Archaeology on the Road, July 2010

Not only are we excited that Team Archaeology is back for our third ride, we are energized to be part of a “Human and Natural History” partnership that allows us expanded opportunities to share the story of Iowa’s amazing past. Once again there will be archaeologists along for the ride, as well as at Expo and this year at roadside locations Day One, Five and Six. Don’t hesitate to ask about the history of the first people to travel this landscape as well as the stories of each generation that has contributed to what we know of ourselves today. We will also feature information about the landscape and natural resources of Iowa you will encounter along the route through our partnering colleagues specializing in geology, hydrology, and other earth sciences. Enjoy using this booklet as your guide to the week’s activities and please help yourself to free materials from our outreach booth about our shared past and the natural world we depend on. Ride smart, be safe, and when you get home, be sure to tell your friends and neighbors about Iowa archaeology!

Inaugural adress: The concept of biostratigraphy: the view point of a stratigrapher

Colleagues, Ladies and Gentlemen. My presence here is due to accidental circumstances and I must confess that I feel a little embarassed by the fact Both your scientific quality and the worlwide acceptance of the results achieved by you in your research fields make me prudent and, to a certain extent, cautious.

Archaeology on the Road, July 2011

Not only are we excited that Team Archaeology is back for our third ride, we are energized to be part of a “Human and Natural History” partnership that allows us expanded opportunities to share the story of Iowa’s amazing past. Once again there will be archaeologists along for the ride, as well as at Expo and this year at roadside locations Day One, Five and Six. Don’t hesitate to ask about the history of the first people to travel this landscape as well as the stories of each generation that has contributed to what we know of ourselves today. We will also feature information about the landscape and natural resources of Iowa you will encounter along the route through our partnering colleagues specializing in geology, hydrology, and other earth sciences. Enjoy using this booklet as your guide to the week’s activities and please help yourself to free materials from our outreach booth about our shared past and the natural world we depend on. Ride smart, be safe, and when you get home, be sure to tell your friends and neighbors about Iowa archaeology!

Urinalysis and pre-renal acute kidney injury: time to move on.

Urinary indices are classically believed to allow differentiation of transient (or pre-renal) acute kidney injury (AKI) from persistent (or acute tubular necrosis) AKI. However, the data validating urinalysis in critically ill patients are weak. In the previous issue of Critical Care, Pons and colleagues demonstrate in a multicenter observational study that sodium and urea excretion fractions as well as urinary over plasma ratios performed poorly as diagnostic tests to separate such entities. This study confirms the limited diagnostic and prognostic ability of urine testing. Together with other studies, this study raises more fundamental questions about the value, meaning and pathophysiologic validity of the pre-renal AKI paradigm and suggests that AKI (like all other forms of organ injury) is a continuum of injury that cannot be neatly divided into functional (pre-renal or transient) or structural (acute tubular necrosis or persistent).

How to measure cortical folding from MR images: a step-by-step tutorial to compute local gyrification index.

Cortical folding (gyrification) is determined during the first months of life, so that adverse events occurring during this period leave traces that will be identifiable at any age. As recently reviewed by Mangin and colleagues(2), several methods exist to quantify different characteristics of gyrification. For instance, sulcal morphometry can be used to measure shape descriptors such as the depth, length or indices of inter-hemispheric asymmetry(3). These geometrical properties have the advantage of being easy to interpret. However, sulcal morphometry tightly relies on the accurate identification of a given set of sulci and hence provides a fragmented description of gyrification. A more fine-grained quantification of gyrification can be achieved with curvature-based measurements, where smoothed absolute mean curvature is typically computed at thousands of points over the cortical surface(4). The curvature is however not straightforward to comprehend, as it remains unclear if there is any direct relationship between the curvedness and a biologically meaningful correlate such as cortical volume or surface. To address the diverse issues raised by the measurement of cortical folding, we previously developed an algorithm to quantify local gyrification with an exquisite spatial resolution and of simple interpretation. Our method is inspired of the Gyrification Index(5), a method originally used in comparative neuroanatomy to evaluate the cortical folding differences across species. In our implementation, which we name local Gyrification Index (lGI(1)), we measure the amount of cortex buried within the sulcal folds as compared with the amount of visible cortex in circular regions of interest. Given that the cortex grows primarily through radial expansion(6), our method was specifically designed to identify early defects of cortical development. In this article, we detail the computation of local Gyrification Index, which is now freely distributed as a part of the FreeSurfer Software (http://surfer.nmr.mgh.harvard.edu/, Martinos Center for Biomedical Imaging, Massachusetts General Hospital). FreeSurfer provides a set of automated reconstruction tools of the brain's cortical surface from structural MRI data. The cortical surface extracted in the native space of the images with sub-millimeter accuracy is then further used for the creation of an outer surface, which will serve as a basis for the lGI calculation. A circular region of interest is then delineated on the outer surface, and its corresponding region of interest on the cortical surface is identified using a matching algorithm as described in our validation study(1). This process is repeatedly iterated with largely overlapping regions of interest, resulting in cortical maps of gyrification for subsequent statistical comparisons (Fig. 1). Of note, another measurement of local gyrification with a similar inspiration was proposed by Toro and colleagues(7), where the folding index at each point is computed as the ratio of the cortical area contained in a sphere divided by the area of a disc with the same radius. The two implementations differ in that the one by Toro et al. is based on Euclidian distances and thus considers discontinuous patches of cortical area, whereas ours uses a strict geodesic algorithm and include only the continuous patch of cortical area opening at the brain surface in a circular region of interest.

Rapid disease emergence through horizontal gene transfer between eukaryotes.

Among different species of eukaryotes, the extent and evolutionary significance of horizontal gene transfer remains poorly understood. A newly published study by Friesen and colleagues indicates that a recent gene transfer between two species of fungi has enabled the recipient to rapidly acquire high virulence on wheat. The study highlights a mechanism by which diseases can suddenly emerge, but also brings up the controversial issues of how horizontal gene transfer occurs and whether fungal incompatibility barriers to gene flow are more 'leaky' than was previously thought.

Low E2F1 transcript levels are a strong determinant of favorable breast cancer outcome.

INTRODUCTION: We investigated whether mRNA levels of E2F1, a key transcription factor involved in proliferation, differentiation and apoptosis, could be used as a surrogate marker for the determination of breast cancer outcome. METHODS: E2F1 and other proliferation markers were measured by quantitative RT-PCR in 317 primary breast cancer patients from the Stiftung Tumorbank Basel. Correlations to one another as well as to the estrogen receptor and ERBB2 status and clinical outcome were investigated. Results were validated and further compared with expression-based prognostic profiles using The Netherlands Cancer Institute microarray data set reported by Fan and colleagues. RESULTS: E2F1 mRNA expression levels correlated strongly with the expression of other proliferation markers, and low values were mainly found in estrogen receptor-positive and ERBB2-negative phenotypes. Patients with low E2F1-expressing tumors were associated with favorable outcome (hazard ratio = 4.3 (95% confidence interval = 1.8-9.9), P = 0.001). These results were consistent in univariate and multivariate Cox analyses, and were successfully validated in The Netherlands Cancer Institute data set. Furthermore, E2F1 expression levels correlated well with the 70-gene signature displaying the ability of selecting a common subset of patients at good prognosis. Breast cancer patients' outcome was comparably predictable by E2F1 levels, by the 70-gene signature, by the intrinsic subtype gene classification, by the wound response signature and by the recurrence score. CONCLUSION: Assessment of E2F1 at the mRNA level in primary breast cancer is a strong determinant of breast cancer patient outcome. E2F1 expression identified patients at low risk of metastasis irrespective of the estrogen receptor and ERBB2 status, and demonstrated similar prognostic performance to different gene expression-based predictors.

Bilateral Sequential NAION: A Comparison of Visual Outcomes in Fellow Eyes Using Quantitative Analysis of Goldmann Visual Fields

Purpose: Previous studies of the visual outcome in bilateral non-arteritic anterior ischemic optic neuropathy (NAION) have yielded conflicting results, specifically regarding congruity between fellow eyes. Prior studies have used measures of acuity and computerized perimetry but none has compared Goldmann visual field outcomes between fellow eyes. In order to better define the concordance of visual loss in this condition, we reviewed our cases of bilateral sequential NAION, including measures of visual acuity, pupillary function and both pattern and severity of visual field loss.Methods: We performed a retrospective chart review of 102 patients with a diagnosis of bilateral sequential NAION. Of the 102 patients, 86 were included in the study for analysis of final visual outcome between the affected eyes. Visual function was assessed using visual acuity, Goldmann visual fields, color vision and RAPD. A quantitative total visual field score and score per quadrant was analyzed for each eye using the numerical Goldmann visual field scoring method previously described by Esterman and colleagues. Based upon these scores, we calculated the total deviation and pattern deviation between fellow eyes and between eyes of different patients. Statistical significance was determined using nonparametric tests.Results: A statistically significant correlation was found between fellow eyes for multiple parameters, including logMAR visual acuity (P = 0.0101), global visual field (P = 0.0001), superior visual field (P = 0.0001), and inferior visual field (P = 0.0001). In addition, the mean deviation of both total (P = 0.0000000007) and pattern (P = 0.000000004) deviation analyses was significantly less between fellow eyes ("intra"-eyes) than between eyes of different patients ("inter"-eyes).Conclusions: Visual function between fellow eyes showed a fair to moderate correlation that was statistically significant. The pattern of vision loss was also more similar in fellow eyes than between eyes of different patients. These results may help allow better prediction of visual outcome for the second eye in patients with NAION. These findings may also be useful for evaluating efficacy of therapeutic interventions.

Superantigens and retroviral infection: insights from mouse mammary tumor virus.

Superantigens induce a vigorous immune response by stimulating T cells that express particular T-cell receptor V beta chains. Mouse mammary tumor virus is a milk-transmitted retrovirus that encodes such a superantigen. Paradoxically, as discussed by Werner Held and colleagues, the strong superantigen-induced immune response permits the survival of the virus via T-cell dependent clonal expansion of infected B cells.

Clinically assessed consequences of workplace physical violence

OBJECTIVES: To assess consequences of physical violence at work and identify their predictors. METHODS: Among the patients in a medicolegal consultation from 2007 to 2010, the subsample of workplace violence victims (n = 185) was identified and contacted again in average 30 months after the assault. Eighty-six victims (47 %) participated. Ordinal logistic regression analyses assessed the effect of 9 potential risk factors on physical, psychological and work consequences summarized in a severity score (0-9). RESULTS: Severity score distribution was as follows: 4+: 14 %; 1-3: 42 %; and 0: 44 %. Initial psychological distress resulting from the violence was a strong predictor (p < 0.001) of the severity score both on work and long-term psychological consequences. Gender and age did not reach significant levels in multivariable analyses even though female victims had overall more severe consequences. Unexpectedly, only among workers whose jobs implied high awareness of the risk of violence, first-time violence was associated with long-term psychological and physical consequences (p = 0.004). Among the factors assessed at follow-up, perceived lack of employers' support or absence of employer was associated with higher values on the severity score. The seven other assessed factors (initial physical injuries; previous experience of violence; preexisting health problems; working alone; internal violence; lack of support from colleagues; and lack of support from family or friends) were not significantly associated with the severity score. CONCLUSIONS: Being a victim of workplace violence can result in long-term consequences on health and employment, their severity increases with the seriousness of initial psychological distress. Support from the employer can help prevent negative outcomes.

Foreword (2004)

This is the first issue of Geologica Acta dedicated to the memory of Professor Francesc Calvet, whose life was cut short in January 2002 when he was only 54. Francesc was a man with great human qualities, a distinguished scientist and an inspiring teacher who was held in high esteem by all those who knew him. His academic achievements, talent and friendly personality attracted numerous colleagues and students. Unfailingly courteous and polite, he was passionately committed to social justice and was a staunch defender of freedom of conscience and tolerance.

Foreword (2007)

This is the second issue of Geologica Acta dedicated to the memory of Professor Francesc Calvet, who passed away in January 2002. Francesc was a man with great human qualities, a distinguished scientist and an inspiring teacher who was held in high esteem by all those who knew him. The first volume contained six papers on specific areas of research in which Francesc was engaged, and a biography (Geologica Acta, volume 2, Nº 4, 2004). This second volume is made up of contributions by colleagues and former students who wish to salute Francesc Calvet as an outstanding geologist and teacher. The papers included in this volume are also subjects in which Francesc was closely involved.

A circuit-based gatekeeper for adult neural stem cell proliferation: Parvalbumin-expressing interneurons of the dentate gyrus control the activation and proliferation of quiescent adult neural stem cells.

Newborn neurons are generated in the adult hippocampus from a pool of self-renewing stem cells located in the subgranular zone (SGZ) of the dentate gyrus. Their activation, proliferation, and maturation depend on a host of environmental and cellular factors but, until recently, the contribution of local neuronal circuitry to this process was relatively unknown. In their recent publication, Song and colleagues have uncovered a novel circuit-based mechanism by which release of the neurotransmitter, γ-aminobutyric acid (GABA), from parvalbumin-expressing (PV) interneurons, can hold radial glia-like (RGL) stem cells of the adult SGZ in a quiescent state. This tonic GABAergic signal, dependent upon the activation of γ(2) subunit-containing GABA(A) receptors of RGL stem cells, can thus prevent their proliferation and subsequent maturation or return them to quiescence if previously activated. PV interneurons are thus capable of suppressing neurogenesis during periods of high network activity and facilitating neurogenesis when network activity is low.

Support for a colleague

As collaborators of Anders Pape Møller, we were shocked and surprised to read that he was accused of data fabrication ("Ecologists roiled by misconduct case," G. Vogel, F. Proffitt, R. Stone, News of the Week, 30 Jan., p. 606). We have never had cause to be concerned about any aspect of our collaborations with Møller. He is an amazing scientist, and his great organizational skills are a model for how to be productive in the face of competing time demands. Most of us are capable of much more than we actually accomplish, but we lack the dedication and self-discipline to follow through like Anders Møller. This is the secret of his phenomenal effectiveness that has been so puzzling to the scientific community. His achievements may have caused negative responses from some of his competitors. We would like to see a full, objective, and independent inquiry into the allegations. Our experience tells us that Anders Møller has an exceptionally complete focus on any task at hand, be it fieldwork, data analysis, or paper writing; this, combined with more than a little natural talent, is sufficient to explain his exceptional productivity. We have worked with him on a variety of projects, including collecting data, sometimes under arduous conditions, and in all our dealings with him, his behavior has been beyond reproach. We would ask colleagues to restrain from further public condemnation until such time as any allegations have been proven beyond doubt.

Nouveau programme de formation en médecine interne générale: implications pour les médecins de premier recours [The new postgraduate training program in general internal medicine: implications for the primary care physician].

The Swiss postgraduate training program in general internal medicine is now designed as a competency-based curriculum. In other words, by the end of their training, the residents should demonstrate a set of predefined competences. Many of those competences have to be learnt in outpatient settings. Thus, the primary care physicians have more than ever an important role to play in educating tomorrows doctors. A competency-based model of training requires a regular assessment of the residents. The mini-CEX (mini-Clinical Evaluation eXercise) is the assessment tool proposed by the Swiss institute for postgraduate and continuing education. The mini-CEX is based on the direct observation of the trainees performing a specific task, as well as on the ensuing feedback. This article aims at introducing our colleagues in charge of residents to the mini-CEX, which is a useful tool promoting the culture of feedback in medical education.