Synthetic biology: putting synthesis into biology.
The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself--encompassing many branches of science and across many scales of application. New DNA synthesis and assembly techniques have made routine customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery--a self-replicating organism--is being pursued at this moment. The aim of this article is to dissect and organize these various components of synthetic biology into a coherent picture.


An unusual presentation of a dural arteriovenous fistula of the sphenoparietal sinus.
Dural arteriovenous fistulae (DAVFs) are a rare form of intracranial arteriovenous malformation. We present the case of a patient who presented in a previously undescribed manner with facial swelling and bruising initially misdiagnosed as cellulitis. He was found subsequently to have DAVFs of the sphenoparietal sinus that had hemorrhaged. The rarity of DAVFs at this location may account for this unique presentation. Successful treatment was achieved by transarterial embolization.


Occupational exposure to extremely low-frequency magnetic fields and the risk of ALS: A systematic review and meta-analysis.
We performed a meta-analysis to examine associations of occupational exposure to extremely-low frequency magnetic fields (ELF-MF) with amyotrophic lateral sclerosis (ALS). Epidemiologic studies were identified in EMBASE and MEDLINE, in reference lists and a specialist database. We included studies that reported risk estimates of ALS in association with occupational ELF-MF exposure. Summary relative risks (RR) or odds ratios (OR) were obtained with random effect meta-analysis, and analyses were stratified by type of exposure assessment. This was done to evaluate whether observed heterogeneity between studies could be explained with differences in the way the exposure had been determined. We included 20 studies in our meta-analysis. Overall, studies reported a slightly increased risk of ALS in those exposed to higher levels of ELF-MF compared to lower levels with a summary RR (sRR) of 1.14 (95% Confidence Interval [CI] 1.00-1.30) and for workers in electrical occupations (sRR 1.41, CI 1.05-1.92), but with large heterogeneity between studies (I2 > 70%). Self-reported exposure or occupations determined from death certificates did not show increased risks. Highest-longest types of exposure translated into increased risks of ALS if the studies had evaluated the whole occupational history, in contrast to evaluating only few points in time (e.g., from census records); sRR were 1.89 (CI 1.31-2.73, I2 0%) and 1.06 (CI 0.75-1.57, I2 76%), respectively. In this meta-analysis, we observed an increased risk of ALS in workers occupationally exposed to ELF-MF. Results of studies depended on the quality of the exposure assessment. Bioelectromagnetics. 39:156-163, 2018. © 2018 Wiley Periodicals, Inc.


Treatment planning optimisation based on imaging tumour proliferation and cell density.
Functional imaging could provide valuable information on the distribution of biological factors that influence the outcome of radiation therapy. Tumour proliferation and cell density in particular could be imaged with dedicated metabolic tracers and could thus be used for the biological optimisation of the treatment plans. The feasibility of individualising treatment planning using proliferation and density information has been investigated through simulations of heterogeneous tumours taking into account the cell density and proliferation rates. The predicted outcome was used to estimate the success of the individualisation of dose distributions. The results have shown that tumour control could be increased through the escalation of doses to proliferating foci with a relative reduction of doses to slowly proliferating regions of the tumour. This suggests that individualisation of treatment planning taking into account proliferation information creates the premises for further reduction of the doses to the surrounding regions which would consequently lead to an increased sparing of the normal tissues. Cell density has been shown to be another important factor that could be used for optimisation, albeit of a lower weight than proliferation. However, associated with proliferation it could lead to treatment failure if the trouble foci are underdosed. In conclusion, treatment optimisation based on imaged proliferation could improve both tumour control and normal tissue sparing.


Reliability of accelerometry to assess impact loads of jumping and landing tasks.
Overuse injuries, resulting from repetitive subacute impact loading, are a problem in high-performance sports. Monitoring of impact loading may aid in the prevention of these injuries. The current study aimed to establish the intra-day and inter-day reliability of a tri-axial accelerometer to assess impact loading during jumping and landing tasks. Twelve participants wore an accelerometer on their upper and lower back. They performed a continuous hopping task as well as drop landings and rebound jumps from three drop heights (37.5, 57.5 and 77.5 cm), peak resultant acceleration (PRA) was calculated for all tasks. The tasks were performed twice, one week apart at the same time of day. The difference in the mean, intra-class correlation coefficient, coefficient of variation and Cohen's effect size were calculated as measures of reliability. PRA showed good intra-day reliability for the hopping task. Inter-day reliability of the PRA was moderate to good across all tasks. Reliability of PRA was slightly higher when accelerations were recorded on the lower back compared to the upper back. To assess impact loading, during continuous hopping, drop landings and rebound jumps, PRA recorded at both the upper and lower back appears to be a reliable measure.


Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions.
Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone.


Composite lithium electrode with mesoscale skeleton via simple mechanical deformation.
Lithium metal-based batteries are attractive energy storage devices because of high energy density. However, uncontrolled dendrite growth and virtually infinite volume change, which cause performance fading and safety concerns, have limited their applications. Here, we demonstrate that a composite lithium metal electrode with an ion-conducting mesoscale skeleton can improve electrochemical performance by locally reducing the current density. In addition, the potential for short-circuiting is largely alleviated due to side deposition of mossy lithium on the three-dimensional electroactive surface of the composite electrode. Moreover, the electrode volume only slightly changes with the support of a rigid and stable scaffold. Therefore, this mesoscale composite electrode can cycle stably for 200 cycles with low polarization under a high areal current density up to 5 mA/cm2. Most attractively, the proposed fabrication process, which only involves simple mechanical deformation, is scalable and cost effective, providing a new strategy for developing high performance and long lifespan lithium anodes.


Reproducibility and uncertainty of wastewater turbidity measurements.
Turbidity monitoring is a valuable tool for operating sewer systems, but it is often considered as a somewhat tricky parameter for assessing water quality, because measured values depend on the model of sensor, and even on the operator. This paper details the main components of the uncertainty in turbidity measurements with a special focus on reproducibility, and provides guidelines for improving the reproducibility of measurements in wastewater relying on proper calibration procedures. Calibration appears to be the main source of uncertainties, and proper procedures must account for uncertainties in standard solutions as well as non linearity of the calibration curve. With such procedures, uncertainty and reproducibility of field measurement can be kept lower than 5% or 25 FAU. On the other hand, reproducibility has no meaning if different measuring principles (attenuation vs. nephelometry) or very different wavelengths are used.


Survivin is not an independent prognostic factor for patients with upper tract urothelial carcinoma: a multi-institutional study.
Several small single-center studies have reported conflicting results on the prognostic value of survivin expression in upper tract urothelial carcinoma (UTUC) following radical nephroureterectomy. We attempted to validate the prognostic utility of survivin using a large multi-institutional cohort. Survivin expression was evaluated by immunohistochemistry in tumor tissue from 732 patients with unilateral, sporadic UTUC treated with radical nephroureterectomy between 1990 and 2008 at 7 centers. Survivin expression was considered altered when at least 10% of the tumor cells stained positive. Associations of altered survivin expression with recurrence-free survival (RFS) and cancer-specific survival (CSS) were evaluated using Cox proportional hazards regression models. Altered survivin expression was observed in 288 (39.3%) tumors and was associated with more advanced pathological tumor stages (P<0.001), lymph node metastases (P<0.001), lymphovascular invasion (P<0.001), tumor necrosis (P = 0.027), and tumor architecture (P<0.001). Median follow-up was 35 (16-64) months. There were 191 (25.4%) patients who experienced disease recurrence, and 165 patients (21.9%) died of the disease. In the univariable analysis, altered survivin expression was significantly associated with worse RFS and CSS (each P<0.001); however, altered survivin expression did not achieve independent predictive status on multivariable models (P = 0.24 and P = 0.53). Similarly, survivin was not independently associated with outcomes in subgroup analyses, including patients with high-grade tumors. In UTUC, altered survivin expression is associated with worse clinicopathological features and worse RFS and CSS. However, it does not appear to be independently associated with cancer outcomes when considering standard prognostic factors.


De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.
It remains a challenge to perform de novo assembly using next-generation sequencing (NGS). Despite the availability of multiple sequencing technologies and tools (e.g., assemblers) it is still difficult to assemble new genomes at chromosome resolution (i.e., one sequence per chromosome). Obtaining high quality draft assemblies is extremely important in the case of yeast genomes to better characterise major events in their evolutionary history. The aim of this work is two-fold: on the one hand we want to show how combining different and somewhat complementary technologies is key to improving assembly quality and correctness, and on the other hand we present a de novo assembly pipeline we believe to be beneficial to core facility bioinformaticians. To demonstrate both the effectiveness of combining technologies and the simplicity of the pipeline, here we present the results obtained using the Dekkera bruxellensis genome. In this work we used short-read Illumina data and long-read PacBio data combined with the extreme long-range information from OpGen optical maps in the task of de novo genome assembly and finishing. Moreover, we developed NouGAT, a semi-automated pipeline for read-preprocessing, de novo assembly and assembly evaluation, which was instrumental for this work. We obtained a high quality draft assembly of a yeast genome, resolved on a chromosomal level. Furthermore, this assembly was corrected for mis-assembly errors as demonstrated by resolving a large collapsed repeat and by receiving higher scores by assembly evaluation tools. With the inclusion of PacBio data we were able to fill about 5 % of the optical mapped genome not covered by the Illumina data.


Absence of age and gender effects on the pharmacokinetics of a single 500-milligram oral dose of levofloxacin in healthy subjects.
The influence of age and gender on the pharmacokinetics of levofloxacin in healthy subjects receiving a single oral 500-mg dose of levofloxacin was investigated in this parallel design study. Six young males (aged 18 to 40 years), six elderly males (aged > or = 65 years), six young females (aged 18 to 40 years), and six elderly females (aged > or = 65 years) were enrolled and completed the study. The study reveals that the bioavailability (rate and extent) of levofloxacin was not affected by either age or gender. In both age (young and elderly) and gender (male and female) groups of subjects, peak concentrations in plasma were reached at approximately 1.5 h after dosing; renal clearance of levofloxacin accounted for approximately 77% of total body clearance, and approximately 76% of the administered dose was recovered unchanged in urine over the 36 h of collection. The apparent differences in the calculated pharmacokinetic parameters for levofloxacin between the age groups (young versus elderly) and between the gender groups (males versus females) could be explained by differences in renal function among the subjects. A single dose of 500 mg of levofloxacin administered orally to both young and old, male and female healthy subjects was found to be safe and well tolerated. As the differences in levofloxacin kinetics between the young and the elderly or the males and the females are limited and are mainly related to the renal function of the subjects, dose adjustment based on age or gender alone is not necessary.


Long-term outcomes of total elbow arthroplasty for distal humeral fracture: results from a prior randomized clinical trial.
Total elbow arthroplasty (TEA) is a reliable treatment for elderly patients with comminuted intra-articular distal humeral fractures. However, the longevity and long-term complications associated with this procedure are unknown. The objectives of this study were to examine long-term outcomes and implant survival in elderly patients undergoing TEA for fracture. Patients from a previously published randomized controlled trial of 42 patients in which TEA was compared with open reduction-internal fixation (ORIF) were followed up long term. Patients were aged 65 years or older with comminuted intra-articular distal humeral fractures. Outcomes included patient-reported grading of function and pain, revision surgical procedures, and implant survival. Data were obtained for 40 patients, 15 treated with ORIF and 25 treated with TEA, with a mean follow-up period of 12.5 years for surviving patients and 7.7 years for deceased patients. The reoperation rate was 3 of 25 in the TEA group and 4 of 15 in the ORIF group (P = .39). Of the 25 patients with TEAs, only 1 required (early) revision arthroplasty; 7 were living with their original arthroplasty, and 15 died with a well-functioning implant in situ. Three were lost to follow-up. TEA is an effective and reliable procedure for the treatment of comminuted distal humeral fractures in the elderly patient. Our study reveals reliable implant long-term survival, with no patient requiring a late revision. For the majority of these patients, a well-performed TEA will give them a well-functioning elbow for life and will be the last elbow procedure required.


Calpain inhibitor inhibits p35-p25-Cdk5 activation, decreases tau hyperphosphorylation, and improves neurological function after spinal cord hemisection in rats.
Aberrant calpain activation is a key mediator of neuron death. We examined the cell-permeable calpain inhibitor MDL28170 in the pathophysiological processes after spinal cord injury (SCI) including p35-p25- cyclin-dependent kinase-5 (Cdk5) activation, tau hyperphosphorylation, neuron cell death, calpain I activation, astrogliosis, and microglia activation. Our study showed that intrathecal administration of MDL28170 improved neurologic dysfunction, prevented neuron loss, decreased the number of apoptotic cells, and abated astrogliosis and microglia activation 7 days after spinal cord hemisection in rats. Reverse transcription polymerase chain reaction demonstrated calpain inhibition significantly attenuated the ratio of proapoptotic Bax/anti-apoptotic Bcl-2 mRNA in the lesion and penumbra after SCI. Calpain, the calcium-activated proteolytic enzyme, was found to digest p35 to its truncated product, p25. Moreover, abnormal Cdk5 activation by p25 and subsequent tau hyperphosphorylation triggers pathologic events leading to neurodegeneration and neurofibrillary tangles. We found p35-p25-Cdk5 activation and tau hyperphosphorylation in SCI, and then we showed that intrathecal MDL28170 treatment could diminish p35 truncation, and abrogate aberrant tau phosphorylation. Double labeling of calpain I and phosphorylated tau (AT8) in the same cells of spinal cord lesion further implicated pathogenesis of SCI. In conclusion, MDL28170 abated calpain I activation, inhibited apoptosis and neuron loss, quenched microglia and astrocyte activation, and significantly improved neurologic deficit one week after spinal cord hemisection. The neuroprotective mechanisms of calpain inhibitor in SCI could be attenuating upregulation of Bax/Bcl-2 ratio, preventing p35 truncation in the lesion and penumbra, and abrogating tau hyperphosphorylation.


Downregulation of uPA/uPAR inhibits intermittent hypoxia-induced epithelial-mesenchymal transition (EMT) in DAOY and D283 medulloblastoma cells.
Hypoxia is known to induce overexpression of the urokinase plasminogen activator (uPA) and its receptor (uPAR) and thus overexpression promotes uPAR-mediated survival signaling in various cancers. Moreover, hypoxia/ overexpression of uPAR in cancer cells promote the epithelial-mesenchymal transition (EMT) and thereby invasiveness and metastasis. In this study, we show that intermittent hypoxia has a more pronounced effect than chronic hypoxia and contributes to EMT, invasion and migration in medulloblastoma cells. Intermittent hypoxia induced expression of mesenchymal markers (i.e., SNAIL, Vimentin and N-cadherin) and reduced expression of epithelial markers (i.e., Zo-1, E-cadherin) in medulloblastoma cells. Further, intermittent hypoxia also leads to enhancement in cell invasion, migration and angiogenesis in medulloblastoma cells. Intermittent hypoxia also inhibited expression of pro-anti-apoptotic proteins (Bax and Bad), and induced expression of anti-pro-apoptotic proteins (Bcl2 and Bcl-xL), and activation of ERK in medulloblastoma cells. Transcriptional inactivation of either uPA or uPAR inhibits the intermittent hypoxia-induced invasion and migration, and expression of Vimentin. uPA/ uPAR downregulation also induces E-cadherin expression and inhibits activation of ERK. Thus, transcriptional inactivation of either uPA or uPAR enhances the apoptotic response in medulloblastoma cells exposed to intermittent hypoxia. This study provides evidence of the anti-tumor efficacy of down-regulation of uPA or uPAR in medulloblastoma tumors to target hypoxia-induced cell EMT, invasion and migration, to achieve better therapeutic outcomes in the treatment of malignant medulloblastoma.


Beta-catenin/Tcf-4 inhibition after progastrin targeting reduces growth and drives differentiation of intestinal tumors.
Aberrant activation of the beta-catenin/Tcf-4 transcriptional complex represents an initiating event for colorectal carcinogenesis, shifting the balance from differentiation toward proliferation in colonic crypts. Here, we assessed whether endogenous progastrin, encoded by a target gene of this complex, was in turn able to regulate beta-catenin/Tcf-4 activity in adenomatous polyposis coli (APC)-mutated cells, and we analyzed the impact of topical progastrin depletion on intestinal tumor growth in vivo. Stable or transient RNA silencing of the GAST gene was induced in human tumor cells and in mice carrying a heterozygous Apc mutation (APCDelta14), which overexpress progastrin but not amidated or glycine-extended gastrin. Depletion of endogenous progastrin production strongly decreased intestinal tumor growth in vivo through a marked inhibition of constitutive beta-catenin/Tcf-4 activity in tumor cells. This effect was mediated by the de novo expression of the inhibitor of beta-catenin and Tcf-4 (ICAT), resulting from a down-regulation of integrin-linked kinase in progastrin-depleted cells. Accordingly, ICAT down-regulation was correlated with progastrin overexpression and Tcf-4 target gene activation in human colorectal tumors, and ICAT repression was detected in the colon epithelium of tumor-prone, progastrin-overexpressing mice. In APCDelta14 mice, small interfering RNA-mediated progastrin depletion not only reduced intestinal tumor size and numbers, but also increased goblet cell lineage differentiation and cell apoptosis in the remaining adenomas. Thus, depletion of endogenous progastrin inhibits the tumorigenicity of APC-mutated colorectal cancer cells in vivo by promoting ICAT expression, thereby counteracting Tcf-4 activity. Progastrin targeting strategies should provide an exciting prospect for the differentiation therapy of colorectal cancer.


Ecology of H3 avian influenza viruses in Korea and assessment of their pathogenic potentials.
To determine the genetic origins of novel H3 avian influenza viruses of chickens and ducks in Korea, genetic characterization of H3 avian influenza viruses isolated from live poultry markets and migratory aquatic birds in South Korea during 2004-2006 was conducted. Phylogenetic analysis revealed that at least four novel genotypes of H3N2 and two genotypes of H3N6 avian influenza viruses were co-circulating in backyard poultry of Korea. The viruses were reassortants between H9N2 viruses of Korean chickens and unknown influenza viruses of migratory birds. Genetic comparison of H3 viruses from live bird markets with those from wild bird isolates revealed that certain gene segments of wild bird isolates are related closely to those of Korean group H9N2 viruses isolated from live poultry markets in 2003. Furthermore, animal-challenge studies demonstrated that the pathogenicity of certain avian H3 influenza viruses was altered due to reassortment, leading to H3 avian influenza viruses in Korea that can potentially expand their host range to include mammals. These studies emphasize the continuing need to monitor backyard poultry at live poultry markets to better understand interspecies transmission and the emergence of novel influenza viruses that have the potential to infect humans.


Associations between Parental Concerns about Preschoolers' Weight and Eating and Parental Feeding Practices: Results from Analyses of the Child Eating Behavior Questionnaire, the Child Feeding Questionnaire, and the Lifestyle Behavior Checklist.
Insight into parents' perceptions of their children's eating behaviors is crucial for the development of successful childhood obesity programs. However, links between children's eating behaviors and parental feeding practices and concerns have yet to be established. This study aims to examine associations between parental perceptions of preschoolers' eating behaviors and parental feeding practices. First, it tests the original 8-factor structure of the Child Eating Behavior Questionnaire (CEBQ). Second, it examines the associations with parental feeding practices, measured with the Child Feeding Questionnaire (CFQ). Questionnaires were sent to parents from 25 schools/preschools in Stockholm, Sweden and to parents starting a childhood obesity intervention. The CEBQ factor structure was tested with confirmatory factor analysis (CFA). Associations between CEBQ subscales Food approach and Food avoidance and CFQ factors Restriction, Pressure to eat and Monitoring were examined with structural equation modelling (SEM), adjusting for child and parental characteristics, and parental confidence, measured with the Lifestyle Behavior Checklist (LBC). CFQ Concern for child weight and Perceived responsibility for child eating were used as mediators. 478 parents completed the questionnaires (children: 52% girls, mean age 5.5 years, 20% overweight/obese). A modified 8-factor structure showed an acceptable fit (TLI = 0.91, CFI = 0.92, RMSEA = 0.05 and SRMR = 0.06) after dropping one item and allowing three pairs of error terms to correlate. The SEM model demonstrated that Food approach had a weak direct effect on Restriction, but a moderate (β = 0.30) indirect effect via Concern, resulting in a substantial total effect (β = 0.37). Food avoidance had a strong positive effect on Pressure to eat (β = 0.71). The CEBQ is a valid instrument for assessing parental perceptions of preschoolers' eating behaviors. Parental pressure to eat was strongly associated with children's food avoidance. Parental restriction, however, was more strongly associated with parents' concerns about their children's weights than with children's food approach. This suggests that childhood obesity interventions should address parents' perceptions of healthy weight alongside perceptions of healthy eating.


Steric control of the donor/acceptor interface: implications in organic photovoltaic charge generation.
The performance of organic photovoltaic (OPV) devices is currently limited by modest short-circuit current densities. Approaches toward improving this output parameter may provide new avenues to advance OPV technologies and the basic science of charge transfer in organic semiconductors. This work highlights how steric control of the charge separation interface can be effectively tuned in OPV devices. By introducing an octylphenyl substituent onto the investigated polymer backbones, the thermally relaxed charge-transfer state, and potentially excited charge-transfer states, can be raised in energy. This decreases the barrier to charge separation and results in increased photocurrent generation. This finding is of particular significance for nonfullerene OPVs, which have many potential advantages such as tunable energy levels and spectral breadth, but are prone to poor exciton separation efficiencies. Computational, spectroscopic, and synthetic methods were combined to develop a structure-property relationship that correlates polymer substituents with charge-transfer state energies and, ultimately, device efficiencies.


Evolution of a phage RuvC endonuclease for resolution of both Holliday and branched DNA junctions.
Resolution of Holliday junction recombination intermediates in most Gram-negative bacteria is accomplished by the RuvC endonuclease acting in concert with the RuvAB branch migration machinery. Gram-positive species, however, lack RuvC, with the exception of distantly related orthologues from bacteriophages infecting Lactococci and Streptococci. We have purified one of these proteins, 67RuvC, from Lactococcus lactis phage bIL67 and demonstrated that it functions as a Holliday structure resolvase. Differences in the sequence selectivity of resolution between 67RuvC and Escherichia coli RuvC were noted, although both enzymes prefer to cleave 3' of thymidine residues. However, unlike its cellular counterpart, 67RuvC readily binds and cleaves a variety of branched DNA substrates in addition to Holliday junctions. Plasmids expressing 67RuvC induce chromosomal breaks, probably as a consequence of replication fork cleavage, and cannot be recovered from recombination-defective E. coli strains. Despite these deleterious effects, 67RuvC constructs suppress the UV light sensitivity of ruvA, ruvAB and ruvABC mutant strains confirming that the phage protein mediates Holliday junction resolution in vivo. The characterization of 67RuvC offers a unique insight into how a Holliday junction-specific resolvase can evolve into a debranching endonuclease tailored to the requirements of phage recombination.


Dissociable neural mechanisms underlie currently-relevant, future-relevant, and discarded working memory representations.
In daily life, we use visual working memory (WM) to guide our actions. While attending to currently-relevant information, we must simultaneously maintain future-relevant information, and discard information that is no longer relevant. However, the neural mechanisms by which unattended, but future-relevant, information is maintained in working memory, and future-irrelevant information is discarded, are not well understood. Here, we investigated representations of these different information types, using functional magnetic resonance imaging in combination with multivoxel pattern analysis and computational modeling based on inverted encoding model simulations. We found that currently-relevant WM information in the focus of attention was maintained through representations in visual, parietal and posterior frontal brain regions, whereas deliberate forgetting led to suppression of the discarded representations in early visual cortex. In contrast, future-relevant information was neither inhibited nor actively maintained in these areas. These findings suggest that different neural mechanisms underlie the WM representation of currently- and future-relevant information, as compared to information that is discarded from WM.


Persistent organic pollutants and liver dysfunction biomarkers in a population-based human sample of men and women.
Persistent organic pollutants (POPs) are stable organic compounds generated through different industrial activities. Liver is involved in the metabolism of POPs, and hence exposure to POPs may interfere with liver function. Although a few studies have shown adverse effects of POPs on liver function, large-scale studies involving humans are lacking. We performed this large population-based cross-sectional study to assess the associations between different POPs and liver dysfunction biomarkers. A total of 992 individuals (all aged 70 years, 50% males) were recruited as part of Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) cohort. The total toxic equivalency (TEQ) value was calculated for seven mono-ortho and two non-ortho substituted polychlorinated biphenyls (PCBs) and octachloro-p-dibenzodioxin (OCDD) to assess their toxicological effects. The association of TEQ values, summary measures of 16 PCBs (sum of PCBs) and three organochlorine pesticides (sum of OC pesticides) with liver dysfunction biomarkers (bilirubin; alkaline phosphatase, ALP; alanine aminotransferase, ALT; and gamma-glutamyltransferase, GGT) was analyzed utilizing linear regression analysis. The mono-ortho PCB TEQ values were found to be significantly positively associated with bilirubin (β=0.71, P=0.008), while sum of OC pesticide concentrations was negatively associated with ALP (β=-0.02, P=0.002) after adjusting for various potential confounders. When analyzed individually, a number of different POPs were associated with ALP, ALT and bilirubin. No such association with GGT was observed. Various POPs including PCBs, OCDD and pesticides were associated with the liver dysfunction biomarkers bilirubin, ALT and ALP, suggesting adverse effects on liver function from these environmental pollutants.


Bleeding risks associated with inheritance of the Quebec platelet disorder.
Quebec platelet disorder (QPD) is an autosomal dominant bleeding disorder associated with increased urokinase-type plasminogen activator in platelets and alpha-granule protein degradation. To determine bleeding risks and common manifestations of QPD, a history questionnaire was developed and administered to 127 relatives in a family with QPD. Data entry was done blinded to affected and unaffected status, determined by assays for platelet urokinase-type plasminogen activator (u-PA) and fibrinogen degradation. Odds ratios (ORs), with 95% confidence intervals (CIs), were determined for items queried. Summative bleeding scores for each individual were calculated using items with OR more than 1. Mean ages (34 years; range, 1-89 years) were similar for affected (n = 23) and unaffected (n = 104) family members. Affected individuals had higher mean bleeding scores (P <.0001) and a much higher likelihood (OR > 20) of having bleeding that led to lifestyle changes, bruises that spread lower or as large or larger than an orange or both, joint bleeds, bleeding longer than 24 hours after dental extractions or deep cuts, and received or been recommended other treatments (fibrinolytic inhibitors) for bleeding. Individuals with QPD and exposure(s) to hemostatic challenges had experienced excessive bleeding only when fibrinolytic inhibitors had not been used. These data illustrate that QPD is associated with increased risks of bleeding that can be modified by fibrinolytic inhibitors.


A minimal "push-pull" bistability model explains oscillations between quiescent and proliferative cell states.
A minimal model for oscillating between quiescent and growth/proliferation states, dependent on the availability of a central metabolic resource, is presented. From the yeast metabolic cycles, metabolic oscillations in oxygen consumption are represented as transitions between quiescent and growth states. We consider metabolic resource availability, growth rates, and switching rates (between states) to model a relaxation oscillator explaining transitions between these states. This frustrated bistability model reveals a required communication between the metabolic resource that determines oscillations and the quiescent and growth state cells. Cells in each state reflect memory, or hysteresis of their current state, and "push-pull" cells from the other state. Finally, a parsimonious argument is made for a specific central metabolite as the controller of switching between quiescence and growth states. We discuss how an oscillator built around the availability of such a metabolic resource is sufficient to generally regulate oscillations between growth and quiescence through committed transitions.


Dental metal allergy in patients with oral, cutaneous, and genital lichenoid reactions.
The subject of lichen planus (LP) and dental metal allergy long has been debated. An overwhelming majority of the existing literature focuses on mercury and gold salts in relation to oral lichen planus. Our objective was to expand current knowledge regarding LP and lichenoid lesions (LL) and dental metal allergy by investigating more metals and investigating cutaneous and genital disease in addition to oral disease. Fifty-one patients with known LP or LL were patch tested to a series of dental metals. Patients chose to replace their dental metals or make no revision. A telephone survey was conducted after 1 year to determine disease state. Thirty-eight of 51 patients (74.5%) had at least 1 positive reaction. Twenty-five of 51 patients (49.0%) showed sensitivity to at least 1 mercurial allergen. Prevalence data for patients patch tested by the North American Contact Dermatitis Group (NACDG) from 1996 to 1998 was available for chromate, cobalt, gold, nickel, and thimerosal. The prevalence of positive reactions was higher in our group than in the NACDG group for all 5 of these allergens, and statistical significance was achieved for chromate (P = .028), gold (P = .041), and thimerosal (P = .005). Of patients who had a positive patch test reaction to 1 or more metals, 100% (9 of 9) reported improvement after metal replacement, whereas 62.5% (15 of 24) reported improvement without metal replacement. Sensitization to dental metals is more common among LP and LL patients than in routinely tested patients, and might be an etiologic or triggering factor in the disease.


Spatial Entropy Pursuit for Fast and Accurate Perimetry Testing.
To propose a static automated perimetry strategy that increases the speed of visual field (VF) evaluation while retaining threshold estimate accuracy. We propose a novel algorithm, spatial entropy pursuit (SEP), which evaluates individual locations by using zippy estimation by sequential testing (ZEST) but additionally uses neighboring locations to estimate the sensitivity of related locations. We model the VF with a conditional random field (CRF) where each node represents a location estimate that depends on itself as well as its neighbors. Tested locations are randomly selected from a pool of locations and new locations are added such that they maximally reduce the uncertainty over the entire VF. When no location can further reduce the uncertainty significantly, remaining locations are estimated from the CRF directly. SEP was evaluated and compared to tendency-oriented strategy, ZEST, and the Dynamic Test Strategy by using computer simulations on a test set of 245 healthy and 172 glaucomatous VFs. For glaucomatous VFs, root-mean-square error (RMSE) of SEP was comparable to that of existing strategies (3.4 dB), whereas the number of stimulus presentations of SEP was up to 23% lower than that of other methods. For healthy VFs, SEP had an RMSE comparable to evaluated methods (3.1 dB) but required 55% fewer stimulus presentations. When compared to existing methods, SEP showed improved performances, especially with respect to test speed. Thus, it represents an interesting alternative to existing strategies.


Intracellular and membrane-damaging activities of methyl gallate isolated from Terminalia chebula against multidrug-resistant Shigella spp.
Shigella spp. (Shigella dysenteriae, Shigella flexneri, Shigella boydii and Shigella sonnei) cause bacillary dysentery (shigellosis), which is characterized by bloody mucous diarrhoea. Although a variety of antibiotics have been effective for treatment of shigellosis, options are becoming limited due to globally emerging drug resistance. In the present study, in vitro antibacterial activity of methyl gallate (MG) isolated from Terminalia chebula was determined by performing MIC, minimal bactericidal concentration (MBC) and time-kill kinetic studies. Bacterial membrane-damaging activity of MG was determined by membrane perturbation and transmission electron microscopy (TEM). Cellular drug accumulation, cell infection and assessment of intracellular activities of MG and reference antibiotics were performed using HeLa cell cultures. The bactericidal activity of MG against multidrug-resistant (MDR) Shigella spp. in comparison with other commonly used drugs including fluoroquinolone was demonstrated here. TEM findings in the present study revealed that MG caused the total disintegration of inner and outer membranes, and leakage of the cytoplasmic contents of S. dysenteriae. The level of accumulation of MG and tetracycline in HeLa cells incubated for 24 h was relatively higher than that of ciprofloxacin and nalidixic acid (ratio of intracellular concentration/extracellular concentration of antibiotic for MG and tetracycline>ciprofloxacin and nalidixic acid). The viable number of intracellular S. dysenteriae was decreased in a time-dependent manner in the presence of MG (4 × MBC) and reduced to zero within 20 h. The significant intracellular activities of MG suggested that it could potentially be used as an effective antibacterial agent for the treatment of severe infections caused by MDR Shigella spp.


Fe and Zn co-substituted beta-tricalcium phosphate (β-TCP): Synthesis, structural, magnetic, mechanical and biological properties.
In the present work, Fe3+ and Zn2+ co-substituted β-tricalcium phosphate (β-TCP) has been synthesized by wet co-precipitation method. Co-substitution level in the range from 1 to 5 mol% has been studied. Thermal decomposition of as-prepared precipitates was shown to be affected by introducing of foreign ions, decreasing the decomposition temperature of precursor. It was determined that partial substitution of Ca2+ by Fe3+ and Zn2+ ions leads to the change in lattice parameters, which gradually decrease as doping level increases. Lattice distortion was also confirmed by means of Raman spectroscopy, which showed gradual change of the peaks shape in the Raman spectra. Rietveld refinement and electron paramagnetic resonance study confirmed that Fe3+ ions occupy only one Ca crystallographic site until Fe3+ and Zn2+ substitution level reaches 5 mol%. All co-substituted samples revealed paramagnetic behavior, magnetization of powders was determined to be linearly dependent on concentration of Fe3+ ions. Cytotoxicity of the synthesized species was estimated by in vivo assay using zebrafish (Danio rerio) and revealed non-toxic nature of the samples. Preparation of ceramic bodies from the powders was performed, however the results obtained on Vickers hardness of the ceramics did not show improvement in mechanical properties induced by co-substitution.


ApoE gene polymorphisms, BMD, and fracture risk in elderly men and women: the Rotterdam study.
To study the association between the ApoE gene polymorphism and osteoporosis, we performed an association study in 5,857 subjects from the Rotterdam Study. We did not observe an association between the ApoE polymorphism and osteoporosis in this study, which is thus far the largest study on ApoE and osteoporosis. The E*4 allele of the E*2, E*3, E*4 protein isoform polymorphism in the gene encoding apolipoprotein E (ApoE) has previously been associated with an increased fracture risk. We investigated the association between the ApoE polymorphism and BMD, bone loss, and incident fractures as part of the Rotterdam Study a prospective population-based cohort study of diseases in the elderly. The study population consisted of 5,857 subjects (2,560 men; 3,297 women) for whom data on ApoE genotypes, confounding variables, and follow-up of nonvertebral fractures were available. Data on femoral neck and lumbar spine BMD were available for 4,814 participants. Genotype analyses for bone loss (defined as annualized percent change in BMD at the hip and lumbar spine) and BMD were performed using ANOVA. Fractures were analyzed using a Cox proportional-hazards model and logistic regression. All relative risks were adjusted for age and body mass index. The genotype distribution of the study population was in Hardy-Weinberg equilibrium (p = 0.98) and did not differ by gender. At baseline, mean BMD of the lumbar spine and femoral neck did not differ between the ApoE genotypes of men and women. Bone loss (mean follow-up, 2.0 years) did not differ by ApoE genotype for women and men. During a mean follow-up of 6.6 years, 708 nonvertebral fractures (198 hip fractures and 179 wrist fractures) and 149 incident vertebral fractures occurred. No consistent differences in the distribution of alleles could be observed between subjects with or without these fractures. Our data do not support the hypothesis that the ApoE*4 risk allele is associated with BMD, increased bone loss, or an increased risk of osteoporotic fractures.


Coronal adenomas.
The incidence and morphologic features of coronal adenomas, benign epithelial tumors of the ciliary processes, were studied in 500 autopsy cases. Macroscopically, coronal adenomas are white, globular, often cystic in appearance, of limited growth potential, and found only on the ciliary processes. Microscopically, they contain convoluted sheets or tubes of nonpigmented epithelium, between which are found varying amounts of amorphous eosinophilic, PAS-positive, extracellular material. Coronal adenomas were present in 153 (31%) of 500 cases, were bilateral in 23 (15%), and were thus present in 176 (18%) of the 1,000 eyes examined. Two clinically important complications of coronal adenomas were found, sectoral cataracts and misdiagnosis as iris tumor.


Women bound to be active: differences in long-term physical activity between completers and noncompleters of a book club intervention.
Ideal approaches to increasing long-term physical activity (PA) adherence in women remain unclear. This study used a longitudinal mixed-methods approach to 1) determine the effectiveness of an 8-month book club intervention for increasing PA participation and self-worth, and reducing barriers at 1-year followup; and 2) identify reasons why completers and noncompleters did or did not maintain PA. One year after the cessation of Women Bound to be Active (WBA), completers (participated in posttesting; n = 30) and noncompleters (did not participate in posttesting; n = 22) responded to questionnaires and interviews assessing their body mass index (BMI), current PA participation, barriers, and global self-worth. Compared with noncompleters, completers reported decreases in BMI, higher motivation for PA, higher ratio of benefits to barriers, and more consistent PA. Both groups still reported barriers to PA, especially time; however, completers more often reported strategies for overcoming these barriers. Completers more directly discussed the impact of their improved self-worth on their PA participation. In the future, a greater focus on time management and self-regulation strategies should be emphasized in PA interventions, specifically those that focus on women. This may help to prevent program and long-term PA attrition.


SU-E-I-19: Local Search Clustering Algorithm for DCE-MRI Analysis.
To develop a local search clustering algorithm for analyzing the dynamic contrasted enhanced (DCE)-MRI data for determining the vascular permeability. The clustered signal will have better contrast-to-noise ratio (CNR) and thus can improve the analysis. In DCE-MRI, data often suffer from low CNR. The CNR is particularly poor in central nervous system and could lead to spurious results. We propose a local search clustering algorithm that groups proximal voxels with similar uptake curves and T1 values. The algorithm starts with a seed voxel, and then grows outward to recruit new voxels into a cluster. Once a cluster is formed, all members of the current cluster form a 'seed collection' and the seed point of the cluster becomes the seed collection. The expansions and updates continue with the seed point/collection until the stopping criterion is met. To investigate the effectiveness of our clustering algorithm, we used a 64×64 2D Shepp-Logan phantom. Variations on the T1 values and permeability parameters were applied on different regions in the phantom. The time resolution was set to 30sec and 82 post-contrast data were created. After the DCE-MRI data were generated, Gaussian noise was applied to the images to investigate the effect of noise on the clustering algorithm. DCE analysis was performed on the clustered data and the results were compared against the Result obtained from voxel-by-voxel analysis. The addition of noise degraded the results of DCE estimation. The clustering algorithm on average reduced the errors of the permeability parameters by more than 50% compared to the voxel-by-voxel analysis. We developed a local search clustering algorithm to segment the concentration time curves of the DCE-MRI data. The proposed clustering algorithm enhances the apparent CNR within the clustered data and reduces the errors of the permeability parameters.


Rheb GTPase is a direct target of TSC2 GAP activity and regulates mTOR signaling.
Tuberous sclerosis complex (TSC) is a genetic disease caused by mutation in either TSC1 or TSC2. The TSC1 and TSC2 gene products form a functional complex and inhibit phosphorylation of S6K and 4EBP1. These functions of TSC1/TSC2 are likely mediated by mTOR. Here we report that TSC2 is a GTPase-activating protein (GAP) toward Rheb, a Ras family GTPase. Rheb stimulates phosphorylation of S6K and 4EBP1. This function of Rheb is blocked by rapamycin and dominant-negative mTOR. Rheb stimulates the phosphorylation of mTOR and plays an essential role in regulation of S6K and 4EBP1 in response to nutrients and cellular energy status. Our data demonstrate that Rheb acts downstream of TSC1/TSC2 and upstream of mTOR to regulate cell growth.


Raised tone reveals ATP as a sympathetic neurotransmitter in the porcine mesenteric arterial bed.
The relative importance of ATP as a functional sympathetic neurotransmitter in blood vessels has been shown to be increased when the level of preexisting vascular tone or pressure is increased, in studies carried out in rat mesenteric arteries. The aim of the present study was to determine whether tone influences the involvement of ATP as a sympathetic cotransmitter with noradrenaline in another species. We used the porcine perfused mesenteric arterial bed and porcine mesenteric large, medium and small arteries mounted for isometric tension recording, because purinergic cotransmission can vary depending on the size of the blood vessel. In the perfused mesenteric bed at basal tone, sympathetic neurogenic vasocontractile responses were abolished by prazosin, an α1-adrenoceptor antagonist, but there was no significant effect of α,β-methylene ATP, a P2X receptor-desensitizing agent. Submaximal precontraction of the mesenteric arterial bed with U46619, a thromboxane A2 mimetic, augmented the sympathetic neurogenic vasocontractile responses; under these conditions, both α,β-methylene ATP and prazosin attenuated the neurogenic responses. In the mesenteric large, medium and small arteries, prazosin attenuated the sympathetic neurogenic contractile responses under conditions of both basal and U46619-raised tone. α,β-Methylene ATP was effective in all of these arteries only under conditions of U46619-induced tone, causing a similar inhibition in all arteries, but had no significant effect on sympathetic neurogenic contractions at basal tone. These data show that ATP is a cotransmitter with noradrenaline in porcine mesenteric arteries; the purinergic component was revealed under conditions of partial precontraction, which is more relevant to physiological conditions.


Expression of beta-defensins in the tubotympanum of experimental otitis media.
Since the expression levels of beta-defensins 2-4 were up-regulated in experimental otitis media, they may play a protective role in the pathogenesis of otitis media. Defensins are antimicrobial peptides that play a major role in innate immunity. The goal of this study was to identify the expression of defensins in experimental otitis media of the mouse. The expression of three alpha-defensins (cryptdins, cryptdin-related sequences 1-C (CRS1-C), and CRS4-C) and four beta-defensins (mBD1, mBD2, mBD3, and mBD4) was investigated in the tubotympanum of experimental otitis media in mice by a semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR), and the expression levels of three beta-defensins (mBD2, mBD3, mBD4) were evaluated by Western blotting. The alpha-defensins were not expressed in the tubotympanum. mBD1 was expressed constitutively in normal middle ear mucosa and Eustachian tube mucosa, but up-regulated expression of mBD2, mBD3, and mBD4 was observed with RT-PCR and Western blotting in the tubotympanums in experimental otitis media, while the normal tubotympanums did not express them.


The Mouse Phenome Project.
The laboratory mouse is the organism of choice for many studies in biology and medicine. Reliable phenotypic data are essential for the full utility of genotypic information emerging from efforts to sequence human and mouse genomes. The Mouse Phenome Project has been organized to help accomplish this task by establishing a collection of baseline phenotypic data on commonly used and genetically diverse inbred mouse strains and making this information publicly available through a web-accessible database. The Mouse Phenome Database (MPD) is being developed to manage these data and to provide researchers with tools for exploring both raw phenotypic data and comparative summary analyses. The MPD serves as a repository for detailed protocols and raw data. This resource enables investigators to identify appropriate strains for (1) physiological testing, (2) drug discovery, (3) toxicology studies, (4) mutagenesis, (5) modeling human diseases, (6) QTL analyses and identification of new genes and (7) unraveling the influence of environment on genotype.


The Isolation and Characterization of Kronos, a Novel Caulobacter Rhizosphere Phage that is Similar to Lambdoid Phages.
Despite their ubiquity, relatively few bacteriophages have been characterized. Here, we set out to explore Caulobacter bacteriophages (caulophages) in the rhizosphere and characterized Kronos, the first caulophage isolated from the rhizosphere. Kronos is a member of the Siphoviridae family since it has a long flexible tail. In addition, an analysis of the Kronos genome indicated that many of the predicted proteins were distantly related to those of bacteriophages in the lambdoid family. Consistent with this observation, we were able to demonstrate the presence of cos sites that are similar to those found at the ends of lambdoid phage genomes. Moreover, Kronos displayed a relatively rare head and tail morphology compared to other caulophages but was similar to that of the lambdoid phages. Taken together, these data indicate that Kronos is distantly related to lambdoid phages and may represent a new Siphoviridae genus.


Perception of speech in noise: neural correlates.
The presence of irrelevant auditory information (other talkers, environmental noises) presents a major challenge to listening to speech. The fundamental frequency (F(0)) of the target speaker is thought to provide an important cue for the extraction of the speaker's voice from background noise, but little is known about the relationship between speech-in-noise (SIN) perceptual ability and neural encoding of the F(0). Motivated by recent findings that music and language experience enhance brainstem representation of sound, we examined the hypothesis that brainstem encoding of the F(0) is diminished to a greater degree by background noise in people with poorer perceptual abilities in noise. To this end, we measured speech-evoked auditory brainstem responses to /da/ in quiet and two multitalker babble conditions (two-talker and six-talker) in native English-speaking young adults who ranged in their ability to perceive and recall SIN. Listeners who were poorer performers on a standardized SIN measure demonstrated greater susceptibility to the degradative effects of noise on the neural encoding of the F(0). Particularly diminished was their phase-locked activity to the fundamental frequency in the portion of the syllable known to be most vulnerable to perceptual disruption (i.e., the formant transition period). Our findings suggest that the subcortical representation of the F(0) in noise contributes to the perception of speech in noisy conditions.


Use of manual and powered wheelchair in children with cerebral palsy: a cross-sectional study.
Mobility is important for the cognitive and psychosocial development of children. Almost one third of children with cerebral palsy (CP) are non-ambulant. Wheelchairs can provide independent mobility, allowing them to explore their environment. Independent mobility is vital for activity and participation and reduces the dependence on caregivers. The purpose of this study was to describe the use of manual and powered wheelchair indoors and outdoors in relation to the degree of independent wheelchair mobility or need for assistance in a total population of children with CP. A cross-sectional study was performed including all children aged 3-18 years with CP living in southern Sweden during 2008. Data was extracted from a register and health care programme for children with CP (CPUP). There were a total of 562 children (326 boys, 236 girls) in the register. Information on the child's use of manual and powered wheelchair indoors and outdoors and the performance in self-propelling or need for assistance were analysed related to age, CP subtype and gross motor function. Wheelchairs for mobility indoors were used by 165 (29%) of the 562 children; 61 used wheelchair for independent mobility (32 using manual only, 12 powered only, 17 both) and 104 were pushed by an adult. For outdoor mobility wheelchairs were used by 228 children (41%); 66 used a wheelchair for independent mobility (18 using manual only, 36 powered only, 12 both) and 162 were pushed. The use of wheelchair increased with age and was most frequent in the spastic bilateral and dyskinetic subtypes. Most powered wheelchairs were operated by children at GMFCS level IV. In this total population of children with CP, aged 3-18 years, 29% used a wheelchair indoors and 41% outdoors. A majority using manual wheelchairs needed adult assistance (86%) while powered wheelchairs provided independent mobility in most cases (86%). To achieve a high level of independent mobility, both manual and powered wheelchairs should be considered at an early age for children with impaired walking ability.


The relationship between spirituality and burnout among medical students.
Medical student burnout has been associated with depression, loss of empathy, and suicidal ideation. Spirituality has been identified in previous studies as a protective factor in coping with the stress but has not been examined as a factor in medical student burnout. An internet link to an anonymous survey was sent via email to medical students at a public northeastern medical school; 259/469 (55.2%) completed it. The survey included measures of spirituality, burnout, psychological distress, coping, and general happiness. A Pearson-r correlation showed significant inverse correlations between measures of spirituality and measures of psychological distress/burnout (r's ranging from -.62 to -.14; p's <.01). In contrast, a positive correlation was found between life satisfaction and spirituality (r's .53 to .12; p<.05). Using hierarchical multiple regression with demographics (Step 1), mental health variables (Step 2), and satisfaction and Adaptive coping (Step 3), burnout remained significantly related to lower scores on both spirituality measures (FACIT-SP p<.00 and DSE p<.05). Students having higher levels of spiritual well being and daily spiritual experiences described themselves as more satisfied with their life in general, while students with low scores on spiritual well being and daily spiritual experiences had higher levels of psychological distress and burnout. Spirituality may therefore be a protective factor against burnout in medical students and future studies should explore potential causal relationships.


Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae).
The cyprinid subfamily Oxygastrinae is composed of a diverse group of fishes that has been taxonomically and phylogenetically problematic. Their great variation in appearance, life histories, and trophic diversity resulted in uncertainty regarding their relationships, which led to their historical classification across many disparate subfamilies. The phylogenetic relationships of Oxygastrinae are resolved based on sequence data from four loci: cytochrome b, cytochrome c oxidase I, opsin, and recombination activating gene 1. A combined data matrix consisting of 4114 bp for 144 taxa was compiled and analyzed using maximum likelihood and parsimony optimality criteria. The subfamily Oxygastrinae is recovered as a monophyletic group that includes Ancherythroculter, Aphyocypris, Candidia, Chanodichthys, Ctenopharyngodon, Culter, Distoechodon, Elopichthys, Hainania, Hemiculter, Hemiculterella, Hemigrammocypris, Hypophthalmichthys, Ischikauia, Macrochirichthys, Megalobrama, Metzia, Mylopharyngodon, Nicholsicypris, Nipponocypris, Ochetobius, Opsariichthys, Oxygaster, Parabramis, Parachela, Paralaubuca, Pararasbora, Parazacco, Plagiognathops, Pseudobrama, Pseudohemiculter, Pseudolaubuca, Sinibrama, Squaliobarbus, Toxabramis, Xenocyprioides, Xenocypris, Yaoshanicus, and Zacco. Of these genera, the following were found to be monophyletic: Aphyocypris, Distoechodon, Hypophthalmichthys, Nipponocypris, Opsariichthys, Parachela, Paralaubuca, Plagiognathops, Xenocyprioides, and Xenocypris. The following genera were not monophyletic: Metzia, Hemiculter, Toxabramis, Ancherythroculter, Chanodichthys, Culter, Megalobrama. The remainder are either monotypic or were represented by only a single species. Four genera not examined in this study are provisionally classified in Oxygastrinae: Anabarilius, Longiculter, Pogobrama, and Rasborichthys.


Hybrid treatment of T3 chest wall lung cancer lobectomy.
Nowadays the treatment of patients with non-small cell lung cancer (NSCLC) that invades the chest wall is still questioned. The classic approach is a lobectomy that requires chest wall resection through thoracotomy, but thanks to the progress in the field of thoracoscopic surgery, this procedure can be performed by video-assisted thoracoscopic surgery (VATS). Major advances have been made in recent years both in the surgical technique associated with thoracoscopy and in the instrumentation available today. This has allowed the use of thoracoscopic technique even in advanced disease. To choose to perform complex surgery in assisted video surgery, considerable experience is needed to avoid making mistakes and giving up a better approach for the patient only for any technical difficulties. Thoracoscopy is not currently the preferred intervention for patients with chest wall invasion because there are insufficient studies on the feasibility of lobectomy with thoracoscopic wall resection, although the thoracoscopic approach has reduced mortality and morbidity in lung cancer cases not in advanced stage. We discuss our experience in three patients using hybrid approach with assisted video thoracoscopic lobectomy and a chest wall en-block resection with an alternative method of estimating thoracic wall resection that uses assisted video surgery and hypodermic needles (minimally invasive posterior approach).


Systematic determination of patterns of gene expression during Drosophila embryogenesis.
Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription. As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, we examined 2,179 genes by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos. The photomicrographs were annotated using controlled vocabularies for anatomical structures that are organized into a developmental hierarchy. We also generated a detailed time course of gene expression during embryogenesis using microarrays to provide an independent corroboration of the in situ hybridization results. All image, annotation and microarray data are stored in publicly available database. We found that the RNA transcripts of about 1% of genes show clear subcellular localization. Nearly all the annotated expression patterns are distinct. We present an approach for organizing the data by hierarchical clustering of annotation terms that allows us to group tissues that express similar sets of genes as well as genes displaying similar expression patterns. Analyzing gene-expression patterns by in situ hybridization to whole-mount embryos provides an extremely rich dataset that can be used to identify genes involved in developmental processes that have been missed by traditional genetic analysis. Systematic analysis of rigorously annotated patterns of gene expression will complement and extend the types of analyses carried out using expression microarrays.


Synthesis of some heterofunctionalized penicillanic acid derivatives and investigation of their biological activities.
6-Substituted amino-penicillanic acid esters were synthesized starting with 6-apa. The compounds containing a 1,3-thiazole- or 1,3-thiazolidinone nucleus linked to the penicillanic acid skeleton via a hydrazino linkage were obtained from 6-apa. The treatment of carbonylamino and carbonothioylamino compounds with 4-chlorophenacyl bromide or ethyl bromoacetate gave 6-bis{4-[1,3-thiazol(idinone)amino]benzoyl}amino derivatives of 6-apa. Benzyl derivatives were synthesized in several steps, starting with 4-aminobenzoyl chloride. The treatment of 4-{[3-benzyl-4-oxo-1,3-thia(oxa)zolidin-2-ylidene]amino}benzoyl chlorides with 6-apa in ethanolic solution produced the 6-[bis(4-{[3-benzyl-4-oxo-1,3-thiazolidin-2-ylidene]amino}benzoyl)amino] derivative of penicillanic acid, while the reaction of the same intermediates in DMF gave the mono-substituted amino derivative of 6-apa. The synthesized compounds were screened for their biological activities, and some of them were found to possess good to moderate antimicrobial activity. Moreover, some of the compounds displayed antiurease, anti-β-lactamase, and/or antilipase activities.


Clinical assessment of a foam dressing containing growth factor-enhancing hydrated polyurethanes.
This study assesses a novel dressing concept in venous leg ulcer (VLU) patients. It is based on boosting endogenous growth factor activities synthesised by functional granulation tissue. Patients received treatment for eight weeks with a hydrated polyurethane-containing foam dressing plus concomitant compression therapy. Wound area reduction (WAR), percentage of wounds achieving a relative WAR of ≥40% and ≥60%, wound pain ratings for the last 24 hours and at dressing changes, EQ-5D Quality of Life questionnaire data, dressing handling and safety parameters were recorded. There were 128 patients who received treatment and data for 123 wound treatment courses were documented. Wound area size decreased from 13.3±9.8cm2 to 10.5±12.2cm2 at week eight and median relative WAR was 48.8%. At week eight, a relative WAR ≥40% was reached by 54.5% of the wounds, 41.5% reached a relative WAR of ≥60% and complete healing was observed in 13.5% of wounds. Median wound pain ratings (last 24 hours before dressing change) declined significantly from 30 to 15.5 (100 visual analogue scale [VAS], p=0.0001) and pain at dressing changes from 30 to 12.5 (p≤0.0001). The EQ-5D VAS rating increased from 58.4±19.2mm to 63.1±19.1mm (p=0.0059). This clinical assessment shows that the concept of boosting endogenous growth factors through hydrated polyurethanes has the potential to accelerate WAR in VLU patients while decreasing pain levels and improving quality of life parameters.


Norwegian healthcare professionals' perceptions of patient knowledge and involvement as basis for decision making in hematology.
To investigate how healthcare professionals relate to patients with different levels of knowledge and involvement in their disease and treatment. Qualitative, exploratory approach based on semi-structured interviews. A hematologic outpatient clinic in Norway. 5 nurses and 5 doctors. Semistructured interviews were conducted, recorded on audiotape, transcribed, and analyzed with qualitative techniques. Patient knowledge, patient involvement, and decision making. Study participants perceived that they had stable, basic relationships with patients and were flexible toward patients with different levels of knowledge and involvement. Healthcare professionals grouped patients into four behavior types: passive, withdrawn, uncooperative, and expert. The perceived behaviors formed the basis for relationships involving shared or nonshared decision making. Patients' perceived propensity in mastering medical knowledge affects how healthcare professionals involve them in decision making. Healthcare professionals' tendency to see relationships with patients as asymmetric and stable may inhibit patients' ability to involve themselves in their healthcare decisions. This study's findings can be used to raise awareness of how nurses' biases about patients influence shared decision making. Nurses should be aware of a tendency to exclude patients from decision making if they perceive that patients are incapable of involving themselves.


Antioxidant neolignans from the twigs and leaves of Mitrephora wangii HU.
Two new compounds, odoratisol E (1) and decurrenal A (2), together with 12 known compounds were isolated from the twig and leaf extracts of Mitrephora wangii HU (Annonaceae). All structures were elucidated by spectroscopic methods. The structure of compound (+)-6 was also confirmed by X-ray diffraction analysis. The absolute configurations of odoratisol E and decurrenal A were determined by comparison of their electronic circular dichroism (ECD) spectra with those of related known compounds. Most of the isolated compounds were evaluated for their antioxidant activity using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) assays. Compounds 4 and (+)-6 displayed potent ABTS radical scavenging activity with IC50 values of 11.9 ± 1.8 and 10.8 ± 1.7 μM, respectively, which is better than that of standard compound, ascorbic acid, (IC50 = 19.3 ± 0.1 μM). Compound 9 showed moderate DPPH radical scavenging activity with an IC50 value of 38.7 ± 0.8 μM.


Could an Innovative Training Program Including Contact Sports and Counseling Help Young People With Traits of Psychopathy and A History of School Dropout?
The aim was to assess the effects of a training program inclusive of contact sports and counseling on school dropout, quality of life (QoL) and psychopathologic symptoms in the youth with a history of school dropout and psychopathic personality traits. The Experimental Group (EG) consisted of 32 subjects (male 90.6%; age 19.6±4.3 years); the Control Group (CG) consisted of an equal number matched for gender and age with the same psychological features. At the beginning of the experimental Training Program (T0), both cohorts were assessed by a diagnostic psychiatric interview (SCID ANTAS), the Short Form Health Survey (SF-12) to evaluate QoL, the Psychopathy Checklist - Revised (PCL-R) for the assessment of psychopathic traits, the Self Reporting Questionnaire (SRQ) to measure general psychopathology. At the end of the program (T1), the coorths were evaluated by SF-12 and SRQ. Twenty-seven subjects in the EG (84.4%) completed the course and underwent the evaluation at T1. The SF-12 score significantly increased from T0 to T1 in both groups, albeit this was more evident in the EG than in the CG, owing to an interaction between time and group. SRQ score significantly decreased in the EG from T0 to T1, while in the CG it did not, although the interaction between time and group was not significant. The experimental training program was effective in improving QoL and countering school dropout in young citizens with psychopathic traits. Further studies are needed to clarify if such results are due to a relationship between the practical tasks approach including contact sports and an improvement in mentalization processes.


Stereotactic body radiation therapy in patients with pelvic recurrence from rectal carcinoma.
To investigate the clinical applications of stereotactic body radiation therapy (SBRT) using the CyberKnife system for pelvic recurrence from rectal cancer with a focus on survival and toxicity. Between 2002 and 2006, 23 patients with recurrent rectal cancer were treated with SBRT at our institution. The median follow-up was 31 months. Sites of recurrence were pre-sacral in seven patients and the pelvic wall in 16. SBRT doses ranged from 30 to 51 Gy (median 39 Gy) and were delivered in three fractions. Response to treatment was assessed by computed tomography. Overall and local progression-free survival and toxicities were recorded. Four-year overall survival and local control rates were 24.9 and 74.3%, respectively. No prognostic factor was found to affect patient survival or local progression. One patient developed a severe radiation-related toxicity, but recovered completely after treatment. SBRT for pelvic recurrence was found to be comparable with other modalities with respect to overall survival and complication rates. Further studies are needed to confirm these preliminary results.


Peripheral pulses of oxytocin increase partner preferences in female, but not male, prairie voles.
Centrally administered oxytocin (OT) facilitates social behaviors including the partner preferences that characterize the monogamous social system of prairie voles. In contrast peripherally administered OT generally has been ineffective in influencing central processes including behavior. OT from the posterior pituitary gland is released in pulses into the peripheral circulation. We hypothesized that peripherally administered OT, if delivered in repeated injections mimicking these pulses, would influence behavior. Male and female prairie voles received three subcutaneous injections of OT, a single injection of OT, or isotonic saline. Animals then were placed with an adult member of the opposite sex, designated as a "partner," for a 1-h period of cohabitation, and subsequently tested for preference for the familiar partner versus a comparable stranger. Females treated with pulses of peripheral OT (1, 5, or 20 microg) displayed a significant preference for the partner compared to control females, while females receiving a lower dose of OT (0.1 microg) or a single injection (20 microg) did not. There was also a significant within-group effect as pulsed OT-treated females spent more time with the partner when compared to the stranger, while control females spent equal amounts of time with the partner and stranger. Peripheral pulses of OT were no longer effective in inducing partner preferences when females were pretreated with a selective OT receptor antagonist, administered either peripherally or centrally. In contrast to females, peripheral treatment with OT did not facilitate the formation of partner preferences in males.


Regularization-Free Strain Mapping in Three Dimensions, With Application to Cardiac Ultrasound.
Quantifying dynamic strain fields from time-resolved volumetric medical imaging and microscopy stacks is a pressing need for radiology and mechanobiology. A critical limitation of all existing techniques is regularization: because these volumetric images are inherently noisy, the current strain mapping techniques must impose either displacement regularization and smoothing that sacrifices spatial resolution, or material property assumptions that presuppose a material model, as in hyperelastic warping. Here, we present, validate, and apply the first three-dimensional (3D) method for estimating mechanical strain directly from raw 3D image stacks without either regularization or assumptions about material behavior. We apply the method to high-frequency ultrasound images of mouse hearts to diagnose myocardial infarction. We also apply the method to present the first ever in vivo quantification of elevated strain fields in the heart wall associated with the insertion of the chordae tendinae. The method shows promise for broad application to dynamic medical imaging modalities, including high-frequency ultrasound, tagged magnetic resonance imaging, and confocal fluorescence microscopy.


Implementation of co-trimoxazole prophylaxis and isoniazid preventive therapy for people living with HIV.
To measure progress in implementing co-trimoxazole prophylaxis (CTXp) (trimethoprim plus sulfamethoxazole) and isoniazid preventive therapy (IPT) policy recommendations, identify barriers to the development of national policies and pinpoint challenges to implementation. In 2007 we conducted by e-mail a cross-sectional survey of World Health Organization (WHO) HIV/AIDS programme officers in 69 selected countries having a high burden of infection with HIV or HIV-associated tuberculosis (TB). The specially-designed, self-administered questionnaire contained items covering national policies for CTXp and IPT in people living with HIV, current level of implementation and barriers to developing or implementing these policies. The 41 (59%) respondent countries, representing all WHO regions, comprised 85% of the global burden of HIV-associated TB and 82% of the global burden of HIV infection. Thirty-eight countries (93%) had an established national policy for CTXp, but only 66% of them (25/38) had achieved nationwide implementation. For IPT, 21 of 41 countries (51%) had a national policy but only 28% of them (6/21) had achieved nationwide implementation. Despite significant progress in the development of CTXp policy, the limited availability of co-trimoxazole for this indication and inadequate systems to manage drug supply impeded nationwide implementation. Inadequate intensified tuberculosis case-finding and concerns regarding isoniazid resistance were challenges to the development and implementation of national IPT policies. Despite progress in implementing WHO-recommended CTXp and IPT policies, these interventions remain underused. Urgent steps are required to facilitate the development and implementation of these policies.


Rapid changes in connexin-43 in response to genotoxic stress stabilize cell-cell communication in corneal endothelium.
To determine how corneal endothelial (CE) cells respond to acute genotoxic stress through changes in connexin-43 (Cx43) and gap junction intercellular communication (GJIC). Cultured bovine CE cells were exposed to mitomycin C or other DNA-damaging agents. Changes in the levels, stability, binding partners, and trafficking of Cx43 were assessed by Western blot analysis and immunostaining. Live-cell imaging of a Cx43-green fluorescent protein (GFP) fusion protein was used to evaluate internalization of cell surface Cx43. Dye transfer and fluorescent recovery after photobleaching (FRAP) assessed GJIC. After genotoxic stress, Cx43 accumulated in large gap junction plaques, had reduced zonula occludens-1 binding, and displayed increased stability. Live-cell imaging of Cx43-GFP plaques in stressed CE cells revealed reduced gap junction internalization and degradation compared to control cells. Mitomycin C enhanced transport of Cx43 from the endoplasmic reticulum to the cell surface and formation of gap junction plaques. Mitomycin C treatment also protected GJIC from disruption after cytokine treatment. These results show a novel CE cell response to genotoxic stress mediated by marked and rapid changes in Cx43 and GJIC. This stabilization of cell-cell communication may be an important early adaptation to acute stressors encountered by CE.


1918 Influenza: the mother of all pandemics.
The "Spanish" influenza pandemic of 1918-1919, which caused approximately 50 million deaths worldwide, remains an ominous warning to public health. Many questions about its origins, its unusual epidemiologic features, and the basis of its pathogenicity remain unanswered. The public health implications of the pandemic therefore remain in doubt even as we now grapple with the feared emergence of a pandemic caused by H5N1 or other virus. However, new information about the 1918 virus is emerging, for example, sequencing of the entire genome from archival autopsy tissues. But, the viral genome alone is unlikely to provide answers to some critical questions. Understanding the 1918 pandemic and its implications for future pandemics requires careful experimentation and in-depth historical analysis.


Development and validation of a patient questionnaire to determine New York Heart Association classification.
New York Heart Association (NYHA) classification correlates with quality of life and is useful in tracking changes in status in clinical trials. We explored methods to determine NYHA class in multicenter trials where double-blind conditions could not be maintained. A questionnaire was developed containing 7 major questions based on the standard definitions of NYHA classes. The questionnaire was administered to 116 patients with varying degrees of heart failure. When comparing NYHA determined by physicians at the site to NYHA assigned by 3 independent physician graders, there was an approximate 60% concordance. Concordance between independent reviewers was approximately 75%. Results of repeat grading of 30 randomly selected questionnaires indicated that graders provided the same score 90% of the time. Thus, although there were some differences from the site determination of NYHA class, the questionnaire had good inter- and intragrader reproducibility. In a second group of 103 patients enrolled in an ongoing device-intervention trial, we demonstrated that it is feasible to employ the questionnaire in a multicenter trial. Finally, NYHA class was correlated with quality of life and peak exercise oxygen consumption. A standardized questionnaire provided an approximate 60% concordance in assigning NYHA classification compared to the site assessment with approximately 90% reproducibility. This approach may be useful to determine NYHA classification within the context of clinical trials where blinded conditions are not possible.


Dietary Iron Deficiency Impaired Peripheral Immunity but Did Not Alter Brain Microglia in PRRSV-Infected Neonatal Piglets.
During the postnatal period the developing brain is vulnerable to insults including nutrient insufficiency and infection that may lead to disrupted development and cognitive dysfunction. Since iron deficiency (ID) often presents with immunodeficiency, the objective of this study was to investigate peripheral viremia and inflammation as well as brain microglial phenotype and function when ID and respiratory infection occur simultaneously in a neonatal piglet model. On postnatal day 2 (PD 2) male and female piglets were assigned to one of four treatments and fed either control or ID milk replacer. On PD 8 half the pigs on each diet were inoculated with either vehicle or porcine reproductive and respiratory syndrome virus (PRRSV; P-129). Blood samples were collected prior to inoculation (PD 7) and repeated once weekly. Rectal temperature, feeding score, and sickness behavior were measured daily until PD 28. Hematocrit, hemoglobin, and serum iron were reduced by ID but not PRRSV infection. PRRSV-infected piglets displayed viremia by PD 14; however, those fed control diet had lower viral titer on PD 28, while circulating virus remained elevated in those fed an ID diet, suggesting that ID either impaired immune function necessary for viral clearance or increased viral replication. ID piglets infected with PRRSV displayed reduced sickness behavior compared to those fed control diet on PD 13-15 and 18-20. While ID piglet sickness behavior progressively worsened, piglets fed control diet displayed improved sickness score after PD 21. Microglia isolated from PRRSV piglets had increased MHCII expression and phagocytic activity ex vivo compared to uninfected piglets. ID did not alter microglial activation or phagocytic activity. Similarly, microglial cytokine expression was increased by PRRSV but unaffected by ID, in stark contrast to peripheral blood mononuclear cell (PBMC) cytokine expression, which was increased by infection and generally decreased by ID. Taken together, these data suggest that ID decreases peripheral immune function leading to increased viremia, but immune activity in the brain is protected from acute ID.


Clomiphene-induced acute pancreatitis without hypertriglyceridemia.
Acute pancreatitis may be caused by drugs. In the literature, there are more than 260 different drugs that have been blamed for causing pancreatitis. Among these drugs, only 1 case has been reported as clomiphene-induced acute pancreatitis. However, in this single case, there was concomitant hypertriglyceridemia. We report the case of a woman who developed 2 attacks of acute pancreatitis without hypertriglyceridemia while receiving treatment with clomiphene.


Comparative and quantitative proteomics reveal the adaptive strategies of oyster larvae to ocean acidification.
Decreasing pH due to anthropogenic CO2 inputs, called ocean acidification (OA), can make coastal environments unfavorable for oysters. This is a serious socioeconomical issue for China which supplies >70% of the world's edible oysters. Here, we present an iTRAQ-based protein profiling approach for the detection and quantification of proteome changes under OA in the early life stage of a commercially important oyster, Crassostrea hongkongensis. Availability of complete genome sequence for the pacific oyster (Crassostrea gigas) enabled us to confidently quantify over 1500 proteins in larval oysters. Over 7% of the proteome was altered in response to OA at pHNBS 7.6. Analysis of differentially expressed proteins and their associated functional pathways showed an upregulation of proteins involved in calcification, metabolic processes, and oxidative stress, each of which may be important in physiological adaptation of this species to OA. The downregulation of cytoskeletal and signal transduction proteins, on the other hand, might have impaired cellular dynamics and organelle development under OA. However, there were no significant detrimental effects in developmental processes such as metamorphic success. Implications of the differentially expressed proteins and metabolic pathways in the development of OA resistance in oyster larvae are discussed. The MS proteomics data have been deposited to the ProteomeXchange with identifiers PXD002138 (http://proteomecentral.proteomexchange.org/dataset/PXD002138).


Dissolved organic matter signatures vary between naturally acidic, circumneutral and groundwater-fed freshwaters in Australia.
Dissolved organic matter (DOM) plays important roles in both abiotic and biotic processes within aquatic ecosystems, and these in turn depend on the quality of the DOM. We collected and characterized chromophoric DOM (CDOM) from different Australian freshwater types (circumneutral, naturally acidic and groundwater-fed waterways), climatic regions and seasons. CDOM quality was characterized using absorbance and fluorescence spectroscopy. Excitation emission scans followed by parallel factor (PARAFAC) analysis showed that CDOM was characterized by three main components: protein-like, fulvic-like and humic-like components commonly associated with various waters globally in the Openfluor database. Principal component analysis showed that CDOM quality varied between naturally acidic, circumneutral and groundwater-fed waters, with unique CDOM quality signatures shown for each freshwater type. CDOM quality also differed significantly within some sites between seasons. Clear differences in dominant CDOM components were shown between freshwater types. Naturally acidic waters were dominated by highly aromatic (as indicated by the specific absorbance co-efficient (SAC340) and the specific UV absorbance (SUVA254) values which ranged between 31 and 50 cm2 mg-1 and 3.9-5.7 mg C-1 m-1 respectively), humic-like CDOM of high molecular weight (as indicated by abs254/365 which ranged from 3.8 to 4.3). In contrast, circumneutral waters were dominated by fulvic-like CDOM of lower aromaticity (SAC340: 7-21 cm2 mg-1 and SUVA254: 1.5-3.0 mg C-1 m-1) and lower molecular weight (abs254/365 5.1-9.3). The groundwater-fed site had a higher abundance of protein-like CDOM, which was the least aromatic (SAC340: 2-5 cm2 mg-1 and SUVA254: 0.58-1.1 mg C-1 m-1). CDOM was generally less aromatic, of a lower molecular weight and more autochthonous in nature during the summer/autumn sampling compared to winter/spring. Significant relationships were shown between various CDOM quality parameters and pH. This is the first study to show that different freshwater types (circumneutral, naturally acidic and groundwater-fed) contain distinct CDOM quality signatures in Australia, a continent with unique flora and geology.


Safety, immunogenicity, and transmissibility in humans of CVD 1203, a live oral Shigella flexneri 2a vaccine candidate attenuated by deletions in aroA and virG.
We evaluated the safety and immunogenicity of attenuated Shigella flexneri 2a vaccine candidate CVD 1203, which harbors precise deletions in the plasmid gene virG and in the chromosomal gene aroA. CVD 1203 invades epithelial cells but undergoes minimal intracellular proliferation and cell-to-cell spread. Fasting healthy volunteers, aged 18 to 40 years, were randomly allocated (double-blind design) to receive either CVD 1203 vaccine or placebo, along with sodium bicarbonate buffer, on days 0 and 14, as follows. At the time of the first inoculation, 10 subjects received placebo (group 1) and 22 subjects received either 1.5 x 10(8) (group 2; 11 subjects) or 1.5 x 10(9) (group 3; 11 subjects) CFU of CVD 1203. Fourteen days later, subjects from group 1 received 1.2 x 10(6) CFU of CVD 1203 and subjects from groups 2 and 3 received 1.2 x 10(8) vaccine organisms. Clinical tolerance was dose dependent. After a single dose of CVD 1203 at 10(6), 10(8), or 10(9) CFU, self-limited (<48-h duration) objective reactogenicity (fever, diarrhea, or dysentery) developed in 0, 18, and 72% of subjects, respectively, and in no placebo recipients. CVD 1203 induced immunoglobulin G seroconversion to S. flexneri 2a lipopolysaccharide (LPS) in 30, 45, and 36% of subjects from groups 1, 2, and 3, respectively, and stimulated immunoglobulin A-producing anti-LPS antibody-secreting cells in 60, 91, and 100% of subjects, respectively. After vaccination, significant rises in tumor necrosis factor alpha concentration in serum (groups 1, 2, and 3) and stool (group 2) samples were observed. We conclude that engineered deletions in virG and aroA markedly attenuate wild-type S. flexneri but preserve immunogenicity; however, less reactogenic vaccines are needed.


Towards generating a patient's timeline: extracting temporal relationships from clinical notes.
Clinical records include both coded and free-text fields that interact to reflect complicated patient stories. The information often covers not only the present medical condition and events experienced by the patient, but also refers to relevant events in the past (such as signs, symptoms, tests or treatments). In order to automatically construct a timeline of these events, we first need to extract the temporal relations between pairs of events or time expressions presented in the clinical notes. We designed separate extraction components for different types of temporal relations, utilizing a novel hybrid system that combines machine learning with a graph-based inference mechanism to extract the temporal links. The temporal graph is a directed graph based on parse tree dependencies of the simplified sentences and frequent pattern clues. We generalized the sentences in order to discover patterns that, given the complexities of natural language, might not be directly discoverable in the original sentences. The proposed hybrid system performance reached an F-measure of 0.63, with precision at 0.76 and recall at 0.54 on the 2012 i2b2 Natural Language Processing corpus for the temporal relation (TLink) extraction task, achieving the highest precision and third highest f-measure among participating teams in the TLink track.


Endogenous and rapid serial visual presentation-induced alpha band oscillations in the attentional blink.
The attentional blink (AB) is a deficit in conscious perception of the second of two targets if it follows the first within 200-500 msec. The AB phenomenon has been linked to pre-target oscillatory alpha activity. However, this is based on paradigms that use a rapid serial visual presentation (RSVP) stimulus stream in which the targets are embedded. This distracter stream is usually presented at a frequency of 10 Hz and thus generates a steady-state visual-evoked potential (ssVEP) at the center of the alpha frequency band. This makes the interpretation of alpha findings in the AB difficult. To be able to relate these findings either to the presence of the ssVEP or to an effect of endogenously generated alpha activity, we compared AB paradigms with and without different pre-target distracter streams. The distracter stream was always presented at 12 Hz, and power and intertrial phase coherence were analyzed in the alpha range (8-12 Hz). Without a distracter stream alpha power dropped before target presentation, whereas coherence did not change. Presence of a distracter stream was linked to stronger pre-target power reduction and increased coherence, which were both modulated by distracter stream characteristics. With regard to the AB results indicated that, whereas ssVEP-related power tended to be higher when both targets were detected, endogenous alpha power tended to be lower. We argue that the pattern of results indicates that in the pre-target interval several processes act in parallel. The balance between these processes relates to the occurrence of an AB.


Sequential multiple-assignment randomized trial design of neurobehavioral treatment for patients with metastatic malignant melanoma undergoing high-dose interferon-alpha therapy.
Interferon-alpha therapy, which is used to treat metastatic malignant melanoma, can cause patients to develop two distinct neurobehavioral symptom complexes: a mood syndrome and a neurovegetative syndrome. Interferon-alpha effects on serotonin metabolism appear to contribute to the mood and anxiety syndrome, while the neurovegetative syndrome appears to be related to interferon-alpha effects on dopamine. Our goal is to propose a design for utilizing a sequential, multiple assignment, randomized trial design for patients with malignant melanoma to test the relative efficacy of drugs that target serotonin versus dopamine metabolism during 4 weeks of intravenous, then 8 weeks of subcutaneous, interferon-alpha therapy. Patients will be offered participation in a double-blinded, randomized, controlled, 14-week trial involving two treatment phases. During the first month of intravenous interferon-alpha therapy, we will test the hypotheses that escitalopram will be more effective in reducing depressed mood, anxiety, and irritability, whereas methylphenidate will be more effective in diminishing interferon-alpha-induced neurovegetative symptoms, such as fatigue and psychomotor slowing. During the next 8 weeks of subcutaneous interferon therapy, participants whose symptoms do not improve significantly will be randomized to the alternate agent alone versus escitalopram and methylphenidate together. We present a prototype for a single-center, sequential, multiple assignment, randomized trial, which seeks to determine the efficacy of sequenced and targeted treatment for the two distinct symptom complexes suffered by patients treated with interferon-alpha. Because we cannot completely control for external factors, a relevant question is whether or not 'short-term' neuropsychiatric interventions can increase the number of interferon-alpha doses tolerated and improve long-term survival. This sequential, multiple assignment, randomized trial proposes a framework for developing optimal treatment strategies; however, additional studies are needed to determine the best strategy for treating or preventing neurobehavioral symptoms induced by the immunotherapy interferon-alpha.


Family-centered rounds on pediatric wards: a PRIS network survey of US and Canadian hospitalists.
The goal was to examine pediatric hospitalist rounding practices and characteristics associated with programs conducting family-centered rounds (FCRs). The Pediatric Hospitalist Triennial Survey, sent to a subset of pediatric hospitalists on the Pediatric Research in Inpatient Settings listserv from the United States and Canada, consisted of 63 questions on sociodemographic characteristics, training, practice characteristics, and rounding practices. Among 265 respondents (response rate: 70%), 78% practiced in academic hospitals and 22% in nonacademic hospitals. The prevalences of specific rounding categories were as follows: FCRs, 44%; sit-down, 24%; hallway, 21%; others, 11%. FCRs occurred significantly more often in academic (48%) than nonacademic (31%) hospitals (P = .04). FCRs can include pediatric residents, bedside nurses, charge nurses, case managers, pharmacists, and social workers. Academic settings and higher average daily patient censuses, but not FCRs, were significantly associated with prolonged rounding duration. The most commonly perceived FCR benefits included increased family involvement and understanding, trainee role modeling, and effective team communication. Physical constraints, trainees' apprehensions, and time were the main perceived FCR barriers. Greater perceived benefit/barrier ratios, FCR benefits, and family involvement in care were associated with a greater likelihood of conducting FCRs, whereas a greater number of perceived FCR barriers was associated with not conducting FCRs. FCRs were the most-common rounding category among respondents. FCRs were not associated with a self-reported increase in rounding duration. Successful FCR implementation may require educating staff members and trainees about FCR benefits and addressing FCR barriers.