MPKin-YSTR: Interpretation of Y chromosome STR haplotypes for missing persons cases.
Y chromosome Short Tandem Repeat (STR) haplotypes have been used in assisting forensic investigations primarily for identification and male lineage determination. The current SWGDAM interpretation guidelines for Y-STR typing provide helpful guidance on those purposes but do not address the issue of kinship analysis with Y-STR haplotypes. Because of the high mutation rate of Y-STRs, there are complex missing person cases in which inconsistent Y-STR haplotypes between true paternal lineage relatives will arise and cases with two or more male references in the same lineage and yet differ in their haplotypes. Therefore, more useful methods are needed for interpreting the Y-STR haplotype data. Computational methods and interpretation guidelines have been developed specifically addressing this issue, either using a mismatch-based counting method or a pedigree likelihood ratio method. In this study, a software program, MPKin-YSTR, was developed by implementing those more sophisticated methods. This software should be able to improve the interpretation of complex cases with Y-STR haplotype evidence. Thus, more biological evidence will be interpreted, which in turn will result in more investigation leads to help solve crimes.


Ashley revisited: a response to the critics.
The case of Ashley X involved a young girl with profound and permanent developmental disability who underwent growth attenuation using high-dose estrogen, a hysterectomy, and surgical removal of her breast buds. Many individuals and groups have been critical of the decisions made by Ashley's parents, physicians, and the hospital ethics committee that supported the decision. While some of the opposition has been grounded in distorted facts and misunderstandings, others have raised important concerns. The purpose of this paper is to provide a brief review of the case and the issues it raised, then address 25 distinct substantive arguments that have been proposed as reasons that Ashley's treatment might be unethical. We conclude that while some important concerns have been raised, the weight of these concerns is not sufficient to consider the interventions used in Ashley's case to be contrary to her best interests, nor are they sufficient to preclude similar use of these interventions in the future for carefully selected patients who might also benefit from them.


Methyl donor-deficient diet during development can affect fear and anxiety in adulthood in C57BL/6J mice.
DNA methylation is one of the essential factors in the control of gene expression. Folic acid, methionine and choline (methyl donors)--all nutrients related to one-carbon metabolism--are known as important mediators of DNA methylation. A previous study has shown that long-term administration of a diet lacking in methyl donors caused global DNA hypermethylation in the brain (Pogribny et al., 2008). However, no study has investigated the effects of a diet lacking in methyl donors during the developmental period on emotional behaviors such as fear and anxiety-like behavior in association with gene expressions in the brain. In addition, it has not been elucidated whether a diet supplemented with methyl donors later in life can reverse these changes. Therefore, we examined the effects of methyl donor deficiency during the developmental period on fear memory acquisition/extinction and anxiety-like behavior, and the relevant gene expressions in the hippocampus in juvenile (6-wk) and adult (12-wk) mice. We found that juvenile mice fed a methyl-donor-deficient diet had impaired fear memory acquisition along with decreases in the gene expressions of Dnmt3a and Dnmt3b. In addition, reduced anxiety-like behavior with decreased gene expressions of Grin2b and Gabar2 was observed in both the methyl-donor-deficient group and the body-weight-matched food-restriction group. After being fed a diet supplemented with methyl donors ad libitum, adult mice reversed the alteration of gene expression of Dnmt3a, Dnmt3b, Grin2b and Gabar2, but anxiety-like behavior became elevated. In addition, impaired fear-memory formation was observed in the adult mice fed the methyl-donor-deficient diet during the developmental period. Our study suggested that developmental alterations in the one-carbon metabolic pathway in the brain could have effects on emotional behavior and memory formation that last into adulthood.


Human ovarian cancer stroma contains luteinized theca cells harboring tumor suppressor gene GT198 mutations.
Ovarian cancer is a highly lethal gynecological cancer, and its causes remain to be understood. Using a recently identified tumor suppressor gene, GT198 (PSMC3IP), as a unique marker, we searched for the identity of GT198 mutant cells in ovarian cancer. GT198 has germ line mutations in familial and early onset breast and ovarian cancers and recurrent somatic mutations in sporadic fallopian tube cancers. GT198 protein has been shown as a steroid hormone receptor coregulator and also as a crucial factor in DNA repair. In this study, using GT198 as a marker for microdissection, we find that ovarian tumor stromal cells harboring GT198 mutations are present in various types of ovarian cancer including high and low grade serous, endometrioid, mucinous, clear cell, and granulosa cell carcinomas and in precursor lesions such as inclusion cysts. The mutant stromal cells consist of a luteinized theca cell lineage at various differentiation stages including CD133(+), CD44(+), and CD34(+) cells, although the vast majority of them are differentiated overexpressing steroidogenic enzyme CYP17, a theca cell-specific marker. In addition, wild type GT198 suppresses whereas mutant GT198 protein stimulates CYP17 expression. The chromatin-bound GT198 on the human CYP17 promoter is decreased by overexpressing mutant GT198 protein, implicating the loss of wild type suppression in mutant cells. Together, our results suggest that GT198 mutant luteinized theca cells overexpressing CYP17 are common in ovarian cancer stroma. Because first hit cancer gene mutations would specifically mark cancer-inducing cells, the identification of mutant luteinized theca cells may add crucial evidence in understanding the cause of human ovarian cancer.


Effects of Agaricus brasiliensis mushroom in Walker-256 tumor-bearing rats.
Agaricus brasiliensis is a mushroom native to São Paulo State, Brazil, that is studied for its medicinal proprieties. This work aimed to investigate the antitumoral activity of A. brasiliensis extracts and pure powdered basidiocarp preparation using Walker-256 (W256) tumor-bearing rats, a model for cancer-related cachexia studies. The rats were treated for 14 days by gavage (136 mg/kg) and at the end of the experiment tumors were collected to calculate mass and volume. Blood was collected for determination of plasma glucose, albumin, alanine aminotransferase (ALT), and aspartate aminotransferase (AST). Hepatic and tumor enzymes indicating oxidative stress were also evaluated. The results showed that all 4 treatments (pure powdered basidiocarp and aqueous, acid, and alkaline extracts) significantly reduced tumor size and promoted gain in body weight. Plasmatic analysis showed a reduction in AST level and increased glycemia in the treated rats. Pure basidiocarp preparations improved the liver catalase and superoxide dismutase activity, but did not change the glutathione S-transferase activity. The data collected from the W256 tumor-bearing rats revealed the beneficial effects of A. brasiliensis in tumor treatment, mainly related to cachexia. The benefits can be partly related to antioxidant activity and to reduction of weight loss and tumor growth.


Regulation of thiol environment of the N-demethylation and ring hydroxylation of N,N-dimethyl-4-aminoazobenzene (DAB) by rat liver microsomes.
A study was conducted on the regulation by thiol environment of microsomal metabolism of the azo dye hepatocarcinogen, N,N-dimethyl-4-aminoazobenzene (DAB). Physiological concentrations of glutathione (GSH) stimulated N-demethylation and ring hydroxylation of the dye in normal and phenobarbital (PB)-treated microsomes. However, little effect of GSH was seen with microsomes from beta-naphthoflavone (BNF)-treated rats. The synthetic thiol, dithiothreitol (DTT), stimulated ring-hydroxylation of DAB but inhibited N-demethylation at all concentrations in control nd PB-induced microsomes. A biphasic response to DTT was obtained with BNF microsomes; inhibition of N-demethylation was seen only at low concentrations (0.1 mM) and a return to control values occurred at higher concentrations. DTT inhibition was shown to be specific for the first N-demethylation step, whereas the second was slightly stimulated at concentrations greater than 3.0 mM. Agents which alkylate [N-ethylmaleimide (NEM), p-hydroxymercuribenzoate] or oxidize [5,5'-dithiobis(nitrobenzoic acid) or Ellman's reagent] protein SH groups inhibited DAB metabolism. Inhibition of microsomal NADPH-cytochrome c reductase activity by p-hydroxymercuribenzoate required an order of magnitude more inhibitor than was needed to block DAB metabolism. This suggests that DAB metabolism requires viable SH groups other than those involved in NADPH-cytochrome c reductase activity. NEM, in contrast, inhibited the N-demethylation of DAB and NADPH-cytochrome c reductase at approximately the same concentrations. Ring-hydroxylation was stimulated by high (greater than 1 mM) concentrations of NEM, implying a different enzymic mechanism for this pathway.(ABSTRACT TRUNCATED AT 250 WORDS)


How should efficacy be evaluated in randomized clinical trials of treatments for depression?
The present system of conducting studies of promising antidepressant therapies has evolved through the collaborative efforts of government, industry, and academicians and is costly and inefficient. At least one third of the published clinical trials of approved antidepressants are negative for efficacy, which can be partly explained by the clinical and neurobiological heterogeneity of the depressive disorder and partly because of methodological inadequacies. Unfortunately, too little attention is given to ensuring the reliability of diagnoses and dependent measures, sample sizes are seldom large enough to detect modest yet honestly significant differences, and too many trials are pursued before dose-response characteristics are fully understood. At present, the only data beyond 1 year of treatment--and the only evidence about protection against recurrent depression--come during postmarketing or phase 4 of the drug development process. Moreover, efficacy data for depressed children and adolescents, bipolar depression, psychotic depression, dysthymia, and frail or medically ill elderly patients are rarely available at the time a drug is introduced. Thus, it is remarkable how little clinicians know about a new antidepressant at the time it is first approved for general use. Within a research strategy, tactics that ensure reliability, encourage attention to adherence, and lessen attrition at the outset of a study will increase the power and design sensitivity of a particular trial. Additionally, the issues of research funding-including division of the research pie-and the relationship of the Food and Drug Administration and investigators to the pharmaceutical industry and the National Institute of Mental Health need to be revisited. Finally, extension of a compound's patent life might be considered to expand the necessary postmarketing research. This article describes the process of conducting the clinical trials that support a New Drug Application, discusses issues in evaluating efficacy, and offers suggestions for modifying and improving the drug development process so that clinicians can better judge new drugs.


Referral and counter-referral system between secondary and tertiary care facilities in a children's hospital network of Greater Buenos Aires.
Hospital El Cruce is a tertiary care facility which is part of a healthcare network that has been operating since July 2008 and includes health centers from five municipalities of the South of Greater Buenos Aires. The objective of the study was to describe the referral and counter-referral system at the pediatric intermediate medical care unit of the Hospital El Cruce, the tertiary level care of the network, and secondly to identify the critical points that could go against the consolidation of the network and to analyze the level of knowledge about it. This was a cross-sectional, prospective study conducted at the pediatric intermediate medical care unit of Hospital El Cruce between July 2008 and December 2010. Indicators related to patient admission and discharge were analyzed. A survey was administered to all the heads of the network's pediatric departments in order to assess the level of knowledge they had about it. A total of1677patients were hospitalized; 83.9% were referred from the network. Of all referrals made, 71.1% were accepted. There were 156 patients (9.4%) who were counter-referred to the referring facility. The survey results showed that 70% of heads of pediatric departments were unaware of the range of services provided by the network. Health care exchange was predominantly based on accepting patients referred from secondary care facilities to Hospital El Cruce and a minimum number of counter-referrals to referring facilities, with a radial pattern dynamics. There was scarce knowledge about the availability of the network health service delivery.


Cost-effectiveness analysis of a lidocaine 5% medicated plaster compared with gabapentin and pregabalin for treating postherpetic neuralgia: a german perspective.
This study set out to assess the cost effectiveness of using a 5% lidocaine (lignocaine) medicated plaster for the treatment of postherpetic neuralgia (PHN) compared with gabapentin, pregabalin 300 mg/day or 600 mg/day in German primary care. The analysis took the perspective of the Statutory Health Insurance scheme (GKV). A Markov model was used to calculate the costs (2007) and benefits of the lidocaine plaster, gabapentin 1800 mg/day and pregabalin 300 or 600 mg/day over a 6-month time horizon in elderly patients with PHN who experienced insufficient pain relief with standard analgesics and could not tolerate or had contraindications to tricyclic antidepressants. The model calculated the cost per quality-adjusted life-year (QALY) gained and the cost per additional month without symptoms or intolerable adverse effects. The majority of transition probabilities were obtained from randomized controlled trials identified from a systematic literature review. Further model inputs, including resource use, concomitant medication and long-term efficacy/adherence data, were obtained from a Delphi panel. Utility values were taken from a previous study and age adjusted. Cost data were obtained from official price tariffs. Mortality, indirect costs and costs associated with inpatient treatment were not considered in the present analysis due to the perspective and time horizon employed. Over the 6-month period modelled, the mean total therapy cost per patient treated with the lidocaine plaster was euro911, compared with euro728 for gabapentin, euro875 for pregabalin 300 mg/day and euro977 for pregabalin 600 mg/day. Treatment with the lidocaine plaster was related to greater numbers of QALYs and more months without symptoms or intolerable adverse effects (mean 0.300 QALYs and 4.06 months per patient) than with gabapentin (mean 0.247 QALYs and 2.72 months), pregabalin 300 mg/day (mean 0.253 QALYs and 3.02 months) or pregabalin 600 mg/day (mean 0.256 QALYs and 3.22 months). The lidocaine plaster cost euro3453/QALY gained and euro137 per additional month without adverse effects or symptoms relative to gabapentin and euro766/QALY and euro35 per month without adverse effects or symptoms relative to pregabalin 300 mg/day. The lidocaine plaster dominated pregabalin 600 mg/day, being less costly and more effective. Probabilistic sensitivity analysis indicated that there is a 99.36% chance that the lidocaine plaster is the most clinically effective treatment considered in the analysis and a 99.09% chance that the lidocaine plaster is the most cost-effective treatment of the four therapies considered in the analysis if the GKV is willing to pay at least euro20 000/QALY gained. Extensive deterministic sensitivity analyses demonstrated that the findings are robust. The 5% lidocaine-medicated plaster is a cost-effective treatment option for the management of PHN in Germany compared with gabapentin and both 300 and 600 mg/day of pregabalin.


Respiratory center output following zopiclone or diazepam administration in patients with pulmonary disease.
Mouth occlusion pressure at 0.1 s (P0.1) and minute ventilation (VE) were measured at rest and during progressive hypercapnia in 32 patients. Under double-blind conditions and according to a 2 x 2 Latin-square design, half the patients received one oral dose of diazepam and its placebo. Using the same design, the other half received zopiclone and its placebo. Normocapnic and moderately hypoxemic patients between the ages of 21 and 69 with moderate to severe chronic obstructive pulmonary disease were included in the study. Diazepam produced a statistically significant decrease (p less than 0.05) over its placebo in delta P0.1/delta PETCO2 values following CO2 rebreathing. Zopiclone did not influence either delta P0.1/delta PETCO2 or delta VE/delta PETCO2, but produced a significant increase in respiratory frequency. However, no statistically significant differences were observed between the two active treatments.


Psychosocial functioning before and after surgical treatment for morbid obesity: reliability and validation of the Norwegian version of obesity-related problem scale.
Background. The aims of this study were to translate the Obesity-Related Problem scale (OP scale) into the Norwegian language and test its reliability, validity and responsiveness in a Norwegian sample. Method. The questionnaire (OP scale) was translated from the original language (Swedish) into Norwegian. Patients completed the questionnaire prior to and one year after sleeve gastrectomy. Internal consistency was evaluated using Cronbach's α. Construct validity was tested by correlating the OP-scale with the SF-36 and the Cantril Ladder using the Pearson correlation coefficient. An exploratory and confirmatory factor analysis was used to test the unidimensionality of the OP scale. Responsiveness was tested by assessing changes in the OP scale from baseline to one year post-surgery using the paired sample t-test. Floor and ceiling effect were calculated as percentages. Results. A total of 181 patients (123 women) accepted for bariatric surgery was included in the study. The mean age was 43.1 ± 12.5 years, and mean body mass index (BMI) before surgery was 45 ± 6.9. The mean value of the OP scale at baseline was 63.30 ± 24.43 (severe impairment) and 21.01 ± 20.98 at one year follow-up (mild impairment). Internal consistency was high at baseline (Cronbach's α 0.91). The floor effect was small at baseline and high at one year. The ceiling effect was small at baseline and at one year. Exploratory and conformatory factor analysis showed one factor with a high percent of explained variance. Correlations between OP scale at baseline, SF-36, Cantril Ladder and BMI were statistically significant and in the predicted direction to support validity of the Norwegian OP scale. After one year correlations between the change in OP scale and the change in SF-36 scores, Cantril Ladder and BMI were also statistically significant, except for the change in the Role Physical-scale. The OP scale showed greater responsiveness than either the SF-36 or Cantril Ladder. Conclusion. These results confirm that the Norwegian version of the OP scale is a valid and reliable instrument for measuring psychosocial functioning in patients with clinically severe obesity.


Influence of the prion protein and the apolipoprotein E genotype on the Creutzfeldt-Jakob Disease phenotype.
We investigated the risk associated with the codon 129 polymorphism in the prion protein gene (PRNP) and apolipoprotein E gene (APOE) isoforms for development of Creutzfeldt-Jakob disease (CJD) (n=126) and the possible influences on the disease pathology and its most important clinical characteristics. The PRNP M129V (PRNP129) polymorphism was determined using both DNA extracted from formalin fixed and paraffin embedded brain tissue (n=59) and leukocyte extracted DNA (n=67). In the latter group also the PRNP open reading frame and the APOE genotype were analysed and compared to a neurologically unaffected, age and sex matched control group (n=79). We found that methionine homozygosity of the PRNP129 increases the risk for developing CJD. PRNP129 also influenced the prion accumulation patterns in brain. The APOE 4 allele was an independent risk factor for developing CJD. We further observed a significant dose dependent APOE 4 effect on the number and type of amyloid-beta plaques in the brain of CJD patients.


Trimble GX200 and Riegl LMS-Z390i sensor self-calibration.
This paper aims to establish and develop a calibration model for two time-of-flight terrestrial laser scanners (TLS): Trimble GX200 and Riegl LMS-Z390i. In particular, the study focuses on measurement errors and systematic instrumental errors to compile an error model for TLS. An iterative and robust least squares procedure is developed to compute internal calibration parameters together with a TLS data set geo-reference in an external reference system. To this end, a calibration field is designed that performs as an experimental platform that tests the different laser scanner methods. The experimental results show the usefulness and potential of this approach, especially when high-precision measurements are requires.


Direct detection of Chlamydia trachomatis in urine specimens from symptomatic and asymptomatic men by using a rapid polymerase chain reaction assay.
Screening for Chlamydia trachomatis infection in men has traditionally been limited to men who present with urethral symptoms, thereby limiting the detection of asymptomatic chlamydia infection in men. In order to effectively screen both symptomatic and asymptomatic men, we evaluated a newly developed polymerase chain reaction (PCR) assay, Amplicor C. trachomatis, from Roche Molecular Systems for the detection of C. trachomatis in urine specimens in comparison with urethral culture. A total of 530 male urine specimens were collected from 322 symptomatic and 208 asymptomatic men attending two sexually transmitted disease clinics in Baltimore, Md. The prevalence of C. trachomatis by culture was 9.8% (10.6% in symptomatic men and 8.2% in asymptomatic men). Compared with culture, the sensitivity of the PCR was 92.8%, the specificity was 94.7%, the positive predictive value was 68.4%, and the negative predictive value was 99.1%. Discrepant results between culture and PCR were further analyzed by direct fluorescent-antibody staining of elementary bodies in urine sediment and in culture transport vials and by major outer membrane protein PCR of transport media for specimens with negative culture. The revised sensitivity and specificity of PCR for urine were 95.0 and 99.8%, respectively, and the positive and negative predictive values were 98.7 and 99.1%, respectively. The sensitivity of culture compared with PCR and/or direct fluorescent-antibody staining was 68.4%. These results indicate that the PCR assay is a highly sensitive and specific assay for the detection of C. trachomatis in male urine specimens and provides a noninvasive technique for routine screening of chlamydia infection in both symptomatic and asymptomatic men.


Biological invasions: recommendations for U.S. policy and management.
The Ecological Society of America has evaluated current U.S. national policies and practices on biological invasions in light of current scientific knowledge. Invasions by harmful nonnative species are increasing in number and area affected; the damages to ecosystems, economic activity, and human welfare are accumulating. Without improved strategies based on recent scientific advances and increased investments to counter invasions, harm from invasive species is likely to accelerate. Federal leadership, with the cooperation of state and local governments, is required to increase the effectiveness of prevention of invasions, detect and respond quickly to new potentially harmful invasions, control and slow the spread of existing invasions, and provide a national center to ensure that these efforts are coordinated and cost effective. Specifically, the Ecological Society of America recommends that the federal government take the following six actions: (1) Use new information and practices to better manage commercial and other pathways to reduce the transport and release of potentially harmful species; (2) Adopt more quantitative procedures for risk analysis and apply them to every species proposed for importation into the country; (3) Use new cost-effective diagnostic technologies to increase active surveillance and sharing of information about invasive species so that responses to new invasions can be more rapid and effective; (4) Create new legal authority and provide emergency funding to support rapid responses to emerging invasions; (5) Provide funding and incentives for cost-effective programs to slow the spread of existing invasive species in order to protect still uninvaded ecosystems, social and industrial infrastructure, and human welfare; and (6) Establish a National Center for Invasive Species Management (under the existing National Invasive Species Council) to coordinate and lead improvements in federal, state, and international policies on invasive species. Recent scientific and technical advances provide a sound basis for more cost-effective national responses to invasive species. Greater investments in improved technology and management practices would be more than repaid by reduced damages from current and future invasive species. The Ecological Society of America is committed to assist all levels of government and provide scientific advice to improve all aspects of invasive-species management.


A Patient With Human Herpesvirus 8-Positive Multicentric Castleman's Disease Who Met Criteria for TAFRO Syndrome: Controversy in Practice?
Multicentric Castleman's disease (MCD) is a known entity with characteristics of lymphoproliferative syndrome, characterized by cytokine activation. Its association with human immunodeficiency virus (HIV) is frequently described, as well as its positivity for human herpesvirus 8 (HHV-8). However, some negative patients for the latter (called idiopathic MCD), may have an aggressive spectrum of the disease (characterized by the presence of cytopenia, renal failure, anasarca and organomegaly), known as TAFRO syndrome (thrombocytopenia, anasarca, myelofibrosis, renal dysfunction, and organomegaly). We present the case of a young patient recently diagnosed with HIV infection, in whom MCD was found, and with an aggressive course despite treatment, who met criteria for TAFRO syndrome despite HHV-8 positivity.


Increased risk of anterior uveitis following herpes zoster: a nationwide population-based study.
To investigate the relationship between herpes zoster (HZ) and the subsequent risk of anterior uveitis during the year following an HZ diagnosis, using a nationwide population-based data set. This study used the Taiwan National Health Insurance Research Database. The study cohort consisted of 314,405 patients who received a diagnosis of HZ. The comparison cohort comprised 943,215 randomly selected patients. We tracked each patient for a 1-year period from their index ambulatory care visit to identify those who subsequently received a diagnosis of anterior uveitis. Stratified Cox proportional hazard regressions were performed to compute the adjusted 1-year uveitis-free survival rate, after adjusting for patient's age, sex, and geographic region and the presence of rheumatoid arthritis, psoriasis, mumps, systemic lupus erythematosus, tuberculosis, ankylosing spondylitis, and human immunodeficiency syndrome/AIDS. During the 1-year follow-up period, 2515 (0.2%) of 1,257,620 sampled patients were diagnosed with anterior uveitis: 908 from the study cohort (0.3% of the patients with HZ) and 1607 from the comparison cohort (0.2% of patients without HZ). After adjusting for potential confounders, the hazard ratio of anterior uveitis during the 1-year follow-up period was 1.67 for patients with HZ (P < .001) compared with the comparison cohort. In addition, the hazard ratio of anterior uveitis for patients with HZ ophthalmicus was 13.06 (P < .001) when compared with patients without HZ. The risk of anterior uveitis increased in the year following a diagnosis of HZ. We suggest that patient eye condition be evaluated following diagnosis with HZ.


Spatiotemporal neuromodulation therapies engaging muscle synergies improve motor control after spinal cord injury.
Electrical neuromodulation of lumbar segments improves motor control after spinal cord injury in animal models and humans. However, the physiological principles underlying the effect of this intervention remain poorly understood, which has limited the therapeutic approach to continuous stimulation applied to restricted spinal cord locations. Here we developed stimulation protocols that reproduce the natural dynamics of motoneuron activation during locomotion. For this, we computed the spatiotemporal activation pattern of muscle synergies during locomotion in healthy rats. Computer simulations identified optimal electrode locations to target each synergy through the recruitment of proprioceptive feedback circuits. This framework steered the design of spatially selective spinal implants and real-time control software that modulate extensor and flexor synergies with precise temporal resolution. Spatiotemporal neuromodulation therapies improved gait quality, weight-bearing capacity, endurance and skilled locomotion in several rodent models of spinal cord injury. These new concepts are directly translatable to strategies to improve motor control in humans.


World Association of Sleep Medicine (WASM) 2016 standards for recording and scoring leg movements in polysomnograms developed by a joint task force from the International and the European Restless Legs Syndrome Study Groups (IRLSSG and EURLSSG).
This report presents the results of the work by a joint task force of the International and European Restless Legs Syndrome Study Groups and World Association of Sleep Medicine that revised and updated the current standards for recording and scoring leg movements (LM) in polysomnographic recordings (PSG). First, the background of the decisions made and the explanations of the new rules are reported and then specific standard rules are presented for recording, detecting, scoring and reporting LM activity in PSG. Each standard rule has been classified with a level of evidence. At the end of the paper, Appendix 1 provides algorithms to aid implementation of these new standards in software tools. There are two main changes introduced by these new rules: 1) Candidate LM (CLM), are any monolateral LM 0.5-10 s long or bilateral LM 0.5-15 s long; 2) periodic LM (PLM) are now defined by runs of at least four consecutive CLM with an intermovement interval ≥10 and ≤ 90 s without any CLM preceded by an interval <10 s interrupting the PLM series. There are also new options defining CLM associated with respiratory events. The PLM rate may now first be determined for all CLM not excluding any related to respiration (providing a consistent number across studies regardless of the rules used to define association with respiration) and, subsequently, the PLM rate should also be calculated without considering the respiratory related events. Finally, special considerations for pediatric studies are provided. The expert visual scoringof LM has only been altered by the new standards to require accepting all LM > 0.5 s regardless of duration, otherwise the technician scores the LM as for the old standards. There is a new criterion for the morphology of LM that applies only to computerized LM detection to better match expert visual detection. Available automatic scoring programs will incorporate all the new rules so that the new standards should reduce technician burden for scoring PLMS.


5-Fluorouracil incorporation into DNA of CF-1 mouse bone marrow cells as a possible mechanism of toxicity.
Isolated CF-1 mouse bone marrow cells were exposed for 1 hr to 5-fluorouracil (FUra) at concentrations from 1.8 to 50 microM and then washed and suspended in a soft agar growth medium to assess the effect on toxicity (measured as reduction in colony growth compared to control). These data were used to determine specific toxic concentrations ranging from 25 to 90% lethal doses. Subsequent studies examined in parallel the effect of these toxic concentrations of FUra on the possible sites of toxicity including: (a) inhibition of thymidylate synthetase activity using a modified 3H release assay; (b) incorporation of FUra into RNA (FUra-RNA); and (c) incorporation of FUra into DNA (FUra-DNA). Thymidylate synthetase activity was slightly decreased (75% of control) after 1-hr exposure to a 50% lethal dose and was not significantly further reduced as the FUra concentration was increased to an 85% lethal dose. Furthermore, subsequent exposure of FUra-treated cells to a nontoxic thymidine dose (5 microM) failed to reverse toxicity. FUra-RNA increased during 1-hr exposure to increasing concentrations of FUra (25 to 90% lethal doses). Although initially suggesting a relationship between the level of FUra-RNA and toxicity, subsequent studies in cells exposed to FUra in the presence of uridine demonstrated a significantly decreased toxicity while, at the same time, a minimal decrease of FUra in RNA. In contrast, FUra-DNA was significantly decreased in the presence of uridine and correlated with decreased toxicity. In additional subsequent studies, an apparent decrease in subsequent DNA synthesis was observed (measured by 32P or [3H]thymidine incorporation into DNA) as the level of FUra-DNA increased. In conclusion, FUra is demonstrated to be incorporated into DNA of isolated CF-1 mouse bone marrow cells, and the level of FUra-DNA appears to be closely associated with toxicity and inhibition of further DNA synthesis. The parallel studies of thymidylate synthetase activity and FUra-RNA suggest that FUra-DNA may be an unrecognized mechanism of FUra toxicity in these cells.


Molecular, functional, and pharmacological characterization of the metabotropic glutamate receptor type 5 splice variants: comparison with mGluR1.
The main excitatory neurotransmitter in the brain, glutamate (Glu), activates not only receptor-channels, but also receptors coupled to G-protein called metabotropic Glu receptors (mGluRs). Eight genes coding for mGluRs have been characterized to date giving rise to even more proteins due to alternative splicing phenomena. Here we characterized a splice variant of mGluR5, called mGluR5b which contains a 32 amino acid fragment inserted in the cytoplasmic tail, 50 residues after the 7th transmembrane domain. mGluR5b mRNAs are present in different regions of the adult rat brain and are expressed at a higher level than mGluR5a mRNA. Functional analysis of mGluR5a and mGluR5b revealed that they share all the properties of mGluR1a, but not those of mGluR1b or 1c. Like mGluR1a, both mGluR5a and mGluR5b activate a rapid and transient current in Xenopus oocytes. When expressed in LLC-PK1 cells, they show the same subcellular distribution as mGluR1a, and stimulate both inositol phosphate (IP) and cAMP production. Moreover, cells expressing mGluR5a or mGluR5b, like those expressing mGluR1a have a higher basal PLC activity that is not inhibited by glutamate-pyruvate transaminase (GPT), suggesting that these receptors have an intrinsic activity. Interestingly, the pharmacological profiles of mGluR5a and b are identical, but different from that of mGluR1a. Most agonists, except glutamate, are more potent on mGluR5a/b than on mGluR1a. Interestingly, the mGluR1a antagonists MCPG and 4CPG have no effect on mGluR5a/b; 4C3HPG which is a full antagonist at mGluR1a is a partial agonist at mGluR5a/b. These results indicate that the long C-terminal intracellular domain present only in mGluR1a and mGluR5a/b, although not well conserved, is likely to be involved in the specific functional properties of these receptors. Although the ligand recognition sites of mGluR5a/b and mGluR1a are highly conserved, these receptors have different pharmacology.


Differences in centromere positioning of cycling and postmitotic human cell types.
Centromere positioning in human cell nuclei was traced in non-cycling peripheral blood lymphocytes (G0) and in terminally differentiated monocytes, as well as in cycling phytohemagglutinin-stimulated lymphocytes, diploid lymphoblastoid cells, normal fibroblasts, and neuroblastoma SH-EP cells using immunostaining of kinetochores, confocal microscopy and three-dimensional image analysis. Cell cycle stages were identified for each individual cell by a combination of replication labeling with 5-bromo-2'-deoxyuridine and immunostaining of pKi67. We demonstrate that the behavior of centromeres is similar in all cell types studied: a large fraction of centromeres are in the nuclear interior during early G1; in late G1 and early S phase, centromeres shift to the nuclear periphery and fuse in clusters. Peripheral location and clustering of centromeres are most pronounced in non-cycling cells (G0) and terminally differentiated monocytes. In late S and G2, centromeres partially decluster and migrate towards the nuclear interior. In the rather flat nuclei of adherently growing fibroblasts and neuroblastoma cells, kinetochores showed asymmetrical distributions with preferential kinetochore location close either to the bottom side of the nucleus (adjacent to the growth surface) or to the nuclear upper side. This asymmetrical distribution of centromeres is considered to be a consequence of chromosome arrangement in anaphase rosettes.


X-Ray Nanoscopy of a Bulk Heterojunction.
Optimizing the morphology of bulk heterojunctions is known to significantly improve the photovoltaic performance of organic solar cells, but available quantitative imaging techniques are few and have severe limitations. We demonstrate X-ray ptychographic coherent diffractive imaging applied to all-organic blends. Specifically, the phase-separated morphology in bulk heterojunction photoactive layers for organic solar cells, prepared from a 50:50 blend of poly(3-hexylthiophene) (P3HT) and phenyl-C61-butyric acid methyl ester (PCBM) and thermally treated for different annealing times is imaged to high resolution. Moreover, using a fast-scanning calorimetry chip setup, the nano-morphological changes caused by repeated thermal annealing applied to the same sample could be monitored. X-ray ptychography resolves to better than 100 nm the phase-segregated domains of electron donor and electron acceptor materials over a large field of view within the active layers. The quantitative phase contrast images further allow us to estimate the local volume fraction of PCBM across the photovoltaically active layers. The volume fraction gradient for different regions provides insight on the PCBM diffusion across the depletion zone surrounding PCBM aggregates. Phase contrast X-ray microscopy is under rapid development, and the results presented here are promising for future studies of organic-organic blends, also under in situ conditions, e.g., for monitoring the structural stability during UV-Vis irradiation.


MicroRNAs Associated with Shoulder Tendon Matrisome Disorganization in Glenohumeral Arthritis.
The extracellular matrix (ECM) provides core support which is essential for the cell and tissue architectural development. The role of ECM in many pathological conditions has been well established and ECM-related abnormalities leading to serious consequences have been identified. Though much has been explored in regards to the role of ECM in soft tissue associated pathologies, very little is known about its role in inflammatory disorders in tendon. In this study, we performed microRNA (miRNA) expression analysis in the long head of the human shoulder biceps tendon to identify key genes whose expression was altered during inflammation in patients with glenohumeral arthritis. We identified differential regulation of matrix metalloproteinases (MMPs) that could be critical in collagen type replacement during tendinopathy. The miRNA profiling showed consistent results between the groups and revealed significant changes in the expression of seven different miRNAs in the inflamed tendons. Interestingly, all of these seven miRNAs were previously reported to have either a direct or indirect role in regulating the ECM organization in other pathological disorders. In addition, these miRNAs were also found to alter the expression levels of MMPs, which are the key matrix degrading enzymes associated with ECM-related abnormalities and pathologies. To our knowledge, this is the first report which identifies specific miRNAs associated with inflammation and the matrix reorganization in the tendons. Furthermore, the findings also support the potential role of these miRNAs in altering the collagen type ratio in the tendons during inflammation which is accompanied with differential expression of MMPs.


Career Paths of Pathology Informatics Fellowship Alumni.
The alumni of today's Pathology Informatics and Clinical Informatics fellowships fill diverse roles in academia, large health systems, and industry. The evolving training tracks and curriculum of Pathology Informatics fellowships have been well documented. However, less attention has been given to the posttraining experiences of graduates from informatics training programs. Here, we examine the career paths of subspecialty fellowship-trained pathology informaticians. Alumni from four Pathology Informatics fellowship training programs were contacted for their voluntary participation in the study. We analyzed various components of training, and the subsequent career paths of Pathology Informatics fellowship alumni using data extracted from alumni provided curriculum vitae. Twenty-three out of twenty-seven alumni contacted contributed to the study. A majority had completed undergraduate study in science, technology, engineering, and math fields and combined track training in anatomic and clinical pathology. Approximately 30% (7/23) completed residency in a program with an in-house Pathology Informatics fellowship. Most completed additional fellowships (15/23) and many also completed advanced degrees (10/23). Common primary posttraining appointments included chief medical informatics officer (3/23), director of Pathology Informatics (10/23), informatics program director (2/23), and various roles in industry (3/23). Many alumni also provide clinical care in addition to their informatics roles (14/23). Pathology Informatics alumni serve on a variety of institutional committees, participate in national informatics organizations, contribute widely to scientific literature, and more than half (13/23) have obtained subspecialty certification in Clinical Informatics to date. Our analysis highlights several interesting phenomena related to the training and career trajectory of Pathology Informatics fellowship alumni. We note the long training track alumni complete in preparation for their careers. We believe flexible training pathways combining informatics and clinical training may help to alleviate the burden. We highlight the importance of in-house Pathology Informatics fellowships in promoting interest in informatics among residents. We also observe the many important leadership roles in academia, large community health systems, and industry available to early career alumni and believe this reflects a strong market for formally trained informaticians. We hope this analysis will be useful as we continue to develop the informatics fellowships to meet the future needs of our trainees and discipline.


Support patient search on pathology reports with interactive online learning based data extraction.
Structural reporting enables semantic understanding and prompt retrieval of clinical findings about patients. While synoptic pathology reporting provides templates for data entries, information in pathology reports remains primarily in narrative free text form. Extracting data of interest from narrative pathology reports could significantly improve the representation of the information and enable complex structured queries. However, manual extraction is tedious and error-prone, and automated tools are often constructed with a fixed training dataset and not easily adaptable. Our goal is to extract data from pathology reports to support advanced patient search with a highly adaptable semi-automated data extraction system, which can adjust and self-improve by learning from a user's interaction with minimal human effort. We have developed an online machine learning based information extraction system called IDEAL-X. With its graphical user interface, the system's data extraction engine automatically annotates values for users to review upon loading each report text. The system analyzes users' corrections regarding these annotations with online machine learning, and incrementally enhances and refines the learning model as reports are processed. The system also takes advantage of customized controlled vocabularies, which can be adaptively refined during the online learning process to further assist the data extraction. As the accuracy of automatic annotation improves overtime, the effort of human annotation is gradually reduced. After all reports are processed, a built-in query engine can be applied to conveniently define queries based on extracted structured data. We have evaluated the system with a dataset of anatomic pathology reports from 50 patients. Extracted data elements include demographical data, diagnosis, genetic marker, and procedure. The system achieves F-1 scores of around 95% for the majority of tests. Extracting data from pathology reports could enable more accurate knowledge to support biomedical research and clinical diagnosis. IDEAL-X provides a bridge that takes advantage of online machine learning based data extraction and the knowledge from human's feedback. By combining iterative online learning and adaptive controlled vocabularies, IDEAL-X can deliver highly adaptive and accurate data extraction to support patient search.


Complete Freund's adjuvant-induced intervertebral discitis as an animal model for discogenic low back pain.
Although numerous animal models for low back pain associated with intervertebral disk (IVD) degeneration have been proposed, insufficient data have been provided to make any conclusions regarding pain. Our aim in this study was to determine the reliability of complete Freund's adjuvant (CFA) injection into the rat spine as an animal model representing human discogenic pain. We studied IVD degenerative changes with pain development after a 10-microL CFA injection into the L5-6 IVD of adult rats using behavioral, histologic, and biochemical studies. Serial histologic changes were analyzed to detect degenerative changes. Expression of calcitonin gene-related peptide (CGRP), prostaglandin E (PGE), and inducible nitric oxide synthase (iNOS) were determined using immunohistochemistry or real-time polymerase chain reaction as support data for pain development. In addition, CGRP immunoreactivity (ir) at the IVD was considered indirect evidence of neural ingrowth into the IVD. There was a significant increase of the hindpaw withdrawal response in the CFA group until 7 wk postoperatively (P < 0.05). Histologic analyses revealed progressive degenerative changes of the disks without any damage in adjacent structures, including nerve roots. In the CGRP-ir staining study, the bilateral dorsal horns and IVD had positive ir after intradiscal CFA injection. CGRP mRNA expression was increased in the dorsal root ganglion (DRG) at 2 and 4 wk, whereas PGE and iNOS mRNAs were markedly increased at 2 wk. The increment of CGRP expression was higher in allodynic rats compared with nonallodynic rats. Intradiscal CFA injection led to chronic disk degeneration with allodynia, which was suggested by pain behavior and expression of pain-related mediators. The increment of CGRP, PGE, and iNOS also suggest pain-related signal processing between the IVD and the neural pathway in this animal model. This animal model may be useful for future research related to the pathophysiology and development of novel treatment for spine-related pain.


A Systematic Comparison of Protocols for Recovery of High-Quality RNA from Human Islets Extracted by Laser Capture Microdissection.
The isolation of high-quality RNA from endocrine pancreas sections represents a considerable challenge largely due to the high ribonuclease levels. Laser capture microdissection (LCM) of mammalian islets, in association with RNA extraction protocols, has emerged as a feasible approach to characterizing their genetic and proteomic profiles. However, a validated protocol to obtain high-quality RNA from LCM-derived human pancreas specimens that is appropriate for next-generation sequencing analysis is still lacking. In this study, we applied four methods (Picopure extraction kit, Qiazol protocol, Qiazol + Clean-up kit, and RNeasy Microkit + Carrier) to extract RNA from human islets obtained from both non-diabetic individuals and patients with type 2 diabetes who had undergone partial pancreatectomy, as well as handpicked islets from both non-diabetic and diabetic organ donors. The yield and purity of total RNA were determined by 260/280 absorbance using Nanodrop 100 and the RNA integrity number with a bioanalyzer. The results indicated that among the four methods, the RNeasy MicroKit + Carrier (Qiagen) provides the highest yield and purity.


Serial Xenotransplantation in NSG Mice Promotes a Hybrid Epithelial/Mesenchymal Gene Expression Signature and Stemness in Rhabdomyosarcoma Cells.
Serial xenotransplantation of sorted cancer cells in immunodeficient mice remains the most complex test of cancer stem cell (CSC) phenotype. However, we have demonstrated in various sarcomas that putative CSC surface markers fail to identify CSCs, thereby impeding the isolation of CSCs for subsequent analyses. Here, we utilized serial xenotransplantation of unsorted rhabdomyosarcoma cells in NOD/SCID gamma (NSG) mice as a proof-of-principle platform to investigate the molecular signature of CSCs. Indeed, serial xenotransplantation steadily enriched for rhabdomyosarcoma stem-like cells characterized by enhanced aldehyde dehydrogenase activity and increased colony and sphere formation capacity in vitro. Although the expression of core pluripotency factors (SOX2, OCT4, NANOG) and common CSC markers (CD133, ABCG2, nestin) was maintained over the passages in mice, gene expression profiling revealed gradual changes in several stemness regulators and genes linked with undifferentiated myogenic precursors, e.g., SOX4, PAX3, MIR145, and CDH15. Moreover, we identified the induction of a hybrid epithelial/mesenchymal gene expression signature that was associated with the increase in CSC number. In total, 60 genes related to epithelial or mesenchymal traits were significantly altered upon serial xenotransplantation. In silico survival analysis based on the identified potential stemness-associated genes demonstrated that serial xenotransplantation of unsorted rhabdomyosarcoma cells in NSG mice might be a useful tool for the unbiased enrichment of CSCs and the identification of novel CSC-specific targets. Using this approach, we provide evidence for a recently proposed link between the hybrid epithelial/mesenchymal phenotype and cancer stemness.


Protein-protein-interaction network organization of the hypusine modification system.
Hypusine modification of eukaryotic initiation factor 5A (eIF-5A) represents a unique and highly specific post-translational modification with regulatory functions in cancer, diabetes, and infectious diseases. However, the specific cellular pathways that are influenced by the hypusine modification remain largely unknown. To globally characterize eIF-5A and hypusine-dependent pathways, we used an approach that combines large-scale bioreactor cell culture with tandem affinity purification and mass spectrometry: "bioreactor-TAP-MS/MS." By applying this approach systematically to all four components of the hypusine modification system (eIF-5A1, eIF-5A2, DHS, and DOHH), we identified 248 interacting proteins as components of the cellular hypusine network, with diverse functions including regulation of translation, mRNA processing, DNA replication, and cell cycle regulation. Network analysis of this data set enabled us to provide a comprehensive overview of the protein-protein interaction landscape of the hypusine modification system. In addition, we validated the interaction of eIF-5A with some of the newly identified associated proteins in more detail. Our analysis has revealed numerous novel interactions, and thus provides a valuable resource for understanding how this crucial homeostatic signaling pathway affects different cellular functions.


Effects of Burkholderia pseudomallei and other Burkholderia species on eukaryotic cells in tissue culture.
Burkholderia pseudomallei causes melioidosis, a serious and often fatal bacterial infection. B. pseudomallei can behave as a facultatively intracellular organism and this ability may be important in the pathogenesis of both acute and chronic infection. The uptake of B. pseudomallei and other Burkholderia spp. by cells in tissue culture was examined by electron microscopy. B. pseudomallei can invade cultured cell lines including phagocytic lines such as RAW264, J774 and U937, and non-phagocytic lines such as CaCO-2, Hep2, HeLa, L929, McCoy, Vero and CHO. Uptake was followed by the intracellular multiplication of B. pseudomallei and the induction of cell fusion and multinucleate giant cell formation. Similar effects were produced by B. mallei and B. thailandensis.


Predictors of substance abuse treatment participation among homeless adults.
The current study focuses on the relationships among a trauma history, a substance use history, chronic homelessness, and the mediating role of recent emotional distress in predicting drug treatment participation among adult homeless people. We explored the predictors of participation in substance abuse treatment because enrolling and retaining clients in substance abuse treatment programs is always a challenge particularly among homeless people. Participants were 853 homeless adults from Los Angeles, California. Using structural equation models, findings indicated that trauma history, substance use history and chronicity of homelessness were associated, and were significant predictors of greater recent emotional distress. The most notable result was that recent emotional distress predicted less participation in current substance abuse treatment (both formal and self-help) whereas a substance use history alone predicted significantly more participation in treatment. Implications concerning treatment engagement and difficulties in obtaining appropriate dual-diagnosis services for homeless mentally distressed individuals are discussed.


Presynaptically silent synapses: dormancy and awakening of presynaptic vesicle release.
Synapses represent the main junctures of communication between neurons in the nervous system. In many neurotransmitter systems, a fraction of presynaptic terminals fails to release vesicles in response to action potential stimulation and strong calcium influx. These silent presynaptic terminals exhibit a reversible functional dormancy beyond low vesicle release probability, and dormancy status may have important implications in neural function. Recent advances have implicated presynaptic proteins interacting with vesicles downstream of cAMP and protein kinase A signaling cascades in modulating the number of these mute presynaptic terminals, and dormancy induction may represent a homeostatic neuroprotective mechanism active during pathological insults involving excitotoxicity. Interestingly, dormancy reversal may also be induced during Hebbian plasticity. Here, details of synaptic dormancy, recent insights into the molecular signaling cascades involved, and potential clinical and mechanistic implications of this form of synaptic plasticity are described.


Complex transition metal hydrides incorporating ionic hydrogen: thermal decomposition pathway of Na2Mg2FeH8 and Na2Mg2RuH8.
Complex transition metal hydrides have potential technological application as hydrogen storage materials, smart windows and sensors. Recent exploration of these materials has revealed that the incorporation of anionic hydrogen into these systems expands the potential number of viable complexes, while varying the countercation allows for optimisation of their thermodynamic stability. In this study, the optimised synthesis of Na2Mg2TH8 (T = Fe, Ru) has been achieved and their thermal decomposition properties studied by ex situ Powder X-ray Diffraction, Gas Chromatography and Pressure-Composition Isotherm measurements. The temperature and pathway of decomposition of these isostructural compounds differs considerably, with Na2Mg2FeH8 proceeding via NaMgH3 in a three-step process, while Na2Mg2RuH8 decomposes via Mg2RuH4 in a two-step process. The first desorption maxima of Na2Mg2FeH8 occurs at ca. 400 °C, while Na2Mg2RuH8 has its first maxima at 420 °C. The enthalpy and entropy of desorption for Na2Mg2TH8 (T = Fe, Ru) has been established by PCI measurements, with the ΔHdes for Na2Mg2FeH8 being 94.5 kJ mol(-1) H2 and 125 kJ mol(-1) H2 for Na2Mg2RuH8.


Infant Feeding Practices in China and Ireland: Ireland Chinese Mother Survey.
Introduction: Migration to another country may induce changes in infant feeding practices especially where such practices differ considerably between the two countries. This study was undertaken to compare the infant feeding practices between Chinese mothers who gave birth in Ireland (CMI) with immigrant Chinese mothers who gave birth in China (CMC), and to examine the factors that influence these practices. Methods: A cross-sectional self-administrated survey was conducted among a convenience sample of 322 Chinese mothers living in Ireland. Data were obtained from mailed questionnaires. Infant feeding practices between CMC and CMI were compared by Chi-square or independent sample t-test. Binary logistic regression analyses were further performed to test the differences in infant feeding practices between two groups, after controlling for potential socio-demographic confounders. Results: High breastfeeding initiation rates were found in both groups (CMC: 87.2%; CMI: 75.6%); however sharp reductions in breastfeeding rates at 3 months (49.1%) and 6 months (28.4%) were found among CMI but not CMC (P < 0.05). Introduction of water within 1 week after childbirth was common for CMC in comparison with CMI. CMI were more likely than CMC to introduce infant formula to their child within the first 4 months after childbirth. The timing of introduction of rice porridge, vegetables, fruits and meats did not differ between CMC and CMI. Conclusions: Cultural and perceptional factors, and changes caused by migration contribute to the decline in breastfeeding duration among CMI. Language-specific breastfeeding support and education among Chinese mothers in Ireland is needed, in particular to encourage mothers to breastfeed for 6 months or more.


Analysis of promoter regions of co-expressed genes identified by microarray analysis.
The use of global gene expression profiling to identify sets of genes with similar expression patterns is rapidly becoming a widespread approach for understanding biological processes. A logical and systematic approach to study co-expressed genes is to analyze their promoter sequences to identify transcription factors that may be involved in establishing specific profiles and that may be experimentally investigated. We introduce promoter clustering i.e. grouping of promoters with respect to their high scoring motif content, and show that this approach greatly enhances the identification of common and significant transcription factor binding sites (TFBS) in co-expressed genes. We apply this method to two different dataset, one consisting of micro array data from 108 leukemias (AMLs) and a second from a time series experiment, and show that biologically relevant promoter patterns may be obtained using phylogenetic foot-printing methodology. In addition, we also found that 15% of the analyzed promoter regions contained transcription factors start sites for additional genes transcribed in the opposite direction. Promoter clustering based on global promoter features greatly improve the identification of shared TFBS in co-expressed genes. We believe that the outlined approach may be a useful first step to identify transcription factors that contribute to specific features of gene expression profiles.


New hydroxyproline radiocarbon dates from Sungir, Russia, confirm early Mid Upper Palaeolithic burials in Eurasia.
Sungir (Russia) is a key Mid-Upper Palaeolithic site in Eurasia, containing several spectacular burials that disclose early evidence for complex burial rites in the form of a range of grave goods deposited along with the dead. Dating has been particularly challenging, with multiple radiocarbon dates ranging from 19,160±270 to 28,800±240 BP for burials that are believed to be closely similar in age. There are disparities in the radiocarbon dates of human bones, faunal remains and charcoal found on the floor of burials. Our approach has been to develop compound-specific methods using High Performance Liquid Chromatography (HPLC) to separate single amino acids, such as hydroxyproline, and thereby avoid the known human contamination on the bones themselves. Previously, we applied this technique to obtain radiocarbon dates of ∼30,000 BP for Sungir 2, Sungir 3 and a mammoth bone from the occupation levels of the site. The single amino acid radiocarbon dates were in good agreement with each other compared to all the dates previously reported, supporting their reliability. Here we report new hydroxyproline dates for two more human burials from the same site, Sungir 1 and Sungir 4. All five hydroxyproline dates reported are statistically indistinguishable and support an identical age for the group. The results suggest that compound-specific radiocarbon analysis should be considered seriously as the method of choice when precious archaeological remains are to be dated because they give a demonstrably contaminant-free radiocarbon age. The new ages are, together with the previously dated 'Red Lady of Paviland' human in the British Isles, the earliest for Mid Upper Palaeolithic burial behaviour in Eurasia, and point to the precocious appearance of this form of rite in Europe Russia.


Pushing the optical imaging limits of cancer with multi-frequency-band raster-scan optoacoustic mesoscopy (RSOM).
Angiogenesis is a central cancer hallmark, necessary for supporting tumor growth and metastasis. In vivo imaging of angiogenesis is commonly applied, to understand dynamic processes in cancer development and treatment strategies. However, most radiological modalities today assess angiogenesis based on indirect mechanisms, such as the rate of contrast enhancement after contrast agent administration. We studied the performance of raster-scan optoacoustic mesoscopy (RSOM), to directly reveal the vascular network supporting melanoma growth in vivo, at 50 MHz and 100 MHz, through several millimeters of tumor depth. After comparing the performance at each frequency, we recorded, for the first time, high-resolution images of melanin tumor vasculature development in vivo, over a period of several days. Image validation was provided by means of cryo-slice sections of the same tumor after sacrificing the mice. We show how optoacoustic (photoacoustic) mesoscopy reveals a potentially powerful look into tumor angiogenesis, with properties and features that are markedly different than other radiological modalities. This will facilitate a better understanding of tumor's angiogenesis, and the evaluation of treatment strategies.


Progression of Geographic Atrophy in Age-related Macular Degeneration: AREDS2 Report Number 16.
To analyze the prevalence, incidence, and clinical characteristics of eyes with geographic atrophy (GA) in age-related macular degeneration (AMD), including clinical and genetic factors affecting enlargement. Prospective cohort study within a controlled clinical trial. Age-Related Eye Disease Study 2 (AREDS2) participants, aged 50-85 years. Baseline and annual stereoscopic color fundus photographs were evaluated for GA presence and area. Analyses included GA prevalence and incidence rates, Kaplan-Meier rates, mixed-model regression, and multivariable analysis of the square root of GA, area adjusted for covariates, including clinical/imaging characteristics and genotype. (1) Presence or development of GA; (2) change in the square root of GA area over time. At baseline, 517 eyes (6.2%) of 411 participants (9.8%) had pre-existing GA (without neovascular AMD), with the following characteristics: 33% central, 67% noncentral; and the following configurations: 36% small, 26% solid/unifocal, 24% multifocal, 9% horseshoe/ring, and 6% indeterminate. Of the remaining 6530 eyes at risk, 1099 eyes (17.3%) of 883 participants developed incident GA without prior neovascular disease during mean follow-up of 4.4 years. The Kaplan-Meier rate of incident GA was 19% of eyes at 5 years. In eyes with incident GA, 4-year risk of subsequent neovascular AMD was 29%. In eyes with incident noncentral GA, 4-year risk of central involvement was 57%. GA enlargement rate (following square root transformation) was similar in eyes with pre-existing GA (0.29 mm/year; 95% confidence interval 0.27-0.30) and incident GA (0.28 mm/year; 0.27-0.30). In the combined group, GA enlargement was significantly faster with noncentrality, multifocality, intermediate baseline size, and bilateral GA (P < 0.0001 for interaction in each case) but not with AREDS2 treatment assignment (P = 0.33) or smoking status (P = 0.05). Enlargement was significantly faster with ARMS2 risk (P < 0.0001), C3 non-risk (P = 0.0002), and APOE non-risk (P = 0.001) genotypes. Analyses of AREDS2 data on natural history of GA provide representative data on GA evolution and enlargement. GA enlargement, which was influenced by lesion features, was relentless, resulting in rapid central vision loss. The genetic variants associated with faster enlargement were partially distinct from those associated with risk of incident GA. These findings are relevant to further investigations of GA pathogenesis and clinical trial planning.


Nocturnal heart rate variability following supramaximal intermittent exercise.
To assess the effect of supramaximal intermittent exercise on long-term cardiac autonomic activity, inferred from heart rate variability (HRV). Eleven healthy males performed a series of two consecutive intermittent 15-s runs at 95% VIFT (i.e., speed reached at the end of the 30-15 Intermittent Fitness Test) interspersed with 15 s of active recovery at 45% VIFT until exhaustion. Beat-to-beat intervals were recorded during two consecutive nights (habituation night and 1st night) before, 10 min before and immediately after exercise, as well as 12 h (2nd night) and 36 h (3rd night) after supramaximal intermittent exercise. The HRV indices were calculated from the last 5 min of resting and recovery periods, and the first 10 min of the first estimated slow wave sleep period. Immediate post-supramaximal exercise vagal-related HRV indices were significantly lower than immediate pre-supramaximal exercise values (P < .001). Most vagal-related indices were lower during the 2nd night compared with the 1st night (eg, mean RR intervals, P = .03). Compared with the 2nd night, vagal-related HRV indices were significantly higher during the 3rd night. Variables were not different between the 1st and 3rd nights; however, we noted a tendency (adjusted effect size, aES) for an increased normalized high-frequency component (P = .06 and aES = 0.70) and a tendency toward a decreased low-frequency component (P = .06 and aES = 0.74). Results confirm the strong influence of exercise intensity on short- and long-term postexercise heart rate variability recovery and might help explain the high efficiency of supramaximal training for enhancing indices of cardiorespiratory fitness.


Cola soft drinks for evaluating the bioaccessibility of uranium in contaminated mine soils.
There is a rising need for scientifically sound and quantitative as well as simple, rapid, cheap and readily available soil testing procedures. The purpose of this study was to explore selected soft drinks (Coca-Cola Classic®, Diet Coke®, Coke Zero®) as indicators of bioaccessible uranium and other trace elements (As, Ce, Cu, La, Mn, Ni, Pb, Th, Y, Zn) in contaminated soils of the Mary Kathleen uranium mine site, Australia. Data of single extraction tests using Coca-Cola Classic®, Diet Coke® and Coke Zero® demonstrate that extractable arsenic, copper, lanthanum, manganese, nickel, yttrium and zinc concentrations correlate significantly with DTPA- and CaCl₂-extractable metals. Moreover, the correlation between DTPA-extractable uranium and that extracted using Coca-Cola Classic® is close to unity (+0.98), with reduced correlations for Diet Coke® (+0.66) and Coke Zero® (+0.55). Also, Coca-Cola Classic® extracts uranium concentrations near identical to DTPA, whereas distinctly higher uranium fractions were extracted using Diet Coke® and Coke Zero®. Results of this study demonstrate that the use of Coca-Cola Classic® in single extraction tests provided an excellent indication of bioaccessible uranium in the analysed soils and of uranium uptake into leaves and stems of the Sodom apple (Calotropis procera). Moreover, the unconventional reagent is superior in terms of availability, costs, preparation and disposal compared to traditional chemicals. Contaminated site assessments and rehabilitation of uranium mine sites require a solid understanding of the chemical speciation of environmentally significant elements for estimating their translocation in soils and plant uptake. Therefore, Cola soft drinks have potential applications in single extraction tests of uranium contaminated soils and may be used for environmental impact assessments of uranium mine sites, nuclear fuel processing plants and waste storage and disposal facilities.


How certain is 'certain'? Exploring how the English-language media reported the use of calibrated language in the Intergovernmental Panel on Climate Change's Fifth Assessment Report.
This article presents findings from an analysis of English-language media reports following the publication of the fifth Intergovernmental Panel on Climate Change Assessment Report in September 2013. Focusing on the way they reported the Intergovernmental Panel on Climate Change's use of 'calibrated' language, we find that of 1906 articles relating to the issuing of the report only 272 articles (14.27%) convey the use of a deliberate and systematic verbal scale. The Intergovernmental Panel on Climate Change's carefully calibrated language was rarely discussed or explicated, but in some instances scientists, political actors or journalists would attempt to contextualise or elaborate on the reported findings by using analogies to other scientific principles or examples of taking action despite uncertainty. We consider those analogies in terms of their efficacy in communicating (un)certainty.


Identification of transcription-factor genes expressed in the Arabidopsis female gametophyte.
In flowering plants, the female gametophyte is typically a seven-celled structure with four cell types: the egg cell, the central cell, the synergid cells, and the antipodal cells. These cells perform essential functions required for double fertilization and early seed development. Differentiation of these distinct cell types likely involves coordinated changes in gene expression regulated by transcription factors. Therefore, understanding female gametophyte cell differentiation and function will require dissection of the gene regulatory networks operating in each of the cell types. These efforts have been hampered because few transcription factor genes expressed in the female gametophyte have been identified. To identify such genes, we undertook a large-scale differential expression screen followed by promoter-fusion analysis to detect transcription-factor genes transcribed in the Arabidopsis female gametophyte. Using quantitative reverse-transcriptase PCR, we analyzed 1,482 Arabidopsis transcription-factor genes and identified 26 genes exhibiting reduced mRNA levels in determinate infertile 1 mutant ovaries, which lack female gametophytes, relative to ovaries containing female gametophytes. Spatial patterns of gene transcription within the mature female gametophyte were identified for 17 transcription-factor genes using promoter-fusion analysis. Of these, ten genes were predominantly expressed in a single cell type of the female gametophyte including the egg cell, central cell and the antipodal cells whereas the remaining seven genes were expressed in two or more cell types. After fertilization, 12 genes were transcriptionally active in the developing embryo and/or endosperm. We have shown that our quantitative reverse-transcriptase PCR differential-expression screen is sufficiently sensitive to detect transcription-factor genes transcribed in the female gametophyte. Most of the genes identified in this study have not been reported previously as being expressed in the female gametophyte. Therefore, they might represent novel regulators and provide entry points for reverse genetic and molecular approaches to uncover the gene regulatory networks underlying female gametophyte development.


Population-wide cohort study of statin use for the secondary cardiovascular disease prevention in Scotland in 2009-2017.
To estimate the extent of suboptimal statin use for the secondary prevention of atherosclerotic cardiovascular disease (ASCVD) at different stages of the treatment pathway and identify patient groups at risk of suboptimal treatment. National retrospective cohort study using linked National Health Service Scotland administrative data of adults hospitalised for an ASCVD event (n=167 978) from 2009 to 2017. Proportions of patients initiating, adhering to, discontinuing and reinitiating statins were calculated. We separately examined treatment following myocardial infarction (MI), ischaemic stroke and peripheral arterial disease (PAD) hospitalisations. Multivariable logistic regression and Cox proportional hazards models were used to assess the roles of patient characteristics in the likelihood of initiating and discontinuing statins. Of patients hospitalised with ASCVD, only 81% initiated statin therapy, 40% of whom used high-intensity statin. Characteristics associated with lower odds of initiation included female sex (28% less likely than men), age below 50 years or above 70 years (<50 year-olds 26% less likely, and 70-79, 80-89 and ≥90 year-olds 22%, 49% and 77% less likely, respectively, than 60-69 year-olds), living in the most deprived areas and history of mental health-related hospital admission. Following MI, 88% of patients initiated therapy compared with 81% following ischaemic stroke and 75% following PAD events. Of statin-treated individuals, 24% discontinued treatment. Characteristics associated with discontinuation were similar to those related to non-initiation. Statin use remains suboptimal for the secondary ASCVD prevention, particularly in women and older patients, and following ischaemic stroke and PAD hospitalisations. Improving this would offer substantial benefits to population health at low cost.


Lung cancer after treatment for Hodgkin's disease: focus on radiation effects.
Aspects of radiation-induced lung cancer were evaluated in an international study of Hodgkin's disease. The study population consisted of 227 patients with lung cancer and 455 matched controls. Unique features included dose determinations to the specific location in the lung where each cancer developed and quantitative data on both chemotherapy and tobacco use obtained from medical records. The estimated excess relative risk (ERR) per Gy was 0.15 (95% CI: 0.06-0.39), and there was little evidence of departure from linearity even though lung doses for the majority of Hodgkin's disease patients treated with radiotherapy exceeded 30 Gy. The interaction of radiation and chemotherapy that included alkylating agents was almost exactly additive, and a multiplicative relationship could be rejected (P = 0.017). Conversely, the interaction of radiation and smoking was consistent with a multiplicative relationship, but not with an additive relationship (P < 0.001). The ERR/Gy for males was about four times that for females, although the difference was not statistically significant. There was little evidence of modification of the ERR/Gy by time since exposure (after a 5-year minimum latent period), age at exposure, or attained age. Because of the very high radiation doses received by Hodgkin's disease patients and the immunodeficiency inherent to this lymphoma and that associated with chemotherapy, generalizing these findings to other populations receiving considerably lower doses of radiation should be done cautiously.


Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains.
The respiratory syncytial virus (RSV) group A variant with the 72-nucleotide duplication in the G gene, genotype ON1, was first detected in Kilifi in 2012 and has almost completely replaced circulating genotype GA2 strains. This replacement suggests some fitness advantage of ON1 over the GA2 viruses in Kilifi, and might be accompanied by important genomic substitutions in ON1 viruses. Close observation of such a new virus genotype introduction over time provides an opportunity to better understand the transmission and evolutionary dynamics of the pathogen. We have generated and analysed 184 RSV-A whole-genome sequences (WGSs) from Kilifi (Kenya) collected between 2011 and 2016, the first ON1 genomes from Africa and the largest collection globally from a single location. Phylogenetic analysis indicates that RSV-A circulation in this coastal Kenya location is characterized by multiple introductions of viral lineages from diverse origins but with varied success in local transmission. We identified signature amino acid substitutions between ON1 and GA2 viruses' surface proteins (G and F), polymerase (L), and matrix M2-1 proteins, some of which were positively selected, and thereby provide an enhanced picture of RSV-A diversity. Furthermore, five of the eleven RSV open reading frames (ORFs) (G, F, L, N, and P) formed distinct phylogenetic clusters for the two genotypes. This might suggest that coding regions outside of the most frequently studied G ORF also play a role in the adaptation of RSV to host populations, with the alternative possibility that some of the substitutions are neutral and provide no selective advantage. Our analysis provides insight into the epidemiological processes that define RSV spread, highlights the genetic substitutions that characterize emerging strains, and demonstrates the utility of large-scale WGS in molecular epidemiological studies.


Obstructive azoospermia: a microsurgical success story.
Microsurgical techniques used in the treatment of male factor infertility have provided a revolutionary adjunct to the advent of intracytoplasmic sperm injection used in conjunction with in vitro fertilization. Previously infertile couples may now parent their own biological children and, in some cases, may even conceive naturally owing to technical advances within the past decade. This article outlines the modern methods currently employed to address vasal and epididymal obstruction with special emphasis on the importance of microsurgical techniques. The multiple reconstructive and sperm aspiration techniques at our disposal for treatment of vasal and epididymal obstruction as well as the management of ejaculatory duct obstruction are reviewed. The various procedures discussed allow reproductive urologists to maximize male fertility potential in the era of assisted reproductive technologies.


Defective transforming growth factor beta signaling pathway in head and neck squamous cell carcinoma as evidenced by the lack of expression of activated Smad2.
Transforming growth factor beta (TGF-beta) regulates cell growth and differentiation, in normal squamous epithelium, via specific TGF-beta receptors and intracellular signaling molecules (Smads). We have previously observed that TGF-beta type II receptor (TbetaR-II) expression decreases in squamous cell carcinomas as tumors become less differentiated and more biologically aggressive. However, a small fraction of tumors remain TbetaR-II positive. In this article, we examine the integrity of the other members of the TGF-beta-signaling machinery, the Smad proteins. Thirteen archived head and neck squamous cell carcinomas were selected from the files of the Pathology Department of the H. Lee Moffitt Cancer Center. Protein immunoexpression was quantitated by image analysis in the context of histopathological parameters. Mutation analysis of the MADR2/Smad2 gene was also performed. In both TbetaR-II-positive and TbetaR-II-negative tumors, expression of the non-TGF-beta-specific Smads (4, 6, and 7) was variable, whereas expression of the pathway-specific Smad2 was lost in 38% of the tumors. Expression of the activated, phosphorylated form of this molecule, Smad2-P, was lost in approximately 70% of the tumors. No abnormal mRNA expression and no mutations in the MADR2/Smad2 gene were observed. These results suggest that multiple defects in TGF-beta signaling, both at the receptor and postreceptor level, may play a role in the oncogenesis of head and neck squamous cell carcinoma.


Prehistoric cooking versus accurate palaeotemperature records in shell midden constituents.
The reconstruction of pre-depositional cooking treatments used by prehistoric coastal populations for processing aquatic faunal resources is often difficult in archaeological shell midden assemblages. Besides limiting our knowledge of various social, cultural, economic and technological aspects of shell midden formation, unknown pre-depositional cooking techniques can also introduce large errors in palaeoclimate reconstructions as they can considerably alter the geochemical proxy signatures in calcareous skeletal structures such as bivalve shells or fish otoliths. Based on experimental and archaeological data, we show that carbonate clumped-isotope thermometry can be used to detect and reconstruct prehistoric processing methods in skeletal aragonite from archaeological shell midden assemblages. Given the temperature-dependent re-equilibration of clumped isotopes in aragonitic carbonates, this allows specific processing, cooking or trash dispersal strategies such as boiling, roasting, or burning to be differentiated. Besides permitting the detailed reconstruction of cultural or technological aspects of shell midden formation, this also allows erroneous palaeoclimate reconstructions to be avoided as all aragonitic shells subjected to pre-historic cooking methods show a clear alteration of their initial oxygen isotopic composition.


Sequence and polymorphism analysis of the murine gene encoding histidyl-tRNA synthetase.
The murine histidyl-tRNA synthetase-encoding gene (MMHRS) coding region has been cloned and sequenced. The 1527-bp transcript shows a strikingly similar structural organization to that of its human counterpart, particularly within the three class II aminoacyl-tRNA synthetase structural motifs and the two histidyl-tRNA synthetase signature regions. It is predicted, as in humans, to have a coiled-coil alpha-helical structure that is characteristic of many autoantigens. MMHRS shows some degree of polymorphism at both the DNA and amino-acid levels, although its sequence is well conserved amongst the commonly used laboratory mouse strains.


Macrophage killing of Leishmania amazonensis amastigotes requires both nitric oxide and superoxide.
The requirements for effective and efficient intracellular killing of Leishmania amazonensis by activated macrophages are unknown. Despite resistance to the arginase inhibitor LOHA by intracellular L. amazonensis amastigotes, enhanced replication did not account for the relative resistance of this parasite to macrophage activation. Herein we report that the presence of both superoxide and nitric oxide is necessary for efficient killing of L. amazonensis amastigotes within LPS/IFN-gamma-activated bone marrow-derived macrophages generated from C3H mice. Addition of an extracellular signal-regulated kinase (ERK) inhibitor to L. amazonensis-infected macrophages increased the ability of these activated macrophages to kill L. amazonensis amastigotes. This enhanced macrophage killing through addition of ERK inhibitor was abrogated by inhibition of superoxide or iNOS, whereas inhibiting superoxide had no effect on the killing of L. major. These results suggest that ERK activation may modulate effective macrophage killing, leading to the ability of L. amazonensis to resist elimination within activated macrophages.


Disentangling resting-state BOLD variability and PCC functional connectivity in 22q11.2 deletion syndrome.
Although often ignored in fMRI studies, moment-to-moment variability of blood oxygenation level dependent (BOLD) signals reveals important information about brain function. Indeed, higher brain signal variability has been associated with better cognitive performance in young adults compared to children and elderly adults. Functional connectivity, a very common approach in resting-state fMRI analysis, is scaled for variance. Thus, alterations might be confounded or driven by BOLD signal variance alterations. Chromosome 22q11.2 deletion syndrome (22q11.2DS) is a neurodevelopmental disorder that is associated with a vast cognitive and clinical phenotype. To date, several resting-state fMRI studies reported altered functional connectivity in 22q11.2DS, however BOLD signal variance has not yet been analyzed. Here, we employed PLS correlation analysis to reveal multivariate patterns of diagnosis-related alterations and age-relationship throughout the cortex of 50 patients between 9 and 25 years old and 50 healthy controls in the same age range. To address how functional connectivity in the default mode network is influenced by BOLD signal fluctuations, we conducted the same analysis on seed-to-voxel connectivity of the posterior cingulate cortex (PCC) and compared resulting brain patterns. BOLD signal variance was lower mainly in regions of the default mode network and in the dorsolateral prefrontal cortex, but higher in large parts of the temporal lobes. In those regions, BOLD signal variance was correlated with age in healthy controls, but not in patients, suggesting deviant developmental trajectories from child- to adulthood. Positive connectivity of the PCC within the default mode network as well as negative connectivity towards the frontoparietal network were weaker in patients with 22q11.2DS. We furthermore showed that lower functional connectivity of the PCC was not driven by higher BOLD signal variability. Our results confirm the strong implication of BOLD variance in aging and give an initial insight in its relationship with functional connectivity in the DMN.


Functionally cloned pdrM from Streptococcus pneumoniae encodes a Na(+) coupled multidrug efflux pump.
Multidrug efflux pumps play an important role as a self-defense system in bacteria. Bacterial multidrug efflux pumps are classified into five families based on structure and coupling energy: resistance-nodulation-cell division (RND), small multidrug resistance (SMR), major facilitator (MF), ATP binding cassette (ABC), and multidrug and toxic compounds extrusion (MATE). We cloned a gene encoding a MATE-type multidrug efflux pump from Streptococcus pneumoniae R6, and designated it pdrM. PdrM showed sequence similarity with NorM from Vibrio parahaemolyticus, YdhE from Escherichia coli, and other bacterial MATE-type multidrug efflux pumps. Heterologous expression of PdrM let to elevated resistance to several antibacterial agents, norfloxacin, acriflavine, and 4',6-diamidino-2-phenylindole (DAPI) in E. coli KAM32 cells. PdrM effluxes acriflavine and DAPI in a Na(+)- or Li(+)-dependent manner. Moreover, Na(+) efflux via PdrM was observed when acriflavine was added to Na(+)-loaded cells expressing pdrM. Therefore, we conclude that PdrM is a Na(+)/drug antiporter in S. pneumoniae. In addition to pdrM, we found another two genes, spr1756 and spr1877,that met the criteria of MATE-type by searching the S. pneumoniae genome database. However, cloned spr1756 and spr1877 did not elevate the MIC of any of the investigated drugs. mRNA expression of spr1756, spr1877, and pdrM was detected in S. pneumoniae R6 under laboratory growth conditions. Therefore, spr1756 and spr1877 are supposed to play physiological roles in this growth condition, but they may be unrelated to drug resistance.


A stepwise framework for the normalization of array CGH data.
In two-channel competitive genomic hybridization microarray experiments, the ratio of the two fluorescent signal intensities at each spot on the microarray is commonly used to infer the relative amounts of the test and reference sample DNA levels. This ratio may be influenced by systematic measurement effects from non-biological sources that can introduce biases in the estimated ratios. These biases should be removed before drawing conclusions about the relative levels of DNA. The performance of existing gene expression microarray normalization strategies has not been evaluated for removing systematic biases encountered in array-based comparative genomic hybridization (CGH), which aims to detect single copy gains and losses typically in samples with heterogeneous cell populations resulting in only slight shifts in signal ratios. The purpose of this work is to establish a framework for correcting the systematic sources of variation in high density CGH array images, while maintaining the true biological variations. After an investigation of the systematic variations in the data from two array CGH platforms, SMRT (Sub Mega base Resolution Tiling) BAC arrays and cDNA arrays of Pollack et al., we have developed a stepwise normalization framework integrating novel and existing normalization methods in order to reduce intensity, spatial, plate and background biases. We used stringent measures to quantify the performance of this stepwise normalization using data derived from 5 sets of experiments representing self-self hybridizations, replicated experiments, detection of single copy changes, array CGH experiments which mimic cell population heterogeneity, and array CGH experiments simulating different levels of gene amplifications and deletions. Our results demonstrate that the three-step normalization procedure provides significant improvement in the sensitivity of detection of single copy changes compared to conventional single step normalization approaches in both SMRT BAC array and cDNA array platforms. The proposed stepwise normalization framework preserves the minute copy number changes while removing the observed systematic biases.


Impaired P2X signalling pathways in renal microvascular myocytes in genetic hypertension.
P2X receptors (P2XRs) mediate sympathetic control and autoregulation of renal circulation triggering preglomerular vasoconstriction, which protects glomeruli from elevated pressures. Although previous studies established a casual link between glomerular susceptibility to hypertensive injury and decreased preglomerular vascular reactivity to P2XR activation, the mechanisms of attenuation of the P2XR signalling in hypertension remained unknown. We aimed to analyse molecular mechanisms of the impairment of P2XR signalling in renal vascular smooth muscle cells (RVSMCs) in genetic hypertension. We compared the expression of pertinent genes and P2XR-linked Ca(2+) entry and Ca(2+) release mechanisms in RVSMCs of spontaneously hypertensive rats (SHRs) and their normotensive controls, Wistar Kyoto (WKY) rats. We found that, in SHR RVSMCs, P2XR-linked Ca(2+) entry and Ca(2+) release from the sarcoplasmic reticulum (SR) are both significantly reduced. The former is due to down-regulation of the P2X1 subunit. The latter is caused by a decrease of the SR Ca(2+) load. The SR Ca(2+) load reduction is caused by attenuated Ca(2+) uptake via down-regulated sarco-/endoplasmic reticulum Ca(2+)-ATPase 2b and elevated Ca(2+) leak from the SR via ryanodine receptors (RyRs) and inositol 1,4,5-trisphosphate receptors. Spontaneous activity of these Ca(2+)-release channels is augmented due to up-regulation of RyR type 2 and elevated IP3 production by up-regulated phospholipase C-β1. Our study unravels the cellular and molecular mechanisms of attenuation of P2XR-mediated preglomerular vasoconstriction that elevates glomerular susceptibility to harmful hypertensive pressures. This provides an important impetus towards understanding of the pathology of hypertensive renal injury.


Factors associated with self-reported risk-taking behaviour on ski slopes.
In recent years, discussions have arisen about the potential influence of wearing a ski helmet on an increasing level of risk taking and higher speeds on ski slopes. To evaluate factors associated with self-reported risk-taking behaviour in recreational skiers and snowboarders. Speeds of skiers and snowboarders were measured with a radar speed gun and sex, age, nationality, height, weight and helmet use, used type of gear, self-estimated skill level and self-estimated fitness level were recorded. In addition, participants were asked if they considered themselves as cautious or risk-taking skier or snowboarder. In total, 453 skiers (39.6 (14.8) years) and 74 snowboarders (26.4 (9.6) years) have been interviewed. A stepwise forward logistic regression model revealed five independent factors for a risk-taking behaviour on slopes. Adjusted OR and their 95% CI showed that risk takers were <40 years (OR 2.4, 95% CI 1.51 to 3.80), had a higher skill level (OR 2.1, 95% CI 1.25 to 3.50), were more likely males (OR 2.0, 95% CI 1.22 to 3.26), had a lower body mass index (22.8 vs 24.2) and skied with higher speeds (on average 53 vs 45 km/h) compared to cautious skiers. Risk-taking behaviour on ski slopes is associated with younger age, higher skiing ability, male sex, lower body mass index and on average higher speeds. Helmet use is not associated with riskier behaviour on slopes. In addition, helmet use has to be recommended because helmet use reduces the risk of head injuries among skiers and snowboarders.


Immunopathology of Toxocara canis and Ascaris suum infections of the eye: the role of the eosinophil.
Intravitreal infection of guinea pigs with second-stage larvae of Toxocara canis and second- and fourth-stage larvae of Ascaris suum induced intraocular IgE antibodies and a dense eosinophil infiltration in the anterior chamber and throughout the uveal tract. The eosinophil infiltrate began within 1 day after infection and persisted for as long as 51 days. By day 12 after intravitreal infection, the injected ascarid larvae were surrounded by granulomas which consisted almost entirely of eosinophils. Firm adherence of eosinophils to the parasite cuticle, morphologic alterations and degranulation of eosinophils with the deposition of free eosinophil granules on the parasite surfaces, and ingestion of eosinophils and eosinophil granules by the parasite larvae also were observed. Intravitreal injectionof a soluble antigen derived from third-stage A. suum molting to the fourth-stage in defined media in vitro also induced intraocular IgE antibody and a diffuse ocular eosinophil infiltrate. Dense eosinophil infiltration of the choroid, not immediately adjacent to a parasite larva, was accompanied by destruction of the lverlying outer retina, with cystic changes in the retina and between the retina and the choroid. Few eosinophils were observed within the retina, and the retinal destruction may be the result of direct toxic action of constituents of the choroidal eosinophils. Evidence which indicates that the eosinophil is the principal effector cell in immunity to helminth infections and is cytotoxic for the parasites, possible mechanisms for the induction of the ocular eosinophil infiltrates, and evidence for autotoxicity by eosinophils are briefly reviewed, and the potential roles of the eosinophil in the ocular response to helminth parasites are discussed.


GDNF is a chemoattractant for enteric neural cells.
In situ hybridization revealed that GDNF mRNA in the mid- and hindgut mesenchyme of embryonic mice was minimal at E10.5 but was rapidly elevated at all gut regions after E11, but with a slight delay (0.5 days) in the hindgut. GDNF mRNA expression was minimal in the mesentery and in the pharyngeal and pelvic mesenchyme adjacent to the gut. To examine the effect of GDNF on enteric neural crest-derived cells, segments of E11.5 mouse hindgut containing crest-derived cells only at the rostral ends were attached to filter paper supports and grown in catenary organ culture. With GDNF (100 ng/ml) in the culture medium, threefold fewer neurons developed in the gut explants and fivefold more neurons were present on the filter paper outside the gut explants, compared to controls. Thus, in controls, crest-derived cells colonized the entire explant and differentiated into neurons, whereas in the presence of exogenous GDNF, most crest-derived cells migrated out of the gut explant. This is consistent with GDNF acting as a chemoattractant. To test this idea, explants of esophagus, midgut, superior cervical ganglia, paravertebral sympathetic chain ganglia, or dorsal root ganglia from E11.5-E12.5 mice were grown on collagen gels with a GDNF-impregnated agarose bead on one side and a control bead on the opposite side. Migrating neural cells and neurites from the esophagus and midgut accumulated around the GDNF-impregnated beads, but neural cells in other tissues showed little or no chemotactic response to GDNF, although all showed GDNF-receptor (Ret and GFRalpha1) immunoreactivity. We conclude that GDNF may promote the migration of crest cells throughout the gastrointestinal tract, prevent them from straying out of the gut (into the mesentery and pharyngeal and pelvic tissues), and promote directed axon outgrowth.