Ensouled bodies: The continuity of the theme of ‘the body as instrument’

This paper deals squarely with the concept of instrument, specifically, a music instrument, as a unifying agent. The topic occupied writers from Plato, through Plotinus (3rd century, CE), writers within the period known as the European Latin-based Middle Ages, and, as we will see, beyond. Seen from a historical perspective as it recurs, the topic of “body as instrument” is evidence that mind–body interactive reciprocity is not by any means solely a recent multifaceted biochemical, neurological, psychological, and cognitive, subject of inquiry; but, rather, constituted a carefully-articulated topic of discussion in the past – and, that the results of this encounter of various points of view are indeed useful for us today. Further, that alternative modes of knowledge transmission exist, for example, the allegorical mode.     

Workshops Without Walls: broadening access to science around the world

The National Aeronautics and Space Administration (NASA) Astrobiology Institute (NAI) conducted two "Workshops Without Walls" during 2010 that enabled global scientific exchange--with no travel required. The second of these was on the topic "Molecular Paleontology and Resurrection: Rewinding the Tape of Life." Scientists from diverse disciplines and locations around the world were joined through an integrated suite of collaborative technologies to exchange information on the latest developments in this area of origin of life research. Through social media outlets and popular science blogs, participation in the workshop was broadened to include educators, science writers, and members of the general public. In total, over 560 people from 31 US states and 30 other nations were registered. Among the scientific disciplines represented were geochemistry, biochemistry, molecular biology and evolution, and microbial ecology. We present this workshop as a case study in how interdisciplinary collaborative research may be fostered, with substantial public engagement, without sustaining the deleterious environmental and economic impacts of travel.     

Humor and sexual selection

Recently Geoffrey Miller has suggested that humor evolved through sexual selection as a signal of "creativity," which in turn implies youthfulness, intelligence, and adaptive unpredictability. Drawing upon available empirical studies, I argue that the evidence for a link between humor and creativity is weak and ambiguous. I also find only tenuous support for Miller’s assumption that the attractiveness of the "sense of humor" is to be found in the wittiness of its possessor, since those who use the phrase often seem to associate it with the affects of relatively mirthless "bonding" laughter. Humor, I conclude, may have evolved as an instrument for achieving broad social adhesiveness and for facilitating the individual’s maneuverability within the group, but that it evolved through sexual selection has yet to be convincingly demonstrated. Robert Storey teaches drama and modern fiction at Temple University. In addition to his recent work on literary representation and humor, he has published two books on the French Pierrot figure and articles on such writers as James Joyce, Alain Robbe-Grillet, and David Mamet.     

Analyzing the field of bioinformatics with the multi-faceted topic modeling technique

Background

Bioinformatics is an interdisciplinary field at the intersection of molecular biology and computing technology. To characterize the field as convergent domain, researchers have used bibliometrics, augmented with text-mining techniques for content analysis. In previous studies, Latent Dirichlet Allocation (LDA) was the most representative topic modeling technique for identifying topic structure of subject areas. However, as opposed to revealing the topic structure in relation to metadata such as authors, publication date, and journals, LDA only displays the simple topic structure.

Methods

In this paper, we adopt the Tang et al.’s Author-Conference-Topic (ACT) model to study the field of bioinformatics from the perspective of keyphrases, authors, and journals. The ACT model is capable of incorporating the paper, author, and conference into the topic distribution simultaneously. To obtain more meaningful results, we use journals and keyphrases instead of conferences and bag-of-words.. For analysis, we use PubMed to collected forty-six bioinformatics journals from the MEDLINE database. We conducted time series topic analysis over four periods from 1996 to 2015 to further examine the interdisciplinary nature of bioinformatics.

Results

We analyze the ACT Model results in each period. Additionally, for further integrated analysis, we conduct a time series analysis among the top-ranked keyphrases, journals, and authors according to their frequency. We also examine the patterns in the top journals by simultaneously identifying the topical probability in each period, as well as the top authors and keyphrases. The results indicate that in recent years diversified topics have become more prevalent and convergent topics have become more clearly represented.

Conclusion

The results of our analysis implies that overtime the field of bioinformatics becomes more interdisciplinary where there is a steady increase in peripheral fields such as conceptual, mathematical, and system biology. These results are confirmed by integrated analysis of topic distribution as well as top ranked keyphrases, authors, and journals.

     

The galenic and hippocratic challenges to Aristotle's conception theory

Conclusion As a result of this case study, additional questions arise. These can be cast into at least three groups. The first concerns the development of critical empiricism in the ancient world: a topic of much interest in our own century, expecially with regard to the work of the logical empiricists. Many of the same arguments are present in the ancient world and were hotly debated from the Hippocratic writers through and beyond Galen. Some of the ways in which Galen reacts to Hippocratic and Aristotelian influences may, in part, be explained by Galen's own posture as a so-called Dogmatist. Both the Empirics and the Methodists offered alternative viewpoints on the place, role, and limits of observation in biomedical research. Though I have written on this relationship in the Hippocratic writers and Aristotle,⁴⁴ it remains to be discussed in detailed fashion just how critical empiricism acted in Galen's evaluation of biomedical problems (aporiai). Contrasts between Galen and his predecessors might further clarify this issue both as a historical question and as it affects the construction of biological theory.The second area explores the question of how one develops comprehensive theories. In this respect Galen follows Aristotle's methodology rather closely. Both look at what theories are available to them and then systematically review the problems raised, at the same time refuting what they find inadequate. This is an effective strategy, for it permits utilizing the best features of earlier work to fashion a new whole. Indeed, Galen himself seems to attribute his use of such a methodology to his ecletic medical and philosophical training. Both Aristotle and Galen endeavor to employ techniques of theory integration. That is, they use aspects of theories they have already espoused to deal with new problems. This suggests the emergence of formal, logical coherence as an element in theory evaluation. The obvious drawback is that it can cause mistakes in one area to be repeated and ingrained in other areas. Such errors, because they are at the very core of an explanatory framework, may take centuries to correct. Future studies may shed light on how theory integration acts both in a positive and in a negative way.Finally, this case study offers a glimpse of how science progresses. Even though the advances in medical technology were comparatively minor, there is a great deal more sophistication in the conception theoreis of Aristotle and Galen than was present in the Hippocratic writers. Some of this (in Galen's case) had to do with increased anatomic and physiological knowledge, but most, I believe, is due to the evolution of scientific knowledge. If further work were done specifically on this question, it might document more completely how scientific knowledge on a specific topic evolves. The mode of advancement is primarily through gradual refinement of the types of questions being asked by these ancient authors, and the ramifications of their answers.Ancient theories of conception offer a fine case study in the history and philosophy of how a theory begins the develops. I have tried to suggest some interrelationships among the more important theories, as they focused upon Aristotle's own conception theory. There has been renewed interest in such cases in recent years. It is my hope that future specialized studies will increase our knowledge of method and practice in these important case studies and thereby augment our understanding of the genesis and application of biological theories.     

Dreams and Dreamless Sleep

Dreamless sleep, as subjective experience, is mentioned primarily within Hindu and Buddhist contexts. In the Upanishads, dreamless sleep is presented for the most part as objectless consciousness. Tibetan Buddhists speak of dreamless sleep in terms of a progression of visual experiences consisting of darkness and light. Contemporary discussions of dreaming, unless concerned with Eastern religion or philosophy, do not tend to mention dreamless sleep. For some writers today, dreaming includes all subjective experience during sleep, leaving no room for an experience of dreamless sleep. Some writers describe dreaming as a simulation of waking life. Since not all experience during sleep is simulation, this concept allows for experiences during sleep that may be understood to be other than dreaming. The writer finds it useful to consider simulation as the determining characteristic of dreaming and finds certain other sleep experiences then that are best considered to be dreamless.     

An American in Paris and the origins of the stereomicroscope

A century ago, Horatio S. Greenough, an American living in Paris, persuaded the firm of Carl Zeiss to construct the first low-power stereomicroscope. Fitted by Zeiss with Porro prisms for image erection, this instrument became the ancestor of all stereoscopic dissection microscopes (binoculars) now in use. On the basis of original documents and earlier publications, the present Centennial Essay traces both the history of the Greenough stereomicroscope and the scantily documented life of its inventor, including his probable descent from a family of famous New England sculptors. The aim is to provide some historical background for a truly timeless instrument that was fundamental to developmental biology, beginning almost from the days of its proclamation by Wilhelm Roux.     

Wording effects and the factor structure of the Hospital Anxiety & Depression Scale in HIV/AIDS patients on antiretroviral treatment in South Africa

Background

Given the immense burden of HIV/AIDS on health systems in sub-Saharan Africa and the intricate link between HIV/AIDS and mental health problems, health care providers need a valid and reliable instrument to assess mental health rapidly. The Hospital Anxiety and Depression Scale (HADS) may constitute such an instrument. The aims of this study were to: (1) examine the factor structure of the HADS in a population of South African HIV/AIDS patients on antiretroviral treatment (ART); and (2) identify and control the disturbing influence of systematic wording effects in vulnerable respondent groups.

Methodology/Principal Findings

The translated scale was administered to 716 HIV/AIDS patients enrolled in the public sector ART program in South Africa. A combined confirmatory factor analysis and correlated-traits-correlated-methods framework was used to determine the preferred factor structure of the HADS, while controlling for the disturbing influence of systematic wording effects. When assessing the structure without a negative wording factor, all three factor structures displayed an acceptable fit to the data. The three-factor solution best fitted the data. Addition of a method factor significantly improved the fit of all three factor solutions. Using χ² difference testing, Razavi''s one-factor solution displayed a superior fit compared to the other two factor solutions.

Conclusions

The study outcomes support the use of the HADS as a valid and reliable means to screen for mental health problems in HIV/AIDS patients enrolled in a public-sector ART program in a resource-limited context. The results demonstrate the importance of evaluating and correcting for wording effects when examining the factor structure of the screening instrument in vulnerable patient groups. In light of the inter-relationships between HIV/AIDS and mental health problems and the scarcity of adequate screening tools, additional studies on this topic are required.     

The Neurotic Arthralgia and Myalgia Syndrome

In 1943 Boland and Corr (1) observed that neurosis sometimes displays a similarity to diseases of joints and muscles, and described this as psychogenic rheumatism. Clinically, the latter is manifested, as these writers describe it, by joint and muscle pains of varying intensity and nature, ranging from unpleasant paresthesias to burning sensations.     

Some fallacies in the computation of paternity probabilities.

Legal identification of fathers by means of a "paternity probability" has been used in European courts for decades, and has recently been introduced into American courts and accepted by some of them. The voluminous literature on this topic contains virtually no fundamental criticism of the logical basis for the probabilistic computations. Here I suggest that the "paternity probability" suffers from three basic fallacies: (1) contrary to claims, the figure is not, in fact, the probability that the alleged father is the true father, (2) the denominator of the likelihood ratio used in the computation is driven by (sometimes self-contradictory) assumptions and is not based on facts, and (3) post-inclusionary computations are based on speculation about genotypes that does not constitute scientific evidence. It is recommended that pending the resolution of these difficulties "paternity probabilities" should not be computed or introduced as positive evidence of paternity.     

Development of the AGREE II,part 1: performance,usefulness and areas for improvement

Background

We undertook research to improve the AGREE instrument, a tool used to evaluate guidelines. We tested a new seven-point scale, evaluated the usefulness of the original items in the instrument, investigated evidence to support shorter, tailored versions of the tool, and identified areas for improvement.

Method

We report on one component of a larger study that used a mixed design with four factors (user type, clinical topic, guideline and condition). For the analysis reported in this article, we asked participants to read a guideline and use the AGREE items to evaluate it based on a seven-point scale, to complete three outcome measures related to adoption of the guideline, and to provide feedback on the instrument’s usefulness and how to improve it.

Results

Guideline developers gave lower-quality ratings than did clinicians or policy-makers. Five of six domains were significant predictors of participants’ outcome measures (p < 0.05). All domains and items were rated as useful by stakeholders (mean scores > 4.0) with no significant differences by user type (p > 0.05). Internal consistency ranged between 0.64 and 0.89. Inter-rater reliability was satisfactory. We received feedback on how to improve the instrument.

Interpretation

Quality ratings of the AGREE domains were significant predictors of outcome measures associated with guideline adoption: guideline endorsements, overall intentions to use guidelines, and overall quality of guidelines. All AGREE items were assessed as useful in determining whether a participant would use a guideline. No clusters of items were found more useful by some users than others. The measurement properties of the seven-point scale were promising. These data contributed to the refinements and release of the AGREE II.Evidence-based guidelines are systematically developed statements aimed at assisting clinicians and patients in decisions about appropriate health care for specific clinical circumstances. ¹ Guidelines assist decision-makers in solving system-level and population-level challenges. ^2,3 The potential benefits of guidelines, however, are only as good as the quality of the guidelines themselves. Rigorous development and strategies for reporting are important precursors to successful implementation of the resulting recommendations. ⁴The quality of guidelines is variable, often falling short of basic standards.^5–7 To address this variability, an international team of guideline developers and researchers, the AGREE Collaboration (Appraisal of Guidelines, Research and Evaluation), created a generic instrument to assess the process of guideline development and reporting. The result of this work was the AGREE instrument, a 23-item tool targeting six quality-related domains.^8,9 It became accepted by many as the standard for guideline evaluation.¹⁰As with any new assessment tool, ongoing development of the instrument is required. The AGREE Next Steps Consortium was established to conduct a program of research aimed at improving the AGREE and advancing the overall guideline enterprise. We report on the first of two studies designed to achieve these goals. This study focused on four key issues related to methodology and implementation (Figure 1).Open in a separate windowFigure 1Program of research.First, the original four-point response scale was not in keeping with standards for test construction that are intended to maximize the reliability and discriminability of an instrument and minimize the number of appraisers required to evaluate a guideline.¹¹ To address this issue, we introduced a seven-point response scale, tested its performance and conducted a preliminary analysis of some of its measurement properties.Second, to be of value, the AGREE instrument needs to be easy to apply and needs to generate information that is useful. To generate a reliable estimate of guideline quality, it is recommended that the 23 items of the AGREE instrument be applied by four independent reviewers.^8,9 This process can be cumbersome and resource-intensive. However, no systematic analysis has been undertaken previously to determine if all items of the AGREE instrument generate information that is equally useful across different groups. This fact opens the possibility that fewer than 23 items, and varying combinations of items unique to different users, may be sufficient for evaluation purposes. Therefore, we explored whether evidence exists to inform the development of abridged versions of the AGREE that could be tailored to the unique priorities of different user groups.Third, to be useful as well, the AGREE ratings should be associated with outcomes that are relevant to guideline usage. In keeping with previous findings,⁴ guidelines of higher quality should be more attractive, endorsed or used than those of lower quality. We therefore explored whether these relationships existed and whether they were consistent across different types of users.Finally, given that the AGREE had been in the field for some time, we systematically collected feedback from users on how the items and domains might be improved, updated and refined.In combination with the results of the second study,¹² the data were used by the consortium to craft the AGREE II,¹³ the next version of the AGREE instrument.     

Developing a theory-based instrument to assess the impact of continuing professional development activities on clinical practice: a study protocol

Background

Continuing professional development (CPD) is one of the principal means by which health professionals (i.e. primary care physicians and specialists) maintain, improve, and broaden the knowledge and skills required for optimal patient care and safety. However, the lack of a widely accepted instrument to assess the impact of CPD activities on clinical practice thwarts researchers' comparisons of the effectiveness of CPD activities. Using an integrated model for the study of healthcare professionals' behaviour, our objective is to develop a theory-based, valid, reliable global instrument to assess the impact of accredited CPD activities on clinical practice.

Methods

Phase 1: We will analyze the instruments identified in a systematic review of factors influencing health professionals' behaviours using criteria that reflect the literature on measurement development and CPD decision makers' priorities. The outcome of this phase will be an inventory of instruments based on social cognitive theories. Phase 2: Working from this inventory, the most relevant instruments and their related items for assessing the concepts listed in the integrated model will be selected. Through an e-Delphi process, we will verify whether these instruments are acceptable, what aspects need revision, and whether important items are missing and should be added. The outcome of this phase will be a new global instrument integrating the most relevant tools to fit our integrated model of healthcare professionals' behaviour. Phase 3: Two data collections are planned: (1) a test-retest of the new instrument, including item analysis, to assess its reliability and (2) a study using the instrument before and after CPD activities with a randomly selected control group to explore the instrument's mere-measurement effect. Phase 4: We will conduct individual interviews and focus groups with key stakeholders to identify anticipated barriers and enablers for implementing the new instrument in CPD practice. Phase 5: Drawing on the results from the previous phases, we will use consensus-building methods to develop with the decision makers a plan to implement the new instrument.

Discussion

This project proposes to give stakeholders a theory-based global instrument to validly and reliably measure the impacts of CPD activities on clinical practice, thus laying the groundwork for more targeted and effective knowledge-translation interventions in the future.

     

Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer

Mass spectrometry-based proteomics has greatly benefitted from enormous advances in high resolution instrumentation in recent years. In particular, the combination of a linear ion trap with the Orbitrap analyzer has proven to be a popular instrument configuration. Complementing this hybrid trap-trap instrument, as well as the standalone Orbitrap analyzer termed Exactive, we here present coupling of a quadrupole mass filter to an Orbitrap analyzer. This "Q Exactive" instrument features high ion currents because of an S-lens, and fast high-energy collision-induced dissociation peptide fragmentation because of parallel filling and detection modes. The image current from the detector is processed by an "enhanced Fourier Transformation" algorithm, doubling mass spectrometric resolution. Together with almost instantaneous isolation and fragmentation, the instrument achieves overall cycle times of 1 s for a top 10 higher energy collisional dissociation method. More than 2500 proteins can be identified in standard 90-min gradients of tryptic digests of mammalian cell lysate- a significant improvement over previous Orbitrap mass spectrometers. Furthermore, the quadrupole Orbitrap analyzer combination enables multiplexed operation at the MS and tandem MS levels. This is demonstrated in a multiplexed single ion monitoring mode, in which the quadrupole rapidly switches among different narrow mass ranges that are analyzed in a single composite MS spectrum. Similarly, the quadrupole allows fragmentation of different precursor masses in rapid succession, followed by joint analysis of the higher energy collisional dissociation fragment ions in the Orbitrap analyzer. High performance in a robust benchtop format together with the ability to perform complex multiplexed scan modes make the Q Exactive an exciting new instrument for the proteomics and general analytical communities.     

A solid-state,portable instrument for measurement of chlorophyll luminescence induction in plants

A newly developed compact instrument is described for the measurement of chlorophyll luminescence induction in plants. The instrument operates with a pulsed light emitting diode (LED) as light source and a photodiode as luminescence detector. A special emitter-detector geometry provides for high irradiance of the sample and efficient collection of luminescence by the detector. With insertion of appropriate filters the same probe is also suited for measuring prompt chlorophyll fluorescence. The instrument shows considerable flexibility with respect to pulse frequency, relative lengths of light/dark intervals and luminescence sampling periods. Due to a selective amplifier system only that part of luminescence is processed which is induced by the individual excitation pulses. By this approach, the problem of slow phase accumulation, encountered with conventional phosphoroscopes, is eliminated. Some examples are given for system operation, demonstrating satisfactory performance in measurements with intact leaves and isolated chloroplasts.     

The design of a phonoactograph suitable for study on the influence of pheromones on insect mobility

An instrument for recording changes in insect mobility under the influence of pheromone was described. The instrument was named "phonoactograph" because the intensity of rustle made by insects was utilized as a correlate of their movement. The Colorado beetle males exposed to the action of the female odour increased their mobility significantly.     

Flash fluorometer made from off-the-shelf photographic equipment to measure tissue levels of fluorescein

A device to measure fluorescein in tissue has been constructed from standard photographic equipment--an electronic strobe and a flashmeter both covered with interference filters. The instrument works well in the light and need not touch the area being measured, an advantage over existing fluorometers. The instrument has been used to measure the amount of dye in flaps in rats, pigs, and three humans. The results revealed that the amount of dye in a freshly made flap was rarely as much as in normal skin, and skin with less than 20 percent of the dye of control areas usually sloughed, although there were exceptions. In the future the instrument will be improved, and its readings will be compared to those obtained from radioactive microspheres, the present "gold standard" of techniques to measure vascularity. The instrument can be used to estimate the blood supply to any tissue and seems to be as reliable as the dermofluorometers already on the market.     

Origins of signalling and memory: matters of life versus death

This review focuses on the principles in cell-cell communication and cellular ability to respond to external chemical changes which have been so crucial for the development of life on planet Earth. We now know that the capacity of free-living organisms which evolved more than a billion years ago to respond to intercellular signal molecules, originating either from themselves or from other sources in their vicinity, is so similar possibly even more sophisticated - to that of the cells in our own body, and these findings have had a major impact on our struggle to understand how life has evolved and how it can be maintained. Attention is drawn to the very important topic of mechanisms in cell death, being seen as an aggressive and very powerful instrument in the continuance of life and ability of life to proliferate into a plethora of new species, and use insulin-related material as our paradigm. Such signal molecules (hormones) may have played a major role in cellular maintenance throughout evolution.     

Light scattering measurement in an arc lamp-based flow cytometer

The epi-illumination optics employed in most arc lamp-based flow cytometers may be modified so as to produce a dark-field configuration which facilitates highly sensitive detection of both forward and large angle light scattering in an instrument with a "jet on open surface" flow chamber. Forward scattering is detected at angles upwards from about 2 degrees, while large angle scattering includes angles above 18 degrees. Theoretical considerations suggest that large angle scattering measured around 20 degrees may be as efficient as that measured at 90 degrees for the purpose of distinguishing cells on the basis of intracellular structure. This was supported by the finding that dual parameter light scattering histograms of leukocyte suspensions obtained with the arc lamp-based instrument were closely similar to such histograms recorded with a laser-based instrument with the large angle detector at 90 degrees. Different species of bacteria could be distinguished by means of the dual parameter light scattering device, as could different species of sea algae. The sensitivity of the device is sufficient to measure 0.2 microns polystyrene particles in both forward and large angle scattering.     

Automation of blood film preparation and staining utilizing the technicon autoslide

Evaluation of a prototype Technicon Autoslide, which automatically prepares, fixes, stains, dries labels, and "coverslips" blood films, attached to a Technicon Hemalog D-90 revealed that the instrument prepares high-quality wedge blood smears with uniform distribution of leukocytes, excellent red blood cell and platelet morphology, and adequate staining of normal types of leukocytes. The fixation-staining characteristics did not enable reliable identification of some immature cell types. An additional 200 microliters of blood samples is requred above that required for the Hemalog D-90 in order to prepare a smear. The throughput time of the instrument, from sample aspirate to completion of the blood smear, is 14 min. One sample is completed every 45s. The final glass-slide specimen contains the blood smear sample and its identification and date, embedded in acrylic plastic, which also serves as a coverslip. The instrument can be operated by the D-90 operator with negligible additional effort. The approximate cost of each sample was 8.25 cents. The Autoslide in combination with the Hemalog D-90 should reduce technician time required to prepare, stain, and label blood smears. Its use should reduce the frequency of sample misidentification and provide more uniform quality to slide preparation and staining than is available by current manual techniques. Preliminary studies suggest that Autoslide smears are suitable for use on an image-processing type of automated differential system, and this therefore makes their use possible in a tiered screening system for detection of platelet or red cell abnormalities not recognized by the high-volume cell-counting instruments.