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1.  ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana 
BMC Bioinformatics  2017;18:37.
Background
Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana.
Results
To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www.biw.kuleuven.be/CSB/ARA-PEPs), a repository of putative peptides encoded by sORFs in the A. thaliana genome starting from in-house Tiling arrays, RNA-seq data and other publicly available datasets. ARA-PEPs currently lists 13,748 sORF-encoded peptides with transcriptional evidence. In addition to existing data, we have identified 100 novel transcriptionally active regions (TARs) that might encode 341 novel stress-induced peptides (SIPs). To aid in identification of bioactivity, we add functional annotation and sequence conservation to predicted peptides.
Conclusion
To our knowledge, this is the largest repository of plant peptides encoded by sORFs with transcript evidence, publicly available and this resource will help scientists to effortlessly navigate the list of experimentally studied peptides, the experimental and computational evidence supporting the activity of these peptides and gain new perspectives for peptide discovery.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-016-1458-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12859-016-1458-y
PMCID: PMC5240266  PMID: 28095775
RNA-seq; Tiling arrays; sORFs; Database; Peptides; Arabidopsis thaliana
2.  Altered Source Memory Retrieval is Associated with Pathological Doubt in Obsessive-Compulsive Disorder 
Behavioural brain research  2015;296:53-60.
Individuals with obsessive-compulsive disorder (OCD) often complain of doubt related to memory. As neuropsychological research has demonstrated that individuals with OCD tend to focus on details and miss the larger context, the construct of source (contextual) memory may be particularly relevant to memory complaints in OCD. Memory for object versus contextual information relies on partially distinct regions within the prefrontal cortex, parietal and medial temporal lobe, and may be differentially impacted by OCD. In the present study we sought to test the hypothesis that individuals with OCD exhibit impaired source memory retrieval using a novel memory paradigm-The Memory for Rooms Test (MFRT)- a four-room memory task in which participants walk through four rooms and attempt to encode and remember objects. Demographically matched individuals with OCD and healthy controls studied objects in the context of four rooms, and then completed a memory retrieval test while undergoing functional magnetic resonance imaging (fMRI). While no differences were observed in source memory accuracy, individuals with OCD exhibited greater task related activation in the posterior cingulate cortex (PCC) relative to healthy controls during correct source memory retrieval. During correct object recognition, individuals with OCD failed to recruit the dorsolateral prefrontal(DLPFC)/premotor, left mPFC, and right parietal regions to the same extent as healthy controls. Our results suggest abnormal recruitment of frontal-parietal and PCC regions during source verses object memory retrieval in OCD. Within the OCD group, activation in the PCC and the premotor/DLPFC was associated with greater pathological doubt. This finding is consistent with the observation that OCD patients often experience extreme doubt, even when memory performance is intact.
doi:10.1016/j.bbr.2015.08.031
PMCID: PMC4720123  PMID: 26315458
3.  The human milk oligosaccharide 2′-fucosyllactose attenuates the severity of experimental necrotising enterocolitis by enhancing mesenteric perfusion in the neonatal intestine 
The British journal of nutrition  2016;116(7):1175-1187.
Necrotising enterocolitis (NEC) is a common disease in premature infants characterised by intestinal ischaemia and necrosis. The only effective preventative strategy against NEC is the administration of breast milk, although the protective mechanisms remain unknown. We hypothesise that an abundant human milk oligosaccharide (HMO) in breast milk, 2′-fucosyllactose (2′FL), protects against NEC by enhancing intestinal mucosal blood flow, and we sought to determine the mechanisms underlying this protection. Administration of HMO-2′FL protected against NEC in neonatal wild-type mice, resulted in a decrease in pro-inflammatory markers and preserved the small intestinal mucosal architecture. These protective effects occurred via restoration of intestinal perfusion through up-regulation of the vasodilatory molecule endothelial nitric oxide synthase (eNOS), as administration of HMO-2′FL to eNOS-deficient mice or to mice that received eNOS inhibitors did not protect against NEC, and by 16S analysis HMO-2′FL affected the microbiota of the neonatal mouse gut, although these changes do not seem to be the primary mechanism of protection. Induction of eNOS by HMO-2′FL was also observed in cultured endothelial cells, providing a link between eNOS and HMO in the endothelium. These data demonstrate that HMO-2′FL protects against NEC in part through maintaining mesenteric perfusion via increased eNOS expression, and suggest that the 2′FL found in human milk may be mediating some of the protective benefits of breast milk in the clinical setting against NEC.
doi:10.1017/S0007114516002944
PMCID: PMC5124125  PMID: 27609061
Necrotising enterocolitis; Human milk oligosaccharides; 2′-Fucosyllactose; Endothelial nitric oxide synthase; Breast milk
4.  Comparison of Obese Adults with Poor versus Good Sleep Quality during a Functional Neuroimaging Delay Discounting Task: A Pilot Study 
Psychiatry research  2015;234(1):90-95.
This study aimed to determine if obese adults with poor versus good sleep quality demonstrate reduced self-regulatory capacity and different patterns of neural activation when making impulsive monetary choices. Six obese, good quality sleepers (M age = 44.7 years, M BMI = 83.1 kg/m2) were compared to 13 obese, poor quality sleepers (M age = 42.6, M BMI = 39.2 kg/m2) on sleep and eating behavior and brain activation in prefrontal and insular regions while engaging in a delay discounting task during functional magnetic resonance imaging (fMRI). Poor quality sleepers demonstrated significantly lower brain activation in the right inferior frontal gyrus, right middle frontal gyrus, and bilateral insula when making immediate and smaller (impulsive) monetary choices compared to the baseline condition. Behaviorally, poor compared to good quality sleepers reported higher scores in the night eating questionnaire. Obese adults with poor sleep quality demonstrate decreased brain activation in multiple regions that regulate cognitive control and interceptive awareness, possibly reducing self-regulatory capacity when making immediately gratifying decisions.
doi:10.1016/j.pscychresns.2015.08.011
PMCID: PMC4651827  PMID: 26358975
sleep quality; self-regulation; delay discounting; brain activation; obesity
6.  Investigation of Elimination Rate, Persistent Subpopulation Removal, and Relapse Rates of Mycobacterium tuberculosis by Using Combinations of First-Line Drugs in a Modified Cornell Mouse Model 
Currently, the most effective tuberculosis control method involves case finding and 6 months of chemotherapy. There is a need to improve our understanding about drug interactions, combination activities, and the ability to remove persistent bacteria using the current regimens, particularly in relation to relapse. We aimed to investigate the therapeutic effects of three main components, rifampin (RMP), isoniazid (INH), and pyrazinamide (PZA), in current drug regimens using a modified version of the Cornell mouse model. We evaluated the posttreatment levels of persistent Mycobacterium tuberculosis in the organs of mice using culture filtrate derived from M. tuberculosis strain H37Rv. When RMP was combined with INH, PZA, or INH-PZA, significant additive activities were observed compared to each of the single-drug treatments. However, the combination of INH and PZA showed a less significant additive effect than either of the drugs used on their own. Apparent culture negativity of mouse organs was achieved at 14 weeks of treatment with RMP-INH, RMP-PZA, and RMP-INH-PZA, but not with INH-PZA, when conventional tests, namely, culture on solid agar and in liquid broth, indicated that the organs were negative for bacteria. The relapse rates for RMP-containing regimens were not significantly different from a 100% relapse rate at the numbers of mice examined in this study. In parallel, we examined the organs for the presence of culture filtrate-dependent persistent bacilli after 14 weeks of treatment. Culture filtrate treatment of the organs revealed persistent M. tuberculosis. Modeling of mycobacterial elimination rates and evaluation of culture filtrate-dependent organisms showed promise as surrogate methods for efficient factorial evaluation of drug combinations in tuberculosis in mouse models and should be further evaluated against relapse. The presence of culture filtrate-dependent persistent M. tuberculosis is the likely cause of disease relapse in this modified Cornell mouse model.
doi:10.1128/AAC.02548-15
PMCID: PMC4958161  PMID: 27216065
7.  The effect of surgery on the outcome of treatment for multidrug-resistant tuberculosis: a systematic review and meta-analysis 
BMC Infectious Diseases  2016;16:262.
Background
In 2014 only 50 % of multidrug-resistant tuberculosis (MDR-TB) patients achieved a successful treatment outcome. With limited options for medical treatment, surgery has re-emerged as an adjuvant therapeutic strategy. We conducted a systematic review and meta-analysis to assess the evidence for the effect of surgery as an adjunct to chemotherapy on outcomes of adults treated for MDR-TB.
Methods
Databases and grey literature sources were searched using terms incorporating surgery and MDR-TB. No language or publication type limits were applied. Articles published pre-1990, without a comparator group, or reporting <10 surgical participants were excluded. Two-stage sifting in duplicate was employed. Data on WHO-defined treatment outcomes were abstracted into a standardised database. Study-level risk of bias was evaluated using standardised tools. Outcome-level evidence quality was assessed using GRADE. Forest plots were generated, random effects meta-analysis conducted, and heterogeneity assessed using the I2 statistic.
Results
Of 1024 unique citations identified, 62 were selected for full-text review and 15 retained for inclusion. A further four articles were included after bibliography/citation searching, and one additional unpublished manuscript was identified, giving 20 articles for final inclusion. Six were meta-analyses/systematic reviews and 14 were primary research articles (observational studies).
From the 14 primary research articles, a successful outcome (cured/treatment completed) was reported for 81.9 % (371/453) and 59.7 % (1197/2006) in the surgical and non-surgical group respectively, giving a summary odds ratio of 2.62 (95 % confidence interval 1.94–3.54). Loss to follow-up and treatment failure were lower in the surgery group (both p = 0.01). Overall GRADE quality of evidence for all outcomes considered was “very low”.
Conclusions
This meta-analysis suggests that surgery as an adjunct to chemotherapy is associated with improved treatment outcomes in MDR-TB patients. However, inherent limitations in observational study design, insufficient reporting, and lack of adjustment for confounders, led to grading of the evidence as very low quality. Data on rationale for surgical referral, subsequent outcomes and resource-limited settings are scarce, precluding evidence-based recommendations on the suitability of surgery by patient characteristics or setting. It is hoped that highlighted methodological and reporting gaps will encourage improved design and reporting of future surgical studies for MDR-TB.
Electronic supplementary material
The online version of this article (doi:10.1186/s12879-016-1585-0) contains supplementary material, which is available to authorized users.
doi:10.1186/s12879-016-1585-0
PMCID: PMC4901410  PMID: 27283524
Multi-drug resistant; Extensively drug resistant; Tuberculosis; Surgery; Pneumonectomy; Meta-analysis; Systematic review
8.  Neural Processing of Emotional Musical and Nonmusical Stimuli in Depression 
PLoS ONE  2016;11(6):e0156859.
Background
Anterior cingulate cortex (ACC) and striatum are part of the emotional neural circuitry implicated in major depressive disorder (MDD). Music is often used for emotion regulation, and pleasurable music listening activates the dopaminergic system in the brain, including the ACC. The present study uses functional MRI (fMRI) and an emotional nonmusical and musical stimuli paradigm to examine how neural processing of emotionally provocative auditory stimuli is altered within the ACC and striatum in depression.
Method
Nineteen MDD and 20 never-depressed (ND) control participants listened to standardized positive and negative emotional musical and nonmusical stimuli during fMRI scanning and gave subjective ratings of valence and arousal following scanning.
Results
ND participants exhibited greater activation to positive versus negative stimuli in ventral ACC. When compared with ND participants, MDD participants showed a different pattern of activation in ACC. In the rostral part of the ACC, ND participants showed greater activation for positive information, while MDD participants showed greater activation to negative information. In dorsal ACC, the pattern of activation distinguished between the types of stimuli, with ND participants showing greater activation to music compared to nonmusical stimuli, while MDD participants showed greater activation to nonmusical stimuli, with the greatest response to negative nonmusical stimuli. No group differences were found in striatum.
Conclusions
These results suggest that people with depression may process emotional auditory stimuli differently based on both the type of stimulation and the emotional content of that stimulation. This raises the possibility that music may be useful in retraining ACC function, potentially leading to more effective and targeted treatments.
doi:10.1371/journal.pone.0156859
PMCID: PMC4902194  PMID: 27284693
9.  Resting State Brain Connectivity After Surgical and Behavioral Weight Loss 
Obesity (Silver Spring, Md.)  2015;23(7):1422-1428.
OBJECTIVE
We previously reported changes in food-cue neural reactivity associated with behavioral and surgical weight loss interventions. Resting functional connectivity represents tonic neural activity that may contribute to weight loss success. Here we explore whether intervention type is associated with differences in functional connectivity after weight loss.
METHODS
Fifteen obese participants were recruited prior to adjustable gastric banding surgery. Thirteen demographically matched obese participants were selected from a separate behavioral diet intervention. Resting state fMRI was collected three months after surgery/behavioral intervention. ANOVA was used to examine post-weight loss differences between the two groups in connectivity to seed regions previously identified as showing differential cue-reactivity after weight loss.
RESULTS
Following weight loss, behavioral dieters exhibited increased connectivity between left precuneus/superior parietal lobule (SPL) and bilateral insula pre- to post-meal and bariatric patients exhibited decreased connectivity between these regions pre- to post-meal (pcorrected<.05).
CONCLUSIONS
Behavioral dieters showed increased connectivity pre- to post-meal between a region associated with processing of self-referent information (precuneus/SPL) and a region associated with interoception (insula) whereas bariatric patients showed decreased connectivity between these regions. This may reflect increased attention to hunger signals following surgical procedures, and increased attention to satiety signals following behavioral diet interventions.
doi:10.1002/oby.21119
PMCID: PMC4483156  PMID: 26053145
resting state functional MRI; bariatric surgery; neural mechanisms; weight loss
10.  The effect of early versus late treatment initiation after diagnosis on the outcomes of patients treated for multidrug-resistant tuberculosis: a systematic review 
BMC Infectious Diseases  2016;16:193.
Background
Globally it is estimated that 480 000 people developed multidrug-resistant tuberculosis (MDR-TB) in 2014 and 190 000 people died from the disease. Successful treatment outcomes are achieved in only 50 % of patients with MDR-TB, compared to 86 % for drug susceptible disease. It is widely held that delay in time to initiation of treatment for MDR-TB is an important predictor of treatment outcome. The objective of this review was to assess the existing evidence on the outcomes of multidrug- and extensively drug-resistant tuberculosis patients treated early (≤4 weeks) versus late (>4 weeks) after diagnosis of drug resistance.
Methods
Eight sources providing access to 17 globally representative electronic health care databases, indexes, sources of evidence-based reviews and grey literature were searched using terms incorporating time to treatment and MDR-TB. Two-stage sifting in duplicate was employed to assess studies against pre-specified inclusion and exclusion criteria. Only those articles reporting WHO-defined treatment outcomes were considered for inclusion. Articles reporting on fewer than 10 patients, published before 1990, or without a comparison of outcomes in patient groups experiencing different delays to treatment initiation were excluded.
Results
The initial search yielded 1978 references, of which 1475 unique references remained after removal of duplicates and 28 articles published pre-1990. After title and abstract sifting, 64 papers underwent full text review. None of these articles fulfilled the criteria for inclusion in the review.
Conclusions
Whilst there is an inherent logic in the theory that treatment delay will lead to poorer treatment outcomes, no published evidence was identified in this systematic review to support this hypothesis. Reports of programmatic changes leading to reductions in treatment delay exist in the literature, but attribution of differences in outcomes specifically to treatment delay is confounded by other contemporaneous changes. Further primary research on this question is not considered a high priority use of limited resources, though where data are available, improved reporting of outcomes by time to treatment should be encouraged.
Electronic supplementary material
The online version of this article (doi:10.1186/s12879-016-1524-0) contains supplementary material, which is available to authorized users.
doi:10.1186/s12879-016-1524-0
PMCID: PMC4855810  PMID: 27142682
Multi-drug resistant; Extensively drug resistant; Tuberculosis; Treatment delay; Systematic review
11.  Rationing tests for drug-resistant tuberculosis – who are we prepared to miss? 
BMC Medicine  2016;14:30.
Background
Early identification of patients with drug-resistant tuberculosis (DR-TB) increases the likelihood of treatment success and interrupts transmission. Resource-constrained settings use risk profiling to ration the use of drug susceptibility testing (DST). Nevertheless, no studies have yet quantified how many patients with DR-TB this strategy will miss.
Methods
A total of 1,545 subjects, who presented to Lima health centres with possible TB symptoms, completed a clinic-epidemiological questionnaire and provided sputum samples for TB culture and DST. The proportion of drug resistance in this population was calculated and the data was analysed to demonstrate the effect of rationing tests to patients with multidrug-resistant TB (MDR-TB) risk factors on the number of tests needed and corresponding proportion of missed patients with DR-TB.
Results
Overall, 147/1,545 (9.5 %) subjects had culture-positive TB, of which 32 (21.8 %) had DR-TB (MDR, 13.6 %; isoniazid mono-resistant, 7.5 %; rifampicin mono-resistant, 0.7 %). A total of 553 subjects (35.8 %) reported one or more MDR-TB risk factors; of these, 506 (91.5 %; 95 % CI, 88.9–93.7 %) did not have TB, 32/553 (5.8 %; 95 % CI, 3.4–8.1 %) had drug-susceptible TB, and only 15/553 (2.7 %; 95 % CI, 1.5–4.4 %) had DR-TB. Rationing DST to those with an MDR-TB risk factor would have missed more than half of the DR-TB population (17/32, 53.2 %; 95 % CI, 34.7–70.9).
Conclusions
Rationing DST based on known MDR-TB risk factors misses an unacceptable proportion of patients with drug-resistance in settings with ongoing DR-TB transmission. Investment in diagnostic services to allow universal DST for people with presumptive TB should be a high priority.
doi:10.1186/s12916-016-0576-8
PMCID: PMC4804634  PMID: 27005771
Microscopic-observation drug-susceptibility assay; Multidrug-resistant tuberculosis; Tuberculosis; Drug Susceptibility Testing
12.  The transfer and decay of maternal antibody against Shigella sonnei in a longitudinal cohort of Vietnamese infants 
Vaccine  2016;34(6):783-790.
Highlights
•Shigella sonnei is an emergent and highly drug resistant diarrheal pathogen.•The half-life of maternal S. sonnei IgG in infants is 43 days.•Maternal titer, antibody transfer ratio and gestational age influence birth titer.•Incidence of seroconversion in infants in southern Vietnam is 4/100 infant years.•Children should be vaccinated after 5 months of age if a candidate is licensed.
Background
Shigella sonnei is an emergent and major diarrheal pathogen for which there is currently no vaccine. We aimed to quantify duration of maternal antibody against S. sonnei and investigate transplacental IgG transfer in a birth cohort in southern Vietnam.
Methods and results
Over 500-paired maternal/infant plasma samples were evaluated for presence of anti-S. sonnei-O IgG and IgM. Longitudinal plasma samples allowed for the estimation of the median half-life of maternal anti-S. sonnei-O IgG, which was 43 days (95% confidence interval: 41–45 days). Additionally, half of infants lacked a detectable titer by 19 weeks of age. Lower cord titers were associated with greater increases in S. sonnei IgG over the first year of life, and the incidence of S. sonnei seroconversion was estimated to be 4/100 infant years. Maternal IgG titer, the ratio of antibody transfer, the season of birth and gestational age were significantly associated with cord titer.
Conclusions
Maternal anti-S. sonnei-O IgG is efficiently transferred across the placenta and anti-S. sonnei-O maternal IgG declines rapidly after birth and is undetectable after 5 months in the majority of children. Preterm neonates and children born to mothers with low IgG titers have lower cord titers and therefore may be at greater risk of seroconversion in infancy.
doi:10.1016/j.vaccine.2015.12.047
PMCID: PMC4742520  PMID: 26742945
Shigella; Maternal antibody; Placental transfer; Seroconversion
13.  Induction of a regenerative microenvironment in skeletal muscle is sufficient to induce embryonal rhabdomyosarcoma in p53-deficient mice 
The Journal of pathology  2011;226(1):40-49.
We have previously reported that mice with muscular dystrophy, including mdx mice, develop embryonal rhabdomyosarcoma (eRMS) with a low incidence after 1 year of age and that almost all such tumours contain cancer-associated p53 mutations. To further demonstrate the relevance of p53 inactivation, we created p53-deficient mdx mice. Here we demonstrate that loss of one or both p53 (Trp53) alleles accelerates eRMS incidence in the mdx background, such that almost all Trp53−/− mdx animals develop eRMS by 5 months of age. To ascertain whether increased tumour incidence was due to the regenerative microenvironment found in dystrophic skeletal muscles, we induced muscle regeneration in Trp53+/+ and Trp53−/− animals using cardiotoxin (Ctx). Wild-type (Trp53+/+) animals treated with Ctx, either once every 7 days or once every 14 days from 1 month of age onwards, developed no eRMS; however, all similarly Ctx-treated Trp53−/− animals developed eRMS by 5 months of age at the site of injection. Most of these tumours displayed markers of human eRMS, including over-expression of Igf2 and phosphorylated Akt. These data demonstrate that the presence of a regenerative microenvironment in skeletal muscle, coupled with Trp53 deficiency, is sufficient to robustly induce eRMS in young mice. These studies further suggest that consideration should be given to the potential of the muscle microenvironment to support tumourigenesis in regenerative therapies for myopathies.
doi:10.1002/path.2996
PMCID: PMC4727244  PMID: 21915858
p53; rhabdomyosarcoma; mdx; muscular dystrophy; tumour microenvironment
14.  Brain function predictors and outcome of weight loss and weight loss maintenance 
Contemporary clinical trials  2014;40:218-231.
Obesity rates are associated with public health consequences and rising health care costs. Weight loss interventions, while effective, do not work for everyone, and weight regain is a significant problem. Eating behavior is influenced by a convergence of processes in the brain, including homeostatic factors and motivational processing that are important contributors to overeating. Initial neuroimaging studies have identified brain regions that respond differently to visual food cues in obese and healthy weight individuals that are positively correlated with reports of hunger in obese participants. While these findings provide mechanisms of overeating, many important questions remain. It is not known whether brain activation patterns change after weight loss, or if they change differentially based on amount of weight lost. Also, little is understood regarding biological processes that contribute to long-term weight maintenance. This study will use neuroimaging in participants while viewing food and non-food images. Functional Magnetic Resonance Imaging will take place before and after completion of a twelve-week weight loss intervention. Obese participants will be followed though a 6-month maintenance period. The study will address three aims: 1. Characterize brain activation underlying food motivation and impulsive behaviors in obese individuals. 2. Identify brain activation changes and predictors of weight loss. 3. Identify brain activation predictors of weight loss maintenance. Findings from this study will have implications for understanding mechanisms of obesity, weight loss, and weight maintenance. Results will be significant to public health and could lead to a better understanding of how differences in brain activation relate to obesity.
doi:10.1016/j.cct.2014.12.008
PMCID: PMC4314339  PMID: 25533729
Weight loss; functional Magnetic Resonance Imaging; Obesity
15.  Closed-loop Robots Driven by Short-Term Synaptic Plasticity: Emergent Explorative vs. Limit-Cycle Locomotion 
We examine the hypothesis, that short-term synaptic plasticity (STSP) may generate self-organized motor patterns. We simulated sphere-shaped autonomous robots, within the LPZRobots simulation package, containing three weights moving along orthogonal internal rods. The position of a weight is controlled by a single neuron receiving excitatory input from the sensor, measuring its actual position, and inhibitory inputs from the other two neurons. The inhibitory connections are transiently plastic, following physiologically inspired STSP-rules. We find that a wide palette of motion patterns are generated through the interaction of STSP, robot, and environment (closed-loop configuration), including various forward meandering and circular motions, together with chaotic trajectories. The observed locomotion is robust with respect to additional interactions with obstacles. In the chaotic phase the robot is seemingly engaged in actively exploring its environment. We believe that our results constitute a concept of proof that transient synaptic plasticity, as described by STSP, may potentially be important for the generation of motor commands and for the emergence of complex locomotion patterns, adapting seamlessly also to unexpected environmental feedback. We observe spontaneous and collision induced mode switchings, finding in addition, that locomotion may follow transiently limit cycles which are otherwise unstable. Regular locomotion corresponds to stable limit cycles in the sensorimotor loop, which may be characterized in turn by arbitrary angles of propagation. This degeneracy is, in our analysis, one of the drivings for the chaotic wandering observed for selected parameter settings, which is induced by the smooth diffusion of the angle of propagation.
doi:10.3389/fnbot.2016.00012
PMCID: PMC5067527  PMID: 27803661
closed-loop robots; short-term synaptic plasticity; limit cycles; sensorimotor loop; self-organized locomotion; compliant robot
16.  Neuroimaging of Goal-Directed Behavior in Midlife Women 
Nursing research  2014;63(6):388-396.
Background
Motivational interventions to improve health behaviors based on conventional cognitive and behavioral theories have been extensively studied; however, advances in neuroimaging technology make it possible to assess the neurophysiological basis of health behaviors, such as physical activity. The goals of this approach are to support new interventions to achieve optimal outcomes.
Objectives
This study used functional magnetic resonance imaging (fMRI) to assess differences in brain responses in healthy weight to obese midlife women during a goal-directed decision task.
Methods
Thirty nondiabetic, midlife (age 47-55 years) women with body mass index (BMI) ranging from 18.5 to 40 kg/m2 were recruited. A descriptive, correlational design was used to assess the relationship between brain activations and weight status. Participants underwent a goal-directed behavior task in the fMRI scanner consisting of a learning and implementation phase. The task was designed to assess both goal-directed and habitual behaviors. One participant was omitted from the analysis due to excessive motion (> 4 mm), and six were omitted due to fewer than 50% correct responses on the exit survey. Four participants developed claustrophobia in the scanner and were disqualified from further participation. The remaining 19 participants were included in the final analysis.
Results
Brain responses while participants learned goal-directed behavior showed a positive correlation with BMI in the dorsal medial prefrontal cortex (dmPFC) and a negative correlation with BMI in the insula. During the implementation of goal-directed behavior, brain responses in the dorsolateral prefrontal cortex (dlPFC) negatively correlated with BMI.
Discussion
These results indicate that overweight women activate regions associated with cognitive control to a greater degree than healthy weight women during goal-directed learning. The brain regions activated (dmPFC, dlPFC, insula) are associated with cognitive control and self-regulation. On the other hand, healthy weight women activate regions associated with emotion processing, planning, and self-regulation (lateral orbitofrontal cortex, anterior insula) to a greater degree than overweight women during goal-directed learning and implementation of goal-directed behavior. Overweight women activate cognitive control regions while learning associations between actions and outcomes; however, this is not the case during the implementation phase—which may make it more difficult to transform goals into action (e.g., maintain PA over time). Overall, these results indicate that overweight midlife women respond differently during learning and implementation of actions that lead to positive outcomes during a general test of goal-directed behavior. Future study is needed to assess the transfer of goal-directed and habitual behavior to specific aspects of energy balance to improve health outcomes.
doi:10.1097/NNR.0000000000000060
PMCID: PMC4213232  PMID: 25186027
fMRI; health behavior; neuroimaging; neurophysiology; obesity; women's health
17.  Applying Cases to Solve Ethical Problems: The Significance of Positive and Process-Oriented Reflection 
Ethics & behavior  2012;22(2):113-130.
This study examined the role of reflection on personal cases for making ethical decisions with regard to new ethical problems. Participants assumed the position of a business manager in a hypothetical organization and solved ethical problems that might be encountered. Prior to making a decision for the business problems, participants reflected on a relevant ethical experience. The findings revealed that application of material garnered from reflection on a personal experience was associated with decisions of higher ethicality. However, whether the case was viewed as positive or negative, and whether the outcomes, process, or outcomes and processes embedded in the experience were examined, influenced the application of case material to the new problem. As expected, examining positive experiences and the processes involved in those positive experiences resulted in greater application of case material to new problems. Future directions and implications for understanding ethical decision-making are discussed.
doi:10.1080/10508422.2012.655646
PMCID: PMC4527578  PMID: 26257506
self-reflection; cases; experience; ethical decision-making; knowledge; case analysis; case method
18.  Production of a Shigella sonnei Vaccine Based on Generalized Modules for Membrane Antigens (GMMA), 1790GAHB 
PLoS ONE  2015;10(8):e0134478.
Recently, we developed a high yield production process for outer membrane particles from genetically modified bacteria, called Generalized Modules of Membrane Antigens (GMMA), and the corresponding simple two step filtration purification, enabling economic manufacture of these particles for use as vaccines. Using a Shigella sonnei strain that was genetically modified to produce penta-acylated lipopolysaccharide (LPS) with reduced endotoxicity and to maintain the virulence plasmid encoding for the immunodominant O antigen component of the LPS, scale up of the process to GMP pilot scale was straightforward and gave high yields of GMMA with required purity and consistent results. GMMA were formulated with Alhydrogel and were highly immunogenic in mice and rabbits. In mice, a single immunization containing 29 ng protein and 1.75 ng of O antigen elicited substantial anti-LPS antibody levels. As GMMA contain LPS and lipoproteins, assessing potential reactogenicity was a key aspect of vaccine development. In an in vitro monocyte activation test, GMMA from the production strain showed a 600-fold lower stimulatory activity than GMMA with unmodified LPS. Two in vivo tests confirmed the low potential for reactogenicity. We established a modified rabbit pyrogenicity test based on the European Pharmacopoeia pyrogens method but using intramuscular administration of the full human dose (100 μg of protein). The vaccine elicited an average temperature rise of 0.5°C within four hours after administration, which was considered acceptable and showed that the test is able to detect a pyrogenic response. Furthermore, a repeat dose toxicology study in rabbits using intramuscular (100 μg/dose), intranasal (80 μg/dose), and intradermal (10 μg/dose) administration routes showed good tolerability of the vaccine by all routes and supported its suitability for use in humans. The S. sonnei GMMA vaccine is now in Phase 1 dose-escalation clinical trials.
doi:10.1371/journal.pone.0134478
PMCID: PMC4527750  PMID: 26248044
19.  Evaluation of candidate spermatogonial markers ID4 and GPR125 in testes of adult human cadaveric organ donors 
Andrology  2014;2(4):607-614.
The optimal markers for human spermatogonial stem cells (SSCs) are not known. Among the genes recently linked to SSCs in mice and other animals are the basic helix-loop-helix transcription factor ID4 and the orphan G-protein coupled receptor GPR125. While ID4 and GPR125 are considered putative markers for SSCs, they have not been evaluated for co-expression in human tissue. Further, neither the size nor the character of the human spermatogonial populations that express ID4 and GPR125, respectively, are known. A major barrier to addressing these questions is the availability of healthy adult testis tissue from donors with no known reproductive health problems. To overcome this obstacle, we have employed healthy testicular tissue from a novel set of organ donors (n=16; aged 17-68 years) who were undergoing post-mortem clinical organ procurement. Using immunolabeling, we found that ID4 and GPR125 are expressed on partially overlapping spermatogonial populations and are more broadly expressed in the normal adult human testis. Additionally, we found that expression of ID4 remained stable during aging. These findings suggest that ID4 and GPR125 could be efficacious for identifying previously unrecognized human spermatogonial subpopulations in conjunction with other putative human stem cell markers, both in younger and older donors.
doi:10.1111/j.2047-2927.2014.00226.x
PMCID: PMC4153397  PMID: 24902969
20.  Transmission of Multidrug-Resistant and Drug-Susceptible Tuberculosis within Households: A Prospective Cohort Study 
PLoS Medicine  2015;12(6):e1001843.
Background
The “fitness” of an infectious pathogen is defined as the ability of the pathogen to survive, reproduce, be transmitted, and cause disease. The fitness of multidrug-resistant tuberculosis (MDRTB) relative to drug-susceptible tuberculosis is cited as one of the most important determinants of MDRTB spread and epidemic size. To estimate the relative fitness of drug-resistant tuberculosis cases, we compared the incidence of tuberculosis disease among the household contacts of MDRTB index patients to that among the contacts of drug-susceptible index patients.
Methods and Findings
This 3-y (2010–2013) prospective cohort household follow-up study in South Lima and Callao, Peru, measured the incidence of tuberculosis disease among 1,055 household contacts of 213 MDRTB index cases and 2,362 household contacts of 487 drug-susceptible index cases.
A total of 35/1,055 (3.3%) household contacts of 213 MDRTB index cases developed tuberculosis disease, while 114/2,362 (4.8%) household contacts of 487 drug-susceptible index patients developed tuberculosis disease. The total follow-up time for drug-susceptible tuberculosis contacts was 2,620 person-years, while the total follow-up time for MDRTB contacts was 1,425 person-years. Using multivariate Cox regression to adjust for confounding variables including contact HIV status, contact age, socio-economic status, and index case sputum smear grade, the hazard ratio for tuberculosis disease among MDRTB household contacts was found to be half that for drug-susceptible contacts (hazard ratio 0.56, 95% CI 0.34–0.90, p = 0.017). The inference of transmission in this study was limited by the lack of genotyping data for household contacts. Capturing incident disease only among household contacts may also limit the extrapolation of these findings to the community setting.
Conclusions
The low relative fitness of MDRTB estimated by this study improves the chances of controlling drug-resistant tuberculosis. However, fitter multidrug-resistant strains that emerge over time may make this increasingly difficult.
In this prospective cohort study, Louis Grandjean and colleagues examine the relative fitness of multidrug-resistant versus drug-susceptible tuberculosis for transmission among household contacts in South Lima and Callao, Peru.
Editors' Summary
Background
Tuberculosis—a contagious bacterial disease that usually infects the lungs—is a global public health problem. Every year, 8.6 million people develop active tuberculosis (tuberculosis disease), and at least 1.3 million people die as a result, mainly in resource-limited countries. Mycobacterium tuberculosis, the bacterium that causes tuberculosis, is spread in airborne droplets when people with tuberculosis disease cough or sneeze. Consequently, an individual’s risk of contracting tuberculosis increases with his/her frequency of contact with people who have the disease; people who live in the same household as someone with tuberculosis disease are at particularly high risk. Other risk factors for contracting tuberculosis include living in crowded or insanitary conditions and being immunocompromised because of, for example, infection with HIV. The characteristic symptoms of tuberculosis disease are persistent cough, fever, weight loss, and night sweats. Diagnostic tests for the disease include sputum smear microscopy (microscopic analysis of mucus coughed up from the lungs), the growth of M. tuberculosis from sputum samples, and chest X-rays.
Why Was This Study Done?
Taking several antibiotics (including rifampicin and isoniazid) daily for six months can cure tuberculosis, but the emergence of multidrug-resistant tuberculosis (MDRTB) is making the disease increasingly hard to treat. How badly MDRTB will affect tuberculosis control efforts is likely to depend on the relative “fitness” of multi-drug resistant and drug-susceptible M. tuberculosis strains. The fitness of a pathogen (infectious organism) is its ability to survive, reproduce, be transmitted, and cause disease in another host. Animal and laboratory studies indicate that drug-resistant M. tuberculosis strains are less fit than drug-susceptible strains, but these studies do not account for the clinical, environmental, and socio-economic variables that influence a patient’s ability to cause tuberculosis disease in a contact, and may not accurately measure the relative fitness of M. tuberculosis strains. In this prospective cohort study, the researchers estimate the fitness of drug-resistant tuberculosis relative to drug-susceptible tuberculosis by comparing the incidence of additional cases of tuberculosis disease in households with an MDRTB index case and the incidence in households with a drug-susceptible tuberculosis index case. A prospective cohort study follows a group of people over time to see whether specific baseline characteristics are associated with specific outcomes. The incidence of a disease is the number of new cases in a population over a given time period.
What Did the Researchers Do and Find?
The researchers enrolled 1,055 household contacts of 213 MDRTB index cases (individuals whose disease was resistant to at least rifampicin and isoniazid) and 2,362 household contacts of 487 drug-susceptible tuberculosis index cases living in South Lima and Callao, Peru. During three years of follow-up, 35 (3.3%) of the household contacts of the MDRTB index cases and 114 (4.8%) of the household contacts of the drug-susceptible tuberculosis index cases developed tuberculosis disease. After adjusting for factors likely to affect the transmission of tuberculosis, such as HIV status, socio-economic status, and sputum smear grade of the index case (higher smear grades are associated with a higher risk of tuberculosis transmission), the hazard ratio for tuberculosis disease for household contacts of MDRTB index cases was half that of the household contacts of drug-susceptible tuberculosis index cases. That is, the household contacts of MDRTB index cases contracted tuberculosis disease half as often as those of drug-susceptible tuberculosis index cases.
What Do These Findings Mean?
These findings indicate that, within households, MDRTB has a relatively low fitness compared to drug-susceptible tuberculosis. That is, at least during the first three years following exposure, individuals with MDRTB are less likely to transmit disease to their household contacts than individuals with drug-susceptible tuberculosis. These findings agree with those of previous animal and laboratory studies and with the findings of molecular epidemiology studies that have used genetic methods to estimate M. tuberculosis fitness within populations. Because the researchers did not genetically compare M. tuberculosis strains isolated from the index cases with strains isolated from the household contacts who developed tuberculosis disease, some of these contacts may have become infected outside the household. Moreover, it may not be possible to extrapolate these findings to the community setting. Nevertheless, the low relative fitness of MDRTB reported here improves our chances of controlling the spread of drug-resistant tuberculosis, with the proviso that the emergence of fitter MDRTB strains over time might yet threaten global tuberculosis control efforts.
Additional Information
This list of resources contains links that can be accessed when viewing the PDF on a device or via the online version of the article at http://dx.doi.org/10.1371/journal.pmed.1001843.
The World Health Organization provides information (in several languages) on tuberculosis and on multidrug-resistant tuberculosis; the Global Tuberculosis Report 2014 provides information about tuberculosis around the world; a supplement to the report entitled Drug-Resistant TB—Surveillance and Response is available
The Stop TB Partnership is working towards tuberculosis elimination and provides personal stories about tuberculosis (in English and Spanish); the Tuberculosis Vaccine Initiative (a not-for-profit organization) also provides personal stories about tuberculosis
The US Centers for Disease Control and Prevention provides information about tuberculosis and about drug-resistant tuberculosis (in English and Spanish)
The US National Institute of Allergy and Infectious Diseases also has detailed information on all aspects of tuberculosis
MedlinePlus has links to further information about tuberculosis (in English and Spanish)
doi:10.1371/journal.pmed.1001843
PMCID: PMC4477882  PMID: 26103620
21.  High-dose rifampicin kills persisters, shortens treatment duration, and reduces relapse rate in vitro and in vivo 
Although high-dose rifampicin holds promise for improving tuberculosis control by potentially shortening treatment duration, these effects attributed to eradication of persistent bacteria are unclear. The presence of persistent Mycobacterium tuberculosis was examined using resuscitation promoting factors (RPFs) in both in vitro hypoxia and in vivo murine tuberculosis models before and after treatment with incremental doses of rifampicin. Pharmacokinetic parameters and dose-dependent profile of rifampicin in the murine model were determined. The Cornell mouse model was used to test efficacy of high-dose rifampicin in combination with isoniazid and pyrazinamide and to measure relapse rate. There were large numbers of RPF-dependent persisters in vitro and in vivo. Stationary phase cultures were tolerant to rifampicin while higher concentrations of rifampicin eradicated plate count positive but not RPF-dependent persistent bacteria. In murine infection model, incremental doses of rifampicin exhibited a dose-dependent eradication of RPF-dependent persisters. Increasing the dose of rifampicin significantly reduced the risk of antibiotic resistance emergence. In Cornell model, mice treated with high-dose rifampicin regimen resulted in faster visceral clearance; organs were M. tuberculosis free 8 weeks post-treatment compared to 14 weeks with standard-dose rifampicin regimen. Organ sterility, plate count and RPF-dependent persister negative, was achieved. There was no disease relapse compared to the standard dose regimen (87.5%). High-dose rifampicin therapy results in eradication of RPF-dependent persisters, allowing shorter treatment duration without disease relapse. Optimizing rifampicin to its maximal efficacy with acceptable side-effect profiles will provide valuable information in human studies and can potentially improve current tuberculosis chemotherapy.
doi:10.3389/fmicb.2015.00641
PMCID: PMC4477163  PMID: 26157437
Mycobacterium tuberculosis; rifampicin; persistence; resuscitation promoting factors; mouse model
22.  Understanding paratyphoid infection: study protocol for the development of a human model of Salmonella enterica serovar Paratyphi A challenge in healthy adult volunteers 
BMJ Open  2015;5(6):e007481.
Introduction
This study will develop the first human challenge model of paratyphoid infection which may then be taken forward to evaluate paratyphoid vaccine candidates. Salmonella Paratyphi A is believed to cause a quarter of the estimated 20 million cases of enteric fever annually. Epidemiological evidence also suggests that an increasing proportion of the enteric fever burden is attributable to S. Paratyphi infection meriting further attention and interest in vaccine development. Assessment of paratyphoid vaccine efficacy in preclinical studies is complicated by the lack of a small animal model and the human-restricted nature of the infection. The use of experimental human infection in healthy volunteers provides an opportunity to address these problems in a cost-effective manner.
Methods and analysis
Volunteers will ingest virulent S. Paratyphi A bacteria (NVGH308 strain) with a bicarbonate buffer solution to establish the infectious dose resulting in an ‘attack rate’ of 60–75%. Using an a priori decision-making algorithm, the challenge dose will be escalated or de-escalated to achieve the target attack rate, with the aim of reaching the study end point while exposing as few individuals as possible to infection. The attack rate will be determined by the proportion of paratyphoid infection in groups of 20 healthy adult volunteers, with infection being defined by one or more positive blood cultures (microbiological end point) and/or fever, defined as an oral temperature exceeding 38°C sustained for at least 12 h (clinical end point); 20–80 participants will be required. Challenge participants will start a 2-week course of an oral antibiotic on diagnosis of infection, or after 14 days follow-up.
Ethics and dissemination
The strict eligibility criterion aims to minimise risk to participants and their close contacts. Ethical approval has been obtained. The results will be disseminated in a peer-reviewed journal and presented at international congresses.
Trial registration number
NCT02100397.
doi:10.1136/bmjopen-2014-007481
PMCID: PMC4480031  PMID: 26082464
MICROBIOLOGY; BACTERIOLOGY; IMMUNOLOGY; INFECTIOUS DISEASES
23.  Vaccines against invasive Salmonella disease 
Human Vaccines & Immunotherapeutics  2014;10(6):1478-1493.
Though primarily enteric pathogens, Salmonellae are responsible for a considerable yet under-appreciated global burden of invasive disease. In South and South-East Asia, this manifests as enteric fever caused by serovars Typhi and Paratyphi A. In sub-Saharan Africa, a similar disease burden results from invasive nontyphoidal Salmonellae, principally serovars Typhimurium and Enteritidis. The existing Ty21a live-attenuated and Vi capsular polysaccharide vaccines target S. Typhi and are not effective in young children where the burden of invasive Salmonella disease is highest. After years of lack of investment in new Salmonella vaccines, recent times have seen increased interest in the area led by emerging-market manufacturers, global health vaccine institutes and academic partners. New glycoconjugate vaccines against S. Typhi are becoming available with similar vaccines against other invasive serovars in development. With other new vaccines under investigation, including live-attenuated, protein-based and GMMA vaccines, now is an exciting time for the Salmonella vaccine field.
doi:10.4161/hv.29054
PMCID: PMC4185946  PMID: 24804797
vaccines; Salmonella; nontyphoidal; typhoid; enteric; global health; glycoconjugate; GMMA
24.  Can Neural Activation in Dorsolateral Prefrontal Cortex Predict Responsiveness to Information? An Application to Egg Production Systems and Campaign Advertising 
PLoS ONE  2015;10(5):e0125243.
Consumers prefer to pay low prices and increase animal welfare; however consumers are typically forced to make tradeoffs between price and animal welfare. Campaign advertising (i.e., advertising used during the 2008 vote on Proposition 2 in California) may affect how consumers make tradeoffs between price and animal welfare. Neuroimaging data was used to determine the effects of brain activation in dorsolateral prefrontal cortex (dlPFC) on choices making a tradeoff between price and animal welfare and responsiveness to campaign advertising. Results indicated that activation in the dlPFC was greater when making choices that forced a tradeoff between price and animal welfare, compared to choices that varied only by price or animal welfare. Furthermore, greater activation differences in right dlPFC between choices that forced a tradeoff and choices that did not, indicated greater responsiveness to campaign advertising.
doi:10.1371/journal.pone.0125243
PMCID: PMC4446318  PMID: 26018592
25.  The Association between Mycobacterium Tuberculosis Genotype and Drug Resistance in Peru 
PLoS ONE  2015;10(5):e0126271.
Background
The comparison of Mycobacterium tuberculosis bacterial genotypes with phenotypic, demographic, geospatial and clinical data improves our understanding of how strain lineage influences the development of drug-resistance and the spread of tuberculosis.
Methods
To investigate the association of Mycobacterium tuberculosis bacterial genotype with drug-resistance. Drug susceptibility testing together with genotyping using both 15-loci MIRU-typing and spoligotyping, was performed on 2,139 culture positive isolates, each from a different patient in Lima, Peru. Demographic, geospatial and socio-economic data were collected using questionnaires, global positioning equipment and the latest national census.
Results
The Latin American Mediterranean (LAM) clade (OR 2.4, p<0.001) was significantly associated with drug-resistance and alone accounted for more than half of all drug resistance in the region. Previously treated patients, prisoners and genetically clustered cases were also significantly associated with drug-resistance (OR's 2.5, 2.4 and 1.8, p<0.001, p<0.05, p<0.001 respectively).
Conclusions
Tuberculosis disease caused by the LAM clade was more likely to be drug resistant independent of important clinical, genetic and socio-economic confounding factors. Explanations for this include; the preferential co-evolution of LAM strains in a Latin American population, a LAM strain bacterial genetic background that favors drug-resistance or the "founder effect" from pre-existing LAM strains disproportionately exposed to drugs.
doi:10.1371/journal.pone.0126271
PMCID: PMC4435908  PMID: 25984723

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