Taxane-platinum therapy (TP) has replaced platinum-based therapy  in the postoperative treatment of ovarian cancer patients; however, it is not always effective. TP53 protein plays a differential role in response to DNA-damaging agents and taxanes. We sought to define profiles of patients who benefit the most from TP and also of those who can be treated with PC.We compared the effectiveness of PC/PAC (n = 253) and TP (n = 199) with respect to tumor TP53 accumulation in ovarian cancer patients with FIGO stage IIB-IV disease; this was a non-randomized retrospective study. Immunohistochemical analysis was performed on 452 archival tumors; univariate and multivariate analysis by the Cox's and logistic regression models was performed in all patients and in subgroups with [TP53(+)] and without TP53 accumulation [TP53(-)].The advantage of taxane-platinum therapy over platinum-based therapy was seen in the TP53(+), and not in the TP53(-) group. In the TP53(+) group taxane-platinum therapy enhanced the probability of complete remission (p = .018), platinum sensitivity (p = .014), platinum highly sensitive response (p = .038) and longer survival . Poor tumor differentiation diminished the advantage from taxane-platinum therapy in the TP53(+) group. In the TP53(-) group PC/PAC was at least equally efficient as taxane-platinum therapy and it enhanced the chance of platinum highly sensitive response (p = .010). However, in the TP53(-) group taxane-platinum therapy possibly diminished the risk of death in patients over 53 yrs (p = .077). Among factors that positively interacted with taxane-platinum therapy in some analyses were endometrioid and clear cell type, FIGO III stage, bulky residual tumor, more advanced age of patient and moderate tumor differentiation.Our results suggest that taxane-platinum therapy is particularly justified in patients with TP53(+) tumors or older than 53 years. In the group of patients ≤53 yrs and with TP53(-) tumors platinum-based therapy is possibly equally efficient. We provide hints for planning randomized trials to verify these observations. First-line chemotherapy based on taxanes and platinum derivatives is a standard of care for ovarian cancer patients  ; it replTP53 independent  and without TP53 accumulation [TP53(-)] . In the We also studied the relative efficiency of the main types of chemotherapy (TP versus PC/PAC) in various clinical and pathological subgroups. For example, not only patients with FIGO IIIC disease but also patients with FIGO IIIC disease treated with PC/PAC, and patients with FIGO IIIC disease treated with TP were compared to patients with FIGO IIB/C disease. These analyses were performed in the multivariate models. If the odds of achieving a given endpoint differed significantly between the both chemotherapy groups, it meant that one chemotherapeutic regimen was more efficient in the FIGO IIIC group (in other words it showed an interaction with FIGO IIIC).PC/PAC and TP chemotherapy showed interaction with several clinicopathological parameters. In some patients the interaction was contradictory. For example, TP was more efficient in older patients, but less efficient in patients with undifferentiated tumors. To find out how various parameters and the two main chemotherapeutic regimens contribute to the final clinical effect we counted cumulated odds or hazards as in the example below.Hazards of death in the TP53(+) group were as follows: the PC/PAC treated group served as a reference with HR 1.0 for all factors; risk of death for TP therapy was lower (HR 0.15)  group, complete remission (CR), platinum sensitivity, disease-free survival and overall survival were not influenced by the type of chemotherapy Table . PlatinuAnalysis of the relative efficiency of the two types of chemotherapy revealed that patients with FIGO IIIA/B and IIIC disease, and with endometrioid and clear cell carcinomas would have higher chances of PHS response with taxane-platinum than with platinum-based therapy Table ; howeverOverall survival curves have shown that in the TP53(-) group patient's age over median determined benefits from TP therapy  group enhanced the chances of complete remission, platinum sensitivity and platinum highly sensitive response (PHS) when compared with PC/PAC therapy Table . As to tRisk of death was 6 times lower for patients treated with taxane-platinum than for those treated with PC/PAC Table . There wConcomitant evaluation of three parameters influencing a given clinical endpoint  might suggest that in the TP53(+) group there was a subgroup with higher chances of platinum highly sensitive response with PC/PAC therapy without compromising overall survival. This group was characterized by younger patient's age, residual tumor ≤2 cm, tumor grade 4  with regard to complete remission , platinum sensitivity  and overall survival ; taxane-platinum therapy did not influence disease free survival and the probability of achieving platinum highly sensitive response (PHS). The latter was probably a result of contradictory associations between PHS and the therapies in the TP53(-) and TP53(+) groups.Analysis of interactions revealed advantages or disadvantages of taxane-platinum therapy in some subgroups of patients, in accord with the results presented above, i.e. taxane-platinum therapy was more efficient than PC/PAC in patients with RT > 2 cm , older than 53 years , while it was less advantageous in cases with high tumor grade – G3  and G4 .There are four major randomized studies comparing platinum-based and taxane-platinum therapy (TP) in ovarian cancer patients and they present inconsistent results ,39-41. NOur analysis of the whole group studied shows the superiority of TP over PC/PAC, and in this aspect it is in accord with the results of GOG 111 and OV-10 studies. However, we have possibly identified profiles of ovarian cancer patients who benefit most from first-line taxane-platinum therapy (TP), and also of those in whom platinum-based therapy (PC or PAC) appears at least equally efficient.In our non-randomized retrospective study TP53 protein accumulation in tumor tissue was the main criterion of higher benefits from TP than from PC/PAC chemotherapy; in the TP53-negative group taxane-platinum therapy did not show any clear advantages over platinum-cyclophosphamide therapy. A similar observation was published by Zhao et al  who retrThe observed advantage of taxane-platinum therapy in the group with TP53 accumulation is in accord with some earlier data from experimental and pilot clinical studies -23. The In our study the patient's age over median  appears as another important criterion of advantage of TP over PC/PAC therapy. This factor did not reach statistical significance in multivariate analysis, nevertheless, patients older than 53 years treated with PC/PAC had the worst survival rate. This result means a worse survival for older than for younger patients treated with PC/PAC, as it was shown in our previous multivariate analyses on the PC/PAC group only ,31; TP tOf secondary importance in the criteria of benefits from taxane-platinum therapy observed in our study (in the TP53-positive group only) were bulky residual tumor and moderate tumor differentiation. This partially confirms the results of previous clinical studies showing that TP therapy improves survival in suboptimally debulked patients ,40,46. Ain vivo by paclitaxel in well differentiated than in moderately differentiated tumors [Spectacularly high efficacy of TP in moderately differentiated tumors and much lower in undifferentiated tumors (and concomitantly the opposite for platinum-based therapy) has not been reported previously. Poor tumor differentiation/undifferentiation appears as a factor significantly leveling the benefits from TP therapy in the TP53-positive group. While better effects of platinum-based therapy in undifferentiated tumors might be explained by loss of DNA repair in undifferentiated cells, we could not find a clear explanation for the observed associations between tumor grade and TP therapy. The mechanisms underlying taxol resistance include mutations in the β-tubulin gene -49, diffd tumors .We also observed that patients with endometriod and clear cell carcinomas treated with TP showed a better response than those treated with PC/PAC (in the TP53-negative group only). This may be due to the high expression of apoptosis inhibitor BCL-2 in these histological types and its inactivation by taxanes ,56. HoweA striking observation was the much lower rate of responses to taxane-platinum therapy in FIGO II and IV disease in the TP53-negative group. These may be candidate groups for platinum-based therapy of choice. Due to the small number of cases further clinical studies focused on these subgroups including also FIGO IC-IIA disease may provide greater insight.The results of our analysis are presented and discussed with the limitation that this is a non-randomized retrospective study. Therefore, there is some bias in our analysis related to differences in the material characteristics between the therapies. Nevertheless, the main focus of our study was the analysis across TP53 status and the results have been obtained in a multivariate analysis. Our study suggests the superiority of taxane-platinum therapy in the majority of patients with TP53(+) tumors and in any one older than 53 years. It also questions the necessity of taxane-platinum therapy in some subgroups of younger ovarian cancer patients. We provide hints for planning randomized trials to verify these observations.According to our non-randomized study, TP53 protein accumulation appears as the main factor determining benefits from taxane-platinum therapy in ovarian cancer patients. Another factor may be the more advanced age of the patient. Thus, our study confirms the advantage of taxane-platinum therapy in the majority of patients. Nevertheless, the prospect does exist for a return to platinum-cyclophosphamide therapy in some subgroups of patients, predominantly of those younger than 53 yrs with TP53-negative tumors. Our results give hints for randomized trials.The author(s) declare that they have no competing interests.JK conceived and coordinated the study, reviewed the pathology and immunohistochemistry, interpreted the results and drafted the manuscript. EK performed the statistical analysis with the analysis of interactions. IZ-S, RM, AT, JM, JS, MB participated in the design of the study, carried out patient recruitment, reviewed the clinical material centrally. Other members of the POCSG carried out patient recruitment from the platinum-cyclophosphamide-treated group. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


We report on the establishment of a model for differentiation induction in sarcomas, using the clonal rhabdomyosarcoma cell line BA-HAN-1C. This rhabdomyosarcoma cell line is composed of morphologically undifferentiated mononuclear stem cells, some of which spontaneously fuse to form terminally differentiated multinuclear myotube-like giant cells. The deprivation of fetal calf serum (FCS) or the exposure to retinoic acid, respectively, resulted in a significant inhibition of proliferation (P less than 0.001) and a marked increase in cellular differentiation as shown by a significant increase in the number of myotube-like giant cells (P less than 0.001) and in the creatine kinase activity (P less than 0.05) used as a biochemical marker of differentiation. Furthermore, after exposure to retinoic acid about 30% of the mononuclear tumour cells exhibited morphological features of rhabdomyogenic differentiation, such as bundles of thick and thin myofilaments, which had never been observed in the mononuclear cells of untreated cultures. These results confirm that the inverse linkage between proliferation and differentiation known from embryonic myogenesis is preserved in our rhabdomyosarcoma cell line. The failure to induce terminal differentiation by exposure to retinoic acid in all the cells of our clonal cell line indicates that some tumour cells might epigenetically be blocked from responding to retinoic acid. The temporary growth retardation observed after FCS-deprivation suggests that autocrine stimulation of proliferation may be operating in our cell line, too.


Pleural effusion secondary to ventriculoperitoneal shunt insertion is a rare and potentially life-threatening occurrence.We describe a 14-month-old Caucasian boy who had a ventriculoperitoneal shunt inserted for progressive hydrocephalus of unknown etiology. Two and a half months post-shunt insertion, the patient presented with mild respiratory distress. A chest radiograph revealed a large right pleural effusion and a shunt series demonstrated an appropriately placed distal catheter tip. A subsequent abdominal ultrasound revealed marked ascites. Fluid drained via tube thoracostomy was sent for beta-2-transferrin electrophoresis. A positive test was highly suggestive of cerebral spinal fluid hydrothorax. Post-externalization of the ventriculoperitoneal shunt, the ascites and pleural effusion resolved.Testing for beta-2-transferrin protein in pleural fluid may serve as a useful technique for diagnosing cerebrospinal fluid hydrothorax in patients with ventriculoperitoneal shunts. Mechanical shunting of cerebrospinal fluid (CSF) is an effective treatment for non-obstructive hydrocephalus. In particular, ventriculoperitoneal (VP) shunting has become a preferred method in most clinical centers. Despite the wide acceptance of VP shunting, there are important complications associated with this technique. Common problems include obstruction, mechanical shunt failure and infections  while CSWe report a 14-month-old Caucasian boy with a symptomatic pleural effusion that developed two and a half months post-VP shunt insertion for hydrocephalus of unknown etiology. We will review potential mechanisms behind the development of this complication and discuss the use of beta-2-transferrin for the identification of CSF hydrothorax in children with VP shunts.A 14-month-old Caucasian boy with idiopathic non-obstructive hydrocephalus and a VP shunt presented to the emergency room with a 1-day history of mild respiratory distress without cough or fever. The patient had presented at 11 months of age with a history of enlarging head circumference and developmental delay. A computed tomography (CT) scan of his head at 11 months of age revealed enlargement of the lateral, third and fourth ventricles and a bulky choroid plexus. A right-sided programmable valve VP shunt was inserted at that time.On examination, the 14-month-old patient was found to be afebrile and tachypneic (34 breaths/minute) with mildly increased work of breathing and decreased respiratory sounds in the distal aspect of the right lung. The cardiovascular exam was within normal limits. An examination of the abdomen revealed distension but no hepatomegaly or signs of peritoneal irritation.A chest radiograph Figures  and 2 re9/L, respectively. Further blood work demonstrated an alanine aminotransferase (ALT) level of 46U/L, an aspartate aminotransferase (AST) level of 51U/L, a serum calcium level of 2.61mmol/L and an alkaline phosphatase (ALP) level of 1403U/L. Subsequently, ALP steadily decreased to 498U/L but remained elevated throughout the patient's admission.At the time of admission, venous blood gas, serum electrolytes and creatinine were within normal limits. Blood urea nitrogen and white blood count were mildly elevated at 5.1mmol/L and 12.5 × 10A thoracentesis was performed and a chest tube was inserted which drained >300cc/day of clear, yellow fluid. Around the time of chest tube insertion, the patient was noted to have an increasing abdominal girth, sizeable positive fluid balance and weight gain. An abdominal/pelvic ultrasound revealed marked ascites. Structurally normal major abdominal and pelvic viscera as well as normal vena caval and hepatic venous flows were reported.β2-transferrin assay and was found to be positive. Subsequent to this finding, the VP shunt was externalized followed by a dramatic decrease in chest tube drainage. A repeat chest radiograph revealed resolution of the pleural fluid collection and the chest tube was removed. The patient's abdominal girth decreased and a repeat abdominal/pelvic ultrasound demonstrated resolution of ascites. The patient's externalized ventricular drain was subsequently converted to a ventriculoarterial shunt.A head CT showed no change from a previous scan carried out at 11 months of age. A parallel pleural fluid and CSF analysis was also performed which is detailed in Table β2-transferrin for the diagnosis of CSF hydrothorax in a child with a transudative pleural effusion. Although used previously in other applications, to the best of our knowledge, this is the first reported use of β2-transferrin to detect a CSF pleural effusion in a child with a VP shunt.We report the use of A variety of techniques to investigate ascites and/or pleural effusion in patients with VP shunts have been reported in the literature. Among the described methods is the use of radiopaque contrast. This particular procedure involves the injection of radioactive dye at a point along the shunt pathway followed by subsequent imaging studies to trace the migration of contrast-injected CSF . An alteA novel diagnostic strategy was utilized in the case of our patient. A sample of fluid, drained via tube thoracostomy, was sent for beta-2-transferrin level. This desialated isoform of transferrin is almost exclusively found in the CSF with only minimal amounts present in cochlear perilymph and in the aqueous and vitreous humor of the eye. Multiple studies have validated the use of beta-2-transferrin as a specific marker for CSF leakage with sensitivity and specificity approaching 100% and 95%, respectively . FurtherFollowing externalization of the distal VP tip, our patient's ascites and pleural effusion promptly resolved. This finding, in combination with a positive beta-2-transferrin assay, was highly suggestive of a CSF hydrothorax.The findings of CSF hydrothorax and ascites, as demonstrated in our patient, are rare complications of VP shunts. Reported to occur anywhere from days to years postoperatively, CSF ascites usually develops within the first 2 years after VP shunt placement . In greaWe propose a pathological intraperitoneal process, such as subclinical peritonitis, to account for the development of CSF ascites in our patient. Inflammation of the peritoneal membrane may lead to intraperitoneal accumulation of fluid through the impairment of lymphatic flow  and/or bAs evidence to date suggests that modern shunt materials are inert, alternative sources of peritoneal irritation need to be considered. For example, an immune reaction to a foreign protein such as a vaccine may be enough to precipitate ascites in patients with VP shunts . As the Alternative explanations for CSF ascites in the literature such as excess CSF production, surgical procedures, and high CSF protein are less plausible explanations for our patient's CSF ascites. Firstly, it has been suggested that CSF ascites can result from excessive CSF production, with the excess fluid overwhelming the absorptive capacity of the peritoneum . DespiteLastly, high CSF protein has been proposed as a potential cause of CSF ascites . AccordiThe finding of CSF ascites in our patient can be used to explain the coincident finding of pleural effusion. Taub and Lavyne (2004) suggest three mechanisms to account for the development of CSF hydrothorax post-VP shunt placement . FirstlyConsidering that no surgical complications during VP shunt placement were reported in our patient and that his shunt series at the time of admission was normal, an alternative explanation is required. Thus, it is the third mechanism proposed by Taub and Lavyne, the development of hydrothorax secondary to CSF ascites that offers the most promising explanation for our patient's pleural effusion .In order for CSF ascites to result in pleural effusion, some degree of open communication must exist between the peritoneal cavity and the pleural space. Congenital diaphragmatic defects or weak points in the diaphragm such as the Foramen of Morgagni or Foramen of Bochdalek provide potential conduits. Furthermore, one or more microscopic diaphragmatic communications is likely to be sufficient for the transdiaphragmatic movement of peritoneal fluid . These pAlthough no gross diaphragmatic defect was identified in our patient, the presence of microscopic diaphragmatic communications may have been present. Notably, the tapped pleural fluid characteristics of our patient were found to be in keeping with a transudative effusion. The collected pleural fluid also demonstrated a marginally higher protein concentration than in the patient's CSF fluid. Differences in the solute composition of ventricular-extracted CSF and pleural fluid have been previously demonstrated in patients with pleural effusion secondary to VP shunts . The finIn summary, we present the case of a 14-month-old boy with CSF hydrothorax secondary to VP shunt. Pleural effusion following VP shunt insertion is a rare and potentially life-threatening event and hence requires prompt diagnosis and correction. We report a novel and non-invasive technique by which to identify the presence of CSF in pleural fluid. Beta-2-transferrin assay may serve as a useful new means for the identification of CSF hydrothorax in the context of patients with VP shunts.Written informed consent was obtained from the patient's mother for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.The authors declare that they have no competing interests.Both authors contributed to the conception of this case report. Dr. Jennifer Smith drafted the report while Dr. Eyal Cohen provided critical feedback. Both authors have reviewed and approve of the final version.


The specificity was assessed in the blood of six healthy donors, four patients with non-melanoma cancers of which one patient was treated with granulocyte-colony stimulating factor. Lymph nodes of nine patients without malignant melanoma were tested and four cell lines of various other tumours. Six of the nine non-melanoma lymph nodes were positive in this assay. The sensitivity was tested in a spike experiment in vitro, using a melanoma cell line. The detection limit was ten melanoma cells per 10


Furthermore we show that the size of IgA is crucial in its capability to enhance IL-6 production. Monomeric IgA does not affect basic IL-6 production, whereas dimeric and polymeric IgA enhance IL-6 production up to 3- to 9-fold respectively. Additional studies demonstrate that enhanced IL-6 production by MC is not accompanied by increased proliferation of human mesangial cells, a finding which is distinct from that found with rat mesangial cells. Taken together, these fmdings suggest that deposition of dimeric and polymeric IgA in the mesangial area of human kidneys in IgA nephropathy may amplify local inflammation.Depositions of IgA in the renal glomerular mesangial area are a hallmark of IgA nephropathy, and are thought to be crucial for the onset of inflammation processes in IgA nephropathy. In this report we show that human mesangial cells (MC)


Drug perturbations of human cells lead to complex responses upon target binding. One of the known mechanisms is a (positive or negative) feedback loop that adjusts the expression level of the respective target protein. To quantify this mechanism systems-wide in an unbiased way, drug-induced differential expression of drug target mRNA was examined in three cell lines using the Connectivity Map. To overcome various biases in this valuable resource, we have developed a computational normalization and scoring procedure that is applicable to gene expression recording upon heterogeneous drug treatments. In 1290 drug-target relations, corresponding to 466 drugs acting on 167 drug targets studied, 8% of the targets are subject to regulation at the mRNA level. We confirmed systematically that in particular G-protein coupled receptors, when serving as known targets, are regulated upon drug treatment. We further newly identified drug-induced differential regulation of Lanosterol 14-alpha demethylase, Endoplasmin, DNA topoisomerase 2-alpha and Calmodulin 1. The feedback regulation in these and other targets is likely to be relevant for the success or failure of the molecular intervention. Many drug targets thought to be suitable for therapeutic purposes are subjected to positive or negative feedback loops upon chemical perturbations which might even account for the development of drug tolerance. In this study, we carried out the first systematic analysis of drug-induced differential expression of drug targets using the Connectivity Map, a resource that contains the genome-wide expression profiles of 1309 bioactive small molecules performed on four cultured human cells. The main obstacle in analyzing such a large set of profiles is the non-biological experimental variation across batches. We overcame this by developing a pipeline for strict filtering and state-of-the-art normalization and were able to utilize the Connectivity Map for assessing the drug-induced differential regulation of drug targets. Using the normalized data, we found that at least 8% of the drug-induced drug targets studied are differentially regulated in three cell lines; some of these confirm previous observations in other cell lines. Our work not only quantifies the amount of target expression feedback loops in three human cell lines, but also identifies so far unknown drug-induced target expression changes; some of them can be linked to the development of drug tolerance in patients. Although drugs can perturb biological systems by interacting with different types of biomolecules For the future development of new drugs, the understanding of their mechanisms of action is vital. To tackle this in a large-scale, systemic way, the Connectivity Map (CMap) consortium studied the effects of 1309 bioactive small molecules including more than 800 marketed drugs on genome-wide gene expression in four cultured human cells, One important aspect of a good target is its reliability and vulnerability over long periods. Biological systems are robust in a way that they restore the perturbations caused by drug treatments. Many drug targets thought to be suitable for therapeutic purposes turn out to be less effective than expected or account for adverse side effects STITCH et al. proposed to construct a ‘Prototype List’ of the drug by merging its experiments from cell lines, batches, concentrations and microarray platforms CMap is a searchable database of gene expression profiles drug-induced gene expression profile similarity (DIPS) scores using Gene set enrichment analysis .To reveal systematic biases, the DIPS scores of drug-induced gene expression profiles using biological controls were classified into four drug and batch categories . The DIPWe utilized the large number of treatments to infer the background gene expression (by mean-centering) instead of the few biological controls provided by CMap, in order to eliminate the batch effect. In this way, also common (e.g. stress) responses will be down-weighted to reveal the characteristic expression response of each chemical perturbation.−16). Same conclusions were also derived from the distributions of Pearson correlations for drug-induced gene expression profiles across four drug/batch categories  classification of the World Health Organization (WHO) et al.  are subjected to significant differential expression upon drug treatment  by compaThe identified, differentially regulated drug targets are enriched in G-protein coupled receptors (GPCRs) , in agreIn addition to cross-regulation of multiple drugs through the same signaling pathways, promiscuous drugs targeting multiple proteins may cause complex regulatory networks. In order to explore the cross-regulation of drug targets induced by a promiscuous drug, we searched and found that 259 out of 466 total drugs are multi-target drugs and 4 of these drugs act on multiple differentially regulated drug targets upon drug treatment. For example, Podophyllotoxin used in various chemotherapies is known to target both tubulin beta 2C and DNA topoisomerase 2-alpha. The tubulin beta 2C and DNA topoisomerase 2-alpha mRNAs are both down-regulated upon drug treatment in three cell lines . TherefoWhile the above cases only confirm literature reports in other cell lines or tissues, we also identified new cases of drug-induced expression regulation of drug targets. The significant novel findings are the inhibitor-induced down-regulation of calmodulin 1, DNA topoisomerase 2-alpha and up-regulation of endoplasmin, lanosterol 14-alpha demethylase and cAMP-specific phosphodiesterase 4D . On this data set, filtering was performed in multiple steps as follows: Treatment instances (i.e. one treatment versus vehicle control pair) from three cell lines  were taken into consideration. Only the treatment instances from the production batches containing over twenty-five treatments in HT_HG-U133A platform were selected  Lastly, for each cell line, the highest concentration of treatments was selected discarding lower concentration treatments. Connectivity Map  contains 6100 gene expression profiles of 4 cell lines treated with 1309 distinct small molecules. Data from Connectivity Map was downloaded from the CMAP main website Click here for additional data file.Figure S2Same as (0.40 MB TIF)Click here for additional data file.Figure S3Distributions of the drug-induced gene expression profile similarity scores for drug-drug pairs across four drug/cell line categories. To gain a comprehensive picture of drug concordance across cell lines, we evaluated whether the similarity scores are driven by cell-line specific gene expression. For pairwise comparison of profiles from different cell lines, drug treatments from multiple cell lines were merged into one matrix where only the ‘Present’ probe sets for three cell lines were preserved in the matrix. The DIPS scores on the category of the same drug from different cell lines (D+/C−) are significantly higher than the scores within the category of different drugs from the same cell line (D−/C+)  meaning that the drug response is generally concordant across cell lines.(0.34 MB TIF)Click here for additional data file.Figure S4Distribution of molecular functions of differentially regulated drug-targets  compared to molecular functions of all other targets. Drug target classification is based on the categorization described in ChEMBL with few changes. For instance, for a more detail categorization, the lyase, hydrolase, oxidoreductase and transferase activities were included. If a drug target is identified within multiple categories, the order of the categories introduced was used to choose the first category as the main category to annotate the drug target. (0.97 MB TIF)Click here for additional data file.Figure S5Differentially regulated GPCRs and topoisomerase II of (0.42 MB TIF)Click here for additional data file.Table S1Complete list of statistical tests for the differential regulations of drug-targets. The average difference values for the drug-induced drug-targets are tested against the mRNA changes of the same gene in the population of heterogeneous drug treatments from CMap. Anova is used to assess the significance of the differential expression of drug-induced drug targets in multiple and specific cell lines, respectively. This excel sheet contains the name of the drug-targets with its evaluation in multiple cell lines. Only the drug-targets whose detection call are ‘Present’ in more than one-tenth of the experiments in specified cell line, are pursued for the analysis of differential gene-expression of drug-targets. If the detection call does not specify the required criteria, the column of a drug-target for that cell line is left blank. The q-values reported here are calculated using the FDR correction algorithm.(0.10 MB XLS)Click here for additional data file.


In this studywe determined the effects of the peripheral administrationof both insulin and IGF-1 on cardiovasculardynamics and LSNA following removal of the areapostrema (APX), a major site of blood-brain communication.Insulin infusion in normal rats decreasedMAP but increased HR and LSNA. Wheninsulin was infused in APX rats it also decreased theMAP but the MAP recovered rapidly and plateauedat a level equivalent to normals after 40 min. Insulinsignificantly increased the HR and LSNA in theAPX rats compared to normals. However, when hypoglycemiawas prevented by glucose infusion,the HR and LSNA responses to insulin in the APXrats were similar to normals. IGF-1 also decreasedMAP and to a greater extent in the APX ratscompared to normals but the increased LSNA inAPX rats was equivalent to normals. The APX ratswhen compared to normals had a greater sensitivityto insulin-induced hypoglycemia while IGF-1 decreasedthe plasma glucose to a lesser degree in APXrats. We conclude that insulin and IGF-1 entry intothe CNS at least via the area postrema does notcontribute significantly to the hypotensive responseand that the greater depressor response to IGF-1 islikely due to enhanced vascular sensitivity in APXrats. The increased HR and LSNA following insulinwere likely mediated by an increased reflexiveresponse to hypoglycemia.Previous studies have demonstrated that insulin andIGF-1 both increase lumbar sympathetic nerve activity(LSNA) and decrease mean arterial pressure(MAP). We hypothesized that the peripheral responsesto insulin and IGF-1 are mediated, at leastin part,


Double-antibody radioimmunoassay using a mouse monoclonal anti-CEA (MA/1) has been used to measure CEA in human serum. Low levels of MA/1-binding CEA have been found in serum from normal individuals and moderately raised levels are sometimes associated with certain non-malignant diseases. As with conventional anti-CEA, the MA/1 antibodies can recognize significant amounts of CEA in serum from patients with a variety of solid tumours. However they appear to recognize a different immunodeterminant and possibly a different population of CEA molecules to, or a subset of, those measured by two routine assays. Studies in which the MA/1 assay was directly compared with the results of the Charing Cross routine and Abbott EIA assays have indicated that different immunological forms of CEA may be expressed in the course of tumour progression but no prognostic value was evident in this study. Our results stress the need to resolve immunological specificities expressed by CEA-like molecules and evaluate their clinical importance.


Over 50% of patients with upper limb paresis resulting from stroke face long-term impaired arm function and ensuing disability in daily life. Unfortunately, the number of effective treatments aimed at improving arm function due to stroke is still low. This study aims to evaluate a new therapy for improving arm function in sub-acute stroke patients based on mental practice theories and functional task-oriented training, and to study the predictors for a positive treatment result. It is hypothesized that a six-week, mental practice-based training program  targeting the specific upper extremity skills important to the individual patient will significantly improve both arm function and daily activity performance, as well as being cost effective.One hundred and sixty sub-acute stroke patients with upper limb paresis (MRC grade 1–3) will participate in a single-blinded, multi-centre RCT. The experimental group will undertake a six-week, individually tailored therapy regime focused on improving arm function using mental practice. The control group will perform bimanual upper extremity exercises in addition to regular therapy. Total contact time and training intensity will be similar for both groups. Measurements will be taken at therapy onset, after its cessation and during the follow-up period (after 6 and 12 months). Primary outcome measures will assess upper extremity functioning on the ICF level of daily life activity , while secondary outcome measures cover the ICF impairment level (Brunnstrom-Fu-Meyer test). Level of societal participation (IPA) and quality of life  will also be tested. Costs will be based on a cost questionnaire, and statistical analyses on MAN(C)OVA and GEE .The results of this study will provide evidence on the effectiveness of this mental practice-based rehabilitation training, as well as the cost-effectiveness.Current Controlled Trials [ISRCTN33487341) The incidence of stroke in the Netherlands was 2.2/1000 in 2000 . RecentlSome studies have shown task-oriented treatment to positively affect arm function recovery in stroke patients . More reIn neuroscience, interest in movement imagery has grown in line with improvements in brain mapping techniques. Results from brain imaging experiments suggest that executed and imagined movements share a common neural substrate -10. ThisThe possible benefits of movement imagery on motor performance in acute and chronic stroke patients have been investigated in several studies. Page et al., in a small feasibility study using movement imagery in stroke patients, found a marked improvement in their arm function compared to that of the control group . SimilarThe effects of mental practice on small chronic stroke groups have been reported in several studies -22 usingOnly one article has reported on the long-term effect of mental practice in stroke patients. This was based on an evaluation conducted just one month after training; the conclusions were positive . The effBased on the latest body of evidence, it is hypothesized that mental practice applied in a training regime involving arm function tasks will lead to a significant and long-lasting improvement in stroke patients' arm function. Furthermore, since rehabilitation depends upon the learning of new behaviors (this is associated with brain plasticity), the treatment should include much repetition , start eThe aim of the proposed research project is to systematically investigate the therapeutic potential of a mental practice-based therapy in the  restoration of arm/hand function in sub-acute stroke patients. This aim has led to the following research questions:1. Does a six-week, mental practice-based rehabilitation regime for patients with upper extremity paresis in the sub-acute stroke phase improve arm function and daily activity performance as compared to usual care?2. What are the prognostic factors for a good therapy outcome?3. Is a regime such as that described in (1) cost effective as compared to usual care?A multi-centre, single-blinded, randomized controlled trial will be conducted to evaluate the effects of six weeks of mental practice-based treatment on arm function in unilateral stroke patients. The evaluation will span the full post-stroke year. Assessment will take place upon entry to the study; post-treatment and follow-up assessments will be performed on three moments during the year  randomization scheme including pre-stratification according to two variables: MRC scale of the elbow flexor (dichotomized in score 1 or scores 2–3); and participating hospital. Two sets of opaque, numbered envelopes will be prepared for each site (one each for MRC score 1 and MRC scores 2–3) containing cards indicating the allocated group. When a new patient is registered, a card will be extracted and the relevant occupational therapist informed of the group allocation.In accordance with Dutch stroke rehabilitation guidelines, the intervention group patients will receive their regular therapy  and addist person perspective (an 'over-the-shoulder' view). In the first step, correct task performance is shown on screen combined with a verbal explanation. Five repetitions are given. In the second step, task performance is repeated on screen but without verbal explanation; patients are asked to mentally practice the movement. If they are able to actually perform (part of) the task, they may do so concurrently with the imagination of the movement. Again, five repetitions are given. In the third step, no guidance during task performance is given except a visual and verbal cue indicating the end of the task performance over five repetitions. Patients already familiar with this task can immediately start on step two.Five different mental practice training tasks derived from the Frenchay Activities Index  are avaiDVDs are available for every task for right- and left-handers. Patients must practice at least three times a day for ten minutes each session. During the intervention period, functional arm/hand progress will be evaluated by the occupational therapist every two weeks. If functional level improves, a new task will be chosen and the DVD changed. The total intervention lasts six weeks.Patients in the control group receive therapy as usual. In addition, they will be instructed to practice additional bimanual upper extremity techniques based on conservative neurodevelopmental (NDT) principles . These eMeasurements will be taken upon entry to the study (T0 = baseline) and 6 weeks (T1 = post treatment); 6 months (T2 = short-term follow-up); 9 months  and 12 months (T4 = long term follow up) after T0. They will be performed by a rater blinded for therapy modality, and administered wherever the patient is at the time. A blinding check will be performed after each of the four measurement sessions.Outcome measures and assessment moments are presented in table The following socio-demographic variables will be recorded: age, sex, living situation and educational level. The medical variables include systematically scored, stroke-related neurological variables: lesion site, stroke type (hemorrhagic or ischemic), paresis level and co-morbidity. In the questionnaire, information on demographical variables is retrieved. Medical variables as presented above are derived from the medical file of the referring consultant in rehabilitation medicine. Patients will be asked for permission to use this information of their medical file in the informed consent procedure.The following aspects of cognitive functioning were measured.The Cognitive Log (Cog-log) is a 10-item cognitive screening instrument which measures higher neurocognitive processes including orientation, memory, concentration and executive skills .To asses participants' ability to imagine motor acts, the Vividness of Movement Imagery Questionnaire (VMIQ) will be used . IndividThe Credibility/Expectancy Questionnaire (CEQ), a simple scale for measuring rationale credibility and treatment expectancy in clinical outcome studies will be used. The credibility and expectancy of mental practice and control training is scored by the patient. This questionnaire demonstrated high internal consistency and good test-retest reliability .Physical functioning will be assessed on three different levels, in accordance with the International Classification of Functioning . PatientUpper extremity functioning at the impairment level will be assessed using two instruments, described below.1. 1.1 The arm section of the Fugl-Meyer Test (FMT) contains three different domains: (a) motor function , (b) sensation  and (c) passive joint motion/joint pain [ 0 to 48). Each it 0 to 48) and show 0 to 48),36.1.2 To score spasticity level, the Tardieu Scale will be used. The affected limb is passively moved through range at two velocities – i.e., as fast and as slow as possible (VI). At both velocities, the quality of the muscle reaction to stretch is assessed for each muscle group, and the angle at which the muscle reaction occurred is measured with a hand-held goniometer after the cessation of movement. Spasticity will be scored from 0–4 during the fast stretching velocity. In patients with severe brain injury and impaired consciousness, the Modified Tardieu Scale provides higher test-retest and inter-rater reliability than the Modified Ashworth Scale and may therefore provide a more valid spasticity scale for adults [r adults .2. Upper extremity functioning at the activity level will measured using the following three instruments.2.1 The Wolf Motor Function Test (WMFT) test contains 15 timed and 2 strength tasks (lifting of weighted limb and grip strength), ranging from simple to complex and administered sequentially to each upper extremity while controlling for patient positioning. Trained observers rate quality of movement using a 6-point functional ability scale . Strength and performance time will be recorded by the test administrators. The psychometric properties of the WMFT appear solid [ar solid ,38-40.2.2 The Frenchay Arm Test (FAT) will be used to assess the degree to which the patient is able to actually perform arm hand functions and tasks. It includes an evaluation of performance on five different tasks, and has shown good reliability and validity in stroke patients [patients .2.3 Accelerometery (ACC) will be used to assess upper extremity use in a daily life situation. Patients will wear a 'watch' with an accelerometer inside (Actiwatch [ctiwatch ) on bothThe Actiwatch has shown good validity for assessing daily life activities . In stro3. Functional performance on the level of participation in society and perceived quality of life will be measured using three methods.3.1 The Impact on Participation and Autonomy (IPA) questionnaire. This 39-item questionnaire focuses on two aspects of participation: the perceived participation level in different domains, and the problems encountered [ountered ,47.3.2 The Stroke-Specific Quality of Life (SS-Qol) scale. This includes an overall evaluation of the patient's quality of life compared with their pre-stroke state. Twelve domains are included: personality, energy, language, mobility, vision, upper extremity function, thinking, mood, work/productivity, self care and family and social roles .3.3 The EuroQol 6D (EQ-6D). This is a generic measure scoring quality of life using six domains: mobility, self-care, usual activities, pain/discomfort, anxiety/depression and cognition. Each domain consists of three answer possibilities. Participants are also to rate their current health state on a visual analogue scale from 0 to 100 [0 to 100 .In brief, primary outcome measures for the evaluation of upper extremity functioning focus on the activity level , whereas secondary outcome measures focus on both the impairment (FMT) and participation level .After completing the intervention, participants will be asked to evaluate it by way of a questionnaire. In addition, treatment compliance in both groups will be monitored using diaries recording the daily amount of time patients spend on mental practice training (intervention group) and NDT-based upper extremity training (control group). Compliance can be an important issue in studying patients in the sub-acute stroke phase : poor coBoth direct non-medical and indirect costs will be measured using a cost questionnaire administered to the participants or their proxies at the time of the T0-T4 assessments . An addiDirect non-medical costs include patient times, transportation and out-of-pocket expenses not covered by insurance. Indirect costs would cover productivity losses and informal care by the family or significant others. In line with recommendations in the Dutch manual for costing in economic healthcare evaluations, standardized costs will be used . MedicatThe number of dropouts (patients who prematurely end their participation) and follow-up losses in both training groups will be reported based on descriptive data. Baseline characteristics of compliant and non-compliant participants will be compared. Before examining the intervention's effectiveness, possible differences between the two groups will be determined by comparing baseline characteristics using independent sample T-tests  or Mann Whitney U-tests  in the event of continuous variables. In cases of dichotomous variables, a chi-square test will be used.The effects of mental practice-based therapy on arm function outcome will be evaluated using MAN(C)OVA and GEE  analyses. Deviations from the therapy protocols will be analyzed according to the 'intention-to-treat' principle. If either T2 or T4 data are missing, the 'last-observation-carried-forward' principle will be used. Losses of T0 and/or T1 data will lead to exclusion, and an additional participant will be entered into the project. Subgroup analysis will be performed for potential effect modifiers.To assess whether protocol deviations or care provided outside the intervention have caused bias, the results of the intention-to-treat analysis will be compared to the on-treatment analysis.strength on T0) , cognitive level (Cog-log), credibility and expectancy of training (CEQ), general arm muscle strength  benefit as a function of the ceiling ratio, or society's maximum willingness to pay. A 4-state Markov with 6-month cycle to approximate the time span between medical follow-ups will be used to simulate a long-term, 4-year period. Discounting of costs and outcomes will be undertaken at 4% . UncertaIn this study, the (cost) effectiveness of a mental practice-based training regime in improving arm function and daily activity performance in stroke patients will be evaluated. In addition, prognostic factors for a strong training outcome will be examined. A number of issues were taken into account in designing this study protocol.Firstly, we intend to include tasks that would be appealing for all patients. For this reason, ordinary daily life activities have been chosen. Individual patients will be designated an activity that is currently just out of the reach of their functional abilities; this ought to trigger motivation. Reaching a point where they can perform the task will directly result in an improvement and facilitation of daily life, which will be the participants' reward for good practice. In order to maintain this cycle, the tasks' complexity level will constantly increase depending on improvement in upper extremity function.Secondly, the current intervention training program was tested for feasibility. Patients who fulfilled the inclusion criteria and participated in an outpatient program of Heerlen's hospital department of rehabilitation medicine were included. After a variable baseline period with training as part of usual care, mental practice was added to the program. Patients trained at home were supervised by the rehabilitation team's occupational therapist. In a questionnaire, the compliance and feasibility of the training regime were scored. Participants appeared to experience no problems performing DVD-guided mental practice training guided twice a day for 7 days a week over 6 weeks, and reported good concentration levels during the 10-minute sessions. Only one participant, who showed rapid recovery in functional level, reported a decrease in motivational level. He was able to complete the most complex task (pouring water out of a can) in real life within the training period. Occupational therapists reported that the training program was feasible within the rehabilitation setting; these results were taken into account in designing the study protocol.Thirdly, in choosing the current outcome measures, three different domains of the International Classification of Functioning  were included. The second domain – level of activity – was chosen as the primary outcome measure level, since changes in this domain seem most clinically relevant in daily life performance. Both the ability to perform daily activities (to be measured by the Wolf Motor Function Test) and the level of activity in a daily life situation (to be assessed using accelerometry), are included. In our opinion, additional assessment of real-world impaired arm activity by way of accelerometry is important, since discrepancies between motor capacity as measured by laboratory performance tests and its actual use in daily life can exist.To conclude, this paper described the design of a randomized controlled clinical trial to study the effectiveness of mental practice training aimed at improving upper extremity functioning in stroke patients. The results of this study will provide evidence as to the (cost) effectiveness of the training as well as indicators for effective mental practice training in stroke patients.The author(s) declare that they have no competing interests.JAV is the main researcher and had an initiating role in writing this manuscript. HAS made important contributions during all phases of the study design. FRA designed the cost effectiveness part of the study. BHM, WWE and MMO had an important role in the design of the intervention and will have an important role in study-coordination on the various locations. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


Post-translational stabilization of beta-catenin through mutation of the adenomatous polyposis coli (APC) gene has been proposed as an early step in colorectal carcinogenesis. Beta-catenin may translocate from the cytoplasm to the nucleus, where it might serve as a transcriptional factor to stimulate tumour formation. We investigated intracellular localization of beta-catenin in sporadic colorectal adenomas and cancers as well as familial adenomatous polyposis (FAP). Nuclear over-expression of beta-catenin was observed in 35% (7/20) of intramucosal cancers and 42% (23/55) of invasive cancers but was not seen in any adenomas from sporadic or FAP cases. Cytoplasmic beta-catenin in adenomas was significantly higher than that of normal mucosa in both sporadic and FAP cases. The cytoplasmic intensity index of cancers was significantly higher than that of sporadic adenomas, but the index was not correlated with nuclear expression in cancers. These findings suggest that nuclear translocation of beta-catenin is involved in development of intramucosal cancer rather than adenoma, independent of APC mutations. Cytoplasmic accumulation of beta-catenin may occur in adenomas, but it remains to be determined whether this is a cause or a consequence of colorectal cancer. © 2000 Cancer Research Campaign


The determination of hormone inducible proteins in endocrine tumours may yield information about the presence of hormone dependent tumour cells. We have estimated the high affinity oestradiol binding capacity in primary mammary carcinomata of 57 postmenopausal patients. Glucose-6-phosphate dehydrogenase and lactose synthetase are known from animal experiments to be hormone inducible. Therefore, in biopsies of sufficient size the activity of glucose-6-phosphate dehydrogenase (47 pateints) and lactose synthetase (23 patients) was also studied. It was found that biopsies with high binding capacity also showed high activities of glucose-6-phosphate dehydrogenase and lactose synthetase A protein . No lactose synthetase B protein  has been discovered in the tumours. The present observations may be considered suggestive evidence of a relationship between high oestradiol binding capcity and high activities of the two enzymes on the one hand and hormone dependence of the tumour on the other. However, further clinical studies are required before final conclusions in this respect can be drawn.


In the study of adaptive evolution, it is important to detect the protein coding sites where natural selection is acting. In general, the ratio of the rate of non-synonymous substitutions (Ka) to the rate of synonymous substitutions (Ks) is used to estimate either negative or positive selection for an entire gene region of interest. However, since each amino acid in a region has a different function and structure, the type and strength of natural selection may be different for each amino acid. Specifically, domain sites on the protein are indicative of structurally and functionally important sites. Therefore, Window-sliding tools can be used to detect evolutionary forces acting on mutation sites.This paper reports the development of a web-based tool, WSPMaker (Window-sliding Selection pressure Plot Maker), for calculating selection pressures (estimated by Ka/Ks) in the sub-regions of two protein-coding DNA sequences (CDSs). The program uses a sliding window on DNA with a user-defined window length. This enables the investigation of adaptive protein evolution and shows selective constraints of the overall/specific region(s) of two orthologous gene-coding DNA sequences. The method accommodates various evolutionary models and options such as the sliding window size. WSPmaker uses domain information from Pfam HMM models to detect highly conserved residues within orthologous proteins.WSPMaker is a web tool for scanning and calculating selection pressures (estimated by Ka/Ks) in sub-regions of two protein-coding DNA sequences (CDSs). In researching adaptive evolution processes, it is important to detect protein coding genes that are under an active natural selection process. Traditionally, this is described as the ratio of Ka/Ks. Ka is the rate of non-synonymous substitution and Ks is the rate of synonymous substitution. The Ka/Ks ratio can be used to estimate either negative or positive selection tendencies for genes of interest -3. HowevRecently, the Selecton program  has beenThe most important feature of the WSPMaker is that it compares the selection constraints of domain and non-domain regions. It provides a simple (or effective) method to detect for defining positive and negative selection pressure regions within protein-coding sequences.WSPMaker (Window-sliding Selection pressure Plot Maker) uses the ClustalW sequence alignment tool . As a deWSPMaker implements several different evolutionary models widely used to estimate the level of selection operating on a gene or coding region. In the 'Single Size' option, there are three model pairs . The first pair includes M1a  and M2a (positive selection). The second pair includes M7 (beta) and M8 (beta & ω), while the third pair includes M0 (one ratio) and M3 (discrete). Comparison of these model pairs allows the for statistical testing of the hypothesis that there is positive selection on proteins  against the null hypothesis model. The output is the likelihood of each model, allowing for a comparison using a likelihood ratio test (LRT). The program predicts when a site is undergoing positive selection. In the second option, 'User Defined Size,' there are two models. The Yang and Nielsen model  and the WSPMaker takes a default input data type of user-curated orthologous DNA coding sequence pairs. WSPMaker allows users to submit various sequence formats, such as FASTA, EMBL, GCG, ClustalW, and Phylip/Phylip4, for the input data containing codon-based alignment of paired sequences. WSPMaker provides a choice of one of the 17 NCBI genetic codes  for autoThe results page consists of four sections. They are 1) file download, 2) Ka/Ks graph, 3) Pfam domain position annotation, and 4) Ka/Ks calculation. An example output is shown in Figure Here, we give an example illustrating WSPMaker's use for detecting positive selection Figure .The subset of genes implicated in nervous system development is known to display significantly higher rates of protein evolution in primates than in rodents . The hig.WSPMaker is a useful web-based visualization tool that shows which DNA sub-regions of coding sequences are under strong selection pressure. It can assist researchers in easily detecting candidate genes and partial gene regions for fast base substitution in functional and evolutionary analyses, using its window-sliding visual graphs. The WSPMaker server can be accessed at The authors declare that they have no competing interests.YSL, THK, and TWK wrote the code for WSPMaker. WHC worked on the visual display of the results. GSS designed the overall web site and coordinated the project. YSL wrote the main draft of the paper. All authors have read and approved the final manuscript.


Coral bleaching can be defined as the loss of symbiotic zooxanthellae and/or their photosynthetic pigments from their cnidarian host. This major disturbance of reef ecosystems is principally induced by increases in water temperature. Since the beginning of the 1980s and the onset of global climate change, this phenomenon has been occurring at increasing rates and scales, and with increasing severity. Several studies have been undertaken in the last few years to better understand the cellular and molecular mechanisms of coral bleaching but the jigsaw puzzle is far from being complete, especially concerning the early events leading to symbiosis breakdown. The aim of the present study was to find molecular actors involved early in the mechanism leading to symbiosis collapse.Pocillopora damicornis nubbins was subjected to a gradual increase of water temperature from 28°C to 32°C over 15 days. A second control set kept at constant temperature (28°C). The differentially expressed mRNA between the stressed states (sampled just before the onset of bleaching) and the non stressed states (control) were isolated by Suppression Subtractive Hybridization. Transcription rates of the most interesting genes (considering their putative function) were quantified by Q-RT-PCR, which revealed a significant decrease in transcription of two candidates six days before bleaching. RACE-PCR experiments showed that one of them (PdC-Lectin) contained a C-Type-Lectin domain specific for mannose. Immunolocalisation demonstrated that this host gene mediates molecular interactions between the host and the symbionts suggesting a putative role in zooxanthellae acquisition and/or sequestration. The second gene corresponds to a gene putatively involved in calcification processes (Pdcyst-rich). Its down-regulation could reflect a trade-off mechanism leading to the arrest of the mineralization process under stress.In our experimental procedure, one set of Under thermal stress zooxanthellae photosynthesis leads to intense oxidative stress in the two partners. This endogenous stress can lead to the perception of the symbiont as a toxic partner for the host. Consequently, we propose that the bleaching process is due in part to a decrease in zooxanthellae acquisition and/or sequestration. In addition to a new hypothesis in coral bleaching mechanisms, this study provides promising biomarkers for monitoring coral health. Coral reefs are fascinating ecosystems, characterized by high levels of biodiversity and ecological complexity, high primary productivity and have significant aesthetic and commercial value, particularly in relation to fisheries, tourism and the aquarium industry. In recent decades coral reefs have been dramatically impacted by large-scale disturbances . NaturalOf the broad range of natural and anthropogenic perturbations that affect coral reefs, coral bleaching is recognised as a major disturbance that has the potential to significantly alter the biological and ecological processes that maintain reef communities ,5. This Symbiodinium spp.), commonly referred to as zooxanthellae. This symbiosis breakdown can be the consequence of a large variety of environmental stressors  pH 7.4). The samples were then incubated overnight at 4°C in a moist chamber with the purified IgG at 20 μg.ml-1 in the preceding buffer. The primary antibodies surplus was discarded by multiple rinsing in the saturating medium and samples incubated for 1 h at room temperature with biotinylated anti-rabbit antibodies (secondary antibodies) diluted 1:250 in the saturating medium. After incubation, slides were rinsed with PBS pH 7.4, and samples finally stained for 15 min with streptavidin AlexaFluor 568 1:50 diluted (Molecular probes) and 4',6-diamino-2-phenylindole, DAPI . Sections were mounted in Pro-Long antifade medium (Molecular Probes) and observed with a confocal laser-scanning microscope .Immunolocalization on tissue sections was performed according to a protocol previously described in . BrieflyJVD and GM conceived and coordinated the study, participated in molecular genetic studies  and wrote the manuscript. MA and DA participated in the design and the coordination of the study, drafted the manuscript. ER and DD participated in RACE-PCR experiments and DNA sequencing. LF and JVD helped design and conduct the experimental procedures in the aquaria. YM participated in the molecular modelling of PdC-Lectin. CFP participated in the measurements of zooxanthellae density and drafted the manuscript. ST, ET and DZ performed immunolocalization experiments and drafted the manuscript. All authors read and approved the final manuscript.Top blastx, annotation, GeneBank accession number and specific primers (Q-RT-PCR) of selected ESTs. The data provided represents, Top blast, GeneBank accession number and specific primers used for Q-RT-PCR of selected ESTs.Click here for file


Identification of novel cancer-causing genes is one of the main goals in cancer research. The rapid accumulation of genome-wide protein-protein interaction (PPI) data in humans has provided a new basis for studying the topological features of cancer genes in cellular networks. It is important to integrate multiple genomic data sources, including PPI networks, protein domains and Gene Ontology (GO) annotations, to facilitate the identification of cancer genes.Topological features of the PPI network, as well as protein domain compositions, enrichment of gene ontology categories, sequence and evolutionary conservation features were extracted and compared between cancer genes and other genes. The predictive power of various classifiers for identification of cancer genes was evaluated by cross validation. Experimental validation of a subset of the prediction results was conducted using siRNA knockdown and viability assays in human colon cancer cell line DLD-1.Cross validation demonstrated advantageous performance of classifiers based on support vector machines (SVMs) with the inclusion of the topological features from the PPI network, protein domain compositions and GO annotations. We then applied the trained SVM classifier to human genes to prioritize putative cancer genes. siRNA knock-down of several SVM predicted cancer genes displayed greatly reduced cell viability in human colon cancer cell line DLD-1.Topological features of PPI networks, protein domain compositions and GO annotations are good predictors of cancer genes. The SVM classifier integrates multiple features and as such is useful for prioritizing candidate cancer genes for experimental validations. Cancer is a complex disease whose multi-step progression involves alteration of many genes, including tumor suppressor genes and oncogenes. Although multiple targeted cancer therapeutic agents have been developed based on several known cancer genes, it is expected that many cancer genes remain to be identified . IdentifMost gene products interact in complex cellular networks. It was proposed that direct and indirect interactions often occur between protein pairs whose mutations are attributable to similar disease phenotypes. This concept was utilized to predict phenotypic effects of gene mutations using protein complexes  and idenbona fide cancer genes whose mutations are causally implicated in cancers) [In this study, we took a machine learning approach to investigate various network and functional properties of known cancer genes to predict the likelihood of a gene to be involved in cancer. Although Cancer Gene Census provides a catalogue of currently known cancer causing mutations, many other cancer genes may be yet to be discovered from the rest of the genome. To reduce the false positives in classifying genes not involved in cancer, we extended the comparison of various features in four non-overlapping gene groups, i.e. "cancer genes" from the Cancer Gene Census (cancers) , "COSMICcancers)  (excludicancers)   as the kernel of SVM. We conducted cross-validation to select the parameter gamma for the radial basis function kernel and the parameter c for the cost of training error. Cost weights wi were set based on the ratio between the number of negative examples and the number of positive examples in the training data. Naïve Bayes and logistic regression classifiers were built using default parameters from Weka tools .SVM classifier was built using LIBSVM tools, a library for Support Vector Machines The features used to train the classifiers include degree, clustering coefficient and average length of shortest path to a cancer gene from the PPI network, gene and protein lengths from sequence features, Ka and Ka/Ks from evolutionary features, presence or absence of annotation of selected GO terms and Pfam domains (p < 0.01 from chi-square tests of over- or under-representation in cancer genes compared with non-cancer genes). Continuous features whose distribution deviates significantly from the normal distribution were log transformed, including PPI degree, protein length, gene length, Ka and Ka/Ks.c and gamma, and then a classifier trained using the selected parameter pair was evaluated using the test data . The area under the ROC curve (AUC) was used to measure the performance of different classifiers. ROC curves and AUC values were obtained using the LIBSVM and Weka tools. A classifier with better performance than a random predictor has an AUC between 0.5 and 1.Classifiers were trained and evaluated using cancer genes as positive examples and non-cancer genes as negative examples. 10-fold cross validation experiments were conducted to evaluate the performance of the classifiers. The dataset was randomly divided into ten subsets, each of which has one tenth of the number of examples in the original set and preserves the relative proportion between positive and negative examples. A classifier was trained and tested ten times where each time a different subset was used for testing and the remaining nine subsets were used for training. For SVM classifiers, we conducted 5-fold cross-validation using the training data for each round to select parameter pair DLD-1 (ATCC CCL-221) cells were obtained from the American Type Culture Collection and maintained in High Glucose Dulbecco Modified Essential Media supplemented with 10% Fetal bovine sera and 2 mM L-Glutamine. Gene targeting siRNA duplexes (Dharmacon siGENOME), siGENONE Non-Targeting siRNA #2 (Dharmacon D-001210-02) and siGENOME Non-Targeting siRNA Pool #1 siRNAs were transfected into cells using Lipofectamine 2000 (InVitrogen #11668). siRNA duplexes were transfected at concentrations of 25-30 nM (duplexes) or 100-120 nM (pools), respectively. Lipid-siRNA complexes were formed in OptiMEM Media (Gibco #31985) to which cells were added in antibiotic-free media. Four days following transfection, cell viability was measured with the addition of CellTiter-Glo (Promega #G7570) and luminescence was measured according to manufacturer's instructions using a Perkin Elmer EnVision luminometer.t tests for each siRNA oligo. As there are four siRNAs targeting a given gene, we require at least two of the siRNAs have p-value less than 0.05 and the decrease in cell viability is at least 15% to claim that the gene is essential for cell viability.A viability score is defined as the ratio of CellTiter-Glo readout between transfection of a testing siRNA and that of negative controls (non-targeting siRNAs). A viability score less than 1 indicates decreased cell viability with siRNA targeting a given gene. Viability scores for two replicated transfections using the same siRNA were averaged and statistical significance of reduced viability was evaluated by A comprehensive human PPI network was built via integrating multiple publicly available data sources, including a collection of validated direct interactions , computaTo investigate various PPI network, functional and sequence features of cancer genes and other genes, we selected 9218 well-annotated genes that were included in the PPI network and were assigned with GO terms  and PfamThree topological features of the PPI network were computed for each gene: the network connectivity, the clustering coefficient , and theWe investigated the difference in the enrichment of various protein domains from the Pfam Database  and GO aWe then compared the patterns of Pfam and GO annotations among cancer, COSMIC, OMIM and non-cancer gene groups. We calculated the log-odds ratio for each Pfam domain and GO slim term measuring the differential frequency of being assigned to cancer genes vs. non-cancer genes. GO slim was used because it gives a broad overview of GO ontology content with reduced details. A gene-based log-odds score was subsequently derived as the sum of log-odds ratios for each Pfam domain and GO term assigned to a given gene . Overallt test p-value < 0.001). The median protein length for cancer genes is 591 aa, compared with the median protein length of 487 aa in COSMIC genes, 498 aa in OMIM disease genes and 433 aa in non-cancer genes. With respect to total gene length (including the length of introns and un-translated regions), the median gene length is 51 kb for cancer genes, 31 kb for COSMIC genes, 27.5 kb for OMIM genes and 21.7 kb for non-cancer genes; the median gene length of cancer genes are over two times longer than that of non-cancer genes . OMIM genes are also longer than non-cancer genes ; it was previous shown that disease genes on average are longer than house-keeping genes and other genes in the genome [We studied four sequence related features including protein length, gene length, the number of exons and the number of alternative transcripts Table . Cancer e genome . InteresF test p-value 0.096).With regards to other sequence features we examined, the probability density distributions did not show clear separation between cancer and non-cancer genes regarding the average number of alternative transcripts (data not shown); no significant difference was observed in the number of exons among the four gene groups (ANOVA The non-synonymous mutation rate (Ka) and the ratio of non-synonymous mutation rate (Ka) over synonymous rate (Ks)  between As distinctive patterns were observed between cancer and non-cancer genes from the analyses of PPI networks, annotations of GO and Pfam, sequence and conservation features, we sought to design a classifier to combine the predictive power of each type of feature for identification of cancer genes. Specifically, we considered PPI network features including degree, clustering coefficient and the length of the shortest path to a cancer gene, sequence features including gene and protein lengths, and conservation features including Ka and Ka/Ks ratio. For GO and Pfam features, we selected 79 GO terms and 61 Pfam domains significantly differentially represented in caner genes compared to non-cancer genes by chi-square test (p < 0.01). For a given gene, presence and absence of assignment of each GO term or Pfam domain was encoded as '1' or '0' respectively.Several machine-learning algorithms were investigated in building a classifier to predict novel cancer genes, including naïve Bayes, logistic regression and support vector machines (SVM), all of which have been widely used for pattern classification and regression problems. Naïve Bayes is a simple probabilistic classifier based on Bayes rules and has a strong assumption that the features are independent to each other. Logistic regression is a model used for prediction of the probability of occurrence of an event by fitting data to a logistic curve. SVMs map input examples to a higher dimensional feature space using a kernel function, and identify a separating hyperplane that maximizes the margin or distance from the hyperplane to the nearest positive and negative examples . Classift test p-value 4.3e-18) and OMIM genes ; COSMIC_other genes have higher probability scores than OMIM genes . Specifically, 102 out of 805 COSMIC_mut genes, 72 out of 1386 COSMIC_other genes, and 25 out of 1088 OMIM genes have a probability score no less than 0.5  and the decrease in cell viability is at least 15%. As a result, 6 out of the 16 (37.5%) predicted cancer genes vs. 40 out of the 316 (12.7%) predicted non-cancer genes were selected. Fisher's exact test showed a significant enrichment of genes essential for cell viability in predicted cancer genes vs. non-cancer genes .RNAi-based phenotypic screening has demonstrated its utility in identifying cancer genes and putative drug targets -34. As gFigure Our study represents a first attempt to examine the predictive power of PPI network properties, in combination with an extensive set of structural and functional features, for identification of cancer genes. Compared to OMIM disease genes and non-cancer genes, cancer genes have more interaction partners, higher network density in their neighborhood, and are more closely related to other cancer genes in the PPI network. These observations agree with the notions that cancer genes play a central role in the cellular network and exert functions in an inter-dependant modular fashion. One common concern regarding analysis of PPI network is that the observed higher connectivity of certain group of genes could be a result of a bias in the PPI network, as it could be argued that these genes received more detailed investigations by the research community. To address this concern, it was previously argued that higher number of known interaction partners for cancer genes is likely to be a consequence of higher frequency of promiscuous domains (which interact with a variety of different domains) in caner genes rather than obvious bias in the PPI network . Based oOur study showed that cancer genes have distinctive functional, sequence and evolutionary characteristics from COSMIC, OMIM and non-cancer genes. COSMIC genes and OMIM genes in turn have distinctive features between each other and from non-cancer genes. It should be noted that the OMIM gene set in our study is specific to the context of comparison with cancer genes as we excluded from the OMIM gene set those common between the OMIM database and Cancer Census Genes or COSMIC database. COSMIC genes showed relatively more similarities with cancer genes in many properties, and in fact many COSMIC genes were found to be involved in cancer although they are not included in the Cancer Gene Census database . TherefoSVM classifiers on average perform slightly better than Naïve Bayes and logistic regression. Naïve Bayes performs the worst in our study probably due to the fact that our feature vectors are not orthogonal to each other, which violated the basic assumption of Naïve Bayes models. The theoretical advantage of SVMs is that they simultaneously minimize the empirical classification error and maximize the geometric margin; the idea of maximizing the margin mitigates the problem of over-fitting the training data, which is of particular importance when dealing with large number of features.PPI topological features alone have relatively strong predictive power for identification of cancer genes. Similar to PPI features, GO and Pfam annotations are strong predictors compared to sequence and conservation features. Combining all these features maximize the predictive power Table . With thThe SVM classifier provides a probability score to prioritize candidate cancer genes, which can be followed up by experimental studies, such as siRNA knock down and cell viability assays. Preliminary siRNA studies on predicted cancer genes showed promising leads for further investigations. Interestingly, COSMIC genes with somatic mutations in cancer samples have higher scores than other genes in the COSMIC database Figure . As COSMTopological features of PPI networks, protein domain compositions and GO annotations are good predictors of cancer genes. The SVM classifier integrates multiple features and as such is useful for prioritizing candidate cancer genes for experimental validations. Preliminary siRNA studies on predicted cancer genes showed promising leads for further investigations. The integrative approach using PPI networks is a useful complement to large-scale systematic re-sequencing and other genomic discovery projects for identifying novel cancer genes.PPI: protein-protein interaction; GO: Gene Ontology; SVM: support vector machine; COSMIC: Catalogue Of Somatic Mutations In Cancer; OMIM: Online Mendelian Inheritance in Man; BIND: Biomolecular Interaction Network Database; HPRD: Human Protein Reference Database; KEGG: Kyoto Encyclopedia of Genes and Genomes; ROC: Receiver Operating Characteristic; RBF: radial basis function.The authors declare that they have no competing interests.ZT and LL designed the study. LL and KZ collected the data, performed the data analysis and drafted the manuscript. JL, SC and DD performed the siRNA experiments and prepared the corresponding Method sections. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:Supplementary Table S1-S3. Supplementary Table S1 Comparisons of network topological features among gene groups. Supplementary Table S2 Comparisons of Ka and Ka/Ks among gene groups. Supplementary Table S3 COSMIC and OMIM genes having probability greater than 0.5 from the SVM classifier.Click here for file


Objective: The intent of this study was to determine the efficacy and tolerance of single-dose oral azithromycin in the treatment of pregnant women with endocervical chlamydial carriage.Methods: A retrospective review of clinic records over a two-year period identified pregnant patients treated with a single 1-g dose of azithromycin for chlamydial carriage. The side effects and subsequent chlamydial carriage (test of cure) were noted.Results: A total of 146 pregnant women treated with azithromycin was reviewed. A cure rate of96% was found. Side effects were reported in 5%.Conclusions: A single 1-g oral dose of azithromycin is effective for the treatment of chlamydia and is well tolerated in pregnant women.


The reaction differs from that of its hydrolysis product DADP in a higher specificity anda lower capacity. Both of them induced exposure of the tryptophane residues and labeled Cys374 and theincrease in α-helix content depending on R, but the conformation changes caused by DADP are moresignificant than DDCP at the same R. These are related to the binding of DADP to groups other than thiols.The rate constants of conformation change suggested that DADP quenched the intrinsic fluorescence morerapid. The temporal change in fluorescence of NPM labeled actin has a biphasic feature: in the first 16minutes, the fluorescence was quenched, then it recovered slowly, indicating a multi-step reaction includinghigh affinity platinum binding → labeled Cys374 moving to hydrophilic environment → low affinity platinumbinding → Cys374-related conformation compacting in sequence.The binding of cis-diamminedichloroplatinum (DDCP) and cis-diaquodiammine platinum (DADP) torabbit skeletal muscle G-actin and the consequent conformation changes were studied as the function of thePt/actin molar ratio (R) and time by intrinsic and NPM labeled fluorescence, CD spectra as well as gelfiltrationchromatography. The results indicated that the unhydrolyzed DDCP can react with G-actin inpresence of Cl


An eight year old English boy presented with an abdominal undifferentiated 'Burkitt-like' lymphoma. Lymphoma cells from ascitic fluid were cultured on a human embryo fibroblast feeder layer and, after a short lag period, a cell line (DH-BL) was established which, like the original tumour, was both negative for the Epstein-Barr nuclear antigen (EBNA) and expressed a monoclonal pattern of surface immunoglobulin . DH-BL also possessed the Burkitt-related 8:14 chromosome translocation in all metaphases analysed; no other chromosomal abnormalities were present. The cell surface phenotype of the original biopsy cells and the cultured tumour cells in early passage were investigated using a panel of monoclonal antibodies to B lineage-associated antigens. These antibodies had recently been used to characterise African 'endemic' Burkitt's lymphoma (BL) biopsy cells and their derived cell lines. The cell surface phenotype of this English EBNA negative Burkitt-like lymphoma biopsy was indistinguishable from that previously shown by biopsies of EBNA positive endemic BLs. It therefore appears that both the endemic and sporadic forms of BL, as illustrated by this case, may be derived from the same subset of progenitor cells.