Space: the final frontier

Few things are misunderstood more by biotech startup management teams than the importance of creating working space conductive to innovation and productivity, and compatible with the company's vision. Aesthetics, form and function matter.     

P-TEFb- the final frontier

Cyclin-dependent kinases (CDKs) play a central role in the orderly transition from one phase of the eukaryotic mitotic cell division cycle to the next. In this context, p27^Kip1 (one of the CIP/KIP family of CDK specific inhibitors in mammals) or its functional analogue in other eukarya prevents a premature transition from G1 to S-phase. Recent studies have revealed that expression of a second member of this family, p57^Kip2, is induced as trophoblast stem (TS) cells differentiate into trophoblast giant (TG) cells. p57 then inhibits CDK1 activity, an enzyme essential for initiating mitosis, thereby triggering genome endoreduplication (multiple S-phases without an intervening mitosis). Expression of p21^Cip1, the third member of this family, is also induced in during differentiation of TS cells into TG cells where it appears to play a role in suppressing the DNA damage response pathway. Given the fact that p21 and p57 are unique to mammals, the question arises as to whether one or both of these proteins are responsible for the induction and maintenance of polyploidy during mammalian development.     

Cardiac resynchronization therapy: a meta-analysis of randomized controlled trials

Background

Studies of cardiac resynchronization therapy in addition to an implantable cardioverter defibrillator in patients with mild to moderate congestive heart failure had not been shown to reduce mortality until the recent RAFT trial (Resynchronization/Defibrillation for Ambulatory Heart Failure Trial). We performed a meta-analysis including the RAFT trial to determine the effect of cardiac resynchronization therapy with or without an implantable defibrillator on mortality.

Methods

We searched electronic databases and other sources for reports of randomized trials using a parallel or crossover design. We included studies involving patients with heart failure receiving optimal medical therapy that compared cardiac resynchronization therapy with optimal medical therapy alone, or cardiac resynchronization therapy plus an implantable defibrillator with a standard implantable defibrillator. The primary outcome was mortality. The optimum information size was considered to assess the minimum amount of information required in the literature to reach reliable conclusions about cardiac resynchronization therapy.

Results

Of 3071 reports identified, 12 studies (n = 7538) were included in our meta-analysis. Compared with optimal medical therapy alone, cardiac resynchronization therapy plus optimal medical therapy significantly reduced mortality (relative risk [RR] 0.73, 95% confidence interval [CI] 0.62–0.85). Compared with an implantable defibrillator alone, cardiac resynchronization therapy plus an implantable defibrillator significantly reduced mortality (RR 0.83, 95% CI 0.72–0.96). This last finding remained significant among patients with New York Heart Association (NYHA) class I or II disease (RR 0.80, 95% CI 0.67–0.96) but not among those with class III or IV disease (RR 0.84, 95% CI 0.69–1.07). Analysis of the optimum information size showed that the sequential monitoring boundary was crossed, which suggests no need for further clinical trials.

Interpretation

The cumulative evidence is now conclusive that the addition of cardiac resynchronization to optimal medical therapy or defibrillator therapy significantly reduces mortality among patients with heart failure.Congestive heart failure is currently reaching epidemic proportions in Canada, with 500 000 Canadians affected and 50 000 new patients identified each year.¹ It accounts for more than 100 000 hospital admissions per year and has a one-year mortality ranging from 15% to 50%, depending on the severity of heart failure.² By 2050, the number of patients with heart failure is projected to increase threefold.²Advances in medical therapies have resulted in substantial reductions in mortality associated with congestive heart failure.^3–7 The use of devices has recently become an important adjuvant therapy.⁸ Cardiac resynchronization therapy involves pacing from both the right and left ventricles simultaneously to improve myocardial efficiency (see radiographs in Appendix 1, at www.cmaj.ca/cgi/content/full/cmaj.101685/DC1). Cardiac resynchronization therapy has been shown to reduce morbidity and, when compared with medical therapy alone, to reduce mortality.^9–13 Until recently, it was not shown to reduce mortality among patients who also received an implantable cardioverter defibrillator. Among patients receiving optimal medical therapy, the Resynchronization/Defibrillation for Ambulatory Heart Failure Trial (RAFT) showed the superiority of cardiac resynchronization therapy in addition to an implantable defibrillator over a standard implantable defibrillator in reducing mortality and the combined outcome of death from any cause or hospital admission related to heart failure.¹⁴We performed a meta-analysis to further assess the effect on mortality of cardiac resynchronization therapy with and without an implantable defibrillator among patients with mildly symptomatic and advanced heart failure.     

Unbiased research and the human spirit: the challenges of randomized controlled trials.

Research by Klein and associates provides useful information on the relation between episiotomy and outcomes such as perineal trauma, but the methodologic implications of their work are especially fascinating. Physicians who participated in their randomized controlled trial (RCT) were supposed to adhere to a policy of either liberal or restrictive use of episiotomy according to the study arm to which each patient was assigned. However, some used the procedure for approximately 90% of patients regardless of allocation. Klein and associates'' post-hoc study (see pages 769 to 779 of this issue) sheds light on the relation between physician attitudes and the practice of episiotomy. The author contends that the noncompliance encountered by Klein and associates reflects the fact that randomized trials are anathema to the human spirit. He offers suggestions for making RCTs more meaningful and stresses that, although RCTs are indispensible to the advancement of medical knowledge, they necessitate assiduous attention to matters of design and implementation.     

Respiratory fluoroquinolones for the treatment of community-acquired pneumonia: a meta-analysis of randomized controlled trials

Background

We investigated whether the use of respiratory fluoroquinolones was associated with better clinical outcomes compared with the use of macrolides and β-lactams among adults with pneumonia.

Methods

We searched PubMed, Current Contents, Scopus, EMBASE, ClinicalTrials.gov and Cochrane with no language restrictions. Two reviewers independently extracted data from published trials that compared fluoroquinolones (levofloxacin, moxifloxacin, gemifloxacin) with macrolides or β-lactams or both. A meta-analysis was performed with the clinical outcomes of mortality, treatment success and adverse outcomes.

Results

We included 23 trials in our meta-analysis. There was no difference in mortality among patients who received fluoroquinolones or the comparator antibiotics (OR 0.85, 95% CI 0.65–1.12). Pneumonia resolved in more patients who received fluoroquinolones compared with the comparator antibiotics for the included outcomes in the intention-to-treat population (OR 1.17, 95% CI 1.00–1.36), clinically evaluable population (OR 1.26, 95% CI 1.06–1.50) and the microbiologically assessed population (OR 1.67, 95% CI 1.28–2.20). Fluoroquinolones were more effective than a combination of β-lactam and macrolide (OR 1.39, 95% CI 1.02–1.90). They were also more effective for patients with severe pneumonia (OR 1.84, 95% CI 1.02–3.29), those who required admission to hospital (OR = 1.30, 95% CI 1.04–1.61) and those who required intravenous therapy (OR = 1.44, 15% CI 1.13–1.85). Fluoroquinolones were more effective than β-lactam and macrolide in open-label trials (OR = 1.35, 95% CI 1.08–1.69) but not in blinded randomized controlled trials (OR = 1.13, 95% CI 0.85–1.50).

Interpretation

Fluoroquinolones were associated with higher success of treatment for severe forms of pneumonia; however, a benefit in mortality was not evident. A randomized controlled trial that includes patients with severe pneumonia with or without bacteremia is needed.Community-acquired pneumonia is among the leading reasons for hospital admission¹ and resource consumption.^2,3 It is the most frequent cause of community-acquired infections among patients admitted to intensive care units.⁴ In addition, it is among the leading causes of death worldwide.Physicians must choose an optimal therapeutic regimen that eliminates the infection effectively, minimizes the risk of developing drug resistance and does not compromise the safety of the patient. The combination of β-lactam and macrolide covers the most common possible pathogens involved in the pathogenesis of pneumonia.⁵ More recently, fluoroquinolones with enhanced activity against Streptococcus pneumoniae were introduced in clinical practice. The favourable pharmacokinetic profile of fluoroquinolones allows for once daily administration, often eliminating the need for parenteral treatment. Furthermore, initial treatment with fluoroquinolones was among the predictors of lower treatment failure among patients with pneumonia.⁶In 2007, the Infectious Diseases Society of America and the American Thoracic Society released new guidelines for the management of care for adult patients with community-acquired pneumonia.⁷ In these guidelines, levofloxacin, gemifloxacin and moxifloxacin were reported to be equally effective as the combination of β-lactam and macrolide, and were proposed to be the preferred treatment option for patients who require admission to hospital, as well as for patients with comorbidity who receive treatment as outpatients. In addition to being safe, these fluoroquinolones are more effective against the most common types of bacteria responsible for the development of community-acquired pneumonia.⁷ For example, S. pneumoniae strains are not fully susceptible to ciprofloxacin. On the other hand, trovafloxacin, clinafloxacin, gatifloxacin and other quinolones are not used because of safety concerns or because they are not widely available. The trials that compared fluoroquinolones with other antibiotics regimens for the treatment of pneumonia were designed on the basis of noninferiority (i.e., an antibiotic is equally effective to a comparator), and several were conducted in order to receive approval from the relevant agencies.We sought to examine whether the use of fluoroquinolones was associated with more advantages or disadvantages than the use of macrolides or β-lactams in terms of mortality, resolution of pneumonia and adverse effects.     

Guides to the final frontier of the cytoskeleton: septins in filamentous fungi

Recent investigations have established core principles by which septins can form non-polar filaments in vitro. How cells then assemble, regulate and use septin polymers is still only beginning to be understood. It is clear that there is plasticity and variability in septin organization across diverse species and cell types. Work in the filamentous fungi has been invaluable in discovering this variation in form and function. In particular filamentous fungi display many forms of higher order septin structures and study of septins in these systems has led to insights into septin assembly, dynamics and regulation. Importantly in many cases work in these alternative systems reveal differences to how septins may be organized, functioning or regulated in Saccharomyces cerevisiae. Here I review the novel aspects of septin biology found in filamentous fungi and raise many open questions about these enigmatic polymers that should guide future study.     

Outcomes in registered, ongoing randomized controlled trials of patient education

Background

With the increasing prevalence of chronic noncommunicable diseases, patient education is becoming important to strengthen disease prevention and control. We aimed to systematically determine the extent to which registered, ongoing randomized controlled trials (RCTs) evaluated an educational intervention focus on patient-important outcomes (i.e., outcomes measuring patient health status and quality of life).

Methods

On May 6, 2009, we searched for all ongoing RCTs registered in the World Health Organization International Clinical Trials Registry platform. We used a standardized data extraction form to collect data and determined whether the outcomes assessed were 1) patient-important outcomes such as clinical events, functional status, pain, or quality of life or 2) surrogate outcomes, such as biological outcome, treatment adherence, or patient knowledge.

Principal Findings

We selected 268 of the 642 potentially eligible studies and assessed a random sample of 150. Patient-important outcomes represented 54% (178 of 333) of all primary outcomes and 46% (286 of 623) of all secondary outcomes. Overall, 69% of trials (104 of 150) used at least one patient-important outcome as a primary outcome and 66% (99 of 150) as a secondary outcome. Finally, for 31% of trials (46 of 150), primary outcomes were only surrogate outcomes. The results varied by medical area. In neuropsychiatric disorders, patient important outcomes represented 84% (51 of 61) of primary outcomes, as compared with 54% (32 of 59) in malignant neoplasm and 18% (4 of 22) in diabetes mellitus trials.In addition, only 35% assessed the long-term impact of interventions (i.e., >6 months).

Conclusions

There is a need to improve the relevance of outcomes and to assess the long term impact of educational interventions in RCTs.     

Effects of myo-inositol in women with PCOS: a systematic review of randomized controlled trials

Polycystic ovary syndrome (PCOS) affects 5%-10% of women in reproductive age, and it is the most common cause of infertility due to ovarian dysfunction and menstrual irregularity. Several studies have reported that insulin resistance is common in PCOS women, regardless of the body mass index. The importance of insulin resistance in PCOS is also suggested by the fact that insulin-sensitizing compounds have been proposed as putative treatments to solve the hyperinsulinemia-induced dysfunction of ovarian response to endogenous gonadotropins. Rescuing the ovarian response to endogenous gonadotropins reduces hyperandrogenemia and re-establishes menstrual cyclicity and ovulation, increasing the chance of a spontaneous pregnancy. Among the insulin-sensitizing compounds, there is myo-inosiol (MYO). Previous studies have demonstrated that MYO is capable of restoring spontaneous ovarian activity, and consequently fertility, in most patients with PCOS. With the present review, we aim to provide an overview on the clinical outcomes of the MYO use as a treatment to improve ovarian function and metabolic and hormonal parameters in women with PCOS.     

Dexamethasone and bacterial meningitis. A meta-analysis of randomized controlled trials.

A meta-analysis of 5 randomized, controlled trials using dexamethasone as adjunctive therapy in the treatment of bacterial meningitis in children was done to assess the efficacy in reducing sequelae. A 6th study including both children and adults was analyzed separately. Results of the 5 pediatric studies indicated no significant difference in case-fatality rate between the placebo and dexamethasone groups. Significantly more neurologic sequelae were found in the placebo group during the period from discharge from hospital to 6 weeks after discharge (relative risk [RR] = 1.99, 95% confidence interval [CI] 1.13 to 3.53) and during the period beginning 6 months after discharge (RR = 3.90, 95% CI 1.72 to 8.85). The incidence of neurologic sequelae from 6 weeks to 6 months after discharge, though less with dexamethasone administration, did not reach statistical significance. The frequency of bilateral hearing loss was significantly greater in the placebo group (RR = 4.12, 95% CI 1.74 to 9.79), but unilateral loss was not statistically different in the two groups. Dexamethasone administration in addition to antimicrobial therapy appears to be effective in reducing neurologic sequelae and bilateral hearing loss associated with bacterial meningitis in children.     

Equipoise,design bias,and randomized controlled trials: the elusive ethics of new drug development

The concept of 'equipoise', or the 'uncertainty principle', has been represented as a central ethical principle, and holds that a subject may be enrolled in a randomized controlled trial (RCT) only if there is true uncertainty about which of the trial arms is most likely to benefit the patient. We sought to estimate the frequency with which equipoise conditions were met in industry-sponsored RCTs in rheumatology, to explore the reasons for any deviations from equipoise, to examine the concept of 'design bias', and to consider alternative ethical formulations that might improve subject safety and autonomy. We studied abstracts accepted for the 2001 American College of Rheumatology meetings that reported RCTs, acknowledged industry sponsorship, and had clinical end-points (n = 45), and examined the proportion of studies that favored the registration or marketing of the sponsor's drug. In every trial (45/45) results were favorable to the sponsor, indicating that results could have been predicted in advance solely by knowledge of sponsorship (P < 0.0001). Equipoise clearly was being systematically violated. Publication bias appeared to be an incomplete explanation for this dramatic result; this bias occurs after a study is completed. Rather, we hypothesize that 'design bias', in which extensive preliminary data are used to design studies with a high likelihood of being positive, is the major cause of the asymmetric results. Design 'bias' occurs before the trial is begun and is inconsistent with the equipoise principle. However, design bias increases scientific efficiency, decreases drug development costs, and limits the number of subjects required, probably reducing aggregate risks to participants. Conceptual and ethical issues were found with the equipoise principle, which encourages performance of negative studies; ignores patient values, patient autonomy, and social benefits; is applied at a conceptually inappropriate decision point (after randomization rather than before); and is in conflict with the Belmont, Nuremberg, and other sets of ethical principles, as well as with US Food and Drug Administration procedures. We propose a principle of 'positive expected outcomes', which informs the assessment that a trial is ethical, together with a restatement of the priority of personal autonomy.     

Space as the final frontier in stochastic simulations of biological systems

Recent technological and theoretical advances are only now allowing the simulation of detailed kinetic models of biological systems that reflect the stochastic movement and reactivity of individual molecules within cellular compartments. The behavior of many systems could not be properly understood without this level of resolution, opening up new perspectives of using computer simulations to accelerate biological research. We review the modeling methodology applied to stochastic spatial models, also to the attention of non-expert potential users. Modeling choices, current limitations and perspectives of improvement of current general-purpose modeling/simulation platforms for biological systems are discussed.