HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures

Background  

An accurate rendering of interior surfaces can facilitate the analysis of mechanisms at atomic-level detail, such as the transport of substrates in the ammonia channel. In molecular viewers, one must remove the exterior surface that obscures the channel surface by clipping the viewing plane or manually selecting the channel residues in order to display a partial surface. Neither method is entirely satisfactory, as unwanted additional pieces of surfaces are always generated.     

JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases

Background  

Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language.     

Tools for integrated sequence-structure analysis with UCSF Chimera

Background  

Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a) provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b) facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit); (c) can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d) interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals.     

A standardised protocol for texture feature analysis of endoscopic images in gynaecological cancer

Background  

In the development of tissue classification methods, classifiers rely on significant differences between texture features extracted from normal and abnormal regions. Yet, significant differences can arise due to variations in the image acquisition method. For endoscopic imaging of the endometrium, we propose a standardized image acquisition protocol to eliminate significant statistical differences due to variations in: (i) the distance from the tissue (panoramic vs close up), (ii) difference in viewing angles and (iii) color correction.     

Associations of TV Viewing Duration,Meals and Snacks Eaten When Watching TV,and a TV in the Bedroom with Child Adiposity

Objective

This study aimed to examine the associations of TV parameters with adiposity in early life.

Methods

Data were collected as part of the Born in Bradford (BiB) longitudinal birth cohort study. Child TV viewing duration was parent reported, and BMI, the sum of triceps and subscapular skinfolds, and waist circumference were measured at ~12, 18, 24, and 36 months of age in 1,338 children. Mixed effects models were used to quantify adjusted associations of TV viewing duration with adiposity markers, incorporating data from all time points. Linear regression was used to investigate differences in adiposity levels across frequencies of eating meals and snacks while watching TV at age ~24 months and between children who did and did not have a TV in their bedroom at age ~36 months.

Results

Every 1 h/d of TV viewing was associated with a 0.075‐cm larger (95% CI: 0.0034‐0.15) waist circumference, independent of covariates including sleep duration, dietary factors, and physical activity level. There was no evidence for any other associations.

Conclusions

TV viewing duration is independently associated with abdominal adiposity in young children. Limiting TV viewing from an early age may be important for primary prevention of obesity.     

Television Viewing Time in Hong Kong Adult Population: Associations with Body Mass Index and Obesity

Background

Obesity is increasing dramatically in the Asia-Pacific region particularly China. The population of Hong Kong was exposed to modernization far earlier than the rest of China, reflecting conditions that are likely to be replicated as other Chinese cities undergo rapid change. This study examined the relationship between television viewing and obesity in a Hong Kong sample. Information about the relationship between a key sedentary behavior, TV viewing, and obesity, and its moderation by demographic characteristics may identify sectors of the population at highest risk for excess weight.

Methods

Data were from Hong Kong Family and Health Information Trends Survey (2009–2010), a population-based survey on the public''s use of media for health information and family communication by telephone interviews with 3,016 Hong Kong adults (age≥18 years). TV viewing time, body mass index (BMI), physical activity and other lifestyle variables were analyzed.

Results

Viewing time was longer in women, increased with age but decreased with education level and vigorous physical activity (all P<0.01). Longer TV viewing time was significantly associated with higher BMI (Coefficients B = 0.17, 95% CI: 0.11, 0.24) after adjusting for age, gender, employment status, marital status, education level, smoking activity and vigorous physical activity. This association was stronger in women than men (Coefficients B: 0.19 versus 0.15) and strongest in those aged 18 to 34 years (Coefficients B = 0.35). Furthermore, an hour increase in daily TV viewing was associated with 10% greater odds of being obese.

Conclusions

A significant socioeconomic gradient in television viewing time was observed. TV viewing time positively associated with BMI and obesity. The TV viewing – BMI associations were strongest in women and young adults, suggesting vulnerable groups to target for obesity prevention by decreasing TV viewing.     

Energy Balance Related Behaviour: Personal,Home- and Friend-Related Factors among Schoolchildren in Europe Studied in the ENERGY-Project

Objective

To design interventions that target energy balance-related behaviours, knowledge of primary schoolchildren''s perceptions regarding soft drink intake, fruit juice intake, breakfast consumption, TV viewing and physical activity (PA) is essential. The current study describes personal beliefs and attitudes, home- and friend-related variables regarding these behaviours across Europe.

Design

Cross-sectional study in which personal, family and friend -related variables were assessed by validated questionnaires, and dichotomized as favourable versus unfavourable answers. Logistic regression analyses were conducted to estimate proportions of children giving unfavourable answers and test between-country differences.

Setting

A survey in eight European countries.

Subjects

A total of 7903 10–12 year old primary schoolchildren.

Results

A majority of the children reported unfavourable attitudes, preferences and subjective norms regarding soft drink, fruit juice intake and TV viewing accompanied with high availability and accessibility at home. Few children reported unfavourable attitudes and preferences regarding breakfast consumption and PA. Many children reported unfavourable health beliefs regarding breakfast consumption and TV viewing. Substantial differences between countries were observed, especially for variables regarding soft drink intake, breakfast consumption and TV viewing.

Conclusion

The surveyed children demonstrated favourable attitudes to some healthy behaviours (PA, breakfast intake) as well as to some unhealthy behaviours (soft drink consumption, TV viewing). Additionally, many children across Europe have personal beliefs and are exposed to social environments that are not supportive to engagement in healthy behaviours. Moreover, the large differences in personal, family and friend-related variables across Europe argue for implementing different strategies in the different European countries.     

A tool for comparing different statistical methods on identifying differentially expressed genes

Background  

Many different statistical methods have been developed to deal with two group comparison microarray experiments. Most often, a substantial number of genes may be selected or not, depending on which method was actually used. Practical guidance on the application of these methods is therefore required. We developed a procedure based on bootstrap and a criterion to allow viewing and quantifying differences between method-dependent selections. We applied this procedure on three datasets that cover a range of possible sample sizes to compare three well known methods, namely: t-test, LPE and SAM.     

The Emotional and Attentional Impact of Exposure to One's Own Body in Bulimia Nervosa: A Physiological View

Background

Body dissatisfaction is the most relevant body image disturbance in bulimia nervosa (BN). Research has shown that viewing one''s own body evokes negative thoughts and emotions in individuals with BN. However, the psychophysiological mechanisms involved in this negative reaction have not yet been clearly established. Our aim was to examine the emotional and attentional processes that are activated when patients with BN view their own bodies.

Method

We examined the effects of viewing a video of one''s own body on the physiological (eye-blink startle, cardiac defense, and skin conductance) and subjective (pleasure, arousal, and control ratings) responses elicited by a burst of 110 dB white noise of 500 ms duration. The participants were 30 women with BN and 30 healthy control women. The experimental task consisted of two consecutive and counterbalanced presentations of the auditory stimulus preceded, alternatively, by a video of the participant''s own body versus no such video.

Results

The results showed that, when viewing their own bodies, women with BN experienced (a) greater inhibition of the startle reflex, (b) greater cardiac acceleration in the first component of the defense reaction, (c) greater skin conductance response, and (d) less subjective pleasure and control combined with greater arousal, compared with the control participants.

Conclusion

Our findings suggest that, for women with BN, peripheral-physiological responses to self-images are dominated by attentional processes, which provoke an immobility reaction caused by a dysfunctional negative response to their own body.     

The effect of sensory uncertainty due to amblyopia (lazy eye) on the planning and execution of visually-guided 3D reaching movements

Background

Impairment of spatiotemporal visual processing in amblyopia has been studied extensively, but its effects on visuomotor tasks have rarely been examined. Here, we investigate how visual deficits in amblyopia affect motor planning and online control of visually-guided, unconstrained reaching movements.

Methods

Thirteen patients with mild amblyopia, 13 with severe amblyopia and 13 visually-normal participants were recruited. Participants reached and touched a visual target during binocular and monocular viewing. Motor planning was assessed by examining spatial variability of the trajectory at 50–100 ms after movement onset. Online control was assessed by examining the endpoint variability and by calculating the coefficient of determination (R²) which correlates the spatial position of the limb during the movement to endpoint position.

Results

Patients with amblyopia had reduced precision of the motor plan in all viewing conditions as evidenced by increased variability of the reach early in the trajectory. Endpoint precision was comparable between patients with mild amblyopia and control participants. Patients with severe amblyopia had reduced endpoint precision along azimuth and elevation during amblyopic eye viewing only, and along the depth axis in all viewing conditions. In addition, they had significantly higher R² values at 70% of movement time along the elevation and depth axes during amblyopic eye viewing.

Conclusion

Sensory uncertainty due to amblyopia leads to reduced precision of the motor plan. The ability to implement online corrections depends on the severity of the visual deficit, viewing condition, and the axis of the reaching movement. Patients with mild amblyopia used online control effectively to compensate for the reduced precision of the motor plan. In contrast, patients with severe amblyopia were not able to use online control as effectively to amend the limb trajectory especially along the depth axis, which could be due to their abnormal stereopsis.     

Infrastructure for the life sciences: design and implementation of the UniProt website

Background  

The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) at Georgetown University, and soon afterwards the website was set up as a central entry point to UniProt resources. Requests to this address were redirected to one of the three organisations' websites. While these sites shared a set of static pages with general information about UniProt, their pages for searching and viewing data were different. To provide users with a consistent view and to cut the cost of maintaining three separate sites, the consortium decided to develop a common website for UniProt. Following several years of intense development and a year of public beta testing, the domain was switched to the newly developed site described in this paper in July 2008.     

When What's Left Is Right: Visuomotor Transformations in an Aged Population

Background

There has been little consensus as to whether age-related visuomotor adaptation effects are readily observable. Some studies have found slower adaptation, and/or reduced overall levels. In contrast, other methodologically similar studies have found no such evidence of aging effects on visuomotor adaptation. A crucial early step in successful adaptation is the ability to perform the necessary transformation to complete the task at hand. The present study describes the use of a viewing window paradigm to examine the effects of aging in a visuomotor transformation task.

Methods

Two groups of participants, a young adult control group (age range 18–33 years old, mean age = 22) and an older adult group (age range 62–74, mean age = 68) completed a viewing window task that was controlled by the user via a computer touchscreen. Four visuomotor “flip” conditions were created by varying the relationship between the participant''s movement, and the resultant on-screen movement of the viewing window: 1) No flip 2) X-Axis and Y-axis body movements resulted in the opposite direction of movement of the viewing window. In each of the 3) Flip-X and 4) Flip-Y conditions, the solitary X- or Y-axes were reversed. Response times and movement of the window were recorded.

Conclusions

Older participants demonstrated impairments in performing a required visuomotor transformation, as evidenced by more complex scanning patterns and longer scanning times when compared to younger control participants. These results provide additional evidence that the mechanisms involved in visuomotor transformation are negatively affected by age.     

Changes in cardiovascular disease risk factors from age 9 to 19 and the influence of television viewing

Objective:

The purpose of this study was to determine if time spent watching television is associated with changes in cardiovascular disease (CVD) risk factors from age 9 to 19.

Design and Methods:

Participants were girls enrolled in the NHLBI Growth and Health Study (n = 1,702), and CVD risk factors were measured at ages 10, 12, 14, 16, and 19. Longitudinal quantile regression was used to determine if television viewing was associated with changes in CVD risk factors over time at the 10th, 25th, 50th, 75th, and 90th percentiles of the CVD risk factors.

Results:

In black girls, television viewing (h/wk) was positively associated with sum of skinfolds (mm) at the 75th (0.22, 99% CI, 0.06‐0.38) and 90th percentiles (0.21, 99% CI, 0.05‐0.36), but not at the 10th, 25th, or 50th percentiles. In white girls, television viewing (h/wk) was positively associated with sum of skinfolds (mm) with the strength of the associations progressively stronger toward the upper tail of the skinfold distribution, adjusting for physical activity and other covariates (10th percentile: 0.08, 99% CI, 0.03‐0.13; 90th percentile: 0.42, 99% CI, 0.24‐0.59). All associations were adjusted for physical activity, dietary factors, sleep, and maturation. No associations were observed between television viewing and changes in systolic blood pressure, triglycerides, or cholesterol levels in black or white girls.

Conclusion:

Girls who spent more time watching television had greater increases in sum of skinfolds from age 9 to 19, independent of physical activity levels and other covariates. The associations observed were stronger at the upper tail of the skinfold distribution.     

Viewing the Body after Bereavement Due to Suicide: A Population-Based Survey in Sweden

Background

Research on the assumed, positive and negative, psychological effects of viewing the body after a suicide loss is sparse. We hypothesized that suicide-bereaved parents that viewed their childs body in a formal setting seldom regretted the experience, and that viewing the body was associated with lower levels of psychological morbidity two to five years after the loss.

Methods and Findings

We identified 915 suicide-bereaved parents by linkage of nationwide population-based registries and collected data by a questionnaire. The outcome measures included the Patient Health Questionnaire (PHQ-9). In total, 666 (73%) parents participated. Of the 460 parents (69%) that viewed the body, 96% answered that they did not regret the experience. The viewing was associated with a higher risk of reliving the child''s death through nightmares (RR 1.61, 95% CI 1.13 to 2.32) and intrusive memories (RR 1.20, 95% CI 1.04 to 1.38), but not with anxiety (RR 1.02, 95% CI 0.74 to 1.40) and depression (RR 1.25, 95% CI 0.85 to 1.83). One limitation of our study is that we lack data on the informants'' personality and coping strategies.

Conclusions

In this Swedish population-based survey of suicide-bereaved parents, we found that by and large everyone that had viewed their deceased child in a formal setting did not report regretting the viewing when asked two to five years after the loss. Our findings suggest that most bereaved parents are capable of deciding if they want to view the body or not. Officials may assist by giving careful information about the child''s appearance and other details concerning the viewing, thus facilitating mental preparation for the bereaved person. This is the first large-scale study on the effects of viewing the body after a suicide and additional studies are needed before clinical recommendations can be made.     

Gender Differences in the Motivational Processing of Babies Are Determined by Their Facial Attractiveness

Background

This study sought to determine how esthetic appearance of babies may affect their motivational processing by the adults.

Methodology and Principal Findings

Healthy men and women were administered two laboratory-based tasks: a) key pressing to change the viewing time of normal-looking babies and of those with abnormal facial features (e.g., cleft palate, strabismus, skin disorders, Down''s syndrome and fetal alcohol syndrome) and b) attractiveness ratings of these images. Exposure to the babies'' images produced two different response patterns: for normal babies, there was a similar effort by the two groups to extend the visual processing with lower attractiveness ratings by men; for abnormal babies, women exerted greater effort to shorten the viewing time despite attractiveness ratings comparable to the men.

Conclusions

These results indicate that gender differences in the motivational processing of babies include excessive (relative to the esthetic valuation) motivation to extend the viewing time of normal babies by men vs. shortening the exposure to the abnormal babies by women. Such gender-specific incentive sensitization phenomenon may reflect an evolutionary-derived need for diversion of limited resources to the nurturance of healthy offspring.     

GeneLibrarian: an effective gene-information summarization and visualization system

Background  

Abundant information about gene products is stored in online searchable databases such as annotation or literature. To efficiently obtain and digest such information, there is a pressing need for automated information-summarization and functional-similarity clustering of genes.     

Screen-Based Sedentary Behavior,Physical Activity,and Muscle Strength in the English Longitudinal Study of Ageing

Background

Sarcopenia is associated with loss of independence and ill-health in the elderly although the causes remain poorly understood. We examined the association between two screen-based leisure time sedentary activities (daily TV viewing time and internet use) and muscle strength.

Methods and Results

We studied 6228 men and women (aged 64.9±9.1 yrs) from wave 4 (2008-09) of the English Longitudinal Study of Ageing, a prospective study of community dwelling older adults. Muscle strength was assessed by a hand grip test and the time required to complete five chair rises. TV viewing and internet usage were inversely associated with one another. Participants viewing TV ≥6hrs/d had lower grip strength (Men, B = −1.20 kg, 95% CI, −2.26, −0.14; Women, −0.75 kg, 95% CI, −1.48, −0.03) in comparison to <2hrs/d TV, after adjustment for age, physical activity, smoking, alcohol, chronic disease, disability, depressive symptoms, social status, and body mass index. In contrast, internet use was associated with higher grip strength (Men, B = 2.43 kg, 95% CI, 1.74, 3.12; Women, 0.76 kg, 95% CI, 0.32, 1.20). These associations persisted after mutual adjustment for both types of sedentary behaviour.

Conclusions

In older adults, the association between sedentary activities and physical function is context specific (TV viewing vs. computer use). Adverse effects of TV viewing might reflect the prolonged sedentary nature of this behavior.     

Involvement of lipid rafts in adhesion-induced activation of Met and EGFR

Background  

Cell adhesion has been shown to induce activation of certain growth factor receptors in a ligand-independent manner. However, the mechanism for such activation remains obscure.     

A sugar beet chlorophyll a/b binding protein promoter void of G-box like elements confers strong and leaf specific reporter gene expression in transgenic sugar beet

Background  

Modification of leaf traits in sugar beet requires a strong leaf specific promoter. With such a promoter, expression in taproots can be avoided which may otherwise take away available energy resources for sugar accumulation.     

Pancreatic metastasis from gastric carcinoma: a case report

Background  

The pancreas is a rare but occasionally favored target for metastasis. Metastatic lesions in the pancreas have been described for various primary cancers, such as carcinomas of the lung, the breast, renal cell carcinoma and sarcomas.