An assessment of gene prediction accuracy in large DNA sequences.
One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of both methods and accuracy evaluation measures, most of the sequence sets in which the programs are tested are short genomic sequences, and there is concern that these accuracy measures may not extrapolate well to larger, more challenging data sets. Given the absence of experimentally verified large genomic data sets, we constructed a semiartificial test set comprising a number of short single-gene genomic sequences with randomly generated intergenic regions. This test set, which should still present an easier problem than real human genomic sequence, mimics the approximately 200kb long BACs being sequenced. In our experiments with these longer genomic sequences, the accuracy of GENSCAN, one of the most accurate ab initio gene prediction programs, dropped significantly, although its sensitivity remained high. Conversely, the accuracy of similarity-based programs, such as GENEWISE, PROCRUSTES, and BLASTX was not affected significantly by the presence of random intergenic sequence, but depended on the strength of the similarity to the protein homolog. As expected, the accuracy dropped if the models were built using more distant homologs, and we were able to quantitatively estimate this decline. However, the specificities of these techniques are still rather good even when the similarity is weak, which is a desirable characteristic for driving expensive follow-up experiments. Our experiments suggest that though gene prediction will improve with every new protein that is discovered and through improvements in the current set of tools, we still have a long way to go before we can decipher the precise exonic structure of every gene in the human genome using purely computational methodology.


Electromagnetic surface modes in a magnetized quantum electron-hole plasma.
The propagation of surface electromagnetic waves along a uniform magnetic field is studied in a quantum electron-hole semiconductor plasma. A forward propagating mode is found by including the effect of quantum tunneling. In the classical limit (ħ→0), one of the low-frequency modes found is similar to an experimentally observed one in n-type InSb at room temperature. The surface modes are shown to be significantly modified in the case of high-conductivity semiconductor plasmas where electrons and holes may be degenerate. The effects of the external magnetic field and the quantum tunneling on the surface wave modes are discussed.


Expression of multiple forms of cytochrome P450 mRNAs in primary cultures of rat hepatocytes maintained on matrigel.
Freshly isolated rat hepatocytes rapidly lose their cytochrome P450 (P450) proteins and mRNAs, with no evidence of subsequent restoration, after placement into traditional systems of primary culture on type I collagen. We examined the patterns of expression of 10 constitutively expressed P450 mRNAs in rat hepatocytes cultured for up to 5 days on a matrix of Matrigel, a reconstituted basement membrane that allows inducible expression of some P450s, and compared these patterns with those seen in hepatocytes cultured on type I collagen (Vitrogen). mRNA for each P450 was detected on Northern blots in samples prepared from freshly isolated male rat hepatocytes, and the amount of each mRNA decreased markedly during the first 2 days of culture in cells maintained on either matrix (decreases of 53-97% on Matrigel and 62 to > 99% on Vitrogen), in contrast to the level of NADPH-P450 oxidoreductase mRNA, which increased during this interval. On subsequent days, hepatocytes cultured on Matrigel expressed the individual P450 mRNAs in one of the following four patterns. 1) P450 1A2, 2A2, 2E1, and 3A1/2 mRNAs remained low throughout the 5-day culture period. 2) 2A1 mRNA increased between days 2 and 4 but then decreased on day 5. 3) 2B1/2, 2C6, 2C7, and 4A1 mRNAs increased continually between days 2 and 5, 4) The total mRNAs detected with a 2D probe remained at constant levels between culture days 2 and 5. Our results show that rat hepatocytes cultured on Matrigel in serum-free medium spontaneously reexpress the mRNAs for several constitutive P450s in form-specific patterns, and they suggest that the Matrigel culture system will be useful for identifying the underlying regulatory mechanisms.


Community-based environmental protection in the Brazilian Amazon: Recent history, legal landmarks and expansion across protected areas.
Globally, community-based initiatives are effective in protecting ecosystems and the species within them. In this paper, we analyze the emergence and large-scale expansion of a community-based environmental protection system (the Voluntary Environmental Agents Program - VEA Program) in the Brazilian Amazon and identify factors that have determined its success since its inception, 25 years ago. Collective actions to protect the environment in the region have been undertaken by local people for at least 40 years, before their legal regulation in 2001 by the federal government of Brazil, and by the Amazonas state in 2007. The system is based on territorial surveillance and monitoring, and on guidelines for the better use of the territory and its natural resources. Between 1995 and 2020, the VEA Program expanded into the two protected areas where it was first implemented reaching approximately 9 thousand km2 of area protected by the system. The number of people participating also grew in this period by around 2050%, as did the participation of women, which grew by 5600%. The system was replicated in 37 protected areas in central Amazonia, and currently covers almost 200 thousand km2 of Amazon rainforest. From our analyses we unveil four main factors that may have allowed the VEA Program to expand and flourish: (a) the communities' previous demand for an effective control system, (b) its legal formalization and regulation, (c) the support from external institutions, and (d) the consolidation of community-based management programs to fund actions. These factors shall be further investigated as to confirm their critical role in the success of the VEA Program. We demonstrate that this community-based environmental protection system has established itself as a legitimate form of social control, and as a mechanism of socio-environmental governance in the areas in which it operates. By allowing more effective protection of territories, it generates consensus amongst users for the adequate management of natural resources, especially in contexts where government's actions are absent or inefficient. We claim that this system can be replicated in various parts of the world.


Towards a synthesis of frameworks in nutritional ecology: interacting effects of protein, carbohydrate and phosphorus on field cricket fitness.
Phosphorus has been identified as an important determinant of nutrition-related biological variation. The macronutrients protein (P) and carbohydrates (C), both alone and interactively, are known to affect animal performance. No study, however, has investigated the importance of phosphorus relative to dietary protein or carbohydrates, or the interactive effects of phosphorus with these macronutrients, on fitness-related traits in animals. We used a nutritional geometry framework to address this question in adult field crickets (Gryllus veletis). Our results showed that lifespan, weight gain, acoustic mate signalling and egg production were maximized on diets with different P : C ratios, that phosphorus did not positively affect any of these fitness traits, and that males and females had different optimal macronutrient intake ratios for reproductive performance. When given a choice, crickets selected diets that maximized both lifespan and reproductive performance by preferentially eating diets with low P : C ratios, and females selected diets with a higher P : C ratio than males. Conversely, phosphorus intake was not regulated. Overall, our findings highlight the importance of disentangling the influences of different nutrients, and of quantifying both their individual and interactive effects, on animal fitness traits, so as to gain a more integrative understanding of their nutritional ecology.


Diffusion, adsorption, and desorption of molecular hydrogen on graphene and in graphite.
The diffusion of molecular hydrogen (H2) on a layer of graphene and in the interlayer space between the layers of graphite is studied using molecular dynamics computer simulations. The interatomic interactions were modeled by an Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential. Molecular statics calculations of H2 on graphene indicate binding energies ranging from 41 meV to 54 meV and migration barriers ranging from 3 meV to 12 meV. The potential energy surface of an H2 molecule on graphene, with the full relaxations of molecular hydrogen and carbon atoms is calculated. Barriers for the formation of H2 through the Langmuir-Hinshelwood mechanism are calculated. Molecular dynamics calculations of mean square displacements and average surface lifetimes of H2 on graphene at various temperatures indicate a diffusion barrier of 9.8 meV and a desorption barrier of 28.7 meV. Similar calculations for the diffusion of H2 in the interlayer space between the graphite sheets indicate high and low temperature regimes for the diffusion with barriers of 51.2 meV and 11.5 meV. Our results are compared with those of first principles.


Pantoea abscess mimicking sarcoma in a HTLV-1-infected Indigenous Australian man: Case report and literature review.
Gram-negative bacteria of the genus Pantoea are emerging bacterial causes of diverse sporadic and outbreak-linked infections. Chronic Pantoea abscesses are unusual and may give rise to a differential diagnosis of malignancy. Foreign body retention and host immune defects may be risk factors for such chronic infections.


Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination.
Severe liver abscess infections caused by hypervirulent clonal-group CG23 Klebsiella pneumoniae have been increasingly reported since the mid-1980s. Strains typically possess several virulence factors including an integrative, conjugative element ICEKp encoding the siderophore yersiniabactin and genotoxin colibactin. Here we investigate CG23's evolutionary history, showing several deep-branching sublineages associated with distinct ICEKp acquisitions. Over 80% of liver abscess isolates belong to sublineage CG23-I, which emerged in ~1928 following acquisition of ICEKp10 (encoding yersiniabactin and colibactin), and then disseminated globally within the human population. CG23-I's distinguishing feature is the colibactin synthesis locus, which reportedly promotes gut colonisation and metastatic infection in murine models. These data show circulation of CG23 K. pneumoniae decades before the liver abscess epidemic was first recognised, and provide a framework for future epidemiological and experimental studies of hypervirulent K. pneumoniae. To support such studies we present an open access, completely sequenced CG23-I human liver abscess isolate, SGH10.


Educational Inequalities in Health Behaviors at Midlife: Is There a Role for Early-life Cognition?
Education is a fundamental cause of social inequalities in health because it influences the distribution of resources, including money, knowledge, power, prestige, and beneficial social connections, that can be used in situ to influence health. Recent studies have highlighted early-life cognition as commonly indicating the propensity for educational attainment and determining health and age of mortality. Health behaviors provide a plausible mechanism linking both education and cognition to later-life health and mortality. We examine the role of education and cognition in predicting smoking, heavy drinking, and physical inactivity at midlife using data from the Wisconsin Longitudinal Study (N = 10,317), National Survey of Health and Development (N = 5,362), and National Childhood Development Study (N = 16,782). Adolescent cognition was associated with education but was inconsistently associated with health behaviors. Education, however, was robustly associated with improved health behaviors after adjusting for cognition. Analyses highlight structural inequalities over individual capabilities when studying health behaviors.


Agency and social constraint among victims of domestic minor sex trafficking: A method for measuring free will.
Human agency has been a focus of philosophical and sociological concern from early debates about "free will" to recent themes in poststructuralism. Debates over the proper understanding of structure, agency, and constraint are hindered by the fact that few if any empirical measures of these concepts have been proposed. As sociologists have long recognized, the total results of the decisions of a group's members can be viewed as a distribution, and parameters can be fit to obtain a description of observed distributions. Here we propose the use of negative binomial curve to model population survival outcomes, and suggest that the parameters of such a curve represent reasonable surrogates for measures of agency, opportunity, and constraint when the decision process can be thought of as akin to a Bernoulli process. To provide an illustration of this approach, we discuss participation of legal minors in commercial sex (commonly referred to as victims of domestic minor sex trafficking (VDMST) or commercially sexually exploited children (CSEC)). In popular and advocacy-based accounts, considerable focus has been placed on the relative powerlessness of female VDMST. Using the proposed modeling technique, we test the extent to which male versus female VDMST appear to possess greater agency (or function under more limiting constraint) when deciding whether to remain in sex work or "leave the life". Contrary to existing literature, our results indicate that male and female underage sex workers are experiencing similar levels of agency, and differ mainly in opportunity, and constraint. Other individual circumstances are shown to contribute to varying levels of agency and constraint among sex workers, including street work status, community trouble, drug use, and the availability of an alternative income.


Suitability of Kinect for measuring whole body movement patterns during exergaming.
Exergames provide a challenging opportunity for home-based training and evaluation of postural control in the elderly population, but affordable sensor technology and algorithms for assessment of whole body movement patterns in the home environment are yet to be developed. The aim of the present study was to evaluate the use of Kinect, a commonly available video game sensor, for capturing and analyzing whole body movement patterns. Healthy adults (n=20) played a weight shifting exergame under five different conditions with varying amplitudes and speed of sway movement, while 3D positions of ten body segments were recorded in the frontal plane using Kinect and a Vicon 3D camera system. Principal Component Analysis (PCA) was used to extract and compare movement patterns and the variance in individual body segment positions explained by these patterns. Using the identified patterns, balance outcome measures based on spatiotemporal sway characteristics were computed. The results showed that both Vicon and Kinect capture >90% variance of all body segment movements within three PCs. Kinect-derived movement patterns were found to explain variance in trunk movements accurately, yet explained variance in hand and foot segments was underestimated and overestimated respectively by as much as 30%. Differences between both systems with respect to balance outcome measures range 0.3-64.3%. The results imply that Kinect provides the unique possibility of quantifying balance ability while performing complex tasks in an exergame environment.


Factors affecting the spontaneous cell-mediated cytotoxicity of intestinal mononuclear cells.
This study was performed to determine what factors related to the enzymatic isolation technique and assay conditions may influence the measurement of spontaneous cell-mediated cytotoxicity (SCMC) of mononuclear cells (MNC) isolated from human intestinal mucosa. In 18 studies, the SCMC of freshly isolated cells was 1.8 +/- 0.4% but increased to 12 +/- 3% following 24 hr culture without a change in the proportion of cells with the NK phenotype (Leu-7+). The SCMC tended to plateau with more prolonged culture. Culturing peripheral blood (PB) MNC for 24 hr did not alter SCMC nor the proportion of Leu-7+ cells. However, the suppression of the SCMC of PBMNC preincubated with the supernatant of the collagenase digestion of intestinal mucosa was completely reversed by 24 hr culture. Intestinal MNC were found to suppress the SCMC of autologous PBMNC in mixing experiments. However, 24 hr culture did not affect the degree of suppression and the proportion of T cells of the suppressor-cytotoxic phenotype (Leu-2a+) was also unchanged. It is concluded that the SCMC of intestinal MNC may be accurately assessed following 24 hr culture of the cells to allow recovery from the suppressive influences of the isolation process and that this does not introduce other artefactual problems. However, suppression of cytotoxicity within the assay may result in an underestimation of the SCMC of intestinal MNC when compared to that of PBMNC.


The Earth as a seismic absorption band.
Attenuation of seismic waves indicates that the earth is not perfectly elastic. Dispersion accompanying absorption gives frequency-dependent "elastic" moduli, a fact that must be taken into account when inverting seismic data. Normal mode data are reinverted after correcting for absorption. The correction removes the discrepancy between body wave and free oscillation interpretations of earth structure.


Choroidal Thickness Influences Near-Infrared Reflectance Intensity in Eyes With Geographic Atrophy Due To Age-Related Macular Degeneration.
To evaluate the effects of retinal and choroidal thickness on near-infrared reflectance (NIR) scanning laser ophthalmoscopy in eyes with geographic atrophy (GA) secondary to non-neovascular age-related macular degeneration (AMD). This was a cross-sectional review of the clinical records and multimodal imaging data of eyes diagnosed with GA secondary to non-neovascular AMD. Imaging modalities included color fundus photography, fundus autofluorescence, NIR, and structural spectral-domain optical coherence tomography (SD-OCT). On SD-OCT images, the foveal retina thickness and the subfoveal choroidal thickness were measured by two independent readers. Near-infrared reflectance intensity within areas of GA was subjectively graded as hyperreflective, isoreflective, or hyporeflective and objectively estimated by using ImageJ to calculate the mean gray scale value within each GA area. A linear regression analysis was performed to model the relationship between mean NIR gray scale value and retinal and choroidal thickness. One hundred four eyes of 104 patients with a mean age of 81.3 years (SD: ±8.3) were included. The area of GA was hyperreflective on NIR in 88 eyes (85%), isoreflective in 13 eyes (12%), and hyporeflective in 3 eyes (3%). The mean foveal retinal thickness was 101.5 μm (SD: ±54) showing no significant relationship with mean NIR (P = 0.464); and the mean subfoveal choroidal thickness was 172.6 μm (SD: ±114.7) showing a statistically significant relationship with mean NIR intensity in the linear regression analysis (r = 0.590; r2 = 0.348; P < 0.00001). Variations in choroidal thickness appear to influence NIR intensity in areas of GA and have the potential to affect image interpretation. The recognition of this relationship may provide useful information regarding choroidal thickness.


Enhanced antioxidant capacity and anti-ageing biomarkers after diet micronutrient supplementation.
A growing number of studies confirm an important effect of diet, lifestyle and physical activity on health status, the ageing process and many metabolic disorders. This study focuses on the influence of a diet supplement, NucleVital®Q10 Complex, on parameters related to redox homeostasis and ageing. An experimental group of 66 healthy volunteer women aged 35-55 supplemented their diet for 12 weeks with the complex, which contained omega-3 acids (1350 mg/day), ubiquinone (300 mg/day), astaxanthin (15 mg/day), lycopene (45 mg/day), lutein palmitate (30 mg/day), zeaxanthine palmitate (6 mg/day), L-selenomethionine (330 mg/day), cholecalciferol (30 µg/day) and α-tocopherol (45 mg/day). We found that NucleVital®Q10 Complex supplementation significantly increased total antioxidant capacity of plasma and activity of erythrocyte superoxide dismutase, with slight effects on oxidative stress biomarkers in erythrocytes; MDA and 4-hydroxyalkene levels. Apart from the observed antioxidative effects, the tested supplement also showed anti-ageing activity. Analysis of expression of SIRT1 and 2 in PBMCs showed significant changes for both genes on a mRNA level. The level of telomerase was also increased by more than 25%, although the length of lymphocyte telomeres, determined by RT-PCR, remained unchanged. Our results demonstrate beneficial effects concerning the antioxidant potential of plasma as well as biomarkers related to ageing even after short term supplementation of diet with NucleVital®Q10 Complex.


Modulation of gene expression as a new skin anti-aging strategy.
[corrected] The signs of aging may originate from natural processes or from exposure to the sun, wind, or other environmental factors. To evaluate the anti-aging effects of potential agents researchers must first identify and be able to quantify epidermal markers that change with aging. This paper summarizes the results of studies conducted to evaluate the transcriptional effects of an Aframomum angustifolium seed extract and Malva Sylvestris extract, and the antiaging efficacy of a skin care product containing the Aframomum angustifolium seed extract. The transcriptional effect of an Aframomum angustifolium seed extract on normal human keratinocytes (NHKs) and normal human fibroblasts (NHF) was evaluated in vitro with the use of a low-density DNA array technology. The Malva Sylvestris extract was studied with a commercial DNA macroarray and by a real-time quantitative reverse transcriptase-polymerase chain reaction. The in vitro anti-aging activities of the Malva sylvestris extract were compared with those of all-trans retinoic acid (RA), a well-established topical therapy for photodamage and wrinkles. The genes studied were known to be modified by RA. The anti-aging efficacy of a facial skin care product containing Aframomum angustifolium seed extract was evaluated in a single-center study using image processing analysis and in a 2-center study by evaluation of the photographs by the investigator, independent evaluators, and subjects. In general, the Aframomum angustifolium seed extract strongly modified the gene expression profiles of NHKs and weakly modified the gene expression profiles of NHFs. After incubation with Aframomum angustifolium seed extract, the expressions of 3 antioxidant genes (metallothionein 1, metallothionein 2, and thioredoxin) were increased in NHKs, while expressions of 1 antioxidant gene (glutathione peroxidase) was increased in NHFs. Concerning the Malva sylvestris extract, a cDNA macro-array technology experiment with the reconstructed human epidermis model showed that some genes modulated by treatment with the Malva sylvestris extract are also regulated by RA treatment indicating a similar activity at the mRNA level. In the single-center study, a facial skin care product containing the Aframomum angustifolium seed extract significantly improved the homogeneity of the skin. The areas of the detected objects (skin imperfections) decreased significantly on each studied area of the face and the variance decreased significantly over the entire face. In the 2-center study, 28% percent of the subjects reported a greater than 50% overall global improvement in their skin by the end of the study compared to 11% of the subjects after 4 weeks of treatment. Seventy-six percent of subjects said they would purchase the cream. The authors developed a low-density DNA chip method that permitted the study of the transcriptional effect of Malva Sylvestris extract and of Aframomum angustrifolium seed extract. The gene expression profiles obtained demonstrate the anti-aging properties of these compounds. An in vivo single-center study, performed and analyzed with an assay based on image processing analysis, demonstrated the antiwrinkle activity of a formulation containing the Aframomum angustifolium seed extract. The data obtained in the 2-center study suggests that the cosmeceutical containing Aframomum angustifolium seed extract produces a global rejuvenation effect in terms of redness, pigmentation, and fine lines similar to that noted utilizing an intense pulse light source.


Early onset idiopathic scoliosis.
Children with early onset scoliosis typically present before age 5 years. Radiographic criteria help to distinguish progressive cases from those that will spontaneously resolve. Severe cardiopulmonary problems may occur in untreated progressive cases. A comprehensive evaluation should be performed to identify commonly associated conditions, such as plagiocephaly, congenital heart disease, inguinal hernia, and hip dysplasia. For curves >20 degrees , magnetic resonance imaging of the neural axis is indicated to rule out occult central nervous system lesions. Surgical management should be considered when nonsurgical measures, including bracing and casting, fail to arrest progression. Surgical methods continue to evolve and are primarily directed at obtaining and maintaining curve correction while simultaneously preserving spinal and trunk growth.


Human transgenerational responses to early-life experience: potential impact on development, health and biomedical research.
Mammalian experiments provide clear evidence of male line transgenerational effects on health and development from paternal or ancestral early-life exposures such as diet or stress. The few human observational studies to date suggest (male line) transgenerational effects exist that cannot easily be attributed to cultural and/or genetic inheritance. Here we summarise relevant studies, drawing attention to exposure sensitive periods in early life and sex differences in transmission and offspring outcomes. Thus, variation, or changes, in the parental/ancestral environment may influence phenotypic variation for better or worse in the next generation(s), and so contribute to common, non-communicable disease risk including sex differences. We argue that life-course epidemiology should be reframed to include exposures from previous generations, keeping an open mind as to the mechanisms that transmit this information to offspring. Finally, we discuss animal experiments, including the role of epigenetic inheritance and non-coding RNAs, in terms of what lessons can be learnt for designing and interpreting human studies. This review was developed initially as a position paper by the multidisciplinary Network in Epigenetic Epidemiology to encourage transgenerational research in human cohorts.


Effects of cartilage-derived morphogenetic proteins and osteogenic protein-1 on osteochondrogenic differentiation of periosteum-derived cells.
Localization studies and genetic evidence have implicated cartilage-derived morphogenetic proteins-1, -2 (CDMP-1 and CDMP-2), and osteogenic protein-1 (OP-1) in the osteochondrogenic differentiation of mesenchymal progenitor cells during embryonic development and in postnatal life. Based on their expression pattern and the evidence that periosteum contains mesenchymal cells in the cambium layer that can undergo bone and cartilage formation, we hypothesized that CDMPs and OP-1 may be involved in long bone development and fracture healing. To test this hypothesis, periosteum-derived cells from young calves were cultured as monolayers under serum-free conditions with and without the addition of recombinant CDMP-1, CDMP-2 and OP-1. Phenotypic analysis indicate that periosteum-derived cell populations prepared, expanded, and cultured under the conditions described below, constitutively express messenger RNAs for the bone markers osteocalcin, osteopontin and collagen type I, and the chondrogenic markers collagen type II and aggrecan as determined by RT-PCR. Moreover, histologic examinations showed positive staining for alcian blue and alkaline phosphatase (AP). Treatment of periosteum-derived cells with CDMPs and OP-1 resulted in a dose-dependent increase of cell proliferation; CDMP-2 was less active in this regard. Furthermore, all growth factors enhanced osteogenic differentiation as assessed by a time- and dose-dependent stimulation of AP activity and OP-1 increased messenger RNA expression for osteocalcin and collagen type I. We further examined the effects of CDMPs and OP-1 on chondrogenic differentiation of periosteum-derived cells. Both CDMPs and OP-1 stimulated (35)S-sulfate incorporation into newly synthesized macromolecules with OP-1 having a more pronounced stimulatory effect when compared with CDMP-1 and CDMP-2. Our results indicate that distinct members of the BMP-family increase the mitotic and metabolic activity of periosteum-derived cells. The enhancement of both the chondrogenic and osteogenic differentiation suggests that these growth factors might contribute to the local regulation of bone formation and fracture repair.


Structural and functional characterization of nonstructural protein 2 for its role in hepatitis C virus assembly.
The hepatitis C virus (HCV) is a flavivirus replicating in the cytoplasm of infected cells. The HCV genome is a single-stranded RNA encoding a polyprotein that is cleaved by cellular and viral proteases into 10 different products. While the structural proteins core protein, envelope protein 1 (E1) and E2 build up the virus particle, most nonstructural (NS) proteins are required for RNA replication. One of the least studied proteins is NS2, which is composed of a C-terminal cytosolic protease domain and a highly hydrophobic N-terminal domain. It is assumed that the latter is composed of three trans-membrane segments (TMS) that tightly attach NS2 to intracellular membranes. Taking advantage of a system to study HCV assembly in a hepatoma cell line, in this study we performed a detailed characterization of NS2 with respect to its role for virus particle assembly. In agreement with an earlier report ( Jones, C. T., Murray, C. L., Eastman, D. K., Tassello, J., and Rice, C. M. (2007) J. Virol. 81, 8374-8383 ), we demonstrate that the protease domain, but not its enzymatic activity, is required for infectious virus production. We also show that serine residue 168 in NS2, implicated in the phosphorylation and stability of this protein, is dispensable for virion formation. In addition, we determined the NMR structure of the first TMS of NS2 and show that the N-terminal segment (amino acids 3-11) forms a putative flexible helical element connected to a stable alpha-helix (amino acids 12-21) that includes an absolutely conserved helix side in genotype 1b. By using this structure as well as the amino acid conservation as a guide for a functional study, we determined the contribution of individual amino acid residues in TMS1 for HCV assembly. We identified several residues that are critical for virion formation, most notably a central glycine residue at position 10 of TMS1. Finally, we demonstrate that mutations in NS2 blocking HCV assembly can be rescued by trans-complementation.


Watchful Waiting Versus Surgery of Mildly Symptomatic or Asymptomatic Inguinal Hernia in Men Aged 50 Years and Older: A Randomized Controlled Trial.
To compare if watchful waiting is noninferior to elective repair in men aged 50 years and older with mildly symptomatic or asymptomatic inguinal hernia. The role of watchful waiting in older male patients with mildly symptomatic or asymptomatic inguinal hernia is still not well-established. In this noninferiority trial, we randomly assigned men aged 50 years and older with mildly symptomatic or asymptomatic inguinal hernia to either elective inguinal hernia repair or watchful waiting. Primary endpoint was the mean difference in a 4-point pain/discomfort score at 24 months of follow-up. Using a 0.20-point difference as a clinically relevant margin, it was hypothesized that watchful waiting was noninferior to elective repair. Secondary endpoints included quality of life, event-free survival, and crossover rates. Between January 2006 and August 2012, 528 patients were enrolled, of whom 496 met the inclusion criteria: 234 were assigned to elective repair and 262 to watchful waiting. The mean pain/discomfort score at 24 months was 0.35 [95% confidence interval (CI) 0.28-0.41)] in the elective repair group and 0.58 (95% CI 0.52-0.64) in the watchful waiting group. The difference of these means (MD) was -0.23 (95% CI -0.32 to -0.14). In the watchful waiting group, 93 patients (35·4%) eventually underwent elective surgery and 6 patients (2·3%) received emergent surgery for strangulation/incarceration. Postoperative complication rates and recurrence rates in these 99 operated individuals were comparable with individuals originally assigned to the elective repair group (8.1% vs 15.0%; P = 0.106, 7.1% vs 8.9%; P = 0.668, respectively). Our data could not rule out a relevant difference in favor of elective repair with regard to the primary endpoint. Nevertheless, in view of all other findings, we feel that our results justify watchful waiting as a reasonable alternative compared with surgery in men aged 50 years and older.


Quality Enhancement Research Initiative in stroke: prevention, treatment, and rehabilitation.
Stroke is the third leading cause of death and a leading cause of adult disability in the United States. Both within and outside of the Veterans Health Administration (VHA), the lack of a systematic approach to stroke prevention and treatment may have contributed to reduced rates of compliance with recommended practices and increased rates of stroke. Gaps in the knowledge base inhibit a systematic approach to high-quality care within the veteran population. Initial recommendations for closing those gaps are proposed. In some cases (eg, systematic anticoagulation management), the VHA is perceived as a leader in applied research; therefore, a systematic national policy for implementing these clinics may significantly reduce stroke rates. In other areas (eg, carotid endarterectomy), databases exist that would help advance quality and outcomes, but short-term studies are necessary to establish their utility. To promote strategic improvement in prevention, treatment, and rehabilitation for veterans who may be at risk or have had a stroke, specific objectives are proposed to (1) identify best practices for the effective delivery of long-term anticoagulation and enhance veterans' access to these services, (2) develop risk-adjusted models for the surgical preventive procedure carotid endarterectomy to understand facility variation in outcomes so practices can be improved, (3) define a systematic acute stroke management system so that high-quality stroke-related care can be generalizable to a variety of VHA settings, and (4) assess the impact of poststroke rehabilitation on risk adjustment and the location of outcomes so as to facilitate the implementation of best rehabilitation practices.


Stroke in children.
To summarize 1) the definitions and epidemiological features of stroke in children; 2) the main risk factors that can lead to stroke in pediatrics and neonatology; 3) the main pathophysiological features involved in the genesis of brain injury in stroke; 4) the clinical manifestations and imaging diagnosis; and 5) the latest recommendations concerning the support measures, treatment, and prophylaxis of stroke in children. A review of the literature published in PubMed, EMBASE, and SciELO databases using the search terms stroke, pediatrics, and neonatology was performed, including relevant references from the chosen texts. Stroke in children are rare conditions, with incidence rates among two and eight per 100,000 children up to 14 years, and most cases show an underlying disease such as heart diseases, prothrombotic conditions, sickle-cell disease, and vascular malformations. There are no specific guidelines currently in place for the treatment of stroke in children, although central elements include support treatment, monitoring, and anticoagulation as secondary prevention in certain cases. Prognosis depends on the extent of brain damage and the underlying disease but recurrence rates are high in most cases. Early diagnosis of stroke in children is very important and pediatricians should be aware of the lack of specificity of the symptoms to avoid late sequelae and improve life quality.


Skin antisepsis for reducing central venous catheter-related infections.
The central venous catheter (CVC) is a device used for many functions, including monitoring haemodynamic indicators and administering intravenous medications, fluids, blood products and parenteral nutrition. However, as a foreign object, it is susceptible to colonisation by micro-organisms, which may lead to catheter-related blood stream infection (BSI) and in turn, increased mortality, morbidities and health care costs. To assess the effects of skin antisepsis as part of CVC care for reducing catheter-related BSIs, catheter colonisation, and patient mortality and morbidities. In May 2016 we searched: The Cochrane Wounds Specialised Register; The Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library); Ovid MEDLINE (including In-Process & Other Non-Indexed Citations and Epub Ahead of Print); Ovid EMBASE and EBSCO CINAHL Plus. We also searched clinical trial registries for ongoing and unpublished studies. There were no restrictions with respect to language, date of publication or study setting. We included randomised controlled trials (RCTs) that assessed any type of skin antiseptic agent used either alone or in combination, compared with one or more other skin antiseptic agent(s), placebo or no skin antisepsis in patients with a CVC in place. Two authors independently assessed the studies for their eligibility, extracted data and assessed risk of bias. We expressed our results in terms of risk ratio (RR), absolute risk reduction (ARR) and number need to treat for an additional beneficial outcome (NNTB) for dichotomous data, and mean difference (MD) for continuous data, with 95% confidence intervals (CIs). Thirteen studies were eligible for inclusion, but only 12 studies contributed data, with a total of 3446 CVCs assessed. The total number of participants enrolled was unclear as some studies did not provide such information. The participants were mainly adults admitted to intensive care units, haematology oncology units or general wards. Most studies assessed skin antisepsis prior to insertion and regularly thereafter during the in-dwelling period of the CVC, ranging from every 24 h to every 72 h. The methodological quality of the included studies was mixed due to wide variation in their risk of bias. Most trials did not adequately blind the participants or personnel, and four of the 12 studies had a high risk of bias for incomplete outcome data.Three studies compared different antisepsis regimens with no antisepsis. There was no clear evidence of a difference in all outcomes examined, including catheter-related BSI, septicaemia, catheter colonisation and number of patients who required systemic antibiotics for any of the three comparisons involving three different antisepsis regimens (aqueous povidone-iodine, aqueous chlorhexidine and alcohol compared with no skin antisepsis). However, there were great uncertainties in all estimates due to underpowered analyses and the overall very low quality of evidence presented.There were multiple head-to-head comparisons between different skin antiseptic agents, with different combinations of active substance and base solutions. The most frequent comparison was chlorhexidine solution versus povidone-iodine solution (any base). There was very low quality evidence (downgraded for risk of bias and imprecision) that chlorhexidine may reduce catheter-related BSI compared with povidone-iodine (RR of 0.64, 95% CI 0.41 to 0.99; ARR 2.30%, 95% CI 0.06 to 3.70%). This evidence came from four studies involving 1436 catheters. None of the individual subgroup comparisons of aqueous chlorhexidine versus aqueous povidone-iodine, alcoholic chlorhexidine versus aqueous povidone-iodine and alcoholic chlorhexidine versus alcoholic povidone-iodine showed clear differences for catheter-related BSI or mortality (and were generally underpowered). Mortality was only reported in a single study.There was very low quality evidence that skin antisepsis with chlorhexidine may also reduce catheter colonisation relative to povidone-iodine (RR of 0.68, 95% CI 0.56 to 0.84; ARR 8%, 95% CI 3% to 12%; ; five studies, 1533 catheters, downgraded for risk of bias, indirectness and inconsistency).Evaluations of other skin antiseptic agents were generally in single, small studies, many of which did not report the primary outcome of catheter-related BSI. Trials also poorly reported other outcomes, such as skin infections and adverse events. It is not clear whether cleaning the skin around CVC insertion sites with antiseptic reduces catheter related blood stream infection compared with no skin cleansing. Skin cleansing with chlorhexidine solution may reduce rates of CRBSI and catheter colonisation compared with cleaning with povidone iodine. These results are based on very low quality evidence, which means the true effects may be very different. Moreover these results may be influenced by the nature of the antiseptic solution (i.e. aqueous or alcohol-based). Further RCTs are needed to assess the effectiveness and safety of different skin antisepsis regimens in CVC care; these should measure and report critical clinical outcomes such as sepsis, catheter-related BSI and mortality.


Smoking and long-term risk of type 2 diabetes: the EPIC-InterAct study in European populations.
The aims of this study were to investigate the association between smoking and incident type 2 diabetes, accounting for a large number of potential confounding factors, and to explore potential effect modifiers and intermediate factors. The European Prospective Investigation into Cancer and Nutrition (EPIC)-InterAct is a prospective case-cohort study within eight European countries, including 12,403 cases of incident type 2 diabetes and a random subcohort of 16,835 individuals. After exclusion of individuals with missing data, the analyses included 10,327 cases and 13,863 subcohort individuals. Smoking status was used (never, former, current), with never smokers as the reference. Country-specific Prentice-weighted Cox regression models and random-effects meta-analysis were used to estimate hazard ratios (HRs) for type 2 diabetes. In men, the HRs (95% CI) of type 2 diabetes were 1.40 (1.26, 1.55) for former smokers and 1.43 (1.27, 1.61) for current smokers, independent of age, education, center, physical activity, and alcohol, coffee, and meat consumption. In women, associations were weaker, with HRs (95% CI) of 1.18 (1.07, 1.30) and 1.13 (1.03, 1.25) for former and current smokers, respectively. There was some evidence of effect modification by BMI. The association tended to be slightly stronger in normal weight men compared with those with overall adiposity. Former and current smoking was associated with a higher risk of incident type 2 diabetes compared with never smoking in men and women, independent of educational level, physical activity, alcohol consumption, and diet. Smoking may be regarded as a modifiable risk factor for type 2 diabetes, and smoking cessation should be encouraged for diabetes prevention.


A novel O-linked glycan modulates Campylobacter jejuni major outer membrane protein-mediated adhesion to human histo-blood group antigens and chicken colonization.
Campylobacter jejuni is an important cause of human foodborne gastroenteritis; strategies to prevent infection are hampered by a poor understanding of the complex interactions between host and pathogen. Previous work showed that C. jejuni could bind human histo-blood group antigens (BgAgs) in vitro and that BgAgs could inhibit the binding of C. jejuni to human intestinal mucosa ex vivo. Here, the major flagella subunit protein (FlaA) and the major outer membrane protein (MOMP) were identified as BgAg-binding adhesins in C. jejuni NCTC11168. Significantly, the MOMP was shown to be O-glycosylated at Thr(268); previously only flagellin proteins were known to be O-glycosylated in C. jejuni. Substitution of MOMP Thr(268) led to significantly reduced binding to BgAgs. The O-glycan moiety was characterized as Gal(β1-3)-GalNAc(β1-4)-GalNAc(β1-4)-GalNAcα1-Thr(268); modelling suggested that O-glycosylation has a notable effect on the conformation of MOMP and this modulates BgAg-binding capacity. Glycosylation of MOMP at Thr(268) promoted cell-to-cell binding, biofilm formation and adhesion to Caco-2 cells, and was required for the optimal colonization of chickens by C. jejuni, confirming the significance of this O-glycosylation in pathogenesis.


Electrospun poly(D/L-lactide-co-L-lactide) hybrid matrix: a novel scaffold material for soft tissue engineering.
Electrospinning is a long-known polymer processing technique that has received more interest and attention in recent years due to its versatility and potential use in the field of biomedical research. The fabrication of three-dimensional (3D) electrospun matrices for drug delivery and tissue engineering is of particular interest. In the present study, we identified optimal conditions to generate novel electrospun polymeric scaffolds composed of poly-D/L-lactide and poly-L-lactide in the ratio 50:50. Scanning electron microscopic analyses revealed that the generated poly(D/L-lactide-co-L-lactide) electrospun hybrid microfibers possessed a unique porous high surface area mimicking native extracellular matrix (ECM). To assess cytocompatibility, we isolated dermal fibroblasts from human skin biopsies. After 5 days of in vitro culture, the fibroblasts adhered, migrated and proliferated on the newly created 3D scaffolds. Our data demonstrate the applicability of electrospun poly(D/L-lactide-co-L-lactide) scaffolds to serve as substrates for regenerative medicine applications with special focus on skin tissue engineering.


Elevated intracellular calcium triggers recruitment of the receptor cross-talk accessory protein calcyon to the plasma membrane.
Calcyon is called a "cross-talk accessory protein" because the mechanism by which it enables the typically Gs-linked D1 dopamine receptor to stimulate intracellular calcium release depends on a priming step involving heterologous Gq-linked G-protein-coupled receptor activation. The details of how priming facilitates the D1R calcium response have yet to be precisely elucidated. The present work shows that calcyon is constitutively localized both in vesicular and plasma membrane compartments within HEK293 cells. In addition, surface biotinylation and luminescence assays revealed that priming stimulates a 2-fold increase in the levels of calcyon expressed on the cell surface and that subsequent D1R activation produces further accumulation of the protein in the plasma membrane. The effects of priming and D1R agonists were blocked by nocodazole implicating microtubules in the delivery of calcyon-containing vesicles to the cell surface. Accumulation of calcyon in the plasma membrane correlated well with increased intracellular calcium levels as thapsigargin mimicked, and 2-aminoethoxydiphenylborane abrogated, the effects of priming. KN-62, an inhibitor of calcium/calmodulin-dependent protein kinase II (CaMKII) also blocked the effects of priming and D1R agonists. Furthermore, expression of constitutively active forms of the kinase bypassed the requirement for priming indicating that CaMKII is a key effector in the Ca2+ and microtubule-dependent delivery of calcyon to the cell surface.


Charting the landscape of priority problems in psychiatry, part 2: pathogenesis and aetiology.
This is the second of two companion papers proposing priority problems for research on mental disorders. Whereas the first paper focuses on questions of nosology and diagnosis, this Personal View concerns pathogenesis and aetiology of psychiatric diseases. We hope that this (non-exhaustive and subjective) list of problems, nominated by scientists and clinicians from different fields and institutions, provides guidance and perspectives for choosing future directions in psychiatric science.


Downregulation of high-isoelectric-point extracellular superoxide dismutase mediates alterations in the metabolism of reactive oxygen species and developmental disturbances in hybrid aspen.
Transgenic hybrid aspen (Populus tremula L. x P. tremuloides Michx.) plants expressing a high-isoelectric-point superoxide dismutase (hipI-SOD) gene in antisense orientation were generated to investigate its function. Immunolocalization studies showed the enzyme to be localized extracellularly, in the secondary cell wall of xylem vessels and phloem fibers. The antisense lines of hipI-SOD exhibited a distinct phenotype; growth rate was reduced, stems were thinner and leaves smaller than in wild-type (WT) plants. The abundance of hipI-SOD was reduced in the bark and xylem of plants from these antisense lines. The vascular tissue of transgenic lines became lignified earlier than in WT plants and also showed an increased accumulation of reactive oxygen species (ROS). Xylem fibers and vessels were shorter and thinner in the transgenic lines than in WT plants. The total phenolic content was enhanced in the antisense lines. Furthermore, microarray analysis indicated that several enzymes involved in cell signaling, lignin biosynthesis and stress responses were upregulated in apical vascular tissues of transgenic plants. The upregulation of selected genes involved in lignin biosynthesis was also verified by real-time PCR. The results suggest that, in the transgenic plants, a premature transition into maturation occurs and the process is discussed in terms of the effects of increased accumulation of ROS due to reduced expression of hipI-SOD during development and differentiation.


A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade.
Evidence from mouse chronic viral infection models suggests that CD8+ T cell subsets characterized by distinct expression levels of the receptor PD-1 diverge in their state of exhaustion and potential for reinvigoration by PD-1 blockade. However, it remains unknown whether T cells in human cancer adopt a similar spectrum of exhausted states based on PD-1 expression levels. We compared transcriptional, metabolic and functional signatures of intratumoral CD8+ T lymphocyte populations with high (PD-1T), intermediate (PD-1N) and no PD-1 expression (PD-1-) from non-small-cell lung cancer patients. PD-1T T cells showed a markedly different transcriptional and metabolic profile from PD-1N and PD-1- lymphocytes, as well as an intrinsically high capacity for tumor recognition. Furthermore, while PD-1T lymphocytes were impaired in classical effector cytokine production, they produced CXCL13, which mediates immune cell recruitment to tertiary lymphoid structures. Strikingly, the presence of PD-1T cells was strongly predictive for both response and survival in a small cohort of non-small-cell lung cancer patients treated with PD-1 blockade. The characterization of a distinct state of tumor-reactive, PD-1-bright lymphocytes in human cancer, which only partially resembles that seen in chronic infection, provides potential avenues for therapeutic intervention.


Induction of long-lasting multi-specific CD8+ T cells by a four-component DNA-MVA/HIVA-RENTA candidate HIV-1 vaccine in rhesus macaques.
As a part of a long-term effort to develop vaccine against HIV-1 clade A inducing protective T cell responses in humans, we run mutually complementing studies in humans and non-human primates (NHP) with the aim to maximize vaccine immunogenicity. The candidate vaccine under development has four components, pTHr.HIVA and pTH.RENTA DNA, and modified vaccinia virus Ankara (MVA).HIVA and MVA.RENTA, delivered in a heterologous DNA prime-MVA boost regimen. While the HIVA (Gag/epitopes) components have been tested in NHP and over 300 human subjects, we plan to test in humans the RENTA (reverse transcriptase, gp41, Nef, Tat) vaccines designed to broaden HIVA-induced responses in year 2007. Here, we investigated the four-component vaccine long-term immunogenicity in Mamu-A*01-positive rhesus macaques and demonstrated that the vaccine-induced T cells were multi-specific, multi-functional, readily proliferated to recall peptides and were circulating in the peripheral blood of vaccine recipients over 1 year after vaccine administration. The consensus clade A-elicited T cells recognized 50% of tested epitope variants from other HIV-1 clades. Thus, the DNA-MVA/HIVA-RENTA vaccine induced memory T cells of desirable characteristics and similarities to those induced in humans by HIVA vaccines alone; however, single-clade vaccines may not elicit sufficiently cross-reactive responses.


Methotrexate for high-grade osteosarcoma in children and young adults.
The majority of the currently used treatment protocols for osteosarcoma are based on a combination of doxorubicin, cisplatin, methotrexate (MTX) and/or ifosfamide, of which MTX seems to be one of the most active drugs. However, in the literature, this has not been unambiguously proven. To compare the effectiveness of treatment including MTX with treatment without MTX for children and young adults (up to 21 years) with primary high-grade osteosarcoma. We searched the Cochrane Central Register of Controlled Trials (The Cochrane Library, issue 3, 2008), MEDLINE (1966 to July 2008) and EMBASE (1980 to July 2008). In addition, we searched reference lists of relevant articles, conference proceedings and ongoing trials databases. Randomised controlled trials (RCTs) or controlled clinical trials (CCTs) comparing the effectiveness of treatment including MTX with treatment without MTX in the treatment of paediatric high-grade osteosarcoma. Two reviewers independently performed the study selection. One reviewer performed the data extraction and quality assessment, which was checked by another reviewer. We could not identify any studies in which the only difference between the treatment groups was the use of MTX.We did identify a RCT comparing MTX with cisplatin (n=30 children). The risk of bias in this study was difficult to assess due to a lack of reporting. Survival could not be evaluated, but no evidence of a significant difference in response rate between the treatment groups was identified (RR=0.44; 95% CI 0.17 to 1.13; P=0.09). A significant difference in the occurrence of toxicities in favour of MTX was identified, but with regard to quality of life treatment with cisplatin seemed to give better results.For other combinations of treatment including and not including MTX no studies were identified. Since no RCTs or CCTs in which only the use of MTX differed between the treatment groups were identified, no definitive conclusions can be made about the effects on antitumour efficacy, toxicities and quality of life of the addition of MTX to treatment of children and young adults with primary high-grade osteosarcoma. The same is true for combinations of treatment including and not including MTX other than treatment with MTX versus treatment with cisplatin. Only 1 RCT comparing MTX with cisplatin treatment was available and therefore, no definitive conclusions can be made about the effectiveness of these agents in children and young adults with primary high-grade osteosarcoma. Furthermore, this study was performed in a different treatment era. Nowadays single agent treatment of osteosarcoma is considered inadequate. Based on the currently available evidence, we are not able to give recommendations for the use of MTX in clinical practice. More high quality research is needed.


Genetic schemes and schemata in neurophysiology.
Information in nervous systems is often carried by neural ensembles--groups of neurons in transient functional linkage--and written in a code that involves the spatial locations of active neurons or synapses and the times at which activity occurs. Even in favorable neuroanatomical circumstances, studying neural ensemble function presents a serious experimental challenge. One recent strategy to overcome this challenge relies on protein-based sensors that provide direct optical images of neural activity, and on protein-based effectors that interfere with it. Because these molecules are encodable in DNA, they can be introduced into intact animals by genetic manipulation, and their expression pattern can be tailored to include--exclusively and at the same time comprehensively--the neurons of interest. Circumscribed populations of neurons can thus be studied in virtual isolation at defined stages of intact neural pathways.


Neural dynamics of audiovisual speech integration under variable listening conditions: an individual participant analysis.
Speech perception engages both auditory and visual modalities. Limitations of traditional accuracy-only approaches in the investigation of audiovisual speech perception have motivated the use of new methodologies. In an audiovisual speech identification task, we utilized capacity (Townsend and Nozawa, 1995), a dynamic measure of efficiency, to quantify audiovisual integration. Capacity was used to compare RT distributions from audiovisual trials to RT distributions from auditory-only and visual-only trials across three listening conditions: clear auditory signal, S/N ratio of -12 dB, and S/N ratio of -18 dB. The purpose was to obtain EEG recordings in conjunction with capacity to investigate how a late ERP co-varies with integration efficiency. Results showed efficient audiovisual integration for low auditory S/N ratios, but inefficient audiovisual integration when the auditory signal was clear. The ERP analyses showed evidence for greater audiovisual amplitude compared to the unisensory signals for lower auditory S/N ratios (higher capacity/efficiency) compared to the high S/N ratio (low capacity/inefficient integration). The data are consistent with an interactive framework of integration, where auditory recognition is influenced by speech-reading as a function of signal clarity.


Reversible phase transitions in self-assembled monolayers at the liquid-solid interface: temperature-controlled opening and closing of nanopores.
We present a variable-temperature study of monolayer self-assembly at the liquid-solid interface. By means of in situ scanning tunneling microscopy (STM), reversible phase transitions from a nanoporous low-temperature phase to a more densely packed high-temperature phase are observed. The occurrence of the phase transition and the respective transition temperature were found to depend on the type of solvent and solute concentration. Estimates of the entropic cost and enthalpic gain upon monolayer self-assembly suggest that coadsorption of solvent molecules within the cavities of the nanoporous structure renders this polymorph thermodynamically stable at low temperatures. At elevated temperatures, however, desorption of these relatively weakly bound solvent molecules destabilizes the nanoporous polymorph, and the densely packed polymorph becomes thermodynamically favored. Interestingly, the structural phase transition provides external control over the monolayer morphology and, for the system under discussion, results in an effective opening and closing of supramolecular nanopores in a two-dimensional molecular monolayer.


ADAM9 promotes lung cancer metastases to brain by a plasminogen activator-based pathway.
The transmembrane cell adhesion protein ADAM9 has been implicated in cancer cell migration and lung cancer metastasis to the brain, but the underpinning mechanisms are unclear and clinical support has been lacking. Here, we demonstrate that ADAM9 enhances the ability of tissue plasminogen activator (tPA) to cleave and stimulate the function of the promigratory protein CDCP1 to promote lung metastasis. Blocking this mechanism of cancer cell migration prolonged survival in tumor-bearing mice and cooperated with dexamethasone and dasatinib (a dual Src/Abl kinase inhibitor) treatment to enhance cytotoxic treatment. In clinical specimens, high levels of ADAM9 and CDCP1 correlated with poor prognosis and high risk of mortality in patients with lung cancer. Moreover, ADAM9 levels in brain metastases derived from lung tumors were relatively higher than the levels observed in primary lung tumors. Our results show how ADAM9 regulates lung cancer metastasis to the brain by facilitating the tPA-mediated cleavage of CDCP1, with potential implications to target this network as a strategy to prevent or treat brain metastatic disease.


Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection.
Metagenomic sequence data can be used to detect the presence of infectious viruses and bacteria, but normal microbial flora make this process challenging. We re-analyzed metagenomic RNA sequence data collected during a recent outbreak of acute flaccid myelitis (AFM), caused in some cases by infection with enterovirus D68. We found that among the patients whose symptoms were previously attributed to enterovirus D68, one patient had clear evidence of infection with Haemophilus influenzae, and a second patient had a severe Staphylococcus aureus infection caused by a methicillin-resistant strain. Neither of these bacteria were identified in the original study. These observations may have relevance in cases that present with flaccid paralysis because bacterial infections, co-infections or post-infection immune responses may trigger pathogenic processes that may present as poliomyelitis-like syndromes and may mimic AFM. A separate finding was that large numbers of human sequences were present in each of the publicly released samples, although the original study reported that human sequences had been removed before deposition.


Diagnostic yield and accuracy of coronary CT angiography after abnormal nuclear myocardial perfusion imaging.
We aimed to determine the diagnostic yield and accuracy of coronary CT angiography (CCTA) in patients referred for invasive coronary angiography (ICA) based on clinical concern for coronary artery disease (CAD) and an abnormal nuclear stress myocardial perfusion imaging (MPI) study. We enrolled 100 patients (84 male, mean age 59.6 ± 8.9 years) with an abnormal MPI study and subsequent referral for ICA. Each patient underwent CCTA prior to ICA. We analyzed the prevalence of potentially obstructive CAD (≥50% stenosis) on CCTA and calculated the diagnostic accuracy of ≥50% stenosis on CCTA for the detection of clinically significant CAD on ICA (defined as any ≥70% stenosis or ≥50% left main stenosis). On CCTA, 54 patients had at least one ≥50% stenosis. With ICA, 45 patients demonstrated clinically significant CAD. A positive CCTA had 100% sensitivity and 84% specificity with a 100% negative predictive value and 83% positive predictive value for clinically significant CAD on a per patient basis in MPI positive symptomatic patients. In conclusion, almost half (48%) of patients with suspected CAD and an abnormal MPI study demonstrate no obstructive CAD on CCTA.


MAPK- and glycogen synthase kinase 3-mediated phosphorylation regulates the DEAD-box protein modulator Gle1 for control of stress granule dynamics.
Rapid expression of critical stress response factors is a key survival strategy for diseased or stressed cells. During cell stress, translation is inhibited, and a pre-existing pool of cytoplasmic mRNA-protein complexes reversibly assembles into cytoplasmic stress granules (SGs). Gle1 is a conserved modulator of RNA-dependent DEAD-box proteins required for mRNA export, translation, and stress responses. Proper Gle1 function is critical as reflected by some human diseases such as developmental and neurodegenerative disorders and some cancers linked to gle1 mutations. However, the mechanism by which Gle1 controls SG formation is incompletely understood. Here, we show that human Gle1 is regulated by phosphorylation during heat shock stress. In HeLa cells, stress-induced Gle1 hyperphosphorylation was dynamic, primarily in the cytoplasmic pool, and followed changes in translation factors. MS analysis identified 14 phosphorylation sites in the Gle1A isoform, six of which clustered in an intrinsically disordered, low-complexity N-terminal region flanking the coil-coiled self-association domain. Of note, two mitogen-activated protein kinases (MAPKs), extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK), phosphorylated the Gle1A N-terminal domain, priming it for phosphorylation by glycogen synthase kinase 3 (GSK3). A phosphomimetic gle1A6D variant (in which six putative Ser/Thr phosphorylation sites were substituted with Asp) perturbed self-association and inhibited DEAD-box helicase 3 (X-linked) (DDX3) ATPase activity. Expression of alanine-substituted, phosphodeficient GFP-gle1A6A promoted SG assembly, whereas GFP-gle1A6D enhanced SG disassembly. We propose that MAPKs and GSK3 phosphorylate Gle1A and thereby coordinate SG dynamics by altering DDX3 function.


Early Development of Parvalbumin-, Somatostatin-, and Cholecystokinin-Expressing Neurons in Rat Brain following Prenatal Immune Activation and Maternal Iron Deficiency.
Prenatal maternal infection and maternal iron deficiency during pregnancy are 2 early environmental insults associated with increased risk for schizophrenia in offspring. Substantial evidence suggests that abnormalities in inhibitory γ-aminobutyric acid (GABA) interneuron function, especially in the parvalbumin subtype of GABA interneuron, both developmentally and in adulthood, may contribute mechanistically to cognitive deficits and psychotic symptoms in schizophrenia. This study used a rat model to test whether prenatal immune activation with lipopolysaccharide (LPS; at gestation days, GD, 15 and 16) or maternal iron deficiency (from GD2 to postnatal day P7) or the combination of both insults alters major subtypes of GABAergic interneurons (parvalbumin, somatostatin, cholecystokinin) in brain regions relevant to schizophrenia (medial and dorsolateral prefrontal cortex [PFC], hippocampal CA1 and dentate gyrus, ventral subiculum) in offspring at P14 or P28. Prenatal LPS treatment significantly increased the density of parvalbumin-immunoreactive neurons at P14 in the medial PFC, dorsolateral PFC, and ventral subiculum of offspring born from iron-sufficient but not iron-deficient dams. Prenatal LPS also increased cholecystokinin neuron density in the medial PFC at P28, under both iron-sufficient and iron-deficient conditions. We observed a large increase in parvalbumin neuron density from P14 to P28 in the medial PFC and subiculum across all birth groups, that was not observed in other brain regions, and significant decreases in somatostatin neuron density from P14 to P28 in all brain regions examined across all birth groups, indicating differential developmental trajectories for parvalbumin and somatostatin neurons in various brain regions during this early postnatal period. Thus, it appears that the medial PFC and ventral subiculum, brain regions involved in circuitry modulating ventral tegmental dopamine and nucleus accumbens activities, may be regions vulnerable to effects of prenatal LPS on specific subpopulations of interneurons. It is known that the timing of maturation and expansion of parvalbumin neurons in early development provides threshold levels of inhibition that trigger critical periods for cortical plasticity, leading to long-term circuit consolidation. Thus, our finding of increased parvalbumin neuron density at early developmental times might suggest a mechanism by which an acute prenatal insult like LPS exposure could produce long-term changes in prefrontal cortical or subicular function.


Does Structured Exercise Improve Cognitive Impairment in People with Mild to Moderate Dementia? A Cost-Effectiveness Analysis from a Confirmatory Randomised Controlled Trial: The Dementia and Physical Activity (DAPA) Trial.
Previous studies suggest that physical exercise could slow dementia progression. However, evidence for the cost effectiveness of structured exercise is conflicting and based on small trials. The objective of this study was to compare the cost effectiveness of a tailored, structured, moderate- to high-intensity exercise programme versus usual care in people with mild to moderate dementia. An economic evaluation was conducted from the UK National Health Service and personal social services perspective, based on data from a large randomised controlled trial. The primary clinical outcome was the participant reported ADAS-Cog (Alzheimer's Disease Assessment Scale-Cognitive Subscale) at 12 months. Costs (£; 2014-2015 prices) were collected prospectively over a 12-month follow-up period. A bivariate regression of costs and quality-adjusted life-years (QALYs), with multiple imputation of missing data, was conducted with the view to estimating the incremental cost per QALY gained and the incremental net monetary benefit (INMB) associated with the exercise programme plus usual care versus usual care. Sensitivity analyses were undertaken to assess the impact of uncertainty surrounding aspects of the economic evaluation, and pre-specified subgroup analyses explored heterogeneity in the cost-effectiveness results. Participants (n = 494) were randomised to exercise plus usual care or usual care only. By 12 months the mean ADAS-Cog score had worsened slightly to 25.2 (standard deviation [SD] 12.3) in the exercise arm and 23.8 (SD 10.4) in the usual care: difference - 1.4, 95% confidence interval (CI) - 2.6 to - 0.2 (p = 0.03). The mean (standard error [SE]) costs over 12 months for experimental versus control was £5945 (US$7856) versus £4597 (US$6574), respectively; (difference: £1347 [$1926]; p = 0.0426). Mean (SE) QALY estimates were 0.787 (0.012) versus 0.826 (0.019), respectively (p = 0.090). The probability that the exercise programme is cost effective was < 1% across cost-effectiveness thresholds. INMBs ranged between -£2601 (US$3719) and £2158 (US$3086) at cost-effectiveness thresholds between £15,000 (US$21,450) and £30,000 (US$42,900) per QALY. The cost-effectiveness results remained robust to several sensitivity and subgroup analyses. Building on the clinical results of the trial, which showed that the structured exercise programme evaluated does not slow cognitive impairment in people with mild to moderate dementia, this economic evaluation shows that the programme is not cost effective.


The pleiotropic effects of antithrombotic drugs in the metabolic-cardiovascular-neurodegenerative disease continuum: impact beyond reduced clotting.
Antithrombotic drugs are widely used for primary and secondary prevention, as well as treatment of many cardiovascular disorders. Over the past few decades, major advances in the pharmacology of these agents have been made with the introduction of new drug classes as novel therapeutic options. Accumulating evidence indicates that the beneficial outcomes of some of these antithrombotic agents are not solely related to their ability to reduce thrombosis. Here, we review the evidence supporting established and potential pleiotropic effects of four novel classes of antithrombotic drugs, adenosine diphosphate (ADP) P2Y12-receptor antagonists, Glycoprotein IIb/IIIa receptor Inhibitors, and Direct Oral Anticoagulants (DOACs), which include Direct Factor Xa (FXa) and Direct Thrombin Inhibitors. Specifically, we discuss the molecular evidence supporting such pleiotropic effects in the context of cardiovascular disease (CVD) including endothelial dysfunction (ED), atherosclerosis, cardiac injury, stroke, and arrhythmia. Importantly, we highlight the role of DOACs in mitigating metabolic dysfunction-associated cardiovascular derangements. We also postulate that DOACs modulate perivascular adipose tissue inflammation and thus, may reverse cardiovascular dysfunction early in the course of the metabolic syndrome. In this regard, we argue that some antithrombotic agents can reverse the neurovascular damage in Alzheimer's and Parkinson's brain and following traumatic brain injury (TBI). Overall, we attempt to provide an up-to-date comprehensive review of the less-recognized, beneficial molecular aspects of antithrombotic therapy beyond reduced thrombus formation. We also make a solid argument for the need of further mechanistic analysis of the pleiotropic effects of antithrombotic drugs in the future.


Concentric coil arrays for parallel MRI.
A new type of coil array is proposed that consists of concentrically placed coil elements, each of which is characterized by symmetrically arranged lobes that have alternating current directions. Symmetries in the coil elements' conductor paths allow for the minimization of mutual inductance and noise correlations. In addition, the concentric arrangement of the coil elements provides spatial encoding capabilities in multiple directions, which is valuable when arrays are used with parallel MRI. Simulations are presented that describe the signal-to-noise ratio (SNR) properties of individual concentric array elements, and a four-element prototype concentric array is constructed. This prototype array is compared experimentally with three alternative four-element array designs. The overall SNR of the concentric array is comparable to the SNR of the competing arrays. Reconstruction of twofold undersampled data using the concentric array yields an average g-factor of less than 1.3 in all directions parallel to the plane of the array. There is some degradation in performance when threefold undersampled data are reconstructed, but the array still shows substantial directional invariance compared to alternative designs. Both fully-sampled and undersampled cardiac images acquired using the concentric array are shown. These results suggest that concentric structures can be useful tools for designing specialized coil arrays for parallel MRI.


Multimodality treatment involving radiotherapy for advanced liver-confined hepatocellular carcinoma.
Advanced-stage hepatocellular carcinoma (HCC) has an extremely poor prognosis although sorafenib, which is the treatment of choice, has provided survival benefits. Among advanced diseases, liver-confined HCC, which invades the vasculature without extrahepatic metastasis, requires novel therapeutic management beyond using sorafenib alone. Currently, the Korean Liver Cancer Study Group and National Comprehensive Cancer Network guidelines recommend combined radiotherapy (RT) and chemotherapy for some selected cases. For advanced liver-confined HCC, focal liver irradiation, RT technological development, and optimal selection of RT-suitable patients enable clinicians to use RT-involving multimodality treatments based on oncologic principles, such as concurrent chemoradiotherapy, which represent effective multimodality treatments for several types of malignancy. In this review, we discuss the need to develop novel therapeutic approaches for liver-confined HCC and clinical applications of RT-involving multimodality treatments for advanced liver-confined HCC. RT-involving multimodality treatments can enhance the overall therapeutic successes for advanced liver-confined HCC and also provide potential cures to some patients via conversion to a resectable condition.


Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations.
Independent experimental and computational approaches show agreement concerning arginine/membrane interactions when a single arginine is introduced at selected positions within the membrane-spanning region of acetyl-GGALW(5)LALALAL(12)AL(14)ALALW(19)LAGA-ethanolamide, designated GWALP23. Peptide sequence isomers having Arg in position 12 or position 14 display markedly different behaviors, as deduced by both solid-state NMR experiments and coarse-grained molecular dynamics (CG-MD) simulations. With respect to the membrane normal of DOPC or DPPC lipid bilayer membranes, GWALP23-R14 shows one major state whose apparent average tilt is approximately 10 degrees greater than that of GWALP23. The presence of R14 furthermore induces bilayer thinning and peptide displacement to "lift" the charged guanidinium toward the bilayer surface. By contrast, GWALP23-R12 exhibits multiple states that are in slow exchange on the NMR time scale, with CG-MD simulations indicating two distinct positions with different screw rotation angles in the membrane, along with an increased tendency to exit the lipid bilayer.


EASL Clinical Practice Guidelines on hepatitis E virus infection.
Infection with hepatitis E virus (HEV) is a significant cause of morbidity and mortality, representing an important global health problem. Our understanding of HEV has changed completely over the past decade. Previously, HEV was thought to be limited to certain developing countries. We now know that HEV is endemic in most high-income countries and is largely a zoonotic infection. Given the paradigm shift in our understanding of zoonotic HEV and that locally acquired HEV is now the commonest cause of acute viral hepatitis in many European countries, the focus of these Clinical Practice Guidelines will be on HEV genotype 3 (and 4).


Accuracy of Software-Based Three-Dimensional Root Canal Length Measurements Using Cone-Beam Computed Tomography.
This study aims to evaluate the accuracy of three-dimensional root canal length measurements performed by dentists with different experience levels using a special software based on cone beam com-puted tomography (CBCT). A CBCT scan of an artificial resin maxillary molar was used to train dentists (n=65) in using the software (3D Endo, DentsplySirona, Ballaigues, Switzerland) as part of a continuing education course. At the beginning, each participant completed a questionnaire on endodontic and CBCT experiences. After com-prehensive instructions, each participant performed an entire three-dimensional treatment plan by tracing the root canal anatomy between the apical foramen and the center of the canal orifice and simulating a straight-line access. The final root canal length was indicated after the virtual rubber stop of a simulated instrument was adapted to the adjoining cusp. To evaluate the individual accuracy in terms of trueness and precision, differences between the three-dimensional planning and the actual root canal length (ARCL) were calculated, and statistically analyzed. Mean absolute differences between the measurements with the 3D Endo™ software (n=260) and the ARCL were 0.30±0.22 mm. All measurements were within a limit of ±1 mm. The accuracy of root canal length measurements was significantly influenced by the type of root canal (p<0.0001). The smallest devia-tions were observed for the palatal root canal (0.18±0.13 mm), followed by the mesiobuccal (0.26±0.22 mm), the distobuccal (0.32±0.17 mm), and the second mesiobuccal root canal (0.46±0.24 mm). Within the limitations of this study, the 3D Endo software enables reproducible and accurate root canal length measurements as part of a three-dimensional endodontic treatment plan. However, mea-surements should always be clinically verified, as root canal morphology has a statistically significant influence.


Defining Effective Combinations of Immune Checkpoint Blockade and Oncolytic Virotherapy.
Recent data from randomized clinical trials with oncolytic viral therapies and with cancer immunotherapies have finally recapitulated the promise these platforms demonstrated in preclinical models. Perhaps the greatest advance with oncolytic virotherapy has been the appreciation of the importance of activation of the immune response in therapeutic activity. Meanwhile, the understanding that blockade of immune checkpoints (with antibodies that block the binding of PD1 to PDL1 or CTLA4 to B7-2) is critical for an effective antitumor immune response has revitalized the field of immunotherapy. The combination of immune activation using an oncolytic virus and blockade of immune checkpoints is therefore a logical next step. Here, we explore such combinations and demonstrate their potential to produce enhanced responses in mouse tumor models. Different combinations and regimens were explored in immunocompetent mouse models of renal and colorectal cancer. Bioluminescence imaging and immune assays were used to determine the mechanisms mediating synergistic or antagonistic combinations. Interaction between immune checkpoint inhibitors and oncolytic virotherapy was found to be complex, with correct selection of viral strain, antibody, and timing of the combination being critical for synergistic effects. Indeed, some combinations produced antagonistic effects and loss of therapeutic activity. A period of oncolytic viral replication and directed targeting of the immune response against the tumor were required for the most beneficial effects, with CD8(+) and NK, but not CD4(+) cells mediating the effects. These considerations will be critical in the design of the inevitable clinical translation of these combination approaches. Clin Cancer Res; 21(24); 5543-51. ©2015 AACR.See related commentary by Slaney and Darcy, p. 5417.


Dental tissue proportions and enamel thickness in Neandertal and modern human molars.
The thickness of dental enamel is often discussed in paleoanthropological literature, particularly with regard to differences in growth, health, and diet between Neandertals and modern humans. Paleoanthropologists employ enamel thickness in paleodietary and taxonomic studies regarding earlier hominins, but variation in enamel thickness within the genus Homo has not been thoroughly explored despite its potential to discriminate species and its relevance to studies of growth and development. Radiographic two-dimensional studies indicate that Neandertal molar enamel is thin relative to the thick enamel of modern humans, although such methods have limited accuracy. Here we show that, measured via accurate high-resolution microtomographic imaging, Neandertal molar enamel is absolutely and relatively thinner than modern human enamel at most molar positions. However, this difference relates to the ratio of coronal dentine volume to total crown volume, rather than the quantity of enamel per se. The absolute volume of Neandertal molar enamel is similar to that of modern humans, but Neandertal enamel is deposited over a larger volume of coronal dentine, resulting in lower average (and relative) enamel thickness values. Sample sizes do not permit rigorous intragroup comparisons, but Neandertal molar tissue proportions evince less variation than the modern human sample. Differences in three- and two-dimensional enamel thickness data describing Neandertal molars may be explained by dimensional reduction. Although molar tissue proportions distinguish Neanderthals from recent Homo sapiens, additional study is necessary to assess trends in tissue proportions in the genus Homo throughout the Pleistocene.


Activating primary care COPD patients with multi-morbidity through tailored self-management support.
Given the dearth of COPD self-management interventions that specifically acknowledge multi-morbidity in primary care, we aimed to activate COPD patients through personalised self-management support that recognised the implications of co-morbidities. This single-group experimental study included patients aged 40-84 with a spirometry diagnosis of COPD and at least one co-morbidity. A self-management education programme for COPD in the context of multi-morbidity, based on the Health Belief Model, was tailored and delivered to participants by general practice nurses in face-to-face sessions. At 6 months' follow-up, there was significant improvement in patient activation (p < 0.001), COPD-related quality of life (p = 0.012), COPD knowledge (p < 0.001) and inhaler device technique (p = 0.001), with no significant change in perception of multi-morbidity (p = 0.822) or COPD-related multi-morbidity (0.084). The programme improved patients' self-efficacy for their COPD as well as overall health behaviour. The findings form an empirical basis for further testing the programme in a large-scale randomised controlled trial.


[Atopic dermatitis - current insights into path physiology and management].
Atopic eczema (AE) is a multifaktoriell skin disease caused by a variety of factors such as genetic conditions, alterated skin structure, immunologic deviations, psychological and environmental factors, among others. There are two main subtypes of AE, i.e. the IgE-associated ("extrinsic atopic eczema") and the non-IgE-associated type ("intrinsic atopic eczema") with different prognosis concerning the development of respiratory diseases ("atopy march"). The role of allergens varies: while in early childhood food allergens may play a role, mites and microbial antigens may become more relevant in adolescence and adulthood. Recently, it was demonstrated that Filaggrin is a major gene for atopic eczema. The altered skin structure and a deficiency in antimicrobial peptides favour colonization with Staphylococcus aureus; their enterotoxins with superantigenic activity stimulate activation of T cells and macrophages. Also sensitization to the yeast Malassezia spp. occurs almost exclusively in AE patients. So far, AE skin lesions are orchestrated by the local tissue expression of proinflammatory cytokines and chemokines with activation of T lymphocytes, dendritic cells, macrophages, keratinocytes, mast cells, and eosinophils which lead to the skin inflammatory responses. From the therapeutic point of view, a step wise approach using emollients as a basic treatment is recommended. Modern topical corticosteroids of moderate to medium potency applied once per day and only on several days per week offer an efficient anti-inflammatory treatment with moderate side effects. Topic immunomodulatory drugs (tacrolimus and pimecrolimus) have in addition substantially improved the treatment of AE. Proactive treatment approaches also in disease-free intervals may reduce exacerbations and total drug use. Phototherapy and wet dressings are both efficient and safe additional tools in more severe forms. For generalized severe forms systemic drugs such as Cyclosporin A are very helpful. Various Biologicals and antipruriginous substances are under clinical investigation and may add to an improved therapy in the future.


Antidepressant-like effect of Cordyceps sinensis in the mouse tail suspension test.
Cordyceps sinensis (CS) has been known as a component of traditional medicines that elicit various biological effects such as anti-fatigue, immunomodulatory, and hypoglycemic actions. Since it has been well-established that fatigue is closely related to depression, we used the tail suspension test (TST) in mice to examine the antidepressant-like effects of hot water extract (HWCS) and supercritical fluid extract (SCCS) of CS. Immobility time in the TST was reduced by administration of SCCS (2.5-10 ml/kg, p.o.) dose-dependently though it was not reduced by treatment with HWCS (500-2000 mg/kg, p.o.). Neither HWCS nor SCCS altered locomotor activity in the open field test, excluding the possibility that the effect of SCCS is due to activation of locomotion. Pretreatment with prazosin (an adrenoreceptor antagonist) or sulpiride (a dopamine D2 receptor antagonist) reduced the effect of SCCS on the immobility time. In contrast, pretreatment with p-chlorophenylalanine (p-CPA, a serotonin synthesis inhibitor) did not alter the anti-immobility effect of SCCS. The last finding is consistent with an additional observation that SCCS had no effect on head twitch response induced by 5-hydroxy-L-tryptophan in mice. Taken altogether, these results suggest that SCCS may elicit an antidepressant-like effect by affecting the adrenergic and dopaminergic systems, but not by affecting the serotonergic system.


Design and synthesis of a library of lead-like 2,4-bisheterocyclic substituted thiophenes as selective Dyrk/Clk inhibitors.
The Dyrk family of protein kinases is implicated in the pathogenesis of several diseases, including cancer and neurodegeneration. Pharmacological inhibitors were mainly described for Dyrk1A so far, but in fewer cases for Dyrk1B, Dyrk2 or other isoforms. Herein, we report the development and optimization of 2,4-bisheterocyclic substituted thiophenes as a novel class of Dyrk inhibitors. The optimized hit compounds displayed favorable pharmacokinetic properties and high ligand efficiencies, and inhibited Dyrk1B in intact cells. In a larger selectivity screen, only Clk1 and Clk4 were identified as additional targets of compound 48, but no other kinases frequently reported as off-targets. Interestingly, Dyrk1A is implicated in the regulation of alternative splicing, a function shared with Clk1/Clk4; thus, some of the dual inhibitors might be useful as efficient splicing modulators. A further compound (29) inhibited Dyrk1A and 1B with an IC50 of 130 nM, showing a moderate selectivity over Dyrk2. Since penetration of the central nervous system (CNS) seems possible based on the physicochemical properties, this compound might serve as a lead for the development of potential therapeutic agents against glioblastoma. Furthermore, an inhibitor selective for Dyrk2 (24) was also identified, which might be are suitable as a pharmacological tool to dissect Dyrk2 isoform-mediated functions.


Characterization of dFMR1, a Drosophila melanogaster homolog of the fragile X mental retardation protein.
Fragile X syndrome is the most common inherited form of mental retardation. It is caused by loss of FMR1 gene activity due to either lack of expression or expression of a mutant form of the protein. In mammals, FMR1 is a member of a small protein family that consists of FMR1, FXR1, and FXR2. All three members bind RNA and contain sequence motifs that are commonly found in RNA-binding proteins, including two KH domains and an RGG box. The FMR1/FXR proteins also contain a 60S ribosomal subunit interaction domain and a protein-protein interaction domain which mediates homomer and heteromer formation with each family member. Nevertheless, the specific molecular functions of FMR1/FXR proteins are unknown. Here we report the cloning and characterization of a Drosophila melanogaster homolog of the mammalian FMR1/FXR gene family. This first invertebrate homolog, termed dfmr1, has a high degree of amino acid sequence identity/similarity with the defined functional domains of the FMR1/FXR proteins. The dfmr1 product binds RNA and is similar in subcellular localization and embryonic expression pattern to the mammalian FMR1/FXR proteins. Overexpression of dfmr1 driven by the UAS-GAL4 system leads to apoptotic cell loss in all adult Drosophila tissues examined. This phenotype is dependent on the activity of the KH domains. The ability to induce a dominant phenotype by overexpressing dfmr1 opens the possibility of using genetic approaches in Drosophila to identify the pathways in which the FMR1/FXR proteins function.


Increased risk of low birthweight and small for gestational age infants among women with tuberculosis.
As the relationship between tuberculosis (TB) and fetal outcomes remains unclear, this study used a 3-year nationwide population-based data set to determine the risk of adverse pregnancy outcomes [low birthweight (LBW), preterm birth and small for gestational age (SGA) infants] among women with TB. A cross-sectional retrospective study. Taiwan. Linking the Taiwan birth certificate registry and the Taiwan National Health Insurance Research Dataset, we identified 761 women who gave birth from 2001 to 2003 and who had received medication treatment for TB during their pregnancy, together with 3805 unaffected women matched in terms of age and year of delivery. Conditional logistic regression analyses were performed to compare the risk of LBW, preterm birth and SGA for mothers with TB and unaffected mothers. The risk of LBW, preterm birth and SGA. Mothers diagnosed with TB had significantly higher percentages of LBW (8.5 versus 6.4%, P = 0.033) and SGA (19.7 versus 16.7%, P = 0.048) infants than unaffected mothers. However, there was no significant difference in preterm birth (8.0 versus 8.0%, P = 0.961) between these two groups. The adjusted odds ratios of having LBW and SGA infants for mothers with TB were 1.35 (95% CI = 1.01-1.81) and 1.22 (95% CI = 1.00-1.49), respectively, compared with unaffected mothers. We concluded that women diagnosed with TB during pregnancy are at increased risk for having LBW and SGA babies, compared with unaffected mothers. We suggest that clinicians should make women with TB aware of the potential risks before planning a child.


Continuous association of cadherin with beta-catenin requires the non-receptor tyrosine-kinase Fer.
The function of Type 1, classic cadherins depends on their association with the actin cytoskeleton, a connection mediated by alpha- and beta-catenin. The phosphorylation state of beta-catenin is crucial for its association with cadherin and thus the association of cadherin with the cytoskeleton. We now show that the phosphorylation of beta-catenin is regulated by the combined activities of the tyrosine kinase Fer and the tyrosine phosphatase PTP1B. Fer phosphorylates PTP1B at tyrosine 152, regulating its binding to cadherin and the continuous dephosphorylation of beta-catenin at tyrosine 654. Fer interacts with cadherin indirectly, through p120ctn. We have mapped the interaction domains of Fer and p120ctn and peptides corresponding to these sequences release Fer from p120ctn in vitro and in live cells, resulting in loss of cadherin-associated PTP1B, an increase in the pool of tyrosine phosphorylated beta-catenin and loss of cadherin adhesion function. The effect of the peptides is lost when a beta-catenin mutant with a substitution at tyrosine 654 is introduced into cells. Thus, Fer phosphorylates PTP1B at tyrosine 152 enabling it to bind to the cytoplasmic domain of cadherin, where it maintains beta-catenin in a dephosphorylated state. Cultured fibroblasts from mouse embryos targeted with a kinase-inactivating ferD743R mutation have lost cadherin-associated PTP1B and beta-catenin, as well as localization of cadherin and beta-catenin in areas of cell-cell contacts. Expression of wild-type Fer or culture in epidermal growth factor restores the cadherin complex and localization at cell-cell contacts.


Only two out of five articles by New Zealand researchers are free-to-access: a multiple API study of access, citations, cost of Article Processing Charges (APC), and the potential to increase the proportion of open access.
We studied journal articles published by researchers at all eight New Zealand universities in 2017 to determine how many were freely accessible on the web. We wrote software code to harvest data from multiple sources, code that we now share to enable others to reproduce our work on their own sample set. In May 2019, we ran our code to determine which of the 2017 articles were open at that time and by what method; where those articles would have incurred an Article Processing Charge (APC) we calculated the cost if those charges had been paid. Where articles were not freely available we determined whether the policies of publishers in each case would have allowed deposit in a non-commercial repository (Green open access). We also examined citation rates for different types of access. We found that, of our 2017 sample set, about two out of every five articles were freely accessible without payment or subscription (41%). Where research was explicitly said to be funded by New Zealand's major research funding agencies, the proportion was slightly higher at 45%. Where open articles would have incurred an APC we estimated an average cost per article of USD1,682 (for publications where all articles require an APC, that is, Gold open access) and USD2,558 (where APC payment is optional, Hybrid open access) at a total estimated cost of USD1.45m. Of the paid options, Gold is by far more common for New Zealand researchers (82% Gold, 18% Hybrid). In terms of citations, our analysis aligned with previous studies that suggest a correlation between publications being freely accessible and, on balance, slightly higher rates of citation. This is not seen across all types of open access, however, with Diamond OA achieving the lowest rates. Where articles were not freely accessible we found that a very large majority of them (88% or 3089 publications) could have been legally deposited in an institutional repository. Similarly, only in a very small number of cases had a version deposited in the repository of a New Zealand university made the difference between the publication being freely accessible or not (125 publications). Given that most New Zealand researchers support research being open, there is clearly a large gap between belief and practice in New Zealand's research ecosystem.