Cytokinesis, in which newly formed daughter cells separate, is the culmination of the cell cycle. It is necessary for normal growth and development, and it is also a sine qua non in the pathogenesis of cancers—cells that can't divide can't form tumors, can't metastasize, and can't kill. Therefore, understanding the full range of proteins involved in cytokinesis has both deep theoretical and immediate practical applications. In this issue, Ulrike Eggert and colleagues report results from two complementary screening approaches to identify those proteins and to discover molecules that inhibit them.Drosophila cells, the first screen used almost 20,000 double-stranded RNAs, representing virtually the entire Drosophila genome. A double-stranded RNA pairs with, and causes the destruction of, a matching messenger RNA, thus preventing the encoded protein from being formed, a process called RNA interference (RNAi). The authors identified 214 proteins whose absence prevented cytokinesis. While some of these, including actin and Myosin, were already known to be essential for the process, others were not. The latter included a new discovery, CG4454 , which was found to be one of the handful of proteins deemed most critical to cytokinesis.A cell cannot divide if it lacks a protein vital for cytokinesis or if that protein is inhibited. When that occurs, the cell retains both nuclei, and can be quickly identified by an automated process. Working with Drosophila cells, but this time used over 50,000 “small molecules,” a catchall term for molecules small enough to pass easily into cells. The vast majority of drugs currently in clinical use are small molecules. This screen revealed 50 cytokinesis inhibitors, of which 25, dubbed binucleines, were selected for further characterization. Not surprisingly, several inhibited actin, whose role in cytokinesis is key in contraction of the cytokinesis furrow.The second screen also treated For the purposes of this study, however, binucleines affecting other proteins were even more interesting. By comparing the appearances of binucleate cells from the small-molecule screen with those from the RNAi screen, Eggert et al. identified one molecule and three proteins that caused a similar phenotype, suggesting that the three proteins acted within a single pathway, which the molecule could disrupt. One of the three proteins was CG4454/Borr, and the researchers' results indicated it interacts with Aurora B, an essential but still poorly understood protein that is needed for proper division of the chromosomes. The identified binucleine will be a valuable reagent for exploring the details of the Aurora B pathway.Drosophila, the insights they provide into the cell cycle are likely to be applicable to humans as well. Equally importantly, they provide the proof of principle for a new drug discovery method. A major bottleneck in drug development is target identification—determining which of the cell's thousands of proteins is the right one to inhibit with a drug. The unique aspect of this study is the parallel use of the two approaches—small molecules and RNAi—to provide a “stereoscopic” view of cytokinesis and its inhibition. Working together, they provide a set of proteins and a matched set of inhibitors, the target and the bullet at the same time.While these results are from


The aim of this body of research is to determine whether injuries in the home are more common in particular types of housing. Previous home injuries research has tended to focus on behaviours or the provision of safety equipment to families with young children. There has been little consideration of the physical environment. This study reports methodological developments in database linkage and analysis to improve researchers abilities to utilise large administrative and clinical databases to carry out health and health services research.The study involved linking a database of home injuries obtained from an emergency department surveillance system with an external survey of all homes in an area and population denominators for home types derived from a health service administrative database. Analysis of injury incidence by housing type was adjusted for potential biases due to deprivation and distance to hospital. For non-injured individuals data confidentiality considerations required the deprivation and distance measures be imputed. The process of randomly imputing these variables and the testing of the validity of this approach is detailed.There were 14,081 first injuries in 112,248 residents living in 54,081 homes over a two-year period. The imputation method worked well with imputed and observed measures in the injured group being very similar. Re-randomisation and a repeated analysis gave identical results to the first analysis. One particular housing type had a substantially elevated odds ratio for injury occurrence, OR = 2.07 (95% CI: 1.87 to 2.30).The method of data linkage, imputation and statistical analysis used provides a basis for improved analysis of database linkage studies. Home injuries are frequent and result in greater mortality and morbidity than road traffic injuries. It is eThe present study was designed to utilise three such datasets relating to all residential properties in a defined geographical area in the United Kingdom, the resident population, and their attendances at local hospital emergency departments (EDs). These datasets could not be linked comprehensively at individual level on account of constraints on identifiability of individuals. This article describes the novel challenges that result, and the methodology used to obviate them.This study was carried out as part of the wider Housing and Neighbourhood and Health (HANAH) project. This isAll properties in the study area were viewed externally. Domestic properties were classified into categories based on floor area (four groups), five period groups, and five build types, viz. detached, semi-detached, flat conversions, purpose-built flats, and terraced housing. Ninety-four of the 100 combinations of the three housing type variables were found in the study area. Analysis was carried out at individual property level: analysis at postcode or zip code level was not possible because very few postcodes (13%) comprised a single property type. Postcodes contained an average of 14 properties.Data on injuries treated at EDs were obtained for the period 1999 – 2000 from the All Wales Injury Surveillance System (AWISS) which routinely obtains individual level data from EDs surrounding the study area and is described in detail elsewhere. BrieflyTo obtain denominator data for each property type we used the National Health Service Administrative Register (NHSAR), a list of all people registered with the free-to-use primary care health service in Wales. Data on this system are highly confidential and denominator population profiles were obtained by providing a list of all properties in the ninety four different groups to the NHSAR staff who then matched these with their system and obtained the number of people in each of the property types, subdivided by age and sex. This system has previously been used to obtain small area population data.In analysing data on injury attendance at hospital EDs it is important to take into account the potential confounders of deprivation and access, which are known to be strongly related to injury occurrence and ED attendance respectively. For eacDuring 1999 and 2000, 14,171 out of 112,248 residents made one or more emergency department visits for a home injury. We sought to combine three files comprising individual-level injuries data from an emergency department surveillance system; an external assessment of the built form in all 54,801 homes in the area; and denominator populations for each of ninety-four property types delivered from a health service registration system. Application of logistic regression to model injury risk on built form, property size and age, subject age, sex, deprivation and distance from emergency department jointly necessitates construction of a single linked data file. The objective was to construct an appropriately linked database and hence determine whether injuries occur more commonly in different types of home.The study population of 112,248 individuals made 16,358 ED attendances for home injuries during the study period. The vast majority  of these attendance records included adequate data on age, gender, proximity and Townsend score. These 16,277 attendances involved 14,171 residents of the study area. Thus the average number of visits during the study period among those who ever visited the ED was 1.15, in other words 15% of the visits were repeat visits. The main analyses were constructed to compare the 14,171 first injury records identified as the subject's first attendance at ED for a home injury during the study period with those of the remaining 98,077 subjects. This has the effect of identifying all subjects who had one or more ED attendance for home injury during the study period.The other datasets to be linked were the population distribution by housing group, age and sex  and a file listing 54,913 properties, of which we restrict attention to the 54,801 with complete data. Table Following discussion of preliminary results it was decided to use actual deprivation and proximity scores for the injured, and to impute values randomly according to property type for the uninjured. This is appropriate because risk scores for the remaining variables, age and sex taken together as a forty two category categorical variable, were uncorrelated with risk scores for all other variables (see later), hence imputing according to property type alone and disregarding age and sex is a reasonable strategy.The process of randomly imputing property records, and hence Townsend and proximity scores, to the 112,248 population according to housing type is not trivial. Using ordinary stratified sampling does not work, simply because the number of residents is larger than the number of properties. The overall occupancy ratio was 112,248 residents in 54,801 properties, i.e. 2.05 individuals per property, but this figure varied widely between the 94 property types. For example, for property type 1 there were just under 2 people per property, 114 properties and 226 population. We then choose randomly 114 of the 226 population to match one-to-one to the 114 properties in a random order, leaving the remaining 112 to be matched to a random sample of the 114 properties also in a random order. This simply achieves a maximal degree of representativity with an appropriate degree of randomness. A multi-stage randomisation and linkage process (further details available from the authors) successfully linked the vast majority  of first attendances with the merged population-properties file. This has the effect of producing a merged data file in which the deprivation and distance scores randomly imputed to the uninjured both incorporate the correct means to produce an appropriate degree of adjustment for confounding, and also the correct amount of variation to produce appropriate logistic regression coefficients to perform the adjustment.The resulting linked file, comprising reconstructed data for all 112,248 residents, containing elements originating in population, properties and events files, has complete data for demographics, property type and randomly imputed Townsend and proximity measures. Among the 112,248 subjects, 14,081 are identified as having had one or more attendances for injuries following home accidents. Actual Townsend and proximity measures and the code for injury type 1 are available for each of the 14,081 injured individuals.The actual and imputed Townsend and proximity values were summarised for the injured and uninjured and compared. This was done by t-test, paired or unpaired as appropriate, rather than by non-parametric methods which were associated with a serious loss of power due to the gross discreteness of the small area based, randomly imputed Townsend score. Associations between random and actual Townsend and proximity scores were characterised by Spearman rank correlations. Examination of these results, together with the low correlations of a risk score for age and sex with those for property type variables, Townsend and proximity, suggested it was appropriate to include in the logistic regression model composite Townsend and proximity scores, defined as the actual value in the injured and the randomly imputed value in the uninjured. Property size, age and build type were entered as categorical variables. Preliminary analyses indicated that Townsend score should be included as a continuous variable, but distance from hospital discretised into five categories. On account of the known marked sex-age interaction, sex and subject's age were entered together as a 42-group categorical variable, age being discretised into groups under 1, 1–4, 5–9, ..., 90–94 and 95 and over.The main analysis proceeded as above, using the 14,081 who were ever injured during the study period as the group with the outcome of interest. Both univariate analyses for each explanatory variable in turn and a multivariate analysis were produced.Also, the main analysis was repeated after re-running the randomisation parts of the linkage process. This step is more radical than might appear. In particular, due to the small amount of missing data, the randomised matching program does not pick up exactly the same set of 14,081 events records on both occasions. Essentially, the process draws 14,081 out of 14,114 potentially matchable events.Table Table The effect of the random imputation process was explored in the main logistic regression model. In the final model the effect of age and sex jointly was dominant, followed by build type, then distance, property age, Townsend score  and floor area (p = 0.007). Table The results of the main multiple logistic regression model in table The main methodological finding of the study is that the random imputation process developed here is a reasonable one. This approach enabled us to base analyses on a very large dataset notwithstanding confidentiality issues precluding comprehensive linkage directly at individual level. It is feasible to incorporate randomisation into the linkage process, even when the target group is larger than the source. The reasonableness of the imputation process can be judged by comparison of the actual and imputed variables for the injured population. For the Townsend score the actual and imputed scores are essentially identical in distribution, thus showing that the methodology does not produce a biased result. For the distance variable the mean imputed value is 7.4% higher than the actual distance. Whilst this difference is statistically significant the magnitude of the effect on residual confounding cannot be large, given the odds ratios for attendance rates by distance in Table th (most distant) one. These figures are similar to those obtained in the univariate logistic regression based on the composite distance measure, and suggest that the latter regression coefficients, and hence also those in the multiple regression, may be attenuated by around 10% only.The low correlation between randomly imputed and actual values, for distance from hospital and Townsend score, could result in attenuated regression coefficients and hence underadjustment for the confounding effect of these variables. For distance, which is by far the more influential of the two variables, a logistic regression in which the entire population of 112,248 is assumed to have the same distribution into the 5 distance groups as applies to the 54,801 properties gives odds ratios 1.469, 1.318, 1.445, 1.200 for the first 4 distance categories relative to the 5Of primary importance to the validity of the methodology set out here, the results obtained after a second randomisation were almost identical. The unadjusted analyses for age-sex and housing type were unaltered, as these variables do not come from the random imputation. The analyses for deprivation and proximity and the results of multivariate analyses for build type and other variables were altered, but only to a very minor degree. These results provide considerable reassurance that the random element that was necessary in order to achieve the linkage process introduced very little additional uncertainty into the final analyses.It appears that injured people tend to live in property types more associated with deprivation than the uninjured. Their actual Townsend scores are in line with what we would expect from their property types. On the composite data, i.e. when we replace random by actual Townsend scores for the injured only, there is a substantial difference in mean Townsend score, 0.85 v. 0.70, and all the 0.15 points difference is attributable to a real effect of deprivation on risk.(6). On the composite data (with means 7.73 v. 8.37 km), nearly the whole of the difference (0.57 out of 0.64 km) is attributable to this self-selection effect.Conversely, the injured and uninjured tend to live in property types equally distanced from hospital. The actual distance is less for the injured than the randomly imputed distance, which is in line with the known tendency for hospital attendance for less serious types of injury to be related to proximityThis process is an important methodological development to increase the power of linkage studies when all individual data elements are not available for all individuals. As a result the analysis was based on 112,248 subjects and not on ninety-four groups. Thus, the power to detect important differences is substantially enhanced.Further work is continuing in the relationship between specific features of built type and injury occurrence, using the methodology described in this paper.The author(s) declare that they have no competing interests.All authors contributed to the design of the study. RGN devised the conceptual design of the data imputation and carried out the statistical analysis. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


In the first part of the study healthy controls (n = 18) were compared with euthymic Bipolar Disorder patients (Type I and Type II) who were taking either lithium (n = 14) or sodium valproate (n = 11), and temporal lobe choline/creatine (Cho/Cr) ratios were determined. In the second part we examined a separate group of euthymic Bipolar Disorder Type I patients taking sodium valproate (n = 9) and compared these to controls (n = 11). Here we measured the absolute concentrations of choline in both temporal and frontal lobes.The present study utilized The results from the first part of the study showed that bipolar patients chronically treated with both lithium and sodium valproate had significantly reduced temporal lobe Cho/Cr ratios. In contrast, in the second part of the study, there were no effects of sodium valproate on either absolute choline concentrations or on Cho/Cr ratios in either temporal or frontal lobes.These findings suggest that measuring Cho/Cr ratios may not accurately reflect brain choline concentrations. In addition, the results do not support previous suggestions that either lithium or valproate increases choline concentrations in bipolar patients. Bipolar disorder is a chronic severe mental illness affecting approximately 1% of the adult population. The most widely used mood stabilizer for this condition is lithium , and humin vivo utilizes proton magnetic resonance spectroscopy (1H-MRS). Previous studies of bipolar patients utilizing this methodology have had mixed findings. Overall, while some studies have suggested there may be increased choline concentrations in specific situations [The most appropriate method to measure brain choline concentrations tuations -18, moretuations -27, and tuations . In bothtuations ,30. Nonetuations ,32, althin-vitro study suggested that valproate may inhibit choline acetyltransferase activity [Sodium valproate is also widely used as a mood stabilizer, both alone and in combination with lithium . To dateactivity . In one activity , and incactivity . Nonethe1H-MRS spectra is composed primarily of phosphocholine and glycerophosphocholine, along with free choline, acetylcholine, and cytidine diphosphate choline. Also, we have shown in animal studies that both lithium and valproate can both decrease creatine concentrations [Most of the previous studies have examined Cho/Cr ratios. However, it should be noted that the "choline" resonance peak seen in trations . TherefoIn the first part of the study patients taking either lithium or valproate were examined using the Cho/Cr ratio method, and both Bipolar Type I and Bipolar Type II patients were included who could also be taking other medications. In the second part of this study only Bipolar Type I patients on valproate monotherapy were included, and quantification of choline concentrations was made. Some of the data from the first part of this study has been reported previously .All subjects gave full informed consent, and both studies were approved by the ethics committee at the University of Alberta. Healthy controls were examined using a detailed, but non-standardized, psychiatric interview. They were excluded if there was any personal history, or immediate family history, of psychiatric disorder. For patients, diagnoses were made using DSM-IV criteria for Bipolar Disorder Type I or Type II following detailed psychiatric interview, with additional information being available in almost all cases from long-term psychiatric clinic records. They also had to be taking a dose of either lithium or valproate which maintained their blood levels within the ranges of 0.4–1.2 mmol/l for lithium and 200–700 μmol/l for sodium valproate. Serum lithium and valproate levels were also measured on the day of MRS scanning. Other medications taken by the patient were noted. In the second part of the study the same criteria were used, except that only patients meeting diagnostic criteria for Bipolar Disorder Type I were included, and they had to be on sodium valproate monotherapy. This was done to examine Bipolar Type I patients in more detail, and to remove a possible confounding variable. All patients had to be euthymic for the previous 3 months, as determined by interviews with the patient, and additional interviews with their relatives and bipolar clinic records when available. MRS scans were carried out within 24 hours of this interview.1H measurements.For both studies magnetic resonance experiments were performed using a Magnex 3 T scanner with 80 cm bore equipped with actively shielded gradient, and spectrometer control was provided by an Surrey Medical Imaging System (SMIS) console. The subjects head was immobilized with a restraint system. Signal transmission and reception were achieved using a quadrature birdcage resonator for 1H MR spectra were acquired using the PRESS localization method [1H MRS spectra in which all the major metabolite peaks can be seen.Initially, MRI data were acquired using gradient echo imaging sequences to produce multiple slice images along both coronal and transverse planes. This allowed registration of a 2 × 2 × 3 cm volume-of-interest (VOI) to be selected in the temporal lobe. n method ,40, with3 voxels placed in the cortex of the left frontal lobe, the cortex of the left temporal lobe, and in the external standard solution. The average coordinates [1 and T2 values of the metabolites in the brain and external standard solution, MRS data were collected with different TE values at a constant TR and different TR values at a constant TE both for the healthy volunteers and the patients and also from external standard solution [3), it was not possible to exactly match the voxel size or location between the two studies.To accurately quantify the brain concentration of creatine we used a 125 ml glass sphere containing a solution of 4 mmol creatine as an external standard. The PRESS sequence was used to acquire proton MRS data with TE1 = 25 msec, TE2 = 25 msec, TR = 3000 msec, and 128 scan averages. The MRS data were acquired from three 2 × 2 × 2 cmrdinates ,42 of thb, in millimoles per kg of wet brain, the CSF volume fraction, fcsf, in the spectroscopic voxels must be corrected. Thus, brain metabolite concentrations were calculated as described in the following equation:For quantitative measurement of brain metabolite concentrations we used previously described methodology ,43. In tvoxel is the volume of a 8 cm3 spectroscopic voxel [b represents the number of metabolite molecules per unit voxel in brain.where Vic voxel , and Nb post-hoc Tukey tests. The MRS data was analyzed using Student's unpaired t-test using a significance level of p < 0.05 comparing diagnostic groups (patients vs controls) in each brain region .Means ± SEM were used in the statistical analysis. Sex differences were analyzed using chi-squared, and age differences with ANOVA with A total of 18 healthy controls, 14 bipolar patients taking lithium, and 11 bipolar patients taking valproate completed this study. Of the 14 bipolar patients taking lithium, 7 were Type I and 7 were Type II. In the valproate group, 7 were Type I and 4 were Type II. These groups were studied both separately and together, but as there were no statistically significant differences between the Type I and Type II patients, the results for both types are presented together. Of the 14 bipolar patients taking lithium 12 patients were taking other psychotropic medications: these were benzodiazepines (7 patients), antidepressants (5 patients), and antipsychotics (2 patients). Of the 11 patients taking sodium valproate 10 patients were taking other psychotropic medications: these were benzodiazepines (5 patients), antidepressants (5 patients), and antipsychotics (4 patients).post hoc, p < 0.05).The mean age for the lithium group was 40.43 ± 2.96 years, for the valproate group 35.47 ± 2.27 years, and for the control group was 31.35 ± 2.89 years. These differences were statistically significant , which was attributable to the lithium group being significantly older than the control group , 5 females and 9 males in the lithium group , and 6 females and 5 males in the valproate group .There were no gender differences within the groups: 10 females and 8 males in the control group  as a primary correlate of Choline concentrations. This result has been reported briefly in a previous publication . The meaA total of 11 healthy controls and 9 Bipolar Type I patients taking valproate as monotherapy were entered into this study. The mean age for the control group was 37.3 ± 2.2 years, and for the valproate patients 42.4 ± 3.0 years. These differences were not statistically significant .2 = 0.474, df 1, p > 0.05). The mean serum valproate levels were 472 ± 36 μmol/l, and the range was 284–728 μmol/l.There were no gender differences within the groups: 7 females and 2 males in the valproate group and 5 females and 6 males in the control group  or temporal  lobes  or temporal  lobes . ThirdlWe conclude that, taking all current evidence together including the findings from the present study, it is unlikely that either lithium or valproate significantly alter brain choline concentrations. However, given the large differences in patients populations, medications received, and MRS methodologies it is difficult to directly compare all these studies. In addition, the methodology used to measure choline concentrations can significantly alter the results. Future MRS studies in bipolar patients should, therefore, examine metabolite concentrations rather than a ratio of choline compared to other metabolites.None declared.


The key elements in tuberculosis (TB) control are to cure the individual patient, interrupt transmission of TB to others and prevent the tubercle bacilli from becoming drug resistant. Incomplete treatment may result in excretion of bacteria that may also acquire drug resistance and cause increased morbidity and mortality. Treatment outcome results serves as a tool to control the quality of TB treatment provided by the health care system. The aims of this study were to evaluate the treatment outcome for new cases of culture positive pulmonary TB registered in Norway during the period 1996–2002 and to identify factors associated with non-successful treatment.This was a register-based cohort study. Treatment outcome was assessed according to sex, birthplace, age group, isoniazid (INH) susceptibility, mode of detection and treatment periods . Logistic regression was also used to estimate the odds ratio for treatment success vs. non-success with 95% confidence interval (CI), taking the above variables into account.Among the 655 patients included, the total treatment success rate was 83% (95% CI 80%–86%). The success rates for those born in Norway and abroad were 79% (95% CI 74%–84%) and 86% (95% CI 83%–89%) respectively. There was no difference in success rates by sex and treatment periods. Twenty-two patients (3%) defaulted treatment, 58 (9%) died and 26 (4%) transferred out. The default rate was higher among foreign-born and male patients, whereas almost all who died were born in Norway. The majority of the transferred out group left the country, but seven were expelled from the country. In the multivariate analysis, only high age and initial INH resistance remained as significant risk factors for non-successful treatment.Although the TB treatment success rate in Norway has increased compared to previous studies and although it has reached a reasonable target for treatment outcome in low-incidence countries, the total success rate for 1996–2002 was still slightly below the WHO target of success rate of 85%. Early diagnosis of TB in elderly patients to reduce the death rate, abstaining from expulsion of patients on treatment and further measures to prevent default could improve the success rate further. The key elements in tuberculosis (TB) control are to detect the disease as early as possible and to ensure that those diagnosed complete their treatment and get cured. The World Health Organization (WHO) target for treatment success is 85 percent of all detected smear-positive cases . Even whNorway has about 4.5 million inhabitants, with foreign-born residents comprising 6.9% of the total population in 2002. The proportion of TB cases from foreign-born residents has increased from 19 % in 1986 to 76 % in 2002 [The aims of this study were to evaluate the treatment outcome for new culture positive pulmonary TB cases registered in Norway during the period 1996–2002, and to identify factors associated with non-successful treatment.Mycobacteria. A total of 25 microbiological laboratories isolate M. tuberculosis from patient samples. The laboratory at the Norwegian Institute of Public Health functions as a national reference laboratory for TB. The Pharmacy at the National Hospital is the only pharmacy distributing drugs for TB treatment, and TB prescriptions are compared with the National TB Registry in order to identify cases that may not have been notified. The notification is therefore considered to be quite complete [This was a register-based cohort study. In Norway, there is compulsory nominative notification of all TB cases directly to the National TB Registry. Both suspected and confirmed cases have to be reported by clinicians. Laboratories of clinical microbiology are also required to report all isolates of complete . There iIn this study, we included all new cases with culture positive pulmonary TB notified during 1996–2002. The sputum smear results were not recorded or reported for all cases, especially in the first years of the study period. We therefore based our analysis of treatment outcome on new cases with culture positive pulmonary TB.The mode of detection was determined by information on the notification form. Data on susceptibility to TB drugs was obtained from the notification forms and laboratory reports. In addition to the information in the TB Registry, we used data from the Cause of Death Registry at Statistics Norway to determine the cause of death for those who died under treatment or before start of treatment.Recommended regime for TB treatment in the study period consisted of isoniazid (INH), rifampicin and pyrazinamide in the intensive phase (two months). Ethambutol was added when resistance was suspected such as in foreign-born patients and in previously treated patients. The continuation phase consisted of four months with INH and rifampicin .Directly Observed Therapy (DOT) was used before 2003 on an individual basis. However, we have no data to show how many patients in this study received DOT.cured (finished treatment with negative bacteriology result at the end of treatment), completed treatment , failure (remaining smear/ culture positive at five months despite correct intake of medication), defaulted treatment (patients who interrupted their treatment for two consecutive months or more after registration), died (patients who died due to TB or other cause before or during treatment), transferred out (patients whose treatment results are unknown due to emigration before or during treatment). Patients who changed treatment due to multi-drug resistant TB (MDR-TB), i.e. resistance to both INH and rifampicin, were also defined as failures [The treatment outcome was divided into six categories according to WHO guidelines, with some modifications . These cfailures .Treatment success was defined as the sum of the cases that were cured and that completed treatment.The proportion of patients with a potentially bacteriologically unsuccessful outcome  was also calculated .We used the statistical package SPSS, version 11.0 for data analysis. To estimate the odds ratio for treatment outcome (success vs. non-success), logistic regression analysis was used. Confidence interval (CI) for the odds ratio has also been given. Variables such as sex, birthplace, age group, INH susceptibility, mode of detection and treatment periods  were entered into both univariate and multivariate logistic regression model. P values of less than 0.05 were considered statistically significant.Six hundred and fifty-five new culture positive pulmonary TB patients were included in the study table . Of thesIn our study, the proportion of patients with a potentially bacteriologically unsuccessful outcome  was 8%.The average duration of residence in Norway for foreign-born patients at TB registration was 3.8 (range 1–31) years. There were no differences in the treatment success rates for those who had lived in Norway for less than three years and for those who had stayed longer than three years.Among the 22 patients who defaulted treatment (3%) table , four haThere were 26 patients (4%) who were transferred out table . Of thesAltogether 58 patients (9%) died, 19 (3%) before treatment start and 39 (6%) while on treatment. Of those who died before treatment start, four were diagnosed after death at autopsy. Eighty four percent of those who died were born in Norway. The median age for all who died was 80 years. For those who died before treatment start, the median age was 71 years. For those who died while on treatment, the median age was 81 years and the average duration of treatment was 67 days. Sixteen patients died within 14 days of treatment start. For 23 patients, TB was the primary cause of death. It was the only cause of death for nine of those 23 patients. For further 20 patients, TB was a contributing factor to their death. Fourteen patients died from other diseases than TB. The cause of death was unknown for one patient (table There was no systematic registration of TB/ human immunodeficiency virus (HIV) co-infection at the TB Registry. For those who died while on treatment or before treatment started, HIV disease was registered as the cause of death for two patients table .Table Susceptibility testing for the main TB drugs was done in most of the patients. However, susceptibility testing for streptomycin was done for fewer patients than other main TB drugs. Resistance to INH and streptomycin was most common, and resistance was frequent among foreign-born patients. Of those with MDR-TB, two were born in Norway and eight abroad.Of the 655 patients included in this study, 453 were detected through passive case finding (due to their symptoms). Another 101 patients were discovered through the immigration TB screening program. A total of 52 patients were detected through following ups of close contacts of identified infectious cases (22 cases) and of previous abnormal mass miniature radiology (MMR) (32 cases). The remainder was discovered through other screening programs. No information on mode of detection was available for three patients.In our study, the total treatment success rate for new culture positive pulmonary TB for the period 1996–2002 was 83%. This is close to the WHO target of success rate of 85% of all smear positive cases. However, subgroups of patients contributing to low success rate warrant special attention such as those who defaulted treatment, those who were transferred out and those who died. The first two subgroups mainly comprise patients who were born abroad and the last subgroup mainly comprises patients who were born in Norway. Despite these problems, Norway has reached the reasonable target for treatment outcome in low-incidence countries .Our study shows a default rate of 3%. Higher default rates have been described in other studies such as Vaud County, Switzerland (16%) , HamburgIn the transferred out group, the majority of patients left the country on their own initiative, but seven were expelled. Most of the patients who left the country were on treatment, but we do not have information about their treatment outcome. It is worrying that some of the patients who were expelled moved to countries with political unrest and poorly functioning TB programs. In this group three patients already had isolated INH resistant strains and one had MDR-TB. Expelling patients with TB before completion of treatment is unfortunate, unless it can be guaranteed that adequate treatment will be provided elsewhere. Efforts should be made to ensure the continuity of treatment for patients who move out of the country and, if possible, to allow them to start and complete their treatment, even if they have to leave the country later. The Netherlands have adopted a system where patients are not expelled from the country as long as they are on treatment. According to the new Norwegian manual for TB control and prevention , health The death rate in our study was 9%. Other studies from low TB incidence regions of the world showed death rates among TB patients of 24%, 14% and 6% in Baltimore City, USA , Vaud CoAs indicated in the results section, TB/HIV co-infection is not a common cause of death for TB patients in Norway as most of the patients born in Norway were elderly persons with low risk of HIV and most foreign-born patients were from countries with low levels of HIV infection . TherefoIn the logistic regression model, increasing age and INH resistance were significant risk factors for non-successful treatment. We expected to find that age played a role, since old age in itself will contribute towards higher mortality, partly through co-existing illness. INH is a powerful bactericidal drug and resistance to the drug might reduce the effectiveness of standard short-course treatment . TreatmeAlthough the TB treatment success rate in Norway has increased compared to previous studies and although it has reached a reasonable target for treatment outcome in low-incidence countries, the total success rate for 1996–2002 was still slightly below the WHO target of success rate of 85%. Early diagnosis of TB in elderly patients to reduce the death rate, abstaining from expulsion of patients on treatment and further measures to prevent default could improve the success rate further.CI- Confidence intervalHIV- Human immunodeficiency virusINH- IsoniazidIUATLD- International Union Against Tuberculosis and Lung DiseaseKCNV-Royal Netherlands Tuberculosis AssociationMDR-TB- Multi-drug resistant tuberculosis, i.e. resistance to both isoniazid and rifampicinTB- TuberculosisWHO- World Health OrganizationThe author(s) declare that they have no competing interests.MGF participated in all phases of preparation of the manuscript  and is corresponding author. AT, TWS, EH, ABB and GB have participated the interpretation of results and writing of the manuscript. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


How growth regulators provoke context-specific signals is a fundamental question in developmental biology. In plants, both auxin and brassinosteroids (BRs) promote cell expansion, and it was thought that they activated this process through independent mechanisms. In this work, we describe a shared auxin:BR pathway required for seedling growth. Genetic, physiological, and genomic analyses demonstrate that response from one pathway requires the function of the other, and that this interdependence does not act at the level of hormone biosynthetic control. Increased auxin levels saturate the BR-stimulated growth response and greatly reduce BR effects on gene expression. Integration of these two pathways is downstream from BES1 and Aux/IAA proteins, the last known regulatory factors acting downstream of each hormone, and is likely to occur directly on the promoters of auxin:BR target genes. We have developed a new approach to identify potential regulatory elements acting in each hormone pathway, as well as in the shared auxin:BR pathway. We show that one element highly overrepresented in the promoters of auxin- and BR-induced genes is responsive to both hormones and requires BR biosynthesis for normal expression. This work fundamentally alters our view of BR and auxin signaling and describes a powerful new approach to identify regulatory elements required for response to specific stimuli. Although distinct sets of growth regulators - auxin and brassinosteroids - are required for cell expansion; rather than being independent signals, the response from each pathway requires the other The continuous shaping of plant form is a marvel of signal integration. In early seedling development this is particularly clear, as environmental cues, such as light, profoundly alter the innate morphogenetic program. How diverse pathways merge to determine a discrete cellular growth response is largely unknown. Auxin, the first plant hormone identified, has been implicated in patterning or growth of virtually every plant tissue from earliest embryo to developing fruit . BrassinArabidopsis , a plasma-membrane-localized receptor serine/threonine kinase, is essential for BR perception and accounts for most BR-binding activity in bidopsis . A Shaggbidopsis . When BRbidopsis . Upon BRbidopsis .In contrast to BRs, no auxin receptor has been identified. However, exposure to auxin is known to promote rapid turnover of nuclear Aux/IAA proteins by ubiquitin-mediated targeting to the 26S proteasome . Aux/IAAArabidopsis genome, rekindled interest in the interaction between auxin and BRs, as it was found that a significant percentage of the BR genomic response comprised genes annotated as auxin responsive  length as a quantitative measure of growth. Both hormones are known to induce cell elongation, and exogenous BR treatment has been shown to increase hypocotyl length  and ARF8 (At5g37020) were negatively regulated by BR treatment (see Tables PIN3 (At1g70940), PIN4 (At2g01420), PIN7 (At1g23080), and an AUX1-like gene (At1g77690). Auxin induced the expression of BRI1 and a close paralog, BRL3 (At3g13380), and repressed the expression of another BRI1-like gene, VH1/ BRL2 (At2g01950)  . It is p2g01950) B.det2 plants, which are hypersensitive to exogenous BR treatment, were insensitive to growth at elevated temperature  plants were no longer affected by BR treatment in a yucca background , those with increased transcript levels following auxin treatment only , and those genes whose transcripts were induced following treatment with either hormone . Known plant promoter elements and their annotations were downloaded from PLACE . This approach offers a significant advantage over other background models used to assess enrichment. Permuted distributions reflect real expected frequencies and do not rely on assumptions about genome architecture. In addition, the normal distribution of site frequencies observed with large numbers of permutations allows for the use of powerful parametric statistical methods. Moreover, the ease of filtering based on relative probabilities makes this approach ideally suited to comparisons of promoters regulated in different conditions. In this study, matches were considered significant if a motif was overrepresented in a given set (p < 0.1) and present in at least 10% of group promoters. This analysis identified several motifs specifically enriched in a given group . However, the A, B, and AB groups showed significant enrichment of the core ARF-binding element TGTC in their promoters, perhaps reflecting some sequence divergence between Arabidopsis and soybean, where the element was first identified. A well-characterized synthetic element containing the ARFAT called DR5  gene, which is known to function in BR response , ethylene, ABA, and cytokinin have all been shown to affect hypocotyl elongation , 0.8% phytagar (Gibco-BRL), and one of five concentrations of BL . Seeds on plates were then stratified in the dark at 4 °C for 2 d. Plants were grown in approximately 35 μmol mGUS staining protocol was as described in Arabidopsis seedlings were immersed in 1 μM BL in 0.5× Murashige Minimal Organics Medium  or medium alone for 2.5 h before they were harvested for total RNA preparation. Total RNA from the treated seedlings was used for preparing probes for the microarray experiments, which were carried out according to the protocols provided by the gene chip manufacturer Affymetrix . All experiments used two independent biological replicates. Details of the auxin experiment have been described previously  greater than 0. Data are available at Gene Expression Omnibus; see Nine-day-old, light-grown eviously . Data aneviously . Genes wPlants were treated with hormones as above using treatments of either 1 μM BL, 1 μM indole-3-acetic-acid (auxin), both hormones, or a mock treatment. Total RNA was extracted using a Qiagen  RNAeasy kit and first-strand cDNA was synthesized using an Invitrogen Superscript First-Strand cDNA Synthesis kit. cDNAs were diluted 20-fold and combined with SYBR master mix  for PCR. Primers were as follows: At5g64770 , At1g18400 , At1g10550 , and At4g30290 . At5g15400 (ubiquitin) was used to normalize all values . PCR reactions were performed in triplicate and analyzed using an ABI PRISMA 7700. A standard curve was constructed for each primer using an equal mixture of all cDNAs.We used a Perl script to extract the 500 bp of sequence preceding the 5′ end of each annotated transcription unit in the AGI pseudomolecules annotation (14-May-2003) downloaded from NCBI. These putative promoter sequences begin immediately upstream of the 5′ UTR for transcription units with an annotated 5′ UTR, and upstream of the annotated translational start for the remainder.n genes and extracting 500-bp promoter sequences for the sampled set of genes. Known plant promoter elements and their annotation were downloaded from PLACE  minus the mean count from the 1,000 surrogates (Csurr) relative to the SD from the 1,000 surrogates (SDsurr) . Thus for each motif the p value we calculated was the probability to the right of the observed count calculated on the null distribution derived from sampling promoters randomly from the genome. We considered a motif to be significantly overrepresented if this probability was less than 0.1. These calculations were implemented using Perl scripts and a relational database (MySQL).We analyzed putative promoter regions upstream of auxin- and BR-regulated genes to identify overrepresented promoter elements. One thousand surrogates of each promoter set were created by randomly shuffling the list of genes represented on the Affymetrix ATH1 arrays and then sampling om PLACE . For eacTable S1yucca mutant are shown as compared to WT and following BL treatments. The comparisons from left to right are WT BL- versus mock-treated, WT IAA- versus mock-treated, yucca mock-treated versus WT mock-treated, and yucca BL- versus mock-treated. nc, no change.Effects of increased auxin levels in the (160 KB XLS).Click here for additional data file.Table S2yucca mutant are shown as compared to WT and following BL treatments. The comparisons from left to right are WT BL- versus mock-treated, WT IAA- versus mock-treated, yucca mock-treated versus WT mock-treated, and yucca BL- versus mock-treated. nc, no change.Effects of increased auxin levels in the (169 KB XLS).Click here for additional data file.Table S3ave, average; se, standard error.(64 KB XLS).Click here for additional data file.Table S4ave, average; se, standard error.(64 KB XLS).Click here for additional data file.Table S5ave, average; se, standard error.(63 KB XLS).Click here for additional data file.Table S6ave, average; se, standard error.(26 KB XLS).Click here for additional data file.http://www.ncbi.nlm.nih.gov/geo/) accession numbers for the genes and gene products discussed in this paper are WTBR1 (GSM13423), WTBR2 (GSM13424), WTmock1 (GSM13420), WTmock2 (GSM13421), wtzm1 (GSM13430), wtzm2 (GSM13432), wtzmIAA1 (GSM13433), wtzmIAA2 (GSM13434) and, yuccaBR1 (GSM13428), yuccaBR2 (GSM13429), yuccamock1 (GSM13426), and yuccamock2 (GSM13427).The associated experimental descriptions are available at accession numbers GSE862 (BR effects on WT and yucca seedlings) and GSE863 (auxin effects on seedlings).The Gene Expression Omnibus (


We studied food consumption and nutrient intake in subjects with depressed mood, anxiety and insomnia as indices of compromised mental wellbeing.The study population consisted of 29,133 male smokers aged 50 to 69 years who entered the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study in 1985–1988. This was a placebo-controlled trial to test whether supplementation with alpha-tocopherol or beta-carotene prevents lung cancer. At baseline 27,111 men completed a diet history questionnaire from which food and alcohol consumption and nutrient intake were calculated. The questionnaire on background and medical history included three symptoms on mental wellbeing, anxiety, depression and insomnia experienced in the past four months.Energy intake was higher in men who reported anxiety or depressed mood, and those reporting any such symptoms consumed more alcohol. Subjects reporting anxiety or depressed mood had higher intake of omega-3 fatty acids and omega-6 fatty acids.Our findings conflict with the previous reports of beneficial effects of omega-3 fatty acids on mood. Diet has an effect on mood and cognitive function . There iA double-blind placebo-controlled trial with 30 patients showed that omega-3 essential fatty acid supplements alleviated symptoms in patients with bipolar disorder . In a reA number of studies have shown that acute tryptophan depletion produces depressive symptoms and results in worsening of mood . Folic aIn general, a low-fat diet may have negative effects on mood , and altDepressed subjects tend to consume more carbohydrates in their diets than non-depressed individuals , and theWe set out to study whether food consumption and intake of nutrients in subjects with depressed mood, anxiety and insomnia differed from those in subjects without any such symptoms.This study was based on the cohort of a randomized, double-blind, placebo-controlled primary prevention trial testing the hypothesis that daily supplementation with α-tocopherol or β-carotene reduces the incidence of lung and other cancers . The stuAt baseline, subjects completed a questionnaire on their background and medical history, including three questions on mental wellbeing. These items concerned anxiety, depressed mood and insomnia experienced in the past four months. Height and weight were also measured, and a blood sample was drawn for determining total and high-density lipoprotein (HDL) cholesterol concentrations. Diet and alcohol consumption was assessed from a self-administered dietary history questionnaire , which aDietary nutrient data were analyzed by linking the questionnaire data to the food composition database of the National Public Health Institute, Finland. For analysis, we considered three main groups: principal nutrients, specific nutrients selected on the basis of a priori hypotheses, and certain foods. The principal nutrients were energy, carbohydrates, proteins and fats. The hypothesis-based nutrients were omega-3 and omega-6 fatty acids, lysine, serine, tryptophan, and two vitamins, vitamin D and folic acid. Omega-3 fatty acids from fish consist of long-chain fatty acids, while the omega-3 fatty acids in vegetables are shorter-chain molecules. The food items included were fish, milk, meat, vegetables, margarine, coffee and alcohol. We also evaluated the total energy intake.The trial involved three follow-up visits annually. At each follow-up visit the participants were asked whether they had felt anxiety, depression, or insomnia since the preceding visit (Have you felt feelings of depression in last three months? Have you felt feelings of anxiety in last three months? Have you had insomnia in last three months?). To identify subjects who suffered chronically from these symptoms we took into account the symptoms reported throughout the first follow-up year, i.e. at baseline and the three follow-up visits . Men reporting anxiety, depression, insomnia, or all these symptoms at all four visits were included in these analyses.As potential risk factors, baseline age, body-mass index (BMI), energy intake, alcohol consumption, education level, marital status and smoking were entered into regression models as covariates. Dietary factors were adjusted for energy intake in the models .At study entry, 4314 (16%) men reported depressed mood in the past four months, 6498 24%) feelings of anxiety, and 5550 (21%) insomnia. The mean intake of energy was 1 to 3% greater and consumption of alcohol 30 to 33% greater in subjects with any such symptoms, compared with symptom-free individuals  subjects with depressed mood also had feelings of anxiety, it may be that anxiety is the dominant symptom, and the greater intake of omega-3 and omega-6 fatty acids is primarily related to feelings of anxiety.Previously, it has been suggested that omega-3 fatty acids may alleviate the effects of depressive symptoms but not those of mania . RecentlSubjects with any or all of the symptoms consumed more alcohol than the symptom-free subjects. Subjects with all three symptoms consumed most alcohol of all, and they received 6% of their total energy from alcohol, compared with 4% in subjects with no symptoms. Energy from alcohol, however, did not explain the differences in the mean intake of energy between groups. Body-mass index was lower, despite a higher caloric intake, in subjects with any of the symptoms compared with symptom-free subjects.Subjects reporting insomnia drank more milk than symptom-free subjects, but less coffee. Warm milk has long been taken as a self-medication for insomnia, and our finding among those with insomnia accords with this traditional habit. In addition, they avoided consuming large amounts of coffee, which is known to have impact of sleep. We also found that subjects reporting depressed mood consumed more carbohydrates than subjects with no symptoms. This finding is consistent with the attempt by depressed subjects to alleviate the carbohydrate craving associated with symptoms of depression.Tryptophan intake showed no association with mental wellbeing in our study population. Interestingly, a number of negative studies has been published recently, suggesting that the effects of tryptophan depletion on mood are inconsistent -24, and There are some limitations in our study. Our study was a cross-sectional study, and it cannot provide causal evidence on the association between the diet and symptoms of depression, anxiety or insomnia. The study participants included only men, aged 50 to 69 years, and all were smokers. Our exclusion criteria limit the generalization of our findings, but the study still provides valid and reliable data on a community-based, homogenous sample of older men.Dietary intake and alcohol consumption were assessed with a validated food use questionnaire to measure the habitual dietary intake over the previous year as completely as possible. For most nutrients, both the reproducibility and the validity of this method are 0.6 to 0.7 . For exaThe assessment of self-reported depression was based on a single item only that might have compromised the specificity, but not sensitivity. For example, two questions only may be as effective as more detailed screening instruments in detecting probable cases of major depression . One of The scientific examination of relationships between nutrition and mental wellbeing is a relatively new area of study. Most of the studies focus on the use of dietary supplements, which provide more concentrated amounts of specific nutrients than most food sources. There are few data evaluating food consumption and nutrient intake among subjects with compromised mental health. Our main finding was that we did not find any association between omega-3 fatty acids from fish and mental wellbeing. In general, more attention need to be paid to the intake of nutrients in patients suffering from symptoms of depression, anxiety or insomnia. Further studies are needed to clarify complex associations between the diet and mental wellbeing, and to elucidate their mechanisms of action.


Recent studies have identified long, non-coding genomic regions that are perfectly conserved between human and mouse, termed ultra-conserved regions (UCRs). Here, we focus on UCRs that cluster around genes involved in early vertebrate development; genes conserved over 450 million years of vertebrate evolution.Evolutionarily conserved sequences within or adjoining orthologous genes often serve as critical Based on a high resolution detection procedure, our UCR set enables novel insights into vertebrate genome organization and regulation of developmentally important genes. We find that the genomic positions of deeply conserved UCRs are strongly associated with the locations of genes encoding key regulators of development, with particularly strong positional correlation to transcription factor-encoding genes. Of particular importance is the observation that most UCRs are clustered into arrays that span hundreds of kilobases around their presumptive target genes. Such a hallmark signature is present around several uncharacterized human genes predicted to encode developmentally important DNA-binding proteins.The genomic organization of UCRs, combined with previous findings, suggests that UCRs act as essential long-range modulators of gene expression. The exceptional sequence conservation and clustered structure suggests that UCR-mediated molecular events involve greater complexity than traditional DNA binding by transcription factors. The high-resolution UCR collection presented here provides a wealth of target sequences for future experimental studies to determine the nature of the biochemical mechanisms involved in the preservation of arrays of nearly identical non-coding sequences over the course of vertebrate evolution. The study reports a significant association of a non-transcribed subset of those elements with DNA-binding proteins; an equivalent observation has been made independently by Boffeli et al.[et al. [HoxD gene cluster that are highly conserved across vertebrate genomes.Comparative genome sequence analysis, often termed phylogenetic footprinting, has proven successful for the identification of y regions,2. Recenons[DACH , SOX9 [4x bigene ,6, and He [HOX-D ,8 clustee [HOX-D ). A receli et al. for a li.[et al.  describeIn this paper, we define a set of UCRs using high-resolution criteria that detect segments conserved between the human, mouse and pufferfish genomes. Analysis of this set provides insights into a previously unrealized organizational structure of UCRs in vertebrate genomes. We conclusively show that clusters of UCRs are globally associated with many of the genes that act as master regulators during vertebrate development. The clustered distribution of these regions along chromosomes and, importantly, around their presumptive target genes suggests that gene regulation involves the coordinated action of numerous, widely dispersed elements.We initiated this study by applying comparative genomics to identify putative regulatory regions for a number of evolutionary conserved homeodomain transcription factors that control neural cell fate determination ,13. Whenet al. [To test whether the association of UCRs with regulatory genes reflected a global genomic trend, we identified a comprehensive set of human/mouse/pufferfish UCRs for detailed analysis. We defined minimum requirements for a UCR (see Methods) and performed a genome-scale computational analysis that retrieved 3583 human/mouse/pufferfish UCRs. Since one of the requirements is that the UCRs are not overlapping actively transcribed genomic regions, they would belong to type II UCRs defined by Bejerano et al. .et al.[The median UCR length was 125 bp, but extreme lengths (>1000 bp) were observed. Qualitative assessment of "genescapes", the gene structures, surrounding UCRs revealed them to be present either in introns, in dense clusters around a group of genes or in 'gene deserts' . There appeared to be a strong association between locations of our set of UCRs and genes encoding transcription factors – even stronger than that reported by Bejerano et al. [see AddTo quantitatively assess the characteristics of genes proximal to UCRs, we analyzed the over-representation of gene annotations. We retrieved the InterPro  domain ai.e. the HoxD cluster, Nkx6.1, Nkx2.2 and Pbx3) [for detailed annotated lists of genes associated with UCR clusters, see Additional files  with links to the UCSC genome browser [In order to visualize the distribution of UCR locations across the human genome, we generated a UCR density map for each chromosome see . Figure  browser .IRX) gene clusters. IRX genes are situated in two clusters of three genes each, present on human chromosomes 5 and 16 [We performed a global pairwise comparison of all UCRs, in order to determine if UCR duplication was common across evolution. We discovered only five sets of duplicated UCRs, all of which are adjacent to corresponding duplicated genes. For example, duplicated UCRs are present in the introns of SOX5 (on chromosome 12) and SOX6 (on chromosome 11), two highly similar genes involved in chondrocyte differentiation . Of spec5 and 16 . SimilarThese UCRs occur in arrays of highly conserved regulatory elements spanning large chromosomal regions. The clusters are co-localized with genes encoding key proteins for the regulation of development, with a particular correlation with genes encoding transcription factors. The strength of association between UCRs and diverse classes of DNA binding transcription factors validates that a relatively simple definition of UCRs captures a biologically meaningful set of functional sequences. The presence of non-coding UCRs is predictive for the presence of genes implicated in development, differentiation and malignancies. The list presented in [The human genome contains numerous ultra-conserved regulatory sequences that are shared broadly across vertebrates. ented in  hints atExceptional mechanisms are brought to bear to retain UCRs over hundreds of millions of years of parallel evolution. UCRs are more strongly conserved than sequences encoding identical proteins, and exhibit sequence identity exceeding essentially all known cis-regulatory sequences. The retention properties suggest that UCRs have important functions in the vertebrate genome.The observed UCRs could fall into multiple functional categories, including enhancers of transcription, regulators of chromatin structure and unknown genes for non-coding transcripts. A small subset of UCRs have been identified previously as enhancers of transcription ,3.Drosophila melanogaster [The high conservation and length of UCRs compared to binding sites for single transcription factors suggests that the mode of regulation must involve more than the binding of small number of transcription factors. Homeotypic clusters of binding sites, as seen in developmental genes in nogaster , represeIRX gene clusters. Most of the UCRs have no similarity between the two clusters, with the exception of a set of four UCRs that have retained both mutual sequence similarity and spatial position  resulting in the decrease of mutational frequency in UCRs, or negative pressure consistent with evolutionary selection against such mutations. Given the breadth of possibilities, we leave postulation until further data emerges.et al.[Since Bejerano et al. focused We defined UCRs as non-protein coding genomic regions having a sequence identity > 95% over a 50 bp sliding window of length in human/mouse comparison  window which was progressively slid over each chromosome in 100 kb intervals. The same approach was used to estimate the gene density; specifically by summing the number of bases within the window that aligned with human mRNA (from the UCSC Genome Browser database).Distances between a given gene and UCR on the same chromosome were defined as the shortest distance between the starting points and/or endpoints of UCR and gene in the human genome (UCSC assembly hg15), using EnsEMBL  gene annThe distances from genes within a set  to the closest UCRs were calculated as above. The expected fraction of gene-UCR distances smaller than 8 kb was estimated by simulation: UCR genome coordinates were randomly chosen and distances measured as above. The simulation process was repeated 1000 times and the average fraction reported. In order to estimate if the observed distribution was significantly different from the expected, we used the chi-squared test.For each UCR, the closest upstream and downstream gene within 2 Mbp was identified . EnsEMBL InterPro  domain a. Since the number of tests is considerable, we corrected for multiple sampling using the conservative Bonferroni method [For each domain found in the UCR-proximal genes, we tested the null-hypothesis that the sample and background sets are drawn from the same population versus the alternative hypothesis that the sample set has a higher frequency of the domain, using Fisher's Exact Test  from thei method , in whici method .We used the distances between consecutive UCRs as a statistic indicating clustering. A neutral background distance distribution was created by assigning UCRs genome coordinates randomly, and subsequently measuring distances between consecutive UCRs. This process was repeated 1000 times. We compared the distance distribution between naturally occurring UCRs and the background using the Kolmogorov-Smirnov test , which aAll possible pairs of UCRs were aligned using NCBI BLASTN  with sta3 base pairsUCR – ultraconserved non-coding region; bp – basepairs; kbp – 10AS collected the data and performed most steps of bioinformatic and statistical analysis presented in the paper. He produced all the Figures in the paper and Table Genescape around 50 randomly selected UCRs. Selected UCRs are shown as yellow triangles, other UCRs as light yellow triangles. Genes are colored after domain .Click here for fileGenescape around 50 randomly selected genes. UCRs are shown as as light yellow triangles. Color coding of genes as above.Click here for fileComplete list of protein domains in genes flanking UCRs. Each tested domain is listed along with corrected and uncorrected P-value as in Table Click here for fileComplete list of protein domains in genes with UCR(s) in intron(s) Each tested domain is listed along with corrected and uncorrected P-value as in Table Click here for fileUCR distribution in the human genome UCR density (pink) and gene density (blue) is shown for each chromosome. Densities are calculated as described in Methods.Click here for fileGenes associated with enumerated UCR clusters from Figure Click here for fileExtended list of UCR clusters An extended, but less annotated, version of in [on of in Click here for file


Drosophila.You might say that caspases are obsessed with death. The primary agents of programmed cell death, or apoptosis, caspases kill cells by destroying proteins that sustain cellular processes. Apoptosis, a highly controlled sequence of events that eliminates dangerous or unnecessary cells, contributes to a wide variety of developmental and physiological processes—in a developing embryo, apoptosis creates the space between fingers and adjusts nerve cell populations to match the number of cells they target; in an adult, apoptosis counters cell proliferation to maintain tissue size and density. Now it appears that caspases may also play a role in creating life. As Bruce Hay, Jun Huh, and colleagues report, multiple caspases and caspase regulators are required for the proper formation of free-swimming sperm in the fruitfly Caspases, which typically exist in a quiescent state in nearly all cells, are regulated through a complex network of activators and inhibitors. Once activated, a “caspase cascade” ultimately cleaves and irreversibly alters the function of essential cellular proteins, leading to apoptosis. A few of the dozen-plus known caspases appear to contribute to inflammation responses, but the vast majority are enlisted to kill cells. Not surprisingly, cells keep caspase activation under tight wraps. That's why it's intriguing that multiple caspases normally associated with the induction of cell death participate in this nonapoptotic process.During spermatogenesis, germline precursor cells—the cells that generate sex cells—give rise to 64 haploid spermatids.  Spermatids are connected by intracellular “bridges” that, along with most other cytoplasmic components, must be expelled in a process called “individualization” to create terminally differentiated free-swimming sperm. Protein structures known as investment cones surround each spermatid nucleus and sweep out the neighboring cytoplasm, bridges, and organelles, forming a bulge that eventually detaches as a “waste bag” as it reaches the sperm tail. This process—elimination of cytoplasm and membrane packaging of individual spermatids—also occurs in mammals. Many types of human infertility result when it is disrupted.To explore how caspases affect this process, Hay's group studied the consequences of inhibiting caspase activity (or the activity of specific caspase activators) in the male germline cells of fruitflies. In both cases, they observed that the bulges and waste bags were either abnormally small or absent and that the normal path of investment cone movement was disrupted. The researchers also inspected the flies to look for structural differences and found that spermatids in both mutant strains remained connected by cytoplasmic bridges and retained residual cytoplasm. Together, the authors conclude, these results demonstrate that individualization depends on caspase activity.Hay's team went on to characterize the pathways that activate caspases during sperm individualization. They found that in one pathway, two key activators of caspase-dependent cell death—Ark and Hid —promote the activity or stabilization of the caspase Dronc. A second caspase, Dredd, and its activator Fadd  were also found to be important. Double mutants that removed both Dronc and Dredd activity had more severe defects in individualization than mutants that removed only one or the other, suggesting that these caspases have distinct roles in this process. Interestingly, Drice—the downstream caspase activated just as individualization begins —was not affected by inhibition of Dronc and Dredd. This result, along with the fact that Dronc and Drice were activated at different times and places, suggests that some other mechanism activates Drice. Different apoptosis-related caspases and caspase regulators, the authors conclude, are recruited through different pathways at distinct points in time and space to create individually packaged, free-swimming sperm, a distinctly nonapoptotic process.Drosophila mutants, for example, resemble “cytoplasmic droplet sperm,” a condition seen in infertile men. Insights into the molecular basis of caspase activation in sperm individuation could provide clues to male infertility and suggest possible treatments. Given the widespread role of programmed cell death in supporting processes fundamental to life, perhaps it's not surprising that the agents of apoptosis also support the creation of life.Studies in mice suggest that individualization may occur similarly in mammals, with activation of apoptotic caspase cascades resulting in free-swimming sperm and loss of specific caspase activators causing infertility and defective spermatogenesis. The abnormal differentiation and residual cytoplasm seen in caspase-inhibited


Epidemiological studies suggest that statins, a class of cholesterol-lowering drugs, may lower the risk for Alzheimer disease. The mechanism for this effect is unclear. Alzheimer disease is characterized by accumulation of amyloid deposits in the brain. These deposits are composed of amyloid-beta (Aβ) peptide, a protein fragment that is cleaved off from the amyloid precursor protein APP. APP can be cleaved in two different ways. Amyloidogenic (“amyloid generating”) cleavage by an enzyme called beta-secretase yields “sticky” Aβ peptides that aggregate to form deposits, whereas non-amyloidogenic cleavage by alpha-secretases generates soluble peptides that do not form deposits. Studies in animal models and cell culture suggest that statins might modulate APP processing and shift the balance toward “healthy” (non-amyloidogenic) cleavage.In their quest to understand how statins affect APP processing, Sam Gandy and colleagues focused on a molecule called ROCK1, a kinase enzyme that had recently been implicated in APP processing. The theoretical link between statins and ROCK1 goes as follows: statins inhibit the isoprenoid pathway, isoprenoids are regulators of the enzyme Rho, and Rho in turn activates ROCK1. And while such potential connections could be drawn for any number of molecules, Gandy and colleagues went on to test whether statins exert their effect on APP cleavage by interfering with the isoprenoid/Rho/ROCK1 pathway.Working in mouse neuroblastoma cells, they confirmed that two different statins increased healthy cleavage of APP. When they directly interfered with the isoprenoid/Rho/ROCK1 pathway by adding a drug that inhibits Rho activation, they saw effects similar to those of the statins . The same effects were seen when they transfected the cells with a dominant negative form of ROCK1 ; this outcome shows that the pathway can influence APP cleavage. Most conclusively, when they added a version of ROCK1 that was constitutively  active, they reduced basal levels and abolished statin-stimulated levels of healthy cleavage.Taken together, these results suggest that statins influence APP processing, at least in part, by modulating the isoprenoid pathway and inactivating the ROCK1 kinase. Future studies are necessary to determine whether this mechanism is actually responsible for the apparent clinical benefits of statins. Another question worth exploring further is whether ROCK1 might be a suitable target for therapeutic interventions that aim to decrease harmful, and promote healthy, cleavage of APP.


Research in General Practice requires the participation of General practitioners (GPs). In Germany there is little tradition of research in this field, and GPs are not used to be participants in research. Little is known about German GPs attitudes towards research. Therefore the aim of our study was to assess the willingness of German General Practitioners to participate in primary care research and their attitude towards research in general practice. The results should enable a more successful approach to GPs in further studies.Cross sectional study using semi-structured interviews with a random sample of 76 General Practitioners who participate in the teaching of medical students at the University of Heidelberg.Despite little experience, over 85 % of GPs appreciated research in their field. Important reasons for scepticism about research were the gap between theoretical research and practical work of GPs and the domination of research by specialists. Main barriers for participation are clinical workload, administrative overload and the newly introduced Disease Management Programs. The highest motivation for GPs to participate in research emanates from the will to substantiate their quality of care with solid research data.Financial incentives and personal support e.g. with study nurses are certainly necessary to establish a research culture and to overcome main barriers against participation. The most successful approach to motivate GPs to participate is to convince them that research documents their quality of care. This data may reflect the facts on which the financial resources are provided in the future health care system. Compared to other European countries, Germany still has little of a research tradition in general practice. Increasingly policy-makers have realized that the continuity and the efficacy of the healthcare system have to be improved. For this a well-developed primary medical care system is needed. In recent years a number of new chairs of general practice have been established and a national funding programme was created in order to promote General Practice as an academic discipline in Germany. The University of Heidelberg, which is the oldest university in Germany, is among the beneficiaries of these developments. Despite of a well established network of teaching practices, the research group for general practice and health services research was only created in 2002 . This grWe performed a cross sectional observational study collecting qualitative data. The Ethical Commission of the University of Heidelberg approved the study.A random sample of 76 GPs in the area of Heidelberg was approached for the study. The GPs were selected by choosing every third of an alphabetical list of 250 practices. These GPs were associated with the university by frequently teaching students in their practices. Due to old data, in six cases the GPs did not practice any more. So finally 76 GPs were included. All of the selected GPs were in practice for more than five years. Former studies indicated that relevance of the topic has a positive predictive value for the recruitment rate. Therefore we selected a topic with a high clinical relevance in daily practice: osteoarthritis ,4. BasedNo letters were returned to the university because of wrong addresses. A reminder or anything similar did not follow the first letter. One week after the letter, every GP was called by the principal investigator and was asked – after giving him again information on the study – if she or he wanted to participate. This approach was chosen to get qualitative information of all approached GPs about their willingness to participate and their opinion in general. This way of data collecting has already been used in this field of research and enables not only a high rate of data response, it is also a feasible way of collecting qualitative data . If the We were mainly focused on qualitative information. Therefore the statements of the GPs were grouped and coded by two separate researchers and then discussed in order to agree on the selected categorisation according to the guidelines for qualitative researchers .A total of 18 GPs (23.8%) of the approached GPs was female, 58 GPs (72.2 %) were male. Only two GPs faxed their agreement-sheet within the first week, before they were phoned and interviewed by the principal investigator. During the telephone calls 25 GPs (32.8 %) agreed to participate and promised to fax the sheet. Out of this group 5 GPs (18.5%) sent their fax during the subsequent two weeks. A total of 8 (10.5 %) faxes were returned. Five female (27.7 %) and 22 male GPs agreed (37.9 %) to participate. A total of 27 GPs agreed to participate ultimately.Table As can be seen in table There were three main conclusions that can be drawn out of our interview results. Firstly, the research topic improving the quality of care for patients suffering from osteoarthritis was considered as highly relevant by the interviewed GPs. This is concordant to our assumptions based on epidemiological data, which led to the fictitious research topic. The same reasoning causes GPs to seek support in the daily treatment of patients with osteoarthritis. Consequently this will be subject of future research projects.Secondly, most of the GPs appreciate research in general practice, but a few were very sceptical. German GPs still don't realise it as a professional obligation as their colleagues in countries like e.g. the Netherlands or the United Kingdom, with a much longer tradition in research, do .The third main result of our survey has not yet been shown in former studies. It is the fact that the willingness for participating in research emanates mainly out of the motivation to improve the reputation of family medicine in general by documenting the high quality of care with data attained in solid surveys. This may reflect the increasing self-confidence of German GPs, which are about to expend the influence in the health care system, and their awareness that an own research culture helps to enhance this. Facing decreasing financial resources in the Health care system, GPs may also be aware that a solid database documenting the quality of care will get more important for the distribution of financial resources in the near future.The revealed barriers against participating in studies mentioned in our telephone survey are in line with results from previous studies in other countries . AccordiPrevious studies were mainly focused on formal or external barriers for GPs against participating in research, or revealed approaches that cannot easily be transferred, as e.g. the enrollment of friendly GPs . What thThe author(s) declare that they have no competing interests.TR conceived and performed the study and draft the manuscript. JS participated in the study design. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


Acinetobacter baumanii organisms in Sivas, Turkey over 3 years. We used disk diffusion or standardized microdilution to test the isolates against 18 antibiotics.Gram-negative bacteria cause most nosocomial respiratory infections. At the University of Cumhuriyet, we examined 328 respiratory isolates of Enterobacteriaceae and Klebsiella spp (35%), A. baumanii (27%), and Escherichia coli (15%). Imipenem was the most active agent, inhibiting 90% of Enterobacteriaceae and A. baumanii organisms. We considered approximately 12% of Klebsiella pneumoniae and 21% of E. coli isolates to be possible producers of extended-spectrum beta-lactamase. K. pneumoniae isolates of the extended-spectrum beta-lactamase phenotype were more resistant to imipenem, ciprofloxacin, and tetracycline in our study than they are in other regions of the world.We cultured organisms from sputum (54%), tracheal aspirate (25%), and bronchial lavage fluid (21%). The most common organisms were Our results suggest that imipenem resistance in our region is growing. Pseudomonas aeruginosa in our region [Nosocomial bacterial pneumonia is frequently polymicrobial, with gram-negative bacilli predominating . Becauser region . The curKlebsiella spp (35%), A. baumanii (27%), and E. coli (15%). We also isolated rare organisms such as Stenotrophomonas maltophilia, Burkholderia spp, and Hafnia alvei. All studied Enterobacteriaceae (except Enterobacter spp) were far more susceptible to ticarcillin-clavulanate than to ticarcillin alone, which suggests that the primary mechanism of resistance in these organisms is β-lactamase production.Table K. pneumoniae accounted for 79% of Klebsiella isolates. Klebsiella spp were generally more susceptible to the tested antimicrobials than were Enterobacter spp, Serratia spp, or E. coli. The overall resistance rates to the third-generation cephalosporins  were as follows: Klebsiella spp, 10%–19%; Serratia spp, 16%–33%; and Enterobacter spp, 22%–45%. Serratia spp were less resistant to third-generation cephalosporins than Enterobacter spp. E. coli isolates resistant to piperacillin, gentamicin, and the fluoroquinolones accounted for only 4% of all E. coli isolates. Imipenem was the most active agent against our isolates.A. baumanii. Tobramycin was more effective against A. baumanii than against Enterobacteriaceae. Tobramycin and imipenem were the most active agents against both gentamicin- and ciprofloxacin-resistant A. baumanii  and 11 K. pneumoniae isolates (12.2%). All K. pneumoniae and E. coli isolates with the ESBL phenotype were resistant to tetracycline. Regarding K. pneumoniae isolates, 2 were susceptible to tobramycin, 3 to gentamicin, and 4 to ciprofloxacin, but 8 were susceptible to amikacin and imipenem. Regarding E. coli isolates, 4 were susceptible to tobramycin, 7 to gentamicin, 5 to ciprofloxacin, and 8 to amikacin, but all were susceptible to imipenem.We observed the ESBL phenotype in 10 Klebsiella isolates were more susceptible to third-generation cephalosporins , aztreonam (44.0% vs. 65.6%), and ticarcillin-clavulanate (37.0% vs. 60.3%). Klebsiella spp were 81.6% susceptible to ceftazidime in our study; these rates are 96.6% in North America [Contrary to the findings of the Turkish antimicrobial resistance study group , our KleAcinetobacter spp in respiratory specimens may reflect colonization and not necessarily infection [Acinetobacter infection is the lower respiratory tract, especially in mechanically ventilated patients [Acinetobacter spp were the second most frequent gram-negative bacilli isolated from patients with pneumonia in Latin America [A. baumanii isolates. Susceptibility to imipenem was >95% in Canada [A. baumanii will stimulate the use of carbapenems and possibly increase carbapenem resistance in our region.Although the isolation of nfection , the mospatients . Acineto America . In our n Canada , India [n Canada , and Chin Canada . The higE. coli isolates were susceptible to ciprofloxacin. However, this rate was greater in Europe (95.2%) [E. coli's susceptibility to ceftazidime was >95% in Europe [E. coli isolates. Conversely, E. coli strains were not resistant to imipenem in Europe [Only 75% of our  (95.2%) , North A (95.2%) , and Latn Europe , North An Europe , China [n Europe  but onlyn Europe . Imipenen Europe , Latin An Europe , China [n Europe .Enterobacter spp showed high rates of resistance to broad-spectrum penicillins with or without β-lactamase inhibitors (41.7% resistance to ticarcillin-clavulanate) and third-generation cephalosporins (45.2% resistance to ceftazidime). The high rates of ceftazidime resistance among Enterobacter spp suggests a high prevalence of stably derepressed AmpC cephalosporinase-producing strains. Interestingly, resistance to third-generation cephalosporins, aztreonam, and ticarcillin-clavulanate was higher in our study (28.1%–48.0%) than with the Turkish antimicrobial resistance study group (13.3%–38.3%) [Enterobacter or Serratia isolates were resistant to imipenem. In our study, however, the rates of susceptibility to imipenem were 86.2% for Enterobacter spp and 76.5% for Serratia spp. Imipenem susceptibility for these two species was >95% in other parts of the world [Serratia spp were at least 95% susceptible to ceftazidime in the United States [y group 1.3%–38.3%he world ,13. Mored States , Canada d States , India [K. pneumoniae isolates were 45.4% in Latin America, 24.6% in the Western Pacific, 22.6% in Europe, 7.6% in the United States, and 4.9% in Canada [E. coli isolates were 8.5% in Latin America, 7.9% in the Western Pacific, 5.3% in Europe, 4.2% in Canada, and 3.3% in the United States [E. coli isolates decreased susceptibility to the aminoglycosides, tetracycline, and ciprofloxacin but not imipenem, suggesting the presence of other resistance genes in ESBL-encoding plasmids. Despite the high percentage of ESBL production in E. coli isolates, antibiotics remained reasonably effective with these isolates. Imipenem was active against all ESBL-producing E. coli isolates. E. coli remained 30.0% resistant to gentamicin; this resistance rate was 75.9% in the Western Pacific, 57.8% in Latin America, 25.7% in Europe, and 21.1% in the United States [From 1997 to 1999, ESBL detection rates in n Canada ; this ran Canada . During d States ; this rad States .K. pneumoniae isolates were resistant to imipenem in the United States, Latin America, the Western Pacific region, and Canada [K. pneumoniae strains was 61.1% in Canada, 55.1% in the Western Pacific, 52.0% in Latin America, 49.5% in Europe, and 44.4% in the United States [K. pneumoniae strains was 44.2% in the Western Pacific, 34.6% in the United States, 24.3% in Europe, 23.1% in Latin America, 22.2% in Canada, and 63.6% in our study.Only 0.5%–0.7% of ESBL-producing d Canada . Our ratd States , but thiE. coli isolate. It was resistant to ampicillin, ticarcillin, and piperacillin but susceptible to ceftazidime, ceftriaxone, and aztreonam. This profile suggests an oxacillinase with carbapenemase properties. This finding is interesting because class D enzymes have been found only in Acinetobacter spp [Klebsiella spp were resistant to all β-lactams, including aztreonam. These species were probably expressed a metallo-β-lactamase with additional mechanisms  [We found only one imipenem-resistant cter spp . Two imiduction) .The absence of a confirmation test for the ESBL phenotype limits the impact of our results. On the other hand, it is known that supplemented media (blood) can alter the zone diameters for several agents and bacterial species. Despite these limitations, our data can be used for local therapeutic choices.P. aeruginosa during the same period [We previously presented the antibiotic susceptibility patterns of 249 respiratory isolates of A. baumanii. We accepted all consecutive isolates because we did not attempt to distinguish actual pathogens from colonizing strains. Specimen types consisted of sputum (54.2%), transtracheal/endotracheal aspirates (24.6%), and bronchial lavage fluid (21.2%). We cultured sputum samples that showed no oral contamination in the presence of sputum purulence or a suspected lower respiratory infection.We collected our data from 01/01/1999 to 01/01/2002 at the microbiology laboratory of the University of Cumhuriyet. We processed the data to eliminate duplicate registrations. We excluded any isolates collected within 7 days when they came from the same specimen source of the same patient. We initially identified the isolates using such routine methods as colonial/microscopic morphology and enzymatic characteristics. We confirmed species identification with API-bioMerieux products. We retrospectively analyzed antibiotic susceptibility patterns in 238 respiratory isolates of Enterobacteriaceae members and 90 respiratory isolates of E. coli ATCC 25922 and Staphylococcus aureus ATCC 25923 strains. The disks (Oxoid) contained the following antimicrobials: ampicillin (10 μg), ampicillin/sulbactam (20 μg), piperacillin (100 μg), aztreonam (30 μg), cefazolin (30 μg), cefuroxime (30 μg), cefotaxime (30 μg), ceftriaxone (30 μg), ceftazidime (30 μg), amikacin (30 μg), gentamicin (10 μg), tobramycin (10 μg), ciprofloxacin (5 μg), imipenem (10 μg), tetracycline (30 μg), and cotrimoxazole (25 μg). Until November 1999, our microbiology laboratory based susceptibility rates on disk zone sizes; thereafter, we used a coordinating laboratory to determine the minimal inhibitory concentrations (MICs) of these 18 antimicrobial agents, accomplished with a standardized microdilution technique . We used this system to determine MICs for all strains. We used the NCCLS criteria to identify possible extended-spectrum β-lactamase (ESBL)-producing strains of Klebsiella spp and E. coli when MICs were increased (2 mg/mL) with ceftazidime and/or ceftriaxone and/or aztreonam [We confirmed susceptibility to 18 antimicrobial agents using disk diffusion according to the National Committee for Clinical Laboratory Standards (NCCLS) guidelines , except susceptible. We labeled all resistant and intermediate isolates as resistant. We divided the number of resistant isolates by the total number of isolates that had undergone susceptibility testing.We classified our results into two categories. We labeled strains deemed susceptible by the disk diffusion method or microdilution technique as UG had primary responsibility for study design, collection of data, and writing the manuscript. IA, MZB, TE had intellectual contribution as well as the writing of manuscript. All authors read and approved the final manuscript.