Showing papers by "University of Southern Denmark published in 2008"

SOAP: short oligonucleotide alignment program

Abstract: Summary: We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets. Availability: http://soap.genomics.org.cn Contact: soap@genomics.org.cn

The diploid genome sequence of an Asian individual.

Abstract: Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.

Mangrove Production and Carbon sinks: A revision of global budget estimates

Abstract: results in a conservative estimate of 218 ± 72 Tg C a 1 . When using the best available estimates of various carbon sinks (organic carbon export, sediment burial, and mineralization), it appears that >50% of the carbon fixed by mangrove vegetation is unaccounted for. This unaccounted carbon sink is conservatively estimated at 112 ± 85 Tg C a 1 , equivalent in magnitude to 30–40% of the global riverine organic carbon input to the coastal zone. Our analysis suggests that mineralization is severely underestimated, and that the majority of carbon export from mangroves to adjacent waters occurs as dissolved inorganic carbon (DIC). CO2 efflux from sediments and creek waters and tidal export of DIC appear to be the major sinks. These processes are quantitatively comparable in magnitude to the unaccounted carbon sink in current budgets, but are not yet adequately constrained with the limited published data available so far.

Social network analysis

Abstract: Chapter 1. Introduction to Social Network Analysis Chapter 2. Network Fundamentals Chapter 3. Data Collection Chapter 4. Basic Methods for Analyzing Networks Chapter 5. Advanced Methods for Analyzing Networks References

Proteomic profiling of exosomes: Current perspectives

Abstract: Exosomes are 40-100 nm membrane vesicles of endocytic origin secreted by most cell types in vitro. Recent studies have shown that exosomes are also found in vivo in body fluids such as blood, urine, amniotic fluid, malignant ascites, bronchoalveolar lavage fluid, synovial fluid, and breast milk. While the biological function of exosomes is still unclear, they can mediate communication between cells, facilitating processes such as antigen presentation and in trans signaling to neighboring cells. Exosome-like vesicles identified in Drosophila (referred to as argosomes) may be potential vehicles for the spread of morphogens in epithelia. The advent of current MS-based proteomic technologies has contributed significantly to our understanding of the molecular composition of exosomes. In addition to a common set of membrane and cytosolic proteins, it is becoming increasingly apparent that exosomes harbor distinct subsets of proteins that may be linked to cell-type associated functions. The secretion of exosomes by tumor cells and their implication in the transport and propagation of infectious cargo such as prions and retroviruses such as HIV suggest their participation in pathological situations. Interestingly, the recent observation that exosomes contain both mRNA and microRNA, which can be transferred to another cell, and be functional in that new environment, is an exciting new development in the unraveling exosome saga. The present review aims to summarize the physical properties that define exosomes as specific cell-type secreted membrane vesicles.

Reducing Uncertainties About the Effects of Chemoradiotherapy for Cervical Cancer: A Systematic Review and Meta-Analysis of Individual Patient Data From 18 Randomized Trials

Abstract: Background After a 1999 National Cancer Institute (NCI) clinical alert was issued, chemoradiotherapy has become widely used in treating women with cervical cancer. Two subsequent systematic reviews found that interpretation of the benefits was complicated, and some important clinical questions were unanswered. Patients and Methods We initiated a meta-analysis seeking updated individual patient data from all randomized trials to assess the effect of chemoradiotherapy on all outcomes. We prespecified analyses to investigate whether the effect of chemoradiotherapy differed by trial or patient characteristics. Results On the basis of 13 trials that compared chemoradiotherapy versus the same radiotherapy, there was a 6% improvement in 5-year survival with chemoradiotherapy (hazard ratio [HR] = 0.81, P <.001). A larger survival benefit was seen for the two trials in which chemotherapy was administered after chemoradiotherapy. There was a significant survival benefit for both the group of trials that used platinum-based (HR = 0.83, P = .017) and non-platinum-based (HR = 0.77, P <.009) chemoradiotherapy, but no evidence of a difference in the size of the benefit by radiotherapy or chemotherapy dose or scheduling was seen. Chemoradiotherapy also reduced local and distant recurrence and progression and improved disease-free survival. There was a suggestion of a difference in the size of the survival benefit with tumor stage, but not across other patient subgroups. Acute hematologic and GI toxicity was increased with chemoradiotherapy, but data were too sparse for an analysis of late toxicity. Conclusion These results endorse the recommendations of the NCI alert, but also demonstrate their applicability to all women and a benefit of non-platinum-based chemoradiotherapy. Furthermore, although these results suggest an additional benefit from adjuvant chemotherapy, this requires testing in randomized trials.

Non-contact ACL injuries in female athletes: An International Olympic Committee current concepts statement

Abstract: The incidence of anterior cruciate ligament (ACL) injury remains high in young athletes. Because female athletes have a much higher incidence of ACL injuries in sports such as basketball and team handball than male athletes, the IOC Medical Commission invited a multidisciplinary group of ACL expert clinicians and scientists to (1) review current evidence including data from the new Scandinavian ACL registries; (2) critically evaluate high-quality studies of injury mechanics; (3) consider the key elements of successful prevention programmes; (4) summarise clinical management including surgery and conservative management; and (5) identify areas for further research. Risk factors for female athletes suffering ACL injury include: (1) being in the preovulatory phase of the menstrual cycle compared with the postovulatory phase; (2) having decreased intercondylar notch width on plain radiography; and (3) developing increased knee abduction moment (a valgus intersegmental torque) during impact on landing. Well-designed injury prevention programmes reduce the risk of ACL for athletes, particularly women. These programmes attempt to alter dynamic loading of the tibiofemoral joint through neuromuscular and proprioceptive training. They emphasise proper landing and cutting techniques. This includes landing softly on the forefoot and rolling back to the rearfoot, engaging knee and hip flexion and, where possible, landing on two feet. Players are trained to avoid excessive dynamic valgus of the knee and to focus on the "knee over toe position" when cutting.

European guidelines for the diagnosis and treatment of pelvic girdle pain.

Abstract: A guideline on pelvic girdle pain (PGP) was developed by “Working Group 4” within the framework of the COST ACTION B13 “Low back pain: guidelines for its management”, issued by the European Commission, Research Directorate-General, Department of Policy, Coordination and Strategy. To ensure an evidence-based approach, three subgroups were formed to explore: (a) basic information, (b) diagnostics and epidemiology, and (c) therapeutical interventions. The progress of the subgroups was discussed at each meeting and the final report is based on group consensus. A grading system was used to denote the strength of the evidence, based on the AHCPR Guidelines (1994) and levels of evidence recommended in the method guidelines of the Cochrane Back Review group. It is concluded that PGP is a specific form of low back pain (LBP) that can occur separately or in conjunction with LBP. PGP generally arises in relation to pregnancy, trauma, arthritis and/or osteoarthritis. Uniform definitions are proposed for PGP as well as for joint stability. The point prevalence of pregnant women suffering from PGP is about 20%. Risk factors for developing PGP during pregnancy are most probably a history of previous LBP, and previous trauma to the pelvis. There is agreement that non risk factors are: contraceptive pills, time interval since last pregnancy, height, weight, smoking, and most probably age. PGP can be diagnosed by pain provocation tests (P4/thigh thrust, Patrick’s Faber, Gaenslen’s test, and modified Trendelenburg’s test) and pain palpation tests (long dorsal ligament test and palpation of the symphysis). As a functional test, the active straight leg raise (ASLR) test is recommended. Mobility (palpation) tests, X-rays, CT, scintigraphy, diagnostic injections and diagnostic external pelvic fixation are not recommended. MRI may be used to exclude ankylosing spondylitis and in the case of positive red flags. The recommended treatment includes adequate information and reassurance of the patient, individualized exercises for pregnant women and an individualized multifactorial treatment program for other patients. We recommend medication (excluding pregnant women), if necessary, for pain relief. Recommendations are made for future research on PGP.

Ferruginous Conditions Dominated Later Neoproterozoic Deep-Water Chemistry

Abstract: Earth9s surface chemical environment has evolved from an early anoxic condition to the oxic state we have today. Transitional between an earlier Proterozoic world with widespread deep-water anoxia and a Phanerozoic world with large oxygen-utilizing animals, the Neoproterozoic Era [1000 to 542 million years ago (Ma)] plays a key role in this history. The details of Neoproterozoic Earth surface oxygenation, however, remain unclear. We report that through much of the later Neoproterozoic (

Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis.

Abstract: The nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma) is a key regulator of adipocyte differentiation in vivo and ex vivo and has been shown to control the expression of several adipocyte-specific genes. In this study, we used chromatin immunoprecipitation combined with deep sequencing to generate genome-wide maps of PPARgamma and retinoid X receptor (RXR)-binding sites, and RNA polymerase II (RNAPII) occupancy at very high resolution throughout adipocyte differentiation of 3T3-L1 cells. We identify >5000 high-confidence shared PPARgamma:RXR-binding sites in adipocytes and show that during early stages of differentiation, many of these are preoccupied by non-PPARgamma RXR-heterodimers. Different temporal and compositional patterns of occupancy are observed. In addition, we detect co-occupancy with members of the C/EBP family. Analysis of RNAPII occupancy uncovers distinct clusters of similarly regulated genes of different biological processes. PPARgamma:RXR binding is associated with the majority of induced genes, and sites are particularly abundant in the vicinity of genes involved in lipid and glucose metabolism. Our analyses represent the first genome-wide map of PPARgamma:RXR target sites and changes in RNAPII occupancy throughout adipocyte differentiation and indicate that a hitherto unrecognized high number of adipocyte genes of distinctly regulated pathways are directly activated by PPARgamma:RXR.

Electronic properties of semiconductor nanowires.

Abstract: This paper provides a review of the state-of-the-art electronic-structure calculations of semiconductor nanowires. Results obtained using empirical k.p, empirical tight-binding, semi-empirical pseudopotential, and with ab initio methods are compared. For conciseness, we will restrict our detailed discussions to free-standing plain and modulated nanowires. Connections to relevant experimental data, particularly band gaps and polarization anisotropy, will be made since these results depend crucially on the electronic properties. For completeness, a brief review on the synthesis of nanowires is included.

Men: good health and high mortality. Sex differences in health and aging*

Abstract: This review examines sex differences in health and survival, with a focus on the Nordic countries. There is a remarkable discrepancy between the health and survival of the sexes: men are physically stronger and have fewer disabilities, but have substantially higher mortality at all ages compared with women: the so-called male-female health-survival paradox. A number of proposed explanations for this paradox are rooted in biological, social, and psychological interpretations. It is likely to be due to multiple causes that include fundamental biological differences between the sexes such as genetic factors, immune system responses, hormones, and disease patterns. Behavioral differences such as risk-taking and reluctance to seek and comply with medical treatment may also play a role. Another consideration is that part of the difference may be due to methodological challenges, such as selective non-participation and under-reporting of health problems, and delayed seeking of treatment by men. The Nordic countries provide a unique opportunity for such studies, as they have good-quality data in their national health registers, which cover the whole population, and a long tradition of high participation rates in surveys.

Protein abundance profiling of the Escherichia coli cytosol

Abstract: Knowledge about the abundance of molecular components is an important prerequisite for building quantitative predictive models of cellular behavior. Proteins are central components of these models, since they carry out most of the fundamental processes in the cell. Thus far, protein concentrations have been difficult to measure on a large scale, but proteomic technologies have now advanced to a stage where this information becomes readily accessible. Here, we describe an experimental scheme to maximize the coverage of proteins identified by mass spectrometry of a complex biological sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins, based on the recently developed emPAI approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell. As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal proteins. Proteins involved in energy metabolism as well as those with binding function were also found in high copy number while proteins annotated with the terms metabolism, transcription, transport, and cellular organization were rare. The barrel-sandwich fold was found to be the structural fold with the highest abundance. Highly abundant proteins are predicted to be less prone to aggregation based on their length, pI values, and occurrence patterns of hydrophobic stretches. We also find that abundant proteins tend to be predominantly essential. Additionally we observe a significant correlation between protein and mRNA abundance in E. coli cells. Abundance measurements for more than 1000 E. coli proteins presented in this work represent the most complete study of protein abundance in a bacterial cell so far. We show significant associations between the abundance of a protein and its properties and functions in the cell. In this way, we provide both data and novel insights into the role of protein concentration in this model organism.

Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus

Abstract: Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease characterized by production of autoantibodies and complex genetic inheritance. In a genome-wide scan using 85,042 SNPs, we identified an association between SLE and a nonsynonymous substitution (rs10516487, R61H) in the B-cell scaffold protein with ankyrin repeats gene, BANK1. We replicated the association in four independent case-control sets (combined P = 3.7 x 10(-10); OR = 1.38). We analyzed BANK1 cDNA and found two isoforms, one full-length and the other alternatively spliced and lacking exon 2 (Delta2), encoding a protein without a putative IP3R-binding domain. The transcripts were differentially expressed depending on a branch point-site SNP, rs17266594, in strong linkage disequilibrium (LD) with rs10516487. A third associated variant was found in the ankyrin domain (rs3733197, A383T). Our findings implicate BANK1 as a susceptibility gene for SLE, with variants affecting regulatory sites and key functional domains. The disease-associated variants could contribute to sustained B cell-receptor signaling and B-cell hyperactivity characteristic of this disease.

Motesanib diphosphate in progressive differentiated thyroid cancer.

Abstract: BACKGROUND: The expression of vascular endothelial growth factor (VEGF) is characteristic of differentiated thyroid cancer and is associated with aggressive tumor behavior and a poor clinical outcome. Motesanib diphosphate (AMG 706) is a novel oral inhibitor of VEGF receptors, platelet-derived growth-factor receptor, and KIT. METHODS: In an open-label, single-group, phase 2 study, we treated 93 patients who had progressive, locally advanced or metastatic, radioiodine-resistant differentiated thyroid cancer with 125 mg of motesanib diphosphate, administered orally once daily. The primary end point was an objective response as assessed by an independent radiographic review. Additional end points included the duration of the response, progression-free survival, safety, and changes in serum thyroglobulin concentration. RESULTS: Of the 93 patients, 57 (61%) had papillary thyroid carcinoma. The objective response rate was 14%. Stable disease was achieved in 67% of the patients, and stable disease was maintained for 24 weeks or longer in 35%; 8% had progressive disease as the best response. The Kaplan-Meier estimate of the median duration of the response was 32 weeks (the lower limit of the 95% confidence interval [CI] was 24; the upper limit could not be estimated because of an insufficient number of events); the estimate of median progression-free survival was 40 weeks (95% CI, 32 to 50). Among the 75 patients in whom thyroglobulin analysis was performed, 81% had decreased serum thyroglobulin concentrations during treatment, as compared with baseline levels. The most common treatment-related adverse events were diarrhea (in 59% of the patients), hypertension (56%), fatigue (46%), and weight loss (40%). CONCLUSIONS: Motesanib diphosphate can induce partial responses in patients with advanced or metastatic differentiated thyroid cancer that is progressive. (ClinicalTrials.gov number, NCT00121628.)

A synthesis of atmospheric mercury depletion event chemistry in the atmosphere and snow

Abstract: It was discovered in 1995 that, during the spring time, unexpectedly low concentrations of gaseous elemental mercury (GEM) occurred in the Arctic air. This was surprising for a pollutant known to have a long residence time in the atmosphere; however conditions appeared to exist in the Arctic that promoted this depletion of mercury (Hg). This phenomenon is termed atmospheric mercury depletion events (AMDEs) and its discovery has revolutionized our understanding of the cycling of Hg in Polar Regions while stimulating a significant amount of research to understand its impact to this fragile ecosystem. Shortly after the discovery was made in Canada, AMDEs were confirmed to occur throughout the Arctic, sub-Artic and Antarctic coasts. It is now known that, through a series of photochemically initiated reactions involving halogens, GEM is converted to a more reactive species and is subsequently associated to particles in the air and/or deposited to the polar environment. AMDEs are a means by which Hg is transferred from the atmosphere to the environment that was previously unknown. In this article we review Hg research taken place in Polar Regions pertaining to AMDEs, the methods used to collect Hg in different environmental media, research results of the current understanding of AMDEs from field, laboratory and modeling work, how Hg cycles around the environment after AMDEs, gaps in our current knowledge and the future impacts that AMDEs may have on polar environments. The research presented has shown that while considerable improvements in methodology to measure Hg have been made but the main limitation remains knowing the speciation of Hg in the various media. The processes that drive AMDEs and how they occur are discussed. As well, the role that the snow pack and the sea ice play in the cycling of Hg is presented. It has been found that deposition of Hg from AMDEs occurs at marine coasts and not far inland and that a fraction of the deposited Hg does not remain in the same form in the snow. Kinetic studies undertaken have demonstrated that bromine is the major oxidant depleting Hg in the atmosphere. Modeling results demonstrate that there is a significant deposition of Hg to Polar Regions as a result of AMDEs. Models have also shown that Hg is readily transported to the Arctic from source regions, at times during springtime when this environment is actively transforming Hg from the atmosphere to the snow and ice surfaces. The presence of significant amounts of methyl Hg in snow in the Arctic surrounding AMDEs is important because this species is the link between the environment and impacts to wildlife and humans. Further, much work on methylation and demethylation processes has occurred but these processes are not yet fully understood. Recent changes in the climate and sea ice cover in Polar Regions are likely to have strong effects on the cycling of Hg in this environment; however more research is needed to understand Hg processes in order to formulate meaningful predictions of these changes.

Vertebral endplate signal changes (Modic change): a systematic literature review of prevalence and association with non-specific low back pain.

Abstract: The prevalence of “vertebral endplate signal changes” (VESC) and its association with low back pain (LBP) varies greatly between studies. This wide range in reported prevalence rates and associations with LBP could be explained by differences in the definitions of VESC, LBP, or study sample. The objectives of this systematic critical review were to investigate the current literature in relation to the prevalence of VESC (including Modic changes) and the association with non-specific low back pain (LBP). The MEDLINE, EMBASE, and SveMED databases were searched for the period 1984 to November 2007. Included were the articles that reported the prevalence of VESC in non-LBP, general, working, and clinical populations. Included were also articles that investigated the association between VESC and LBP. Articles on specific LBP conditions were excluded. A checklist including items related to the research questions and overall quality of the articles was used for data collection and quality assessment. The reported prevalence rates were studied in relation to mean age, gender, study sample, year of publication, country of study, and quality score. To estimate the association between VESC and LBP, 2 × 2 tables were created to calculate the exact odds ratio (OR) with 95% confidence intervals. Eighty-two study samples from 77 original articles were identified and included in the analysis. The median of the reported prevalence rates for any type of VESC was 43% in patients with non-specific LBP and/or sciatica and 6% in non-clinical populations. The prevalence was positively associated with age and was negatively associated with the overall quality of the studies. A positive association between VESC and non-specific LBP was found in seven of ten studies from the general, working, and clinical populations with ORs from 2.0 to 19.9. This systematic review shows that VESC is a common MRI-finding in patients with non-specific LBP and is associated with pain. However, it should be noted that VESC may be present in individuals without LBP.

Disruption of an AP-2 alpha binding site in an IRF6 enhancer is associated with cleft lip

Abstract: Previously we have shown that nonsyndromic cleft lip with or without cleft palate (NSCL/P) is strongly associated with SNPs in IRF6 (interferon regulatory factor 6). Here, we use multispecies sequence comparisons to identify a common SNP (rs642961, G>A) in a newly identified IRF6 enhancer. The A allele is significantly overtransmitted (P = 1 x 10(-11)) in families with NSCL/P, in particular those with cleft lip but not cleft palate. Further, there is a dosage effect of the A allele, with a relative risk for cleft lip of 1.68 for the AG genotype and 2.40 for the AA genotype. EMSA and ChIP assays demonstrate that the risk allele disrupts the binding site of transcription factor AP-2alpha and expression analysis in the mouse localizes the enhancer activity to craniofacial and limb structures. Our findings place IRF6 and AP-2alpha in the same developmental pathway and identify a high-frequency variant in a regulatory element contributing substantially to a common, complex disorder.

Human mesenchymal stem cells: from basic biology to clinical applications

Abstract: Mesenchymal stem cells (MSC) are a group of clonogenic cells present among the bone marrow stroma and capable of multilineage differentiation into mesoderm-type cells such as osteoblasts, adipocytes and chondrocytes. Due to their ease of isolation and their differentiation potential, MSC are being introduced into clinical medicine in variety of applications and through different ways of administration. Here, we discuss approaches for isolation, characterization and directing differentiation of human mesenchymal stem cells (hMSC). An update of the current clinical use of the cells is also provided.

Potential developmental neurotoxicity of pesticides used in Europe

Abstract: Pesticides used in agriculture are designed to protect crops against unwanted species, such as weeds, insects, and fungus. Many compounds target the nervous system of insect pests. Because of the similarity in brain biochemistry, such pesticides may also be neurotoxic to humans. Concerns have been raised that the developing brain may be particularly vulnerable to adverse effects of neurotoxic pesticides. Current requirements for safety testing do not include developmental neurotoxicity. We therefore undertook a systematic evaluation of published evidence on neurotoxicity of pesticides in current use, with specific emphasis on risks during early development. Epidemiologic studies show associations with neurodevelopmental deficits, but mainly deal with mixed exposures to pesticides. Laboratory experimental studies using model compounds suggest that many pesticides currently used in Europe – including organophosphates, carbamates, pyrethroids, ethylenebisdithiocarbamates, and chlorophenoxy herbicides – can cause neurodevelopmental toxicity. Adverse effects on brain development can be severe and irreversible. Prevention should therefore be a public health priority. The occurrence of residues in food and other types of human exposures should be prevented with regard to the pesticide groups that are known to be neurotoxic. For other substances, given their widespread use and the unique vulnerability of the developing brain, the general lack of data on developmental neurotoxicity calls for investment in targeted research. While awaiting more definite evidence, existing uncertainties should be considered in light of the need for precautionary action to protect brain development.

From Animals to Animats 10

Abstract: The Animals to Animats Conference brings together researchers from ethology, psychology, ecology, artificial intelligence, artificial life, robotics, engineering, and related fields to further understanding of the behaviors and underlying mechanisms that allow natural and synthetic agents (animats) to adapt and survive in uncertain environments. The work presented focuses on well-defined models--robotic, computer-simulation, and mathematical--that help to characterize and compare various organizational principles or architectures underlying adaptive behavior in both natural animals and animats.

Government responsiveness and political competition in comparative perspective

Abstract: Governments in democratic systems are expected to respond to the issue preferences of citizens. Yet we have a limited understanding of the factors that cause levels of responsiveness to vary across time and between countries. In this article, the authors suggest that political contestation is the primary mechanism driving policy responsiveness and that this, in turn, is mediated by political institutions and government popularity. To test this proposition, the authors analyze the responsiveness of executive policy promises (speeches) and policy actions (public expenditure) in Britain, Denmark, and the United States in the period from 1970 to 2005. These time-series analyses show that higher levels of political contestation are associated with more responsive executives.

Perivascular Spaces and the Two Steps to Neuroinflammation

Abstract: Immune cells enter the central nervous system (CNS) from the circulation under normal conditions for immunosurveillance and in inflammatory neurologic diseases. This review describes the distinct anatomic features of the CNS vasculature that permit it to maintain parenchymal homeostasis and which necessitate specific mechanisms for neuroinflammation to occur. We review the historical evolution of the concept of the blood-brain barrier and discuss distinctions between diffusion/transport of solutes and migration of cells from the blood to CNS parenchyma. The former is regulated at the level of capillaries, whereas the latter takes place in postcapillary venules. We summarize evidence that entry of immune cells into the CNS parenchyma in inflammatory conditions involves 2 differently regulated steps: transmigration of the vascular wall into the perivascular space and progression across the glia limitans into the parenchyma.

In defence of generalized Darwinism

Abstract: Darwin himself suggested the idea of generalizing the core Darwinian principles to cover the evolution of social entities. Also in the nineteenth century, influential social scientists proposed their extension to political society and economic institutions. Nevertheless, misunderstanding and misrepresentation have hindered the realization of the powerful potential in this longstanding idea. Some critics confuse generalization with analogy. Others mistakenly presume that generalizing Darwinism necessarily involves biological reductionism. This essay outlines the types of phenomena to which a generalized Darwinism applies, and upholds that there is no reason to exclude social or economic entities.

Common breast cancer-predisposition alleles are associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers

Abstract: Germline mutations in BRCA1 and BRCA2 confer high risks of breast cancer. However, evidence suggests that these risks are modified by other genetic or environmental factors that cluster in families. A recent genome-wide association study has shown that common alleles at single nucleotide polymorphisms (SNPs) in FGFR2 (rs2981582), TNRC9 (rs3803662), and MAP3K1 (rs889312) are associated with increased breast cancer risks in the general population. To investigate whether these loci are also associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers, we genotyped these SNPs in a sample of 10,358 mutation carriers from 23 studies. The minor alleles of SNP rs2981582 and rs889312 were each associated with increased breast cancer risk in BRCA2 mutation carriers (per-allele hazard ratio [HR] = 1.32, 95% CI: 1.20-1.45, p(trend) = 1.7 x 10(-8) and HR = 1.12, 95% CI: 1.02-1.24, p(trend) = 0.02) but not in BRCA1 carriers. rs3803662 was associated with increased breast cancer risk in both BRCA1 and BRCA2 mutation carriers (per-allele HR = 1.13, 95% CI: 1.06-1.20, p(trend) = 5 x 10(-5) in BRCA1 and BRCA2 combined). These loci appear to interact multiplicatively on breast cancer risk in BRCA2 mutation carriers. The differences in the effects of the FGFR2 and MAP3K1 SNPs between BRCA1 and BRCA2 carriers point to differences in the biology of BRCA1 and BRCA2 breast cancer tumors and confirm the distinct nature of breast cancer in BRCA1 mutation carriers.