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1.  Low frequency depression of H-reflexes in humans with acute and chronic spinal-cord injury 
Experimental brain research  2000;133(2):233-241.
We measured low-frequency depression of soleus H-reflexes in individuals with acute (n=5) and chronic (n=7) spinal-cord injury and in able-bodied controls (n=7). In one acute subject, we monitored longitudinal changes in low-frequency depression of H-reflexes over 44 weeks and examined the relationship between H-reflex depression and soleus-muscle fatigue properties. Soleus H-reflexes were elicited at 0.1, 0.2, 1, 5, and 10 Hz. The mean peak-to-peak amplitude of ten reflexes at each frequency was calculated, and values obtained at each frequency were normalized to 0.1 Hz. H-reflex amplitude decreased with increasing stimulation frequency in all three groups, but H-reflex suppression was significantly larger in the able-bodied and acute groups than in the chronic group. The acute subject who was monitored longitudinally displayed reduced low-frequency depression with increasing time post injury. At 44 weeks post injury, the acute subject’s H-reflex depression was similar to that of chronic subjects, and his soleus fatigue index (assessed with a modified Burke fatigue protocol) dropped substantially, consistent with transformation to faster muscle. There was a significant inverse correlation over the 44 weeks between the fatigue index and the mean normalized H-reflex amplitude at 1, 5, and 10 Hz. We conclude that: (1) the chronically paralyzed soleus muscle displays impaired low-frequency depression of H-reflexes, (2) attenuation of rate-sensitive depression in humans with spinal-cord injury occurs gradually, and (3) changes in H-reflex excitability are generally correlated with adaptation of the neuromuscular system. Possible mechanisms underlying changes in low-frequency depression and their association with neuromuscular adaptation are discussed.
PMCID: PMC4034370  PMID: 10968224
Spasticity; Paralysis; Plasticity; Muscle; Fatigue
2.  Combinatorial Communication in Bacteria: Implications for the Origins of Linguistic Generativity 
PLoS ONE  2014;9(4):e95929.
Combinatorial communication, in which two signals are used together to achieve an effect that is different to the sum of the effects of the component parts, is apparently rare in nature: it is ubiquitous in human language, appears to exist in a simple form in some non-human primates, but has not been demonstrated in other species. This observed distribution has led to the pair of related suggestions, that (i) these differences in the complexity of observed communication systems reflect cognitive differences between species; and (ii) that the combinations we see in non-human primates may be evolutionary pre-cursors of human language. Here we replicate the landmark experiments on combinatorial communication in non-human primates, but in an entirely different species, unrelated to humans, and with no higher cognition: the bacterium Pseudomonas aeruginosa. Using the same general methods as the primate studies, we find the same general pattern of results: the effect of the combined signal differs from the composite effect of the two individual signals. This suggests that advanced cognitive abilities and large brains do not necessarily explain why some species have combinatorial communication systems and others do not. We thus argue that it is premature to conclude that the systems observed in non-human primates are evolutionarily related to language. Our results illustrate the value of an extremely broad approach to comparative research.
doi:10.1371/journal.pone.0095929
PMCID: PMC3997515  PMID: 24759740
3.  Lower Extremity Passive Range of Motion in Community-Ambulating Stroke Survivors 
Background
Physical therapists may prescribe stretching exercises for individuals with stroke to improve joint integrity and to reduce the risk of secondary musculoskeletal impairment. While deficits in passive range of motion (PROM) exist in stroke survivors with severe hemiparesis and spasticity, the extent to which impaired lower extremity PROM occurs in community-ambulating stroke survivors remains unclear. This study compared lower extremity PROM in able-bodied individuals and independent community-ambulatory stroke survivors with residual stroke-related neuromuscular impairments. Our hypothesis was that the stroke group would show decreased lower extremity PROM in the paretic but not the nonparetic side and that decreased PROM would be associated with increased muscle stiffness and decreased muscle length.
Methods
Individuals with chronic poststroke hemiparesis who reported the ability to ambulate independently in the community (n = 17) and age-matched control subjects (n = 15) participated. PROM during slow (5 degrees/sec) hip extension, hip flexion, and ankle dorsiflexion was examined bilaterally using a dynamometer that measured joint position and torque. The maximum angular position of the joint (ANGmax), torque required to achieve ANGmax (Tmax), and mean joint stiffness (K) were measured. Comparisons were made between able-bodied and paretic and able-bodied and nonparetic limbs.
Results
Contrary to our expectations, between-group differences in ANGmax were observed only during hip extension in which ANGmax was greater bilaterally in people post-stroke compared to control subjects (P ≤ 0.05; stroke = 13 degrees, able-bodied = −1 degree). Tmax, but not K, was also significantly higher during passive hip extension in paretic and nonparetic limbs compared to control limbs (P ≤ 0.05; stroke = 40 Nm, able-bodied = 29 Nm). Compared to the control group, Tmax was increased during hip flexion in the paretic and nonparetic limbs of post-stroke subjects (P ≤ 0.05, stroke = 25 Nm, able-bodied = 18 Nm). K in the nonparetic leg was also increased during hip flexion (P ≤ 0.05, nonparetic = 0.52 Nm/degree, able-bodied = 0.37 Nm/degree.)
Conclusion
This study demonstrates that community-ambulating stroke survivors with residual neuromuscular impairments do not have decreased lower extremity PROM caused by increased muscle stiffness or decreased muscle length. In fact, the population of stroke survivors examined here appears to have more hip extension PROM than age-matched able-bodied individuals. The clinical implications of these data are important and suggest that lower extremity PROM may not interfere with mobility in community-ambulating stroke survivors. Hence, physical therapists may choose to recommend activities other than stretching exercises for stroke survivors who are or will become independent community ambulators.
doi:10.1097/NPT.0b013e31816594ea
PMCID: PMC3963266  PMID: 18463552
cerebral vascular accident (CVA); hemiparesis; muscle; range of motion (ROM); spasticity
4.  High-Throughput Chemical Screening for Antivirulence Developmental Phenotypes in Trypanosoma brucei 
Eukaryotic Cell  2014;13(3):412-426.
In the bloodstream of mammalian hosts, the sleeping sickness parasite, Trypanosoma brucei, exists as a proliferative slender form or a nonproliferative, transmissible, stumpy form. The transition between these developmental forms is controlled by a density-dependent mechanism that is important for the parasite's infection dynamics, immune evasion via ordered antigenic variation, and disease transmissibility. However, stumpy formation has been lost in most laboratory-adapted trypanosome lines, generating monomorphic parasites that proliferate uncontrolled as slender forms in vitro and in vivo. Nonetheless, these forms are readily amenable to cell culture and high-throughput screening for trypanocidal lead compounds. Here, we have developed and exploited a high-throughput screen for developmental phenotypes using a transgenic monomorphic cell line expressing a reporter under the regulation of gene control signals from the stumpy-specific molecule PAD1. Using a whole-cell fluorescence-based assay to screen over 6,000 small molecules from a kinase-focused compound library, small molecules able to activate stumpy-specific gene expression and proliferation arrest were assayed in a rapid assay format. Independent follow-up validation identified one hit able to induce modest, yet specific, changes in mRNA expression indicative of a partial differentiation to stumpy forms in monomorphs. Further, in pleomorphs this compound induced a stumpy-like phenotype, entailing growth arrest, morphological changes, PAD1 expression, and enhanced differentiation to procyclic forms. This not only provides a potential tool compound for the further understanding of stumpy formation but also demonstrates the use of high-throughput screening in the identification of compounds able to induce specific phenotypes, such as differentiation, in African trypanosomes.
doi:10.1128/EC.00335-13
PMCID: PMC3957582  PMID: 24442893
5.  Parasite-Derived MicroRNAs in Host Serum As Novel Biomarkers of Helminth Infection 
Background
MicroRNAs (miRNAs) are a class of short non-coding RNA that play important roles in disease processes in animals and are present in a highly stable cell-free form in body fluids. Here, we examine the capacity of host and parasite miRNAs to serve as tissue or serum biomarkers of Schistosoma mansoni infection.
Methods/Principal Findings
We used Exiqon miRNA microarrays to profile miRNA expression in the livers of mice infected with S. mansoni at 7 weeks post-infection. Thirty-three mouse miRNAs were differentially expressed in infected compared to naïve mice (>2 fold change, p<0.05) including miR-199a-3p, miR-199a-5p, miR-214 and miR-21, which have previously been associated with liver fibrosis in other settings. Five of the mouse miRNAs were also significantly elevated in serum by twelve weeks post-infection. Sequencing of small RNAs from serum confirmed the presence of these miRNAs and further revealed eleven parasite-derived miRNAs that were detectable by eight weeks post infection. Analysis of host and parasite miRNA abundance by qRT-PCR was extended to serum of patients from low and high infection sites in Zimbabwe and Uganda. The host-derived miRNAs failed to distinguish uninfected from infected individuals. However, analysis of three of the parasite-derived miRNAs (miR-277, miR-3479-3p and bantam) could detect infected individuals from low and high infection intensity sites with specificity/sensitivity values of 89%/80% and 80%/90%, respectively.
Conclusions
This work identifies parasite-derived miRNAs as novel markers of S. mansoni infection in both mice and humans, with the potential to be used with existing techniques to improve S. mansoni diagnosis. In contrast, although host miRNAs are differentially expressed in the liver during infection their abundance levels in serum are variable in human patients and may be useful in cases of extreme pathology but likely hold limited value for detecting prevalence of infection.
Author Summary
Schistosomiasis is a chronic disease caused by blood flukes that affects over 200 million people worldwide, of which 90% live in Sub-Saharan Africa. In the field setting schistosomiasis caused by S. mansoni is diagnosed by detection of parasite eggs in stool samples using microscopic techniques. Here we investigate the potential of microRNAs (miRNAs), a class of short noncoding RNAs, to act as biomarkers of S. mansoni infection. We have identified a specific subset of murine miRNAs whose expression is significantly altered in the liver between 6–12 weeks post infection. However their abundance in serum is not significantly different between naïve and S. mansoni-infected mice until twelve weeks post infection and they do not display consistent differential abundance in the serum of infected versus uninfected humans. In contrast, three parasite-derived miRNAs (miR-277, bantam and miR-3479-3p) were detected in the serum of infected mice and human patients and the combined detection of these miRNAs could distinguish S. mansoni infected from uninfected individuals from low and high infection intensity areas with 89%/80% or 80%/90% specificity/sensitivity, respectively. These results demonstrate that miRNAs of parasite origin are a new class of serum biomarker for detecting S. mansoni and likely other helminth infections.
doi:10.1371/journal.pntd.0002701
PMCID: PMC3930507  PMID: 24587461
6.  EEG during pedaling: Evidence for cortical control of locomotor tasks 
Objective
This study characterized the brain electrical activity during pedaling, a locomotor-like task, in humans. We postulated that phasic brain activity would be associated with active pedaling, consistent with a cortical role in locomotor tasks.
Methods
Sixty four channels of electroencephalogram (EEG) and 10 channels of electromyogram (EMG) data were recorded from 10 neurologically-intact volunteers while they performed active and passive (no effort) pedaling on a custom-designed stationary bicycle. Ensemble averaged waveforms, 2 dimensional topographic maps and amplitude of the β (13–35 Hz) frequency band were analyzed and compared between active and passive trials.
Results
The peak-to-peak amplitude (peak positive–peak negative) of the EEG waveform recorded at the Cz electrode was higher in the passive than the active trials (p < 0.01). β-band oscillations in electrodes overlying the leg representation area of the cortex were significantly desynchronized during active compared to the passive pedaling (p < 0.01). A significant negative correlation was observed between the average EEG waveform for active trials and the composite EMG (summated EMG from both limbs for each muscle) of the rectus femoris (r = −0.77, p < 0.01) the medial hamstrings (r = −0.85, p < 0.01) and the tibialis anterior (r = −0.70, p < 0.01) muscles.
Conclusions
These results demonstrated that substantial sensorimotor processing occurs in the brain during pedaling in humans. Further, cortical activity seemed to be greatest during recruitment of the muscles critical for transitioning the legs from flexion to extension and vice versa.
Significance
This is the first study demonstrating the feasibility of EEG recording during pedaling, and owing to similarities between pedaling and bipedal walking, may provide valuable insight into brain activity during locomotion in humans.
doi:10.1016/j.clinph.2012.08.021
PMCID: PMC3912946  PMID: 23036179
Electroencephalography; Pedaling; Brain activity
7.  Direction-Dependent Phasing of Locomotor Muscle Activity Is Altered Post-Stroke 
Journal of neurophysiology  2004;92(4):2207-2216.
A major contributor to impaired locomotion post-stroke is abnormal phasing of muscle activity. While inappropriate paretic muscle phasing adapts to changing body orientation, load, and speed, it remains unclear whether paretic muscle phasing adapts to reversal of locomotor direction. We examined muscle phasing in backward pedaling, a task that requires shifts in biarticular but not uniarticular muscle phasing relative to forward pedaling. We hypothesized that if paretic and neurologically intact muscle phasing adapt similarly, then paretic biarticular but not paretic uniarticular muscles would shift phasing in backward pedaling. Paretic and neurologically intact individuals pedaled forward and backward while recording electromyograms (EMGs) from vastus medialis (VM), soleus (SOL), rectus femoris (RF), semimembranosus (SM), and biceps femoris (BF). Changes in muscle phasing were assessed by comparing the probability of muscle activity in forward and backward pedaling throughout 18 pedaling cycles. Paretic uniarticular muscles (VM and SOL) showed phase-advanced activity in backward versus forward pedaling, whereas the corresponding neurologically intact muscles showed little to no phasing change. Paretic biarticular muscles were less likely than neurologically intact biarticular muscles to display phasing changes in backward pedaling. Paretic RF displayed no phase change during backward pedaling, and paretic BF displayed no consistent adaptation to backward pedaling. Paretic SM was the only muscle to display backward/forward phase changes that were similar to the neurologically intact group. We conclude that paretic uniarticular muscles are more susceptible and paretic biarticular muscles are less susceptible to direction-dependent phase shifts, consistent with altered sensory integration and impaired cortical control of locomotion.
doi:10.1152/jn.01207.2003
PMCID: PMC3912995  PMID: 15175363
8.  Is the ICU staff satisfied with the computerized physician order entry? A cross-sectional survey study 
Objective
To evaluate the satisfaction of the intensive care unit staff with a computerized physician order entry and to compare the concept of the computerized physician order entry relevance among intensive care unit healthcare workers.
Methods
We performed a cross-sectional survey to assess the satisfaction of the intensive care unit staff with the computerized physician order entry in a 30-bed medical/surgical adult intensive care unit using a self-administered questionnaire. The questions used for grading satisfaction levels were answered according to a numerical scale that ranged from 1 point (low satisfaction) to 10 points (high satisfaction).
Results
The majority of the respondents (n=250) were female (66%) between the ages of 30 and 35 years of age (69%). The overall satisfaction with the computerized physician order entry scored 5.74±2.14 points. The satisfaction was lower among physicians (n=42) than among nurses, nurse technicians, respiratory therapists, clinical pharmacists and diet specialists (4.62±1.79 versus 5.97±2.14, p<0.001); satisfaction decreased with age (p<0.001). Physicians scored lower concerning the potential of the computerized physician order entry for improving patient safety (5.45±2.20 versus 8.09±2.21, p<0.001) and the ease of using the computerized physician order entry (3.83±1.88 versus 6.44±2.31, p<0.001). The characteristics independently associated with satisfaction were the system's user-friendliness, accuracy, capacity to provide clear information, and fast response time.
Conclusion
Six months after its implementation, healthcare workers were satisfied, albeit not entirely, with the computerized physician order entry. The overall users' satisfaction with computerized physician order entry was lower among physicians compared to other healthcare professionals. The factors associated with satisfaction included the belief that digitalization decreased the workload and contributed to the intensive care unit quality with a user-friendly and accurate system and that digitalization provided concise information within a reasonable time frame.
doi:10.5935/0103-507X.20140001
PMCID: PMC4031891  PMID: 24770682
Medical order entry system; Physician practice patterns; Health care surveys; Attitude of health personnel; Job satisfaction
10.  Lifetime Paid Work and Mental Health Problems among Poor Urban 9-to-13-Year-Old Children in Brazil 
The Scientific World Journal  2013;2013:815218.
Objective. To verify if emotional/behavioral problems are associated with lifetime paid work in poor urban children, when taking into account other potential correlates. Methods. Cross-sectional study focused on 9-to-13-year-old children (n = 212). In a probabilistic sample of clusters of eligible households (women 15–49 years and son/daughter <18 years), one mother-child pair was randomly selected per household (n = 813; response rate = 82.4%). CBCL/6-18 identified child emotional/behavioral problems. Potential correlates include child gender and age, socioeconomic status/SES, maternal education, parental working status, and family social isolation, among others. Multivariate analysis examined the relationship between emotional/behavioral problems and lifetime paid work in the presence of significant correlates. Findings. All work activities were non-harmful (e.g., selling fruits, helping parents at their small business, and baby sitting). Children with lower SES and socially isolated were more involved in paid work than less disadvantaged peers. Children ever exposed to paid work were four times more likely to present anxiety/depression symptoms at a clinical level compared to non-exposed children. Multivariate modeling identified three independent correlates: child pure internalizing problems, social isolation, and low SES. Conclusion. There is an association between lifetime exposure to exclusively non-harmful paid work activities and pure internalizing problems even when considering SES variability and family social isolation.
doi:10.1155/2013/815218
PMCID: PMC3834988  PMID: 24302872
11.  Secretion of Protective Antigens by Tissue-Stage Nematode Larvae Revealed by Proteomic Analysis and Vaccination-Induced Sterile Immunity 
PLoS Pathogens  2013;9(8):e1003492.
Gastrointestinal nematode parasites infect over 1 billion humans, with little evidence for generation of sterilising immunity. These helminths are highly adapted to their mammalian host, following a developmental program through successive niches, while effectively down-modulating host immune responsiveness. Larvae of Heligmosomoides polygyrus, for example, encyst in the intestinal submucosa, before emerging as adult worms into the duodenal lumen. Adults release immunomodulatory excretory-secretory (ES) products, but mice immunised with adult H. polygyrus ES become fully immune to challenge infection. ES products of the intestinal wall 4th stage (L4) larvae are similarly important in host-parasite interactions, as they readily generate sterile immunity against infection, while released material from the egg stage is ineffective. Proteomic analyses of L4 ES identifies protective antigen targets as well as potential tissue-phase immunomodulatory molecules, using as comparators the adult ES proteome and a profile of H. polygyrus egg-released material. While 135 proteins are shared between L4 and adult ES, 72 are L4 ES-specific; L4-specific proteins correspond to those whose transcription is restricted to larval stages, while shared proteins are generally transcribed by all life cycle forms. Two protein families are more heavily represented in the L4 secretome, the Sushi domain, associated with complement regulation, and the ShK/SXC domain related to a toxin interfering with T cell signalling. Both adult and L4 ES contain extensive but distinct arrays of Venom allergen/Ancylostoma secreted protein-Like (VAL) members, with acetylcholinesterases (ACEs) and apyrase APY-3 particularly abundant in L4 ES. Serum antibodies from mice vaccinated with L4 and adult ES react strongly to the VAL-1 protein and to ACE-1, indicating that these two antigens represent major vaccine targets for this intestinal nematode. We have thus defined an extensive and novel repertoire of H. polygyrus proteins closely implicated in immune modulation and protective immunity.
Author Summary
Intestinal helminth parasites are highly prevalent in humans and animals, and survive for long periods by deviating the host immune system. No vaccines are currently available to control these infections. Many helminths invade through barrier surfaces (such as the skin or the digestive tract) and develop through tissue larval stages before reaching their final niche such as the intestinal lumen. We studied the tissue larval stage of a mouse parasite, Heligmosomoides polygyrus, to test whether proteins released by this stage could elicit protective immunity, and found that they indeed constitute very effective vaccine antigens. Proteomic analysis to identify the individual proteins released by the larvae demonstrated that while many products are shared between tissue-dwelling larvae and adults occupying the intestinal lumen, larvae express higher levels of two gene families linked to immunomodulation, namely the Sushi protein family and the ShK toxin family. Antibody analysis of serum from vaccinated mice identified two major antigens recognised by the protective immune response as VAL-1 and ACE-1, which are respectively members of the venom allergen and acetylcholinesterase families. This work establishes that tissue larvae are the source of protective antigens for future vaccines, and highlights their production of two potentially immunomodulatory gene families.
doi:10.1371/journal.ppat.1003492
PMCID: PMC3744408  PMID: 23966853
12.  Clinically Relevant Mutant DNA Gyrase Alters Supercoiling, Changes the Transcriptome, and Confers Multidrug Resistance 
mBio  2013;4(4):e00273-13.
ABSTRACT
Bacterial DNA is maintained in a supercoiled state controlled by the action of topoisomerases. Alterations in supercoiling affect fundamental cellular processes, including transcription. Here, we show that substitution at position 87 of GyrA of Salmonella influences sensitivity to antibiotics, including nonquinolone drugs, alters global supercoiling, and results in an altered transcriptome with increased expression of stress response pathways. Decreased susceptibility to multiple antibiotics seen with a GyrA Asp87Gly mutant was not a result of increased efflux activity or reduced reactive-oxygen production. These data show that a frequently observed and clinically relevant substitution within GyrA results in altered expression of numerous genes, including those important in bacterial survival of stress, suggesting that GyrA mutants may have a selective advantage under specific conditions. Our findings help contextualize the high rate of quinolone resistance in pathogenic strains of bacteria and may partly explain why such mutant strains are evolutionarily successful.
IMPORTANCE
Fluoroquinolones are a powerful group of antibiotics that target bacterial enzymes involved in helping bacteria maintain the conformation of their chromosome. Mutations in the target enzymes allow bacteria to become resistant to these antibiotics, and fluoroquinolone resistance is common. We show here that these mutations also provide protection against a broad range of other antimicrobials by triggering a defensive stress response in the cell. This work suggests that fluoroquinolone resistance mutations may be beneficial under a range of conditions.
doi:10.1128/mBio.00273-13
PMCID: PMC3735185  PMID: 23882012
13.  Regulation of Trypanosoma brucei Total and Polysomal mRNA during Development within Its Mammalian Host 
PLoS ONE  2013;8(6):e67069.
The gene expression of Trypanosoma brucei has been examined extensively in the blood of mammalian hosts and in forms found in the midgut of its arthropod vector, the tsetse fly. However, trypanosomes also undergo development within the mammalian bloodstream as they progress from morphologically ‘slender forms’ to transmissible ‘stumpy forms’ through morphological intermediates. This transition is temporally progressive within the first wave of parasitaemia such that gene expression can be monitored in relatively pure slender and stumpy populations as well as during the progression between these extremes. The development also represents the progression of cells from translationally active forms adapted for proliferation in the host to translationally quiescent forms, adapted for transmission. We have used metabolic labelling to quantitate translational activity in slender forms, stumpy forms and in forms undergoing early differentiation to procyclic forms in vitro. Thereafter we have examined the cohort of total mRNAs that are enriched throughout development in the mammalian bloodstream (slender, intermediate and stumpy forms), irrespective of strain, revealing those that exhibit consistent developmental regulation rather than sample specific changes. Transcripts that cosediment with polysomes in stumpy forms and slender forms have also been enriched to identify transcripts that escape translational repression prior to transmission. Combined, the expression and polysomal association of transcripts as trypanosomes undergo development in the mammalian bloodstream have been defined, providing a resource for trypanosome researchers. This facilitates the identification of those that undergo developmental regulation in the bloodstream and therefore those likely to have a role in the survival and capacity for transmission of stumpy forms.
doi:10.1371/journal.pone.0067069
PMCID: PMC3694164  PMID: 23840587
14.  White matter structural connectivity is associated with sensorimotor function in stroke survivors☆ 
NeuroImage : Clinical  2013;2:767-781.
Purpose
Diffusion tensor imaging (DTI) provides functionally relevant information about white matter structure. Local anatomical connectivity information combined with fractional anisotropy (FA) and mean diffusivity (MD) may predict functional outcomes in stroke survivors. Imaging methods for predicting functional outcomes in stroke survivors are not well established. This work uses DTI to objectively assess the effects of a stroke lesion on white matter structure and sensorimotor function.
Methods
A voxel-based approach is introduced to assess a stroke lesion's global impact on motor function. Anatomical T1-weighted and diffusion tensor images of the brain were acquired for nineteen subjects (10 post-stroke and 9 age-matched controls). A manually selected volume of interest was used to alleviate the effects of stroke lesions on image registration. Images from all subjects were registered to the images of the control subject that was anatomically closest to Talairach space. Each subject's transformed image was uniformly seeded for DTI tractography. Each seed was inversely transformed into the individual subject space, where DTI tractography was conducted and then the results were transformed back to the reference space. A voxel-wise connectivity matrix was constructed from the fibers, which was then used to calculate the number of directly and indirectly connected neighbors of each voxel. A novel voxel-wise indirect structural connectivity (VISC) index was computed as the average number of direct connections to a voxel's indirect neighbors. Voxel-based analyses (VBA) were performed to compare VISC, FA, and MD for the detection of lesion-induced changes in sensorimotor function. For each voxel, a t-value was computed from the differences between each stroke brain and the 9 controls. A series of linear regressions was performed between Fugl-Meyer (FM) assessment scores of sensorimotor impairment and each DTI metric's log number of voxels that differed from the control group.
Results
Correlation between the logarithm of the number of significant voxels in the ipsilesional hemisphere and total Fugl-Meyer score was moderate for MD (R2 = 0.512), and greater for VISC (R2 = 0.796) and FA (R2 = 0.674). The slopes of FA (p = 0.0036), VISC (p = 0.0005), and MD (p = 0.0199) versus the total FM score were significant. However, these correlations were driven by the upper extremity motor component of the FM score (VISC: R2 = 0.879) with little influence of the lower extremity motor component (FA: R2 = 0.177).
Conclusion
The results suggest that a voxel-wise metric based on DTI tractography can predict upper extremity sensorimotor function of stroke survivors, and that supraspinal intraconnectivity may have a less dominant role in lower extremity function.
Highlights
•An intrinsic voxel-based structural connectivity metric is proposed.•The metric enhances the impact of stroke lesions on the distant voxels.•Whole-brain extralesional anatomical connectivity predicts functional outcome.•Functional impact of a lesion is determined by residual anatomical connectivity.•Connectivity to the posterior parietal cortex is a key to sensorimotor function.
doi:10.1016/j.nicl.2013.05.009
PMCID: PMC3777792  PMID: 24179827
DTI, diffusion tensor imaging; FA, fractional anisotropy; FOV, field of view; FM, Fugl-Meyer; LDV, log difference volume; LE, lower extremity; MD, mean diffusivity; TE, echo time; TFIRE, Tactful Functional Imaging Research Environment; TR, repetition time; UE, upper extremity; VISC, voxel-wise indirect structural connectivity; Voxel-wise structural connectivity; Tractography; Diffusion tensor imaging; Stroke; Sensorimotor function; Lesion analysis
15.  Choice of Bacterial Growth Medium Alters the Transcriptome and Phenotype of Salmonella enterica Serovar Typhimurium 
PLoS ONE  2013;8(5):e63912.
The type of bacterial culture medium is an important consideration during design of any experimental protocol. The aim of this study was to understand the impact of medium choice on bacterial gene expression and physiology by comparing the transcriptome of Salmonella enterica SL1344 after growth in the widely used LB broth or the rationally designed MOPS minimal medium. Transcriptomics showed that after growth in MOPS minimal media, compared to LB, there was increased expression of 42 genes involved in amino acid synthesis and 23 genes coding for ABC transporters. Seven flagellar genes had decreased expression after growth in MOPS minimal medium and this correlated with a decreased motility. In both MOPS minimal medium and MEM expression of genes from SPI-2 was increased and the adhesion of S. Typhimurium to intestinal epithelial cells was higher compared to the levels after growth in LB. However, SL1344 invasion was not significantly altered by growth in either MOPs minimal media or MEM. Expression of SPI-2 was also measured using chromosomal GFP reporter fusions followed by flow cytometry which showed, for the first time, that the reduction in SPI-2 transcript after growth in different media related to a reduction in the proportion of the bacterial population expressing SPI-2. These data highlight the profound differences in the global transcriptome after in vitro growth in different media and show that choice of medium should be considered carefully during experimental design, particularly when virulence related phenotypes are being measured.
doi:10.1371/journal.pone.0063912
PMCID: PMC3660369  PMID: 23704954
16.  Sex determination in the social amoeba Dictyostelium discoideum 
Science (New York, N.Y.)  2010;330(6010):1533-1536.
The genetics of sex determination remains mysterious in many organisms including some that are otherwise well-studied. Here we report the discovery and analysis of the mating-type locus of the model organism Dictyostelium discoideum. Three forms of a single genetic locus specifies this species’ three mating-types: two versions of the locus are entirely different in sequence, and the third resembles a composite of the other two. Single, unrelated genes are sufficient to determine two of the mating-types, while homologues of both these genes are required in the composite type. The key genes encode polypeptides that possess no recognisable similarity to established protein families. Sex determination in the social amoebae thus appears to use regulators unrelated to any currently known.
doi:10.1126/science.1197423
PMCID: PMC3648785  PMID: 21148389
17.  Blood–brain barrier breakdown as a novel mechanism underlying cerebral hyperperfusion syndrome 
Journal of neurology  2009;257(4):615-620.
Cerebral hyperperfusion syndrome (CHS) may occur as a severe complication following surgical treatment of carotid stenosis. However, the mechanism inducing neurological symptoms in CHS remains unknown. We describe a patient with CHS presenting with seizures 24 h following carotid endarterectomy. Imaging demonstrated early ipsilateral blood–brain barrier (BBB) breakdown with electroencephalographic evidence of cortical dysfunction preceding brain edema. Using in vitro experiments on rat cortical tissue, we show that direct exposure of isolated brain slices to a serum-like medium induces spontaneous epileptiform activity, and that neuronal dysfunction is triggered by albumin. We propose BBB breakdown and subsequent albumin extravasation as a novel pathogenic mechanism underlying CHS and a potential target for therapy.
doi:10.1007/s00415-009-5384-z
PMCID: PMC3625729  PMID: 20361293
Albumin; Blood–brain barrier; Cerebral hyperperfusion syndrome; Magnetic resonance imaging; Seizure; Astrocytes; TGF-βR
18.  A pilot study to measure upper extremity H-reflexes following neuromuscular electrical stimulation therapy after stroke 
Neuroscience letters  2013;535:1-6.
Upper extremity (UE) hemiparesis persists after stroke, limiting hand function. Neuromuscular electrical stimulation (NMES) is an effective intervention to improve UE recovery, although the underlying mechanisms are not fully understood. Our objective was to establish a reliable protocol to measure UE agonist–antagonist forearm monosynaptic reflexes in a pilot study to determine if NMES improves wrist function after stroke. We established the between-day reliability of the H-reflex in the extensor carpi radialis longus (ECRL) and flexor carpi radialis (FCR) musculature for individuals with prior stroke (n = 18). The same-day generation of ECRL/FCR H-reflex recruitment curves was well tolerated, regardless of age or UE spasticity. The between-day reliability of the ECRL H-reflex was enhanced above FCR, similar to healthy subjects [20], with the Hmax the most reliable parameter quantified in both muscles. H-reflex and functional measures following NMES show the potential for NMES-induced increases in ECRL Hmax, but confirmation requires a larger clinical study. Our initial results support the safe, easy, and efficacious use of in-home NMES, and establish a potential method to measure UE monosynaptic reflexes after stroke.
doi:10.1016/j.neulet.2012.11.063
PMCID: PMC3592334  PMID: 23313593
Stroke; H-reflex; FCR; ECRL; Upper extremity spasticity; Neuromuscular electrical stimulation
19.  Reciprocal inhibition post-stroke is related to reflex excitability and movement ability 
Objective
Decreased reciprocal inhibition (RI) of motor neurons may contribute to spasticity after stroke. However, decreased RI is not a uniform observation among stroke survivors, suggesting that this spinal circuit may be influenced by other stroke-related characteristics. The purpose of this study was to measure RI post-stroke and to examine the relationship between RI and other features of stroke.
Methods
RI was examined in 15 stroke survivors (PAR) and 10 control subjects by quantifying the effect of peroneal nerve stimulation on soleus H-reflex amplitude. The relationship between RI and age, time post-stroke, lesion side, walking velocity, Fugl-Meyer, Ashworth, and Achilles reflex scores was examined.
Results
RI was absent and replaced by reciprocal facilitation in 10 of 15 PAR individuals. Reciprocal facilitation was associated with low Fugl-Meyer scores and slow walking velocities but not with hyperactive Achilles tendon reflexes. There was no relationship between RI or reciprocal facilitation and time post-stroke, lesion side, or Ashworth score.
Conclusions
Decreased RI is not a uniform finding post-stroke and is more closely related to walking ability and movement impairment than to spasticity.
Significance
Phenomena other than decreased RI may contribute to post-stroke spasticity.
doi:10.1016/j.clinph.2012.04.023
PMCID: PMC3592335  PMID: 22613030
Spasticity; Rehabilitation; Hemiparesis; CVA
21.  A gene expression atlas of the domestic pig 
BMC Biology  2012;10:90.
Background
This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering.
Results
The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed a network analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they sub-divide into functional groups that may control cellular gastrointestinal development.
Conclusions
As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites http://biogps.org and http://www.macrophages.com/pig-atlas.
doi:10.1186/1741-7007-10-90
PMCID: PMC3814290  PMID: 23153189
pig; porcine; Sus scrofa; microarray; transcriptome; transcription network; pathway; gastrointestinal tract
22.  Correction: The Transcriptional Response of Caenorhabditis elegans to Ivermectin Exposure Identifies Novel Genes Involved in the Response to Reduced Food Intake 
PLoS ONE  2012;7(8):10.1371/annotation/259d774f-6c58-4df8-bce5-74a3c9160270.
doi:10.1371/annotation/259d774f-6c58-4df8-bce5-74a3c9160270
PMCID: PMC3439517
23.  Ants farm subterranean aphids mostly in single clone groups - an example of prudent husbandry for carbohydrates and proteins? 
Background
Mutualistic interactions are wide-spread but the mechanisms underlying their evolutionary stability and ecological dynamics remain poorly understood. Cultivation mutualisms in which hosts consume symbionts occur in phylogenetically diverse groups, but often have symbiont monocultures for each host. This is consistent with the prediction that symbionts should avoid coexistence with other strains so that host services continue to benefit relatives, but it is less clear whether hosts should always favor monocultures and what mechanisms they might have to manipulate symbiont diversity. Few mutualisms have been studied in sufficient genetic detail to address these issues, so we decided to characterize symbiont diversity in the complex mutualism between multiple root aphid species and Lasius flavus ants. After showing elsewhere that three of these aphid species have low dispersal and mostly if not exclusively asexual reproduction, we here investigate aphid diversity within and between ant nest mounds.
Results
The three focal species (Geoica utricularia, Forda marginata and Tetraneura ulmi) had considerable clonal diversity at the population level. Yet more than half of the ant mounds contained just a single aphid species, a significantly higher percentage than expected from a random distribution. Over 60% of these single-species mounds had a single aphid clone, and clones tended to persist across subsequent years. Whenever multiple species/clones co-occurred in the same mound, they were spatially separated with more than 95% of the aphid chambers containing individuals of a single clone.
Conclusions
L. flavus “husbandry” is characterized by low aphid “livestock” diversity per colony, especially at the nest-chamber level, but it lacks the exclusive monocultures known from other cultivation mutualisms. The ants appear to eat most of the early instar aphids, so that adult aphids are unlikely to face limited phloem resources and scramble competition with other aphids. We suggest that such culling of carbohydrate-providing symbionts for protein ingestion may maintain maximal host yield per aphid while also benefitting the domesticated aphids as long as their clone-mates reproduce successfully. The cost-benefit logic of this type of polyculture husbandry has striking analogies with human farming practices based on slaughtering young animals for meat to maximize milk-production by a carefully regulated adult livestock population.
doi:10.1186/1471-2148-12-106
PMCID: PMC3499235  PMID: 22747564
Cultivation mutualism; Host-symbiont conflict; Symbiont competition; Monoculture; Clonal mixing
24.  Impact of intensive care unit admission during morning bedside rounds and mortality: a multi-center retrospective cohort study 
Critical Care  2012;16(3):R72.
Introduction
Recent data have suggested that patient admission during intensive care unit (ICU) morning bedside rounds is associated with less favorable outcome. We undertook the present study to explore the association between morning round-time ICU admissions and hospital mortality in a large Canadian health region.
Methods
A multi-center retrospective cohort study was performed at five hospitals in Edmonton, Canada, between July 2002 and December 2009. Round-time ICU admission was defined as occurring between 8 and 11:59 a.m. Multivariable logistic regression analysis was used to explore the association between round-time admission and outcome.
Results
Of 18,857 unique ICU admissions, 2,055 (10.9%) occurred during round time. Round-time admissions were more frequent in community hospitals compared with tertiary hospitals (12.0% vs. 10.5%; odds ratio [OR] 1.16; 95% CI, 1.05-1.29, P < 0.004) and from the ward compared with the emergency department (ED) or operating theater (17.5% vs. 9.2%; OR 2.1; 95% CI, 1.9-2.3, P < 0.0001). Round-time admissions were more often medical than surgical (12.6% vs. 6.6%; OR 2.06; 95% CI, 1.83-2.31, P < 0.0001), had more comorbid illness (11.9% vs. 10.5%; OR 1.15; 95% CI, 1.04-1.27, P < 0.008) and higher APACHE II score (22.2 vs. 21.3, P < 0.001), and were more likely to have a primary diagnosis of respiratory failure (37.0% vs. 31.3%, P < 0.001) or sepsis (11.1% vs. 9.0%, P = 0.002). Crude ICU mortality (15.3% vs. 11.6%; OR 1.38; 95% CI, 1.21-1.57, P < 0.0001) and hospital mortality (23.9% vs. 20.6%; OR 1.21; 95% CI, 1.09-1.35, P < 0.001) were higher for round-time compared with non-round-time admissions. In multi-variable analysis, round-time admission was associated with increased ICU mortality (OR 1.19, 95% CI, 1.03-1.38, P = 0.017) but was not significantly associated with hospital mortality (OR 1.02; 95% CI, 0.90-1.16, P = 0.700). In the subgroup admitted from the ED, round-time admission showed significantly higher ICU mortality (OR 1.54; 95% CI, 1.21-1.95; P < 0.001) and a trend for higher hospital mortality (OR 1.22; 95% CI, 0.99-1.51, P = 0.057).
Conclusions
Approximately 1 in 10 patients is admitted during morning rounds. These patients are more commonly admitted from the ward and are burdened by comorbidities, are non-operative, and have higher illness severity. These patients admitted during morning rounds have higher observed ICU mortality but no difference in hospital mortality.
doi:10.1186/cc11329
PMCID: PMC3580614  PMID: 22554100
25.  Soleus H-Reflex Recruitment Is Not Altered in Persons With Chronic Spinal Cord Injury 
Objective
To determine whether spasticity in persons with spinal cord injury (SCI) is associated with elevated monosynaptic reflex excitability.
Design
One-way experimental.
Setting
Research laboratory.
Participants
Convenience sample of 9 subjects (8 men, 1 woman) with chronic and complete SCI and 20 persons (14 men, 6 women) with no neurologic impairment. Subjects with SCI exhibited lower-extremity spasticity as indicated by velocity-dependent increased resistance to passive muscle stretch, abnormally brisk deep tendon reflexes, involuntary lower-extremity flexion and/or extension spasms, and clonus.
Intervention
Soleus H-reflex recruitment curves were elicited in all subjects.
Main Outcome Measures
Soleus H-reflex threshold (HTH), gain (HGN), and amplitude (HPP).
Results
There was no difference between subjects with and without SCI in HTH, HGN, or HPP.
Conclusions
Spasticity in people with chronic and complete SCI was not associated with increased excitability of the connections between Ia afferent projections and motoneurons. Factors extrinsic to these connections may have a role in spasticity caused by SCI.
PMCID: PMC3298881  PMID: 15129411
H-reflex; Muscle spasticity; Paralysis; Rehabilitation; Soleus muscle; Spinal cord injuries

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