Biomedical subjects

Helen Johnson

Publications and source records attributed to Helen Johnson.

10 recordsLinked to original sources

PubMed2006

PYCHEM: a multivariate analysis package for python.

UNLABELLED: We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines. AVAILABILITY: http://sourceforge.net/projects/pychem

Algorithms↗

PubMed2006

Mortality in southern England during the 2003 heat wave by place of death.

More than 2000 deaths were attributed to the August 2003 heat wave in England and Wales. We analysed excess mortality in southern England during the heat wave by place of death. Excess mortality was 33 per cent in those aged 75 and over and 13.5 per cent in the under 75 age group during the 10 day heat wave. Among those aged 75 and over, deaths at home increased by 33 per cent and deaths in nursing homes increased by 42 per cent. Around one quarter of the heat wave attributable deaths occurred in care homes, but this is likely to be an underestimate as some residents may have been admitted to hospital before death. There is a need for further research to assess the risk of heat-related mortality in hospital in-patients and the residents of care homes in order to improve prevention strategies.

Aged↗

PubMed2005

Motor awareness without perceptual awareness.

The control of action has traditionally been described as "automatic". In particular, movement control may occur without conscious awareness, in contrast to normal visual perception. Studies on rapid visuomotor adjustment of reaching movements following a target shift have played a large part in introducing such distinctions. We suggest that previous studies of the relation between motor performance and perceptual awareness have confounded two separate dissociations. These are: (a) the distinction between motoric and perceptual representations, and (b) an orthogonal distinction between conscious and unconscious processes. To articulate these differences more clearly, we propose a new measure of motor awareness, based on subjects' ability to reproduce the spatial details of reaching movements they have just made. Here we focus on the dissociation between motor awareness and perceptual awareness that may occur when subjects make rapid visuomotor adjustments to reaching movements following a target shift. In experiment 1, motor awareness was dissociated from perceptual awareness of a target shift during reaching movement. Participants' reproduction of movement endpoints following visuomotor adjustment was independent of whether they saw the target shift or not. Experiment 2 replicated this result, and further showed that neither motor awareness nor motor performance were disrupted by TMS over the parietal cortex. The neural mechanisms underlying motor awareness, and the implications for theories of consciousness, are discussed.

Adult↗

PubMed2005

Experience modulates automatic imitation.

Action observation gives rise to activation in corresponding areas of the premotor and primary motor cortices. We tested the hypothesis that this activation depends on visual-motor connections established through correlated experience of observing and executing the same action. Previous work has shown that hand opening and hand closing gestures are facilitated when subjects observe the movement they are performing, relative to a condition in which they observe a different movement from the one they are performing. Experiment 1 replicated this finding in a simple reaction time (RT) procedure using stimulus-response (SR) movements in orthogonal planes. This implies that the effect is an example of automatic imitation, an instruction-independent tendency to execute movements that are topologically similar to those observed, and not merely an example of spatially compatible responding. In Experiment 2, the automatic imitation effect found in Experiment 1 was abolished by a brief period of training in which subjects responded to hand opening by closing their hands, and to hand closing by opening their hands. This outcome is consistent with the hypothesis that, rather than being innate, the cortical connections mediating motor activation by action observation are formed through experience.

Adult↗

PubMed2005

Toward supportive data collection tools for plant metabolomics.

Over recent years, a number of initiatives have proposed standard reporting guidelines for functional genomics experiments. Associated with these are data models that may be used as the basis of the design of software tools that store and transmit experiment data in standard formats. Central to the success of such data handling tools is their usability. Successful data handling tools are expected to yield benefits in time saving and in quality assurance. Here, we describe the collection of datasets that conform to the recently proposed data model for plant metabolomics known as ArMet (architecture for metabolomics) and illustrate a number of approaches to robust data collection that have been developed in collaboration between software engineers and biologists. These examples also serve to validate ArMet from the data collection perspective by demonstrating that a range of software tools, supporting data recording and data upload to central databases, can be built using the data model as the basis of their design.

Arabidopsis↗

PubMed2005

The impact of the 2003 heat wave on mortality and hospital admissions in England.

This article quantifies the impact of the heat wave, 4 to 13 August 2003, on mortality and emergency hospital admissions in England by region and age group. The August 2003 heat wave was associated with a large short-term increase in mortality, particularly in London. Overall in England there were 2,091 (17 per cent) excess deaths. Worst affected were those over the age of 75. The greatest increase of any region in England was in London in the over 75 age group with 522 excess deaths (59 per cent). Excess hospital admissions of 16 per cent were recorded in London for the over 75s. Temperatures in England were unusually hot. Ozone and particulate matter concentrations were also elevated during the heat wave. Estimated excess mortality was greater than for other recent heat waves in the UK.

Adolescent↗

PubMed2005

Mortality from suicide and drug-related poisoning by day of the week in England and Wales, 1993-2002.

This article describes the pattern of mortality by day of the week in deaths from suicide and drug-related poisoning. An increased proportion of suicides occurred on Mondays, while the single day on which the largest number of suicides occurred was 1st January 2000, a Saturday. Together these suggest an effect of entering a new time period. The pattern for drug-related poisonings varied according to the coroner's verdict. An increased proportion of deaths from drug abuse/dependence and accidental drug-related poisoning deaths occurred on Saturdays among males, while the most common day of death for drug-related poisoning deaths with a suicide verdict was Monday for both sexes.

Drug Overdose↗

PubMed2004

Consistent chronostasis effects across saccade categories imply a subcortical efferent trigger.

Saccadic chronostasis refers to the subjective temporal lengthening of the first visual stimulus perceived after an eye movement, and is most commonly experienced as the "stopped clock" illusion. Other temporal illusions arising in the context of movement (e.g., "intentional binding") appear to depend upon the volitional nature of the preceding motor act. Here we assess chronostasis across different saccade types, ranging from highly volitional (self-timed saccades, antisaccades) to highly reflexive (peripherally cued saccades, express saccades). Chronostasis was similar in magnitude across all these conditions, despite wide variations in their neural bases. The illusion must therefore be triggered by a "lowest common denominator" signal common to all the conditions tested and their respective neural circuits. Specifically, it is suggested that chronostasis is triggered by a low-level signal arising in response to efferent signals generated in the superior colliculus.

Adult↗

PubMed2003

The effect of attentional cueing on conscious awareness of stimulus and response.

Attending to a cued location in space leads to faster reaction times when a stimulus is presented there. The reasons for this attentional effect, and its specific locus in the information-processing chain between stimulus and response, remain unclear. One suggestion is that attention speeds the conscious detection of stimuli. Surprisingly, this possibility appears not to have been tested directly. To resolve this question, we asked subjects to make simple responses to lateralised targets that followed either a valid, invalid or neutral cue, and to judge the perceived time of the target onset, or of their response, by delayed report of the position of a clock hand. Our results showed that only a small and non-significant part of the attentional effect is due to delayed conscious awareness of the stimulus. The greater part of the attentional effect is localised either subsequent to conscious detection of stimuli or occurs in a separate, parallel processing stream from that which generates the motor response.

Adult↗

PubMed2002

Action and awareness in pointing tasks.

Subjects' awareness of motor corrections was investigated in a double-step pointing task. An unpredictable lateral target displacement of 10 cm, either left or right, during an ongoing reaching movement led to corrections of the trajectory. Subjects were required either to follow the target (pointing) or move in the opposite direction (anti-pointing). The target jump elicited rapid corrections to the movement in the direction of the target shift. These corrections were in some sense involuntary as they sometimes occurred in anti-point trials, when subjects were instructed to correct in the opposite direction to the target jump. The instructed correction away from the target in anti-point trials occurred later than the correction towards the target in standard pointing. Subjects were also asked to report their awareness of the motor correction they had just made by immediately reproducing each movement. In normal pointing, subjects showed reduced and delayed awareness, suggesting that the corrections were at least partly automatic. Anti-pointing corrections did not show this dissociation between performance and awareness. We suggest that anti-point corrections, but not standard pointing corrections, involve an additional supervisory system. This system is characterised by its slow operation and its access to conscious awareness.

Adult↗