Hydrogen sulphide decreases IL-1β-induced activation of fibroblast-like synoviocytes from patients with osteoarthritis.
Balneotherapy employing sulphurous thermal water is still applied to patients suffering from diseases of musculoskeletal system like osteoarthritis (OA) but evidence for its clinical effectiveness is scarce. Since the gasotransmitter hydrogen sulphide (H2 S) seems to affect cells involved in degenerative joint diseases, it was the objective of this study to investigate the effects of exogenous H2 S on fibroblast-like synoviocytes (FLS), which are key players in OA pathogenesis being capable of producing pro-inflammatory cytokines and matrix degrading enzymes. To address this issue primary FLS derived from OA patients were stimulated with IL-1β and treated with the H2 S donor NaHS. Cellular responses were analysed by ELISA, quantitative real-time PCR, phospho-MAPkinase array and Western blotting. Treatment-induced effects on cellular structure and synovial architecture were investigated in three-dimensional extracellular matrix micromasses. NaHS treatment reduced both spontaneous and IL-1β-induced secretion of IL-6, IL-8 and RANTES in different experimental settings. In addition, NaHS treatment reduced the expression of matrix metallo-proteinases MMP-2 and MMP-14. IL-1β induced the phosphorylation of several MAPkinases. NaHS treatment partially reduced IL-1β-induced activation of several MAPK whereas it increased phosphorylation of pro-survival factor Akt1/2. When cultured in spherical micromasses, FLS intentionally established a synovial lining layer-like structure; stimulation with IL-1β altered the architecture of micromasses leading to hyperplasia of the lining layer which was completely inhibited by concomitant exposure to NaHS. These data suggest that H2 S partially antagonizes IL-1β stimulation via selective manipulation of the MAPkinase and the PI3K/Akt pathways which may encourage development of novel drugs for treatment of OA.


Data and programming code from the studies on the learning curve for radical prostatectomy.
Our group analyzed a multi-institutional data set to address the question of how the outcomes of surgery for prostate cancer are affected by surgeon-specific factors. The cohort consists of 9076 patients treated by open radical prostatectomy at one of four US academic institutions 1987 - 2003. The primary analyses focused on 7765 patients without neoadjuvant therapy. The most well-known finding is that of a surgical "learning curve", with rates of prostate cancer cure strongly dependent on surgeon experience. In this "data note", we provide the raw data set, as well as well-annotated programming code for the main analyses. Data include markers of cancer severity (stage, grade and prostate-specific antigen level), cancer outcome, and surgeon variables such as training and experience.


Co3O4 nanowire@NiO nanosheet arrays for high performance asymmetric supercapacitors.
Herein, we report a simple and facile sequential hydrothermal process for the synthesis of Co3O4 nanowire@NiO nanosheet arrays (CNAs). The as-synthesized CNAs were characterized in detail using various analytical techniques, which confirmed the high crystallinity, purity, and high-density growth of these nanomaterials. From an application point of view, the as-synthesized CNAs were directly used as supercapacitor electrodes, revealing a specific capacitance of up to 2018 mF cm-2 at a current density of 2 mA cm-2. Furthermore, a flexible asymmetric supercapacitor was fabricated using the as-synthesized CNAs as the anode and activated carbon as the cathode, which revealed a specific capacitance of 134.6 mF cm-2 at a current density of 2 mA cm-2. In addition, the supercapacitor showed excellent capacity retention of 73.5% after 10 000 cycles at a current density of 10 mA cm-2.


Sarcoidosis succumbs to antibiotics--implications for autoimmune disease.
From time to time there have been reports of autoimmune disease succumbing to tetracycline antibiotics, but many have assumed this was due to coincidence, or to some ill-defined 'anti-inflammatory property' of the tetracyclines. But now the inflammation of sarcoidosis has succumbed to antibiotics in two independent studies. This review examines the cell wall deficient (antibiotic resistant) bacteria which have been found in tissue from patients with sarcoidosis. It examines how such bacteria can infect the phagocytes of the immune system, and how they may therefore be responsible for not only sarcoid inflammation, but also for other autoimmune disease. Proof positive of a bacterial pathogenesis for Sarcoidosis includes not only the demonstrated ability of these studies to put the disease into remission, but also the severity of Jarisch-Herxheimer shock resulting from endotoxin release as the microbes are killed. Studies delineating the hormone responsible for phagocyte differentiation in the Th1 immune response, 1,25-dihydroxyvitamin D, are discussed, and its utility as a marker of Th1 immune inflammation is reviewed. Finally, data showing that the behavior of this hormone is also aberrant in rheumatoid arthritis, systemic lupus erythematosus, and Parkinson's, raise the possibility that these diseases may also have a CWD bacterial pathogenesis.


Anatomical feasibility of performing a nerve transfer from the femoral branch to bilateral pelvic nerves in a cadaver: a potential method to restore bladder function following proximal spinal cord injury.
Nerve transfers are an effective means of restoring control to paralyzed somatic muscle groups and have recently been shown to be effective in denervated detrusor muscle in a canine model. A cadaveric study was performed to examine the anatomical feasibility of transferring femoral muscular nerve branches to vesical branches of the pelvic nerve as a method of potentially restoring innervation to control the detrusor muscle in humans. Twenty cadavers were dissected bilaterally to expose pelvic and femoral muscular nerve branches. Ease of access and ability to transfer the nerves were assessed, as were nerve cross-sectional areas. The pelvic nerve was accessed at the base of the bladder, inferior to the ureter, and accompanied by inferior vesical vessels. Muscular branches of the femoral nerve to the vastus medialis and intermedius muscles (L-3 and L-4 origins) were followed distally for 17.4 ± 0.8 cm. Two muscle branches were split from the femoral nerve trunk, and tunneled inferior to the inguinal ligament. One branch was moved medially toward the base of the bladder and linked to the ipsilateral pelvic nerve. The second branch was tunneled superior to the bladder and linked to the contralateral pelvic nerve. The cross-sectional area of the pelvic nerve vesical branch was 2.60 ± 0.169 mm(2) (mean ± SEM), and the femoral nerve branch at the suggested transection site was 4.40 ± 0.41 mm2. Use of femoral nerve muscular branches from the vastus medialis and intermedius muscles for heterotopic nerve transfer of bilateral pelvic nerves is surgically feasible, based on anatomical location and cross-sectional areas.


Adaptation of a Mice Doppler Echocardiography Platform to Measure Cardiac Flow Velocities for Embryonic Chicken and Adult Zebrafish.
Ultrasonography is the most widely used imaging technique in cardiovascular medicine. In this technique, a piezoelectric crystal produces, sends, and receives high frequency ultrasound waves to the body to create an image of internal organs. It enables practical real time visualization in a non-invasive manner, making the modality especially useful to image dynamic cardiac structures. In the last few decades, echocardiography has been applied to in vivo cardiac disease models, mainly to rodents. While clinical echocardiography platforms can be used for relatively large animals such as pigs and rats, specialized systems are needed for smaller species. Theoretically, as the size of the imaged sample decreases, the frequency of the ultrasound transducer needed to image the sample increases. There are multiple modes of echocardiography imaging. In Doppler mode, erythrocytes blood flow velocities are measured from the frequency shift of the sent ultrasound waves compared to received echoes. Recorded data are then used to calculate cardiac function parameters such as cardiac output, as well as the hemodynamic shear stress levels in the heart and blood vessels. The multi-mode (i.e., b-mode, m-mode, Pulsed Doppler, Tissue Doppler, etc.) small animal ultrasound systems in the market can be used for most in vivo cardiac disease models including mice, embryonic chick and zebrafish. These systems are also associated with significant costs. Alternatively, there are more economical single-mode echocardiography platforms. However, these are originally built for mice studies and they need to be tested and evaluated for smaller experimental models. We recently adapted a mice Doppler echocardiography system to measure cardiac flow velocities for adult zebrafish and embryonic chicken. We successfully assessed cardiac function and hemodynamic shear stress for normal as well as for diseased embryonic chicken and zebrafish. In this paper, we will present our detailed protocols for Doppler flow measurements and further cardiac function analysis on these models using the setup. The protocols will involve detailed steps for animal stabilization, probe orientation for specific measurements, data acquisition, and data analysis. We believe this information will help cardiac researchers to establish similar echocardiography platforms in their labs in a practical and economical manner.


Carbon footprint and cost-effectiveness of cataract surgery.
This article raises awareness about the cost-effectiveness and carbon footprint of various cataract surgery techniques, comparing their relative carbon emissions and expenses: manual small-incision cataract surgery (MSICS), phacoemulsification, and femtosecond laser-assisted cataract surgery. As the most commonly performed surgical procedure worldwide, cataract surgery contributes significantly to global climate change. The carbon footprint of a single phacoemulsification cataract surgery is estimated to be comparable to that of a typical person's life for 1 week. Phacoemulsification has been estimated to be between 1.4 and 4.7 times more expensive than MSICS; however, given the lower degree of postoperative astigmatism and other potential complications, phacoemulsification may still be preferable to MSICS in relatively resource-rich settings requiring high levels of visual function. Limited data are currently available regarding the environmental and financial impact of femtosecond laser-assisted cataract surgery; however, in its current form, it appears to be the least cost-effective option. Cataract surgery has a high value to patients. The relative environmental impact and cost of different types of cataract surgery should be considered as this treatment becomes even more broadly available globally and as new technologies are developed and implemented.


Monocyte trafficking to hepatic sites of bacterial infection is chemokine independent and directed by focal intercellular adhesion molecule-1 expression.
Recruitment of CCR2(+)Ly6C(high) monocytes to sites of infection is essential for efficient clearance of microbial pathogens. Although CCR2-mediated signals promote monocyte emigration from bone marrow, the contribution of CCR2 to later stages of monocyte recruitment remains unresolved. In this article, we show that CCR2 deficiency markedly worsens hepatic Listeria monocytogenes infection because Ly6C(high) monocytes are retained in the bone marrow. Intravenously transferred, CCR2-deficient Ly6C(high) monocytes traffic normally to hepatic foci of infection and contribute to bacterial clearance. Pertussis toxin treatment of adoptively transferred monocytes does not impair their intrahepatic trafficking, suggesting that chemokine signaling, once CCR2(+)Ly6C(high) monocytes emigrate from the bone marrow, is not required for monocyte localization to sites of bacterial infection in the liver. Expression of ICAM-1 is induced in close proximity to foci of bacterial infection in the liver, including on CD31(+) endothelial cells, and blockade of CD11b and CD44 diminishes monocyte localization to these hepatic foci. Our studies demonstrated that Ly6C(high) monocyte recruitment from the bloodstream to the L. monocytogenes-infected liver does not require chemokine receptor-mediated signals but instead is principally dependent on integrin- and extracellular matrix-mediated monocyte adhesion.


Salivary proteins associated with hyperglycemia in diabetes: a proteomic analysis.
Effective monitoring of glucose levels is necessary for patients to achieve greater control over their diabetes. However, only about a quarter of subjects with diabetes who requires close serum glucose monitoring, regularly check their serum glucose daily. One of the potential barriers to patient compliance is the blood sampling requirement. Saliva and its protein contents can be altered in subjects with diabetes, possibly due to changes in glycemic control. We propose here that salivary proteomes of subjects with diabetes may be different based on their glycemic control as reflected in A1C levels. A total of 153 subjects with type 1 or 2 diabetes were recruited. Subjects in each type of diabetes were divided into 5 groups based on their A1C levels; <7, 7-8, 8-9, 9-10, >10. To examine the global proteomic changes associated with A1C, the proteomic profiling of pooled saliva samples from each group was created using label-free quantitative proteomics. Similar proteomic analysis for individual subjects (N=4, for each group) were then applied to examine proteins that may be less abundant in pooled samples. Principle component analysis (PCA) and cluster analysis (p<0.01 and p<0.001) were used to define the proteomic differences. We, therefore, defined the salivary proteomic changes associated with A1C changes. This study demonstrates that differences exist between salivary proteomic profiles in subjects with diabetes based on the A1C levels.


Upregulation of defensins in burn sheep small intestine.
The aim of this study was to visualize and localize the sheep antimicrobials, beta-defensins 1, 2, and 3, (SBD-1, SBD-2, SBD-3), sheep neutrophil defensin alpha (SNP-1), and the cathelicidin LL-37 in sheep small intestine after burn injury, our hypothesis being that these compounds would be upregulated in an effort to overcome a compromised endothelial lining. Response to burn injury includes the release of proinflammatory cytokines and systemic immune suppression that, if untreated, can progress to multiple organ failure and death, so protective mechanisms have to be initiated and implemented. Tissue sections were probed with antibodies to the antimicrobials and then visualized with fluorescently labeled secondary antibodies and subjected to fluorescence deconvolution microscopy and image reconstruction. In both the sham and burn samples, all the aforementioned antimicrobials were seen in each of the layers of small intestine, the highest concentration being localized to the epithelium. SBD-2, SBD-3, and SNP-1 were upregulated in both enterocytes and Paneth cells, while SNP-1 and LL-37 showed increases in both the inner circular and outer longitudinal muscle layers of the muscularis externa following burn injury. Each of the defensins, except SBD-1, was also seen in between the muscle layers of the externa and while burn caused slight increases of SBD-2, SBD-3, and SNP-1 in this location, LL-37 content was significantly decreased. That while each of these human antimicrobials is present in multiple layers of sheep small intestine, SBD-2, SBD-3, SNP-1, and LL-37 are upregulated in the specific layers of the small intestine.


Development of a high-throughput bead based assay system to measure HIV-1 specific immune signatures in clinical samples.
The monitoring and assessment of a broadly neutralizing antibody (bnAb) based HIV-1 vaccine require detailed measurements of HIV-1 binding antibody responses to support the detection of correlates of protection. Here we describe the development of a flexible, high-throughput microsphere based multiplex assay system that allows monitoring complex binding antibody signatures. Studying a panel of 13 HIV-1 antigens in a parallel assessment of different IgG subclasses (IgG1, IgG2 and IgG3) we demonstrate the potential of our strategy. The technical advances we describe include means to improve antigen reactivity using directed neutravidin-biotin immobilization of antigens and biotin saturation to reduce background. A particular emphasis of our study was to provide tools for the assessment of reproducibility and stability of the assay system and strategies to control for variations allowing the application in high-throughput assays, where reliability of single measurements needs to be guaranteed.


Increased dosage of the MSN1 gene restores invertase expression in yeast mutants defective in the SNF1 protein kinase.
The SNF1 protein kinase is required for expression of the invertase gene in response to glucose deprivation in Saccharomyces cerevisiae. We selected for genes that in multicopy suppress the invertase defect of temperature-sensitive snf1 mutants. Increased dosage of the MSN1 gene restores high-level, regulated invertase expression in snf1-ts mutants, and disruption of MSN1 in the wild type reduces invertase expression a fewfold. MSN1 gene dosage does not affect SNF1 protein kinase activity in vitro. MSN1 encodes a 43-kilodalton protein, and a MSN1-beta-galactosidase fusion protein was localized in the nucleus. A LexA-MSN1 fusion protein, when bound to a lexA operator, activates transcription of an adjacent promoter. In vitro synthesized MSN1 protein exhibits weak, nonspecific DNA-binding activity.


Protein prenylation is required for aldosterone-stimulated Na+ transport.
Aldosterone stimulation of transcellular Na+ flux in polarized epithelial cells is dependent on at least one transmethylation reaction, but the substrate of this signaling step is unknown. Because it is clear that the majority of cellular protein methylation occurs in conjunction with protein prenylation, we examined the importance of prenylation to aldosterone-stimulated Na+ transport in the A6 cell line. Lovastatin, an inhibitor of the first committed step of the mevalonate pathway, inhibits the natriferic effect of aldosterone but does not inhibit insulin-stimulated Na+ flux. The addition of a farnesyl group does not appear to be involved in aldosterone's action. Neither alpha-hydroxyfarne-sylphosphonic acid, an inhibitor of farnesyl:protein transferase, nor N-acetyl-S-farnesyl-L-cysteine, an inhibitor of farnesylated protein methylation, inhibits the hormone-induced increase in Na+ transport. In contrast, N-acetyl-S-geranyl-geranyl-L-cysteine, an inhibitor of geranylgeranyl protein methylation, completely abolishes the aldosterone-induced increase in Na+ flux with no effect on insulin-mediated Na+ transport or cellular protein content. These data indicate that methylation of a geranylgeranylated protein is involved in aldosterone's natriferic action.


Male Fischer 344/N rats show a progressive central impairment of the hypothalamic-pituitary-adrenal axis with advancing age.
We investigated the effects of aging on the regulation of hypothalamic-pituitary-adrenal function and hippocampal steroid receptors in a series of in vivo and in vitro studies conducted in healthy intact 2-, 8-, 18-, and 24-month-old male Fischer 344/N rats. Basal plasma ACTH levels were similar among age groups, and basal plasma corticosterone levels showed a significant aging-associated decline. Two i.v. doses (2 and 20 micrograms/kg BW) of rat CRF elicited significantly greater and delayed ACTH and greater corticosterone responses in older rats, consistent with the pattern encountered in hypothalamic CRF deficiency. In contrast, the i.v. injection of a muscarinic agonist, arecoline, elicited similar ACTH and corticosterone responses in all age groups. An i.v. injection of ACTH-(1-24) evoked lower corticosterone responses in the older (18- and 24-month-old) than in the younger (2- and 8-month-old) groups of rats, consistent with an impairment of hypothalamic-pituitary-adrenal axis function in older animals. Steady state mRNA levels of mineralocorticoid and glucocorticoid receptors were significantly decreased in the hippocampus of the 8-, 18-, and 24-month-old rats, compatible with maturational, rather than senescent, changes. CRF mRNA levels in the paraventricular nucleus of the hypothalamus, CRF content, and in vitro secretion by whole explanted hypothalami were progressively and significantly reduced with age, whereas the steady state levels of arginine vasopressin mRNA were significantly increased with age. Steady state levels of POMC mRNA were decreased, and ACTH content and in vitro secretion by corticotrophs were increased with age in the anterior pituitary. We conclude that male Fischer 344/N rats show a progressive hypothalamic CRH deficiency with advancing age, which appears to be associated with elevated production of arginine vasopressin in the hypothalamus.


Evaluation of a community intervention program in Japan using Framingham risk score and estimated 10-year coronary heart disease risk as outcome variables: a non-randomized controlled trial.
Community-based programs are being widely adopted in the struggle to prevent cardiovascular diseases. No study has been conducted in Japan to evaluate the effects of a community-based health promotion program by using the Framingham risk score and 10-year CHD risk as outcome variables. The aim of the present study was to assess the effects of a program involving 6-month intervention and 18-month follow-up using such outcomes. Participants (n = 1,983, 39.5% women, mean age 63.4 years) were selected for the study in 2008. Of these 1,983, 347 (42.4% women) subjects received the 6-month intervention. The intervention included individual counseling and group sessions, among others. After 18 months, 1,278 participants (intervention group: 238, control group: 1,040) were followed up. Changes in the Framingham risk score and 10-year coronary heart disease (CHD) risk were evaluated. ANCOVA and multiple logistic models adjusted for baseline value, age, sex and intervention times were used. The results showed that the differences in the Framingham risk score and mean 10-year CHD risk were significant in the intervention group compared with the control group after 6-month follow-up (-0.46 and -1.12, respectively) and were also significant after 18-month follow-up (-0.39 and -0.85, respectively). The proportion of those with intermediate 10-year CHD risk (> = 10%) was significantly lower at 6 months (OR 0.30, 95% CI 0.12-0.74) and at 18 months (OR 0.41, 95% CI 0.19-0.92). The six-month intervention program effectively decreased estimated 10-year CHD risk and the effects were still present at 18-month follow-up. UMIN-CTR: UMIN000008163.


Increased monocyte activation with age among HIV-infected long term non-progressor children: implications for early treatment initiation.
The key to newer therapeutic and eradication approaches often lies in understanding slow disease progression in HIV infection. The paediatric population has been poorly studied in this regard. We aimed to describe a cohort of perinatally infected long-term nonprogressor (LTNP) children living with HIV in India and to evaluate the immune biomarkers of disease progression. LTNPs (ART-naïve, with a CD4 count ≥ 500 cells/μL at age ≥ 7 years) among the cohort of HIV-infected children were identified and monitored longitudinally, and their CD4 T-cell counts and plasma viral loads were measured every 6 months. The plasma monocyte/macrophage activation markers, namely soluble CD14 (sCD14), soluble CD163 (sCD163) and interferon-inducible protein-10 (IP-10) were measured by enzyme-linked immunosorbent assay (ELISA) in LTNPs and progressors. The Mann-Whitney U-test was used to compare the two groups and P values < 0.05 were considered statistically significant. Spearman's rank or Pearson's correlation coefficient (r) was calculated to determine the associations between variables. Among 378 children living with HIV-1 surveyed in our cohort, 40 (10.6%) were LTNPs. Longitudinal analysis of the LTNP data showed that both CD4 count and viral load declined significantly with age (P < 0.0001 for both). Plasma sCD14 levels were significantly (P < 0.005) higher in progressors and sCD163 levels were significantly (P < 0.0001) higher in LTNPs. The prevalence of LTNPs in our cohort of perinatally infected children living with HIV was 10.6%. We observed a trend for associations between the increasing sCD163 monocyte/macrophage activation marker levels, declining CD4 counts and the gradual loss of nonprogressor status with age in the LTNPs. These findings underscore the need for early antiretroviral therapy in those children with proven slow disease progression.


The Acute and Chronic Cognitive and Cerebral Blood Flow Effects of a Sideritis scardica (Greek Mountain Tea) Extract: A Double Blind, Randomized, Placebo Controlled, Parallel Groups Study in Healthy Humans.
The presence of polyphenols such as hydroxy-cinnamic acids and flavonoids in Sideritis scardica (Greek mountain tea) are likely responsible for the cognitive and mood effects of its consumption and this could be underpinned by the ability of such polyphenols to prevent monoamine neurotransmitter reuptake and to increase cerebral blood flow (CBF). The current study extends the small amount of Sideritis scardica literature in humans by assessing both cognitive and mood outcomes in a sample of older adults, as well as blood pressure (BP) and CBF, in a subsample, utilizing near-infrared spectroscopy (NIRS). This randomized, double-blind, placebo-controlled, parallel groups trial randomized N = 155, 50⁻70-year-old male and female participants who were assessed for the cognitive (N = 140), mood (N = 142), BP (N = 133) and CBF (N = 57) effects of two doses of Greek mountain tea (475 and 950 mg) as well as an active control of 240 mg Ginkgo biloba, and a placebo control, following acute consumption (Day 1) and following a month-long consumption period (Day 28). Relative to the placebo control, 950 mg Greek mountain tea evinced significantly fewer false alarms on the Rapid Visual Information Processing (RVIP) task on Day 28 and significantly reduced state anxiety following 28 days consumption (relative also to the active, Ginkgo control). This higher dose of Greek mountain tea also attenuated a reduction in accuracy on the picture recognition task, on Day 1 and Day 28, relative to Ginkgo and both doses of Greek mountain tea trended towards significantly faster speed of attention on both days, relative to Ginkgo. Both doses of Greek mountain tea, relative to placebo, increased oxygenated haemoglobin (HbO) and oxygen saturation (Ox%) in the prefrontal cortex during completion of cognitively demanding tasks on Day 1. The higher dose also evinced greater levels of total (THb) and deoxygenated (Hb) haemoglobin on Day 1 but no additional effects were seen on CBF on Day 28 following either dose of Greek mountain tea. Ginkgo biloba led to lower levels of Ox% and higher levels of Hb on Day 1 and lower levels of both HbO and THb on Day 28. The significantly improved cognitive performance following Greek mountain tea on Day 1 could be due to significant modulation of the CBF response. However, these improvements on Day 28 are more likely to be due to the reductions in state anxiety and, taken together, suggests that the former mechanism is more likely to facilitate acute cognitive effects and the latter more likely to underpin more prolonged cognitive improvements.


The lysine- and glutamic acid-rich protein KERP1 plays a role in Entamoeba histolytica liver abscess pathogenesis.
The parasite Entamoeba histolytica colonizes the large bowel where it may persist as an asymptomatic luminal gut infection, which changes to virulence. Parasite invasion of the intestine leads to dysentery and spreads to the liver, where amoebae form abscesses. We took advantage of changes in virulence that occurs after long-term in vitro culture of E. histolytica strains. Using microarrays, we concluded that virulence correlates with upregulation of key genes involved in stress response, including molecular chaperones, ssp1 and peroxiredoxin; as well as the induction of unknown genes encoding lysine-rich proteins. Seven of these were retained with respect to their lysine content higher than 25%. Among them, we found KERP1, formerly identified as associated to parasite surface and involved in the parasite adherence to host cells. Experimentally induced liver abscesses, using molecular beacons and protein analysis, allowed us to draw a parallel between the intricate upregulation of kerp1 gene expression during abscess development and the increased abundance of KERP1 in virulent trophozoites. Following its characterization as a marker for the progression of infection, KERP1 was also seen to be a virulence marker as trophozoites affected in kerp1 expression by an antisense strategy were unable to form liver abscesses.


A Lead-In with Silibinin Prior to Triple-Therapy Translates into Favorable Treatment Outcomes in Difficult-To-Treat HIV/Hepatitis C Coinfected Patients.
The efficacy of first-generation protease inhibitor based triple-therapy against hepatitis C virus (HCV) infection is limited in HIV/HCV-coinfected patients with advanced liver fibrosis and non-response to previous peginterferon-ribavirin. These patients have a low chance of achieving a sustained virologic response (SVR) using first generation triple-therapy, with a success rate of only 20%. We investigated the efficacy and safety of lead-in therapy with intravenous silibinin followed by triple-therapy in this difficult-to-treat patient group. Inclusion criteria were HIV/HCV coinfection with advanced liver fibrosis and documented previous treatment failure on peginterferon-ribavirin. The intervention was a lead-in therapy with intravenous silibinin 20 mg/kg/day for 14 days, followed by triple-therapy (peginterferon-ribavirin and telaprevir) for 12 weeks, and peginterferon-ribavirin alone for 36 weeks. Outcome measurements were HCV-RNA after silibinin lead-in and during triple-therapy, SVR data at week 12, and safety and tolerability of silibinin. We examined sixteen HIV/HCV-coinfected patients with previous peginterferon-ribavirin failure, of whom 14 had a fibrosis grade METAVIR ≥F3. All were on successful antiretroviral therapy. Median (IQR) HCV-RNA decline after silibinin therapy was 2.65 (2.1-2.8) log10 copies/mL. Fifteen of sixteen patients (94%) had undetectable HCV RNA at weeks 4 and 12, eleven patients (69%) showed end-of-treatment response (i.e., undetectable HCV-RNA at week 48), and ten patients (63%) reached SVR at week 12 (SVR 12). Six of the sixteen patients (37%) did not reach SVR 12: One patient had rapid virologic response (RVR) (i.e., undetectable HCV-RNA at week 4) but stopped treatment at week 8 due to major depression. Five patients had RVR, but experienced viral breakthroughs at week 21, 22, 25, or 32, or a relapse at week 52. The HIV RNA remained below the limit of detection in all patients during the complete treatment period. No serious adverse events and no significant drug-drug interactions were associated with silibinin. A lead-in with silibinin before triple-therapy was safe and highly effective in difficult-to-treat HIV/HCV coinfected patients, with a pronounced HCV-RNA decline during the lead-in phase, which translates into 63% SVR. An add-on of intravenous silibinin to standard of care HCV treatment is worth further exploration in selected difficult-to-treat patients. ClinicalTrials.gov NCT01816490.


Improving the aseptic transfer procedures in hospital pharmacies part A: methods for the determination of the surface bioburden on ampoules and vials.
To develop methods for surface bioburden determination of ampoules and vials to be used in the validation of the disinfection procedures and in routine monitoring of ampoules and vials. The surface bioburdens of ampoules and vials are determined before and after disinfection by contact plates and total immersion. The mean surface bioburdens of non-disinfected ampoules and vials taken straight from the original boxes are 2.4 and 5.01 cfu (total immersion; n = 20), and 0.97 and 0.94 cfu (contact plates; n = 60). The mean surface bioburdens of ampules and vials after disinfection by wiping are 1.15 and 7.50 cfu (total immersion; n = 20), and 0.12 and 0.10 cfu (contact plates; n = 60). The high number of cfu on vials (total immersion) indicate hidden cfu around the neck not removable by wiping and not detected by contact plates. Total immersion needs special laboratory facilities and is expensive (about €50 a sample). Therefore, it is less appropriate for use in routine monitoring. However, because of the high recovery, it is the method of choice for the validation of the disinfection procedure. Surface bioburden determination by contact plates is relatively simple. Non-flat surfaces cannot be reached, but the recovery from the touched flat part of the surface is high (around 50%). The recovery from swabs is low (around 10%). Another disadvantage of swabs is the laboratory work after sampling. We therefore advise contact plates for routine monitoring. To get a reliable value of the mean surface bioburden at least 30 samples need to be examined. Total immersion is the method of choice for the determination of the effectiveness of a disinfection procedure for ampoules and vials. Contact plate is the method of choice for routine monitoring of the surfaces of ampoules and vials.


Motivation and academic achievement in medical students.
Despite their ascribed intellectual ability and achieved academic pursuits, medical students' academic achievement is influenced by motivation. This study is an endeavor to examine the role of motivation in the academic achievement of medical students. In this cross-sectional correlational study, out of the total 422 medical students, from 4th to final year during the academic year 2007-2008, at School of Medicine, Isfahan University of Medical Sciences, 344 participated in completion of the Inventory of School Motivation (ISM), comprising 43 items and measuring eight aspects of motivation. The gold standard for academic achievement was their average academic marks at pre-clinical and clinical levels. Data were computer analyzed by running a couple of descriptive and analytical tests including Pearson Correlation and Student's t-student. Higher motivation scores in areas of competition, effort, social concern, and task were accompanied by higher average marks at pre-clinical as well as clinical levels. However, the latter ones showed greater motivation for social power as compared to the former group. Task and competition motivation for boys was higher than for girls. In view of our observations, students' academic achievement requires coordination and interaction between different aspects of motivation.


Long-term maintenance of undifferentiated human embryonic and induced pluripotent stem cells in suspension.
Traditionally, undifferentiated pluripotent human embryonic and induced pluripotent stem cells (hESCs and hiPSCs) have been expanded as monolayer colonies in adhesion culture, both in the presence or absence of feeder cells. However, the use of pluripotent stem cells poses the need to scale-up current culture methods. Herein, we present the cultivation of 2 hESC lines (Royan H5 and Royan H6) and 2 hiPSC lines (hiPSC1 and hiPSC4) as carrier-free suspension aggregates for an extended period of time. The cells proliferated over multiple passages kept a stable karyotype, which successfully maintained an undifferentiated state and pluripotency, as determined by marker expressions in addition to in vitro spontaneous and directed differentiation. Additionally, these cells can be easily frozen and thawed without losing their proliferation, karyotype stability, and developmental potential. Transcriptome analysis of the 3 lines revealed that the adherent culture condition was nearly identical to the suspension culture in Royan H5 and hiPSC1, but not in Royan H6. It remains unclear whether this observation at the transcript level is biologically significant. In comparison with recent reports, our study presents a low-cost procedure for long-term suspension expansion of hESCs and hiPSCs with the capability of freeze/thawing, karyotype stability, and pluripotency. Our results will pave the way for scaled up expansion and controlled differentiation of hESCs and hiPSCs needed for cell therapy, research, and industrial applications in a bioreactor culture system.


Hospitalized prevalence and 5-year mortality for IBD: record linkage study.
To establish the hospitalized prevalence of severe Crohn's disease (CD) and ulcerative colitis (UC) in Wales from 1999 to 2007; and to investigate long-term mortality after hospitalization and associations with social deprivation and other socio-demographic factors. Record linkage of administrative inpatient and mortality data for 1467 and 1482 people hospitalised as emergencies for > or = 3 d for CD and UC, respectively. The main outcome measures were hospitalized prevalence, mortality rates and standardized mortality ratios for up to 5 years follow-up after hospitalization. Hospitalized prevalence was 50.1 per 100 000 population for CD and 50.6 for UC. The hospitalized prevalence of CD was significantly higher (P < 0.05) in females (57.4) than in males (42.2), and was highest in people aged 16-29 years, but the prevalence of UC was similar in males (51.0) and females (50.1), and increased continuously with age. The hospitalized prevalence of CD was slightly higher in the most deprived areas, but there was no association between social deprivation and hospitalized prevalence of UC. Mortality was 6.8% and 14.6% after 1 and 5 years follow-up for CD, and 9.2% and 20.8% after 1 and 5 years for UC. For both CD and UC, there was little discernible association between mortality and social deprivation, distance from hospital, urban/rural residence and geography. CD and UC have distinct demographic profiles. The higher prevalence of hospitalized CD in more deprived areas may reflect higher prevalence and higher hospital dependency.


Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi.
Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity in the Orbiliomycetes suggested that this mechanism was present early in the evolution of the filamentous ascomycetes.


Inducible expression of N-methyl-D-aspartate receptor, and delta and mu opioid receptor messenger RNAs and protein in the NT2-N human cell line.
Retinoic acid treatment of NT-era2/cl.D1 (NT2) cells, a human teratocarcinoma cell line, yields 95% pure cultures of terminally differentiated neuronal cells. Concomitant with their terminal differentiation into neurons, NT2 cells are induced by retinoic acid to express neuronal N-methyl-D-aspartate receptor channels, which are fully functional. We determined the effects of retinoic acid-induced differentiation of NT2 cells on the levels of N-methyl-D-aspartate, delta opioid and mu opioid receptor messenger RNAs. RNA levels were measured using quantitative solution hybridization assays. The riboprobes were complementary to major portions of the coding regions of the N-methyl-D-aspartate, delta opioid and mu opioid receptor complementary DNAs. After four weeks of exposure to 10 microM retinoic acid, followed by four weeks of treatment with mitotic inhibitors (1 microM of cytosine arabinoside, 10 microM of fluorodeoxyuridine and 10 microM of uridine) the levels of N-methyl-D-aspartate receptor messenger RNA in differentiated NT2-N cells increased 10-fold, delta opioid receptor messenger RNA increased three-fold, and mu opioid receptor messenger RNA increased four-fold. Northern blot analysis revealed two transcripts for the N-methyl-D-aspartate receptor messenger RNA (4.2 and 4.4 kb) and two transcripts for delta opioid receptor messenger RNA (7.0 and 11.0 kb). To determine whether the increases in messenger RNAs were accompanied by an increased synthesis of the respective proteins, we examined the immunoperoxidase localization of N-methyl-D-aspartate receptor and delta opioid receptor antisera. N-Methyl-D-aspartate receptor-like immunoreactivity was seen within the cell bodies as well as on the processes of the retinoic acid-differentiated cells. Although delta opioid receptor-like immunoreactivity was detected within the soma of isolated cells prior to retinoic acid treatment, the apparent number of these labelled cells and their ramified processes were markedly enhanced following retinoic acid differentiation. These results demonstrate parallels between the inducible expression of the N-methyl-D-aspartate and opioid receptor messenger RNAs and proteins during the acquisition of the fully differentiated neuronal phenotype in cultured NT2 cells. Retinoic acid-differentiated NT2 cells express increased levels for the N-methyl-D-aspartate, delta opioid and mu opioid receptor messenger RNAs, providing the opportunity to study the interactions among these receptor systems in human terminally differentiated neuronal cells in culture.


Determinants of HbA1c in nondiabetic Dutch adults: genetic loci and clinical and lifestyle parameters, and their interactions in the Lifelines Cohort Study.
Glycated haemoglobin (HbA1c) is associated with cardiovascular disease risk in individuals without diabetes, and its use has been recommended for diagnosing diabetes. Therefore, it is important to gain further understanding of the determinants of HbA1c. The aim of this study was to investigate the effects of genetic loci and clinical and lifestyle parameters, and their interactions, on HbA1c in nondiabetic adults. Population-based cohort study. Three northern provinces of the Netherlands. A total of 2921 nondiabetic adults participating in the population-based LifeLines Cohort Study. Body mass index (BMI), waist circumference, HbA1c, fasting plasma glucose (FPG) and erythrocyte indices were measured. Data on current smoking and alcohol consumption were collected through questionnaires. Genome-wide genotyping was performed, and 12 previously identified single-nucleotide polymorphisms (SNPs) were selected for replication and categorized as 'glycaemic' and 'nonglycaemic' SNPs according to their presumed mechanism(s) of action on HbA1c. Genetic risk scores (GRSs) were calculated as the sum of the weighted effect of HbA1c-increasing alleles. Age, gender, BMI, FPG, mean corpuscular haemoglobin, mean corpuscular haemoglobin concentration, current smoking and alcohol consumption were independent predictors of HbA1c, together explaining 26.2% of the variance in HbA1c, with FPG contributing 10.9%. We replicated three of the previously identified SNPs and the GRSs were also found to be independently associated with HbA1c. We found a smaller effect of the 'nonglycaemic GRS' in females compared with males and an attenuation of the effect of the GRS of all 12 SNPs with increasing BMI. Our results suggest that a substantial portion of HbA1c is determined by nonglycaemic factors. This should be taken into account when considering the use of HbA1c as a diagnostic test for diabetes.


Comparison of the immunogenicity and protection against bovine tuberculosis following immunization by BCG-priming and boosting with adenovirus or protein based vaccines.
There is a requirement for vaccines or vaccination strategies that confer better protection against TB than the current live attenuated Mycobacterium bovis Bacillus Calmette-Guerin (BCG) vaccine for use in cattle. Boosting with recombinant viral vectors expressing mycobacterial proteins, such as Ag85A, has shown a degree of promise as a strategy for improving on the protection afforded by BCG. Experiments in small animal models have indicated that broadening the immune response to include mycobacterial antigens other than Ag85A, such as Rv0288, induced by boosting with Ad5 constructs has a direct effect on the protection afforded against TB. Here, we compared the immunogenicity and protection against challenge with M. bovis afforded by boosting BCG-vaccinated cattle with a human type 5 (Ad5)-based vaccine expressing the mycobacterial antigens Ag85A (Ad5-85A); or Ag85A, Rv0251, Rv0287 and Rv0288 (Ad5-TBF); or with protein TBF emulsified in adjuvant (Adj-TBF). Boosting with TBF broaden the immune response. The kinetics of Ad5-TBF and Adj-TBF were shown to be different, with effector T cell responses from the latter developing more slowly but being more durable than those induced by Ad5-TBF. No increase in protection compared to BCG alone was afforded by Ad5-TBF or Adj-TBF by gross pathology or bacteriology. Using histopathology, as a novel parameter of protection, we show that boosting BCG vaccinated cattle with Ad5-85A induced significantly better protection than BCG alone.


Human polymerase kappa uses a template-slippage deletion mechanism, but can realign the slipped strands to favour base substitution mutations over deletions.
Polymerases belonging to the DinB class of the Y-family translesion synthesis DNA polymerases have a preference for accurately and efficiently bypassing damaged guanosines. These DinB polymerases also generate single-base (-1) deletions at high frequencies with most occurring on repetitive 'deletion hotspot' sequences. Human DNA polymerase kappa (hPolκ), the eukaryotic DinB homologue, displays an unusual efficiency for to extend from mispaired primer termini, either by extending directly from the mispair or by primer-template misalignment. This latter property explains how hPolκ creates single-base deletions in non-repetitive sequences, but does not address how deletions occur in repetitive deletion hotspots. Here, we show that hPolκ uses a classical Streisinger template-slippage mechanism to generate -1 deletions in repetitive sequences, as do the bacterial and archaeal homologues. After the first nucleotide is added by template slippage, however, hPolκ can efficiently realign the primer-template duplex before continuing DNA synthesis. Strand realignment results in a base-substitution mutation, minimizing generation of more deleterious frameshift mutations. On non-repetitive sequences, we find that nucleotide misincorporation is slower if the incoming nucleotide can correctly basepair with the nucleotide immediately 5' to the templating base, thereby competing against the mispairing with the templating base.


Influence of disparity on fixation and saccades in free viewing of natural scenes.
Humans select relevant locations in a scene by means of stimulus-driven bottom-up and context-dependent top-down mechanisms. These have mainly been investigated by recording eye movements under 2D natural or 3D artificial stimulation conditions. Here we try to close that obvious gap and presented 2D and 3D versions of natural, pink, and white noise images to human subjects. Importantly, ground truth distance was obtained for all image pairs by laser scanning. Recording eye movements, we investigated the influence of disparity information and of higher order scene correlations on basic saccade properties and on saliency of bottom-up information. Our results show that the removal of higher order correlations changed saccadic rate, length and main sequence, and the subjects' explorative behavior. Introduction of disparity information countered these effects and alleviated differences between image categories. Disparity information had no effect on the saliency of monocular image features like luminance and texture contrast; however, without higher order correlations these features were uncorrelated to fixation locations. An analysis of binocular image features revealed that participants fixated closer locations earlier than more distant locations. Importantly, this also held for 2D natural images. Taken together, we conclude that depth information changes basic eye movement properties and provides a salient image feature.


Luminescent multifunctional lanthanides-based metal-organic frameworks.
Metal-organic frameworks based on trivalent lanthanides (LnMOFs) are a very promising class of materials for addressing the challenges in engineering of luminescent centres. Lanthanide-bearing phosphors find numerous applications in lighting, optical communications, photonics and biomedical devices. In this critical review we discuss the potential of LnMOFs as multifunctional systems, which combine light emission with properties such as microporosity, magnetism, chirality, molecule and ion sensing, catalysis and activity as multimodal imaging contrast agents. We argue that these materials present a unique chance of observing synergy between several of these properties, such as the coupling between photoluminescence and magnetism. Moreover, an integrated approach towards the design of efficient, stable, cheap, environmentally-friendly and multifunctional luminescent LnMOFs is still missing. Although research into LnMOFs is at its early stage and much basic knowledge is still needed, the field is ripe for new ideas, which will enable sensor devices and photonic prototypes to become a commercial reality (81 references).


Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus.
Varicella zoster virus (VZV) is a human pathogenic alphaherpesvirus harboring a relatively large DNA molecule. The VZV transcriptome has already been analyzed by microarray and short-read sequencing analyses. However, both approaches have substantial limitations when used for structural characterization of transcript isoforms, even if supplemented with primer extension or other techniques. Among others, they are inefficient in distinguishing between embedded RNA molecules, transcript isoforms, including splice and length variants, as well as between alternative polycistronic transcripts. It has been demonstrated in several studies that long-read sequencing is able to circumvent these problems. In this work, we report the analysis of the VZV lytic transcriptome using the Oxford Nanopore Technologies sequencing platform. These investigations have led to the identification of 114 novel transcripts, including mRNAs, non-coding RNAs, polycistronic RNAs and complex transcripts, as well as 10 novel spliced transcripts and 25 novel transcription start site isoforms and transcription end site isoforms. A novel class of transcripts, the nroRNAs are described in this study. These transcripts are encoded by the genomic region located in close vicinity to the viral replication origin. We also show that the ORF63 exhibits a complex structural variation encompassing the splice sites of VZV latency transcripts. Additionally, we have detected RNA editing in a novel non-coding RNA molecule. Our investigations disclosed a composite transcriptomic architecture of VZV, including the discovery of novel RNA molecules and transcript isoforms, as well as a complex meshwork of transcriptional read-throughs and overlaps. The results represent a substantial advance in the annotation of the VZV transcriptome and in understanding the molecular biology of the herpesviruses in general.


Viral hepatitis status does not affect survival in patients with hepatocellular carcinoma.
There have been few studies on the impact of viral etiology on the prognosis in patients with hepatocellular carcinoma (HCC). The aim of this study was to evaluate the clinical characteristics and survival of patients with viral hepatitis-associated HCC (V-HCC), compared to patients with HCC of non-hepatitis B, non-hepatitis C (NBNC-HCC) etiology. We performed a retrospective analysis of all patients with HCC treated at our comprehensive cancer center from 2000 through 2014. Patients were divided into two groups according to their viral hepatitis status. Presentation patterns, treatments, and survival data were analyzed. We evaluated 366 patients: 233 patients (63.7%) had V-HCC while 133 (36.3%) patients had NBNC-HCC. V-HCC patients were younger (P<0.0001) and more likely to be male (P=0.001). Decompensated cirrhosis was more prevalent in V-HCC patients (P=0.01). There was no difference in the resectability rate or disease stage. In patients with resectable disease, those with V-HCC were less likely to undergo hepatectomy (23.7% vs. 38%; P=0.04) for more advanced liver disease. The estimated median survival for V-HCC was 13 months compared to 16 months in NBNC-HCC patients (P=0.57). On multivariate analysis, disease stage (P<0.0001) and Child-Pugh class (P<0.0001) were independent factors affecting survival, but viral status was not (P=0.75). Despite presenting with more advanced cirrhosis and being less likely to undergo surgery, V-HCC patients had similar survival to patients with NBNC-HCC.


The transcription factor PU.1 is involved in macrophage proliferation.
PU.1 is a tissue-specific transcription factor that is expressed in cells of the hematopoietic lineage including macrophages, granulocytes, and B lymphocytes. Bone marrow-derived macrophages transfected with an antisense PU.1 expression construct or treated with antisense oligonucleotides showed a decrease in proliferation compared with controls. In contrast, bone marrow macrophages transfected with a sense PU.1 expression construct displayed enhanced macrophage colony-stimulating factor (M-CSF)-dependent proliferation. Interestingly, there was no effect of sense or antisense constructs of PU.1 on the proliferation of the M-CSF-independent cell line, suggesting that the response was M-CSF dependent. This was further supported by the finding that macrophages transfected with a sense or an antisense PU.1 construct showed, respectively, an increased or a reduced level of surface expression of receptors for M-CSF. The enhancement of proliferation seems to be selective for PU.1, since transfections with several other members of the ets family, including ets-2 and fli-1, had no effect. Various mutants of PU.1 were also tested for their ability to affect macrophage proliferation. A reduction in macrophage proliferation was found when cells were transfected with a construct in which the DNA-binding domain of PU.1 was expressed. The PEST (proline-, glutamic acid-, serine-, and threonine-rich region) sequence of the PU.1 protein, which is an important domain for protein-protein interactions in B cells, was found to have no influence on PU.1-enhanced macrophage proliferation when an expression construct containing PU.1 minus the PEST domain was transfected into bone marrow-derived macrophages. In vivo, PU.1 is phosphorylated on several serine residues. The transfection of plasmids containing PU.1 with mutations at each of five serines showed that only positions 41 and 45 are critical for enhanced macrophage proliferation. We conclude that PU.1 is necessary for the M-CSF-dependent proliferation of macrophages. One of the proliferation-relevant targets of this transcription factor could be the M-CSF receptor.


A systematic review of time studies to assess the impact of patient transfers on nurse workload.
Patients in hospital are increasingly being moved between clinical units and between bedspaces; however, the impact of patient transfers and bedspace moves on nurses' workload is not known. Time studies are an established observational research method that can be used to determine the duration of time taken to perform an activity or process. This review systematically searched four databases for literature published between 2000 and 2013 for observational time study techniques and patient transfers as a nurse activity. Eleven publications from three countries were included in the review. All studies used timing techniques to explore nurse work associated with the transfer process. The review highlights the duration of time spent by nurses on certain aspects of the transfer process. However, as few studies published results from timings, the impact on nurse time is likely to be higher than indicated. Further research is recommended.


Anti-racist pedagogy: challenges faced by faculty of color in predominantly white schools of nursing.
Despite the significant effects of systems of oppression on health, nursing education tends not to include anti-racist pedagogy in its curricula, preferring instead to focus more narrowly on culture. This narrow focus allows nurses to depoliticize discussions of race and other social differences, largely ignoring the influence that systems of oppression, imperialism, and historical trauma have had on health in marginalized populations. In contrast, anti-racist pedagogy educates students in ways that make racialized power relations explicit, deconstruct the social construction of race, and analyze interlocking systems of oppression that serve to marginalize and exclude some groups while privileging others. This article describes anti-racist pedagogy from the perspective of a faculty member of color, drawing on personal experience and a review of the anti-racist pedagogical literature. Specifically, this article highlights some of the personal and professional challenges faced by faculty of color when engaged in anti-racist pedagogy in predominantly white schools of nursing.


Characterization of a canine homolog of hepatitis C virus.
An estimated 3% of the world's population is chronically infected with hepatitis C virus (HCV). Although HCV was discovered more than 20 y ago, its origin remains obscure largely because no closely related animal virus homolog has been identified; furthermore, efforts to understand HCV pathogenesis have been hampered by the absence of animal models other than chimpanzees for human disease. Here we report the identification in domestic dogs of a nonprimate hepacivirus. Comparative phylogenetic analysis of the canine hepacivirus (CHV) confirmed it to be the most genetically similar animal virus homolog of HCV. Bayesian Markov chains Monte Carlo and associated time to most recent common ancestor analyses suggest a mean recent divergence time of CHV and HCV clades within the past 500-1,000 y, well after the domestication of canines. The discovery of CHV may provide new insights into the origin and evolution of HCV and a tractable model system with which to probe the pathogenesis, prevention, and treatment of diseases caused by hepacivirus infection.


Temporal association of infant immunisation with pneumococcal conjugate vaccine on the ecology of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus nasopharyngeal colonisation in a rural South African community.
Immunisation of children with pneumococcal conjugate vaccines (PCV) may affect the bacterial-ecology of the nasopharynx, including colonisation by Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus. The aim of this study was to evaluate the effect of infant PCV-immunisation on the nasopharyngeal ecology of these potentially pathogenic bacteria in a rural African setting. Two cross sectional surveys were undertaken from May to October in 2009 (Period-1) which coincided with the introduction of 7-valent PCV (PCV7) and in May-October 2011 (Period-2). Consenting household members, where there was a child <2 years of age in residence, had nasopharyngeal swabs undertaken for culture. From Period-1 to Period-2 in children 0-2 years and 3-12 years, prevalence of overall S. pneumoniae colonisation decreased from 74.9% to 67.0% (p<0.001) and H. influenzae declined among children 3-12 years (55.1-45.3%, p<0.001) but not among those <2 years. The prevalence of S. aureus remained unchanged in all children. Competitive associations were found between S. pneumoniae and S. aureus and between H. influenzae and S. aureus among children. In individuals >12 years, the prevalence of colonisation decreased from 11.2% to 6.8%, 16.7% to 8.8% and 31.2% to 23.7% for S. pneumoniae, H. influenzae and S. aureus, respectively; p<0.001 for all comparions. Synergistic relationships for S. aureus with H. influenzae and S. pneumoniae were observed in both periods among this group.


The cultural moral right to a basic minimum of accessible health care.
(1) The conception of a cultural moral right is useful in capturing the social-moral realities that underlie debate about universal health care. In asserting such rights, individuals make claims above and beyond their legal rights, but those claims are based on the society's existing commitments and moral culture. In the United States such a right to accessible basic health care is generated by various empirical social facts, primarily the conjunction of the legal requirement of access to emergency care with widely held principles about unfair free riding and just sharing of costs between well and ill. The right can get expressed in social policy through either single-payer or mandated insurance. (2) The same elements that generate this right provide modest assistance in determining its content, the structure and scope of a basic minimum of care. They justify limits on patient cost sharing, require comparative effectiveness, and make cost considerations relevant. They shed light on the status of expensive, marginally life extending, last-chance therapies, as well as life support for PVS patients. They are of less assistance in settling contentious debates about screening for breast and prostate cancer and treatments for infertility and erectile dysfunction, but even there they establish a useful framework for discussion. Scarcity of resources need not be a leading conceptual consideration in discerning a basic minimum. More important are the societal elements that generate the cultural moral right to a basic minimum.


X chromosome inactivation and the Xist gene.
Recent years have seen rapid progress towards understanding the molecular mechanisms involved in X chromosome inactivation (X inactivation). This progress has largely revolved around the discovery of the X inactive specific transcript (Xist) gene, which is known now to represent the master switch locus regulating X inactivation. In adult cells Xist is transcribed exclusively from the inactive X chromosome. The transcript has no apparent protein-coding potential and is retained in the nucleus in close association with the domain occupied by the inactive X chromosome. It is thus thought to represent a functional RNA molecule which acts as the primary signal responsible for the propagation of X inactivation. Developmental regulation of Xist correlates with the developmental timing of X inactivation. Recent results have demonstrated that Xist is both necessary and sufficient for X inactivation. Goals for the future are to understand the mechanism of Xist regulation which underlies the establishment of appropriate X inactivation patterns and to determine how Xist RNA participates in the process of propagating inactivation in cis.


Association between atopy and herpetic eye disease: results from the pacific ocular inflammation study.
Immune dysregulation in patients with atopy has been hypothesized to increase susceptibility to viral infections. Herpetic eye disease (due to herpes simplex and herpes zoster) is a significant cause of visual impairment, and data on an association between this sight-threatening disease and atopy are limited. To assess the association between atopy and herpetic eye disease, including herpes simplex virus (HSV) ocular disease and herpes zoster ophthalmicus (HZO). Retrospective, population-based case-control study from January 1, 2006, through December 31, 2007, at Kaiser Permanente Hawaii, a multispecialty managed care organization serving approximately 15% of the general Hawaiian population. Participants were 217,061 patients enrolled in the Kaiser Permanente Hawaii health plan during the study period. Clinical diagnosis of HSV ocular disease or HZO during the study period determined by an initial search of the electronic medical record of Kaiser Permanente Hawaii and then confirmed through individual medical record review by a uveitis and cornea fellowship-trained ophthalmologist. Atopic disease status was determined based on International Classification of Diseases, Ninth Revision codes for patients with HSV ocular disease or HZO and 2 control groups, each randomly selected at a 4:1 ratio of controls to cases. One hundred fourteen patients with HSV ocular disease and 137 patients with HZO were identified. Using the age- and sex-matched controls, patients who had atopy had a 2.6-fold (95% CI, 1.6-4.2; P < .001) higher odds of having HSV ocular disease compared with patients who did not have atopy. Similarly, patients with atopy had a 1.8-fold (95% CI, 1.2-2.8; P = .01) increased odds of having HZO. Patients with 2 or more atopic conditions had an 8.9-fold (95% CI, 3.5-22.6; P < .001) higher odds of having HSV ocular disease and a 2.9-fold (95% CI, 1.1-7.7; P = .04) higher odds of having HZO. AND RELEVANCE The association between atopy and herpetic eye disease may be explained by various factors, including immunologic dysfunction in patients with atopy. Clinically, these results could help support the diagnosis of herpetic eye disease in these patients.


Linking water uptake with rooting patterns in grassland species.
Water availability strongly governs grassland primary productivity, yet this resource varies dramatically in time (seasonally) and space (with soil depth and topography). It has long been assumed that co-occurring species differ in their partitioning of water use by depth, but direct evidence is lacking. We report data from two growing seasons (2004-2005) in which we measured the isotopic signature of plant xylem water from seven species (including C(3) forbs and shrubs and C(4) grasses) growing along a topographic gradient at the Konza Prairie Biological Station. Plant xylem stable oxygen isotope ratio (delta(18)O) values were compared to soil water delta(18)O profiles, recent rainfall events, and groundwater. Species varied in both their temporal patterns of water use and their responses to seasonal droughts in both years. During wet periods, species differences in water use were minimal, with common dependency on recent rainfall events stored in the upper soil layers. However, during dry periods, most C(3) species used proportionally more water from deeper portions of the soil profile relative to the C(4) grasses. Plants in uplands used more shallow soil water compared to those in lowlands, with the greatest differences across the topographic gradient occurring during dry periods. While the documented vertical root distribution varies by species and growth form in this grassland, each of the species we measured appeared to compete for the same surface layer soil moisture when water was not limiting. Thus, our results suggest that variation in precipitation history and landscape positions are greater determinants of water-use patterns than would be expected based on absolute rooting depth.


A medical informatics perspective on decision support systems. Findings from the yearbook 2012 section on decision support.
To summarize current excellent research in the field of computer-based decision support systems in health and healthcare. We provide a synopsis of the articles selected for the IMIA Yearbook 2012, from which we attempt to draft a synthetic overview of the activity and new trends in the field. While the state of the research in the field of medical decision support systems is illustrated by a set of fairly heterogeneous studies, it is possible to identify fundamental aspects of the fields, e.g. Decision Support Systems for Computerized Provider Order Entry, both for physicians and pharmacists, as well as more specific developments such as instruments to improve processing of data related to Clinical Trials and applications to capture family health history. The best paper selection of articles on decision support shows examples of excellent research on methods concerning original development as well as quality assurance of previously reported studies. This selected set of scientific investigations clearly question the way decision support systems are deployed in clinical environments as these systems seem to have little impact on patient safety and even could harm the patient. Furthermore, while significant research efforts are invested into translational & "omics" medicine, it is interesting to observe that simple data capture applications can reasonably lead to positive changes in healthcare.


The evaluation of the amount of cis- and trans-urocanic acid in the stratum corneum by Raman spectroscopy.
Urocanic acid (UCA) is a major component in the epidermis which absorbs ultraviolet light (UV) and is isomerized from the trans to the cis form upon UV exposure. This study aimed to evaluate the amounts of cis- and trans-UCA in the stratum corneum (SC) in vivo using Raman spectroscopy. UV damage has previously been investigated by calculating the amount of trans-UCA by fitting Raman spectra. cis-UCA at pH 5.0 was also included in the fitting algorithm in this study. For validation, the SC was stripped from the subjects and the levels of cis- and trans-UCA were measured using high performance liquid chromatography (HPLC). Comparison between these two methods was performed at UV exposure and non-UV exposure sites on the volar forearm of 10 healthy Japanese subjects. Finally, the protective capacity of sunscreen was evaluated by Raman spectroscopy on the volar forearm of 18 healthy subjects. The amount of cis-UCA increased and the amount of trans-UCA decreased after UV exposure when measured by Raman spectroscopy. This was confirmed by HPLC analysis of the SC stripped from the same area of skin used in the Raman measurement. The protection against the increase in the cis-UCA and decrease in the trans-UCA amount after UV exposure by the application of sunscreen products was observed using Raman spectroscopy. The results show this method can be used to measure cis- and trans-UCA levels in vivo.


PD-L1+ aneuploid circulating tumor endothelial cells (CTECs) exhibit resistance to the checkpoint blockade immunotherapy in advanced NSCLC patients.
Sustained angiogenesis and increased PD-L1 expression on endothelial and carcinoma cells contribute toward fostering an immunosuppressive microenvironment suitable for tumor growth. PD-L1+ CTCs were reported to associate with poor prognosis in NSCLC patients. However, whether or not aneuploid circulating tumor endothelial cells (CTECs) express PD-L1, then serve as a surrogate biomarker to evaluate immunotherapy efficacy remains unknown. In this study, a novel SE-iFISH strategy was established to comprehensively quantify and characterize a full spectrum of aneuploid CTCs and CTECs in advanced NSCLC patients subjected to second-line anti-PD-1 (nivolumab) immunotherapy. In situ co-detection of diverse subtypes of aneuploid CTCs and CTECs expressing PD-L1 and Vimentin was performed. The present clinical study demonstrated that significant amounts of PD-L1+ aneuploid CTCs and CTECs could be detected in histopathologic hPD-L1- patients. In contrast to decreased PD-L1+ CTCs, the number of multiploid PD-L1+ CTECs (≥tetrasomy 8) undergoing post-therapeutic karyotype shifting increased in patients along with tumor progression following anti-PD-1 treatment. Progressive disease (PD) lung cancer patients possessing multiploid PD-L1+ CTECs had a significantly shorter PFS compared to those without PD-L1+ CTECs. In carcinoma patients, aneuploid CTCs and CTECs may exhibit a functional interplay with respect to tumor angiogenesis, progression, metastasis, and response to immunotherapy.


Evaluating the community education programme of an insecticide-treated bed net trial on the Kenyan coast.
Increased interest in the potential contribution of insecticide-impregnated bed nets (ITBN) to malaria control has led to research efforts to determine the impact and sustainability of ITBN programmes in differing environments. There is a need to develop effective, feasible educational strategies that will both inform and motivate community members, and thus maximize the correct usage of ITBN. This is especially true in communities where indigenous usage of bed nets is low. This paper describes the educational component of a randomized controlled community intervention trial of ITBN, with childhood malaria morbidity as an outcome. The educational approach and messages for the ITBN trial were developed from anthropological survey data collected 4 years before the trial, and from community surveys conducted by project researchers. Low levels of understanding amongst mothers of the aetiological link between mosquitos and malaria led to the exclusion of the term 'malaria' from the initial educational messages promoting the use of ITBN. Appropriate individuals within the existing district health care structure were trained as community educators in the project. These educators conducted intensive teaching in the community through public meetings and group teaching in the first 6 months of the trial. The impact of these initial activities was assessed through interviews with a random sample of 100 mothers and 50 household heads. This allowed the identification of messages which had not been well understood and further educational methods were chosen to address the areas pinpointed. The community assessment also demonstrated that, in 1994, over 90% of mothers understood a protective role for bed nets against malaria and the ITBN education messages were changed to take account of this. The school programme was evaluated through determining outreach (the number of households accessed), changes in participant children's knowledge, post-teaching assessment of mothers' knowledge and discussions with parent-teacher associations. It was shown that 40% of intervention homes with children in the target group were accessed, participant children learned the educational messages well (scores increased from a pre-teaching mean of 59% to a post-teaching mean of 92%) and a high level of awareness of the ITBN trial was achieved in these homes (75%). However, specific messages of the education programmed were not well transferred to the home (30%). The discussion emphasises the need for allocation of adequate resources for education in programmes dependent on achieving a change in community practices. We also describe the value of ongoing communication between programme planners and a target population in maximizing the effectiveness of messages and methods used.


Development of a Provisional Core Domain Set for Polymyalgia Rheumatica: Report from the OMERACT 12 Polymyalgia Rheumatica Working Group.
The Outcome Measures in Rheumatology (OMERACT) polymyalgia rheumatica (PMR) working group aims to develop a core set of outcome measures to be used in clinical trials for PMR. Previous reports from OMERACT 11 included a qualitative study of the patient experience and a preliminary literature review. A 3-round Delphi survey of clinicians and patients with PMR was undertaken to identify a candidate core domain set for PMR research. Additionally, a literature review of outcome measures and their respective measurement instruments was undertaken. Meetings of patient research partners and clinicians were convened to review face validity of the provisional core domain set, which was subsequently presented and discussed at the OMERACT 12 congress. Of the 60 clinicians taking part in round 1, 55 took part in round 2 and 51 in round 3. Of the 55 patients who took part in round 1, 46 and 35 took part in subsequent rounds. In total, 91% of participants in round 3 deemed the resulting draft core domain set reasonable. The literature review identified 28 studies for full review. Measurement instruments for each proposed domain were identified. Clinicians are highly aware of glucocorticoid-related adverse effects, but there is relatively little evidence about their true prevalence and severity, especially in PMR. A provisional core domain set, presented for clinical trials in PMR, comprises acute phase markers, physical function, death, glucocorticoid-related adverse events, and development of giant cell arteritis. Measurement instruments are suggested that may cover each domain, but these require formal validation for clinical trials in PMR.


High failure rate after internal fixation and beneficial outcome after arthroplasty in treatment of displaced femoral neck fractures in patients between 55 and 70 years.
Background and purpose - The treatment of patients between 55 and 70 years with displaced intracapsular femoral neck fracture remains controversial. We compared internal fixation (IF), bipolar hemiarthroplasty (HA) and total hip arthroplasty (THA) in terms of mortality, reoperations and patient-reported outcome by using data from the Norwegian Hip Fracture Register. Patients and methods - We included 2,713 patients treated between 2005 and 2012. 1,111 patients were treated with IF, 1,030 with HA and 572 patients with THA. Major reoperations (defined as re-osteosynthesis, secondary arthroplasty, exchange, or removal of prosthesis components and Girdlestone procedure), patient-reported outcome measures (satisfaction, pain, and health-related quality of life (EQ5D) after 4 and 12 months), 1-year mortality, and change in treatment methods over the study period were investigated. Results - Major reoperations occurred in 27% after IF, 3.8% after HA and 2.8% after THA. 549 patients (20% of total study population) answered both questionnaires. Compared with IF, patients treated with THA were more satisfied after 4 and 12 months, reported less pain after 4 months and 12 months, had a higher EQ5D-index score after 4 months and 12 months, and EQ-VAS score after 4 months. Compared with IF, patients treated with HA were more satisfied and reported less pain after 4 months. EQ5D-index and EQ-VAS were similar. Patients treated with HA had higher 1-year mortality and had more comorbidities than both the THA and IF group. All these differences were statistically and clinically significant. Interpretation - This study showed high reoperation rate after IF and better patient-reported outcome after both THA and HA with medium follow-up. Patients selected for HA represented a frailer group than patients treated with THA or IF.


Pulsed field gel electrophoresis: a review of application and interpretation in the molecular epidemiology of infectious disease.
Over the years, approaches to the epidemiological analysis of infectious disease have undergone a remarkable evolutionary transition moving from phenotypic to molecular in nature. As discussed here, the quest for a clearer comparison of genomic relatedness between bacterial clinical isolates has involved four generations of molecular iteration. First generation plasmid analysis gave way to a second generation use of restriction enzymes and probes. This was followed by third generation pulsed field gel electrophoresis (PFGE) and PCR-based methods with movement now to fourth-generation DNA sequence-based approaches. Remarkably, despite (or perhaps because of) its more than 20-year history as a typing method, PFGE has demonstrated exceptional staying power. The reasons for this endurance as well as the pros and cons of PFGE use are examined in this review. In broad context the history and technology behind PFGE are considered. Issues commonly influencing the quality of PFGE data and its analysis are discussed. Specifics regarding the mechanics of DNA preparation, restriction-enzyme digestion, and proper conditions for electrophoresis are detailed and, most importantly for any approach to epidemiological assessment, issues regarding the analysis and interpretation of PFGE data are explored.


Delineating the impact of machine learning elements in pre-microRNA detection.
Gene regulation modulates RNA expression via transcription factors. Post-transcriptional gene regulation in turn influences the amount of protein product through, for example, microRNAs (miRNAs). Experimental establishment of miRNAs and their effects is complicated and even futile when aiming to establish the entirety of miRNA target interactions. Therefore, computational approaches have been proposed. Many such tools rely on machine learning (ML) which involves example selection, feature extraction, model training, algorithm selection, and parameter optimization. Different ML algorithms have been used for model training on various example sets, more than 1,000 features describing pre-miRNAs have been proposed and different training and testing schemes have been used for model establishment. For pre-miRNA detection, negative examples cannot easily be established causing a problem for two class classification algorithms. There is also no consensus on what ML approach works best and, therefore, we set forth and established the impact of the different parts involved in ML on model performance. Furthermore, we established two new negative datasets and analyzed the impact of using them for training and testing. It was our aim to attach an order of importance to the parts involved in ML for pre-miRNA detection, but instead we found that all parts are intricately connected and their contributions cannot be easily untangled leading us to suggest that when attempting ML-based pre-miRNA detection many scenarios need to be explored.


Effect of tumour shrinkage on the biological effectiveness of permanent brachytherapy implants.
A tumour shrinkage factor is incorporated into previously derived linear-quadratic (LQ) formulae which allowed radiobiological assessment of the efficacy of permanently implanted radionuclides. The new formulations relate the biologically effective dose (BED) to radionuclide half-life, recovery half-life, tumour radiosensitivity, potential doubling time and linear shrinkage rate. Specific attention has been given to the following radionuclides: gold-198 (half-life, 2.7 days), palladium-103 (half-life, 17 days), ytterbium-169 (half-life, 32 days) and iodine-125 (half-life, 60 days). For each nuclide the log cell kill resulting from typically prescribed doses was calculated for a range of tumour clonogen doubling times at various radiosensitivities and linear shrinkage rates. It is shown that even relatively modest shrinkage rates are capable of enhancing the clinical potential of the longer-lived nuclides. However, even though the effect of tumour shrinkage is minimal in the case of gold-198, for fast growing and/or insensitive tumours there are fewer radiobiological uncertainties associated with the use of this nuclide. The revised equations may also have applications in certain types of biologically targeted radiotherapy.


Changes in bronchoalveolar lavage inflammatory cells in asthmatic patients treated with high dose inhaled beclomethasone dipropionate.
Using serial bronchoalveolar lavage (BAL), we have studied changes in the airway inflammatory cell populations in 20 asthmatic patients, before and after treatment with inhaled beclomethasone dipropionate (BDP), 2,000 micrograms daily in an uncontrolled study. There was a significant improvement in asthma severity, as measured by symptom score and airways responsiveness, and there were significant reductions in the total BAL eosinophil, epithelial cell and mast cell counts, with a significant increase in the percentage BAL lymphocyte count. No significant correlations were found between the changes in airway inflammatory cell numbers and the reduction in asthma severity. In contrast, the fall in ROS generation by the pulmonary macrophage and granulocyte populations was nonsignificant, but the improvement in airways responsiveness was positively correlated to the reduction in the unstimulated pulmonary macrophage activity. Although these data are uncontrolled, the results are compatible with previous studies in suggesting an effect of steroids on the eosinophil, mast cell and epithelial cell in asthmatic airways. They also highlight the probable importance of the luminal lymphocyte population and pulmonary macrophage activation within the asthmatic airway, the beneficial modulatory effect of inhaled BDP treatment upon them, and the relative steroid-resistance of pulmonary inflammatory cell activity.


Alignment-free design of highly discriminatory diagnostic primer sets for Escherichia coli O104:H4 outbreak strains.
An Escherichia coli O104:H4 outbreak in Germany in summer 2011 caused 53 deaths, over 4000 individual infections across Europe, and considerable economic, social and political impact. This outbreak was the first in a position to exploit rapid, benchtop high-throughput sequencing (HTS) technologies and crowdsourced data analysis early in its investigation, establishing a new paradigm for rapid response to disease threats. We describe a novel strategy for design of diagnostic PCR primers that exploited this rapid draft bacterial genome sequencing to distinguish between E. coli O104:H4 outbreak isolates and other pathogenic E. coli isolates, including the historical hæmolytic uræmic syndrome (HUSEC) E. coli HUSEC041 O104:H4 strain, which possesses the same serotype as the outbreak isolates. Primers were designed using a novel alignment-free strategy against eleven draft whole genome assemblies of E. coli O104:H4 German outbreak isolates from the E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium website, and a negative sequence set containing 69 E. coli chromosome and plasmid sequences from public databases. Validation in vitro against 21 'positive' E. coli O104:H4 outbreak and 32 'negative' non-outbreak EHEC isolates indicated that individual primer sets exhibited 100% sensitivity for outbreak isolates, with false positive rates of between 9% and 22%. A minimal combination of two primers discriminated between outbreak and non-outbreak E. coli isolates with 100% sensitivity and 100% specificity. Draft genomes of isolates of disease outbreak bacteria enable high throughput primer design and enhanced diagnostic performance in comparison to traditional molecular assays. Future outbreak investigations will be able to harness HTS rapidly to generate draft genome sequences and diagnostic primer sets, greatly facilitating epidemiology and clinical diagnostics. We expect that high throughput primer design strategies will enable faster, more precise responses to future disease outbreaks of bacterial origin, and help to mitigate their societal impact.


Monocytoid differentiation of freshly isolated human myeloid leukemia cells and HL-60 cells induced by the glutamine antagonist acivicin.
Previously we showed that starvation of HL-60 promyelocytic leukemia cells for a single essential amino acid induced irreversible differentiation into more mature monocyte-like cells. Although not an essential amino acid, glutamine is important in the growth of normal and neoplastic cells. The glutamine analogue, alpha S,5S-alpha-amino-3-chloro-4,5-dihydro-5-isoxazoleacetic acid (acivicin) inhibits several glutamine-utilizing enzymes and therefore depletes cells of certain metabolic end products. The current study was designed to examine in vitro the effects of acivicin on growth and differentiation of several established human myeloid leukemia cell lines, including the HL-60 cell line, and of freshly isolated cells from patients with acute nonlymphocytic leukemia (ANLL). Four-day culture of HL-60 cells with acivicin at concentrations of 0.1 to 10.0 micrograms/mL (0.56 to 56 nmol/L) decreased cell growth by 33% to 88% as compared with untreated control cells. Viability of cells was greater than 92% for untreated cells and 93% to 41% for acivicin-treated cells. Cells treated with acivicin differentiated along a monocytic pathway as shown by increased H2O2 production and alpha-naphthyl butyrate esterase (NSE) content. Differentiation was time and dose dependent, and was irreversible. Changes in H2O2 production and NSE content were partially abrogated by co-culture with 10 mmol/L exogenous cytidine and guanosine but not by co-culture with other nucleosides or glutamine. At these concentrations of acivicin, differentiation was associated with expression of the N-formyl-methyl-leucyl-phenylalanine-receptor (FMLP-R) on 8% to 29% of cells as compared with 8% for control cells. Acivicin potentiated the differentiating effects of interferon-gamma, tumor necrosis factor, dihydroxyvitamin D3, dimethylsulfoxide, and retinoic acid. Culture of cells from the U937 (monoblastic), K562 (erythroleukemia), and KG-1 (myeloblastic) cell lines resulted in decreased growth and viability, but not consistently in differentiation. Acivicin decreased survival of freshly isolated ANLL cells and increased their H2O2 production and NSE content. These results suggest that the glutamine analogue acivicin may be useful as a differentiating agent with antileukemia activity in patients with ANLL.


Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.
The study of cancer genomes now routinely involves using next-generation sequencing technology (NGS) to profile tumours for single nucleotide variant (SNV) somatic mutations. However, surprisingly few published bioinformatics methods exist for the specific purpose of identifying somatic mutations from NGS data and existing tools are often inaccurate, yielding intolerably high false prediction rates. As such, the computational problem of accurately inferring somatic mutations from paired tumour/normal NGS data remains an unsolved challenge. We present the comparison of four standard supervised machine learning algorithms for the purpose of somatic SNV prediction in tumour/normal NGS experiments. To evaluate these approaches (random forest, Bayesian additive regression tree, support vector machine and logistic regression), we constructed 106 features representing 3369 candidate somatic SNVs from 48 breast cancer genomes, originally predicted with naive methods and subsequently revalidated to establish ground truth labels. We trained the classifiers on this data (consisting of 1015 true somatic mutations and 2354 non-somatic mutation positions) and conducted a rigorous evaluation of these methods using a cross-validation framework and hold-out test NGS data from both exome capture and whole genome shotgun platforms. All learning algorithms employing predictive discriminative approaches with feature selection improved the predictive accuracy over standard approaches by statistically significant margins. In addition, using unsupervised clustering of the ground truth 'false positive' predictions, we noted several distinct classes and present evidence suggesting non-overlapping sources of technical artefacts illuminating important directions for future study. Software called MutationSeq and datasets are available from http://compbio.bccrc.ca.


CXCR4 mRNA expression in colon, esophageal and gastric cancers and hepatitis C infected liver.
We have recently demonstrated by Northern blot and RT-PCR that the mRNA expression of the alpha-chemokine hIRH/SDF-1alpha is reduced in hepatocellular carcinoma (HCC), several digestive tract cancers and premalignant colon adenomas, and that its receptor CXCR4 mRNA expression is reduced in HCC. Here we investigate the expression of CXCR4 mRNA expression in several digestive tract cancers and hepatitis C viral (HCV) infected liver, a premalignant condition. There was no difference in the CXCR4 mRNA expression in colon, esophageal or gastric cancers compared to non-cancerous tissues. This is significantly different from the reduced expression we have seen with hepatocellular carcinoma (p<0.05). To better refine regional tumor or hepatic cytokine mRNA analysis within a biopsy sample we describe a micro-isolation technique for RNA extraction from portal and triad areas of liver biopsies or other small malignant or non-malignant biopsy samples suitable for use in RT-PCR and differential display reactions. In HCV liver biopsies, the expression of hIRH and its receptor CXCR4 mRNA, corrected for G3PDH, was not significantly different from that of control non-HCV (steatosis) biopsies. CXCR4 is expressed on leukocytes and its expression was predicted to correlate with hepatic inflammation. CXCR4 receptor mRNA expression did correlate significantly with that of its ligand hIRH/SDF-1alpha (p=0.001), and with the severity of fibrosis (p<0.05), but not with portal inflammation (p<0.10), piecemeal necrosis (p<0.10), lobular inflammation (p>0.10), the presence of lymphoid aggregates (p>0.10), or the total histological activity index (p=0.07). There was no difference in expression of hIRH or CXCR4 between responders and non-responders to interferon (IFN) treatment, while as a control, the responder group of patients did show a higher expression of IFNalpha receptor than the non-responder group (p=0.05).


Feelings of revenge, retaliation motive, and posttraumatic stress reactions in crime victims.
Individuals with posttraumatic stress disorder (PTSD) are often said to experience strong feelings of revenge. However, there is a need for confirmatory empirical studies. Therefore, in a study of 174 victims of violent crimes, the relation between feelings of revenge and posttraumatic stress reactions was investigated. Feelings of revenge were correlated with intrusion and hyperarousal but not with avoidance. Feelings of revenge explained incremental variance of intrusion and hyperarousal when the variance explained by victimological variables was controlled. The retaliation motive implied in feelings of revenge did not account for the relation between feelings of revenge and posttraumatic stress reactions. However, the relation was moderated by the time since victimization. Therefore, feelings of revenge must presumably be regarded as a maladaptive coping reaction to experienced injustice, but not in the first period after victimization.


Outlook for soviet oil.
Public debate about Soviet oil has become more widespread in the past 5 years, but during this period Soviet petroleum exports have ceased to be made available by volume. Soviet oil consumption has usually been estimated by deducting exports from total production. This article takes the alternative approach, using Soviet statistics from a variety of sources, to build up a sectoral pattern of Soviet oil demand and to consider this in the broader context of total Comecon energy supply and demand. From this focus future prospects for the Comecon energy balance are analyzed.


Detection of Cryptosporidium species and sources of contamination with Cryptosporidium hominis during a waterborne outbreak in north west Wales.
As part of investigations into the cause of a waterborne outbreak of Cryptosporidium hominis infection linked to a mains water supply, surface waters and wastewater treatment plants were tested for Cryptosporidium spp. Oocyst counts in base flow surface water samples ranged from nil to 29 per 10 l. Oocyst counts in effluent from a community wastewater treatment plant were up to 63 fold higher and breakout from one septic tank five logs higher. There were no peak (storm) flow events during the investigation. C. hominis, four named genotypes (cervine, muskrat II, rat, W19) and six new small subunit ribosomal RNA gene sequences were identified. Four of the new sequences were closely related to Cryptosporidium muskrat genotype I, one was closely related to the fox genotype and one to Cryptosporidium canis. C. hominis was found extensively in the catchment, but only at sites contaminated by wastewater, and in the treated water supply to the affected area. All were gp60 subtype IbA10G2, the outbreak subtype. Multiple routes of contamination of the reservoir were identified, resulting in persistent detection of low numbers of oocysts in the final water. This work demonstrates the utility of genotyping Cryptosporidium isolates in environmental samples during outbreak investigations.