The trouble with replication

Anticoagulant factor V: factors affecting the integration of novel scientific discoveries into the broader framework

Since its initial discovery in the 1940s, factor V has long been viewed as an important procoagulant protein in the coagulation cascade. However, in the later part of the 20th century, two different scientists proposed novel anticoagulant roles for factor V. Philip Majerus proposed the first anticoagulant function for factor V in 1983, yet ultimately it was not widely accepted by the broader scientific community. In contrast, Björn Dahlbäck proposed a different anticoagulant role for factor V in 1994. While this role was initially contested, it was ultimately accepted and integrated into the scientific framework. In this paper, I present a detailed historical account of these two anticoagulant discoveries and propose three key reasons why Dahlbäck's anticoagulant role for factor V was accepted whereas Majerus' proposed role was largely overlooked. Perhaps most importantly, Dahlbäck's proposed anticoagulant role was of great clinical interest because the discovery involved the study of an important subset of patients with thrombophilia. Soon after Dahlbäck's 1994 work, this patient population was shown to possess the factor V Leiden mutation. Also key in the ultimate acceptance of the second proposed anticoagulant role was the persistence of the scientist who made the discovery and the interest in and ability of others to replicate and reinforce this work. This analysis of two different yet similar discoveries sheds light on factors that play an important role in how new discoveries are incorporated into the existing scientific framework.

Order of the major constituents in sign languages: implications for all language

A survey of reports of sign order from 42 sign languages leads to a handful of generalizations. Two accounts emerge, one amodal and the other modal. We argue that universal pressures are at work with respect to some generalizations, but that pressure from the visual modality is at work with respect to others. Together, these pressures conspire to make all sign languages order their major constituents SOV or SVO. This study leads us to the conclusion that the order of S with regard to verb phrase (VP) may be driven by sensorimotor system concerns that feed universal grammar.

Hände weg von der Maus

Zur Bestimmung der Leistungshändigkeit müssen Personen mit der dominanten und nicht-dominanten Hand verschiedene repräsentative motorische Aufgaben realisieren. In zwei quasi-experimentellen Studien mit links- und rechtshändigen Probanden wurde geprüft, ob die manuelle Erfahrung einen Einfluss auf die Leistung in zwei kleinmotorischen Auge-Hand-Koordinationsaufgaben, einer Stift- (S-PA) und einer Cursor-Positionierungsaufgabe (C-PA), hat. Es zeigte sich, dass a) bei der ungeübten S-PA die Probanden generell bessere Leistungen mit ihrer dominanten Hand erzielen und b) bei der C-PA die Leistungen der Linkshänder durch die manuellen Erfahrungen mit der Maus-Konfiguration moderiert werden: Linkshändige „Linksmäuser“ erzielen mit der linken Hand bessere Leistungen als linkshändige „Rechtsmäuser“, wohingegen sich die Leistungen mit der rechten Hand nicht unterscheiden. Motorische Leistungen in Lateralitätsstudien sollten daher nicht mit einer Computermaus erfasst und konsequenterweise auch keine Computermaus-Items in Lateralitätsfragebögen berücksichtigt werden.

Considering trauma exposure in the context of genetics studies of posttraumatic stress disorder: a systematic review

BACKGROUND

Posttraumatic stress disorder (PTSD) is a debilitating anxiety disorder. Surveys of the general population suggest that while 50-85% of Americans will experience a traumatic event in their lifetime, only 2-50% will develop PTSD. Why some individuals develop PTSD following trauma exposure while others remain resilient is a central question in the field of trauma research. For more than half a century, the role of genetic influences on PTSD has been considered as a potential vulnerability factor. However, despite the exponential growth of molecular genetic studies over the past decade, limited progress has been made in identifying true genetic variants for PTSD.

METHODS

In an attempt to aid future genome wide association studies (GWAS), this paper presents a systematic review of 28 genetic association studies of PTSD. Inclusion criteria required that 1) all participants were exposed to Criterion A traumatic events, 2) polymorphisms of relevant genes were genotyped and assessed in relation to participants' PTSD status, 3) quantitative methods were used, and 4) articles were published in English and in peer-reviewed journals. In the examination of these 28 studies, particular attention was given to variables related to trauma exposure (e.g. number of traumas, type of trauma).

RESULTS

Results indicated that most articles did not report on the GxE interaction in the context of PTSD or present data on the main effects of E despite having data available. Furthermore, some studies that did consider the GxE interaction had significant findings, underscoring the importance of examining how genotypes can modify the effect of trauma on PTSD. Additionally, results indicated that only a small number of genes continue to be studied and that there were marked differences in methodologies across studies, which subsequently limited robust conclusions.

CONCLUSIONS

As trauma exposure is a necessary condition for the PTSD diagnosis, this paper identifies gaps in the current literature as well as provides recommendations for how future GWAS studies can most effectively incorporate trauma exposure data in both the design and analysis phases of studies.

Cardiac cell repair therapy: a clinical perspective

From bone marrow transplants 5 decades ago to the most recent stem cell-derived organ transplants, regenerative medicine is increasingly recognized as an emerging core component of modern practice. In cardiovascular medicine, innovation in stem cell biology has created curative solutions for the treatment of both ischemic and nonischemic cardiomyopathy. Multiple cell-based platforms have been developed, harnessing the regenerative potential of various natural and bioengineered sources. Clinical experience from the first 1000 patients (approximately) who have received stem cell therapy worldwide indicates a favorable safety profile with modest improvement in cardiac function and structural remodeling in the setting of acute myocardial infarction or chronic heart failure. Further investigation is required before early adoption and is ongoing. Broader application in practice will require continuous scientific advances to match each patient with the most effective reparative phenotype, while ensuring optimal cell delivery, dosing, and timing of intervention. An interdisciplinary effort across the scientific and clinical community within academia, biotechnology, and government will drive the successful realization of this next generation of therapeutic agents for the "broken" heart.

Cardiac cell repair therapy: a clinical perspective

From bone marrow transplants 5 decades ago to the most recent stem cell-derived organ transplants, regenerative medicine is increasingly recognized as an emerging core component of modern practice. In cardiovascular medicine, innovation in stem cell biology has created curative solutions for the treatment of both ischemic and nonischemic cardiomyopathy. Multiple cell-based platforms have been developed, harnessing the regenerative potential of various natural and bioengineered sources. Clinical experience from the first 1000 patients (approximately) who have received stem cell therapy worldwide indicates a favorable safety profile with modest improvement in cardiac function and structural remodeling in the setting of acute myocardial infarction or chronic heart failure. Further investigation is required before early adoption and is ongoing. Broader application in practice will require continuous scientific advances to match each patient with the most effective reparative phenotype, while ensuring optimal cell delivery, dosing, and timing of intervention. An interdisciplinary effort across the scientific and clinical community within academia, biotechnology, and government will drive the successful realization of this next generation of therapeutic agents for the "broken" heart.

Stem cells for ischemic brain injury: a critical review

No effective therapy is currently available to promote recovery following ischemic stroke. Stem cells have been proposed as a potential source of new cells to replace those lost due to central nervous system injury, as well as a source of trophic molecules to minimize damage and promote recovery. We undertook a detailed review of data from recent basic science and preclinical studies to investigate the potential application of endogenous and exogenous stem cell therapies for treatment of cerebral ischemia. To date, spontaneous endogenous neurogenesis has been observed in response to ischemic injury, and can be enhanced via infusion of appropriate cytokines. Exogenous stem cells from multiple sources can generate neural cells that survive and form synaptic connections after transplantation in the stroke-injured brain. Stem cells from multiple sources cells also exhibit neuroprotective properties that may ameliorate stroke deficits. In many cases, functional benefits observed are likely independent of neural differentiation, although the exact mechanisms remain poorly understood. Future studies of neuroregeneration will require the demonstration of function in endogenously born neurons following focal ischemia. Further, methods are currently lacking to demonstrate definitively the therapeutic effect of newly introduced neural cells. Increased plasticity following stroke may facilitate the functional integration of new neurons, but the loss of appropriate guidance cues and supporting architecture in the infarct cavity will likely impede the restoration of lost circuitry. Thus careful investigation of the mechanisms underlying trophic benefits will be essential. Evidence to date suggests that continued development of stem cell therapies may ultimately lead to viable treatment options for ischemic brain injury.

Methodology capture: discriminating between the "best" and the rest of community practice

Background

The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This makes it difficult to keep track of available bioinformatics software, let alone the most suitable protocols in a specific research area. To remedy this we present an approach for capturing methodology from literature in order to identify and, thus, define best practice within a field.

Results

Our approach is to implement data extraction techniques on the full-text of scientific articles to obtain the set of experimental protocols used by an entire scientific discipline, molecular phylogenetics. Our methodology for identifying methodologies could in principle be applied to any scientific discipline, whether or not computer-based. We find a number of issues related to the nature of best practice, as opposed to community practice. We find that there is much heterogeneity in the use of molecular phylogenetic methods and software, some of which is related to poor specification of protocols. We also find that phylogenetic practice exhibits field-specific tendencies that have increased through time, despite the generic nature of the available software. We used the practice of highly published and widely collaborative researchers ("expert" researchers) to analyse the influence of authority on community practice. We find expert authors exhibit patterns of practice common to their field and therefore act as useful field-specific practice indicators.

Conclusion

We have identified a structured community of phylogenetic researchers performing analyses that are customary in their own local community and significantly different from those in other areas. Best practice information can help to bridge such subtle differences by increasing communication of protocols to a wider audience. We propose that the practice of expert authors from the field of evolutionary biology is the closest to contemporary best practice in phylogenetic experimental design. Capturing best practice is, however, a complex task and should also acknowledge the differences between fields such as the specific context of the analysis.

Stem cells and cardiac repair: a critical analysis

Utilizing stem cells to repair the damaged heart has seen an intense amount of activity over the last 5 years or so. There are currently multiple clinical studies in progress to test the efficacy of various different cell therapy approaches for the repair of damaged myocardium that were only just beginning to be tested in preclinical animal studies a few years earlier. This rapid transition from preclinical to clinical testing is striking and is not typical of the customary timeframe for the progress of a therapy from bench-to-bedside. Doubtless, there will be many more trials to follow in the upcoming years. With the plethora of trials and cell alternatives, there has come not only great enthusiasm for the potential of the therapy, but also great confusion about what has been achieved. Cell therapy has the potential to do what no drug can: regenerate and replace damaged tissue with healthy tissue. Drugs may be effective at slowing the progression of heart failure, but none can stop or reverse the process. However, tissue repair is not a simple process, although the idea on its surface is quite simple. Understanding cells, the signals that they respond to, and the keys to appropriate survival and tissue formation are orders of magnitude more complicated than understanding the pathways targeted by most drugs. Drugs and their metabolites can be monitored, quantified, and their effects correlated to circulating levels in the body. Not so for most cell therapies. It is quite difficult to measure cell survival except through ex vivo techniques like histological analysis of the target organ. This makes the emphasis on preclinical research all the more important because it is only in the animal studies that research has the opportunity to readily harvest the target tissues and perform the detailed analyses of what has happened with the cells. This need for detailed and usually time-intensive research in animal studies stands in contrast to the rapidity with which therapies have progressed to the clinic. It is now becoming clear through a number of notable examples that progress to the clinic may have occurred too quickly, before adequate testing and independent verification of results could be completed (Check, Nature 446:485-486, 2007; Chien, J Clin Investig 116:1838-1840, 2006; Giles, Nature 442:344-347, 2006). Broad reproducibility and transfer of results from one lab to another has been and always will be essential for the successful application of any cell therapy. So, what is the prognosis for cell therapy to repair heart damage? Will there be an approved cell therapy, or multiple ones, or will it require combinations of more than one cell type to be successful? These are questions often asked. The answers are difficult to know and even more difficult to predict because there are so many variables associated with cell-based therapies. There is much about the biology of cell systems that we still do not understand. Much of the pluripotency or transdifferentiation phenomena (see below) being observed go against accepted and well-tested principles for cell development and fate choice, and has caused a reevaluation of long-accepted theories. Clearly, new pathways for tissue repair and regeneration have been uncovered, but will these new pathways be sufficient to effect significant tissue repair and regeneration? Despite the false starts so far, there is the strong likelihood one or possibly multiple cell therapies will succeed. Clearly, important information has been gained, which should better guide the field to achieving success. When there is the successful verification in patients of a cell therapy, there will be an explosion of technological advances around the approach(es) that succeed. Whatever cells get approved accompanying them will be: more effective delivery methods; growth and storage methods; combination therapies, mixes of cells or cells + gene therapies; combinations with biomaterials and technologies for immune protection, allowing allografting. There are many parallel paths of technology development waiting to be brought together once there is an effective cellular approach. The coming years will no doubt bring some exciting developments.

Multipotent cells can be generated in vitro from several adult human organs (heart, liver, and bone marrow)

The aims of our study were to verify whether it was possible to generate in vitro, from different adult human tissues, a population of cells that behaved, in culture, as multipotent stem cells and if these latter shared common properties. To this purpose, we grew and cloned finite cell lines obtained from adult human liver, heart, and bone marrow and named them human multipotent adult stem cells (hMASCs). Cloned hMASCs, obtained from the 3 different tissues, expressed the pluripotent state-specific transcription factors Oct-4, NANOG, and REX1, displayed telomerase activity, and exhibited a wide range of differentiation potential, as shown both at a morphologic and functional level. hMASCs maintained a human diploid DNA content, and shared a common gene expression signature, compared with several somatic cell lines and irrespectively of the tissue of isolation. In particular, the pathways regulating stem cell self-renewal/maintenance, such as Wnt, Hedgehog, and Notch, were transcriptionally active. Our findings demonstrate that we have optimized an in vitro protocol to generate and expand cells from multiple organs that could be induced to acquire morphologic and functional features of mature cells even embryologically not related to the tissue of origin.

Trick or treat?

The purpose of this article is to draw attention to current transgressions in scientific writing and to promote commitment to ethical standards and good science. All participants of any research project, particularly under interdiciplinary team approach, should not only play an active role on the management and carrying out of their study but also ensure that their study is not fraudulent. Manuscript fabrication, data and/or figure manupilation, piracy (plagiarism), sloppy research, and transgressions in authorship are reasons for loss of scientific value and records, retraction of articles, and application of a variety of sanctions.

Molecular evidence-based medicine: evolution and integration of information in the genomic era

Evidence-based medicine and molecular medicine have both been influential in biomedical research in the last 15 years. Despite following largely parallel routes to date, the goals and principles of evidence-based and molecular medicine are complementary and they should be converging. I define molecular evidence-based medicine as the study of medical information that makes sense of the advances of molecular biological disciplines and where errors and biases are properly appreciated and placed in context. Biomedical measurement capacity improves very rapidly. The exponentially growing mass of hypotheses being tested requires a new approach to both statistical and biological inference. Multidimensional biology requires careful exact replication of research findings, but indirect corroboration is often all that is achieved at best. Besides random error, bias remains a major threat. It is often difficult to separate bias from the spirit of scientific inquiry to force data into coherent and 'significant' biological stories. Transparency and public availability of protocols, data, analyses and results may be crucial to make sense of the complex biology of human disease and avoid being flooded by spurious research findings. Research efforts should be integrated across teams in an open, sharing environment. Most research in the future may be designed, performed, and integrated in the public cyberspace.