Frequency-dependent selection with dominance: a window onto the behavior of the mean fitness.
Selection in which fitnesses vary with the changing genetic composition of the population may facilitate the maintenance of genetic diversity in a wide range of organisms. Here, a detailed theoretical investigation is made of a frequency-dependent selection model, in which fitnesses are based on pairwise interactions between the two phenotypes at a diploid, diallelic, autosomal locus with complete dominance. The allele frequency dynamics are fully delimited analytically, along with all possible shapes of the mean fitness function in terms of where it increases or decreases as a function of the current allele frequency in the population. These results in turn allow possibly the first complete characterization of the dynamical behavior by the mean fitness through time under frequency-dependent selection. Here the mean fitness (i) monotonically increases, (ii) monotonically decreases, (iii) initially increases and then decreases, or (iv) initially decreases and then increases as equilibrium is approached. We analytically derive the exact initial and fitness conditions that produce each dynamic and how often each arises. Computer simulations with random initial conditions and fitnesses reveal that the potential decline in mean fitness is not negligible; on average a net decrease occurs 20% of the time and reduces the mean fitness by >17%.


Immunologic effects of national cholesterol education panel step-2 diets with and without fish-derived N-3 fatty acid enrichment.
Reductions in dietary fat, saturated fat, and cholesterol have been recommended to reduce the risk of heart disease in our society. The effects of these modifications on human cytokine production and immune responses have not been well studied. 22 subjects > 40 yr of age were fed a diet approximating that of the current American (14.1% of calories as saturated fatty acids, [SFA], 14.5% monounsaturated fatty acids [MUFA], 6.1% [n-6] polyunsaturated fatty acids [PUFA], 0.8% [n-3] PUFA, and 147 mg cholesterol/1,000 calories) for 6 wk, after which time they consumed (11 in each group) one of the two low-fat, low-cholesterol, high-PUFA diets based on National Cholesterol Education Panel (NCEP) Step 2 recommendations (4.0-4.5% SFA, 10.8-11.6% MUFA, 10.3-10.5% PUFA, 45-61 mg cholesterol/1,000 calories) for 24 wk. One of the NCEP Step 2 diets was enriched in fish-derived (n-3) PUFA (low-fat, high-fish: 0.54% or 1.23 g/d eicosapentaenoic acid [EPA] and docosahexaenoic acid [DHA] [121-188 g fish/d]) and the other low in fish-derived (n-3) PUFA (low-fat, low-fish [0.13% or 0.27 g/d EPA and DHA] [33 g fish/d]). Measurements of in vivo and in vitro indexes of immune responses were taken after each dietary period. Long-term feeding of low-fat, low-fish diet enriched in plant-derived PUFA increased blood mononuclear cell mitogenic response to the T cell mitogen Con A, IL-1 beta, and TNF production and had no effect on delayed-type hypersensitivity skin response, IL-6, GM-CSF, or PGE2 production. In contrast, the low-fat, high-fish diet significantly decreased the percentage of helper T cells whereas the percentage of suppressor T cells increased. Mitogenic responses to Con A and delayed-type hypersensitivity skin response as well as the production of cytokines IL-1 beta, TNF, and IL-6 by mononuclear cells were significantly reduced after the consumption of the low-fat, high-fish diet (24, 40, 45, 35, and 34%, respectively; P < 0.05 by two-tailed Student's t test except for IL-1 beta and TNF, which is by one-tailed t test). Our data are consistent with the concept that the NCEP Step 2 diet that is high in fish significantly decreases various parameters of the immune response in contrast to this diet when it is low in fish. Such alterations may be beneficial for the prevention and treatment of atherosclerotic and inflammatory diseases but may be detrimental with regard to host defense against invading pathogens.


Molecular architecture and conservation of an immature human endogenous retrovirus.
The human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus in the human genome and is activated and expressed in many cancers and amyotrophic lateral sclerosis. We present the immature HERV-K capsid structure at 3.2 Å resolution determined from native virus-like particles using cryo-electron tomography and subtomogram averaging. The structure shows a hexamer unit oligomerized through a 6-helix bundle, which is stabilized by a small molecule analogous to IP6 in immature HIV-1 capsid. The HERV-K immature lattice is assembled via highly conserved dimer and trimer interfaces, as detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the linker between the N-terminal and the C-terminal domains of CA occurs during HERV-K maturation. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.


Cell cycle-dependent nuclear retention of p53 by E2F1 requires phosphorylation of p53 at Ser315.
We show here that the cell cycle-dependent DNA-binding and transcriptional activity of p53 correlates with E2F expression in human primary fibroblasts. E2F1 binds and stimulates DNA-binding, transactivation and apoptotic functions of p53 but not p63 and p73. E2F1 binds residues 347-370 of p53 and enhances nuclear retention of Ser315 phosphorylated p53. This regulation of p53 by E2F1 is cell cycle dependent, as the cellular distribution of Ser315 phosphorylated p53 is associated with the periodic expression of E2F and cyclin A throughout the cell cycle. This is the first demonstration that the activities of p53 are regulated during the cell cycle by E2F/p53 interactions and that phosphorylation of p53 at Ser315 is required for this regulation.


Inflammation of the fetal ovine skin following in utero exposure to Ureaplasma parvum.
There is increasing evidence linking in utero infection and inflammation to preterm birth. Many commensal urogenital tract microorganisms, including the Mycoplasmas and Ureaplasmas, are commonly detected in association with preterm birth. Using an ovine model of sterile fetal inflammation, we demonstrated previously that the fetal skin generates a robust inflammatory response following in utero exposure to lipopolysaccharides from Escherichia coli. The fetal skin's response to colonization of the amniotic fluid by viable microorganisms remains unstudied. We hypothesised that in utero infection with Ureaplasma parvum serovar 3 would induce a proinflammatory response in the fetal skin. We found that (1) cultured fetal keratinocytes (the primary cellular constituent of the epidermis) respond to U. parvum exposure in vitro by increasing the expression of the chemotactant monocyte chemoattractant protein 1 (MCP-1) but not interleukin 1β (IL-1β), IL-6, IL-8, or tumor necrosis factor-α (TNF-α); (2) the fetal skin's response to 7 days of U. parvum exposure is characterized by elevated expression of MCP-1, TNF-α, and IL-10; and (3) the magnitude of inflammatory cytokine/chemokine expression in the fetal skin is dependent on the duration of U parvum exposure. These novel findings provide further support for the role of the fetal skin in the development of fetal inflammation and the preterm birth that may follow.


Passive Smoke Exposure and Its Effects on Cognition, Sleep, and Health Outcomes in Overweight and Obese Children.
Passive smoke exposure (PSE) may be a risk factor for childhood overweight and obesity and is associated with worse neurocognitive development, cognition, and sleep in children. The purpose of the study is to examine the effects of PSE on adiposity, cognition, and sleep in overweight and obese children using an objective measure of PSE. Overweight or obese children (n = 222) aged 7-11 (9.4 ± 1.1 years; 58% black; 58% female; 85% obese) were recruited from schools near Augusta, Georgia, over the course of the school year from 2003-2006 for a clinical trial, with data analyzed in 2009-2010. Passive smoke exposure was measured with plasma cotinine. Health, cognitive, and sleep measures and parent report of smoke exposure were obtained. Overweight and obese children with PSE had greater overall and central adiposity than nonexposed overweight and obese children (p < 0.03). However, PSE was unrelated to prediabetes, insulin resistance, or visceral fat. PSE was linked to poorer cognitive scores (p < 0.04) independent of adiposity, but was not related to sleep-disordered breathing. PSE is associated with fatness and poorer cognition in children. Tailored interventions that target multiple health risk factors including nutrition, physical activity, and tobacco use in children and families are needed to prevent adverse health outcomes related to tobacco use and obesity.


Barriers and facilitators of medicines reconciliation at transitions of care in Ireland - a qualitative study.
Medication error at transitions of care is common. The implementation of medicines reconciliation processes to improve this issue has been recommended by many regulatory and safety organisations. The aim of this study was to gain insight from healthcare professionals on the barriers and facilitators to the medicines reconciliation implementation process. Semi-structured interviews were conducted in Ireland with a wide range of healthcare professionals (HCPs) involved with medicines reconciliation at transitions of care. Thematic analysis was undertaken using an adaptation of a combined theoretical framework of Grol, Cabana and Sluisveld to classify the barriers and facilitators to implementation of medicines reconciliation. Thirty-five participants were interviewed, including eleven community pharmacists (CPs), eight hospital pharmacists (HPs), nine hospital consultants (HCs), five general practitioners (GPs), and two non-consultant hospital doctors (NCHDs). Themes were categorized into barriers and facilitators. Barriers included resistance from existing professional cultures, staff interest and training, poor communication and minimal information and communications technology (ICT) support. Solutions (facilitators) suggested included supporting effective multidisciplinary teams, greater involvement of pharmacists in medicines reconciliation, ICT solutions (linked prescribing databases, decision support systems) and increased funding to provide additional (e.g. admission and discharge reconciliation) and more advanced services (e.g. community pharmacist delivered medicines use review). Medicines reconciliation is advocated as a solution to the known problem of medication error at transitions of care. This study identifies the key challenges and potential solutions that policy makers, managers and HCPs should consider when reviewing the practices and processes of medicines reconciliation in their own organisations.


Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors.
Selective inhibitors could help unveil the mechanisms by which inhibition of poly(ADP-ribose) polymerases (PARPs) elicits clinical benefits in cancer therapy. We profiled 10 clinical PARP inhibitors and commonly used research tools for their inhibition of multiple PARP enzymes. We also determined crystal structures of these compounds bound to PARP1 or PARP2. Veliparib and niraparib are selective inhibitors of PARP1 and PARP2; olaparib, rucaparib, and talazoparib are more potent inhibitors of PARP1 but are less selective. PJ34 and UPF1069 are broad PARP inhibitors; PJ34 inserts a flexible moiety into hydrophobic subpockets in various ADP-ribosyltransferases. XAV939 is a promiscuous tankyrase inhibitor and a potent inhibitor of PARP1 in vitro and in cells, whereas IWR1 and AZ-6102 are tankyrase selective. Our biochemical and structural analysis of PARP inhibitor potencies establishes a molecular basis for either selectivity or promiscuity and provides a benchmark for experimental design in assessment of PARP inhibitor effects.


Protrusio acetabuli in Marfan syndrome. History, diagnosis, and treatment.
Marfan syndrome is an autosomal dominant disorder of connective tissue, with ocular, skeletal, and cardiovascular manifestations. Protrusio acetabuli is a criterion for the diagnosis of Marfan syndrome. Prolonged protrusio acetabuli may result in secondary osteoarthritic changes in the hip joint. Radiographic criteria for protrusio acetabuli include an abnormally positioned acetabular line, a center-edge angle of Wiberg of >40 degrees, and crossing of the teardrop by the ilioischial line. In a skeletally immature patient with Marfan syndrome in whom the triradiate physis of the acetabulum is still open, closure of the triradiate physis can interrupt and decrease the progression of the deformity. In older patients, valgus intertrochanteric osteotomy and eventually total hip arthroplasty are the only methods available for correction of the protrusio acetabuli.


Intra-articular injections of sodium hyaluronate (Hyalgan®) in osteoarthritis of the knee. a randomized, controlled, double-blind, multicenter trial in the Asian population.
The efficacy and tolerability of 500-730 kDa sodium hyaluronate (Hyalgan®) for treatment of osteoarthritis (OA) pain has been established in clinical trials, but few data are available in the Asian population. We conducted a randomized, double-blind, multicenter, placebo-controlled study to evaluate the efficacy and tolerability of this preparation in a Taiwanese population. Two hundred patients with mild to moderate OA of the knee were randomized to receive five weekly intra-articular injections of sodium hyaluronate or placebo. The primary efficacy outcome was the change from baseline to Week 25 in patients' evaluation of pain using a 100-mm visual analog scale (VAS) during the 50-foot walking test. Additional outcomes included Western Ontario and McMaster Universities (WOMAC) scores, time on the 50-foot walking test, patient's and investigator's subjective assessment of effectiveness, acetaminophen consumption, and the amounts of synovial fluid. The Hyalgan® treatment group showed a significantly greater improvement from baseline to Week 25 in VAS pain on the 50-foot walking test than the placebo group (p = 0.0020). The Hyalgan® group revealed significant improvements from baseline to week 25 in WOMAC pain and function score than the placebo group (p = 0.005 and 0.0038, respectively) Other outcomes, such as time on the 50-foot walking test and subjective assessment of effectiveness, did not show any significant difference between groups. Both groups were safe and well tolerated. The present study suggests that five weekly intra-articular injections of sodium hyaluronate are well tolerated, can provide sustained relief of pain, and can improve function in Asian patients with osteoarthritis of the knee. Therapeutic study, Level I-1a (randomized controlled trial with a significant difference).


Transition from pediatric to adult care for youth diagnosed with type 1 diabetes in adolescence.
Youth with type 1 diabetes mellitus are at risk for poor glycemic control as they age into adulthood. The aim of this study was to describe sociodemographic and clinical correlates of poor glycemic control associated with the transfer of care from pediatric to adult diabetes providers among a cohort of youth with type 1 diabetes diagnosed in adolescence. Analyses included 185 adolescent participants with recently diagnosed type 1 diabetes in the SEARCH for Diabetes in Youth Study with pediatric care at baseline who were age ≥18 years at follow-up. Demographic and clinical factors were measured by survey and laboratory results. Survival analysis was used to estimate the age of transition. Logistic regression analysis assessed the association of demographic and clinical factors with the transition of care and poor glycemic control at follow-up. Fifty-seven percent of participants had transitioned to adult diabetes care providers by the follow-up visit. The estimated median age of transition of care was 20.1 years (95% confidence interval 19.8-20.4). Older age, lower baseline glycosylated hemoglobin, and less parental education were independently associated with increased odds of transition. The odds of poor glycemic control at follow-up were 2.5 times higher for participants who transitioned to adult care compared with those who remained in pediatric care. Transferring from pediatric to adult care, experienced by more than half the sample, was associated with an increased risk of poor glycemic control at follow-up. These findings suggest that young adults need additional support when moving to adult care.


Association between endogenous sex steroid hormones and inflammatory biomarkers in US men.
Sex steroid hormones and inflammatory biomarkers are both associated with the development and progression of chronic diseases, but their interrelationship is relatively uncharacterized. We examined the association of sex hormones and sex hormone-binding globulin (SHBG) with biomarkers of inflammation, C-reactive protein (CRP) and white blood cell (WBC) count. The study included data from 809 adult men in the National Health and Nutrition Examination Survey 1999-2004. Geometric means and 95% confidence intervals were estimated separately for CRP and WBC concentrations by sex steroid hormones and SHBG using weighted linear regression models. Higher concentrations of total (slope per one quintile in concentration, -0.18; p-trend, 0.001) and calculated free (slope, -0.13; p-trend, 0.03) testosterone were statistically significantly associated with lower concentrations of CRP, but not with WBC count. Men in the bottom quintile of total testosterone (≤3.3 ng/mL), who might be considered to have clinically low testosterone, were more likely to have elevated CRP (≥3 mg/L) compared with men in the top four quintiles (OR, 1.61; 95% CI, 1.00-2.61). Total and calculated free estradiol (E2) were positively associated with both CRP (Total E2: slope, 0.14; p-trend, <0.001; Free E2: slope, 0.15; p-trend, <0.001) and WBC (Total E2: slope, 0.02; p-trend, 0.08; Free E2: slope, 0.02; p-trend, 0.02) concentrations. SHBG concentrations were inversely associated with WBC count (slope, -0.03; p-trend, 0.04), but not with CRP. These cross-sectional findings are consistent with the hypothesis that higher androgen and lower oestrogen concentrations may have an anti-inflammatory effect in men.


Observation of an arsenic adduct in an acetyl esterase crystal structure.
The crystal structures of an acetyl esterase, HerE, and its complex with an inhibitor dimethylarsinic acid have been determined at 1.30- and 1.45-A resolution, respectively. Although the natural substrate for the enzyme is unknown, HerE hydrolyzes the acetyl groups from heroin to yield morphine and from phenyl acetate to yield phenol. Recently, the activity of the enzyme toward heroin has been exploited to develop a heroin biosensor, which affords higher sensitivity than other currently available detection methods. The crystal structure reveals a single domain with the canonical alpha/beta hydrolase fold with an acyl binding pocket that snugly accommodates the acetyl substituent of the substrate and three backbone amides that form a tripartite oxyanion hole. In addition, a covalent adduct was observed between the active site serine and dimethylarsinic acid, which inhibits the enzyme. This crystal structure provides the first example of an As-containing compound in a serine esterase active site and the first example of covalent modification of serine by arsenic. Thus, the HerE complex reveals the structural basis for the broad scope inhibition of serine hydrolases by As(V)-containing organic compounds.


Denture plaque and adherence of Candida albicans to denture-base materials in vivo and in vitro.
The aim of this paper is to review our understanding of the mechanisms and clinical significance of adhesion of C. albicans to denture-base materials in relation to denture plaque and denture-related stomatitis. Earlier reports in the literature of a 65% prevalence level of denture-related stomatitis seem to be exaggerated. More recent studies indicate that denture-related stomatitis is considerably less common, particularly in normal healthy subjects. The etiology of the condition is discussed in this review, and although much of the literature supports the view that the condition is strongly associated with C. albicans, this is not always so. In some subjects, the cause appears to be related to a non-specific plaque. This review also considers the role of denture plaque in the pathogenesis of denture-related stomatitis, the sequential development of denture plaque, and its colonization by Candida organisms. Designing controlled in vivo studies is difficult, and as a consequence, many investigators have had to resort to in vitro studies. The majority of these studies have attempted to investigate the hydrophobicity of C. albicans, relating the surface free-energy of denture-base materials, particularly acrylic resin, to that of the organism. Surprisingly little work has been directed at surface roughness and how it affects retention of organisms. Further, no attention has been paid to the properties and character of the surface, other than average surface roughness, as it affects adhesion. A comparison of results from in vitro studies on the effect on adhesion of pre-coating the surfaces of denture-base materials with saliva has produced equivocal conclusions. This is largely due to little standardization of experimental protocols between studies, particularly in the collection and handling of the saliva used. In conclusion, the review strongly supports the suggestion that adherence of C. albicans to denture-base materials in vitro is related to the hydrophobicity of the organism. The clinical significance of the observation and the mechanisms for the development and maturation of denture plaque are yet to be understood. There is a clear need for further investigation of other factors that may moderate the adhesion of organisms and subsequent colonization of denture-base materials.


Disposition of the 14C-labeled phosphorothioate oligonucleotide ISIS 2105 after intravenous administration to rats.
5'-TTGCTTCCATCTTCCTCGTC-3' (ISIS 2105) is a phosphorothioate oligodeoxynucleotide currently being evaluated as an intralesional antiviral drug for the treatment of genital warts that are caused by the human papillomavirus. ISIS 2105, labeled with 14C (at the carbon-2 position of thymine) was administered as a single i.v. injection (3.6 mg/kg) to female Sprague-Dawley rats to assess the disposition of the drug. After i.v. administration of [14C]2105, blood radioactivity disappeared in a multiexponential manner with the half-lives of the phases equal to 0.4, 1.9, 7.1 and 5.1 hr. The initial volume of distribution was 22 ml and the postdistribution volume of distribution was 1076 ml, which indicated an extensive distribution of radioactivity. The apparent blood clearance was 14.7 ml/hr. The radioactivity in the expired air accounted for 51% of the administered dose over the 10-day period. Urinary and fecal radioactivity accounted for 15% and 5% of the administered dose, respectively. The major sites of radioactivity uptake were the liver (up to 22.6% of the dose), kidneys (renal cortex, up to 14% of the dose), bone marrow (up to 14% of the dose), skin (up to 13% of the dose) and skeletal muscle (up to 9% of the dose). Other tissues contained approximately 1% or less of the dose. The overall recovery of radioactivity 10 days postdosing was 95.1 +/- 7.5% (mean +/- S.D.) of the administered single dose. The radioactivity in the blood was almost completely in the plasma during the course of the study. In the plasma, the radioactivity was extensively bound to proteins, as assessed by size-exclusion high-performance liquid chromatography (HPLC), in samples up to 8 hr postdosing. Retention data on size-exclusion HPLC and in vitro incubations using purified proteins suggested that the plasma proteins that bound [14C]2105 were albumin and alpha 2-macroglobulin. The complex formed between the plasma proteins and [14C]2105-derived radioactivity was dissociated on anion-exchange HPLC to indicate that the great majority of plasma radioactivity coeluted with intact [14C]2105 in samples that contained sufficient radioactivity for analysis. There was a time-dependent decrease in the proportion of hepatic and renal radioactivity that coeluted with the intact [14C]2105 during the course of the study. The urine did not contain radioactivity that eluted with intact [14C]2105 on anion-exchange HPLC.


SV40 and human cancer: a review of recent data.
An unknown proportion of formalin-inactivated poliovirus vaccine lots administered to millions of US residents between 1955 and 1963 was contaminated with small amounts of infectious simian virus 40 (SV40), a polyomavirus of the rhesus macaque. It has been reported that mesothelioma, brain tumors, osteosarcoma and non-Hodgkin lymphoma (NHL) contain SV40 DNA sequences and that SV40 infection introduced into humans by the vaccine probably contributed to the development of these cancers. The Immunization Safety Review Committee of the Institute of Medicine (IOM) reviewed this topic in 2002. The present review of recent studies showed that the earlier results describing the recovery of SV40 DNA sequences from a large proportion of the above tumors were not reproducible and that most studies were negative. Contamination with laboratory plasmids was identified as a possible source of false positive results in some previous studies. The low-level immunoreactivity of human sera to SV40 was very likely the result of cross-reactivity with antibodies to the SV40-related human polyomaviruses BKV and JCV, rather than of authentic SV40 infection. SV40 sero-reactivity in patients with the suspect tumors was no greater than that in controls. In epidemiologic studies, the increased incidence of some of the suspect tumors in the 1970s to 1980s was not related to the risk of exposure to SV40-contaminated vaccines. In summary, the most recent evidence does not support the notion that SV40 contributed to the development of human cancers.


Doxorubicin kinetics and effects on lung cancer cell lines using in vitro Raman micro-spectroscopy: binding signatures, drug resistance and DNA repair.
Raman micro-spectroscopy is a non-invasive analytical tool, whose potential in cellular analysis and monitoring drug mechanisms of action has already been demonstrated, and which can potentially be used in pre-clinical and clinical applications for the prediction of chemotherapeutic efficacy. To further investigate such potential clinical application, it is important to demonstrate its capability to differentiate drug mechanisms of action and cellular resistances. Using the example of Doxorubicin (DOX), in this study, it was used to probe the cellular uptake, signatures of chemical binding and subsequent cellular responses, of the chemotherapeutic drug in two lung cancer cell lines, A549 and Calu-1. Multivariate statistical analysis was used to elucidate the spectroscopic signatures associated with DOX uptake and subcellular interaction. Biomarkers related to DNA damage and repair, and mechanisms leading to apoptosis were also measured and correlated to Raman spectral profiles. Results confirm the potential of Raman spectroscopic profiling to elucidate both drug kinetics and pharmacodynamics and differentiate cellular drug resistance associated with different subcellular accumulation rates and subsequent cellular response to DNA damage, pointing towards a better understanding of drug resistance for personalised targeted treatment.


miRNA biomarkers in cyst fluid augment the diagnosis and management of pancreatic cysts.
The diagnosis of pancreatic cystic lesions has increased dramatically. Most are benign, whereas some, such as intraductal papillary mucinous neoplasms (IPMN), represent precursors of pancreatic adenocarcinoma. Therapeutic stratification of IPMNs is challenging without precise information on dysplasia grade and presence of invasion. We assessed the diagnostic benefit of using miRNAs as biomarkers in pancreatic cyst fluid, focusing on IPMNs because of their frequency and malignant potential. RNA was extracted from 55 microdissected formalin-fixed, paraffin-embedded (FFPE) IPMN specimens, and 65 cyst fluid specimens aspirated following surgical resection. Expression of 750 miRNAs was evaluated with TaqMan miRNA Arrays using 22 FFPE and 15 cyst fluid specimens. Differential expression of selected miRNA candidates was validated in 33 FFPE and 50 cyst fluid specimens using TaqMan miRNA Assays. We identified 26 and 37 candidate miRNAs that distinguish low-grade from high-grade IPMNs using FFPE and cyst fluid specimens, respectively. A subset of 18 miRNAs, selected from FFPE and cyst fluid data, separated high-grade IPMNs from low-grade IPMNs, serous cystadenomas (SCA) and uncommon cysts, such as solid pseudopapillary neoplasms (SPN) and cystic pancreatic neuroendocrine tumors (PanNET). A logistic regression model using nine miRNAs allowed prediction of cyst pathology implying resection (high-grade IPMNs, PanNETs, and SPNs) versus conservative management (low-grade IPMNs, SCAs), with a sensitivity of 89%, a specificity of 100%, and area under the curve of 1. We found candidate miRNAs that helped identify patients with high-grade IPMN and exclude nonmucinous cysts. These classifiers will require validation in a prospective setting to ultimately confirm their clinical usefulness.


The molecular basis of oligomeric organization of the human M3 muscarinic acetylcholine receptor.
G protein-coupled receptors, including the M3 muscarinic acetylcholine receptor, can form homo-oligomers. However, the basis of these interactions and the overall organizational structure of such oligomers are poorly understood. Combinations of site-directed mutagenesis and homogenous time-resolved fluorescence resonance energy transfer studies that assessed interactions between receptor protomers at the surface of transfected cells indicated important contributions of regions of transmembrane domains I, IV, V, VI, and VII as well as intracellular helix VIII to the overall organization. Molecular modeling studies based on both these results and an X-ray structure of the inactive state of the M3 receptor bound by the antagonist/inverse agonist tiotropium were then employed. The results could be accommodated fully by models in which a proportion of the cell surface M3 receptor population is a tetramer with rhombic, but not linear, orientation. This is consistent with previous studies based on spectrally resolved, multiphoton fluorescence resonance energy transfer. Modeling studies furthermore suggest an important role for molecules of cholesterol at the dimer + dimer interface of the tetramer, which is consistent with the presence of cholesterol at key locations in many G protein-coupled receptor crystal structures. Mutants that displayed disrupted quaternary organization were often poorly expressed and showed immature N-glycosylation. Sustained treatment of cells expressing such mutants with the muscarinic receptor inverse agonist atropine increased cellular levels and restored both cell surface delivery and quaternary organization to many of the mutants. These observations suggest that organization as a tetramer may occur before plasma membrane delivery and may be a key step in cellular quality control assessment.


Depressive Symptoms and the Link with Academic Performance among Rural Taiwanese Children.
Previous studies reflect a high prevalence of depressive symptoms among Taiwanese adolescents (ages 13-18), but there is an absence of literature related to the risk of depression of children in Taiwan (ages 6-12), particularly among potentially vulnerable subgroups. To provide insight into the distribution of depressive symptoms among children in rural Taiwan and measure the correlation between academic performance, we conducted a survey of 1655 randomly selected fourth and fifth-grade students at 92 sample schools in four relatively low-income counties or municipalities. Using the Center for Epidemiological Studies-Depression Scale (CES-D) we assessed the prevalence of depressive symptoms in this sample, in addition to collecting other data, such as performance on a standardized math test as well as information on a number of individual and household characteristics. We demonstrate that the share of children with clinically significant symptoms is high: 38% of the students were at risk of general depression (depression score ≥ 16) and 8% of the students were at risk of major depression (depression score > 28). The results of the multivariate regression and heterogeneous analysis suggest that poor academic performance is closely associated with a high prevalence of depressive symptoms. Among low-performing students, certain groups were disproportionately affected, including girls and students whose parents have migrated away for work. Results also suggest that, overall, students who had a parent who was an immigrant from another country were at greater risk of depression. These findings highlight the need for greater resource allocation toward mental health services for elementary school students in rural Taiwan, particularly for at-risk groups.


Cluster consensus in discrete-time networks of multiagents with inter-cluster nonidentical inputs.
In this paper, cluster consensus of multiagent systems is studied via inter-cluster nonidentical inputs. Here, we consider general graph topologies, which might be time-varying. The cluster consensus is defined by two aspects: intracluster synchronization, the state at which differences between each pair of agents in the same cluster converge to zero, and inter-cluster separation, the state at which agents in different clusters are separated. For intra-cluster synchronization, the concepts and theories of consensus, including the spanning trees, scramblingness, infinite stochastic matrix product, and Hajnal inequality, are extended. As a result, it is proved that if the graph has cluster spanning trees and all vertices self-linked, then the static linear system can realize intra-cluster synchronization. For the time-varying coupling cases, it is proved that if there exists T > 0 such that the union graph across any T-length time interval has cluster spanning trees and all graphs has all vertices self-linked, then the time-varying linear system can also realize intra-cluster synchronization. Under the assumption of common inter-cluster influence, a sort of inter-cluster nonidentical inputs are utilized to realize inter-cluster separation, such that each agent in the same cluster receives the same inputs and agents in different clusters have different inputs. In addition, the boundedness of the infinite sum of the inputs can guarantee the boundedness of the trajectory. As an application, we employ a modified non-Bayesian social learning model to illustrate the effectiveness of our results.


Clinical and epidemiological predictors of transmission in Severe Acute Respiratory Syndrome (SARS).
Only a minority of probable SARS cases caused transmission. We assess if any epidemiological or clinical factors in SARS index patients were associated with increased probability of transmission. We used epidemiological and clinical data on probable SARS patients admitted to Tan Tock Seng Hospital. Using a case-control approach, index patients who had probable SARS who subsequently transmitted the disease to at least one other patient were analysed as "cases" against patients with no transmission as "controls", using multivariate logistic regression analysis. 98 index patients were available for analysis (22 with transmission, 76 with no transmission). Covariates positively associated with transmission in univariate analysis at p < 0.05 included delay to isolation (Day 7 of illness or later), admission to a non-isolation facility, pre-existing chronic respiratory disease and immunosuppressive disease, need for oxygen, shortness of breath, vomiting, and higher lactate dehydrogenase levels and higher neutrophil counts. In the multivariate analysis, only three factors were significant: delay to isolation, admission to a non-isolation facility and higher lactate dehydrogenase levels of >650 IU/L (OR 6.4, 23.8 and 4.7 respectively). Clinical and epidemiological factors can help us to explain why transmission was observed in some instances but not in others.


Still reduced cardiovascular mortality 12 years after supplementation with selenium and coenzyme Q10 for four years: A validation of previous 10-year follow-up results of a prospective randomized double-blind placebo-controlled trial in elderly.
Selenium and coenzyme Q10 are both necessary for optimal cell function in the body. The intake of selenium is low in Europe, and the endogenous production of coenzyme Q10 decreases as age increases. Therefore, an intervention trial using selenium and coenzyme Q10 for four years as a dietary supplement was performed. The main publication reported reduced cardiovascular mortality as a result of the intervention. In the present sub-study the objective was to determine whether reduced cardiovascular (CV) mortality persisted after 12 years, in the supplemented population or in subgroups with diabetes, hypertension, ischemic heart disease or reduced functional capacity due to impaired cardiac function. From a rural municipality in Sweden, four hundred forty-three healthy elderly individuals were included. All cardiovascular mortality was registered, and no participant was lost to the follow-up. Based on death certificates and autopsy results, mortality was registered. After 12 years a significantly reduced CV mortality could be seen in those supplemented with selenium and coenzyme Q10, with a CV mortality of 28.1% in the active treatment group, and 38.7% in the placebo group. A multivariate Cox regression analysis demonstrated a reduced CV mortality risk in the active treatment group (HR: 0.59; 95%CI 0.42-0.81; P = 0.001). In those with ischemic heart disease, diabetes, hypertension and impaired functional capacity we demonstrated a significantly reduced CV mortality risk. This is a 12-year follow-up of a group of healthy elderly participants that were supplemented with selenium and coenzyme Q10 for four years. Even after twelve years we observed a significantly reduced risk for CV mortality in this group, as well as in subgroups of patients with diabetes, hypertension, ischemic heart disease or impaired functional capacity. The results thus validate the results obtained in the 10-year evaluation. The protective action was not confined to the intervention period, but persisted during the follow-up period. The mechanisms behind this effect remain to be fully elucidated, although various effects on cardiac function, oxidative stress, fibrosis and inflammation have previously been identified. Since this was a small study, the observations should be regarded as hypothesis-generating. Clinicaltrials.gov NCT01443780.


Oligomerization of recombinant and endogenously expressed human histamine H(4) receptors.
In this study, we report the homo- and hetero-oligomerization of the human histamine H(4)R by both biochemical (Western blot and immobilized metal affinity chromatography) and biophysical [bioluminescence resonance energy transfer and time-resolved fluorescence resonance energy transfer (tr-FRET)] techniques. The H(4)R receptor is the most recently discovered member of the histamine family of G-protein-coupled receptors. Using specific polyclonal antibodies raised against the C-terminal tail of the H(4)R, we demonstrate the presence of H(4)R oligomers in human embryonic kidney 293 and COS-7 cells heterologously overexpressing H(4)Rs and putative native H(4)R oligomers in human phytohaemagglutinin blasts endogenously expressing H(4)Rs. Moreover, we show that H(4)R homo-oligomers are formed constitutively, are formed at low receptor densities (300 fmol/mg of protein), and are present at the cell surface, as detected by tr-FRET. The formation of these oligomers is independent of N-glycosylation and is not modulated by H(4)R ligands, covering the full spectrum of agonists, neutral antagonists, and inverse agonists. Although we show H(4)R homo-oligomer formation at physiological expression levels, the detection of H(1)R-H(4)R hetero-oligomers was achieved only at higher H(1)R expression levels and are most likely not physiologically relevant.


Quantifying the economic value and quality of life impact of earlier influenza vaccination.
Influenza vaccination is administered throughout the influenza disease season, even as late as March. Given such timing, what is the value of vaccinating the population earlier than currently being practiced? We used real data on when individuals were vaccinated in Allegheny County, Pennsylvania, and the following 2 models to determine the value of vaccinating individuals earlier (by the end of September, October, and November): Framework for Reconstructing Epidemiological Dynamics (FRED), an agent-based model (ABM), and FluEcon, our influenza economic model that translates cases from the ABM to outcomes and costs [health care and lost productivity costs and quality-adjusted life-years (QALYs)]. We varied the reproductive number (R0) from 1.2 to 1.6. Applying the current timing of vaccinations averted 223,761 influenza cases, $16.3 million in direct health care costs, $50.0 million in productivity losses, and 804 in QALYs, compared with no vaccination (February peak, R0 1.2). When the population does not have preexisting immunity and the influenza season peaks in February (R0 1.2-1.6), moving individuals who currently received the vaccine after September to the end of September could avert an additional 9634-17,794 influenza cases, $0.6-$1.4 million in direct costs, $2.1-$4.0 million in productivity losses, and 35-64 QALYs. Moving the vaccination of just children to September (R0 1.2-1.6) averted 11,366-1660 influenza cases, $0.6-$0.03 million in direct costs, $2.3-$0.2 million in productivity losses, and 42-8 QALYs. Moving the season peak to December increased these benefits, whereas increasing preexisting immunity reduced these benefits. Even though many people are vaccinated well after September/October, they likely are still vaccinated early enough to provide substantial cost-savings.


HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server.
We have constructed a relational database of hemoglobin variants and thalassemia mutations, called HbVar, which can be accessed on the web at http://globin.cse.psu.edu. Extensive information is recorded for each variant and mutation, including a description of the variant and associated pathology, hematology, electrophoretic mobility, methods of isolation, stability information, ethnic occurrence, structure studies, functional studies, and references. The initial information was derived from books by Dr. Titus Huisman and colleagues [Huisman et al., 1996, 1997, 1998]. The current database is updated regularly with the addition of new data and corrections to previous data. Queries can be formulated based on fields in the database. Tables of common categories of variants, such as all those involving the alpha1-globin gene (HBA1) or all those that result in high oxygen affinity, are maintained by automated queries on the database. Users can formulate more precise queries, such as identifying "all beta-globin variants associated with instability and found in Scottish populations." This new database should be useful for clinical diagnosis as well as in fundamental studies of hemoglobin biochemistry, globin gene regulation, and human sequence variation at these loci.


Salvia divinorum: from recreational hallucinogenic use to analgesic and anti-inflammatory action.
Salvia divinorum is a herbal plant native to the southwest region of Mexico. Traditional preparations of this plant have been used in illness treatments that converge with inflammatory conditions and pain. Currently, S. divinorum extracts have become popular in several countries as a recreational drug due to its hallucinogenic effects. Its main active component is a diterpene named salvinorin A (SA), a potent naturally occurring hallucinogen with a great affinity to the κ opioid receptors and with allosteric modulation of cannabinoid type 1 receptors. Recent biochemical research has revealed the mechanism of action of the anti-inflammatory and analgesic effect of SA at the cellular and molecular level. Nevertheless, because of their short-lasting and hallucinogenic effect, the research has focused on discovering a new analogue of SA that is able to induce analgesia and reduce inflammation with a long-lasting effect but without the hallucinatory component. In this review, we explore the role of S. divinorum, SA and its analogues. We focus mainly on their analgesic and anti-inflammatory roles but also mention their psychoactive properties.


Peripheral proteins and smooth membrane from erythrocyte ghosts. Segregation of ATP-utilizing enzymes into smooth membrane.
Erythrocytes and their isolated membranes display ATP-dependent endocytosis. To localize the enzymes responsible for this phenomenon, the erythrocyte membranes (ghosts) were fractionated under conditions which retained ATPase activity. Fractionation of the ghosts resulted in three fractions: spectrin-actin, the peripheral proteins soluble in high salt, and the smooth membrane containing integral proteins. On the average, 87% of the protein and 88% of the phosphorus of the original ghosts were recovered in these fractions, and all of the kinds of ATP-splitting activities of the membrane were recovered in the smooth membrane. A tiny ATPase activity, detectable by special methodology in spectrinactin, could have been due to contamination with membranous material. Although the purified spectrin-actin did not have a significant ATPase of its own, it stimulated the Ca2+, Mg2+-ATPase of the smooth membrane significantly, suggesting a cooperative interaction between these two fractions. This segregation of the ATPase activities into the smooth membrane, combined with the energy dependence of endocytosis, showed that the smooth membrane must be involved in the energy production for endocytosis. The possibility that the spectrin-actin filaments cooperate with a myosinlike ATPase in the membrane to generate membrane movements is discussed.


Drivers of the Distribution of Fisher Effort at Lake Alaotra, Madagascar.
Understanding how fishers make decisions is important for improving management of fisheries. There is debate about the extent to which small-scale fishers follow an ideal free distribution (IFD) - distributing their fishing effort efficiently according to resource availability rather than being influenced by social factors or personal preference. Using detailed data from 1800 fisher catches and from semi-structured interviews with over 700 fishers at Lake Alaotra, the largest inland fishery in Madagascar, we show that fishers generally conform to IFD. However, there were differences in catch: effort relationships between fishers using different gear types as well as other revealing deviations from the predictions of IFD. Fishers report routine as the primary determinant of their choice of fishing location, explaining why they do not quickly respond to changes in catch at a site. Understanding the influences on fishers' spatial behaviour will allow better estimates of costs of fishing policies on resource users, and help predict their likely responses. This can inform management strategies to minimise the negative impacts of interventions, increasing local support for and compliance with rules.


Simulated dataset of corn response to nitrogen over thousands of fields and multiple years in Illinois.
Nitrogen (N) fertilizer recommendations for corn (Zea mays L.) in the US Midwest have been a puzzle for several decades, without agreement among stakeholders for which methodology is the best to balance environmental and economic outcomes. Part of the reason is the lack of long-term data of crop responses to N over multiple fields since trial data is often limited in the number of soils and years it can explore. To overcome this limitation, we designed an analytical platform based on crop simulations run over millions of farming scenarios over extensive geographies. The database was calibrated and validated using data from more than four hundred trials in the region. This dataset can have an important role for research and education in N management, machine leaching, and environmental policy analysis. The calibration and validation procedure provides a framework for future gridded crop model studies. We describe dataset characteristics and provide thorough descriptions of the model setup.


Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum.
Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains. We developed a novel, model-based approach for Bayesian inference on biological network data that centres on approximate Bayesian computation, or likelihood-free inference. Instead of computing the intractable likelihood of the protein network topology, our method summarizes key features of the network and, based on these, uses a MCMC algorithm to approximate the posterior distribution of the model parameters. This allowed us to reliably fit a flexible mixture model that captures hallmarks of evolution by gene duplication and subfunctionalization to protein interaction network data of Helicobacter pylori and Plasmodium falciparum. The 80% credible intervals for the duplication-divergence component are [0.64, 0.98] for H. pylori and [0.87, 0.99] for P. falciparum. The remaining parameter estimates are not inconsistent with sequence data. An extensive sensitivity analysis showed that incompleteness of PIN data does not largely affect the analysis of models of protein network evolution, and that the degree sequence alone barely captures the evolutionary footprints of protein networks relative to other statistics. Our likelihood-free inference approach enables a fully Bayesian analysis of a complex and highly stochastic system that is otherwise intractable at present. Modelling the evolutionary history of PIN data, it transpires that only the simultaneous analysis of several global aspects of protein networks enables credible and consistent inference to be made from available datasets. Our results indicate that gene duplication has played a larger part in the network evolution of the eukaryote than in the prokaryote, and suggests that single gene duplications with immediate divergence alone may explain more than 60% of biological network data in both domains.


CD109 deficiency induces osteopenia with an osteoporosis-like phenotype in vivo.
Osteoporosis is a global public health problem that is increasing along with an aging population. A major determinant of osteoporosis is high bone turnover, which results from osteoclast activation. CD109 is a glycosylphosphatidylinositol-anchored glycoprotein, a deficiency that leads to a psoriasis-like skin inflammation in mice. Although the expression of CD109 has been reported in mouse pre-osteoclast cells, its function in osteoclasts in vivo remains largely unknown. To investigate the physiological role of CD109 in bone metabolism, we analyzed bones from wild-type and CD109-deficient adult mice. Micro-computed tomography analysis of the femur (thigh bone) showed that bone volume was lower in CD109-deficient mice than in wild-type mice. Bone histomorphometric analysis showed not only a reduction in bone volume but also an increase in bone turnover in CD109-deficient mice as compared with wild-type mice. Additionally, we measured serum levels of several markers of bone turnover and found a significant increase in the N-terminal telopeptide of type I collagen, a bone resorption marker, as well as alkaline phosphatase, a bone formation marker, in CD109-deficient mice. These results indicate that CD109 deficiency induces a high-turnover, osteoporosis-like phenotype, which suggests that CD109 plays a role in bone metabolism in vivo.


Diurnal cortisol and mental well-being in middle and older age: evidence from four cohort studies.
We conducted an individual participant meta-analysis to test the hypothesis that cortisol patterns indicative of dysregulated hypothalamic-pituitary-adrenal axis functioning would be prospectively associated with poorer well-being at follow-up. Four large UK-based cohort studies. Those providing valid salivary or serum cortisol samples (n=7515 for morning cortisol; n=1612 for cortisol awakening response) at baseline (age 44-82) and well-being data on the Warwick Edinburgh Mental Wellbeing Scale at follow-up (0-8 years) were included. Well-being was not associated with morning cortisol, diurnal slope or awakening response though a borderline association with evening cortisol was found. Adjusting for sex and follow-up time, each 1 SD increase in evening cortisol was associated with a -0.47 (95% CI -1.00 to 0.05) point lower well-being. This was attenuated by adjustment for body mass index, smoking and socioeconomic position. Between-study heterogeneity was low. This study does not support the hypothesis that diurnal cortisol is prospectively associated with well-being up to 8 years later. However, replication in prospective studies with cortisol samples over multiple days is required.


Perceived neighborhood environment and physical activity in 11 countries: do associations differ by country?
Increasing empirical evidence supports associations between neighborhood environments and physical activity. However, since most studies were conducted in a single country, particularly western countries, the generalizability of associations in an international setting is not well understood. The current study examined whether associations between perceived attributes of neighborhood environments and physical activity differed by country. Population representative samples from 11 countries on five continents were surveyed using comparable methodologies and measurement instruments. Neighborhood environment × country interactions were tested in logistic regression models with meeting physical activity recommendations as the outcome, adjusted for demographic characteristics. Country-specific associations were reported. Significant neighborhood environment attribute × country interactions implied some differences across countries in the association of each neighborhood attribute with meeting physical activity recommendations. Across the 11 countries, land-use mix and sidewalks had the most consistent associations with physical activity. Access to public transit, bicycle facilities, and low-cost recreation facilities had some associations with physical activity, but with less consistency across countries. There was little evidence supporting the associations of residential density and crime-related safety with physical activity in most countries. There is evidence of generalizability for the associations of land use mix, and presence of sidewalks with physical activity. Associations of other neighborhood characteristics with physical activity tended to differ by country. Future studies should include objective measures of neighborhood environments, compare psychometric properties of reports across countries, and use better specified models to further understand the similarities and differences in associations across countries.


Rad50 is dispensable for the maintenance and viability of postmitotic tissues.
The majority of spontaneous chromosome breakage occurs during the process of DNA replication. Homologous recombination is the primary mechanism of repair of such damage, which probably accounts for the fact that it is essential for genome integrity and viability in mammalian cells. The Mre11 complex plays diverse roles in the maintenance of genomic integrity, influencing homologous recombination, checkpoint activation, and telomere maintenance. The complex is essential for cellular viability, but given its myriad influences on genomic integrity, the mechanistic basis for the nonviability of Mre11 complex-deficient cells has not been defined. In this study we generated mice carrying a conditional allele of Rad50 and examined the effects of Rad50 deficiency in proliferative and nonproliferative settings. Depletion of Rad50 in cultured cells caused extensive DNA damage and death within 3 to 5 days of Rad50 deletion. This was not associated with gross telomere dysfunction, suggesting that the telomeric functions of the Mre11 complex are not required for viability. Rad50 was also dispensable for the viability of quiescent liver and postmitotic Purkinje cells of the cerebellum. These findings support the idea that the essential functions of the Mre11 complex are associated with DNA replication and further suggest that homologous recombination is not essential in nondividing cells.


Specific phobia in older adults: evidence from the national epidemiologic survey on alcohol and related conditions.
This study aims to investigate: 1) the association of specific phobia with childhood parental loss and recent stressful life events; 2) the coexistence of specific phobia and major depressive disorders (MDDs); and 3) the impact of specific phobia on medical conditions, obesity, health service utilization, and health-related quality of life. Cross-sectional observational study. The National Epidemiologic Survey on Alcohol and Related Conditions (2001-2002), a national representative survey of the noninstitutionized U.S. household population. The 8,205 respondents aged 65 and above. Specific phobia was assessed using the Alcohol Use Disorder and Associated Disabilities Interview Schedule-Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition version. Demographic characteristics, psychosocial risk factors, psychiatric disorders, health-related quality of life, obesity, medical conditions, and health service utilization were measured. The current and lifetime prevalence of specific phobia were 4.51% and 6.05%, respectively. Multivariate analyses revealed that specific phobia was more common among younger age groups, women, and those who reported stressful life events but less common among foreign-born individuals. In addition, MDD was significantly related to lifetime specific phobia. Specific phobia was also significantly related to a lower health-related quality of life and two medical conditions. Our prevalence rates of specific phobia in the elderly are at the lower end of the ranges identified in the previous studies. The correlation between specific phobia and MDD raises further questions about the nature of specific phobia in the elderly. This study supports the notion that specific phobia has a strong impact on the quality of life in old age.


Conventional and technical diving surveys reveal elevated biomass and differing fish community composition from shallow and upper mesophotic zones of a remote United States coral reef.
The world's coral reefs appear to be in a global decline, yet most previous research on coral reefs has taken place at depths shallower than 30 m. Mesophotic coral ecosystem (depths deeper than ~30 m) studies have revealed extensive, productive habitats and rich communities. Despite recent advances, mesophotic coral ecosystems remain understudied due to challenges with sampling at deeper depths. The few previous studies of mesophotic coral ecosystems have shown variation across locations in depth-specific species composition and assemblage shifts, potentially a response to differences in habitat or light availability/water clarity. This study utilized scuba to examine fish and benthic communities from shallow and upper mesophotic (to 45 m) zones of Flower Garden Banks National Marine Sanctuary (FGBNMS, 28°0'N; 93°50'W) from 2010-2012. Dominant planktivores were ubiquitous in shallow and upper mesophotic habitats, and comparisons with previous shallow research suggest this community distribution has persisted for over 30 years. Planktivores were abundant in shallow low-relief habitats on the periphery of the coral reef, and some of these sites that contained habitat transitioning from high to low relief supported high biomass of benthic predators. These peripheral sites at FGBNMS may be important for the trophic transfer of oceanic energy to the benthic coral reef. Distinct differences between upper mesophotic and shallow communities were also observed. These included greater overall fish (as well as apex predator) biomass in the upper mesophotic, differences in apex predator community composition between depth zones, and greater percent cover of algae, rubble, sand, and sponges in the upper mesophotic. Greater fish biomass in the upper mesophotic and similar fish community composition between depth zones provide preliminary support that upper mesophotic habitats at FGBNMS have the capacity to serve as refugia for the shallow-water reefs. Diving surveys of the upper mesophotic and shallow-water coral reef have revealed valuable information concerning the reef fish community in the northern Gulf of Mexico, with implications for the conservation of apex predators, oceanic coral reefs, and the future management of FGBNMS.


Evaluating phenotype and genotype of drug-resistant strains in herpesviruses.
The isolation of drug-resistant strains of herpesviruses, including Herpes Simplex Virus type I (HSV-1) and type 2 (HSV-2), Varicella-Zoster Virus (VZV), and cytomegalovirus (CMV), has been reported with increasing frequency in immunocompromised patients and is a matter of major concern. Determination of antiviral drug susceptibilities is a prerequisite for the management of drug-resistant herpesvirus infections. Phenotyping studies should be correlated with genotyping, i.e., characterization of the mutations in the target genes. The isolation of drug-resistant virus in the laboratory and the determination of their phenotype and genotype may be useful to clarify the mechanisms of selective drug action. We describe here the procedures used for in vitro selection of drug-resistant herpesvirus mutants and the determination of their patterns of drug-susceptibility. The subcloning of the HSV-1 DNA polymerase gene is described as an example of the methodology followed to determine the mutation(s) in the drug-target viral gene that are associated with the resistant phenotype. To avoid the introduction of mutations by PCR amplification, all subcloning experiments were executed directly on viral DNA. Viral DNA was prepared from each plaque-purified viral strain and a 3.4 kb BamHI fragment containing 87% of the HSV-1 DNA polymerase gene coding region was purified and further digested with SacI; the two resulting fragments were subcloned into pU18 and propagated in Escherichia coli. Plasmid DNA was isolated and the inserts were sequenced using dideoxynucleotide chain termination method with T7 DNA polymerase and Taq DNA polymerase in an automated laser fluorescent DNA sequencer. pUC/M13 reverse, universal primers and oligonucleodite primers based on the wild-type virus sequence were used. The nucleotide sequences of the DNA polymerase genes of the different mutants was then compared with the nucleotide sequence of the wild-type HSV-1 KOS strain.


Biophysical characterization of organelle-based RNA/protein liquid phases using microfluidics.
Living cells contain numerous membrane-less RNA/protein (RNP) bodies that assemble by intracellular liquid-liquid phase separation. The properties of these condensed phase droplets are increasingly recognized as important in their physiological function within living cells, and also through the link to protein aggregation pathologies. However, techniques such as droplet coalescence analysis or standard microrheology do not always enable robust property measurements of model RNA/protein droplets in vitro. Here, we introduce a microfluidic platform that drives protein droplets into a single large phase, which facilitates viscosity measurements using passive microrheology and/or active two-phase flow analysis. We use this technique to study various phase separating proteins from structures including P granules, nucleoli, and Whi3 droplets. In each case, droplets exhibit simple liquid behavior, with shear rate-independent viscosities, over observed timescales. Interestingly, we find that a reported order of magnitude difference between the timescale of Whi3 and LAF-1 droplet coalescence is driven by large differences in surface tension rather than viscosity, with implications for droplet assembly and function. The ability to simultaneously perform active and passive microrheological measurements enables studying the impact of ATP-dependent biological activity on RNP droplets, which is a key area for future research.


The Helminth-Derived Immunomodulator AvCystatin Reduces Virus Enhanced Inflammation by Induction of Regulatory IL-10+ T Cells.
Respiratory Syncytial Virus (RSV) is a major pathogen causing low respiratory tract disease (bronchiolitis), primarily in infants. Helminthic infections may alter host immune responses to both helminths and to unrelated immune triggers. For example, we have previously shown that filarial cystatin (AvCystatin/Av17) ameliorates allergic airway inflammation. However, helminthic immunomodulators have so far not been tested in virus-induced disease. We now report that AvCystatin prevents Th2-based immunopathology in vaccine-enhanced RSV lung inflammation, a murine model for bronchiolitis. AvCystatin ablated eosinophil influx, reducing both weight loss and neutrophil recruitment without impairing anti-viral immune responses. AvCystatin also protected mice from excessive inflammation following primary RSV infection, significantly reducing neutrophil influx and cytokine production in the airways. Interestingly, we found that AvCystatin induced an influx of CD4+ FoxP3+ interleukin-10-producing T cells in the airway and lungs, correlating with immunoprotection, and the corresponding cells could also be induced by adoptive transfer of AvCystatin-primed F4/80+ macrophages. Thus, AvCystatin ameliorates enhanced RSV pathology without increasing susceptibility to, or persistence of, viral infection and warrants further investigation as a possible therapy for virus-induced airway disease.


National Science Foundation-sponsored workshop report. Draft plan for soybean genomics.
Recent efforts to coordinate and define a research strategy for soybean (Glycine max) genomics began with the establishment of a Soybean Genetics Executive Committee, which will serve as a communication focal point between the soybean research community and granting agencies. Secondly, a workshop was held to define a strategy to incorporate existing tools into a framework for advancing soybean genomics research. This workshop identified and ranked research priorities essential to making more informed decisions as to how to proceed with large scale sequencing and other genomics efforts. Most critical among these was the need to finalize a physical map and to obtain a better understanding of genome microstructure. Addressing these research needs will require pilot work on new technologies to demonstrate an ability to discriminate between recently duplicated regions in the soybean genome and pilot projects to analyze an adequate amount of random genome sequence to identify and catalog common repeats. The development of additional markers, reverse genetics tools, and bioinformatics is also necessary. Successful implementation of these goals will require close coordination among various working groups.


Post-heparin plasma lipoprotein lipase and hepatic lipase in normal subjects and in patients with hypertriglyceridaemia: correlations to sex, age and various parameters of triglyceride metabolism.
1. A selective immunochemical method was used to measure post-heparin plasma lipoprotein lipase and hepatic lipase activity in eighty-two normal subjects and in twenty patients with type IIb, IV or V hypertriglyceridaemia. In twenty-six normal subjects the activity of post-heparin plasma lipases was compared with the kinetic parameters of endogenous plasma triglyceride metabolism. 2. The activity of post-heparin lipoprotein lipase was significantly higher in normal females than in males, whereas the activity of hepatic lipase showed an opposite sex ratio. The activity of lipoprotein lipase decreased with age both in males and females, whereas no significant age variation was observed in the activity of hepatic lipase. 3. In normal subjects a highly significant negative correlation was present in both sexes between the activity of post-heparin plasma lipoprotein lipase and fasting serum triglyceride concentration, but not between the activity of post-heparin hepatic lipase and serum triglycerides. 4. The fractional removal rate of endogenous triglycerides was positively correlated to the activity of lipoprotein lipase but not to the activity of hepatic lipase. No relationship was found between the activities of post-heparin plasma lipases and the absolute turnover of serum triglycerides. 5. The mean activity of post-heparin plasma lipo-protein lipase was significantly lower in subjects with hyperprebetalipoproteinaemia than in normal individuals. However, many hypertriglyceridaemic patients had lipoprotein lipase within the normal range and there was no correlation between serum triglyceride concentration and the activity of post-heparin lipases. 6. All three patients with fasting chylomicronaemia had low post-heparin lipoprotein lipase activity. Several subjects with high post-heparin plasma hepatic lipase activity were present in the group with hyperprebetalipoproteinaemia, but the mean value of the hepatic lipase was not significantly different from normal.


Evolution in the Understanding of Autism Spectrum Disorder: Historical Perspective.
The study of the evolution in the diagnosis and treatment of autism is a lesson in the dangers of medical beliefs or doctrines that are not grounded in medical science. The early descriptions of autism suggested that it was the result of childhood psychoses or psychodynamic disturbances of parent-child relationships. This flawed conceptualization of autism spectrum disorders (ASD) gave way to advances in medical science, which have established ASD as a neurobiological disorder of early brain development. There are many genetic, epigenetic, metabolic, hormonal, immunological, neuroanatomical and neurophysiological etiologies of ASD, as well as an array of gastrointestinal and other systemic co-morbid disorders. Thus, ASD are a biologically heterogeneous population with extensive neurodiversity. Early identification and understanding of ASD is crucial; interventions at younger ages are associated with improved outcomes. The advent of understanding the biological sub-phenotypes of ASD, along with targeted medical therapies, coupled with a multimodal therapeutic approach that encompasses behavioral, educational, social, speech, occupational, creative arts, and other forms of therapies has created a new and exciting era for individuals with ASD and their families: "personalized" and "precision" medical care based upon underlying biological sub-phenotypes and clinical profiles. For many individuals and their families dealing with the scourge of autism, their long and frustrating diagnostic journey is beginning to come to an end, with a hope for improved outcomes and quality of life.


Survival and Margin Status in Head and Neck Radiation-Induced Sarcomas and De Novo Sarcomas.
Objective To describe histologic subtypes and oncologic outcomes among patients with radiation-induced and de novo sarcomas of the head and neck. Study Design Retrospective case series with chart review. Setting Tertiary academic center. Subject and Methods In total, 166 adult patients with sarcoma of the head and neck treated from January 1, 1985, to January 1, 2010, were included. Tumors were characterized as radiation induced (15.1%) vs de novo sarcomas (84.9%). Clinical and tumor characteristics were compared. The primary outcomes were overall survival (OS) and disease-specific survival (DSS). Results Radiation-induced sarcomas were more likely to be high grade ( P = .006) and advanced stage ( P = .03). Chondrosarcoma was more common in de novo tumors ( P = .02) while leiomyosarcoma ( P = .01), sarcoma not otherwise specified ( P = .02), and undifferentiated pleomorphic sarcoma ( P < .001) were more common in radiation-induced sarcomas. Radiation-induced sarcomas were associated with statistically significantly worse DSS ( P = .019) and OS ( P = .005) compared with de novo sarcomas, but when only high-grade soft tissue sarcomas were analyzed, neither DSS ( P = .48) nor OS ( P = .29) differed. Margin status was a significant predictor of survival as both R0 and R1 resections correlated with statistically better DSS and OS compared with R2 ( P < .001) resections and patients treated with radiation therapy/chemoradiation therapy alone ( P = .005). Conclusion Radiation-induced sarcomas of the head and neck correlate with worse survival compared with de novo tumors; however, when controlling for tumor grade and resection status, there is no statistically significant difference in observed outcomes.


3D Laser Triangulation for Plant Phenotyping in Challenging Environments.
To increase the understanding of how the plant phenotype is formed by genotype and environmental interactions, simple and robust high-throughput plant phenotyping methods should be developed and considered. This would not only broaden the application range of phenotyping in the plant research community, but also increase the ability for researchers to study plants in their natural environments. By studying plants in their natural environment in high temporal resolution, more knowledge on how multiple stresses interact in defining the plant phenotype could lead to a better understanding of the interaction between plant responses and epigenetic regulation. In the present paper, we evaluate a commercial 3D NIR-laser scanner (PlantEye, Phenospex B.V., Herleen, The Netherlands) to track daily changes in plant growth with high precision in challenging environments. Firstly, we demonstrate that the NIR laser beam of the scanner does not affect plant photosynthetic performance. Secondly, we demonstrate that it is possible to estimate phenotypic variation amongst the growth pattern of ten genotypes of Brassica napus L. (rapeseed), using a simple linear correlation between scanned parameters and destructive growth measurements. Our results demonstrate the high potential of 3D laser triangulation for simple measurements of phenotypic variation in challenging environments and in a high temporal resolution.


Adjacent upstream superhelical writhe influences an Escherichia coli promoter as measured by in vivo strength and in vitro open complex formation.
This work investigates the effect on transcription of superhelical writhe located in the region immediately upstream of the -35 consensus sequence of Escherichia coli promoters. A set of double-stranded oligonucleotides, each with an unique DNA configuration, were designed, synthesized and substituted into an area of naturally occurring right-handed superhelical curvature immediately upstream of the beta-lactamase promoter in plasmid pUC19. All the mutants showed reduced promoter activities in E. coli cells. However, rightward superhelical writhe clearly facilitated transcription when compared with the effect produced by a straight DNA segment. Leftward writhe greatly repressed transcription. A plane curve showed an intermediate effect. This phenomenon was due not only to the difference in the ability of the segment to drive an open complex formation, but also to the difference in the binding affinity of RNA polymerase to the promoter. The positive effect of rightward writhe was also observed in vivo for the promoter of the tetracycline resistance gene of pBR322. The sense and extent of superhelical writhe of a DNA curvature seem to determine its influence on promoter activity.


Protein-templated gold nanoparticle synthesis: protein organization, controlled gold sequestration, and unexpected reaction products.
Emerging applications that exploit the properties of nanoparticles for biotechnology require that the nanoparticles be biocompatible or support biological recognition. These types of particles can be produced through syntheses that involve biologically relevant molecules (proteins or natural extracts, for example). Many of the protocols that rely on these molecules are performed without a clear understanding of the mechanism by which the materials are produced. We have investigated a previously described reaction in which gold nanoparticles are produced from the reaction of chloroauric acid and proteins in solution. We find that modifications to the starting conditions can alter the product from the expected solution-suspended colloids to a product where colloids are formed within a solid, fibrous protein structure. We have interrogated this synthesis, exploiting the change in products to better understand this reaction. We have evaluated the kinetics and products for 7 different proteins over a range of concentrations and temperatures. The key factor that controls the synthetic outcome (colloid or fiber) is the concentration of the protein relative to the gold concentration. We find that the observed fibrous structures are more likely to form at low protein concentrations and when hydrophilic proteins are used. An analysis of the reaction kinetics shows that AuNP formation occurs faster at lower protein (fiber-forming) concentrations than at higher protein (colloid-forming) concentrations. These results contradict traditional expectations for reaction kinetics and protein-fiber formation and are instructive of the manner in which proteins template gold nanoparticle production.


Should more patients continue aspirin therapy perioperatively?: clinical impact of aspirin withdrawal syndrome.
To provide an evidence-based focused review of aspirin use in the perioperative period along with an in-depth discussion of the considerations and risks associated with its preoperative withdrawal. For patients with established cardiovascular disease, taking aspirin is considered a critical therapy. The cessation of aspirin can cause a platelet rebound phenomenon and prothrombotic state leading to major adverse cardiovascular events. Despite the risks of aspirin withdrawal, which are exacerbated during the perioperative period, standard practice has been to stop aspirin before elective surgery for fear of excessive bleeding. Mounting evidence suggests that this practice should be abandoned. We performed a PubMed and Medline literature search using the keywords aspirin, withdrawal, and perioperative. We manually reviewed relevant citations for inclusion. Clinicians should employ a patient-specific strategy for perioperative aspirin management that weighs the risks of stopping aspirin with those associated with its continuation. Most patients, especially those taking aspirin for secondary cardiovascular prevention, should have their aspirin continued throughout the perioperative period. When aspirin is held preoperatively, the aspirin withdrawal syndrome may significantly increase the risk of a major thromboembolic complication. For many operative procedures, the risk of perioperative bleeding while continuing aspirin is minimal, as compared with the concomitant thromboembolic risks associated with aspirin withdrawal. Those cases where aspirin should be stopped include patients undergoing intracranial, middle ear, posterior eye, intramedullary spine, and possibly transurethral prostatectomy surgery.


In Vitro and In Vivo Antitumor and Anti-Inflammatory Capabilities of the Novel GSK3 and CDK9 Inhibitor ABC1183.
Glycogen synthase kinase-3s (GSK3α and GSK3β) are constitutively active protein kinases that target over 100 substrates, incorporate into numerous protein complexes, and regulate such vital cellular functions as proliferation, apoptosis, and inflammation. Cyclin-dependent kinase 9 (CDK9) regulates RNA production as a component of positive transcription elongation factor b and promotes expression of oncogenic and inflammatory genes. Simultaneous inhibition of these signaling nodes is a promising approach for drug discovery, although previous compounds exhibit limited selectivity and clinical efficacy. The novel diaminothiazole ABC1183 is a selective GSK3α/β and CDK9 inhibitor and is growth-inhibitory against a broad panel of cancer cell lines. ABC1183 treatment decreases cell survival through G2/M arrest and modulates oncogenic signaling through changes in GSK3, glycogen synthase, and β-catenin phosphorylation and MCL1 expression. Oral administration, which demonstrates no organ or hematologic toxicity, suppresses tumor growth and inflammation-driven gastrointestinal disease symptoms, owing in part to downregulation of tumor necrosis factor α and interleukin-6 proinflammatory cytokines. Therefore, ABC1183 is strategically poised to effectively mitigate multiple clinically relevant diseases.


Low-Energy Electron Diffraction: Improved experimental methods provide new information on the structure of surfaces of solids.
This discussion of a few preliminary experiments with nickel points out some of the potential uses of low energy electron diffraction in improving our understanding of many types of surface phenomena. The first, and probably the most basic use, is in the study of clean surfaces. As illustrated in this article, the physical properties of the surface layer of atoms may be totally unlike those in the bulk of the crystal. It is necessary to understand such phenomena before a thorough understanding of chemical effects on surfaces can be achieved. The adsorption of gases, oxidation and corrosion, and the formation of epitaxial layers can all be studied in great detail by low energy electron diffraction.


Increased strength of the scapular stabilizer and lumbar muscles after twelve weeks of Pilates training using the Reformer machine: A pilot study.
The aim of this work was to analyze muscle strength in Pilates novices who used the Reformer equipment during twelve training sessions. Twenty-four healthy young female volunteers, who were non-smokers and did not exercise regularly, were split into a control group (mean age 28 ± 4 years and BMI 24.55 ± 3.21 kg/m2) and a training group (mean age 29 ± 4 years and BMI 22.69 ± 2.87 kgm2). The data were checked for normality using the Kolmogorov-Smirnov test, and were then analyzed using the t-test (p < 0.05). After the training sessions, there were statistically significant differences between the groups for the scapular stabilizer muscles (p = 0.0263) and the lumbar muscles (p = 0.0001). For the scapular stabilizers, the initial/final values were 14.69 ± 2.80/14.79 ± 2.89 (control group) and 15.99 ± 3.54/17.44 ± 2.88 (Pilates group). The corresponding values for the lumbar muscles were 53.83 ± 11.66/53.28 ± 11.14 (control group) and 54.75 ± 10.27/64.80 ± 10.20 (Pilates group). After twelve sessions of Pilates with the Reformer equipment, there were improvements in lumbar extensor and scapular stabilizer strength. Several benefits are reported by practitioners of Pilates, but until now, there has been limited scientific evidence of the improvement of strength in the trunk and limbs after application of the technique.


Structural brain development between childhood and adulthood: Convergence across four longitudinal samples.
Longitudinal studies including brain measures acquired through magnetic resonance imaging (MRI) have enabled population models of human brain development, crucial for our understanding of typical development as well as neurodevelopmental disorders. Brain development in the first two decades generally involves early cortical grey matter volume (CGMV) increases followed by decreases, and monotonic increases in cerebral white matter volume (CWMV). However, inconsistencies regarding the precise developmental trajectories call into question the comparability of samples. This issue can be addressed by conducting a comprehensive study across multiple datasets from diverse populations. Here, we present replicable models for gross structural brain development between childhood and adulthood (ages 8-30years) by repeating analyses in four separate longitudinal samples (391 participants; 852 scans). In addition, we address how accounting for global measures of cranial/brain size affect these developmental trajectories. First, we found evidence for continued development of both intracranial volume (ICV) and whole brain volume (WBV) through adolescence, albeit following distinct trajectories. Second, our results indicate that CGMV is at its highest in childhood, decreasing steadily through the second decade with deceleration in the third decade, while CWMV increases until mid-to-late adolescence before decelerating. Importantly, we show that accounting for cranial/brain size affects models of regional brain development, particularly with respect to sex differences. Our results increase confidence in our knowledge of the pattern of brain changes during adolescence, reduce concerns about discrepancies across samples, and suggest some best practices for statistical control of cranial volume and brain size in future studies.


Moderating effects of age, gender and education on the associations of perceived neighborhood environment attributes with accelerometer-based physical activity: The IPEN adult study.
The study's purpose was to examine age, gender, and education as potential moderators of the associations of perceived neighborhood environment variables with accelerometer-based moderate-to-vigorous physical activity (MVPA). Data were from 7273 adults from 16 sites (11 countries) that were part of a coordinated multi-country cross-sectional study. Age moderated the associations of perceived crime safety, and perceiving no major physical barriers to walking, with MVPA: positive associations were only found in older adults. Perceived land use mix-access was linearly (positive) associated with MVPA in men, and curvilinearly in women. Perceived crime safety was related to MVPA only in women. No moderating relationships were found for education. Overall the associations of adults' perceptions of environmental attributes with MVPA were largely independent of the socio-demographic factors examined. These findings are encouraging, suggesting that efforts to optimize the perceived built and social environment may act in a socially-equitable manner to facilitate MVPA.


Genotypic difference in silicon uptake and expression of silicon transporter genes in rice.
Rice (Oryza sativa) is a highly silicon (Si)-accumulating species that shows genotypic differences in Si accumulation. We investigated the physiological and molecular mechanisms involved in the genotypic difference in Si uptake between the japonica var. Nipponbare and the indica var. Kasalath. Both the Si concentration in the shoot and the Si uptake per root dry weight were higher in Nipponbare than in Kasalath grown in either soil or nutrient solution. The Si uptake by a single root was also higher in Nipponbare than in Kasalath. A kinetics study showed that Nipponbare and Kasalath had a similar K(m) value, whereas the V(max) was higher in Nipponbare. The expression of two Si transporter genes (Low silicon rice 1 [Lsi1] and Lsi2) investigated using real-time reverse transcription polymerase chain reaction revealed higher expression of both genes in Nipponbare than in Kasalath. Immunostaining with Lsi1 and Lsi2 antibodies revealed a similar pattern of subcellular localization of these two Si transporters in both varieties; Lsi1 and Lsi2 were localized at the distal and proximal sides, respectively, of both exodermis and endodermis of the roots. These results revealed that the genotypic difference in the Si accumulation results from the difference in abundance of Si transporters in rice roots.


Subinhibitory Concentrations of Disinfectants Promote the Horizontal Transfer of Multidrug Resistance Genes within and across Genera.
The greater abundances of antibiotic resistance genes (ARGs) in point-of-use tap and reclaimed water than that in freshly treated water raise the question whether residual disinfectants in distribution systems facilitate the spread of ARGs. This study investigated three widely used disinfectants (free chlorine, chloramine, and hydrogen peroxide) on promoting ARGs transfer within Escherichia coli strains and across genera from Escherichia coli to Salmonella typhimurium. The results demonstrated that subinhibitory concentrations (lower than minimum inhibitory concentrations [MICs]) of these disinfectants, namely 0.1-1 mg/L Cl2 for free chlorine, 0.1-1 mg/L Cl2 for chloramine, and 0.24-3 mg/L H2O2, led to concentration-dependent increases in intragenera conjugative transfer by 3.4-6.4, 1.9-7.5, and 1.4-5.4 folds compared with controls, respectively. By comparison, the intergenera conjugative frequencies were slightly increased by approximately 1.4-2.3 folds compared with controls. However, exposure to disinfectants concentrations higher than MICs significantly suppressed conjugative transfer. This study provided evidence and insights into possible underlying mechanisms for enhanced conjugative transfer, which involved intracellular reactive oxygen species formation, SOS response, increased cell membrane permeability, and altered expressions of conjugation-relevant genes. The results suggest that certain oxidative chemicals, such as disinfectants, accelerate ARGs transfer and therefore justify motivations in evaluating disinfection alternatives for controlling antibiotic resistance. This study also triggers questions regarding the potential role of environmental chemicals in the global spread of antibiotic resistance.


Inferring branching pathways in genome-scale metabolic networks.
A central problem in computational metabolic modelling is how to find biochemically plausible pathways between metabolites in a metabolic network. Two general, complementary frameworks have been utilized to find metabolic pathways: constraint-based modelling and graph-theoretical path finding approaches. In constraint-based modelling, one aims to find pathways where metabolites are balanced in a pseudo steady-state. Constraint-based methods, such as elementary flux mode analysis, have typically a high computational cost stemming from a large number of steady-state pathways in a typical metabolic network. On the other hand, graph-theoretical approaches avoid the computational complexity of constraint-based methods by solving a simpler problem of finding shortest paths. However, while scaling well with network size, graph-theoretic methods generally tend to return more false positive pathways than constraint-based methods. In this paper, we introduce a computational method, ReTrace, for finding biochemically relevant, branching metabolic pathways in an atom-level representation of metabolic networks. The method finds compact pathways which transfer a high fraction of atoms from source to target metabolites by considering combinations of linear shortest paths. In contrast to current steady-state pathway analysis methods, our method scales up well and is able to operate on genome-scale models. Further, we show that the pathways produced are biochemically meaningful by an example involving the biosynthesis of inosine 5'-monophosphate (IMP). In particular, the method is able to avoid typical problems associated with graph-theoretic approaches such as the need to define side metabolites or pathways not carrying any net carbon flux appearing in results. Finally, we discuss an application involving reconstruction of amino acid pathways of a recently sequenced organism demonstrating how measurement data can be easily incorporated into ReTrace analysis. ReTrace is licensed under GPL and is freely available for academic use at http://www.cs.helsinki.fi/group/sysfys/software/retrace/. ReTrace is a useful method in metabolic path finding tasks, combining some of the best aspects in constraint-based and graph-theoretic methods. It finds use in a multitude of tasks ranging from metabolic engineering to metabolic reconstruction of recently sequenced organisms.


Preliminary investigation of the mechanisms underlying the effects of manipulation: exploration of a multivariate model including spinal stiffness, multifidus recruitment, and clinical findings.
Prospective case series. To examine spinal stiffness in patients with low back pain (LBP) receiving spinal manipulative therapy (SMT), evaluate associations between stiffness characteristics and clinical outcome, and explore a multivariate model of SMT mechanisms as related to effects on stiffness, lumbar multifidus (LM) recruitment, and status on a clinical prediction rule (CPR) for SMT outcomes. Mechanisms underlying the clinical effects of SMT are poorly understood. Many explanations have been proposed, but few studies have related potential mechanisms to clinical outcomes or considered multiple mechanisms concurrently. Patients with LBP were treated with two SMT sessions over 1 week. CPR status was assessed at baseline. Clinical outcome was based on the Oswestry disability index (ODI). Mechanized indentation measures of spinal stiffness and ultrasonic measures of LM recruitment were taken before and after each SMT, and after 1 week. Global and terminal stiffness were calculated. Multivariate regression was used to evaluate the relationship between stiffness variables and percentage ODI improvement. Zero-order correlations among stiffness variables, LM recruitment changes, CPR status, and clinical outcome were examined. A path analysis was used to evaluate a multivariate model of SMT effects. Forty-eight patients (54% women) had complete stiffness data. Significant immediate decreases in global and terminal stiffness occurred post-SMT regardless of outcome. ODI improvement was related to greater immediate decrease in global stiffness (P = 0.025), and less initial terminal stiffness (P = 0.01). Zero-order correlations and path analysis supported a multivariate model suggesting that clinical outcome of SMT is mediated by improvements in LM recruitment and immediate decrease in global stiffness. Initial terminal stiffness and CPR status may relate to outcome though their relationship with LM recruitment. The underlying mechanisms explaining the benefits of SMT appear to be multifactorial. Both spinal stiffness characteristics and LM recruitment changes appear to play a role.


Reasons given by patients for participating, or not, in Phase 1 cancer trials.
Communication with patients contemplating Phase 1 cancer trial participation can be challenging. Controversy exists as to whether they are provided with sufficient information to give genuinely informed consent. We present data examining the reasons patients gave for trial entry. Following discussions with oncologists about Phase 1 trials, participants completed a 19-item study specific 'accept or decline measure' exploring hope, expectations of benefit, altruism, concerns, and general perceptions of the trial information. They also completed 2 standardised questionnaires measuring psychological morbidity and predisposition towards optimism. Forty patients completed the study questionnaires. Patients were generally optimistic with few concerns about the experimental nature of Phase 1 trials. Most 36/40 (90%) consented to trial entry. Fifty-one percent thought the trial was the only treatment option available. The four main reasons for trial entry were: expectation of some medical benefit (21%); trial the best available option (21%); to maintain hope (15%) and to help with research (13%). Only one patient gave altruism as their main reason for trial participation. Patients considering Phase 1 trials may be a self-selected group with optimistic expectations of personal benefit driving trial entry rather than altruism. Achieving genuinely informed consent and avoidance of therapeutic misconceptions in such patients may be difficult.


Who is being deceived? The experimental demands of wearing a backpack.
A growing literature argues that wearing a heavy backpack makes slopes look steeper and distances seem longer (e.g., Proffitt, 2006). To test for effects of experimental demand characteristics in a backpack experiment, we manipulated the experimental demand of the backpack and then used a postexperiment questionnaire to assess participants' beliefs about the purpose of the backpack. For participants in the low-demand condition, an elaborate deception was used to provide an alternative explanation of the requirement to wear a heavy backpack (i.e., that it held EMG equipment). The highest slope judgments were found for those undeceived participants who guessed that the backpack was intended to affect their slope perception and also reported that they thought they were affected by it. When persuaded that the backpack served another purpose, participants' slope estimates were no different from those of participants not wearing a backpack. These findings suggest that backpack effects, and other reported effects of effort on perception, are judgmental biases that result from the social, not physical, demands of the experimental context.