leaks.

Methods
A pilot prospective self controlled clinical trial was conducted in patients undergoing LVRS. Each patient was treated with BioGlue on one side and pericardial buttress on the other side as an adjunct to the staple line. The sides were randomised for adjuncts with each patient acting as his own control. Duration of air leak, intercostal drainage and time to chest drain removal were the study end points.

Results
10 patients undergoing the procedure were recruited between December 2005 and October 2007. There were 6 men and the mean age was 59.8 ± 4.9 years. There was one mortality due to multi-organ failure. The BioGlue treated side had a shorter mean duration of air-leak (3.0 ± 4.6 versus 6.5 ± 6.9 days), lesser chest drainage volume (733 ± 404 ml versus 1001 ± 861) and shorter time to chest drain removal (9.7 ± 10.6 versus 11.5 ± 11.1 days) compared with Peri-strips.

Conclusion
This study demonstrates comparable efficacy of BioGlue and Peri-strips, however there is a trend favouring the BioGlue treated side in terms of reduction in air-leak, chest drainage volumes, duration of chest drainage and significant absence of complications. A larger sample size is needed to validate this result.
An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules
Authors: Qin Huaxia , Chan Michael WY , Liyanarachchi Sandya , Balch Curtis , Potter Dustin , Souriraj Irene J , Cheng Alfred SL , Agosto-Perez Francisco J , Nikonova Elena V , Yan Pearlly S , Lin Huey-Jen , Nephew Kenneth P , Saltz Joel H , Showe Louise C , Huang Tim HM , Davuluri Ramana V 
Published: July 2009

Abstract

Background
The TGF-β/SMAD pathway is part of a broader signaling network in which crosstalk between pathways occurs. While the molecular mechanisms of TGF-β/SMAD signaling pathway have been studied in detail, the global networks downstream of SMAD remain largely unknown. The regulatory effect of SMAD complex likely depends on transcriptional modules, in which the SMAD binding elements and partner transcription factor binding sites (SMAD modules) are present in specific context.

Results
To address this question and develop a computational model for SMAD modules, we simultaneously performed chromatin immunoprecipitation followed by microarray analysis (ChIP-chip) and mRNA expression profiling to identify TGF-β/SMAD regulated and synchronously coexpressed gene sets in ovarian surface epithelium. Intersecting the ChIP-chip and gene expression data yielded 150 direct targets, of which 141 were grouped into 3 co-expressed gene sets (sustained up-regulated, transient up-regulated and down-regulated), based on their temporal changes in expression after TGF-β activation. We developed a data-mining method driven by the Random Forest algorithm to model SMAD transcriptional modules in the target sequences. The predicted SMAD modules contain SMAD binding element and up to 2 of 7 other transcription factor binding sites (E2F, P53, LEF1, ELK1, COUPTF, PAX4 and DR1).

Conclusion
Together, the computational results further the understanding of the interactions between SMAD and other transcription factors at specific target promoters, and provide the basis for more targeted experimental verification of the co-regulatory modules.
Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions
Authors: Pache Roland A , Babu M Madan , Aloy Patrick 
Published: July 2009

Abstract

Background
Understanding how individual genes contribute towards the fitness of an organism is a fundamental problem in biology. Although recent genome-wide screens have generated abundant data on quantitative fitness for single gene knockouts, very few studies have systematically integrated other types of biological information to understand how and why deletion of specific genes give rise to a particular fitness effect. In this study, we combine quantitative fitness data for single gene knock-outs in yeast with large-scale interaction discovery experiments to understand the effect of gene deletion on the modular architecture of protein complexes, under different growth conditions.

Results
Our analysis reveals that genes in complexes show more severe fitness effects upon deletion than other genes but, in contrast to what has been observed in binary protein-protein interaction networks, we find that this is not related to the number of complexes in which they are present. We also find that, in general, the core and attachment components of protein complexes are equally important for the complex machinery to function. However, when quantifying the importance of core and attachments in single complex variations, or isoforms, we observe that this global trend originates from either the core or the attachment components being more important for strain fitness, both being equally important or both being dispensable. Finally, our study reveals that different isoforms of a complex can exhibit distinct fitness patterns across growth conditions.

Conclusion
This study presents a powerful approach to unveil the molecular basis for various complex phenotypic profiles observed in gene deletion experiments. It also highlights some interesting cases of potential functional compensation between protein paralogues and suggests a new piece to fit into the histone-code puzzle.
Identification and characterization of novel amphioxus microRNAs by Solexa sequencing
Authors: Chen Xi , Li Qibin , Wang Jin , Guo Xing , Jiang Xiangrui , Ren Zhiji , Weng Chunyue , Sun Guoxun , Wang Xiuqiang , Liu Yaping , Ma Lijia , Chen Jun-Yuan , Wang Jun , Zen Ke , Zhang Junfeng , Zhang Chen-Yu 
Published: July 2009

Abstract
Background
microRNAs (miRNAs) are endogenous small non-coding RNAs that regulate gene expression at the post-transcriptional level. While the number of known human and murine miRNAs is continuously increasing, information regarding miRNAs from other species such as amphioxus remains limited.

Results
We combined Solexa sequencing with computational techniques to identify novel miRNAs in the amphioxus species B. belcheri (Gray). This approach allowed us to identify 113 amphioxus miRNA genes. Among them, 55 were conserved across species and encoded 45 non-redundant mature miRNAs, whereas 58 were amphioxus-specific and encoded 53 mature miRNAs. Validation of our results with microarray and stem-loop quantitative RT-PCR revealed that Solexa sequencing is a powerful tool for miRNA discovery. Analyzing the evolutionary history of amphioxus miRNAs, we found that amphioxus possesses many miRNAs unique to chordates and vertebrates, and these may thus represent key steps in the evolutionary progression from cephalochordates to vertebrates. We also found that amphioxus is more similar to vertebrates than are tunicates with respect to their miRNA phylogenetic histories.

Conclusions
Taken together, our results indicate that Solexa sequencing allows the successful discovery of novel miRNAs from amphioxus with high accuracy and efficiency. More importantly, our study provides an opportunity to decipher how the elaboration of the miRNA repertoire that occurred during chordate evolution contributed to the evolution of the vertebrate body plan.
Testing the use/disuse hypothesis: pectoral and leg muscle changes in captive barnacle geese Branta leucopsis during wing moult
Authors: Portugal Steven J. , Thorpe Susannah K. S. , Green Jonathan A. , Myatt Julia P. , Butler Patrick J. 
Published: July 2009

SUMMARY
Previous studies on wild moulting waterfowl have demonstrated that flight and leg muscles experience periods of hypertrophy and atrophy. This is thought to be in response to the change in use of the locomotor muscles as described in the use/disuse hypothesis. We tested this hypothesis using captive barnacle geese. Forty geese were dissected before, during and after wing moult, to determine the changes in mass and functional capacity of the flight and leg muscles. Physiological cross sectional areas (PCSA) and mean fascicle lengths of functional muscle groups were calculated to ascertain the force-producing capabilities of the flight and leg muscles. At the onset of moult, flight muscle mass was at a minimum, having atrophied by 35% compared with pre-moult levels, but it returned to pre-moult levels by the end of wing moult. By contrast, the leg muscles hypertrophied during wing moult by 29%,and the PCSA of individual muscle groups increased substantially. Increases in mass, PCSA and fascicle length of individual leg muscle groups during moult suggest that, when flightless, the leg muscles are functionally adapted to provide greater force and/or manoeuvrability to the birds, to aid ground-based escape from predators. Through studying captive animals that are unable to fly, it has been possible to conclude that the major changes in leg and flight muscle in moulting captive geese cannot be explained through use or disuse. Instead, changes seem to be compensatory or to occur in anticipation of changes in locomotor patterns.
A body composition model to estimate mammalian energy stores and metabolic rates from body mass and body length, with application to polar bears
Authors: Molnár Péter K. , Klanjscek Tin , Derocher Andrew E. , Obbard Martyn E. , Lewis Mark A. 
Published: July 2009

SUMMARYMany species experience large fluctuations in food availability and depend on energy from fat and protein stores for survival, reproduction and growth. Body condition and, more specifically, energy stores thus constitute key variables in the life history of many species. Several indices exist to quantify body condition but none can provide the amount of stored energy. To estimate energy stores in mammals, we propose a body composition model that differentiates between structure and storage of an animal. We develop and parameterize the model specifically for polar bears (Ursus maritimus Phipps)but all concepts are general and the model could be easily adapted to other mammals. The model provides predictive equations to estimate structural mass,storage mass and storage energy from an appropriately chosen measure of body length and total body mass. The model also provides a means to estimate basal metabolic rates from body length and consecutive measurements of total body mass. Model estimates of body composition, structural mass, storage mass and energy density of 970 polar bears from Hudson Bay were consistent with the life history and physiology of polar bears. Metabolic rate estimates of fasting adult males derived from the body composition model corresponded closely to theoretically expected and experimentally measured metabolic rates. Our method is simple, non-invasive and provides considerably more information on the energetic status of individuals than currently available methods.
Carbon and nitrogen stable isotope turnover rates and diet–tissue discrimination in Florida manatees (Trichechus manatus latirostris)
Authors: Alves-Stanley Christy D. , Worthy Graham A. J. 
Published: July 2009

SUMMARY
The Florida manatee (Trichechus manatus latirostris) is a herbivorous marine mammal that occupies freshwater, estuarine and marine habitats. Despite being considered endangered, relatively little is known about its feeding ecology. The present study expands on previous work on manatee feeding ecology by providing critical baseline parameters for accurate isotopic data interpretation. Stable carbon and nitrogen isotope ratios were examined over a period of more than 1 year in the epidermis of rescued Florida manatees that were transitioning from a diet of aquatic forage to terrestrial forage (lettuce). The mean half-life for 13C turnover was 53 and 59 days for skin from manatees rescued from coastal and riverine regions,respectively. The mean half-life for 15N turnover was 27 and 58 days, respectively. Because of these slow turnover rates, carbon and nitrogen stable isotope analysis in manatee epidermis is useful in summarizing average dietary intake over a long period of time rather than assessing recent diet. In addition to turnover rate, a diet–tissue discrimination value of 2.8‰ for 13C was calculated for long-term captive manatees on a lettuce diet. Determining both turnover rate and diet–tissue discrimination is essential in order to accurately interpret stable isotope data.
Intensity of activation and timing of deactivation modulate elastic energy storage and release in a pennate muscle and account for gait-specific initiation of limb protraction in the horse
Authors: Lichtwark Glen A. , Watson Johanna C. , Mavrommatis Sophia , Wilson Alan M. 
Published: July 2009

SUMMARY
The equine biceps brachii (biceps) initiates rapid limb protraction through a catapult mechanism. Elastic strain energy is slowly stored in an internal tendon and is then rapidly released to protract the forelimb. The muscle fibres are short, have little scope for length change and can therefore only shorten slowly compared with the speed at which the whole muscle must shorten,which makes them poor candidates for driving rapid limb protraction. We suggest that the muscle fibres in the biceps act to modulate the elastic energy output of the muscle–tendon unit (MTU) to meet the demands of locomotion under different conditions. We hypothesise that more elastic strain energy is stored and released from the biceps MTU during higher speed locomotion to accommodate the increase in energy required to protract the limb and that this can be achieved by varying the length change and activation conditions of the muscle. We examined the work performed by the biceps during trot and canter using an inverse dynamics analysis (IDA). We then used excised biceps muscles to determine how much work could be performed by the muscle in active and passive stretch–shorten cycles. A muscle model was developed to investigate the influence of changes in activation parameters on energy storage and energy return from the biceps MTU. Increased biceps MTU length change and increased work performed by the biceps MTU were found at canter compared with at trot. More work was performed by the ex vivo biceps MTU following activation of the muscle and by increasing muscle length change. However, the ratio of active to passive work diminished with increasing length change. The muscle model demonstrated that duration and timing of activation during stretch–shorten cycles could modulate the elastic energy storage and return from the biceps. We conclude that the equine biceps MTU acts as a tuneable spring and the contractile component functions to modulate the energy required for rapid forelimb protraction at different speeds.
Endothermy in birds: underlying molecular mechanisms
Authors: Walter Isabel , Seebacher Frank 
Published: July 2009

SUMMARY
Endothermy is significant in vertebrate evolution because it changes the relations between animals and their environment. How endothermy has evolved in archosaurs (birds, crocodiles and dinosaurs) is controversial especially because birds do not possess brown adipose tissue, the specialized endothermic tissue of mammals. Internal heat production is facilitated by increased oxidative metabolic capacity, accompanied by the uncoupling of aerobic metabolism from energy (ATP) production. Here we show that the transition from an ectothermic to an endothermic metabolic state in developing chicken embryos occurs by the interaction between increased basal ATP demand(Na+/K+-ATPase activity and gene expression), increased oxidative capacity and increased uncoupling of mitochondria; this process is controlled by thyroid hormone via its effect on PGC1α and adenine nucleotide translocase (ANT) gene expression. Mitochondria become more uncoupled during development, but unlike in mammals, avian uncoupling protein(avUCP) does not uncouple electron transport from oxidative phosphorylation and therefore plays no role in heat production. Instead, ANT is the principal uncoupling protein in birds. The relationship between oxidative capacity and uncoupling indicates that there is a continuum of phenotypes that fall between the extremes of selection for increased heat production and increased aerobic activity, whereas increased cellular ATP demand is a prerequisite for increased oxidative capacity.
Thermal activation of escape swimming in post-hatching Xenopus laevis frog larvae
Authors: Sillar Keith T. , Robertson R. Meldrum 
Published: July 2009

SUMMARY
Survival requires the selection of appropriate behavioural responses in the face of danger. With respect to the threat of predation, both the decision to escape and the underlying neuronal mechanisms have been extensively studied,but processes that trigger evasion of abiotic stressors, which are potentially hazardous to survival, are less well understood. Here, we document the interplay between rhythmic locomotory and `C-start' escape swimming in Xenopus frog larvae when exposed to hyperthermic conditions. As temperature rises, swim cycle frequency increases while swim bout duration decreases, until swimming can no longer be initiated by sensory stimuli. Above a critical higher temperature, more intense sequences of spontaneous high amplitude C-start escape activity occur. Each C-start is followed by a few cycles of fast rhythmic swimming in which activity alternates between the two sides. The initial, high amplitude ventral root burst of an escape sequence propagates rostrocaudally approximately threefold faster than subsequent cycles. The high conduction velocity of this initial burst is consistent with the activation of a Mauthner neuron, one of a pair of giant reticulospinal neurons in fish and amphibians. In support of the involvement of a Mauthner neuron, unilateral lesions of the caudal hindbrain eliminated escape activity on the operated side, but activity remained on the un-operated side. Behaviourally, tadpoles responded to temperature ramps with a sequence of C-start responses in which the body arced through ∼130° in 22 ms,followed by high frequency swimming. These results suggest that high temperature activates the Mauthner neurons to trigger C-start escape behaviour.
Effects of crowding on ornithine–urea cycle enzyme mRNA expression and activity in gulf toadfish (Opsanus beta)
Authors: Laberge Tammy , Walsh Patrick J. , McDonald M. Danielle 
Published: July 2009

SUMMARY
The gulf toadfish (Opsanus beta) is a facultatively ureotelic fish that excretes primarily urea under conditions of crowding or confinement. To examine the relationship between ammonia production, urea production and the ornithine–urea cycle (O–UC) enzyme activity and mRNA expression,we subjected toadfish to two-day and seven-day crowding regimes. Plasma cortisol levels were measured and liver tissue was assayed for ammonia and urea concentrations. Liver glutamine synthetase (GS), carbamoyl phosphate synthetase III (CPS), ornithine carbamoyl transferase (OCT) and arginase (ARG)activities were also measured. Quantitative PCR was utilized to determine liver GS, CPS, OCT, ARG, argininosuccinate synthetase (ASS) and argininosuccinate lyase (ASL) mRNA expression. Hepatic ammonia concentrations decreased with increased duration of crowding whereas liver urea and circulating cortisol levels increased. An elevation in enzyme activity with increased duration of crowding was observed for all four O-UC enzymes examined. By contrast, mRNA expression was variable for the O–UC enzymes and only CPS and ASS had mRNA expression levels that were elevated in crowded fish. These results suggest that the activities of O–UC enzymes are better predictors for urea production than O–UC enzyme mRNA expression levels.
The evolution of speed, size and shape in modern athletics
Authors: Charles Jordan D. , Bejan Adrian 
Published: July 2009

SUMMARYIn the present study, we show that the fastest runners and swimmers are becoming not only faster but also heavier, taller and more slender. During the past century, the world record speeds for 100 m-freestyle and 100 m-dash have increased with body mass (M) raised to the power 1/6, in accordance with the constructal scaling of animal locomotion. The world records also show that the speeds have increased in proportion with body heights (H)raised to the power 1/2, in accordance with animal locomotion scaling. If the athlete's body is modeled with two length scales (H, body width L), the (M, H) data can be used to calculate the slenderness of the body, H/L. The world records show that the body slenderness is increasing very slowly over time.