Understanding Dysphagia Care in the Community Setting.
Factors including health policy reform and the aging population are increasing demand for quality healthcare in the community. People with dysphagia are supported by speech-language pathologists (SLPs) in hospital and community settings; however, little is known about the nature of dysphagia services offered by SLPs in the community. The aim of this study was to investigate SLP services and practices provided to community-based adults with dysphagia. A national cohort (n = 144) of SLPs working with community-based clients with dysphagia completed an online survey. Results revealed that clients with neurological conditions comprised the largest proportion of the caseload. Primary referral sources were family doctors (42.4%) or other health professionals (37.5%), with low rates of self-referral. Services were primarily delivered via individual sessions (84.1%), usually within the client's home (80% saw clients at home). While many clinicians were using both clinical and instrumental assessments, half had to refer clients to the other services to access instrumental assessment. Most provided assessment and rehabilitation services, though a few (28.5%) reported using formal outcome or quality-of-life measures. Only 43.8% referred or encouraged clients or caregivers to access support or social groups and a few SLPs incorporated social participation or client well-being aspects in treatment. Speech-language pathology (SLP) practices in the community appear similar to what occurs in the acute setting, which are inherently biomedical. This may not be optimal care for clients with dysphagia who live at home and their caregivers. Further exploration about what clients and caregivers want from community-based SLP services is warranted.


Dengue virus NS1 protein conveys pro-inflammatory signals by docking onto high-density lipoproteins.
The dengue virus nonstructural protein 1 (NS1) is a secreted virulence factor that modulates complement, activates immune cells and alters endothelial barriers. The molecular basis of these events remains incompletely understood. Here we describe a functional high affinity complex formed between NS1 and human high-density lipoproteins (HDL). Collapse of the soluble NS1 hexamer upon binding to the lipoprotein particle leads to the anchoring of amphipathic NS1 dimeric subunits into the HDL outer layer. The stable complex can be visualized by electron microscopy as a spherical HDL with rod-shaped NS1 dimers protruding from the surface. We further show that the assembly of NS1-HDL complexes triggers the production of pro-inflammatory cytokines in human primary macrophages while NS1 or HDL alone do not. Finally, we detect NS1 in complex with HDL and low-density lipoprotein (LDL) particles in the plasma of hospitalized dengue patients and observe NS1-apolipoprotein E-positive complexes accumulating overtime. The functional reprogramming of endogenous lipoprotein particles by NS1 as a means to exacerbate systemic inflammation during viral infection provides a new paradigm in dengue pathogenesis.


The use of microtracers in food-effect trials: An alternative study design for toxic drugs with long half-lives exemplified by the case for alectinib.
The traditional design of food-effect studies has a high patient burden for toxic drugs with long half-lives (e.g., anticancer agents). Microtracers could be used to assess food-effect in patients without influencing their ongoing treatment. The feasibility of a microtracer food-effect study during steady-state of the therapeutic drug was investigated in an in silico simulation study with alectinib as an example for a relative toxic drug with a long half-life. Microtracer pharmacokinetics were simulated based on a previously published population pharmacokinetic model and used for estimation of a model with and a model without food as a covariate on oral bioavailability of alectinib (assuming a 40% food-effect). Power was defined as the fraction of clinical trials where a significant (p < 0.01) food-effect was identified. The proposed study design of 10 patients on steady-state treatment, 10 blood samples collected within 24 h after administration and an assumed food-effect of 40% had a power of 99.9%. The mean estimated food-effect was 39.8% (80% confidence interval: 31.0%-48.6%). The feasibility of microtracer food-effect studies was demonstrated. The design of the microtracer food-effect study allowed estimation of the food-effect with minimal influence on therapeutic treatment and reducing patient burden compared to the traditional study design for toxic drugs with long half-lives.


Atherosclerosis and arterial blood pressure in mice.
Increased blood pressure is a consistent risk factor for the development of atherosclerotic diseases in humans, although the basis for this relationship is unknown. Genetically engineered mice are now commonly used to study mechanisms of atherosclerosis. More recently, blood pressure can be reliably measured in conscious mice using either tail cuff or telemetric techniques. Thus, mouse models permit the investigation of the complex interactions of blood pressure and atherogenesis. Most mouse models exhibiting hypertension have increased atherosclerotic lesion size, although there have been exceptions to these findings. Also, there are several reports that have used methods to decrease blood pressure and demonstrated reduced atherosclerosis. In contrast, there are many studies in which atherosclerosis has been altered without changes in blood pressure, and conversely, studies in which blood pressure changes did not alter atherosclerosis. Studies that have specifically defined the role of elevated systolic blood pressure on the development of atherosclerosis have uniformly demonstrated that pressure per se is not responsible for changes in lesion development. Thus, while increased systolic blood pressure is frequently associated with atherosclerosis, the stimulus for the hypertension appears to be the major determinant of atherogenesis rather than pressure per se. A consistent theme in the literature has been that perturbations of the renin angiotensin system display the strongest correlations between blood pressure and atherosclerosis.


Functional analysis of protein kinase CK2 of the human malaria parasite Plasmodium falciparum.
Protein kinase CK2 (casein kinase 2) is a eukaryotic serine/threonine protein kinase with multiple substrates and roles in diverse cellular processes, including differentiation, proliferation, and translation. The mammalian holoenzyme consists of two catalytic alpha or alpha' subunits and two regulatory beta subunits. We report the identification and characterization of a Plasmodium falciparum CK2alpha orthologue, PfCK2alpha, and two PfCK2beta orthologues, PfCK2beta1 and PfCK2beta2. Recombinant PfCK2alpha possesses protein kinase activity, exhibits similar substrate and cosubstrate preferences to those of CK2alpha subunits from other organisms, and interacts with both of the PfCK2beta subunits in vitro. Gene disruption experiments show that the presence of PfCK2alpha is crucial to asexual blood stage parasites and thereby validate the enzyme as a possible drug target. PfCK2alpha is amenable to inhibitor screening, and we report differential susceptibility between the human and P. falciparum CK2alpha enzymes to a small molecule inhibitor. Taken together, our data identify PfCK2alpha as a potential target for antimalarial chemotherapeutic intervention.


A progress study of 100 cancer patients treated by acupressure for chemotherapy-induced vomiting after failure with the pharmacological approach.
The recent rediscovery of the natural traditional medical sciences has contributed to improve the treatment of the human diseases and, in particular, it has been shown that the pharmacological approach is not the only possible strategy in the treatment of nausea and vomiting, since bioenergetic approaches, such as acupressure and acupuncture, may also counteract the onset of vomiting due to different causes. Previous preliminary clinical studies had already suggested a possible efficacy of acupressure also in the treatment of chemotherapy-induced vomiting resistant to the classical antiemetic drugs. The aim of this study was to confirm these preliminary data. The study was performed in 100 consecutive metastatic solid tumour patients, who underwent chemotherapy for their advanced neoplastic disease, and who had no benefit from the standard antiemetic agents, including corticosteroids, antidopaminergics and 5-HT 3R-antagonists. Acupressure was made by a stimulation of PC6 acupoint. The emetic symptomatology was reduced by acupressure in 68/100 (68%) patients, without significant differences in relation to tumour histotype. The lowest efficacy was observed in patients treated by anthracycline-containing regimens, without, however, statistically significant differences with respect to the other chemotherapeutic combinations. This study confirms previous preliminary clinical results, which had already suggested the potential efficacy of acupressure in the treatment of vomiting due to cancer chemotherapy. Therefore, acupressure may be successfully included within the therapeutic strategies of cancer chemotherapy-induced vomiting.


Intracellular effects of free radicals and reactive oxygen species in cardiac muscle.
Oxygen-derived free radicals (FRs) and other reactive oxygen species (ROS) have been implicated in the deleterious aspects of myocardial infarction, neutrophil infiltration and post-ischaemic reperfusion. We studied their actions on the main intracellular organelles of Ca-compartmentation and force production (the sarcoplasmic reticulum (SR) and myofilaments) in rat heart preparations by using two forms of chemical 'skinning'. We recorded Ca(2+)-activated isometric tension or, in saponin-treated trabeculae where SR function is maintained, either tension alone or tension and [Ca2+] transients evoked by caffeine. A single, brief application of xanthine/xanthine oxidase (generating superoxide; O2-) rapidly and irreversibly inhibits Ca(2+)-activated force with a dose- and time-dependent action. The kinetics of residual force production are slowed. Rigor induction (by ATP withdrawal) before and during exposure to .O2- prevents this action, suggesting the .O2(-)-sensitive site is occluded in rigor. Myofilament Ca-sensitivity and SR function were unaffected by .O2- or physiologically relevant [H2O2] (< 10 microM). Briefly applying 10-50 microM hypochlorous acid (HOCl) increased Ca-sensitivity and resting tension, but reduced Ca-activated force, in a manner consistent with 'rigor-like' crossbridges being involved. HOCl also provoked spontaneous Ca-release but reduced net SR Ca-uptake. Electron microscopy reveals that the myofilament lattice suffers a characteristic disruption by HOCl but not by .O2-. We conclude that FRs and ROS associated with myocyte dysfunction, reperfusion and inflammation could contribute to post-ischaemic myocardial dysfunction.


Different populations of macrophages use either the vitronectin receptor or the phosphatidylserine receptor to recognize and remove apoptotic cells.
One of the key features associated with programmed cell death in many tissues is the phagocytosis of apoptotic bodies by macrophages. Removal of apoptotic cells occurs before their lysis, indicating that these cells, during the development of apoptosis, express specific surface changes recognized by macrophages. We have compared the mechanisms by which four different macrophage populations recognize apoptotic cells. Murine macrophages elicited into the peritoneal cavity with either of two different phlogistic agents were able to phagocytose apoptotic cells. This phagocytosis was inhibited by phosphatidylserine (PS), regardless of the species (human or murine) or type (lymphocyte or neutrophil) of the apoptotic cell. In contrast, the murine bone marrow macrophage, like the human monocyte-derived macrophage, utilized the vitronectin receptor, an alpha v beta 3 integrin, for the removal of apoptotic cells, regardless of their species or type. That human macrophages are capable, under some circumstances, of recognizing PS on apoptotic cells was suggested by the observation that PS liposomes inhibited phagocytosis by phorbol ester-treated THP-1 cells. These results suggest that the mechanism by which apoptotic cells are recognized and phagocytosed by macrophages is determined by the subpopulation of macrophages studied.


Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins.
Double-bond photoisomerization in molecules such as the green fluorescent protein (GFP) chromophore can occur either via a volume-demanding one-bond-flip pathway or via a volume-conserving hula-twist pathway. Understanding the factors that determine the pathway of photoisomerization would inform the rational design of photoswitchable GFPs as improved tools for super-resolution microscopy. In this communication, we reveal the photoisomerization pathway of a photoswitchable GFP, rsEGFP2, by solving crystal structures of cis and trans rsEGFP2 containing a monochlorinated chromophore. The position of the chlorine substituent in the trans state breaks the symmetry of the phenolate ring of the chromophore and allows us to distinguish the two pathways. Surprisingly, we find that the pathway depends on the arrangement of protein monomers within the crystal lattice: in a looser packing, the one-bond-flip occurs, whereas, in a tighter packing (7% smaller unit cell size), the hula-twist occurs.


Implant survival and radiographic outcome of total hip replacement in patients less than 20 years old.
Background and purpose - Total hip replacement (THR) is not recommended for children and very young teenagers because early and repetitive revisions are likely. We investigated the clinical and radiographic outcomes of THR performed in children and teenage patients. Patients and methods - We included 111 patients (132 hips) who underwent THR before 20 years of age. They were identified in the Norwegian Arthroplasty Register, together with information on the primary diagnosis, types of implants, and any revisions that required implant change. Radiographs and Harris hip score (HHS) were also evaluated. Results - The mean age at primary THR was 17 (11-19) years and the mean follow-up time was 14 (3-26) years. The 10-year survival rate after primary THR (with the endpoint being any revision) was 70%. 39 patients had at least 1 revision and 16 patients had 2 or more revisions. In the latest radiographs, osteolysis and atrophy were observed in 19% and 27% of the acetabulae and 21% and 62% of the femurs, respectively. The mean HHS at the final follow-up was 83 (15-100). Interpretation - The clinical score after THR in these young patients was acceptable, but many revisions had been performed. However, young patients with developmental dysplasia of the hip had lower implant survival. Moreover, the bone stock in these patients was poor, which could complicate future revisions.


Accurate electromechanical characterization of soft molecular monolayers using piezo force microscopy.
We report a new methodology for the electromechanical characterization of organic monolayers based on the implementation of dual AC resonance tracking piezo force microscopy (DART-PFM) combined with a sweep of an applied DC field under a fixed AC field. This experimental design allows calibration of the electrostatic component of the tip response and enables the use of low spring constant levers in the measurement. Moreover, the technique is shown to determine both positive and negative piezo response. The successful decoupling of the electrostatic component from the mechanical response will enable more quantitative electromechanical characterization of molecular and biomaterials and should generate new design principles for soft bio-compatible piezoactive materials. To highlight the applicability, our new methodology was used to successfully characterize the piezoelectric coefficient (d 33) of a variety of piezoactive materials, including self-assembled monolayers made of small molecules (dodecane thiol, mercaptoundecanoic acid) or macromolecules (peptides, peptoids), as well as a variety of inorganic materials, including lead zirconate titanate [PZT], quartz, and periodically poled lithium niobate [PPLN]. Due to high differential capacitance, the soft organic monolayers demonstrated exceedingly large electromechanical response (as high as 250 pm V-1) but smaller d 33 piezocoefficients. Finally, we find that the capacitive electrostatic response of the organic monolayers studied are significantly larger than conventional inorganic piezoelectric materials (e.g., PZT, PPLN, quartz), suggesting organic electromechanical materials applications can successfully draw from both piezo and electrostatic responses.


Kinetic and thermodynamic hysteresis imposed by intercalation of proflavine in ferrocene-modified double-stranded DNA.
Surface-confined immobilized redox species often do not show the expected zero peak separation in slow-scan cyclic voltammograms. This phenomenon is frequently associated to experimental drawbacks and hence neglected. However, a nonzero peak separation, which is common to many electrochemical systems with high structural flexibility, can be rationally assigned to a thermodynamic hysteresis. To study this phenomenon, a surface-confined redox species was used. Specifically, a DNA strand which is tagged with ferrocene (Fc) moieties at its 5' end and its complementary capture probe is thiolated at the 3' end was self-assembled in a monolayer at a Au electrode with the Fc moieties being located at the bottom plane of the double-stranded DNA (dsDNA). The DNA-bound Fc undergoes rapid electron transfer with the electrode surface as evaluated by fast scan cyclic voltammetry. The electron transfer is sensitive to the ion transport along the DNA strands, a phenomenon which is modulated upon specific intercalation of proflavine into surface-bound dsDNA. The electron transfer rate of the Fc(0/+) redox process is influenced by the cationic permselectivity of the DNA monolayer. In addition to the kinetic hindrance, a thermodynamic effect correlated with changes in the activity coefficients of the Fc(0/+) moieties near the gold-dsDNA interface is observed and discussed as source of the observed hysteresis causing the non-zero peak separation in the voltammograms.


Rectal pH in well and unwell infants.
Prompt antibiotic treatment for infants with sepsis has the potential to save lives. A rectal formulation of an antibiotic could be used at a village level before referral to hospital. The development of such a preparation needs to take into account the rectal pH of infants that will affect drug partitioning and absorption. Rectal pH measurements were taken in 100 well and 45 unwell infants. We also measured rectal pH in 14 infants sequentially over the course of their illness. The mean rectal pH was 6.75 with no significant difference in well or unwell infants. The mean (95% CI) rectal pH of well neonates was significantly lower than that of older infants (>28 days): 6.47 (6.29-6.65) vs. 6.90 (6.68 to 7.12) p = 0.003.


Assessing the accuracy of blood RNA profiles to identify patients with post-concussion syndrome: A pilot study in a military patient population.
Mild traumatic brain injury (mTBI) is a complex, neurophysiological condition that can have detrimental outcomes. Yet, to date, no objective method of diagnosis exists. Physical damage to the blood-brain-barrier and normal waste clearance via the lymphatic system may enable the detection of biomarkers of mTBI in peripheral circulation. Here we evaluate the accuracy of whole transcriptome analysis of blood to predict the clinical diagnosis of post-concussion syndrome (PCS) in a military cohort. Sixty patients with clinically diagnosed chronic concussion and controls (no history of concussion) were recruited (retrospective study design). Male patients (46) were split into a training set comprised of 20 long-term concussed (> 6 months and symptomatic) and 12 controls (no documented history of concussion). Models were validated in a testing set (control = 9, concussed = 5). RNA_Seq libraries were prepared from whole blood samples for sequencing using a SOLiD5500XL sequencer and aligned to hg19 reference genome. Patterns of differential exon expression were used for diagnostic modeling using support vector machine classification, and then validated in a second patient cohort. The accuracy of RNA profiles to predict the clinical diagnosis of post-concussion syndrome patients from controls was 86% (sensitivity 80%; specificity 89%). In addition, RNA profiles reveal duration of concussion. This pilot study shows the potential utility of whole transcriptome analysis to establish the clinical diagnosis of chronic concussion syndrome.


Induction of intestinal Th17 cells by segmented filamentous bacteria.
The gastrointestinal tract of mammals is inhabited by hundreds of distinct species of commensal microorganisms that exist in a mutualistic relationship with the host. How commensal microbiota influence the host immune system is poorly understood. We show here that colonization of the small intestine of mice with a single commensal microbe, segmented filamentous bacterium (SFB), is sufficient to induce the appearance of CD4(+) T helper cells that produce IL-17 and IL-22 (Th17 cells) in the lamina propria. SFB adhere tightly to the surface of epithelial cells in the terminal ileum of mice with Th17 cells but are absent from mice that have few Th17 cells. Colonization with SFB was correlated with increased expression of genes associated with inflammation and antimicrobial defenses and resulted in enhanced resistance to the intestinal pathogen Citrobacter rodentium. Thus, manipulation of this commensal-regulated pathway may provide new opportunities for enhancing mucosal immunity and treating autoimmune disease.


Clinical Outcome of Febrile Tanzanian Children with Severe Malnutrition Using Anthropometry in Comparison to Clinical Signs.
Children with malnutrition compared with those without are at higher risk of infection, with more severe outcomes. How clinicians assess nutritional risk factors in febrile children in primary care varies. We conducted a post hoc subgroup analysis of febrile children with severe malnutrition enrolled in a randomized, controlled trial in primary care centers in Tanzania. The clinical outcome of children with severe malnutrition defined by anthropometric measures and clinical signs was compared between two electronic clinical diagnostic algorithms: ePOCT, which uses weight-for-age and mid-upper arm circumference to identify and manage severe malnutrition, and ALMANACH, which uses the clinical signs of edema of both feet and visible severe wasting. Those identified as having severe malnutrition by the algorithms in each arm were prescribed antibiotics and referred to the hospital. From December 2014 to February 2016, 106 febrile children were enrolled and randomized in the parent study, and met the criteria to be included in the present analysis. ePOCT identified 56/57 children with severe malnutrition using anthropometric measures, whereas ALMANACH identified 2/49 children with severe malnutrition using clinical signs. The proportion of clinical failure, defined as the development of severe symptoms by day 7 or persisting symptoms at day 7 (per-protocol), was 1.8% (1/56) in the ePOCT arm versus 16.7% (8/48) in the Algorithm for the MANagement of Childhood illnesses arm (risk difference -14.9%, 95% CI -26.0%, -3.8%; risk ratio 0.11, 95% CI 0.01, 0.83). Using anthropometric measures to identify and manage febrile children with severe malnutrition may have resulted in better clinical outcomes than by using clinical signs alone.


Marine cyanophages exhibit local and regional biogeography.
Biogeographic patterns have been demonstrated for a wide range of microorganisms. Nevertheless, the biogeography of marine viruses has been slower to emerge. Here we investigate biogeographic patterns of marine cyanophages that infect Synechococcus sp. WH7803 across multiple spatial and temporal scales. We compared cyanophage myoviral communities from nine coastal sites in Southern New England (SNE), USA, one site in Long Island NY, and four sites from Bermuda's inshore waters by assaying cyanophage isolates using the myoviral g43 DNA polymerase gene. Cyanophage community composition varied temporally at each of the sites. Further, 6 years of sampling at one Narragansett Bay site revealed annual seasonal variations in community composition, driven by the seasonal reoccurrence of specific viral taxa. Although the four Bermuda communities were similar to one another, they were significantly different than the North American coastal communities, with almost no overlap of taxa between the two regions. Among the SNE sites, cyanophage community composition also varied significantly and was correlated with the body of water sampled (e.g. Narragansett Bay, Cape Cod Bay, Vineyard Sound), although here, the same viral taxa were found at multiple sites. This study demonstrates that marine cyanophages display striking seasonal and spatial biogeographic patterns.


Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave.
Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin-Benson-Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO2-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.


Novel genetic sex markers reveal high frequency of sex reversal in wild populations of the agile frog (Rana dalmatina) associated with anthropogenic land use.
Populations of ectothermic vertebrates are vulnerable to environmental pollution and climate change because certain chemicals and extreme temperatures can cause sex reversal during early ontogeny (i.e. genetically female individuals develop male phenotype or vice versa), which may distort population sex ratios. However, we have troublingly little information on sex reversals in natural populations, due to unavailability of genetic sex markers. Here, we developed a genetic sexing method based on sex-linked single nucleotide polymorphism loci to study the prevalence and fitness consequences of sex reversal in agile frogs (Rana dalmatina). Out of 125 juveniles raised in laboratory without exposure to sex-reversing stimuli, 6 showed male phenotype but female genotype according to our markers. These individuals exhibited several signs of poor physiological condition, suggesting stress-induced sex reversal and inferior fitness prospects. Among 162 adults from 11 wild populations in North-Central Hungary, 20% of phenotypic males had female genotype according to our markers. These individuals occurred more frequently in areas of anthropogenic land use; this association was attributable to agriculture and less strongly to urban land use. Female-to-male sex-reversed adults had similar body mass as normal males. We recorded no events of male-to-female sex reversal either in the laboratory or in the wild. These results support recent suspicions that sex reversal is widespread in nature, and suggest that human-induced environmental changes may contribute to its pervasiveness. Furthermore, our findings indicate that sex reversal is associated with stress and poor health in early life, but sex-reversed individuals surviving to adulthood may participate in breeding.


Differences between plasma and adipose tissue biomarkers of carotenoids and tocopherols.
Biomarkers of dietary exposure or nutritional status are sought actively to overcome limitations of traditional dietary methodology. We compared plasma and adipose tissue biomarkers for carotenoids and tocopherols. The data consisted of samples from 91 men and 122 women, ages 45-70 years, from the control group of the European Community Multicentre Study on Antioxidants, Myocardial Infarction, and Cancer of the Breast (EURAMIC) Study. Pearson correlations between plasma and adipose tissue measurements for beta-carotene, lycopene, and alpha-tocopherol adjusted for smoking status displayed low, although significant, correlations of 0.39, 0.24, and 0.39, respectively. The correlation was further stratified by sex. After being corrected for measurement error using deattenuation factors obtained from a reproducibility study, the stratified correlation coefficients were as high as 0.80 for beta-carotene in men, 0.62 for lycopene in women, and 0.52 for alpha-tocopherol in women. In addition, plasma and adipose tissue measurements from the myocardial infarction (MI) subset of the EURAMIC study population were used to evaluate the odds of MI, adjusting for confounders. We found that the concentration of lycopene in plasma was not positively associated significantly with MI (odds ratio, 1.78; P = 0.26). Adipose tissue lycopene, in contrast to reports elsewhere on the total population, showed an inverse association with MI (odds ratio, 0.62; P = 0.15). These results suggest that plasma and adipose carotenoids represent different markers for nutritional status and cannot be used interchangeably in epidemiological and dietary validation studies.


Brain age prediction: Cortical and subcortical shape covariation in the developing human brain.
Cortical development is characterized by distinct spatial and temporal patterns of maturational changes across various cortical shape measures. There is a growing interest in summarizing complex developmental patterns into a single index, which can be used to characterize an individual's brain age. We conducted this study with two primary aims. First, we sought to quantify covariation patterns for a variety of cortical shape measures, including cortical thickness, gray matter volume, surface area, mean curvature, and travel depth, as well as white matter volume, and subcortical gray matter volume. We examined these measures in a sample of 869 participants aged 5-18 from the Healthy Brain Network (HBN) neurodevelopmental cohort using the Joint and Individual Variation Explained (Lock et al., 2013) method. We validated our results in an independent dataset from the Nathan Kline Institute - Rockland Sample (NKI-RS; N = 210) and found remarkable consistency for some covariation patterns. Second, we assessed whether covariation patterns in the brain can be used to accurately predict a person's chronological age. Using ridge regression, we showed that covariation patterns can predict chronological age with high accuracy, reflected by our ability to cross-validate our model in an independent sample with a correlation coefficient of 0.84 between chronologic and predicted age. These covariation patterns also predicted sex with high accuracy (AUC = 0.85), and explained a substantial portion of variation in full scale intelligence quotient (R2 = 0.10). In summary, we found significant covariation across different cortical shape measures and subcortical gray matter volumes. In addition, each shape measure exhibited distinct covariations that could not be accounted for by other shape measures. These covariation patterns accurately predicted chronological age, sex and general cognitive ability. In a subset of NKI-RS, test-retest (<1 month apart, N = 120) and longitudinal scans (1.22 ± 0.29 years apart, N = 77) were available, allowing us to demonstrate high reliability for the prediction models obtained and the ability to detect subtle differences in the longitudinal scan interval among participants (median and median absolute deviation of absolute differences between predicted age difference and real age difference = 0.53 ± 0.47 years, r = 0.24, p-value = 0.04).


A new view on grasping.
Reaching out for object is often described as consisting of two components that are based on different visual information. Information about the object's position and orientation guides the hand to the object, while information about the object's shape and size determines how the fingers move relative to the thumb to grasp it. We propose an alternative description, which consists of determining suitable positions on the object - on the basis of its shape, surface roughness, and so on - and then moving one's thumb and fingers more or less independently to these positions. We modeled this description using a minimum-jerk approach, whereby the finger and thumb approach their respective target positions approximately orthogonally to the surface. Our model predicts how experimental variable such as object size, movement speed, fragility, and required accuracy will influence the timing and size of the maximum aperture of the hand. An extensive review of experimental studies on grasping showed that the predicted influences correspond to human behavior.


Quality scores for 32,000 genomes.
More than 80% of the microbial genomes in GenBank are of 'draft' quality (12,553 draft vs. 2,679 finished, as of October, 2013). We have examined all the microbial DNA sequences available for complete, draft, and Sequence Read Archive genomes in GenBank as well as three other major public databases, and assigned quality scores for more than 30,000 prokaryotic genome sequences. Scores were assigned using four categories: the completeness of the assembly, the presence of full-length rRNA genes, tRNA composition and the presence of a set of 102 conserved genes in prokaryotes. Most (~88%) of the genomes had quality scores of 0.8 or better and can be safely used for standard comparative genomics analysis. We compared genomes across factors that may influence the score. We found that although sequencing depth coverage of over 100x did not ensure a better score, sequencing read length was a better indicator of sequencing quality. With few exceptions, most of the 30,000 genomes have nearly all the 102 essential genes. The score can be used to set thresholds for screening data when analyzing "all published genomes" and reference data is either not available or not applicable. The scores highlighted organisms for which commonly used tools do not perform well. This information can be used to improve tools and to serve a broad group of users as more diverse organisms are sequenced. Unexpectedly, the comparison of predicted tRNAs across 15,000 high quality genomes showed that anticodons beginning with an 'A' (codons ending with a 'U') are almost non-existent, with the exception of one arginine codon (CGU); this has been noted previously in the literature for a few genomes, but not with the depth found here.


Review of the effects of glycerol-containing hyperhydration solutions on gastric emptying and intestinal absorption in humans and in rats.
Glycerol-induced hyperhydration (GIH) has been shown to improve fluid retention and endurance performance compared with water-induced hyperhydration. The goal of this article is to report on what is known and unknown about how glycerol-containing hyperhydration solutions (GCHSs) are processed at the stomach and intestine level, propose strategies to improve the efficacy of GIH, and provide research questions for future studies. Through statistical analyses, it is demonstrated that the effectiveness of GCHSs in increasing fluid retention is maximized when fluid ingestion is in the upper range of what is normally administered by studies (~26 ml/kg body weight) and the duration of the protocol is no longer than the time it takes for the glycerol-fluid load to be totally or nearly completely integrated inside the body. The rate of gastric emptying and intestinal absorption of GCHSs is unknown. However, based on an analysis of indirect evidence obtained from human studies, it is proposed that most glycerol (~80 g) and fluid (~1,700 ml) ingested during a typical GIH protocol can be integrated inside the body within 60-90 min. Whether the stress associated with competition could alter these figures is unknown. Research in rats indicates that combining glycerol with glucose at a 3:1 ratio accelerates intestinal absorption of both glycerol and water, thereby potentially improving the efficacy of GIH. Human studies must be conducted to determine how GCHSs are processed by the gastrointestinal system and whether adding glucose to GCHSs could improve the technique's efficacy.


In vitro synthesis of short DNA pieces by DNA polymerase alpha from mouse myeloma.
The DNA chain elongation mechanisms of mouse DNA polymerases alpha and beta have been analyzed by using denatured DNA with a (dT)n block at the 3'-end as a template in combination with RNA ((rA)12-20)primer. The (rA)12-20-primed DNA product synthesized by DNA polymerase alpha was 3-5 s in size even after prolonged reaction; instead of a size increase, the number of 3-5 s molecules increased with the reaction time. The size of products was not affected by differences in 3H-labeled substrate (dATP or dTTP), enzyme amount, KCl concentration, or the length of 3'-(dT)n blocks. On the other hand, DNA polymerase beta synthesized long DNA products by a highly distributive reaction mechanism. 3-5 sDNA pieces synthesized by DNA polymerase alpha were not elongated any further by DNA polymerase alpha, but were converted into long DNA chains by DNA polymerase beta. The results imply that DNA polymerase alpha recognizes the size of the product DNA, and shuts off further elongation.


Analysis of amino acids by miniaturised isotachophoresis.
A method allowing the miniaturised isotachophoretic analysis of amino acids has been developed. To overcome the problems of carbonate contamination which occur when performing separations at alkaline pH levels glycolate was used as the leading ion. Addition of magnesium to the leading electrolyte as a counter species was found to improve the separations. The method has been used on a poly(methyl methacrylate) microdevice with integrated on-column conductivity detectors. The behaviour of a range of common amino acids was investigated and successful separations of up to seven amino acids were made. Good linearity was observed with calibration curves for aspartic acid and phenylalanine over the range 0.063-1.0 mM. Limits of detection for these two species were calculated to be 0.060 and 0.018 mM, respectively.


Early apoptosis of rod photoreceptors in Rpe65(-/-) mice is associated with the upregulated expression of lysosomal-mediated autophagic genes.
RPE65-related Leber's congenital amaurosis (LCA) is a rod-cone dystrophy whose clinical outcome is mainly attributed to the loss of rod photoreceptors followed by cone degeneration. Pathogenesis in Rpe65(-/-) mice is characterized by a slow and progressive degeneration of rods dependent on the constitutive activation of unliganded opsin. We previously reported that this opsin-mediated apoptosis of rods was dependent on Bcl-2-apoptotic pathway and Bax-induced pro-death activity. In this study, we report early initial apoptosis in the newly differentiated retina of Rpe65(-/-) mice. Apoptotic photoreceptors were identified as rods and resulted from pathological phototransduction signaling. This wave of early apoptosis triggered Bcl-2-related pathway and Bax apoptotic activity, while activation of the caspases was not induced. Following cellular stress, multiple signaling pathways are initiated which either commit cells to death or trigger pro-survival responses including autophagy. We report that Bcl-2-related early rod apoptosis was associated with the upregulation of autophagy markers including chaperone-mediated autophagy (CMA) substrate receptor LAMP-2 and lysosomal hydrolases Cathepsin S and Lysozyme. This suggests that lysosomal-mediated autophagy may be triggered in response to early rod apoptosis in Rpe65-LCA disease. These results highlight that Rpe65-related primary stress induces early signaling events, which trigger Bax-induced-apoptotic pathway and autophagy-mediated cellular response. These events may determine retinal cell fate, progression and severity of the disease.


The management of male subfertility by in vitro fertilisation techniques.
Although IVF was developed for the treatment of tubal infertility, it is clear that it has a significant application in treatment of couples where the problem is one of male subfertility. This is particularly relevant because, despite the developments in reproductive medicine, in most males there is no identifiable cause for the poor semen quality. Therefore, for these men there is no efficacious method of treatment. Varicocele ligation and the use of agents such as clomiphene citrate, mesterolone empirical antibiotic therapy, and anabolic steroids have not been show to be beneficial when subject to controlled trials. The concept of improving the chance of fertilisation by taking the oocytes to the sperm in vitro is therefore the first feasible therapeutic option available to these subfertile couples. However, these possibilities should not obviate the need for a thorough assessment of the subfertile male and continuing research into the basis of male infertility. During the past decade new methods of sperm preparation, modified methods of insemination, and the use of microinjection have been developed. IVF is now a realistic option for couples if the male is subfertile. It has been suggested by some critics of these techniques that the brunt of the discomfort and risk has to be borne by the women where the problem appears to be solely with the male partner. Nevertheless, as having children is a 'couple' decision, prospective couples need to consider whether such procedures are acceptable to them.(ABSTRACT TRUNCATED AT 250 WORDS)


[Diagnosis of legionellosis by microagglutination test--comparison to indirect immunofluorescent antibody method].
We studied the micro-agglutination method (MAT) for the diagnosis of legionellosis. Serum samples were collected from 44 clinically legionellosis suspected patients (17 positive with indirect immunofluorescent antibody technique [IFA] and 27 IFA negatives) and 20 healthy adults (25-30 years old). MAT showed negative results with sera collected from healthy adults and IFA negative patients, 8 out of 17 cass of IFA positive patients showed positive results in MAT. The remaining 9 cases out of 17 were negative in MAT judging from our criteria (1:256 in single serum or fourfold rise to 1:128 in pair sera). MAT had good proportion to IFA in samples collected within three weeks after onset of each disease. All sera that became positive in MAT were sampled within four weeks after onset of each illness. It was noted that MAT was mainly related to IgM-class antibodies. These relationships must be decided by investigating more cases of legionellosis. According to the result of this study, the MAT method was thought to be useful for rapid diagnosis of legionellosis.


Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.
The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.


Superior temporal sulcus and social cognition in dangerous drivers.
Understanding the neural systems underpinning social cognition is a primary focus of contemporary social neuroscience. Using functional magnetic resonance imaging (fMRI), the present study asked if brain activity reflecting socio-cognitive processes differs between individuals according to their social behavior; namely, between a group of drivers with frequent traffic offenses and a group with none. Socio-cognitive processing was elicited by employing videos from a traffic awareness campaign, consisting of reckless and anti-social driving behavior ending in tragic consequences, and control videos with analogous driving themes but without such catastrophic endings. We investigated whether relative increases in brain function during the observation of these campaign stimuli compared with control videos differed between these two groups. To develop the results of our previous study we focused our analyses on superior temporal sulcus/gyrus (STS/STG). This revealed a bigger increase in brain activity within this region during the campaign stimuli in safe compared with dangerous drivers. Furthermore, by thematically coding drivers' verbal descriptions of the stimuli, we also demonstrate differences in STS reactivity according to drivers' scores on two indices of socio-cognitive processing: subjects' perceived consequences of actors' actions, and their affective evaluation of the clips. Our results demonstrate the influence of social behavior and socio-cognitive processing on STS reactivity to social stimuli, developing considerably our understanding of the role of this region in social cognition.


Molecular Basis of the Interaction of the Human Protein Tyrosine Phosphatase Non-receptor Type 4 (PTPN4) with the Mitogen-activated Protein Kinase p38γ.
The human protein tyrosine phosphatase non-receptor type 4 (PTPN4) prevents cell death induction in neuroblastoma and glioblastoma cell lines in a PDZ·PDZ binding motifs-dependent manner, but the cellular partners of PTPN4 involved in cell protection are unknown. Here, we described the mitogen-activated protein kinase p38γ as a cellular partner of PTPN4. The main contribution to the p38γ·PTPN4 complex formation is the tight interaction between the C terminus of p38γ and the PDZ domain of PTPN4. We solved the crystal structure of the PDZ domain of PTPN4 bound to the p38γ C terminus. We identified the molecular basis of recognition of the C-terminal sequence of p38γ that displays the highest affinity among all endogenous partners of PTPN4. We showed that the p38γ C terminus is also an efficient inducer of cell death after its intracellular delivery. In addition to recruiting the kinase, the binding of the C-terminal sequence of p38γ to PTPN4 abolishes the catalytic autoinhibition of PTPN4 and thus activates the phosphatase, which can efficiently dephosphorylate the activation loop of p38γ. We presume that the p38γ·PTPN4 interaction promotes cellular signaling, preventing cell death induction.


Support for the vascular depression hypothesis in late-life depression: results of a 2-site, prospective, antidepressant treatment trial.
Research on vascular depression has used 2 approaches to subtype late-life depression, based on executive dysfunction or white matter hyperintensity severity. To evaluate the relationship of neuropsychological performance and white matter hyperintensity with clinical response in late-life depression. Two-site, prospective, nonrandomized controlled trial. Outpatient clinics at Washington University and Duke University. A total of 217 subjects aged 60 years or older met DSM-IV criteria for major depression, scored 20 or more on the Montgomery-Asberg Depression Rating Scale (MADRS), and received vascular risk factor scores, neuropsychological testing, and magnetic resonance imaging; they were excluded for cognitive impairment or severe medical disorders. Fazekas rating was conducted to grade white matter hyperintensity lesions. Intervention Twelve weeks of sertraline treatment, titrated by clinical response. Main Outcome Measure Participants' MADRS scores over time. Baseline neuropsychological factor scores correlated negatively with baseline Fazekas scores. A mixed model examined effects of predictor variables on MADRS scores over time. Baseline episodic memory (P = .002), language (P = .007), working memory (P = .01), processing speed (P < .001), executive function factor scores (P = .002), and categorical Fazekas ratings (P = .05) predicted MADRS scores, controlling for age, education, age of onset, and race. Controlling for baseline MADRS scores, these factors remained significant predictors of decrease in MADRS scores, except for working memory and Fazekas ratings. Thirty-three percent of subjects achieved remission (MADRS < or =7). Remitters differed from nonremitters in baseline cognitive processing speed, executive function, language, episodic memory, and vascular risk factor scores. Comprehensive neuropsychological function and white matter hyperintensity severity predicted MADRS scores prospectively over a 12-week treatment course with selective serotonin reuptake inhibitors in late-life depression. Baseline neuropsychological function differentiated remitters from nonremitters and predicted time to remission in a proportional hazards model. Predictor variables correlated highly with vascular risk factor severity. These data support the vascular depression hypothesis and highlight the importance of linking subtypes based on neuropsychological function and white matter integrity. clinicaltrials.gov Identifier: NCT00045773.


Planned direct dual-modality treatment of complex broad-necked intracranial aneurysms: four technical case reports.
Treatment of complex, broad-based intracranial aneurysms with either microsurgical clipping or endovascular coiling alone is sometimes impossible. In this study, we report the planned combined endovascular and microsurgical treatment of four complex, wide-necked aneurysms in four patients. Three of the four patients presented with subarachnoid hemorrhage. The fourth patient presented with a progressive neurological deficit secondary to an associated arteriovenous malformation. Three of the aneurysms were located in the posterior circulation (two broad-necked basilar apex aneurysms and one bilobed vertebrobasilar junction aneurysm with a wide-necked ventral component). The fourth aneurysm was a broad-based paraclinoid/cavernous-carotid lesion. One of the patients with a basilar apex aneurysm and the patient with the paraclinoid aneurysm underwent surgery intended to create a narrow neck that would be amenable to future coiling. The patient with the bilobed vertebrobasilar junction aneurysm underwent surgery to treat the broad-necked ventral lobe, whereas the dorsal lobe, with the neck partially buried in the brainstem, was treated endovascularly. The second patient with a basilar apex aneurysm was in poor clinical condition after subarachnoid hemorrhage and was therefore treated with coil embolization to reduce the risk of rebleeding. After the patient made a good clinical recovery, the residual aneurysm was surgically clipped. Angiographic follow-up documented the complete obliteration of all four aneurysms. Clinically, all patients had good to excellent outcomes after a follow-up period of 6 to 30 months. Complex, broad-necked aneurysms that may be difficult to treat with a single mode of therapy can be safely and successfully treated with a combination of endovascular and microsurgical techniques. For patients with broad-based aneurysms that are difficult to access surgically without incurring significant morbidity, microsurgical clipping may be used as the initial procedure to create a smaller neck. Alternatively, for patients who are in poor clinical condition after subarachnoid hemorrhage and who harbor a broad-necked aneurysm in a surgically formidable location, partial coiling may be used initially to reduce the short-term risk of rebleeding.


Highly selective ratiometric fluorescent probe for Au3+ and its application to bioimaging.
The 4-propargylamino-1,8-naphthalimide based fluorescent probe 1 has been explored as a sensor for selective detection of Au(3+). 4-Amino-1,8-naphthalimides, that possess typical intramolecular charge transfer (ICT) electronic characteristics, have been widely used as versatile platforms for fluorescent probes. The newly designed probe 1 contains a propargylamine moiety at C-4 of the naphthalimide chromophore that reacts with Au(3+) to generate a product that has distinctly different electronic properties from 1. Specifically, the probe undergoes a remarkable change in its absorption spectrum upon addition of Au(3+) that is associated with a distinct color change from yellow to light pink. In addition, a blue shift of ca. 56 nm also takes place in the emission spectra of the probe. Consequently, 1 serves as a reaction-based sensor or so called chemodosimeter for Au(3+). Importantly, surfactants enhance the rate of reaction of 1 with Au(3+), thus, enhancing its use as a real time sensor. Finally, the results of studies probing its application to bioimaging of Au(3+) in live cells show that the probe 1 has a unique ability to sense Au(3+) in cells and, in particular, in lipid droplets within cells.


Probable rapid eye movement sleep behavior disorder, nocturnal disturbances and quality of life in patients with Parkinson's disease: a case-controlled study using the rapid eye movement sleep behavior disorder screening questionnaire.
Increasing evidence provides a clear association between rapid eye movement sleep behavior disorders (RBD) and Parkinson's disease (PD), but the clinical features that determine the co-morbidity of RBD and PD are not yet fully understood. We evaluated the characteristics of nocturnal disturbances and other motor and non-motor features related to RBD in patients with PD and the impact of RBD on their quality of life. Probable RBD (pRBD) was evaluated using the Japanese version of the RBD screening questionnaire (RBDSQ-J). A significantly higher frequency of pRBD was observed in PD patients than in the controls (RBDSQ-J ≥ 5 or ≥ 6: 29.0% vs. 8.6%; 17.2% vs. 2.2%, respectively). After excluding restless legs syndrome and snorers in the PD patients, the pRBD group (RBDSQ-J≥5) showed higher scores compared with the non-pRBD group on the Parkinson's disease sleep scale-2 (PDSS-2) total and three-domain scores. Early morning dystonia was more frequent in the pRBD group. The Parkinson's Disease Questionnaire (PDQ-39) domain scores for cognition and emotional well-being were higher in the patients with pRBD than in the patients without pRBD. There were no differences between these two groups with respect to the clinical subtype, disease severity or motor function. When using a cut-off of RBDSQ-J = 6, a similar trend was observed for the PDSS-2 and PDQ-39 scores. Patients with PD and pRBD had frequent sleep onset insomnia, distressing dreams and hallucinations. The stepwise linear regression analysis showed that the PDSS-2 domain "motor symptoms at night", particularly the PDSS sub-item 6 "distressing dreams", was the only predictor of RBDSQ-J in PD. Our results indicate a significant impact of RBD co-morbidity on night-time disturbances and quality of life in PD, particularly on cognition and emotional well-being. RBDSQ may be a useful tool for not only screening RBD in PD patients but also predicting diffuse and complex clinical PD phenotypes associated with RBD, cognitive impairment and hallucinations.


Managing outbreaks of highly contagious diseases in prisons: a systematic review.
There are reports of outbreaks of COVID-19 in prisons in many countries. Responses to date have been highly variable and it is not clear whether public health guidance has been informed by the best available evidence. We conducted a systematic review to synthesise the evidence on outbreaks of highly contagious diseases in prison. We searched seven electronic databases for peer-reviewed articles and official reports published between 1 January 2000 and 28 July 2020. We included quantitative primary research that reported an outbreak of a given contagious disease in a correctional facility and examined the effects of interventions. We excluded studies that did not provide detail on interventions. We synthesised common themes using the Synthesis Without Meta-analysis (SWiM) guideline, identified gaps in the literature and critically appraised the effectiveness of various containment approaches. We identified 28 relevant studies. Investigations were all based in high-income countries and documented outbreaks of tuberculosis, influenza (types A and B), varicella, measles, mumps, adenovirus and COVID-19. Several themes were common to these reports, including the public health implications of infectious disease outbreaks in prison, and the role of interagency collaboration, health communication, screening for contagious diseases, restriction, isolation and quarantine, contact tracing, immunisation programmes, epidemiological surveillance and prison-specific guidelines in addressing any outbreaks. Prisons are high-risk settings for the transmission of contagious diseases and there are considerable challenges in managing outbreaks in them. A public health approach to managing COVID-19 in prisons is required. CRD42020178827.


Filter forensics: microbiota recovery from residential HVAC filters.
Establishing reliable methods for assessing the microbiome within the built environment is critical for understanding the impact of biological exposures on human health. High-throughput DNA sequencing of dust samples provides valuable insights into the microbiome present in human-occupied spaces. However, the effect that different sampling methods have on the microbial community recovered from dust samples is not well understood across sample types. Heating, ventilation, and air conditioning (HVAC) filters hold promise as long-term, spatially integrated, high volume samplers to characterize the airborne microbiome in homes and other climate-controlled spaces. In this study, the effect that dust recovery method (i.e., cut and elution, swabbing, or vacuuming) has on the microbial community structure, membership, and repeatability inferred by Illumina sequencing was evaluated. The results indicate that vacuum samples captured higher quantities of total, bacterial, and fungal DNA than swab or cut samples. Repeated swab and vacuum samples collected from the same filter were less variable than cut samples with respect to both quantitative DNA recovery and bacterial community structure. Vacuum samples captured substantially greater bacterial diversity than the other methods, whereas fungal diversity was similar across all three methods. Vacuum and swab samples of HVAC filter dust were repeatable and generally superior to cut samples. Nevertheless, the contribution of environmental and human sources to the bacterial and fungal communities recovered via each sampling method was generally consistent across the methods investigated. Dust recovery methodologies have been shown to affect the recovery, repeatability, structure, and membership of microbial communities recovered from dust samples in the built environment. The results of this study are directly applicable to indoor microbiota studies utilizing the filter forensics approach. More broadly, this study provides a better understanding of the microbial community variability attributable to sampling methodology and helps inform interpretation of data collected from other types of dust samples collected from indoor environments.


Effects of Enterococcus faecalis fsr genes on production of gelatinase and a serine protease and virulence.
Three agr-like genes (fsrA, fsrB, and fsrC, for Enterococcus faecalis regulator) were found upstream of the previously reported gelatinase gene (gelE) and a downstream putative serine protease gene (sprE; accession number Z12296) of Enterococcus faecalis OG1RF. The deduced amino acid sequence of fsrA shows 26% identity and 38% similarity to Staphylococcus aureus AgrA (the response regulator of the accessory gene regulator system in the agr locus), FsrB shows 23% identity and 41% similarity to S. aureus AgrB, and FsrC shows 23% identity and 36% similarity to S. aureus AgrC (the sensor transducer of Agr system). Northern blot analysis suggested that gelE and sprE are cotranscribed and that fsrB and fsrC are also cotranscribed in OG1RF. Northern blot analysis of fsrA, fsrB, fsrC, gelE, and sprE insertion mutants showed that fsrB, fsrC, gelE, and sprE are not expressed in fsrA, fsrB, and fsrC mutants, while insertion in an open reading frame further upstream of fsrA did not effect the expression of these genes, suggesting that agr-like genes may be autoregulated and that they regulate gelE and sprE expression, as further confirmed by complementation of fsr gene mutations with a 6-kb fragment which contains all three fsr genes in the shuttle vector, pAT18. Testing of 95 other isolates of E. faecalis showed that 62% produced gelatinase (Gel(+)), while 91% (including all Gel(+) strains) hybridized to a gelE probe; 71% (including all Gel(+) strains) hybridized to an fsr probe, corroborating the conclusion that both gelE and fsr are necessary for gelatinase production. Testing of fsrA, fsrB, and sprE mutants in a mouse peritonitis model showed that sprE and agr-like gene mutants resulted in highly significantly prolonged survival compared to the parent strain OG1RF, a finding similar to what we had previously shown for a gelE mutant. These results suggest that sprE and agr-like genes contribute to the virulence of E. faecalis OG1RF in this model.


The Mechanisms for Within-Host Influenza Virus Control Affect Model-Based Assessment and Prediction of Antiviral Treatment.
Models of within-host influenza viral dynamics have contributed to an improved understanding of viral dynamics and antiviral effects over the past decade. Existing models can be classified into two broad types based on the mechanism of viral control: models utilising target cell depletion to limit the progress of infection and models which rely on timely activation of innate and adaptive immune responses to control the infection. In this paper, we compare how two exemplar models based on these different mechanisms behave and investigate how the mechanistic difference affects the assessment and prediction of antiviral treatment. We find that the assumed mechanism for viral control strongly influences the predicted outcomes of treatment. Furthermore, we observe that for the target cell-limited model the assumed drug efficacy strongly influences the predicted treatment outcomes. The area under the viral load curve is identified as the most reliable predictor of drug efficacy, and is robust to model selection. Moreover, with support from previous clinical studies, we suggest that the target cell-limited model is more suitable for modelling in vitro assays or infection in some immunocompromised/immunosuppressed patients while the immune response model is preferred for predicting the infection/antiviral effect in immunocompetent animals/patients.


Enteric outbreaks in long-term care facilities and recommendations for prevention: a review.
Outbreaks of enteric illness in long-term care facilities (LTCFs) were reviewed to identify preventative recommendations. Systematic review methodology identified outbreak reports of gastrointestinal illness in LTCFs either published or that occurred from January 1997 to June 2007. The inclusion criteria captured 75 outbreaks; 23 (31%) associated with bacterial agents and 52 (69%) with viral agents. Transmission was mainly foodborne (52%) for those of bacterial origin and person-to-person (71%) for viral outbreaks. Norovirus infection was associated with 58% of hospitalizations. Sixty deaths were reported, about half from Salmonella infections. Recommendations for foodborne outbreaks emphasized appropriate sourcing and preparation of eggs, staff training, and temperature control during food preparation. Recommendations from outbreaks transmitted person-to-person centred on controlling residents' movements, effective environmental cleaning and disinfection, cancelling social events and restricting visitors, excluding ill staff, encouraging effective hand hygiene, and preventing cross-contamination through gloving and gowning. In none of the 75 published outbreak reports were the suggested recommendations evaluated for effectiveness in controlling the outbreak. Applied research of this type could greatly help in the acceptance of prevention and control strategies.


Extraordinary Adaptive Plasticity of Colorado Potato Beetle: "Ten-Striped Spearman" in the Era of Biotechnological Warfare.
Expanding from remote areas of Mexico to a worldwide scale, the ten-striped insect, the Colorado potato beetle (CPB, Leptinotarsa decemlineata Say), has risen from being an innocuous beetle to a prominent global pest. A diverse life cycle, phenotypic plasticity, adaptation to adverse conditions, and capability to detoxify or tolerate toxins make this insect appear to be virtually "indestructible". With increasing advances in molecular biology, tools of biotechnological warfare were deployed to combat CPB. In the last three decades, genetically modified potato has created a new challenge for the beetle. After reviewing hundreds of scientific papers dealing with CPB control, it became clear that even biotechnological means of control, if used alone, would not defeat the Colorado potato beetle. This control measure once again appears to be provoking the potato beetle to exhibit its remarkable adaptability. Nonetheless, the potential for adaptation to these techniques has increased our knowledge of this pest and thus opened possibilities for devising more sustainable CPB management programs.


Impact of subthreshold membrane potential on synaptic responses at dendritic spines of layer 5 pyramidal neurons in the prefrontal cortex.
Glutamatergic inputs onto cortical pyramidal neurons are received and initially processed at dendritic spines. AMPA and NMDA receptors generate both synaptic potentials and calcium (Ca) signals in the spine head. These responses can in turn activate a variety of Ca, sodium (Na), and potassium (K) channels at spines. In principle, the roles of these receptors and channels can be strongly regulated by the subthreshold membrane potential. However, the impact of different receptors and channels has usually been studied at the level of dendrites. Much less is known about their influence at spines, where synaptic transmission and plasticity primarily occur. Here we examine single-spine responses in the basal dendrites of layer 5 pyramidal neurons in the mouse prefrontal cortex. Using two-photon microscopy and two-photon uncaging, we first show that synaptic potentials and Ca signals differ at resting and near-threshold potentials. We then determine how subthreshold depolarizations alter the contributions of AMPA and NMDA receptors to synaptic responses. We show that voltage-sensitive Ca channels enhance synaptic Ca signals but fail to engage small-conductance Ca-activated K (SK) channels, which require greater numbers of inputs. Finally, we establish how the subthreshold membrane potential controls the ability of voltage-sensitive Na channels and K channels to influence synaptic responses. Our findings reveal how subthreshold depolarizations promote electrical and biochemical signaling at dendritic spines by regulating the contributions of multiple glutamate receptors and ion channels.


A FAS-ligand variant associated with autoimmune lymphoproliferative syndrome in cats.
British shorthair (BSH) kittens in multiple litters died as a result of a severe non-neoplastic lymphoproliferative disease that showed many similarities with human autoimmune lymphoproliferative syndrome (ALPS). Human ALPS is caused by inherited defects in FAS-mediated lymphocyte apoptosis and the possibility of similar defects was investigated in BSH cats. The whole genomes of two affected kittens were sequenced and compared to 82 existing cat genomes. Both BSH kittens had homozygous insertions of an adenine within exon 3 of the FAS-ligand gene. The resultant frameshift and premature stop codon were predicted to result in a severely truncated protein that is unlikely to be able to activate FAS. Three additional affected BSH kittens were homozygous for the variant, while 11 of 16 unaffected, but closely related, BSH cats were heterozygous for the variant. All BSH cats in the study were from a population with significant inbreeding. The variant was not identified in a further survey of 510 non-BSH cats. Identification of a genetic defect in the FAS-mediated apoptosis pathway confirms that the lymphoproliferative disease in BSH cats fulfills the diagnostic criteria for ALPS in humans. These results will enable the development of a genetic test to detect BSH carrier animals.


Individual differences in risk preference predict neural responses during financial decision-making.
We investigated the neural correlates of subjective valuations during a task involving risky choices about lotteries. Because expected value was held constant across all lotteries, decisions were influenced by subjective preferences, which manifest behaviorally as risk-seeking or risk-averse attitudes. To isolate structures encoding risk preference during choice, we probed for areas showing increased activation as a function of selected risk-level. Such response patterns were obtained in anterior (ACC) and posterior cingulate cortex (PCC), superior frontal gyrus, caudate nucleus, and substantia nigra. Behavioral results revealed the presence of risk-averse and risk-neutral individuals. In parallel, brain signals revealed modulation of activity by risk attitude during choice. Correlations between risk-seeking attitudes and neural activity during risky choice were obtained in superior and inferior frontal gyri, medial and lateral orbitofrontal cortex, and parahippocampal gyrus, while correlations with risk-averse attitudes were found in the caudate. The dynamics of neural responses relevant to each stage of the task (decision, anticipation, outcome) were investigated via timeseries and conjunction analyses. Though the networks engaged in each of the task stages were mostly distinct, regions within ACC, PCC and caudate were consistently activated during each decision-making phase. These results demonstrate (1) that subjective assessments of risk, as well as individual attitudes toward risk, play a significant role in modulating activity within brain regions recruited during decision-making, and (2) that ACC, PCC and caudate are relevant during each phase of a decision-making task requiring subjective valuations, strengthening the role of these regions in self-referential subjective valuations during choice.


Are you HIV invincible? A probabilistic study of discordant couples in the context of HIV transmission.
A number of factors have been identified that are related to sexual and injecting HIV transmission. We developed a probabilistic mathematical model to put these factors together and interpret risks in the context of individual behavior among injecting drug-using (IDU) couples in St. Petersburg, Russia. Some HIV-discordant couples have unprotected sex and sometimes inject drugs together but stay discordant for a long time, while some individuals acquire HIV on the first encounter. We considered existing estimates of HIV transmission risks through injecting and sexual contacts to develop a predictive survival model for an individual who is exposed to HIV through intimate relationships. We computed simulated survival curves for a number of behavioral scenarios and discussed sources of simulated uncertainty. We then applied the model to a longitudinal study of HIV-discordant couples and validated the model's forecast. Although individual prediction of seroconversion time appeared impossible, the ability to rank behavioral patterns in terms of HIV risk and to estimate the probability of survival HIV-free will be important to educators and counselors.


A study of titanium release into body organs following the insertion of single threaded screw implants into the mandibles of sheep.
Titanium is generally considered a safe metal to use in implantation but some studies have suggested that particulate titanium may cause health problems either at the site overlying the implant or in distant organs, particularly after frictional wear of a medical prosthesis. It was the purpose of this investigation to study the levels of dissemination of titanium from threaded screw type implants following placement of single implants in sheep mandibles. Twelve sheep were implanted with a single 10x3.75mm self-tapping implant for time intervals of one, four and eight to 12 weeks. Four unoperated sheep served as controls. Regional lymph nodes, lungs, spleens and livers were dissected, frozen and subsequently analysed by Graphite Furnace Atomic Absorption Spectroscopy. Results associated with successful implants showed no statistically significant different levels of titanium in any organ compared to controls, although some minor elevations in titanium levels within the lungs and regional lymph nodes were noted. Two implants failed to integrate and these showed higher levels of titanium in the lungs (2.2-3.8 times the mean of the controls) and regional lymph nodes (7-9.4 times the levels in controls). Debris from a single implant insertion is at such a low level that it is unlikely to pose a health problem. Even though the number of failed implants was low, multiple failed implants may result in considerably more titanium release which can track through the regional lymph nodes. Results suggest that sheep would be an excellent model for following biological changes associated with successful and failed implants and the effect this may have on titanium release.


Fluorogenic Probe for Detecting Active Matrix Metalloproteinase-3 (MMP-3) in Plasma and Peripheral Blood Neutrophils to Indicate the Severity of Rheumatoid Arthritis.
Diagnosis of patients with rheumatoid arthritis (RA) is essential for early and accurate drug treatment to protect the patient from joint bone erosion and relieve symptoms of the disease. In some cases, the RA patient's X-ray images and other clinical diagnostic methods are often difficult to distinguish from different diseases, such as gout, osteoarthritis, and other inflammatory conditions. Thus, methods for diagnosis of disease activity and real-time monitoring of therapeutic effect and accurate differentiation from other bone diseases are needed. In this article, we suggest a matrix metalloproteinase-3 (MMP-3)-specific protease-activated probe immobilized in vitro kit and cell staining for flow cytometry analysis as methods to support clinical diagnosis. To overcome interindividual differences, we used phorbol 12-myristate 13-acetate (PMA)-activated plasma from 269 RA patients, 49 osteoarthritis patients, and 30 healthy volunteers. The in vitro kit developed for PMA-activated plasma showed potential for identifying disease severity and distinguishing RA from other bone diseases. In particular, expression of active MMP-3 increased until the moderate disease activity and then sharply decreased at severe disease. We suggest an analysis of intracellular MMP-3-specific protease-activated probe staining by flow cytometry. Compared with anti-MMP-3 antibody staining, the results for active MMP-3 in neutrophils using the probe exactly matched the results obtained with the in vitro kit. We also confirmed that expression of active MMP-3 was mainly from neutrophils. Together, these results suggest that the MMP-3-specific protease-activated probe might be a promising noninvasive tool for accurate diagnosis of disease severity and differentiation from similar bone diseases as well as for monitoring therapeutic efficacy.


Modified immunotherapies against Alzheimer's disease: toward safer and effective amyloid clearance.
Alzheimer's disease (AD) is characterized by the deposition of amyloid plaques, loss of neurons, neuritic degeneration, accumulation of fibrillary tangles in neurons, and a progressive loss of cognitive function. Amyloid-β peptide (Aβ) appears to play a pivotal role in the development of AD. Clearance of Aβ from the brain represents an important therapeutic strategy for prevention and treatment of AD. Immunotherapy targeting Aβ is effective to remove the peptide from the brain. However, it is associated with detrimental adverse effects, such as autoimmune meningoencephalitis and microhemorrhage. These are presumably the results of brain infiltration of provoked autoimmune T lymphocytes in response to Aβ vaccination and release of proinflammatory cytokines from microglia activated by the immune complex of Aβ and antibodies. An improvement of the safety of the immunotherapy is a major goal of the immunotherapy study. Here, we review the mechanisms involved in modified immunological strategies, as well as their adverse effects. We discuss the following: the development of B epitope vaccines to avoid activation of autoimmune T lymphocytes; DNA vaccines containing appropriate immunostimulatory and immunomodulatory sequences to induce the desired humoral immune responses; antibody modifications to avoid activation of microglia and subsequent release of proinflammatory cytokines; single chain antibodybased gene therapy; immunotherapy targeting Aβ oligomers; modulation of antibody delivery approach and dose; and application of autoantibodies against Aβ. These ultimately represent future directions of therapeutic approaches toward safer and effective Aβ clearance.


Ultrastructural characteristics of tau filaments in tauopathies: immuno-electron microscopic demonstration of tau filaments in tauopathies.
The microtubule-associated protein tau aggregates into filaments in the form of neurofibrillary tangles, neuropil threads and argyrophilic grains in neurons, in the form of variable astrocytic tangles in astrocytes and in the form of coiled bodies and argyrophilic threads in oligodendrocytes. These tau filaments may be classified into two types, straight filaments or tubules with 9-18 nm diameters and "twisted ribbons" composed of two parallel aligned components. In the same disease, the fine structure of tau filaments in glial cells roughly resembles that in neurons. In sporadic tauopathies, individual tau filaments show characteristic sizes, shapes and arrangements, and therefore contribute to neuropathologic differential diagnosis. In frontotemporal dementias caused by tau gene mutations, variable filamentous profiles were observed in association with mutation sites and insoluble tau isoforms, including straight filaments or tubules, paired helical filament-like filaments, and twisted ribbons. Pre-embedding immunoelectron microscopic studies were carried out using anti-3-repeat tau and anti-4-repeat tau specific antibodies, RD3 and RD4. Straight tubules in neuronal and astrocytic Pick bodies were immunolabeled by the anti-3-repeat tau antibody. The anti-4-repeat tau antibody recognized abnormal tubules comprising neurofibrillary tangles, coiled bodies and argyrophilic threads in progressive supranuclear palsy (PSP) and corticobasal degeneration. In the pre-embedding immunoelectron microscopic study using the phosphorylated tau AT8 antibody, tuft-shaped astrocytes of PSP were found to be composed of bundles of abnormal tubules in processes and perikarya of protoplasmic astrocytes. In this study, the 3-repeat tau or 4-repeat tau epitope was detected in situ at the ultrastructural level in abnormal tubules in representative pathological lesions in Pick's disease, PSP and corticobasal degeneration.


The effect of transforming growth factor beta1 gene polymorphisms in ankylosing spondylitis.
To determine whether genetic polymorphisms in or near the transforming growth factor beta1 (TGFB1) locus were associated with susceptibility to or severity of ankylosing spondylitis (AS). Five intragenic single-nucleotide polymorphisms (SNP) and three microsatellite markers flanking the TGFB1 locus were genotyped. Seven hundred and sixty-two individuals from 184 multiplex families were genotyped for the microsatellite markers and two of the promoter SNPs. One thousand and two individuals from 212 English and 170 Finnish families with AS were genotyped for all five intragenic SNPs. A structured questionnaire was used to assess the age of symptom onset, disease duration and disease severity scores, including the BASDAI (Bath Ankylosing Spondylitis Disease Activity Index) and BASFI (Bath Ankylosing Spondylitis Functional Index). A weak association was noted between the rare TGFB1 +1632 T allele and AS in the Finnish population (P = 0.04) and in the combined data set (P = 0.03). No association was noted between any other SNPs or SNP haplotype and AS, even among those families with positive non-parametric linkage scores. The TGFB1 +1632 polymorphism was also associated with a younger age of symptom onset (English population, allele 2 associated with age of onset greater by 4.2 yr, P = 0.05; combined data set, allele 2 associated with age of onset greater by 3.2 yr, P = 0.02). A haplotype of coding region SNPs (TGFB1 +869/+915+1632 alleles 2/1/2) was associated with age of symptom onset in both the English parent-case trios and the combined data set (English data set, haplotype 2/1/2 associated with age of onset greater by 4.9 yr, P = 0.03; combined data set, haplotype 2/1/2 associated with greater age of onset by 4.2 yr, P = 0.006). Weak linkage with AS susceptibility was noted and the peak LOD score was 1.3 at distance 2 cM centromeric to the TGFB1 gene. No other linkage or association was found between quantitative traits and the markers. This study suggests that the polymorphisms within the TGFB1 gene play at most a small role in AS and that other genes encoded on chromosome 19 are involved in susceptibility to the disease.


Biosynthesis of the aminocyclitol subunit of hygromycin A in Streptomyces hygroscopicus NRRL 2388.
The antibacterial activity of hygromycin A (HA) arises from protein synthesis inhibition and is dependent upon a methylenedioxy bridged-aminocyclitol moiety. Selective gene deletions and chemical complementation in Streptomyces hygroscopicus NRRL 2388 showed that the hyg18 and hyg25 gene products, proposed to generate a myo-inositol intermediate, are dispensable for HA biosynthesis but contribute to antibiotic yields. Hyg8 and Hyg17, proposed to introduce the amine functionality, are essential for HA biosynthesis. Hyg6 is a methyltransferase acting on the aminocyclitol, and a Deltahyg6 mutant produces desmethylenehygromycin A. Deletion of hyg7, a metallo-dependant hydrolase homolog gene, resulted in methoxyhygromycin A production, demonstrating that the corresponding gene product is responsible for the proposed oxidative cyclization step of methylenedioxy bridge formation. The methyl/methylene group is not required for in vitro protein synthesis inhibition but is essential for activity against Escherichia coli.


Anti-laminin-1 autoantibodies, pregnancy loss and endometriosis.
Laminin-1 is a major component and multifunctional glycoprotein of basement membranes that consists of three different subunits, alpha1, beta1 and gamma11 chains. It is the earliest synthesized network-forming protein during embryogenesis and plays an important role in embryonic development, embryonic implantation and placentation. We have recently shown that IgG anti-laminin-1 antibodies were significantly associated with recurrent first-trimester miscarriages and with subsequent pregnancy outcome. Interestingly, these antibodies were also observed in patients with endometriosis-associated infertility but not in patients with other causes of infertility, including tubal factors, hormonal and uterine abnormalities. Laminin-alpha1, -beta1 and -gamma1 mRNAs have been detected in 90% of endometriotic lesions and all laminin-alpha1, -beta1 and -gamma1 chains were localized in the basement membranes of glandular epithelium in endometriotic peritoneal lesions. Western blot analysis showed that anti-laminin-1 antibodies from those patients reacted with all laminin-1's chains. ELISA also confirmed that one of the target epitopes for these antibodies was located in a particular region of the laminin-1 molecule, i.e. the carboxyl-terminal globular G domain of alpha1 chain. IgM monoclonal anti-laminin-1 autoantibody, that we recently established, also recognized the G domain. Anti-laminin-1 antibodies from mice immunized with "mouse" laminin-1, caused a higher fetal resorption rate with lower embryonic and placental weights. Thus, anti-laminin-1 antibodies may be important in development of autoimmune-mediated reproductive failures and the assessment of the antibodies may provide a novel non-invasive diagnosis of endometriosis.


Pattern recognition reveals sex-dependent neural substrates of sexual perception.
Sex differences in brain activity evoked by sexual stimuli remain elusive despite robust evidence for stronger enjoyment of and interest toward sexual stimuli in men than in women. To test whether visual sexual stimuli evoke different brain activity patterns in men and women, we measured hemodynamic brain activity induced by visual sexual stimuli in two experiments with 91 subjects (46 males). In one experiment, the subjects viewed sexual and nonsexual film clips, and dynamic annotations for nudity in the clips were used to predict hemodynamic activity. In the second experiment, the subjects viewed sexual and nonsexual pictures in an event-related design. Men showed stronger activation than women in the visual and prefrontal cortices and dorsal attention network in both experiments. Furthermore, using multivariate pattern classification we could accurately predict the sex of the subject on the basis of the brain activity elicited by the sexual stimuli. The classification generalized across the experiments indicating that the sex differences were task-independent. Eye tracking data obtained from an independent sample of subjects (N = 110) showed that men looked longer than women at the chest area of the nude female actors in the film clips. These results indicate that visual sexual stimuli evoke discernible brain activity patterns in men and women which may reflect stronger attentional engagement with sexual stimuli in men.


Autonomous and non-cell autonomous etiology of ciliopathy associated structural birth defects.
Ciliopathies are associated with wide spectrum of structural birth defects (SBD), indicating important roles for cilia in development. Here we provide novel insights into the temporospatial requirement for cilia in SBDs arising from deficiency in Ift140 , an intraflagellar transport protein regulating ciliogenesis. Ift140 deficient mice exhibit cilia defects accompanied by wide spectrum of SBDs including macrostomia (craniofacial defects), exencephaly, body wall defects, tracheoesophageal fistula, randomized heart looping, congenital heart defects (CHD), lung hypoplasia, renal anomalies, and polydactyly. Tamoxifen inducible CAG-Cre deletion of a floxed Ift140 allele between E5.5 to 9.5 revealed early requirement for Ift140 in left-right heart looping regulation, mid to late requirement for cardiac outflow septation and alignment, and late requirement for craniofacial development and body wall closure. Surprisingly, CHD was not observed with four Cre drivers targeting different lineages essential for heart development, but craniofacial defects and omphalocele were observed with Wnt1-Cre targeting neural crest and Tbx18-Cre targeting epicardial lineage and rostral sclerotome through which trunk neural crest cells migrate. These findings revealed cell autonomous role of cilia in cranial/trunk neural crest mediated craniofacial and body wall closure defects, while non-cell autonomous multi-lineage interactions underlie CHD pathogenesis, revealing unexpected developmental complexity for CHD associated with ciliopathy.


Why does vasodilatation occur during syncope?
1. Syncopal or near syncopal episodes have been observed in five subjects who stood or were tilted and in whom blood samples were being taken. 2. In all subjects bradycardia and hypotension developed before the onset of symptoms. Increases in plasma adrenaline concentrations occurred in all subjects, beginning before the faint. Changes in plasma noradrenaline concentrations were variable: in three subjects there was a marked fall and in the other two subjects an increase. Plasma vasopressin increased in all subjects. 3. Increase in plasma adrenaline may be contributing to the vasodilatation and arterial hypotension which occur during syncope.


Dose-adjusted EPOCH chemotherapy for untreated peripheral T-cell lymphomas: a multicenter phase II trial of West-JHOG PTCL0707.
The standard CHOP therapy for peripheral T-cell lymphoma has resulted in unsatisfactory outcomes and it is still not clear what is the optimal front-line therapy. We conducted a multicenter phase II study of dose-adjusted etoposide, doxorubicin, and cyclophosphamide with vincristine and prednisone (EPOCH) for untreated peripheral T-cell lymphoma patients. In this prospective study, 41 patients were treated with dose-adjusted-EPOCH as initial therapy: peripheral T-cell lymphoma-not otherwise specified, n=21; angioimmunoblastic T-cell lymphoma, n=17; anaplastic lymphoma kinase-positive anaplastic large cell lymphoma, n=2; and anaplastic lymphoma kinase-negative anaplastic large cell lymphoma, n=1. Median patient age was 64 years (range: 32-79 years). According to the International Prognostic Index criteria, 51.2% were at high-intermediate or high risk. The overall response and complete response rates were 78.0% [95% confidence interval (CI): 62.4-89.4%] and 61.0% (95%CI: 44.5-75.8%), respectively. At the median follow up of 24.0 months, the 2-year progression-free survival and overall survival were 53.3% (95%CI: 36.4-67.5%) and 73.2% (95%CI: 56.8-84.1%), respectively. The younger patients (≤ 60 years old) had a high response rate (overall response 94.1% and complete response 70.6%) and survival rate (progression-free survival 62.5% and overall survival 82.4%). The most common grade ≥ 3 adverse events were neutropenia (74.5%), anemia (40.8%), thrombocytopenia (22.0%), and febrile neutropenia (9.0%). Dose-adjusted-EPOCH had a high response rate with a tolerable toxicity profile. Our results indicate that dose-adjusted-EPOCH is a reasonable first-line approach for peripheral T-cell lymphoma patients and may improve outcomes.


A survey of early and advanced gastric cancer treatment by surgeons in Thailand.
This study shows the first survey of patterns about surgeons' approaches and current practices in early and advanced gastric cancer in Thailand. Gastric cancer is a significant health problem worldwide. International guidelines for treatment differ in their recommendations including the accompanying therapy, but the condition is potentially curable. Surgeons have played an important role in Thailand but the limitation of institutional resources and the practices for gastric cancer vary between treatment options. The aim of this study is to investigate the current practices and approaches of Thai surgeons in relation to early and advanced gastric cancer treatment. A survey was conducted on 112 surgeons who claimed to have performed clinical practice upon gastric cancer patients. Information was collected on participant demographic data, the practices approaches in early and advanced stage without metastasis and the preferable adjuvant chemotherapy. The majority of participants were 100 general surgeons (89.4%). The preferred early gastric cancer treatment proved to be endoscopic resection 83.9%, cT1bN0 group preferred laparoscopic surgery 75.9%, cT2-T4aN0 group preferred open surgery 67.8%, cT4bN0 group preferred open surgery with En bloc resection 85.7% and cN+ group preferred open surgery 70.5%. For adjuvant treatment with chemotherapy, the study showed the surgeons who prescribed and treated by themselves was 41.9%. The preferred adjuvant regimens were S-1 50.9% and capecitabine and oxaliplatin 31.3%. This study is the first survey of the patterns of surgeons' approaches and current practices in early and advanced gastric cancer in Thailand.


Modelling hurricane exposure and wind speed on a mesoclimate scale: a case study from Cusuco NP, Honduras.
High energy weather events are often expected to play a substantial role in biotic community dynamics and large scale diversity patterns but their contribution is hard to prove. Currently, observations are limited to the documentation of accidental records after the passing of such events. A more comprehensive approach is synthesising weather events in a location over a long time period, ideally at a high spatial resolution and on a large geographic scale. We provide a detailed overview on how to generate hurricane exposure data at a meso-climate level for a specific region. As a case study we modelled landscape hurricane exposure in Cusuco National Park (CNP), Honduras with a resolution of 50 m×50 m patches. We calculated actual hurricane exposure vulnerability site scores (EVVS) through the combination of a wind pressure model, an exposure model that can incorporate simple wind dynamics within a 3-dimensional landscape and the integration of historical hurricanes data. The EVSS was calculated as a weighted function of sites exposure, hurricane frequency and maximum wind velocity. Eleven hurricanes were found to have affected CNP between 1995 and 2010. The highest EVSS's were predicted to be on South and South-East facing sites of the park. Ground validation demonstrated that the South-solution (i.e. the South wind inflow direction) explained most of the observed tree damage (90% of the observed tree damage in the field). Incorporating historical data to the model to calculate actual hurricane exposure values, instead of potential exposure values, increased the model fit by 50%.


Motif kernel generated by genetic programming improves remote homology and fold detection.
Protein remote homology detection is a central problem in computational biology. Most recent methods train support vector machines to discriminate between related and unrelated sequences and these studies have introduced several types of kernels. One successful approach is to base a kernel on shared occurrences of discrete sequence motifs. Still, many protein sequences fail to be classified correctly for a lack of a suitable set of motifs for these sequences. We introduce the GPkernel, which is a motif kernel based on discrete sequence motifs where the motifs are evolved using genetic programming. All proteins can be grouped according to evolutionary relations and structure, and the method uses this inherent structure to create groups of motifs that discriminate between different families of evolutionary origin. When tested on two SCOP benchmarks, the superfamily and fold recognition problems, the GPkernel gives significantly better results compared to related methods of remote homology detection. The GPkernel gives particularly good results on the more difficult fold recognition problem compared to the other methods. This is mainly because the method creates motif sets that describe similarities among subgroups of both the related and unrelated proteins. This rich set of motifs give a better description of the similarities and differences between different folds than do previous motif-based methods.


CD44 expression and modulation on human neuroblastoma tumours and cell lines.
The human CD44 cell surface glycoprotein has been involved in a variety of functions including lymphocyte homing, extracellular cell matrix attachment and tumour metastasis. A large family of variants or isoforms, generated by alternative splicing of a single gene, has been reported to be involved in the malignant process, by conferring metastatic potential to non-metastatic cells. Neuroblastoma is a tumour characterised by an aggressive and metastatic behaviour in advanced stages, with amplification of the MYCN protooncogene. In this report, we show that the CD44 standard molecule was highly expressed in the majority of tumours of stages 1-3, in all stage 4s and ganglioneuromas, but only in a subset of stage 4 tumours. A lack of CD44 expression was observed in all MYCN amplified stage 4 tumours, thus demonstrating a highly significant inverse relationship between MYCN amplification and CD44 expression in neuroblastoma. In addition, the expression of 4 different CD44 isoforms was measured on all specimens and was always found to be negative. Using neuroblastoma cell lines and MYCN expressing transfectants, we show that CD44 expression by neuroblastoma cell lines is not directly related to MYCN amplification, but is associated to the stage of differentiation or lineage, and to the tumorigenic properties of the cells. In addition, CD44 expression can be upmodulated parallel to differentiation or maturation as induced by retinoic acid, bromodeoxyuridine or phorbol ester. In contrast, cytokines such as IFN gamma, TNF alpha, or growth factors such as bFGF, SCF and TGF beta were ineffective in modulating CD44 expression.