A revised definition of the metabolic syndrome predicts coronary artery disease and ischemic stroke after adjusting for low density lipoprotein cholesterol in a 13-year cohort study of Japanese: the Suita study.
Recently, several major organizations have proposed a unified definition for the metabolic syndrome (MetS), which should be evaluated in multiethnic groups. The effect of Mets on the incidence of cardiovascular disease needs to be assessed after adjusting for serum low density lipoprotein cholesterol (LDLC), a major risk factor for atherosclerotic diseases. This is especially needed to be evaluated in Asian populations with low incidence of coronary artery disease (CAD). We conducted a 13-year prospective study of 4939 Japanese living in an urban area. The MetS was defined using a unified classification that included cut-off points for waist circumference in Asians. The multivariable adjusted hazard ratios (HRs) of MetS for CAD and stroke were calculated using a Cox proportional model adjusted for other potential confounding factors with LDLC. During the follow-up period, there were 155 cases of CAD and 204 of stroke including 118 cerebral infarctions. In participants under 65 years old, the multivariable HRs of MetS for CAD were 1.21 (95% C.I., 0.64-2.28) in men and 4.44 (95% C.I., 1.73-11.4) in women; the HRs for ischemic stroke were 3.24 (95% C.I., 1.55-6.77) in men and 3.99 (95% C.I., 1.34-11.8) in women. In participants aged 65 years old and over, MetS only showed a significant association with CAD in men (HR 1.89, 95% C.I., 1.11-3.21). Serum LDLC was associated with increased risk of CAD in men irrespective of age group; however, it was not associated with CAD in women. There was no association between serum LDLC and ischemic stroke in any group stratified by sex and the age of 65. These results indicate that the new uniform MetS definition is useful for detecting high risk individuals, especially for middle-aged population. However, continuous screening for hypercholesterolemia is necessary to prevent CAD, especially in men, even in Asian countries such as Japan.


The evolution of plasmid-carried antibiotic resistance.
Antibiotic resistance represents a significant public health problem. When resistance genes are mobile, being carried on plasmids or phages, their spread can be greatly accelerated. Plasmids in particular have been implicated in the spread of antibiotic resistance genes. However, the selective pressures which favour plasmid-carried resistance genes have not been fully established. Here we address this issue with mathematical models of plasmid dynamics in response to different antibiotic treatment regimes. We show that transmission of plasmids is a key factor influencing plasmid-borne antibiotic resistance, but the dosage and interval between treatments is also important. Our results also hold when plasmids carrying the resistance gene are in competition with other plasmids that do not carry the resistance gene. By altering the interval between antibiotic treatments, and the dosage of antibiotic, we show that different treatment regimes can select for either plasmid-carried, or chromosome-carried, resistance. Our research addresses the effect of environmental variation on the evolution of plasmid-carried antibiotic resistance.


Cumulative incidence of cancer after solid organ transplantation.
Solid organ transplantation recipients have elevated cancer incidence. Estimates of absolute cancer risk after transplantation can inform prevention and screening. The Transplant Cancer Match Study links the US transplantation registry with 14 state/regional cancer registries. The authors used nonparametric competing risk methods to estimate the cumulative incidence of cancer after transplantation for 2 periods (1987-1999 and 2000-2008). For recipients from 2000 to 2008, the 5-year cumulative incidence, stratified by organ, sex, and age at transplantation, was estimated for 6 preventable or screen-detectable cancers. For comparison, the 5-year cumulative incidence was calculated for the same cancers in the general population at representative ages using Surveillance, Epidemiology, and End Results data. Among 164,156 recipients, 8520 incident cancers were identified. The absolute cancer risk was slightly higher for recipients during the period from 2000 to 2008 than during the period from 1987 to 1999 (5-year cumulative incidence: 4.4% vs. 4.2%; P = .006); this difference arose from the decreasing risk of competing events (5-year cumulative incidence of death, graft failure, or retransplantation: 26.6% vs. 31.9%; P < .001). From 2000 to 2008, the 5-year cumulative incidence of non-Hodgkin lymphoma was highest at extremes of age, especially in thoracic organ recipients (ages 0-34 years: range, 1.74%-3.28%; aged >50 years; range, 0.36%-2.22%). For recipients aged >50 years, the 5-year cumulative incidence was higher for colorectal cancer (range, 0.33%-1.94%) than for the general population at the recommended screening age (aged 50 years: range, 0.25%-0.33%). For recipients aged >50 years, the 5-year cumulative incidence was high for lung cancer among thoracic organ recipients (range, 1.16%-3.87%) and for kidney cancer among kidney recipients (range, 0.53%-0.84%). The 5-year cumulative incidence for prostate cancer and breast cancer was similar or lower in transplantation recipients than at the recommended ages of screening in the general population. Subgroups of transplantation recipients have a high absolute risk of some cancers and may benefit from targeted prevention or screening.


Integral equations formulation of plasmonic transmission lines.
In this paper, a comprehensive integral equation formulation of plasmonic transmission lines is presented for the first time. Such lines are made up of a number of metallic strips with arbitrary shapes and dimensions immersed within a stack of planar dielectric or metallic layers. These lines support a number of propagating modes. Each mode has its own phase constant, attenuation constant, and field distribution. The presented integral equation formulation is solved using the Method of Moments (MoM). It provides all the propagation characteristics of the modes. The new formulation is applied to a number of plasmonic transmission lines, such as: single rectangular strip, horizontally coupled strips, vertically coupled strips, triangular strip, and circular strip. The numerical study is performed in the frequency (wavelength) range of 150-450 THz (0.66-2.0 μm). The results of the proposed technique are compared with those obtained using Lumerical mode solution, and CST. Very good agreement has been observed. The main advantage of the MoM is its intrinsic speed for this type of problem compared to general purpose solvers.


Interaction of calcium ions with lecithin and sphingomyelin monolayers.
Dipalmitoyl lecithin and sphingomyelin monolayers have similar limiting areas, whereas their surface potentials are strikingly different. The double bond at the 4-5 position in sphingomyelin acts as an induced dipole in relation to the surface potentials. This was confirmed by the surface potential of hydrogenated sphingomyelin. The binding of calcium to lecithin and sphingomyelin monllayers resulted in an increase in surface potential. This increase was greater for the dipalmitoyl lecithin monolayer as compared to that for sphingomyelin. It is concluded that the binding of calcium ions to springomyelin monolayers is significantly reduced by the presence of the hydroxyl group at the 3-carbon position of the molecule.


A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.
Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material.


Effects of charging and perpendicular electric field on the properties of silicene and germanene.
Using first-principles density functional theory calculations, we showed that electronic and magnetic properties of bare and Ti adatom adsorbed single-layer silicene and germanene, which are charged or subjected to a perpendicular electric field, can be modified to attain new functionalities. In particular, when subjected to a perpendicular electric field, buckled atoms have the symmetry between their planes broken, opening a gap at the Dirac points. The occupation of 3d orbitals of the adsorbed Ti atom changes with charging or applied electric field, inducing significant changes in magnetic moment. We predict neutral silicene uniformly covered by Ti atoms to become a half-metal at a specific value of coverage and hence allow the transport of electrons in one spin direction, but block the opposite direction. These calculated properties, however, exhibit a dependence on the size of the vacuum spacing between periodically repeating silicene and germanene layers, if they are treated using a plane wave basis set within periodic boundary conditions. We clarified the cause of this spurious dependence and show that it can be eliminated by the use of a local orbital basis set.


Gene therapy: principles and potential.
Gene therapy is a new and provocative means of treating human malignancy. Insight into the mechanisms of growth and growth regulation within cancer cells has offered multiple potential methods for genetic intervention. The application of gene therapy to prostate cancer is in its infancy. The development of both adenoviral and retroviral replication deficient vectors has provided the ability consistently to transfer genes into cancer cells. Although the ideal gene for transfer has not yet been clearly identified, many genes capable of altering the biological behaviour of prostate cancer exist. Selection of the appropriate gene is highly dependent on the desired therapeutic outcome. A gene therapy strategy, whether dependent on ex vivo or in vivo transfection, must ultimately be tailored to meet the specific needs of the disease to be treated. The potential to treat locally confined disease, preventing subsequent metastasis, or widespread metastatic disease exists. The ultimate success of a prostate cancer gene therapy strategy will rely on comprehensive investigation of the biology of the tumour and careful planning of an effective intervention.


Egg Production and Donation: A New Frontier in the Global Landscape of Cross-Border Reproductive Care: Ethical Concerns.
Cross-border reproductive care (CBRC) is a multifaceted phenomenon. It may involve both the movement of patients to undertake assisted reproductive treatment through technologies otherwise denied and the movement of assisted reproduction professionals, egg and sperm donors and surrogates, as well as the importing and exporting of gametes. The reasons for CBRC vary between countries. In this global landscape, the search for donor oocytes is one of the main reasons for patients seeking cross-border reproductive care. The egg market has led to ethical and political concerns about the means of procuring donor oocytes, the possibility of exploiting economically underprivileged women mainly in poor countries, and the issue of the responsibility and accountability of medical doctors and fertility clinics. Ethical concerns relating to international egg donation are discussed with special focus on the issues of compensation/ reimbursement, the health and welfare of women donating eggs, informed consent to donation, the possible conflict of interest for physicians involved in egg donation programmes, and equity in the distribution of economic resources from CBRC. Finally, the need for global solutions to this global issue is underlined.


Avian incubation inhibits growth and diversification of bacterial assemblages on eggs.
Microbial infection is a critical source of mortality for early life stages of oviparous vertebrates, but parental defenses against infection are less well known. Avian incubation has been hypothesized to reduce the risk of trans-shell infection by limiting microbial growth of pathogenic bacteria on eggshells, while enhancing growth of commensal or beneficial bacteria that inhibit or competitively exclude pathogens. We tested this hypothesis by comparing bacterial assemblages on naturally incubated and experimentally unincubated eggs at laying and late incubation using a universal 16S rRNA microarray containing probes for over 8000 bacterial taxa. Before treatment, bacterial assemblages on individual eggs from both treatment groups were dissimilar to one another, as measured by clustering in non-metric dimensional scaling (NMDS) ordination space. After treatment, assemblages of unincubated eggs were similar to one another, but those of incubated eggs were not. Furthermore, assemblages of unincubated eggs were characterized by high abundance of six indicator species while incubated eggs had no indicator species. Bacterial taxon richness remained static on incubated eggs, but increased significantly on unincubated eggs, especially in several families of Gram-negative bacteria. The relative abundance of individual bacterial taxa did not change on incubated eggs, but that of 82 bacterial taxa, including some known to infect the interior of eggs, increased on unincubated eggs. Thus, incubation inhibits all of the relatively few bacteria that grow on eggshells, and does not appear to promote growth of any bacteria.


In vitro antiproliferative effect of vanadium complexes bearing 8-hydroxyquinoline-based ligands - the substituent effect.
This is the first comprehensive study demonstrating the antiproliferative effect of vanadium complexes bearing 8-hydroxyquinoline (quinH) ligands, including the parent and -CH3 (Me), -NO2, -Cl and -I substituted ligands, on HCT116 and A2780 cancer cell lines. To determine the structure-cytotoxicity relationships seven six-coordinate oxovanadium(v) complexes [VO(OMe)(5,7-(Me)2-quin)2] (1), [VO(OMe)(5,7-Cl2-quin)2] (2), [VO(OMe)(5,7-Cl,I-quin)2] (3), [VO(OMe)(5,7-I2-quin)2] (4), [VO(OMe)(5-NO2-quin)2] (5), [VO(OMe)(5-Cl-quin)2] (6), and [VO(OMe)(quin)2] (7) were investigated. The cytotoxicity of 8-hydroxyquinoline oxovanadium(v) complexes is higher in the A2780 cell line (lower IC50) than that observed for the widely used chemotherapeutic agent, cisplatin, while displaying low cytotoxicity for normal human primary fibroblasts. Substituents introduced into the 8-hydroxyquinoline backbone reduced the antiproliferative effect of the vanadium complexes, and the complexes with the ligand substituted only in the 5 position (5 and 6) were more cytotoxic than those with substituents in the 5,7 positions of the quin backbone (1-4). Depending on the substituent type, the cytotoxicity of 1-4 followed the trend: -Cl > -CH3 > -I. Incubation of A2780 cancer cells with IC50 concentrations of complexes 5, 6 and 7 promoted cellular detachment, possibly through membrane destabilization, and triggered apoptosis and necrosis. ROS production might be responsible for the cell death mechanism observed particularly in the A2780 cells exposed to complexes 5 and 6.


Formation of Spherulitic J-Aggregates from the Coassembly of Lithocholic Acid and Cyanine Dye.
Supramolecular aggregates of organic dyes through noncovalent interactions have attracted great interest because they exhibit collective optical and excitonic properties. We report the formation of spherulitic J-aggregates from the coassembly of lithocholic acid (LCA) and 3,3'-diethylthiacarbocyanine iodide (DiSC2(3)) in ammonia solution. Each spherulite contains a core, which serves as a nucleus for the growth of radially oriented J-aggregate fibrils. We find that the growth of spherulitic J-aggregates exhibits a sigmoidal kinetic curve with an initial lag time, followed by a period of rapid growth and a finally slow approach to equilibrium.


SSNMR of biosilica-entrapped enzymes permits an easy assessment of preservation of native conformation in atomic detail.
Bioinspired silica coprecipitates of enzymes find a wide range of applications for analysis and catalysis in industrial and academic research. Here we used SSNMR as a proxy for the 3D structure of enzymes trapped in bioinspired silica. We show that it is easy to assess whether the enzymes retain their native conformation in atomic detail. We thus propose SSNMR as a rapid and reliable tool to analyze this kind of samples at high resolution.


Progress in Animal Models of Pancreatic Ductal Adenocarcinoma.
As a common gastrointestinal tumor, the incidence of pancreatic cancer has been increasing in recent years. The disease shows multi-gene, multi-step complex evolution from occurrence to dissemination. Furthermore, pancreatic cancer has an insidious onset and an extremely poor prognosis, so it is difficult to obtain cinical specimens at different stages of the disease, and it is, therefore, difficult to observe tumorigenesis and tumor development in patients with pancreatic cancer. At present, no standard protocols stipulate clinical treatment of pancreatic cancer, and the benefit rate of new targeted therapies is low. For this reason, a well-established preclinical model of pancreatic cancer must be established to allow further exploration of the occurrence, development, invasion, and metastasis mechanism of pancreatic cancer, as well as to facilitate research into new therapeutic targets. A large number of animal models of pancreatic cancer are currently available, including a cancer cell line-based xenograft, a patient-derived xenograft, several mouse models (including transgenic mice), and organoid models. These models have their own characteristics, but they still cannot perfectly predict the clinical outcome of the new treatment. In this paper, we present the distinctive features of the currently popular pancreatic cancer models, and discuss their preparation methods, clinical relations, scientific purposes and limitations.


Meta-analysis: prognostic value of survivin in patients with hepatocellular carcinoma.
The expression of survivin is a promising prognostic indicator for some carcinomas. However, evidence for the prognostic value of survivin with respect to survival in hepatocellular carcinoma remains controversial. To conduct a systematic review of studies evaluating survivin expression in hepatocellular carcinoma as a prognostic indicator. The relevant literature was searched using PubMed, EMBASE, and Chinese biomedicine databases, and two meta-analyses were performed. One studied the association between survivin expression and the overall survival of patients with hepatocellular carcinoma, whereas the other studied the association between survivin expression and disease-free survival. Studies were pooled, and summary hazard ratios (HRs) were calculated. Subgroup analyses were also conducted. Fourteen eligible studies with a total of 890 patients were included in this study. Two meta-analyses were performed according to the different outcomes by which prognosis was valued. The combined HR of the overall survival studies was 2.33 (95% CI: 1.65-3.31). The combined HR of disease-free survival studies was 2.13 (95% CI: 1.65-2.75). These data appeared to be significant when stratified by detection method, the language of publication, and HR estimate. The heterogeneities were highly significant (I(2)>50%) when subgroup analyses of overall survival rate were conducted, whereas little heterogeneity was found when subgroup analyses of disease-free survival rate were carried out. The positive expression of survivin in the cytoplasm was significantly correlated with poor prognosis in HCC (HR>1). This study showed that survivin expression was correlated with poor prognosis in patients with hepatocellular carcinoma, regardless whether they were assessed by overall survival or disease-free survival.


DART-seq: an antibody-free method for global m6A detection.
N6-methyladenosine (m6A) is a widespread RNA modification that influences nearly every aspect of the messenger RNA lifecycle. Our understanding of m6A has been facilitated by the development of global m6A mapping methods, which use antibodies to immunoprecipitate methylated RNA. However, these methods have several limitations, including high input RNA requirements and cross-reactivity to other RNA modifications. Here, we present DART-seq (deamination adjacent to RNA modification targets), an antibody-free method for detecting m6A sites. In DART-seq, the cytidine deaminase APOBEC1 is fused to the m6A-binding YTH domain. APOBEC1-YTH expression in cells induces C-to-U deamination at sites adjacent to m6A residues, which are detected using standard RNA-seq. DART-seq identifies thousands of m6A sites in cells from as little as 10 ng of total RNA and can detect m6A accumulation in cells over time. Additionally, we use long-read DART-seq to gain insights into m6A distribution along the length of individual transcripts.


Structural variability, topological analysis and photocatalytic properties of neoteric Cd(II) coordination polymers based on semirigid bis(thiazolylbenzimidazole) and different types of carboxylic acid linkers.
A series of novel Cd(II) coordination complexes, formulated as {[Cd(btbb)0.5(p-phda)]·H2O}n (), [Cd(btbb)0.5(oba)]n (), {[Cd2(btbb)(m-bdc)2(H2O)]·2H2O}n (), {[Cd(btbb)0.5(btec)0.5(H2O)]·2H2O}n (), [Cd(btbb)0.5(o-bdc)]n () and {[Cd2(btbb)(bptc)(H2O)]·4H2O}n () (btbb = 1,4-bis(2-(4-thiazolyl)benzimidazol-1-ylmethyl)benzene, H2phda = phenylenediacetic acid, H2oba = 4,4'-oxybis(benzoic acid), m-H2bdc = 1,3-benzenedicarboxylic acid, H4btec = 1,2,4,5-benzenetetracarboxylate, o-H2bdc = 1,2-benzenedicarboxylic acid, H4bptc = 3,3',4,4'-benzophenone tetracarboxylic acid), have been obtained by solvothermal/hydrothermal reactions for the exploration of efficient photocatalytic degradation of organic dye pollutants. Complex features a 6-connected 3D pcu α-Po primitive cubic topology net with the point symbol 4(12)·6(3). Interestingly, complexes , and contain left- and right-handed helical chains (: a 2-fold interpenetrating 3D architecture with {4(12)·6(3)}-pcu topology network; : a (3,6)-connected net with a vertex symbol (4(2)·5(4)·6(6)·7·8(2))(4·6(2)); : a (3,4)-connected 3,4L83 topology net with point symbol (4(2)·6)(4(2)·6(3)·8)). Complex exhibits a (3,4)-connected 3,4T48 topology net with point symbol (8(4)·10(2))(8·10(2)), while complex possesses a (3,5)-connected 3,5L2 topology with the point symbol (4(2)·6)(4(2)·6(7)·8). Furthermore, the photophysical studies indicate that the relatively narrow optical energy gaps of complexes (<2.30 eV) calculated from the diffuse reflectivity spectra reflect their outstanding semiconductive nature. The photocatalytic properties of complexes were studied in detail, and the results demonstrate their good photocatalytic activities in methylene blue (MB) degradation reactions, especially for complexes , and (: 91.4%, : 92.7%, : 86.7%).


PI4P and BLOC-1 remodel endosomal membranes into tubules.
Intracellular trafficking is mediated by transport carriers that originate by membrane remodeling from donor organelles. Tubular carriers contribute to the flux of membrane lipids and proteins to acceptor organelles, but how lipids and proteins impose a tubular geometry on the carriers is incompletely understood. Using imaging approaches on cells and in vitro membrane systems, we show that phosphatidylinositol-4-phosphate (PI4P) and biogenesis of lysosome-related organelles complex 1 (BLOC-1) govern the formation, stability, and functions of recycling endosomal tubules. In vitro, BLOC-1 binds and tubulates negatively charged membranes, including those containing PI4P. In cells, endosomal PI4P production by type II PI4-kinases is needed to form and stabilize BLOC-1-dependent recycling endosomal tubules. Decreased PI4KIIs expression impairs the recycling of endosomal cargoes and the life cycles of intracellular pathogens such as Chlamydia bacteria and influenza virus that exploit the membrane dynamics of recycling endosomes. This study demonstrates how a phospholipid and a protein complex coordinate the remodeling of cellular membranes into functional tubules.


How long are elderly patients followed up with mammography after the diagnosis of breast cancer? A single-centre experience in a developing country.
The effect of breast cancer on elderly South African (SA) patients is not well characterised. The lack of data with regard to disease burden, post-treatment surveillance and breast cancer relapse poses a challenge to providing optimum follow-up care to this group of patients. To assess the effect of breast cancer and adherence to post-treatment surveillance programmes among the local elderly population attending the breast oncology clinics at Addington and Inkosi Albert Luthuli Central hospitals in Durban, KwaZulu-Natal, SA. A retrospective review was undertaken of all patients aged ≥65 years diagnosed with breast cancer during 2007. Hospital records were reviewed for a period of 5 years to ascertain the stage of the disease, treatment received, adherence to post-treatment surveillance mammograms, incidence of new mammographic findings and recurrence, site of recurrence, mode of detection of recurrence, disease-free survival, and overall survival rates at 5 years. In our study, the incidence of breast cancer in the elderly population was 26.7%. A significant percentage of patients (56.3%) were diagnosed at an advanced stage of disease. Of the 46.9% who had received surveillance mammography, only 6.3% received their post-treatment surveillance mammograms on time, in accordance with international recommendations. New mammographic findings were detected in 26.7% of patients during the 5-year follow-up. During the follow-up period, 15.6% of the total number of study patients presented with disease recurrence. Eighty percent of cases of recurrence were detected clinically. The overall survival at 5 years was 65.6%. Our study highlights the significant number of elderly patients with advanced disease at diagnosis, poor compliance with internationally recommended annual post-treatment surveillance mammograms, and the relatively low overall 5-year survival rate compared with that of international studies.


Evaluation of epiduroscopy for detection of vertebral canal and spinal cord lesions in dogs.
OBJECTIVE To evaluate the potential usefulness of epiduroscopy for clinical diagnosis and treatment of vertebral canal and spinal cord lesions in dogs. SAMPLE Cadavers of 6 mixed-breed dogs. PROCEDURES Dogs were positioned in sternal recumbency, and an endoscope was introduced into the lumbosacral epidural space. A fiberscope (diameter, 0.9 mm; length, 30 cm) was used for 3 dogs, and a videoscope (diameter, 2.8 mm; length, 70 cm) was used for the other 3 dogs. Visibility and identities of anatomic structures were recorded, and maneuverability of the endoscopes was assessed. Extent of macroscopic tissue damage was evaluated by manual dissection of the vertebral canal at the end of the procedure. RESULTS Intermittent saline (0.9% NaCl) solution infusion, CO2 insufflation, and endoscope navigation improved visualization by separating the epidural fat from the anatomic structures of interest. Images obtained with the fiberscope were small and of poor quality, making identification of specific structures difficult. Maneuverability of the fiberscope was difficult, and target structures could not be reliably reached or identified. Maneuverability and image quality of the videoscope were superior, and spinal nerve roots, spinal dura mater, epidural fat, and blood vessels could be identified. Subsequent manual dissection of the vertebral canal revealed no gross damage in the spinal cord, nerve roots, or blood vessels. CONCLUSIONS AND CLINICAL RELEVANCE A 2.8-mm videoscope was successfully used to perform epiduroscopy through the lumbosacral space in canine cadavers. Additional refinement and evaluation of the technique in live dogs is necessary before its use can be recommended for clinical situations.


Evolution of biosynthetic pathways: a common ancestor for threonine synthase, threonine dehydratase and D-serine dehydratase.
The Bacillus subtilis genes encoding threonine synthase (thrC) and homoserine kinase (thrB) have been cloned via complementation of Escherichia coli thr mutants. Determination of their nucleotide sequences indicates that the thrC stop codon overlaps the thrB start codon; this genetic organization suggests that the two genes belong to the same operon, as in E. coli. However, the gene order is thrC-thrB in B. subtilis whereas it is thrB-thrC in the thr operon of E. coli. This inversion of the thrC and thrB genes between E. coli and B. subtilis is indicative of a possible independent construction of the thr operon in these two organisms. In other respects, comparison of the predicted amino acid sequences of the B. subtilis and E. coli threonine synthases with that of Saccharomyces cerevisiae threonine dehydratase and that of E. coli D-serine dehydratase revealed extensive homologies between these pyridoxal phosphate-dependent enzymes. This sequence homology, which correlates with similarities in the catalytic mechanisms of these enzymes, indicates that these proteins, catalyzing different reactions in different metabolic pathways, may have evolved from a common ancestor.


STAT3 and SMAD1 signaling in Medaka embryonic stem-like cells and blastula embryos.
The activation and transcriptional activity of signal transducer and activator of transcription 3 (STAT3) is essential for maintaining mouse embryonic stem (ES) cell cultures in an undifferentiated state. However, reports from human and monkey ES-cell culture suggest that STAT3 is dispensable for pluripotency in these systems. At the same time, BMP signaling via smad1 was shown to be able to counteract STAT3 signaling in murine ES-cell cultures, while it influences differentiation in multifaceted ways in other cellular contexts. Hence, the question arises whether the signaling situation found in mice or primates and human ES-cells represent the rule or the exception. With this study, we want to contribute an answer to this question from an evolutionary perspective. Therefore, we analyzed the expression and activation status of the Medaka (Oryzias latipes) STAT3 and SMAD1 in Medaka ES-cell-like cultures and their in vivo counterpart, the Medaka blastula embryo. While SMAD signaling is active in the culture system as well as in blastula embryos, our results indicate that STAT3 is inactive and can thus not be involved in pluripotency control of blastula cells or their derived pluripotent in vitro counterparts. These results suggest that the signaling pathways active in the mouse ES-cell culture system represent the exception, while inactivity of STAT3 is apparently the rule in vertebrate ES-cell cultures.


Radical chemistry of 8-oxo-7,8-dihydro-2'-deoxyadenosine and 8-oxo-7,8-dihydro-2'-deoxyguanosine: a pulse radiolysis study.
The reactions of oxidizing ((•)OH, N(3)(•), and SO(4)(•-)) and reducing (e(aq)(-)) radicals with 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxoG) and 8-oxo-7,8-dihydro-2'-deoxyadenosine (8-oxoA) have been studied by pulse radiolysis to elucidate the initial free radical processes in their oxidation since these oxidized purines are readily oxidized in DNA. The second-order rate constants for the reaction of the (•)OH with 8-oxoA and 8-oxoG were determined to be 4.3 × 10(9) and 4.8 × 10(9) dm(3) mol(-1) s(-1), respectively. Similar values were also obtained with the N(3)(•) radical, the respective values being 8.8 × 10(9) and 3.8 × 10(9) dm(3) mol(-1) s(-1). The transient absorption spectrum following reaction of 8-oxoA with (•)OH is assigned to the C4- and C5-OH adducts which then undergo dehydration (k = 5.1 × 10(3) s(-1)) to give a reducing neutral N-centered radical. 8-oxoG, on the other hand, either reacts by H abstraction from the amino group attached to C2, which undergoes fast tautomerization or the resulting (•)OH adduct which rapidly dehydrates (k > 1.7 × 10(6) s(-1)) to give the species corresponding to the one-electron oxidized product. The transient absorption spectrum measured for the reaction of the N(3)(•) with 8-oxoG is identical to that obtained with the (•)OH at pH 10. The rate determining step is the formation of the radical cation which then rapidly loses a proton to form the neutral radical. It is estimated that 85% of (•)OH adducts are oxidizing while 13% are reducing. The yields of the reducing radicals on reaction of e(aq)(-) with 8-oxoA or 8-oxoG amount to ∼43 and 77% of the respective yield of e(aq)(-), whereas the extent of formation of any oxidizing radicals is ≤2%. In summary, radical intermediates from 8-oxoA or 8-oxoG and their redox potentials have been determined so that 8-oxoA and 8-oxoG, if preformed endogenously, may act as primary sinks for oxidized DNA damage if present close to DNA radicals induced radiolytically.


Utilization of kaolin processing waste for the production of porous ceramic bodies.
The kaolin processing industry generates large amounts of waste in producing countries such as Brazil. The aim of this study was to characterize kaolin processing waste and evaluate its suitability as an alternative ceramic raw material for the production of porous technical ceramic bodies. The waste material was physically and chemically characterized and its thermal behaviour is described. Several formulations were prepared and sintered at different temperatures. The sintered samples were characterized to determine their porosity, water absorption, firing shrinkage and mechanical strength. Fired samples were microstructurally analysed by X-ray diffraction and scanning electron microscopy. The results indicated that the waste consisted of quartz, kaolinite, and mica, and that ceramic formulations containing up to 66% of waste can be used for the production of ceramics with porosities higher than 40% and strength of about 70 MPa.


Immunodeficiency scoring index to predict poor outcomes in hematopoietic cell transplant recipients with RSV infections.
We developed an immunodeficiency scoring index for respiratory syncytial virus (ISI-RSV) infection, based on a cohort of 237 allogeneic hematopoietic cell transplant (allo-HCT) recipients, that can predict the risk of progression to lower respiratory tract infection (LRTI) and RSV-associated mortality. A weighted index was calculated using adjusted hazard ratios for immunodeficiency markers. Based on the ISI-RSV (range, 0-12), patients were stratified into low (0-2), moderate (3-6), and high (7-12) risk groups. A significant trend of increasing incidence of LRTI and RSV-associated mortality was observed as the risk increased from low to moderate to high (P < .001). Patients in the high-risk group had the greatest benefit of ribavirin-based therapy at the upper respiratory tract infection stage and the highest risk for progression to LRTI and death when antiviral therapy was not given (6.5 [95% confidence interval (CI), 1.8-23.6] and 8.1 [95% CI, 1.1-57.6], respectively). The ISI-RSV is designed to stratify allo-HCT recipients with RSV infection into groups according to their risk for progression to LRTI and RSV-associated mortality. Identification of high-risk groups using this index would distinguish patients who would benefit the most from antiviral therapy, mainly with aerosolized ribavirin. The ISI-RSV should be validated in a multi-institutional study.


Schedule shifts, cancer and longevity: good, bad or indifferent?
Prompted by a recent report of the possible carcinogenic effect of shiftwork focusing on the disruption of circadian rhythms, we review studies involving shifts in schedule implemented at varying intervals in unicells, insects and mammals, including humans. Results indicate the desirability to account for a broader-than-circadian view. They also suggest the possibility of optimizing schedule shifts by selecting intervals between consecutive shifts associated with potential side-effects such as an increase in cancer risk. Toward this goal, marker rhythmometry is most desirable. The monitoring of blood pressure and heart rate present the added benefit of assessing cardiovascular disease risks resulting not only from an elevated blood pressure but also from abnormal variability in blood pressure and/or heart rate of normotensive as well as hypertensive subjects.


The EEG effects of THIP (Gaboxadol) on sleep and waking are mediated by the GABA(A)delta-subunit-containing receptors.
THIP (4,5,6,7-tetrahydroisoxazolo-[5,4-c]pyridine-3-ol, Gaboxadol) is a selective gamma-aminobutyric acid (GABA)(A) agonist, acting in vitro with high potency and efficacy at the extrasynaptic GABA(A)delta-containing receptors. THIP was suggested to be a potential hypnotic to treat insomnia, and it is currently in clinical trial. Here we assessed whether the GABA(A)delta-containing receptors mediate in vivo the effect of THIP on sleep and the sleep electroencephalogram (EEG). We performed EEG recordings in a mouse model deficient in the GABA(A)delta-subunit gene (delta(-/-) mice) and in wild-type littermate controls. THIP (4 and 6 mg/kg intraperitoneally) induced an abnormal EEG pattern, resulting in dramatic changes in the waking and non-rapid eye movement (NREM) sleep EEG spectra in wild-type mice. Indeed, a massive increase in EEG power lasting 2-3 h occurred in both the frontal and parietal derivation, especially in frequencies below 6 Hz. All effects were more prominent in the frontal EEG. Furthermore, the highest dose of THIP lengthened REM sleep latency and suppressed REM sleep. In contrast, vigilance states and sleep latencies were not affected in delta(-/-) mice. Moreover, only minor changes were observed in the NREM sleep EEG spectrum after THIP injection in the delta-subunit-deficient mice. The present findings do not indicate a sleep-promoting effect of THIP in mice, which is in accordance with a previous report in this species. Moreover, our results in vivo demonstrate that THIP acts preferentially at GABA(A) receptors containing the delta-subunit.


Vertical distribution of water in the atmosphere of venus: a simple thermochemical explanation.
Several lines of evidence concerning the vertical abundance profile of water in the atmosphere of Venus lead to strikingly unusual distributions (the water vapor abundance decreases sharply in the immediately vicinity of the surface) or to serious conflicts in the profiles (different infrared bands suggest water abundances that are discrepant by a factor of 2.5 to 10). These data sets can be reconciled if (i) water molecules associate with carbon dioxide and sulfur trioxide to make gaseous carbonic acid and sulfuric acid in the lower atmosphere, and (ii) the discrepant 0.94-micrometer water measurements are due to gaseous sulfuric acid, requiring it to be a somewhat stronger absorber than water vapor inthis wavelength region. A mean total water abundance of 50 +/- 20 parts per million and a near-surface free water vapor abundance of 10 +/- 4 parts per million are derived.


Oxidative metabolism of lansoprazole by human liver cytochromes P450.
The aim of this work was to identify the form(s) of human cytochrome P450 (P450) involved in the hepatic biotransformation of lansoprazole to its two main metabolites, i.e., the sulfone and the hydroxy derivative. In liver microsomes, the production of the sulfone of lansoprazole correlated with the level of P450 3A4, cyclosporin oxidase, and the production of the hydroxy derivative, as well as of omeprazole sulfone. The production of hydroxylansoprazole moderately correlated with the level of P450 3A4, cyclosporin oxidase, and (S)-mephenytoin 4'-hydroxylase. The production of the sulfone and of the hydroxy derivative of lansoprazole was significantly inhibited by anti-P450 3A4 antibodies, by cyclosporin and ketoconazole, and by tolbutamide. Anti-P450 2C8 and 2C3 antibodies moderately inhibited the biotransformation of lansoprazole, whereas they completely inhibited (S)-mephenytoin 4'-hydroxylase activity under the same conditions. In primary cultures of human hepatocytes, the biotransformation of lansoprazole and the oxidation of cyclosporin were strongly increased by rifampicin and phenobarbital, whereas (S)-mephenytoin 4'-hydroxylation was not. beta-Naphthoflavone did not induce the formation of the sulfones but stimulated the production of hydroxylansoprazole. Among several forms of cDNA-expressed human P450s, 3A4 generated significant amounts of the sulfones of lansoprazole and omeprazole and 2C18 was active for the production of hydroxylansoprazole but inactive in the 4'-hydroxylation of (S)-mephenytoin. We conclude that P450 3A4 is the major enzyme involved in the production of the sulfone of lansoprazole and that this P450, as well as P450 2C18 and/or another 2C-related form, could contribute to the production of hydroxylansoprazole.


Tapping the Potential of DNA Delivery with Electroporation for Cancer Immunotherapy.
Cancer is a worldwide leading cause of death, and current conventional therapies are limited. The search for alternative preventive or therapeutic solutions is critical if we are going to improve outcomes for patients. The potential for DNA vaccines in the treatment and prevention of cancer has gained great momentum since initial findings almost 2 decades ago that revealed that genetically engineered DNA can elicit an immune response. The combination of adjuvants and an effective delivery method such as electroporation is overcoming past setbacks for naked plasmid DNA (pDNA) as a potential preventive or therapeutic approach to cancer in large animals and humans. In this chapter, we aim to focus on the novel advances in recent years for DNA cancer vaccines, current preclinical data, and the importance of adjuvants and electroporation with emphasis on prostate, melanoma, and cervical cancer.


Defining and ranking effects of individual agents based on survival times of cancer patients treated with combination chemotherapies.
An important problem in oncology is comparing chemotherapy (chemo) agents in terms of their effects on survival or progression-free survival time. When the goal is to evaluate individual agents, a difficulty commonly encountered with observational data is that many patients receive a chemo combination including two or more agents. Because agents given in combination may interact, quantifying the contribution of each individual agent to the combination's overall effect is problematic. Still, if on average combinations including a particular agent confer longer survival, then that agent may be considered superior to agents whose combinations confer shorter survival. Motivated by this idea, we propose a definition of individual agent effects based on observational survival data from patients treated with many different chemo combinations. We define an individual agent effect as the average of the effects of the chemo combinations that include the agent. Similarly, we define the effect of each pair of agents as the average of the effects of the combinations including the pair. Under a Bayesian regression model for survival time in which the chemo combination effects follow a hierarchical structure, these definitions are used as a basis for estimating the posterior effects and ranks of the individual agents, and of all pairs of agents. The methods are illustrated by a data set arising from 224 pediatric brain tumor patients treated with over 27 different chemo combinations involving seven chemo agents.


Metacognition and Reading: Comparing Three Forms of Metacognition in Normally Developing Readers and Readers with Dyslexia.
Metacognition refers to 'cognition about cognition' and includes metacognitive knowledge, strategies and experiences (Efklides, 2008; Flavell, 1979). Research on reading has shown that better readers demonstrate more metacognitive knowledge than poor readers (Baker & Beall, 2009), and that reading ability improves through strategy instruction (Gersten, Fuchs, Williams, & Baker, 2001). The current study is the first to specifically compare the three forms of metacognition in dyslexic (N = 22) versus normally developing readers (N = 22). Participants read two factual texts, with learning outcome measured by a memory task. Metacognitive knowledge and skills were assessed by self-report. Metacognitive experiences were measured by predictions of performance and judgments of learning. Individuals with dyslexia showed insight into their reading problems, but less general knowledge of how to approach text reading. They more often reported lack of available reading strategies, but groups did not differ in the use of deep and surface strategies. Learning outcome and mean ratings of predictions of performance and judgments of learning were lower in dyslexic readers, but not the accuracy with which metacognitive experiences predicted learning. Overall, the results indicate that dyslexic reading and spelling problems are not generally associated with lower levels of metacognitive knowledge, metacognitive strategies or sensitivity to metacognitive experiences in reading situations.


Diagnosis and management of chronic daily headache.
Chronic daily headache (CDH) is a descriptive term that encompasses multiple headache diagnoses and affects approximately 4% of the general adult population. Chronic daily headache results in significant pain and suffering with substantial impact on quality of life, and enormous economic costs to society. Although most patients with primary CDH suffer from chronic migraine or chronic tension-type headache, other primary and secondary headache disorders can also manifest as a CDH syndrome. For CDH management to succeed, secondary headaches need to be ruled out with proper investigations when judged necessary. If the diagnosis of primary CDH is established, diagnosis of the specific CDH subtype is imperative to institute appropriate treatment. The diagnosis and management of distinct CDH entities, chronic migraine, chronic tension-type headache, new daily persistent headache, and hemicrania continua, are the primary forms of CDH and the emphasis of this review. Although, strictly speaking, medication overuse headache is a secondary form of CDH, it is also highlighted in this review given its frequent association with primary CDH.


Comparison of Genetic Variants and Manifestations of OTUD6B-Related Disorder: The First Mexican Case.
The intellectual disability syndrome characterized by seizures and dysmorphic features was initially described in 2017 and was associated with genetic variants in the OTUD6B gene, identified by exome sequencing (ES) in a large cohort. This multisystem disorder primarily affects the central nervous system, the gastrointestinal, and the skeletal systems. In this article, we describe the first Mexican patient diagnosed by ES. The homozygous c.433C>T (p.Arg145*) variant of the OTUD6B gene confirmed this intellectual disability syndrome. In addition to seizures and other more frequently reported manifestations of this condition, this is the third patient with associated hypothyroidism and hypogammaglobulinemia, underscoring the value of screening for these conditions in other patients. The current challenge with this patient is to ensure medical management of his seizures and provide him with a better quality of life. The possibilities of additional therapeutic approaches may increase by understanding the physiopathology of the involved pathways.


Transfer of genetic therapy across human populations: molecular targets for increasing patient coverage in repeat expansion diseases.
Allele-specific gene therapy aims to silence expression of mutant alleles through targeting of disease-linked single-nucleotide polymorphisms (SNPs). However, SNP linkage to disease varies between populations, making such molecular therapies applicable only to a subset of patients. Moreover, not all SNPs have the molecular features necessary for potent gene silencing. Here we provide knowledge to allow the maximisation of patient coverage by building a comprehensive understanding of SNPs ranked according to their predicted suitability toward allele-specific silencing in 14 repeat expansion diseases: amyotrophic lateral sclerosis and frontotemporal dementia, dentatorubral-pallidoluysian atrophy, myotonic dystrophy 1, myotonic dystrophy 2, Huntington's disease and several spinocerebellar ataxias. Our systematic analysis of DNA sequence variation shows that most annotated SNPs are not suitable for potent allele-specific silencing across populations because of suboptimal sequence features and low variability (>97% in HD). We suggest maximising patient coverage by selecting SNPs with high heterozygosity across populations, and preferentially targeting SNPs that lead to purine:purine mismatches in wild-type alleles to obtain potent allele-specific silencing. We therefore provide fundamental knowledge on strategies for optimising patient coverage of therapeutics for microsatellite expansion disorders by linking analysis of population genetic variation to the selection of molecular targets.


Different contributions of chemokine N-terminal features attest to a different ligand binding mode and a bias towards activation of ACKR3/CXCR7 compared with CXCR4 and CXCR3.
Chemokines and their receptors form an intricate interaction and signalling network that plays critical roles in various physiological and pathological cellular processes. The high promiscuity and apparent redundancy of this network makes probing individual chemokine/receptor interactions and functional effects, as well as targeting individual receptor axes for therapeutic applications, challenging. Despite poor sequence identity, the N-terminal regions of chemokines, which play a key role in their activity and selectivity, contain several conserved features. Thus far little is known regarding the molecular basis of their interactions with typical and atypical chemokine receptors or the conservation of their contributions across chemokine-receptor pairs. We used a broad panel of chemokine variants and modified peptides derived from the N-terminal region of chemokines CXCL12, CXCL11 and vCCL2, to compare the contributions of various features to binding and activation of their shared receptors, the two typical, canonical G protein-signalling receptors, CXCR4 and CXCR3, as well as the atypical scavenger receptor CXCR7/ACKR3, which shows exclusively arrestin-dependent activity. We provide molecular insights into the plasticity of the ligand-binding pockets of these receptors, their chemokine binding modes and their activation mechanisms. Although the chemokine N-terminal region is a critical determinant, neither the most proximal residues nor the N-loop are essential for binding and activation of ACKR3, as distinct from binding and activation of CXCR4 and CXCR3. These results suggest a different interaction mechanism between this atypical receptor and its ligands and illustrate its strong propensity to activation.


Informal caregivers and the risk of nursing home admission among individuals enrolled in the program of all-inclusive care for the elderly.
We sought to determine whether participants in the Program of All-Inclusive Care for the Elderly (PACE) with an informal caregiver have a higher or lower risk of nursing home admission than those without caregivers. We performed a secondary data analysis of 3,189 participants aged 55 years or older who were enrolled in 11 PACE programs during the period from June 1, 1990 through June 30, 1998. Cox proportional hazard models determined whether having any caregiver, as well as specific caregiver characteristics, such as either living separately from the enrollee, being over the age of 75 years, providing personal care, not reducing or quitting work to provide care, or not being a spouse, predicted time to nursing home admission. Fewer than half of the participants (49.4%) lived with a caregiver, and 12.4% had no caregiver. Individuals who lived with their caregiver were frailer than either those who lived separately or those without a caregiver. We measured frailty in terms of functional and cognitive status, incontinence, and multiple behavioral disturbances. The presence of a caregiver did not change the risk for institutionalization. None of the caregiver characteristics were associated with a higher risk of nursing home admission. Unlike individuals in the general population, participants in PACE who lack an informal caregiver are not at higher risk of institutionalization. Further research is required to ascertain whether PACE's comprehensive formal services compensate for the lack of informal caregiving in limiting the risk for institutionalization.


Non-pathogenic Neisseria: members of an abundant, multi-habitat, diverse genus.
The genus Neisseria contains the important pathogens Neisseria meningitidis and Neisseria gonorrhoeae. These Gram-negative coccoid bacteria are generally thought to be restricted to humans and inhabit mucosal surfaces in the upper respiratory and genito-urinary tracts. While the meningococcus and gonococcus have been widely studied, far less attention has been paid to other Neisseria species. Here we review current knowledge of the distribution of commensal Neisseria in humans and other hosts. Analysis of the microbiome has revealed that Neisseria is an abundant member of the oropharyngeal flora, and we review its potential impact on health and disease. Neisseria also exhibit remarkable diversity, exhibiting both coccoid and rod-shaped morphologies, as well as environmental strains which are capable of degrading complex organic molecules.


American Society of Hematology 2020 guidelines for management of venous thromboembolism: treatment of deep vein thrombosis and pulmonary embolism.
Venous thromboembolism (VTE), which includes deep vein thrombosis (DVT) and pulmonary embolism (PE), occurs in ∼1 to 2 individuals per 1000 each year, corresponding to ∼300 000 to 600 000 events in the United States annually. These evidence-based guidelines from the American Society of Hematology (ASH) intend to support patients, clinicians, and others in decisions about treatment of VTE. ASH formed a multidisciplinary guideline panel balanced to minimize potential bias from conflicts of interest. The McMaster University GRADE Centre supported the guideline development process, including updating or performing systematic evidence reviews. The panel prioritized clinical questions and outcomes according to their importance for clinicians and adult patients. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to assess evidence and make recommendations, which were subject to public comment. The panel agreed on 28 recommendations for the initial management of VTE, primary treatment, secondary prevention, and treatment of recurrent VTE events. Strong recommendations include the use of thrombolytic therapy for patients with PE and hemodynamic compromise, use of an international normalized ratio (INR) range of 2.0 to 3.0 over a lower INR range for patients with VTE who use a vitamin K antagonist (VKA) for secondary prevention, and use of indefinite anticoagulation for patients with recurrent unprovoked VTE. Conditional recommendations include the preference for home treatment over hospital-based treatment for uncomplicated DVT and PE at low risk for complications and a preference for direct oral anticoagulants over VKA for primary treatment of VTE.


Effects of low-level laser therapy (LLLT) in the development of exercise-induced skeletal muscle fatigue and changes in biochemical markers related to postexercise recovery.
Randomized crossover double-blinded placebo-controlled trial. To investigate if low-level laser therapy (LLLT) can affect biceps muscle performance, fatigue development, and biochemical markers of postexercise recovery. Cell and animal studies have suggested that LLLT can reduce oxidative stress and inflammatory responses in muscle tissue. But it remains uncertain whether these findings can translate into humans in sport and exercise situations. Nine healthy male volleyball players participated in the study. They received either active LLLT (cluster probe with 5 laser diodes; lambda = 810 nm; 200 mW power output; 30 seconds of irradiation, applied in 2 locations over the biceps of the nondominant arm; 60 J of total energy) or placebo LLLT using an identical cluster probe. The intervention or placebo were applied 3 minutes before the performance of exercise. All subjects performed voluntary elbow flexion repetitions with a workload of 75% of their maximal voluntary contraction force until exhaustion. Active LLLT increased the number of repetitions by 14.5% (mean +/- SD, 39.6 +/- 4.3 versus 34.6 +/- 5.6; P = .037) and the elapsed time before exhaustion by 8.0% (P = .034), when compared to the placebo treatment. The biochemical markers also indicated that recovery may be positively affected by LLLT, as indicated by postexercise blood lactate levels (P<.01), creatine kinase activity (P = .017), and C-reactive protein levels (P = .047), showing a faster recovery with LLLT application prior to the exercise. We conclude that pre-exercise irradiation of the biceps with an LLLT dose of 6 J per application location, applied in 2 locations, increased endurance for repeated elbow flexion against resistance and decreased postexercise levels of blood lactate, creatine kinase, and C-reactiveprotein. Performance enhancement, level 1b.


Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila.
Genome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study, we propose the use of array-based comparative genomic hybridization (aCGH) in order to identify orthologous genes with high sequence divergence. Here we discuss experimental design, statistical power, success rate, sources of variation and potential confounding factors. We used a spotted PCR product microarray platform from Drosophila melanogaster to assess sequence divergence on a gene-by-gene basis in three fully sequenced heterologous species (D. sechellia, D. simulans, and D. yakuba). Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence. We found a consistent and linear relationship between hybridization ratio and sequence divergence of the sample to the platform species. At higher levels of sequence divergence (< 92% sequence identity to D. melanogaster) approximately 84% of features had significantly less hybridization to the array in the heterologous species than the platform species, and thus could be identified as "diverged". At lower levels of divergence (>or= 97% identity), only 13% of genes were identified as diverged. While approximately 40% of the variation in hybridization ratio can be accounted for by variation in sequence identity of the heterologous sample relative to D. melanogaster, other individual characteristics of the DNA sequences, such as GC content, also contribute to variation in hybridization ratio, as does technical variation. Here we demonstrate that aCGH can accurately be used as a proxy to estimate genome-wide divergence, thus providing an efficient way to evaluate how evolutionary processes and genomic architecture can shape species diversity in non-model systems. Given the increased number of species for which microarray platforms are available, comparative studies can be conducted for many interesting lineages in order to identify highly diverged genes that may be the target of natural selection.


Green Tea Epigallocatechin-3-Gallate Suppresses Autoimmune Arthritis Through Indoleamine-2,3-Dioxygenase Expressing Dendritic Cells and the Nuclear Factor, Erythroid 2-Like 2 Antioxidant Pathway.
The activity of one of the major catechins in Green Tea, the polyphenol (-)-epigallocatechin-3-gallate (EGCG), has been shown to have a variety of health benefits. Recent studies suggest that EGCG can modulate both the innate and adaptive arms of the immune system. The goal of the current studies was to examine the immunomodulatory effects and mechanisms of action of EGCG on experimental arthritis in mice. EGCG (10 mg/kg) was administered by oral gavage after CIA induction, while control mice were administered phosphate buffered saline (PBS). Disease mechanisms were studied in both groups of mice. Phenotypes were examined using repeated measure analysis of variance (ANOVA) and data from in vitro and ex vivo experiments were analyzed for significance using the Mann-Whitney U test. EGCG treatment ameliorated clinical symptoms and reduced histological scores in arthritic mice. Serum type-II collagen-specific immunoglobulin (Ig) IgG2a antibodies were significantly lower in EGCG-fed mice compared to PBS-treated mice. EGCG significantly suppressed T cell proliferation and relative frequencies of CD4 T cells, CD8 T cells and B cell subsets including marginal zone B cells, T1 and T2 transitional B cells, while increasing the frequency of CD4(+) Foxp3(+) regulatory T cells (Tregs) and indoleamine-2,3-dioxygenase (IDO) expression by CD11b(+) dendritic cells (DC). Splenic CD11b(+) DC from EGCG fed mice induced an increased frequency of Tregs via an IDO-dependent mechanism in in vitro cultures. Importantly, joint homogenates from EGCG-fed mice exhibited significantly increased levels of Nuclear Factor, Erythroid 2-Like 2 (Nrf-2) and Heme oxygenase-1 (HO-1) compared with PBS-fed mice. This is the first report of upregulation of the Nrf-2 antioxidant pathway in EGCG-mediated immunoregulation. EGCG ameliorated experimental arthritis in mice by eliciting IDO-producing DCs, increasing frequencies of T regs and inducing the activation of the Nrf-2 antioxidant pathway. It remains to be established whether EGCG is useful for the prevention and treatment of rheumatoid arthritis and other inflammatory disorders.


The spectrum and outcome of surgical sepsis in Pietermaritzburg, South Africa.
Sepsis is a leading cause of morbidity and mortality worldwide, and the incidence appears to be increasing. In the resource-limited environment in low- and middle-income countries, the management of surgical sepsis (SS) continues to represent a significant portion of the workload for most general surgeons. To describe the spectrum of SS seen at a busy emergency department, and categorise the outcomes. The Pietermaritzburg Metropolitan Trauma Service (PMTS) and Pietermaritzburg Metropolitan Surgical Service (PMSS) in KwaZulu-Natal Province, South Africa (SA), maintain a prospective electronic registry. All patients with features of sepsis among emergency general surgical patients >15 years of age admitted to the PMSS over the period January 2012 - January 2015 were identified. From this cohort, all patients with sepsis that required surgical source control or who had a documented surgical source of sepsis (i.e. had SS) were selected for analysis. Of a total of 6 020 adult surgical patients on the database, a cohort of 1 240 acute surgical patients with features of sepsis were identified, and 675 with SS were then analysed further. Of the 675 patients, 49.2% were male, and the mean age was 46 years (standard deviation (SD) 19); 47.0% presented to the PMSS directly from within the metropolitan area, while the remaining 53.0% were referred from hospitals outside the area. Physiological parameters (mean values) on presentation were as follows: systolic blood pressure 123 mmHg (standard deviation (SD) 23), respiratory rate 22 breaths/min (SD 5.2), heart rate 107 bpm (SD 19), temperature 37°C (SD 2) and white cell count 20 × 109/L (SD 8). Of the patients, 21.6% were known to be HIV-positive, 13.5% (91/675) were negative and 64.9% were of unknown status; 57.6% had intra-abdominal sepsis, 26.1% diabetes-related limb sepsis and the remaining 16.3% soft-tissue infections; 17.5% required intensive care unit admission, with a mean length of stay of 4 days (SD 4), and 30.7% developed complications. In this last group (n=207), a total of 313 morbidities were identified. The overall mortality rate was 12.7% (86/675). The mortality rate for intra-abdominal sepsis was 13.1%, for diabetic foot sepsis 14.2% and for necrotising fasciitis 27.3%. The spectrum of SS in SA is different to that seen in the developed world. Intra-abdominal sepsis is the most common SS and is overwhelmingly caused by acute appendicitis. Diabetic foot infection is a major cause of SS, reflecting the increasing burden of non-communicable chronic diseases in SA.


Migraine and risk of hemorrhagic stroke: a study based on data from general practice.
We investigated the association between hemorrhagic stroke and migraine using data from The Health Improvement Network database. We ascertained 1,797 incident cases of intracerebral hemorrhage (ICH) and 1,340 of subarachnoid hemorrhage (SAH). Density-based sampling was used to select 10,000 controls free from hemorrhagic stroke. Using unconditional logistic regression models, we calculated the risk of hemorrhagic stroke associated with migraine, adjusting for age, sex, calendar year, alcohol, body mass index, hypertension, previous cerebrovascular disease, oral contraceptive use, and health services utilization.The risk (odds ratio [OR]) of ICH among migraineurs was 1.2 (95% confidence interval [CI] 0.9-1.5), and of SAH was (1.2, 95% CI 0.9-1.5). The association with ICH was stronger for migraine diagnosed ≥20 years prior to ICH (OR 1.6, 95% CI 1.0-2.4), but not with SAH (OR 1.1, 95% CI 0.6-2.1). In analyses stratified by migraine type and gender, the OR of ICH in women with migraine with aura was 1.7 (95% CI 0.9-3.4) and the corresponding OR of SAH in women was 1.2 (95% CI 0.6-2.3). No clear increased risk of ICH or SAH was observed in migraineurs.


v-myb and v-ets cooperate for the mitogenic stimulation of primary fibroblasts by avian E26 retrovirus.
By using a series of deletion mutants, we have shown that the stimulation of fibroblast growth by E26 requires the cooperation of the two oncogenes, v-myb and v-ets, fused in the nuclear viral product. Of the two DNA-binding domains, only one must be present to promote anchorage-independent growth, whereas that of v-myb is required to allow growth in low serum medium. Furthermore, the v-ets oncogene comprises multifunctional domains.


Low-frequency and rare variants may contribute to elucidate the genetics of major depressive disorder.
Major depressive disorder (MDD) is a common but serious psychiatric disorder with significant levels of morbidity and mortality. Recent genome-wide association studies (GWAS) on common variants increase our understanding of MDD; however, the underlying genetic basis remains largely unknown. Many studies have been proposed to explore the genetics of complex diseases from a viewpoint of the "missing heritability" by considering low-frequency and rare variants, copy-number variations, and other types of genetic variants. Here we developed a novel computational and statistical strategy to investigate the "missing heritability" of MDD. We applied Hamming distance on common, low-frequency, and rare single-nucleotide polymorphism (SNP) sets to measure genetic distance between two individuals, and then built the multi-dimensional scaling (MDS) pictures. Whole-exome genotyping data from a Los Angeles Mexican-American cohort (203 MDD and 196 controls) and a European-ancestry cohort (473 MDD and 497 controls) were examined using our proposed methodology. MDS plots showed very significant separations between MDD cases and healthy controls for low-frequency SNP set (P value < 2.2e-16) and rare SNP set (P value = 7.681e-12). Our results suggested that low-frequency and rare variants may play more significant roles in the genetics of MDD.


Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics.
Increasingly, large phylogenomic data sets include transcriptomic data from nonmodel organisms. This not only has allowed controversial and unexplored evolutionary relationships in the tree of life to be addressed but also increases the risk of inadvertent inclusion of paralogs in the analysis. Although this may be expected to result in decreased phylogenetic support, it is not clear if it could also drive highly supported artifactual relationships. Many groups, including the hyperdiverse Lissamphibia, are especially susceptible to these issues due to ancient gene duplication events and small numbers of sequenced genomes and because transcriptomes are increasingly applied to resolve historically conflicting taxonomic hypotheses. We tested the potential impact of paralog inclusion on the topologies and timetree estimates of the Lissamphibia using published and de novo sequencing data including 18 amphibian species, from which 2,656 single-copy gene families were identified. A novel paralog filtering approach resulted in four differently curated data sets, which were used for phylogenetic reconstructions using Bayesian inference, maximum likelihood, and quartet-based supertrees. We found that paralogs drive strongly supported conflicting hypotheses within the Lissamphibia (Batrachia and Procera) and older divergence time estimates even within groups where no variation in topology was observed. All investigated methods, except Bayesian inference with the CAT-GTR model, were found to be sensitive to paralogs, but with filtering convergence to the same answer (Batrachia) was observed. This is the first large-scale study to address the impact of orthology selection using transcriptomic data and emphasizes the importance of quality over quantity particularly for understanding relationships of poorly sampled taxa.


Maternal cortisol disproportionately impacts fetal growth in male offspring: evidence from the Philippines.
Lower birth weight (BW) reoccurs across generations, but the intermediate mechanisms remain poorly understood. One potential pathway involves cortisol, which may be elevated in women born small and in turn could lead to fetal growth restriction in offspring. To test this possibility, we evaluated whether BW predicts hypothalamic-pituitary-adrenal (HPA) function in the nonpregnant state in a cohort of young Filipino women, and whether differences in HPA function predict offspring BW. Multiple regression relating maternal BW, adult salivary cortisol profiles and recalled offspring BW (N = 488) among participants of the Cebu Longitudinal Health and Nutrition Survey. Maternal BW related inversely to evening cortisol in adulthood (P < 0.04). Maternal BW and evening cortisol were both stronger predictors of male than of female BW (maternal BW: P < 0.0001 for males; P = 0.07 for females; bedtime cortisol: P = 0.003 for males; P = 0.3 for females). Waking and 30-min postwaking cortisol did not predict offspring BW. Controlling for evening cortisol did not diminish the relationship between maternal and offspring BW in males or females. Being born small predicted higher evening cortisol in adulthood among these young mothers. Lower maternal BW and elevated evening cortisol independently predicted giving birth to lower BW offspring, with effects greatest and only significant among males. We speculate that sex differences in sensitivity to maternal stress hormones could help explain the stronger relationships between BW and cardiovascular disease (CVD) risk factors reported among the males in this and other populations.


Expression of aryl hydrocarbon receptor nuclear translocator enhances cisplatin resistance by upregulating MDR1 expression in cancer cells.
The identification of molecular pathways in cancer cells is important for understanding the cells' underlying biology and for designing effective cancer therapies. We demonstrate that the expression of aryl hydrocarbon receptor nuclear translocator (ARNT) is critical during the development of cisplatin resistance. The reduced expression of ARNT was correlated with cisplatin-induced cell death in drug-sensitive cells. In addition, suppression of ARNT reversed the characteristics of cisplatin-resistant cells, making these cells cisplatin-sensitive, and significantly enhanced caspase-3 activation, DNA fragmentation, and apoptosis. The inhibition of colony formation, regulated by cisplatin, was more significant in ARNT-knockdown cells than in parental cells. In a xenograft analysis of severe combined immunodeficiency mice, cisplatin also efficiently inhibited ARNT-deficient c4 tumors but not ARNT-containing vT2 tumor formation. Furthermore, the downregulation of multidrug resistance 1 (MDR1) expression and retention of drugs in cells caused by suppression of ARNT, resulting in the resensitization of drug-resistant cells to cisplatin, was observed. When overexpressed, ARNT interacted with Sp1 to enhance the expression of MDR1 through Sp1-binding sites on the MDR1 promoter, resulting in a reversal of the effect of cisplatin on cell death. In addition, ARNT-induced MDR1 expression was inhibited in Sp1-knockdown cells. These results reveal previously unrecognized, multifaceted functions of ARNT in establishing the drug-resistant properties of cancer cells by the upregulation of MDR1, highlighting ARNT's potential as a therapeutic target in an important subset of cancers.


Colonoscopy vs. Fecal Immunochemical Test in Reducing Mortality From Colorectal Cancer (CONFIRM): Rationale for Study Design.
Colorectal cancer (CRC) is preventable through screening, with colonoscopy and fecal occult blood testing comprising the two most commonly used screening tests. Given the differences in complexity, risk, and cost, it is important to understand these tests' comparative effectiveness. The CONFIRM Study is a large, pragmatic, multicenter, randomized, parallel group trial to compare screening with colonoscopy vs. the annual fecal immunochemical test (FIT) in 50,000 average risk individuals. CONFIRM examines whether screening colonoscopy will be superior to a FIT-based screening program in the prevention of CRC mortality measured over 10 years. Eligible individuals 50-75 years of age and due for CRC screening are recruited from 46 Veterans Affairs (VA) medical centers. Participants are randomized to either colonoscopy or annual FIT. Results of colonoscopy are managed as per usual care and study participants are assessed for complications. Participants testing FIT positive are referred for colonoscopy. Participants are surveyed annually to determine if they have undergone colonoscopy or been diagnosed with CRC. The primary endpoint is CRC mortality. The secondary endpoints are (1) CRC incidence (2) complications of screening colonoscopy, and (3) the association between colonoscopists' characteristics and neoplasia detection, complications and post-colonoscopy CRC. CONFIRM leverages several key characteristics of the VA's integrated healthcare system, including a shared medical record with national databases, electronic CRC screening reminders, and a robust national research infrastructure with experience in conducting large-scale clinical trials. When completed, CONFIRM will be the largest intervention trial conducted within the VA (ClinicalTrials.gov identifier: NCT01239082).


Interplay of overweight and insulin resistance on hypertension development.
Obesity and hypertension are associated, possibly through causal pathways involving insulin resistance and metabolic derangements. We aimed to investigate in a whites sample if overweight or obese persons without insulin resistance are at risk of developing hypertension or blood pressure progression. In a meta-analysis, using multivariable-adjusted mixed-effects logistic regression models, we investigated the risks of hypertension development and blood pressure progression by combinations of relative weight classes and presence or absence of insulin resistance (defined as highest vs. lower three quartiles using the homeostatic model assessment method) in the Uppsala Longitudinal Study of Adult Men (n = 2322) and the Prospective Investigation of the Vasculature in Uppsala Seniors studies (n = 1066). These two samples, consisting mainly of middle-aged and elderly men, provided 1846 observations for the development of hypertension in normotensive individuals and 4223 observations for progressing to a higher blood pressure stage. During a median of 10 years of follow-up, 884 (47.9%) developed hypertension and 1639 (38.8%) progressed to a higher blood pressure stage. Overweight or obese persons without insulin resistance had an increased risk of hypertension development [odds ratio (OR) 1.46, 95% confidence interval 1.14-1.88] and blood pressure progression (OR 1.32, 1.10-1.59) compared with normal-weight persons without insulin resistance. According to this study, being overweight or obese without insulin resistance increases the risk of hypertension and blood pressure progression. This adds to the evidence that overweight and obesity may be harmful per se, and that overweight and obesity without glucometabolic derangements are not benign conditions.


Translating policies into practice: a framework to prevent childhood obesity in afterschool programs.
Afterschool programs (3-6 p.m.) are positioned to play a critical role in combating childhood obesity. To this end, state and national organizations have developed policies related to promoting physical activity and guiding the nutritional quality of snacks served in afterschool programs. No conceptual frameworks, however, are available that describe the process of how afterschool programs will translate such policies into daily practice to reach eventual outcomes. Drawing from complex systems theory, this article describes the development of a framework that identifies critical modifiable levers within afterschool programs that can be altered and/or strengthened to reach policy goals. These include the policy environment at the national, state, and local levels; individual site, afterschool program leader, staff, and child characteristics; and existing outside organizational partnerships. Use of this framework and recognition of its constituent elements have the potential to lead to the successful and sustainable adoption and implementation of physical activity and nutrition policies in afterschool programs nationwide.


Retrospective medical record review of an osteopathic manipulative medicine hospital consultation service.
In the first half of the 20th century, nearly all osteopathic physicians used osteopathic manipulative medicine (OMM) in the care of hospitalized patients. Over the past few decades, however, inpatient OMM care has declined and is more commonly provided by OMM specialists. To retrospectively evaluate the details of a specialty-level OMM inpatient consultation service. Inpatient OMM consultations that took place at Northeast Regional Medical Center in Kirksville, Missouri, between July 1998 and March 2008 were identified from billing records. Consultations were reviewed for demographic information, admission location, postoperative status, intensive care unit and mechanical ventilation usage, admission and discharge diagnoses, consultation reasons and final diagnoses, areas of somatic dysfunction treated and types of osteopathic manipulative treatment (OMT) techniques used, and hospital length of stay (LOS). A total of 1509 OMM consultations were identified (580 for male patients [38%]; 929 for female patients [62%]; mean [SD] age, 54 [31] years [range, 0-99 years]), representing 11% of all inpatient consultations. Of these, 1372 consultations (91%) were initiated in the inpatient acute care facility, 87 (6%) in the inpatient acute rehabilitation facility, and 50 (3%) in the skilled nursing facility. Further, 265 consultations (18%) were for postoperative patients, 187 (12%) were for patients in the intensive care unit, and 54 (4%) were for patients receiving mechanical ventilation at the time of the consultation. The most common admission diagnoses were hypertension, routine newborn care, lower respiratory infection, chronic obstructive pulmonary disease, and gastrointestinal symptoms. The most common reasons for OMM consultation were chest/rib pain, spinal pain, lower respiratory infection (adjunctive treatment), cranial asymmetry, and infant feeding disorder. The most common types of OMT techniques used were myofascial release, balanced ligamentous tension, muscle energy, soft tissue, and inhibition. The mean (SD) LOS was 5.7 (3.3) days (range, 0-48 days), while the mean (SD) number of days the patient received OMT was 3.1 (2.2) days. Medical records reviewed in the current study revealed that OMM consultations were ordered primarily for musculoskeletal complaints, respiratory problems (adjunctive treatment), and newborn care. A variety of OMT techniques were used. Further retrospective study is warranted to determine if OMM had an effect on LOS.


Processing strawberries to different products alters contents of vitamin C, total phenolics, total anthocyanins, and antioxidant capacity.
Strawberries were processed to juice, nectar, wine, and puree. For investigation of the antioxidant capacity as well as the contents of ascorbic acid, total phenolics and total anthocyanins, samples were taken after different stages of production to determine the effects of processing. The content of vitamin C was measured spectrophotometrically. The total phenolic content was analyzed by using the Folin-Ciocalteu method, and the amount of total anthocyanins was determined by using the pH-differential method. Two different methods-the trolox equivalent antioxidant capacity assay and the ferric reducing antioxidant power test-were used to determine the hydrophilic antioxidant capacity. This study showed the decrease of all investigated parameters within processing strawberries to different products. The content of ascorbic acid decreased with production time and processing steps, especially during heat treatment. The investigations on total phenolics in strawberry products proved fining to be a mild method to clarify berry juices and wines without removing high amounts of total phenolics. Fermentation did not lead to heavy losses of total phenolics, probably due to polymerization and condensation of monomer phenolics such as anthocyanins. Total anthocyanins and the hydrophilic antioxidant capacity decreased while using high temperatures. Anthocyanins also decreased considerably during the processing of wines, mainly caused by fermentation and pasteurization.


The role of heterogeneous environment and docetaxel gradient in the emergence of polyploid, mesenchymal and resistant prostate cancer cells.
The ability of a population of PC3 prostate epithelial cancer cells to become resistant to docetaxel therapy and progress to a mesenchymal state remains a fundamental problem. The progression towards resistance is difficult to directly study in heterogeneous ecological environments such as tumors. In this work, we use a micro-fabricated "evolution accelerator" environment to create a complex heterogeneous yet controllable in-vitro environment with a spatially-varying drug concentration. With such a structure we observe the rapid emergence of a surprisingly large number of polyploid giant cancer cells (PGCCs) in regions of very high drug concentration, which does not occur in conventional cell culture of uniform concentration. This emergence of PGCCs in a high drug environment is due to migration of diploid epithelial cells from regions of low drug concentration, where they proliferate, to regions of high drug concentration, where they rapidly convert to PGCCs. Such a mechanism can only occur in spatially-varying rather than homogeneous environments. Further, PGCCs exhibit increased expression of the mesenchymal marker ZEB1 in the same high-drug regions where they are formed, suggesting the possible induction of an epithelial to mesenchymal transition (EMT) in these cells. This is consistent with prior work suggesting the PGCC cells are mediators of resistance in response to chemotherapeutic stress. Taken together, this work shows the key role of spatial heterogeneity and the migration of proliferative diploid cells to form PGCCs as a survival strategy for the cancer population, with implications for new therapies.


Long-acting injectable antipsychotics: an underutilized treatment option.
In this issue, Kane and colleagues report on the efficacy of aripiprazole long-acting injection (LAI) in the treatment of an acute episode of schizophrenia. At 10 weeks of treatment, both psychopathology and functioning were improved in patients treated with aripiprazole compared to placebo, with an acceptable tolerability and safety profile. The outcomes suggest that aripiprazole long-acting is a viable treatment option for patients experiencing an acute episode of schizophrenia.


Trash to treasure Retcam.
Digital fundus imaging is being used in diagnosis, documentation, and sharing of many retinal diseases and hence forms an essential part of ophthalmology. The use of smartphones for the same has been ever increasing. There is a need for simpler devices to couple the 20D lens and smartphone so as to take fundus photographs which can help in fundus documentation. This article describes a simple inexpensive technique of preparing a smartphone fundus photography device (Trash To Treasure (T3) Retcam) from the used materials in the clinics within minutes. This article will also review the optical principles of the T3 Retcam and describe the step-by-step method to record good-quality retinal image/videos. This inexpensive device is made by recycling and modifying the plastic hand sanitizer bottle in the clinics/hospitals which can be used for documenting, diagnosing, screening, and academic purposes.


Protein microarrays for personalized medicine.
Over the last 10 years, DNA microarrays have achieved a robust analytical performance, enabling their use for analyzing the whole transcriptome or for screening thousands of single-nucleotide polymorphisms in a single experiment. DNA microarrays allow scientists to correlate gene expression signatures with disease progression, to screen for disease-specific mutations, and to treat patients according to their individual genetic profiles; however, the real key is proteins and their manifold functions. It is necessary to achieve a greater understanding of not only protein function and abundance but also their role in the development of diseases. Protein concentrations have been shown to reflect the physiological and pathologic state of an organ, tissue, or cells far more directly than DNA, and proteins can be profiled effectively with protein microarrays, which require only a small amount of sample material. Protein microarrays have become well-established tools in basic and applied research, and the first products have already entered the in vitro diagnostics market. This review focuses on protein microarray applications for biomarker discovery and validation, disease diagnosis, and use within the area of personalized medicine. Protein microarrays have proved to be reliable research tools in screening for a multitude of parameters with only a minimal quantity of sample and have enormous potential in applications for diagnostic and personalized medicine.


The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.
DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (>94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium's lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.


ATP-sensitive K+ channels in pancreatic beta-cells. Spare-channel hypothesis.
Since their discovery in pancreatic beta-cells, ATP-sensitive K+ channels in the cell membrane have been thought to mediate glucose-induced beta-cell depolarization, which is required for triggering the voltage-dependent Ca2+ uptake subserving insulin release. The theory is that metabolism of glucose (and other fuel molecules) increases intracellular ATP or possibly other metabolites that diffuse to the membrane and inhibit the opening of ATP-sensitive K+ channels. This slows the efflux of positively charged K+ and depolarizes the cell. A recurrent source of confusion regarding this idea stems from the early observation that these channels are so exquisitely sensitive to intracellular ATP that channel opening is predicted to be approximately 99% inhibited under physiological conditions. To account for this apparent discrepancy, various mechanisms have been proposed that might render the channels less sensitive to intracellular ATP. We use a simple mathematical model to demonstrate that there is no major discrepancy and that, in fact, given the electrophysiological mechanisms existing in the beta-cell, the extreme sensitivity of the channels to ATP is appropriate and even mandatory for their physiological function.


Preclinical Efficacy for AKT Targeting in Clear Cell Carcinoma of the Ovary.
The aim of this study was to determine the role of AKT as a therapeutic target in ovarian clear cell carcinoma (CCC), an aggressive, chemoresistant histologic subtype of ovarian cancer. AKT activation was assessed by immunohistochemistry (IHC) using human tissue microarrays of primary ovarian cancers, composed of both CCC and serous adenocarcinoma (SAC). The growth-inhibitory effect of AKT-specific targeting by the small-molecule inhibitor, perifosine, was examined using ovarian CCC cell lines in vitro and in vivo. Finally, the activity of perifosine was examined using in CCC-derived tumors that had acquired resistance to anti-VEGF or chemotherapeutics such as bevacizumab or cisplatin, respectively. Interestingly, AKT was frequently activated both in early-stage and advanced-stage CCCs. Treatment of CCC cells with perifosine attenuated the activity of AKT-mTORC1 signaling, inhibited proliferation, and induced apoptosis. The effect of perifosine was more profound under conditions of high AKT activity compared with low AKT activity. Increased AKT activation and enhanced sensitivity to perifosine were observed in the context of cisplatin-resistant CCC. Treatment with perifosine concurrently with cisplatin significantly enhanced the antitumor effect of cisplatin. Moreover, perifosine showed significant antitumor activity in CCC-derived tumors that had acquired resistance to bevacizumab or cisplatin. Collectively, these data reveal that AKT is frequently activated in ovarian CCCs and is a promising therapeutic target in aggressive forms of ovarian cancer. AKT-targeted therapy has value in a first-line setting as well as a second-line treatment for recurrent disease developing after platinum-based chemotherapy or bevacizumab treatment.


Childbirths and risk of female predominant and other autoimmune diseases in a population-based Danish cohort.
To evaluate the possible biological role of pregnancy on the risk of autoimmune diseases we assessed associations between reproductive history and subsequent risk of autoimmune diseases characterized by female predominance and other autoimmune diseases. Our study cohort comprised 4.6 million Danes born since 1935 for whom a complete record of childbirths was available. Cohort members were followed for hospital contacts for 31 autoimmune diseases from 1982 to 2008. Female predominant autoimmune diseases were those with a female:male sex ratio >2:1. Ratios of first hospitalization rates were calculated using Poisson regression, adjusting for potential confounding by age, birth cohort, calendar period and marital status. During 45.5 million person-years of follow-up 102,260 women were hospitalized with one or more autoimmune diseases. Overall, compared with childless women, women with children were at a relative risk of 1.04 (1.02-1.06) for any autoimmune diseases, 1.11 (1.08-1.14) for female predominant and 0.97 (0.95-1.00) for other autoimmune diseases. Possibly biologically related associations with parity were found for Hashimoto thyroiditis (1.11; 1.00-1.24), Graves' disease (1.19; 1.14-1.24), erythema nodosum (1.15; 1.01-1.32), psoriasis (1.08; 1.01-1.15), sarcoidosis (1.17; 1.06-1.28) and systemic lupus erythematosus (0.83; 0.74-0.93). Especially the one-year postpartum period was associated with an increased risk of Hashimoto thyroiditis, Graves' disease and sarcoidosis. Overall, parity was associated with an 11% increased risk of female predominant autoimmune diseases. Pregnancies resulting in liveborn children therefore seem to contribute only little to the general female predominance in autoimmune diseases. However, for a number of autoimmune diseases; especially autoimmune thyroid diseases, erythema nodosum and sarcoidosis parity might somehow be involved in disease development.


A kingdom-specific protein domain HMM library for improved annotation of fungal genomes.
Pfam is a general-purpose database of protein domain alignments and profile Hidden Markov Models (HMMs), which is very popular for the annotation of sequence data produced by genome sequencing projects. Pfam provides models that are often very general in terms of the taxa that they cover and it has previously been suggested that such general models may lack some of the specificity or selectivity that would be provided by kingdom-specific models. Here we present a general approach to create domain libraries of HMMs for sub-taxa of a kingdom. Taking fungal species as an example, we construct a domain library of HMMs (called Fungal Pfam or FPfam) using sequences from 30 genomes, consisting of 24 species from the ascomycetes group and two basidiomycetes, Ustilago maydis, a fungal pathogen of maize, and the white rot fungus Phanerochaete chrysosporium. In addition, we include the Microsporidion Encephalitozoon cuniculi, an obligate intracellular parasite, and two non-fungal species, the oomycetes Phytophthora sojae and Phytophthora ramorum, both plant pathogens. We evaluate the performance in terms of coverage against the original 30 genomes used in training FPfam and against five more recently sequenced fungal genomes that can be considered as an independent test set. We show that kingdom-specific models such as FPfam can find instances of both novel and well characterized domains, increases overall coverage and detects more domains per sequence with typically higher bitscores than Pfam for the same domain families. An evaluation of the effect of changing E-values on the coverage shows that the performance of FPfam is consistent over the range of E-values applied. Kingdom-specific models are shown to provide improved coverage. However, as the models become more specific, some sequences found by Pfam may be missed by the models in FPfam and some of the families represented in the test set are not present in FPfam. Therefore, we recommend that both general and specific libraries are used together for annotation and we find that a significant improvement in coverage is achieved by using both Pfam and FPfam.


Non-hexagonal Large-Pitch Fibers for enhanced mode discrimination.
Photonic-Crystal Fibers (PCF) are among the most promising concepts to achieve large mode field areas suitable for the reduction of nonlinearities in fibers. Differential mode propagation loss is the cornerstone of effective single-mode behavior in passive and core-pumped active PCFs. In this work, we explore non-hexagonal PCF designs with increased mode discrimination in comparison to the classical hexagonal PCF designs. It is shown that a pentagonal design can increase the mode discrimination and, simultaneously, also improve the beam quality of Large-Pitch Fibers with mode field diameters well beyond 100 µm.