PALM-IST constructs protein interaction network and pathway information data relevant to the text search using multiple data mining tools and assembles them to create a meta-interaction network. It also analyzes scientific collaboration by extraction and creation of “co-authorship network,” for a given search context. Hence, this useful combination of literature and data mining provided in PALM-IST can be used to extract novel protein-protein interaction (PPI), to generate meta-pathways and further to identify key crosstalk and bottleneck proteins. PALM-IST is available at www.hpppi.iicb.res.in/ctm.Manual curation of biomedical literature has become extremely tedious process due to its exponential growth in recent years. To extract meaningful information from such large and unstructured text, newer and more efficient mining tool is required. Here, we introduce PALM-IST, a computational platform that not only allows users to explore biomedical abstracts using keyword based text mining but also extracts biological entity ( In today’s age of “big data biology” embraced with overwhelming amount of publication records and of high-throughput data, automated and efficient text and data mining platforms are absolutely essential to access and present biological information into more computable and comprehensible form121213141516171819202122e.g., diseases). Hence, implementation of an accurate, robust and automated platform aiming to integrate mining, interaction and pathway data towards development of meta-interaction networks is due.However, for meaningful knowledge discovery, more sophisticated amalgamation of literature analysis and biomedical data mining is required where text-mining solutions integrate with other data resources containing information regarding pathways, protein-protein interactions, gene expression and functional genomics. Intelligent combination of text and data mining might help researchers to discover hitherto undiscovered knowledge about novel protein-protein interaction information, gene-disease, and gene-drug relation. Scattered examples are available where information about gene-gene interactions2930Here, we present PALM-IST, which aims to provide intelligent combination of literature analysis and biomedical data mining. In PALM-IST, a user not only receives more relevant text results for various combination keywords but also can access important information regarding genes/proteins, gene expression, interactions, biological pathways, drug-disease association that are deemed to be connected to the search result. To the best of our knowledge, PALM-IST is the only platform where text mining, database retrieval (data mining), and pathway assembly have been done simultaneously. PALM-IST constructs and assembles protein network and pathway information data relevant to the search using multiple data mining tools. Biological pathways  of the observed proteins and their PPI network are overlaid to provide a meta-interaction network of cellular systems. Such assemblies of pathways can prove to be crucial for generation of novel meta-pathways containing key crosstalk and bottleneck proteins. PALM-IST also emphasized on scientific collaboration in the form of “co-authorship network,” in which nodes represent author name and edges represent co-authorship connection. Co-authorship networks are useful and can tell interesting features of academic communities. Thus, PALM-IST can become an important platform to aid large scale system biology based research where multiple genes/proteins and pathways are required to be examined to simultaneously for better understanding of the cellular complexity.e.g., glioblastoma or haemophilia) and author  based searches can be performed simultaneously and/or separately. All primary keywords along with their synonyms and acronyms are searched using AND  or OR (specified as “|” symbol) Boolean gates in NCBI PubMedA two tier keyword (primary and secondary) based search engine is introduced in PALM-IST server. Topic (The output of the PALM-IST server can be subdivided into five parts. Following section briefly describes each of the output using an example set of keywords (primary and secondary) based search. e.g., modulate, elevate, etc.). PALM-IST provides a unique option of simultaneous literature mining using multiple secondary keywords where abstracts are sorted for all possible combination of secondary query words. 63992 abstract containing articles are retrieved using an example literature search with primary keywords “Glioblastoma|Glioma|Brain tumor|Brain cancer” (“|” denotes OR gate) and secondary keywords like “EGFR<new line>TP53<new line>Erlotinib|Gefitinib”. Results for all single secondary keywords and in combination are mutually exclusive. Synonyms of genes for secondary keywords  are automatically used in abstract search. For example, out of 63992 abstracts only 2 abstracts were found where all the three secondary keywords or their synonyms are present. However, this could easily be done using advance keywords search in PubMed, but to retrieve abstracts for the other combinations, such as EGFR and Erlotinib|Gefitinib or TP53 and EGFR, it would require separate PubMed searches. In PALM-IST abstracts for all the combinations can be retrieved in single search. This becomes really useful option when a large number of secondary keywords are required to be searched. Result for secondary keywords can be used to write the summary of abstract, which in principle can be utilized for refined and curated text search.Abstracts retrieved for primary keyword based search are displayed and highlighted with the bio-entity words  and relation terms (st level and 2nd level interacting protein) for each observed protein is displayed with subcellular compartmentalization. Biological pathways with which each observed protein is involved are shown in a network display where crosstalk proteins (proteins that connect multiple pathways) are identified and emphasized. Biological pathways  of the observed proteins and their PPI network are overlaid to provide a meta-interaction network of cellular systems. Secondary information including gene summary, gene loci, Swiss-Prot/Ensembl code, three dimensional structure, and single nucleotide polymorphism (SNP) for each observed gene are provided on mouse click. Molecular expression data of the listed genes are provided where users can find up- and down-regulation patterns of those genes in numerous experimental conditionsThis section of the PALM-IST server deals with entity recognition of genes/proteins and tagging of abstracts containing the gene/protein names or their synonyms. It provides a list of human genes/proteins that are frequently found in the abstracts yielded by the primary and secondary keywords based search. Protein-protein interaction (PPIs) with two tiers of interaction  proteins to create a meta-interaction network. This broadens the scope of visualizing large interaction and pathway information data within a single visualization window. Co-occurrence based connections between multiple genes can be extracted within this section of the PALM-IST server. Authors and co-authorship networks extracted from the publications in which the particular protein and the primary keywords co-occur is also generated.Glioblastoma OR Glioma OR Brain tumor OR Brain cancer as primary keywords. Top 10 most frequently found genes/proteins within these abstracts are TP53 , EGFR , GFAP , AKT1 , VEGF , MGMT , PTEN , BCL2 , EGF  and TNF. All together 1272 unique protein-protein interactions including 332 interacting proteins were extracted for these 10 proteins. Merging of pathways involving these 10 proteins yielded 73 unique pathways and 1366 crosstalk proteins that connect at least two pathways. Mitogen-activated protein kinase 3 and 1 (MAPK3 and MAPK1), phosphatidylinositol-4,5-bisphosphate 3-kinase (PIK3 family), AKT1 , mitogen-activated protein kinase kinase 1 (MAP2K1) and RAS p21 protein activator (RAS) turn out to be the top 5 enzymes that crosslink maximum numbers of biological pathways .For example, 9923 genes were found from 63992 PubMed abstracts obtained with Abstracts yielded by primary and secondary keywords based search are scanned and sorted based on the presence of 925 approved drugs and 3813 disease names. Biological pathways  related to these drugs and diseases are presented. Similar to the gene/protein section, co-occurrence based connections between multiple drugs and diseases can be extracted within this section of the PALM-IST server. Names of the experts or authors who are frequently publishing scientific papers related to the drugs and diseases observed within the searched abstracts are presented in tabular and network display.Glioblastoma OR Glioma OR Brain tumor OR Brain cancer as primary keywords, most frequent gene-drug-disease triads are found to be MGMT-Temozolomide-Glioma (534 abstracts), VEGF-Bevacizumab-Glioma (156 abstracts), EGFR-Erlotinib-Glioma (99 abstracts), etc. Similarly, most frequent gene-disease-process triad combinations are EGFR-Glioma|Glioblastoma-Growth (1301 abstracts), VEGFA-Glioma|Glioblastoma-Growth (800 abstracts), MGMT-Glioma|Glioblastoma-Methylation (609 abstracts), AKT1-Glioma|Glioblastoma-Signaling (598 abstracts), VEGFA-Neoplasms-Angiogenesis (377 abstracts), etc. In addition to the triads, various combinations of pairs of genes, drugs, diseases, and biological processes are also extracted from the searched abstracts based on their co-occurrence. The observation of MGMT (O-6-methylguanine-DNA methyltransferase), Temozolomide and methylation as the most frequently observed (515 abstracts) gene-drug-biological process triad is in fact quite fascinating and can act as a proof of concept for the discovery of new knowledge of association between genes, drugs, diseases, and biological processes. The strong co-occurrence of MGMT, Temozolomide and methylation extracted by PALM-IST clearly indicates crucial association of them with Glioma. This is indeed the case as some tumors become sensitive to Temozolamide, via epigenetic silencing of MGMT/AGT geneIn this section PALM-IST offers text based co-occurrence of genes, drugs, diseases, and biological processes. Triad combinations of gene-drugs-disease and gene-disease-process are extracted and most frequent combinations are provided in tabular and network display option. For example, for the abstracts obtained with Glioblastoma OR Glioma OR Brain tumor OR Brain cancer as primary keywords, most papers are published from United States Of America (20945 papers) while most frequent authors and co-authors are Darell D Bigner from Duke University and Henry S Friedman from Duke University Neurosurgery Division who are renowned experts of the Glioma field for the last few decades. These author and co-author’s networks not only provide an idea about the experts of the fields but are also quite useful in revealing many interesting features of academic communities37Author’s statistics and network is an interesting feature of PALM-IST server. It provides detailed countrywide publication statistics represented in tabular and interactive global map format. Similarly, most frequent authors and their co-authoring relationship for a given literature search are provided in network based display using Cytoscape Weberica 2095 papers i.e., “Glioblastoma|Glioma|Brain tumor|Brain cancer”), various other disease names were used as query keywords. These diseases were grouped into four categories: a) metabolic disease, b) cancer, c) infectious disease and d) other diseases. Other than the above mentioned example primary keyword  outperformed the MetaMapDisease name recognition aided by the DNorm40The Comparative Toxicogenomics DatabaseThe co-authorship network and network derived features were verified against published networks provided in the PubNetBiomedical literature scan is critical to understand large amount of data generated in experiments and to retrieve novel information from them. PALM-IST constructs and assembles protein network and pathway information data relevant to the gene/proteins frequently observed within the searched text. Hence, PALM-IST can become an important platform to aid large scale system biology based research where multiple genes/proteins and pathways are required to be examined simultaneously for better understanding of the cellular complexity. A key challenge in cell biology is to understand the interconnectivity between its biochemical pathways with respect to extracellular signals. Hence, the assembled/interconnected network (supra-network) constructed via PALM-IST applications can help in generating new hypotheses and can discover emergent properties of the biological systems.PALM-IST is developed on CGI-PERL based web architecture. Multiple keywords of varied nature, such as genes, disease, drug, author names or any other word(s) can be provided as primary keyword input. Similarly, secondary keywords can also be mined in all possible combinations on abstracts retrieved from the primary keyword based search.Information regarding genes, diseases, drugs, pathways, interactions, and expression data were collected from various well-established resources  based text search, A is the number of publications that involve an observed bio-entity  where B is the number of publications that do not contain that particular bio-entity term. Similarly, C is the publications containing the bio-entity term  but not the query term(s) while D does not contain the particular bio-entity  and the query term(s), but contain other bio-entity  name. Y denotes the number of publication in which at least one bio-entity term is found  but not the query term(s). XCA, YCC, and NCZ [can also be represented as equation Eq. e.g., TP53 or Gefitinib). PHGD equation Eq. Score equation Eq. (3) is the log transformation of the probability. As the combinations may result in very large numbers leading to very low probability values, we have utilized a log2 conversion followed by a division with a constant number (100). Higher the Score better is the significance of association between the bio-entity and the query term(s).For a given primary query term(s) (Score in Eq. (4) for co-occurrence based relation between two entities is calculated using the mutual informatione.g., genes, proteins, drugs, diseases, etc to facilitate their functional classificationBiological entity recognition (BER) is a part of named entity recognition (NER) where textual data is mined to identify6364PALM-IST extracts relations based on co-occurrence of bio-entities and presents in tabular and interactive network visualization manner aiding to understand the relationship between gene-gene, protein-protein, gene-disease-drug, disease-drug, gene-drug, gene-processes-disease and gene-processes. Indexing of association table is performed based on common publication containing two/three bio-entities. These associations as solely based on co-occurrence at abstract level. This approach is based on the assumption that co-occurrence of multiple biomedical concept in the same abstract is an indication of a functional link between those bio-entities.Indexing and Scoring section for details). Triad combinations of gene-drugs-disease and gene-disease-process are extracted based on abstracts with three bio-entities and most frequent combinations are provided in tabular and network display option. Triad combination score is calculated based on hypergeometric test (see Indexing and Scoring section for details). Network of co-occurrence can be visualized using Cytoscape web display where, nodes are bio-entities and edge represents abstracts connecting the corresponding bio-entities. Bio-entities are color coded according to their types and edge width is set on the basis of number of abstracts in which those bio-entities are co-occurred.Protein-protein interaction (PPI) data were collected from the STRINGMySql based indexing is used to extract country statistics, authors and co-authors name. Google maps API is used to point country wise publication information on world map. Further, most frequent authors for a given text search is also extracted and co-authorship networks of the most frequent authors are provided within network based display using Cytoscape webBioCreative task IIPerformance of the algorithms/programs was evaluated by calculating the Recall, Precision and F-measure using the following formulaeTrue and false positives are the number of bio-entities that were identified correctly and incorrectly, respectively.S. M. collected and organized the data, developed the server and drafted the manuscript. S. C. drafted the manuscript and coordinated the project. All authors read and approved the final manuscript.How to cite this article: Mandloi, S. and Chakrabarti, S. PALM-IST: Pathway Assembly from Literature Mining - an Information Search Tool. Sci. Rep.5, 10021; doi: 10.1038/srep10021 (2015).Supplementary File 1


The aim of this study was to examine, among treatment-seeking individuals with current BN: i) the proportion of those with an AN history (AN+); ii) whether AN+ patients differed from those without an AN history (AN-) in terms of eating disorder (ED) or general psychopathology; and iii) whether AN+ and AN-patients responded differently to CBT-E, in terms of symptoms reduction and attrition rates. Participants were 221 outpatients at the Centre for Clinical Interventions (CCI) Eating Disorders Service, WA. All participants were ≥16 years and met DSM-IV criteria for BN. Results showed that initially, AN+ patients had significantly lower BMI and a longer time since first ED diagnosis. The groups did not differ on levels of general psychopathology at presentation, rates of attrition or in the proportion achieving BN remission. Multilevel linear modelling showed that frequency of binge eating, vomiting and laxative misuse, and scores for EDEQ, perfectionism, depression, anxiety, stress and distress tolerance all improved significantly over treatment, but there was no difference improvement between AN+ and AN-patients. Results suggest that a history of AN does not detrimentally affect individuals' rates of recovery from BN or improvement in mental health factors, and supports a transdiagnostic approach to treatment.


HIV treatment is only manageable with access to adequate medical care and effective treatment. Gardner et al.  developeTwo hundred thirty five clients, not in medical care and or individuals who have not reached viral suppression have been identified and enrolled. The implementation of this intervention includes emphasis on the importance of follow-up and retention beyond the initial medical appointment, addressing non-HIV medical care, and understanding barriers to attaining viral suppression. A local and national rigorous mixed-methods evaluation is embedded in the thread of the intervention, tracking outcomes at six-month intervals, over an eighteen- month period.We have been able to obtain desired changes in health and clinical outcomes for our cohort over an eighteen-month period. Viral suppression has trended from 41% at enrollment to 59% within six months, 71% within 12-months, and 65% after 18-months of enrollment . At six-months after enrollment, 87% of clients were retained in medical care. By conducting an extensive local and national evaluation, our model clearly highlights and refines best practices for training patient navigators to implement a navigation program to meet the ever-changing needs of HIV-positive individuals.AIDS United, Access2Care Initiative.


Several studies have investigated the factors associated with the return of spontaneous circulation (ROSC) in out-of-hospital cardiac arrest (OHCA) cases. The most analyzed factor is pre-hospital resuscitation, such as an early phone call for the ambulance, bystander cardiopulmonary resuscitation (CPR), presentation with ventricular fibrillation, and medication. The blood gas parameters have not yet been reported as a predictive factor for ROSC.-), hemoglobin, natrium, potassium, lactate, and glucose concentration on admission were able to predict ROSC in patients with OHCA.This study aimed to determine whether the blood pH, partial carbon dioxide pressure (PC02), bicarbonate  were measured and compared between the ROSC-achieving patients (ROSC group) and those who did not achieve ROSC (non-ROSC group).We performed a retrospective observational study of 186 OHCA patients who visited the emergency department of our hospital from January 2008 to December 2013. Bystander CPR status, initial cardiac rhythm, cause of arrest, the time from call receipt to hospital arrival, sex, age, and parameters of blood gas . The PC02 and potassium levels on admission were significantly higher in the non-ROSC group . The glucose concentrations were significantly lower in the non-ROSC group (149 mg/dl vs. 258 mg/dl p < 0.01). There were no statistically significant differences between both groups for other blood gas parameters. On multivariate analysis, bystander CPR as well as PC02, potassium, and glucose levels were independently associated with ROSC.A high blood PC02 level, a high potassium level, and low glucose level measured in OHCA patients on arrival at the hospital is predictive of a poor outcome for ROSC.


Food avoidance is still considered the gold-standard treatment for food allergy (FA). However, recently it has been consolidating the theory that, where possible, the food intake might facilitate the induction of desensitization and tolerance, resulting more effective and safer -if we consider the possibility of accidental ingestion- than a strict avoidance diet .Furthermore, specific oral immunotherapy (OIT) is the unique active treatment for IgE-mediated FAs .Studies have shown short-term efficacy: namely theOIT-ability to induce desensitization (loss of responsiveness to food-antigen during continuous assumption of OIT-doses) -5. ConveRecent data have shown that a key role in the induction of tolerance by OIT is played by a subgroup of regulatory T cells known as “induced T reg” (iTreg) ,7. EpigeAbout safety, allergic reactions occurred in the majority of patients treated. They are primarily mild reactions, severe in about 4%; however, no threatening-life events nor death has been reported . FrequenCareful clinical monitoring by qualified personnel in a medical environment is essential. Consequently, OIT costs are high.In all immunotherapy treatments, safety is of paramount importance. Therefore, when severe adverse reactions occur, OIT should be stopped and revaluated.Several efforts have been made to perfect OIT: e.g.antigens with reduced allergenicity and adjuvants inducing faster immune responses of “protection”. Particularly promising is OIT associated with omalizumab, anti-IgE antibody, resulting safe and able to accelerate the desensitization compared to traditional protocols -12.Further researches are needed in order to verify the degree of long-term safety as well as the long-term efficacy of OIT.Given the interest and the celerity of development of this field of research in the recent years, we are confident in the near achievement of a personalized treatment, planned, safe and effective, to be used in clinical practice.


M. tuberculosis growth in at least one of the first three sputum cultures. Demographics, symptoms, and radiographic findings on initial presentation were compared between the two groups. Of 99 subjects diagnosed with PTB, 21 met the criteria of Cx- PTB. Cx- compared to Cx+ subjects presented with a significantly lower frequency of cough , sputum production , weight loss , and frequency of cavitation on chest CT . Our findings should raise awareness that neither a positive culture nor the hallmark symptoms are invariably associated with early TB disease.Intervention at the earliest possible stage of pulmonary tuberculosis (PTB) reduces morbidity for the individual and transmission for the community. We characterize the clinical and radiographic manifestations of sputum culture-negative (Cx-) PTB in order to facilitate awareness of this under recognized and likely early disease state. In this cross-sectional sub-study, we reviewed the medical records of HIV-uninfected PTB patients enrolled from 2006–2014 within the context of a TB biomarker study in New York City. Cx- PTB was defined as clinical and/or radiographic presentation consistent with PTB, three initial mycobacterial sputum cultures negative, and no evidence of other respiratory disease. Diagnosis was confirmed by clinical and radiographic improvement on antituberculous treatment and/or culture, nucleic acid, or histological confirmation from a specimen other than the initial three sputa. Cx+ PTB was defined as above but with  Mycobacterium tuberculosis (Mtb) transmission, and thus is cornerstone to TB control. The gold standard for TB diagnosis continues to be confirmation by culture or nucleic acid amplification assay, with culture typically being the more sensitive method [With an estimated nine million new cases and about 1.5 million associated deaths annually, active tuberculosis (TB) continues to be a major cause of morbidity and mortality worldwide [e method , 3. Howee method , and sugCx- TB is likely to be less transmissible and more amenable to treatment with fewer drugs for shorter treatment duration. Thus, a low threshold for starting empiric antituberculous therapy is encouraged in patients with a high suspicion for Cx- TB and no evidence of other respiratory diseases. Dutt et al. showed that the relapse rate for an abbreviated four month treatment for Cx- TB was the same as that of standard 12 month therapy for Cx+ TB . In agreRadiographically demonstrable disease in asymptomatic Cx- HIV-uninfected individuals can be construed as an early disease state based on its likelihood of progression despite a low mycobacterial burden (reviewed in ). In a cAbsent a gold standard, studies characterizing Cx- PTB are best performed in settings where an exhaustive radiological, microbiologic, pathological and serologic evaluation can be undertaken leading to a definitive diagnosis other than TB, or to a TB diagnosis based on specimens other than the initial three sputum samples. In New York City (NYC), a locale with both a high burden of TB in its large foreign born population and ample resources for an exhaustive diagnostic evaluation, approximately 27% of TB cases are reported to be Cx- .We hypothesized that Cx- PTB patients present with fewer symptoms, shorter symptom duration, and less radiographic abnormalities compared to those with Cx+ PTB. Therefore, our primary objectives were (1) to assess the presence and duration of TB-associated symptoms in Cx- compared to Cx+ PTB patients; and (2) to compare the radiographic abnormalities of Cx- to those of Cx+ PTB. Our secondary objectives were (1) to assess whether there are differences in demographic characteristics between Cx- and Cx+ PTB patients; and (2) to investigate trends in clinical and radiographic characteristics when comparing Cx-, Sm- Cx+, and smear-positive (Sm+) Cx+ PTB in a three-group analysis, with specific comparisons of each smear group with Cx- TB.In this cross-sectional sub-study, we reviewed the medical records of patients diagnosed with PTB during the time of July 2006 through July 2014 in four public hospital centers in NYC . The subjects were all TB suspects who were consecutively enrolled within the context of an ongoing TB biomarker study . InclusiThis study was conducted in accordance with the amended Declaration of Helsinki, approved by the institutional review boards of the Albert Einstein College of Medicine and the New York University School of Medicine. Written informed consent was obtained from all patients.Legionella, Histoplasma, and pneumococcal urine antigen tests as they became FDA approved and available, and serology for fungal and parasitic organisms as indicated such as serum antigens for Cryptococcus neoformans or serum antibodies for Strongyloides. Cx- PTB was confirmed by an Mtb-positive culture, nucleic acid detection, or histological diagnosis in a specimen other than the initial three sputa, or, as per CDC recommendation, clinical and/or radiographic improvement attributable to antituberculous treatment [Following the guidelines provided by American Thoracic Society and the CDC , 12, andreatment . DiagnosDemographic measurements included age, sex, race, foreign-birth, and time in the US among foreign-born subjects. Symptoms included subject-reported presence and duration of cough, sputum production, fever, night sweats, weight loss > 1.81 kg, and hemoptysis at the time of initial presentation. Radiological findings were based on the first chest X-ray obtained at initial presentation, and chest computer tomography (CT) scan if performed upon initial presentation. The location, extent and characteristics  of radiographic pulmonary abnormalities were recorded.Sputa were processed in the local hospital laboratories as per CDC guidelines . Mycobact test or Mann-Whitney U test for two-group and the ANOVA or Kruskal-Wallis rank test for three-group comparisons. Categorical variables were compared by the Pearson’s chi-square test without correction for continuity or the Fisher’s exact test.Statistical analysis was performed using STATA software, version 13.1 IC . The α was set at < 0.05. Normality and homoscedasticity assumptions were assessed for continuous variables, which were analyzed by the Of 113 subjects diagnosed with TB, 14 extrapulmonary-only cases were excluded. Of the 99 subjects included for analysis, 21 had Cx- PTB. All Cx- PTB patients had at least one major TB risk factor (history of a positive tuberculin skin test or origin from a TB-endemic country) and had upper-lobe and/or miliary infiltrates on either chest x-ray and/or CT. Of these 21, 14 had Mtb confirmed in another specimen other than the initial three sputa by either culture, nucleic acid techniques, or histology consistent with TB . Among tP for trend = 0.01), sputum production (P for trend < 0.01), weight loss (P for trend = 0.01), and any symptom (P for trend = 0.01).No significant demographic differences were observed between Cx- and Cx+ subjects . Ten subP for trend = 0.04) and CT (P for trend < 0.01). The dataset is included as a supplementary file Click here for additional data file.


Quercus ilex, a multiplex (SYPRO-Ruby and Pro-Q DPS) staining of high-resolution 2-DE gels was used. By using this protocol it was possible to detect changes in protein-abundance and/or phosphorylation status. This simple approach could be a good complementary alternative to the enrichment protocols used in the search for phosphoprotein candidates. While 482 spots were visualized with SYPRO-Ruby, 222 were with Pro-Q DPS. Statistically significant differences in spot intensity were observed among samples, these corresponding to 85 SYPRO-Ruby-, 20 Pro-Q-DPS-, and 35 SYPRO-Ruby and Pro-Q-DPS-stained spots. Fifty-five phosphoprotein candidates showing qualitative or quantitative differences between samples were subjected to MALDI-TOF-TOF MS analysis, with 20 of them being identified. Identified proteins belonged to five different functional categories, namely: carbohydrate and amino acid metabolism, defense, protein folding, and oxidation-reduction processes. With the exception of a putative cyclase, the other 19 proteins had at least one orthologous phosphoprotein in Arabidopsis thaliana, Medicago truncatula, N. tabacum, and Glycine max. Out of the 20 identified, seven showed differences in intensity in Pro-Q-DPS but not in SYPRO-Ruby-stained gels, including enzymes of the glycolysis and amino acid metabolism. This bears out that theory the regulation of these enzymes occurs at the post-translational level by phosphorylation with no changes at the transcriptional or translational level. This is different from the mechanism reported in orthodox seeds, in which concomitant changes in abundance and phosphorylation status have been observed for these enzymes.As a preliminary step in the phosphoproteome analysis of germinating seeds (0 and 24 h after seed imbibition) and early grown seedlings (216 h after seed imbibition) from a non-orthodox sp.  Quercus ilex L. subsp. ballota [Desf.] Samp.) is the dominant tree species in natural forest ecosystems over large areas of the Western Mediterranean Basin , mainly phosphorylation. Phosphorylation is a ubiquitous and reversible PTM, which determines protein conformation, stability and activity . Germination and seedling growth were performed at 22 ± 1°C for up to 10 days in darkness as described in Liu et al. . UndamagMr-values were calculated by mobility comparisons with protein standard markers  run in a separate marker lane on the SDS-gel, while pI was determined by using a 5–8 linear scale over the total length of the IPG strips.Tissue samples were ground to a fine powder in liquid nitrogen using a mortar and pestle . Protein extracts were obtained from embryo axes of mature  and germinated seeds (24 h after imbibition when the radicle just emerged) and from seedling radicles , Figure . Proteinhttp://lgsun.grc.nia.nih.gov/anova/index.html)  analysis was performed with PDQuest 8.0.1 software (Bio-Rad)  was used for protein identification running over non-redundant NCBI protein, UniprotKB, and Quercus  was based on the MOWSE score, and confirmed by the accurate overlapping of the matched peptides with the major peaks of the mass spectrum. Proteins with statistically significant (p < 0.05) hits were positively assigned identification. Identified phosphoprotein sequences downloaded from UniprotKB, NCBI nr or available in Quercus_DB  pathway, using Blast2GO , or according to annotations in UniProtKB protein database.Spots with differential abundance were automatically excised , transferred to multiwell 96 plates, and digested with modified porcine trypsin  by using a ProGest (Genomics Solution) digestion station. In-gel digestion was performed as decribed by Shevchenko et al. . PeptideQ. ilex in three different stages, mature seeds (just before imbibition), germinated seeds (24 h after imbibition), and early grown seedlings (216 h after imbibition)  and phosphorylation status (Pro-Q DPS-stained spots) throughout the seed germination and early seedling growth of ) Figure . In the Mr (6–116 kDa) ranges  and Mr 6–16 kDa ras Figure .Consistent Pro-Q DPS stained spots, present in all the three biological replicates, were subjected to statistical, ANOVA and PCA, analysis, with 55, out of the 222, showing significant variations (spot volume) between samples Table . Both quTwo-dimensional biplots indicating associations between experimental samples and protein spots were generated by principal component analysis (PCA) in NIA array analysis tools Figure . The conhttp://www.p3db.org/)  staining of high-resolution 2-DE gels was used. With this protocol it was possible to detect changes in protein-abundance and/or phosphorylation status, identifying, at the same time, candidate phosphoproteins. This simple technique could be a good complementary alternative to the enrichment protocols used in the search for phosphoprotein  biological interpretation of the data, as discussed below, fits in very well with what is known about the regulation of the identified proteins by phosphorylation. The percentage of phosphorylated proteins detected in our experimental system was of 46%, with similar figures reported for chickpea seedlings  or simultaneous, multiplex (protein abundance and phosphorylation pattern) proteomics analysis by using a similar  strategy has been used in the analysis of mature orthodox seed and seed germination process in model and crop plant species, including Arabidopsis, rice, soybean, rapeseed and maize , phosphoglycerate kinase  and glucose-1-phosphate adenylyltransferase   Table , increme4) Table . An incrOn the contrary, for enzymes of the amino acid metabolism  and chaperones  a decrease in their phosphorylation signal was observed Table . Some isprotein folding, has been described decreasing during rice germination , involved in Q. ilex seed germination. The phosphoproteome analysis suggested that the metabolic machinery present in the recalcitrant seeds receives a signal to activate and resume/summarize the most important metabolic pathways in Q. ilex to start the germination and the establishment of the seedlings. In orthodox seeds, changes in abundance, together with differences in their phosphorylation status, were observed for these enzymes. Thus, this is one of the differences between orthodox and non-orthodox seeds that may explain their different behavior  and amino acid metabolic pathways (glutamate decarboxylase) and protein folding (heat shock protein 60) did not change in abundance during germination and growth but their phosphorylation status increased suggesting regulation at the post-translational level. Alterations in the phosphorylation status of proteins related to glycolysis and amino acid metabolism are in agreement considering that these pathways must increase from mature seeds to germinated seeds and seedling. To test these hypotheses it is necessary identify the phosphorylation sites, but this work constitutes an initiation in the study of the molecular mechanism involved in The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


It is an open question as to whether differential developmental trajectories, potentially representing underlying pathophysiological processes, can form the basis of a more useful typology in young persons who present for mental health care.A cohort of 605 young people was recruited from youth mental health services that target the early phases of anxiety, mood or psychotic disorders. Participants were assigned to one of three clinical sub-types  according to putative developmental trajectories.The distribution of subtypes was: 51% anxiety-depression, 25% mania-fatigue and 24% developmental-psychotic, with key differences in demographic, clinical, family history and neuropsychological characteristics. When analyses were limited to 286 cases with ‘attenuated’ or sub-threshold syndromes, the pattern of differences was similar. Multinomial logistic regression demonstrated that compared to the developmental-psychotic subtype, both the mania-fatigue and anxiety-depression subtypes were younger and more depressed at presentation, but less functionally impaired. Other discriminating variables between the developmental-psychotic and mania-fatigue sub-types were that the latter were significantly more likely to have a family history of bipolar disorder but have less likelihood of impaired verbal learning; whilst the anxious-depression group were more anxious, more likely to have a family history of depression, and had a higher premorbid IQ level.This cross-sectional evaluation provides preliminary support for differing developmental trajectories in young persons presenting for mental health care. Prospective follow-up is needed to examine the predictive validity of this approach and its relationships to underlying pathophysiological mechanisms. The optimal meta-structure for differentiation of the major psychotic, bipolar and unipolar mood disorders for use in either clinical practice or clinical or related genetic, neurobiological or psychological research remains controversial -13. The A further consideration is whether such novel studies are better conducted closer to onset of the major disorders, where confounding factors arising as a result of chronicity, prolonged exposure to treatments or developments of secondary morbidities are less important ,17-21. WResearchers have also increasingly highlighted the added value of incorporating clinical staging alongside traditional diagnostic formulations, especially for assessing those initial, less specific clinical presentations that are common in young people when they first present for specialist care ,23-27. WWe have proposed that there are at least three pathways are common and observable in youth mental health cohorts , and thaImportantly, the DEV-PSY group is at the heart of current research domain criteria (RDoC) initiative proposed by the NIMH, and is hypothesized to be associated with autism, schizophrenia and/or psychotic phenomena -34. It iThe final  sub-type comprises individuals who frequently reported childhood anxiety, but later show evidence of heightened stress-sensitivity and an evolving depressive disorder (but without evidence of a ‘fatigue’ profile); this is the ANX-DEP sub-type . This moThe first step in testing the validity of these proposed clinical sub-types is to examine:(i) Which demographic, clinical, family history, childhood phenotype, and neuropsychological characteristics are most strongly associated with cases allocated to each sub-type;(ii) If the same patterns of clinical and neuropsychological characteristics are evident in cases presenting with a sub-threshold or attenuated clinical syndrome (i.e. stage 1b); and,(iii) Which combination of variables best distinguish between the MAN-FAT, DEV-PSY and ANX-DEP sub-types after controlling for symptoms and functional impairment at the time of presentation to the youth mental health services.and (iii) agreed to participate in longitudinal follow-up interviews .With approval from the University of Sydney Human Research Ethics Committee, consecutive cases presenting with mood and/or psychotic symptoms to youth mental health services in and around Sydney were invited to participate in a detailed multi-level clinical assessment. Individuals were included in the study cohort if they: (i) were willing and able to give written informed consent ; (ii) presented to the clinical services with sub-threshold mood and/or psychotic symptoms or with a mood or psychotic syndrome; Exclusion criteria for all potential participants were: medical instability or lack of capacity to give informed consent (as determined by a psychiatrist), history of neurological disease , medical illness known to impact cognitive and brain function , and/or clinically evident intellectual and/or developmental disability, and/or insufficient English to participate in the research protocol.All patients were receiving clinician-based case management and relevant psychosocial interventions at the time of assessment. Additionally, patients who were treated with psychotropic medications were assessed under ‘treatment as usual’ conditions, whereby their normal medications were not altered. At the time of assessment, 27% (163/605) of patients were not taking psychotropic medications; 44% (267/605) were taking an anti-depressant; 38% (229/605) an antipsychotic medication; and 13% (80/605) were taking a mood stabiliser.An independent reviewer (DH) allocated cases to one of the three proposed sub-groups on the basis of the description of the clinical presentation alone (i.e. without reference to any information from the structured research assessment). Any cases presenting with depressive symptoms only, with no evidence of psychotic or manic features, and no indication of atypical symptoms were allocated to the ANX-DEP group. The reviewer was blinded to all other clinical and historical information, so cases were excluded (N = 86) from this cross-sectional study if they could not be allocated to one of the three sub-types.Structured clinical interviews were undertaken by trained researchers  to establish the following:Demographics and key characteristics: age, gender, and years of education were recorded. In addition, age at onset of psychiatric symptoms was assessed. Egeland et al. [a) d et al.  noted thPersonal and family history of mental disorders: the primary clinical diagnosis was assessed using DSM-IV criteria, and lifetime history of other axis 1 disorders such as Autistic Spectrum and Attention Deficit Hyperactivity Disorder (ADHD) were recorded. Current comorbidities, such as substance misuse disorder, were also assessed using general questions supplemented by the 10-item Alcohol Use Disorders Identification Test   AUDIT; ,54). We . We Pers  [c) BPRS-24)  to quantBPRS-24) ), whilstBPRS-24) , In addiBPRS-24)  and the BPRS-24) .Social functioning: the clinician completed the observer-rated social and occupational functioning assessment scale (SOFAS) [d)  (SOFAS) ; this isNeuropsychological profile: premorbid intelligence (‘predicted IQ’) was estimated on the basis of performance on the Word Reading subtest of the Wide Range Achievement Test 4 [e) t Test 4  for thost Test 4  for thost Test 4 . These wt Test 4 ,64; ‘verα = .01. Group differences in demographic, clinical and neuropsychological variables were assessed via ANOVA or chi-square tests where relevant. Analyses of differences between sub-types were repeated for a selected sample of cases rated as stage 1b or stage 2+ . If equality of variance was compromised (according to Levene’s test) the corrected degrees of freedom and p-values were reported. To control for the effects of age, neuropsychological variables were converted to ‘demographically corrected’ standardized scores (i.e. z-scores) using established norms for TMT [Statistical analyses were performed using SPSS for Windows 20.0. Cases with missing data were excluded list-wise from the analyses. All statistical tests were 2-tailed and used a significance level of  for TMT  and RAVL for TMT . Prior t for TMT .  was used to assess the combination of factors and variables that best differentiated between clinical subtypes. The DEV-PSY group was selected as the reference category and the forward (likelihood ratio) procedure was used for the regression. Variables were entered into the model if they had p values lower than 0.01.The variables included in the model were: gender, age at onset, age at presentation to youth services, predicted IQ, and ratings on the HDRS, K-10, SIAS, and SOFAS. Neuropsychological measures  and family history of depression, anxiety, bipolar and schizophrenic disorders all met inclusion criteria. Predictors of sub-group membership are reported using B, exp(B), 95% confidence intervals (95% ci) and significance levels . The Cox and Snell pseudo RThe study sample comprised of 605 individuals with a mean age of 19.9 ; about 50% (n = 304) were female. Just over half of the study participants were classified in the ANX-DEP  group, with about a quarter in either the MAN-FAT  or DEV-PSY  groups. While these characteristics closely reflect the demographics and case mix of the clinical services from which the cohort was recruited, study participants demonstrated slightly higher symptom levels .As shown in Table As shown in Table 2 = 56.2; df = 2; p < 0.001). Comparison of clinical and neuropsychological profiles between cases rated as stage 1b compared to stage 2+ suggested that between group differences were evident for stage 1b cases with regards to age at presentation, age at first treatment, years in education and predicted IQ; impairments in functioning and general behavioral disturbance were less marked in the stage 1b compared to stage 2, but the pattern of differences was consistent. There were marginal changes in gender distribution , depression severity , and distress levels . The pattern of significant neuropsychological differences remained the same, although the overall levels of impairments were less marked in the stage 1b compared to stage 2+ in the DEV-PSY group (data available from the corresponding author).About half of study participants  were rated as being at stage 1b at the time of assessment; a significantly higher proportion of cases in the ANX-DEP  and MAN-FAT  groups were regarded as presenting with sub-threshold syndromes compared to the DEV-PSY group   included the following: age at presentation, HDRS, SOFAS, SIAS, family history of depression and bipolar disorder, and verbal learning, . The DEV-PSY subtype differed from both the MAN-FAT and the ANX-DEP groups on age at presentation to youth mental health services (DEV-PSY older), HDRS scores (less depressed) and SOFAS scores (more impaired). Furthermore, DEV-PSY cases were more likely than MAN-FAT cases to show impaired verbal learning (RAVLT sum score) and less likely to have a family history of bipolar disorders. Compared to the ANX-DEP, the DEV-PSY group were less anxious (SIAS), less likely to have a family history of depression, and more likely to have a lower predicted IQ level.As shown in Table Before discussing the findings in detail, it is useful to highlight two issues. First, this cohort of young people has significant levels of symptoms, functional impairment, distress and suicidal ideation that warrant clinical intervention; and that this need for care and treatment is apparent whether or not the presenting symptoms reached current thresholds for diagnostic caseness -68. SecoIn this study we examine the similarities and differences between three putative developmental trajectories that lead to adolescent-onset disorders – namely, ANX-DEP, MAN-FAT, and DEV-PSY disorders. These sub-types draw, in part, on historical distinctions between depressive disorders driven by heightened sensitivity to environmental stressors thresholds, circadian-based mood disorders  and psychotic disorders with or without affective components (broadly defined and often linked to evidence of earlier deviations in brain development). The study also seeks to apply these concepts to young people with attenuated syndromes before the symptoms progress to classical, more easily distinguished, or more stable syndromes. As such, this tripartite model builds on established diagnostic categories, extending them to sub-threshold presentations via the use of a clinical staging framework, and further refining them by classifying cases on the basis of a putative clinical phenotype linked to a proposed underlying pathophysiology and illness trajectory. However, it differs from other historical approaches to classifications that have traditionally given more weight to psychotic symptoms - because these were perceived as most relevant to diagnostic hierarchies ,13,69. OThe differential demographic , developmental (lower IQ and higher rate of diagnosed ADHD in the DEV-PSY subgroup), and phenotypic  characteristics are consistent with the findings of other longitudinal, clinical and epidemiological studies and lend support to the proposed model of sub-types ,41,70,71The patterns of neuropsychological impairment strongly differentiated the DEV-PSY group from the mood sub-types, particularly with regards to verbal learning and memory, and to a lesser extent to processing speed. These profiles are consistent with other neuropsychological studies in young people across the mood disorders and psychosis spectrum ,63. The Finally, it is important to acknowledge some important study limitations. First, the cohort represents a sub-sample of referrals to youth mental health services and biases in referral processes and/or the exclusion of cases that could not be classified could have influenced our findings. Although we have evidence that the sample reflects the case mix in the clinical service, we cannot rule out biases entirely, so replication of the study is necessary -68. It iThis cross-sectional study of 605 young people presenting for mental health care provides provisional support for a model that differentiates subjects into three subgroups  based largely on differential childhood and adolescent trajectories. While the model shares key concepts with more traditional contrasts between psychotic and non-psychotic disorders, it proposes the differentiation of two mood disorder types based largely on changes in motor or psychic activation or the presence of prior or concurrent anxiety. While this tripartite model is supported by key differences in clinical, family history and neuropsychological characteristics, relevant prospective and comparative intervention studies are now required to test its predictive validity.ADHD: Attention deficit hyperactivity disorder; ANX-DEP: Anxiety-depression; ANOVA: Analysis of variance; AUDIT: Alcohol use disorders identification test; BPRS: Brief psychiatric rating scale; CBT: Cognitive behavioural therapy; DEV-PSY: Developmental-psychotic; DSM: Diagnostic and statistical manual of mental disorders; ECT: Electroconvulsive therapy; HDRS: Hamilton depression rating scale; ICD: International classification of diseases; IQ: Intelligence quotient; K-10: Kessler-10; MAN-FAT: Mania-fatigue; MRI: Magnetic resonance imaging; MNLR: Multi-nomial logistic regression; NIMH: National institute of mental health; RDoC: Research domain criteria; SIAS: Social interaction anxiety scale; SOFAS: Social and occupational functioning assessment scale; SPSS: Statistical product and service solutions; SSRI: Selective serotonin reuptake inhibitor; TMT: Trail-making test; RAVLT: Rey auditory verbal learning test; WRAT: Wide range achievement test; WTAR: Wechsler test of adult reading; YMRS: Young mania rating scale.Professor Hickie is a Board Member of Psychosis Australia Trust. From 2012, he has been a Commissioner in Australia’s new National Mental Health Commission. He was until January 2012 a director of headspace: the national youth mental health foundation. Prof Hickie was previously chief executive officer (till 2003) and clinical adviser (till 2006) of beyondblue, an Australian National Depression Initiative. He is supported principally for clinical research in depression and health services and population health initiatives related to anxiety and depression by an NHMRC Australian Medical Research Fellowship (2007–12) and now by an NHMRC Senior Principal Research Fellowship (2013-17). He has led projects for health professionals and the community supported by governmental, community agency and pharmaceutical industry partners  for the identification and management of depression and anxiety. He has received honoraria for presentations of his own work at educational seminars supported by a number of non-government organisations and the pharmaceutical industry . He has served on advisory boards convened by the pharmaceutical industry in relation to specific antidepressants, including nefazodone, duloxetine, and desvenlafaxine. He leads an investigator-initiated study of the effects of agomelatine on circadian parameters  and has participated in a multicentre clinical trial of agomelatine effects on sleep architecture in depression and a Servier-supported study of major depression and sleep disturbance in primary care settings. In addition to national and international Government-based grant bodies, investigator-initiated mental health research at the BMRI he has been supported by various pharmaceutical manufacturers (including Servier and Pfizer) and not-for-profit entities .Dr Daniel Hermens is currently supported by a grant from the NSW Ministry of Health, Mental Health and Drug & Alcohol Office as well as an NHMRC Australia Fellowship (awarded to Professor Hickie). He has received honoraria for educational seminars from Janssen-Cilag and Eli Lilly.Professor Jan Scott is an unpaid advisor or committee member for the following: International Early Psychiatry Association, International Societies of Affective Disorders and of Bipolar Disorders, UK Bipolar Organization (Manic Depression Fellowship), International Bipolar Disorders Fellowship. She has ongoing funding from the UK MRC, UK NHS FSF and UK NHS RfPB programmes for research on mood disorders, bipolar II disorders, predicting transition in ‘at risk’ populations and development of psychological therapies. Her other mental health research has been supported by a UK NHS SDO grant and funds provided to the NTW NHS Trust by Astra-Zeneca and Janssen-Cilag for investigator initiated studies on mood disorders, psychosis and medication adherence. She has received honoraria for presentations of her own work at educational seminars supported by a number of non-government organizations and the pharmaceutical industry and has also served on advisory boards convened by the pharmaceutical industry mainly in respect of her research interest in medication adherence .Dr Elizabeth Scott is the (unpaid) Clinical Director of Headspace Services at the BMRI, the (unpaid) Co-ordinator of the Youth Mental Health Research Program at the BMRI, and Deputy Director of St Vincent’s Private Hospital Young Adult Mental Health Unit. She has received honoraria for educational seminars related to the clinical management of depressive disorders supported by Servier and Eli-Lilly pharmaceuticals. She has participated in a national advisory board for the antidepressant compound Pristiq, manufactured by Pfizer.IBH and DFH prepared the initial draft manuscript. IBH and EMS supervised and verified all clinical assessments. DFH and JS conducted the statistical analyses. IBH, DFH, SN and EMS conceived the study design. JS, AG and NG provided key interpretation of the clinical data and participated in various aspects of the study design and analysis. All authors contributed significantly to the interpretation of the data as well as having read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-244X/13/303/prepub


In 2013, in the National Institute for Infectious Diseases "Prof. Dr. Matei Balş" Bucharest has been applied post-exposure guidelines in 112 cases of occupational exposure to blood and other biological products and was not registered any cases of HIV transmission.A 22 year old, young police-officer presented in our service for human bite wounds, resulting from intervention in a case of intrafamilial aggression. The aggressor, was known as drug-addicted, co-infected HCV/HIV and he had bleeding in the mouth. He was under antiretroviral therapy for about nine months . Exposed person comes to our service in the first two hours of the incident, without performing initial wound toilet. We started antiretroviral prophylaxis (ARVP) with CBV+LPV/r.At eight days after ARVP, the exposed-person developed a generalized maculopapular rash; in the absence of other clinical manifestations the eruption is interpreted as post-drug side effects. The young man returned to our clinic after another three days (range in which in his own initiative stopped prophylaxis), and we decided to change the antiretroviral regimen with DRV/r + TDF + FTC. Reevaluation after a month recorded that he remained asymptomatic and fourth generation ELISA tests were negative. Reassessment at 12 weeks showed serological tests positive , indicating a recent retroviral infection. We find the same HIV sub-type (F) and the same resistance mutations in those two patients, confirming HIV infection to policeman from the aggressor. New patient initially had HIV-RNA = 210,977 copies/mL, CD4 = 789 cells/cmm and was included in the cohort of individuals with recent HIV infection; antiretroviral therapy is initiated with TDF + DRV/r + RAL. After a month of treatment the HIV-RNA = 161 copies/mL blood, HIV-RNA from CFS was undetectable and anti-HCV were negative.It is the first case of accidental post-exposure  to contaminated blood HIV infection in which we applied post-exposure protocol.It illustrates:- The importance of adherence to antiretroviral medication;- The consideration of acute retroviral syndrome in the presence of a maculopapular rash;- The importance of choosing prophylactic regimen when we know treatment history and possible resistance mutations if the source person is known to be HIV positive.- Should be monitored more frequently and more complete (HIV-RNA), including people with occupational non-medical exposure.


The aim of the study was to examine the effectiveness of an intensive inpatient three-week multimodal therapy. We focused especially on the impact on the multimodal therapy outcome of the pre-admission number of treatment types patients had received and of medical specialist groups patients had consulted.155 patients with chronic low back pain and indication for multimodal therapy were evaluated with respect to pain intensity, depression, anxiety, well-being, and pre-admission health care utilization. In our controlled clinical trial we compared N = 66 patients on the waiting list with N = 89 patients who received immediate treatment. The waiting list patients likewise attended multimodal therapy after the waiting period. Longitudinal post-treatment data for both were collected at three- and twelve-month follow-ups. The impact of pre-admission health care utilization on multimodal therapy outcome (post) was analysed by structural equation model.Compared to the control group, multimodal therapy patients’ pain intensity and psychological variables were significantly reduced. Longitudinal effects with respect to pre-measures were significant at three-month follow-up for pain intensity (ES = -0.48), well-being (ES = 0.78), anxiety (ES = -0.33), and depression (ES = -0.30). Effect sizes at twelve-month follow-up were small for anxiety (ES = -0.22), and moderate for general well-being (ES = 0.61). Structural equation model revealed that a higher number of pre-admission treatment types was associated with poorer post-treatment outcomes in pain intensity, well-being, and depression.Multimodal therapy proved to be effective with regard to improvements in pain intensity, depression, anxiety, and well-being. The association between treatment effect and number of pre-admission pain treatment types suggests that patients would benefit more from attending multimodal therapy in an earlier stage of health care. Access to outpatient medical services is almost barrier-free in the German health system, that is, without any “gate-keeping-system.” This includes consultations with most medical specialists . In orthThe treatment algorithm for managing low back pain first recommends:consultation in a multimodal setting for an interdisciplinary assessment after 8–12 weeks of pain,and/or4–6 weeks out of work due to low back pain,and/orsignificant indication of a risk of chronicity , 7.In reality, patients in multimodal therapy report suffering from low back pain for many years and reveal a long history of consultations and various treatments. Most of these patients already report seriously reduced physical and emotional functioning due to low back pain , 9.Existing studies revealed several predictors of reduced pain intensity in patients with chronic low back pain following multimodal Therapy (MMT) , 11. PreThe present study aims to evaluate an intensive, three-week inpatient MMT for patients with chronic low back pain, focusing on the impact that the amount of healthcare utilization has on the outcome of MMT. The aims and hypotheses are:Evaluating the effectiveness of MMT: Compared to waiting group, patients receiving MMT were expected to improve significantly from pre- to post-treatment.Prospective evaluation at three- and twelve-month follow-ups: We hypothesized that patients would improve significantly in pain-related and psychological variables following MMT. We expected those improvements to decrease by three- and twelve-month follow-up intervals.Impact of healthcare utilization on MMT outcome: We hypothesized that the amount of pre-admission healthcare utilization would predict responses to MMT. We expected that more utilization leads to less improvement.Prior to the investigation, all participants gave written informed consent. The study was approved by the local ethics committee .0), the beginning of MMT (t1), the end of MMT (t2), and three (t3) and twelve months (t4) to follow up. Analyses for the first hypothesis were based on a pre-post-two-group design. The control group  was compared with immediately-treated patients . The outcome measures were assessed at the end of the waiting period (t1) for the waiting group and at the end of MMT (t2) for the group receiving treatment immediately. As the pre-test we used t0 (control group) resp. t1 (intervention group). The analysis for the second hypothesis was based on a one-group longitudinal design. Accordingly, all time points were considered and all patients  were included in the statistical analysis.Assessments were conducted at the beginning of the waiting time (t1 (pre-MMT-treatment) and t2 (post-MMT-treatment) of all patients (N = 155) were considered. Pre-admission healthcare utilization, pre-treatment pain intensity, depression, anxiety, and well-being served as predictors for post-treatment pain intensity, depression, anxiety, and well-being.To analyze the impact of healthcare utilization on MMT outcome (third hypothesis) the intervals tParticipants were recruited in a regular, naturalistic, German pain management setting. Criteria for participation were: (1) chronic (duration >3 months) low back pain as predominant pain condition, (2) indication for attending MMT, (3) sufficient understanding of the German language, and (4) aged between 18 and 70 years. Indication criteria for MMT were based on the German guidelines for managing non-specific low back pain. During a three-day inpatient pre-treatment multi-disciplinary pain assessment the indication was verified by an interdisciplinary team .within the study period (2008 to 2011); 182 patients proved to be eligible for MMT. Twenty-seven patients refused to sign the informed consent and were excluded. Finally, 155 patients were included in the study. Of these, sixty-six patients had a waiting period (waiting group) of at least three months prior to MMT. Patients waited for different reasons . Treatment as usual was carried out during the waiting period. Eighty-nine patients were treated immediately with MMT. N = 330 patients with chronic low back pain attended the pain center The Central Hospital in Bad Berka, Germany provides inpatient pre-treatment multi-disciplinary pain assessment (three days) and, if indicated, an intensive, three-week inpatient MMT. The main aim of the MMT was to improve functional capacity, reduce pain intensity, improve emotional functioning and well-being, and increase the patients’ knowledge of bio-psycho-social pain mechanisms and pain-related coping-strategies.An interdisciplinary therapeutic team  performed an individually-adjusted treatment within a standard schedule . Regular team meetings for the evaluation of individual treatment progress were carried out. Medical treatment consisted of modification of analgesic medication and also frequently withdrawal of medication in case of lack of effectiveness or an increasing burden of side effects. Behavioral management included education , biofeedback and cognitive-behavioral therapy  offered by psychologists. Furthermore, patients received physiotherapy  and active training sessions  offered by trained physiotherapists.All patients of the MMT group underwent pre-treatment multidisciplinary pain assessment. This included physical examination, functional testing, and further investigations to exclude red flags . Moreover psychological-, psychosomatic- or psychiatric diagnostic factors have been evaluated. The assessment team consisted of physicians , psychologists/psychotherapists, pain nurses, and physiotherapists. Based on the medical and psychological findings, an individualized treatment was recommended by the assessment team.The primary outcome was pain intensity . Secondary outcomes were depression, anxiety and well-being .German Pain Questionnaire of the German Section of the IASP (DSF: )et al. (2006) reported much lower rates for Germany. Among the European countries, Germany and Norway showed the fewest number of pain management specialist consultations, with 10% and 8% respectively. Italy and France were in the top positions with 42% and 40%, respectively, which represents chronic pain patients with at least one consultation [With regard to pre-admission healthcare utilization we found that the number of patients who had consultations with pain management specialists was 34.2% in the sample. Breivik ultation . The eleThe treatment that patients received before attending the pain center predominantly consisted of medication, physiotherapy, massage, and local injections. These are almost exclusively passive procedures, which overall are not recommended by the current guidelines for the management of low back pain . MassagAt last associations between the effectiveness of MMT and pre-admission healthcare utilization were examined. Results of the structural equation model indicate that, with an increasing number of different types of treatments received before MMT, a more negative treatment outcome has to be expected in pain intensity, general well-being, and depression after therapy. This corresponds with findings of previous researchers , 12. ThiIt could be considered whether patients with an elevated use of different treatment types might have higher scores in pain-related and psychological factors already prior to treatment. For our analyses this assumption does not hold because we statistically-controlled for baseline pain-related and psychological factors. Furthermore the generalizability is limited by the fact that we considered baseline measures only. It is still possible that these patients will have worse pain conditions in earlier stages of their treatment history. On the other hand, patients with elevated numbers of treatment types might generally have less benefit from pain treatments, including MMT. This leads to the suggestion that patients would benefit more from attending MMT in an earlier stage of healthcare utilization.Several limitations must be noted. The generalizability of the results is potentially limited. The sample consisted of consecutively-included patients from only one pain clinic.Due to the waiting setting , there was no real control group for the whole study period. Therefore no comparison with other treatments or pain conditions was possible. The waiting subgroup was a naturally formed group, and no randomization could be applied. But we found no differences with regard to pre-test values between waiting group and intervention group. Additionally, selection effects were handled by controlling pre-treatment measures in the statistical model and computation of adjusted means. A further limitation refers to the assessment of pain disability which is an important outcome measure in therapy with pain conditions . UnfortThe treatment effects of the MMT suggest that patients with chronic low back pain benefit from the intensive three-week inpatient MMT. This underlines the importance of treating low back pain with relation to physical as well as psychological aspects. The association between treatment effect and number of different pre-admission pain treatment types suggests that patients would benefit more from attending MMT in an earlier stage of healthcare utilization, thus avoiding elevated use of multiple treatment types.S1 Data(SAV)Click here for additional data file.


Risk factor burden and clinical characteristics of patients with coronary artery disease (CAD) differ among ethnic groups. We related biomarkers to CAD severity in Caucasians, Chinese, Indians and Malays.n = 2033) we compared levels of five cardiovascular biomarkers: N-terminal pro-brain natriuretic peptide (NTproBNP), high-sensitivity C-reactive protein (hsCRP), cystatin C (CysC), myeloperoxidase (MPO) and high-sensitivity troponin I (hsTnI). We assessed ethnicity-specific associations of biomarkers with CAD severity, quantified by the SYNTAX score.In the Dutch-Singaporean UNICORN coronary angiography cohort . MPO levels were higher in Caucasians than in Indians , hsTnI levels were higher in Malays than in Caucasians and Indians  and hsTnI levels were higher in Chinese than in Caucasians . We found modifying effects of ethnicity on the association of biomarkers with SYNTAX score. NTproBNP associated more strongly with the SYNTAX score in Malays than Caucasians . For MPO levels the association was stronger in Malays than Caucasians . Differing biomarker cut-off levels were found for the ethnic groups.Adjusted for baseline differences, NTproBNP levels were significantly higher in Malays than in Chinese and Caucasians (72.1 vs. 34.4 and 41.1 pmol/l, When corrected for possible confounders we observe ethnicity-specific differences in biomarker levels. Moreover, biomarkers associated differently with CAD severity, suggesting that ethnicity-specific cut-off values should be considered. Coronary artery disease (CAD) is highly prevalent worldwide but over the next few decades the majority of deaths due to CAD will occur in Asia . EvidencBlood-derived biomarkers are noninvasive tools that can be indicative of CAD severity. Population means of biomarker levels differ among ethnic groups . HoweverIn this study we aimed to define inter-ethnic differences in the association of these biomarkers with CAD severity, quantified by the SYNTAX score .This study was conducted using the parallel United CORoNary biobanks, the UNICORN cohort , consisting of consecutive patients undergoing coronary angiography recruited from two sites: the University Medical Center Utrecht, the Netherlands and the National University Hospital, Singapore. The institutional review boards of both centres approved of this study, which conforms to the declaration of Helsinki.Patients were enrolled between September 2010 and March 2013. Patients from four ethnic groups were enrolled, namely Caucasians in the Netherlands and Chinese, Indians and Malays in Singapore. Blood was sampled from the arterial sheath, inserted at commencement of the coronary angiography procedure and immediately stored at − 80 °C.Risk factor profiles were documented at or around the time of coronary angiography. Coronary angiograms were categorised into four groups: no/minor CAD, single-vessel disease, double-vessel disease and triple-vessel disease .Plasma levels of NTproBNP, hsCRP, CysC and MPO were measured at the University Medical Center Utrecht, the Netherlands, using a semi-automated ELISA robot . Commercial antibody combinations were used to quantify NTproBNP , hsCRP , CysC  and MPO . In brief, maxisorb plates were coated with mouse anti-human NTproBNP, hsCRP, CysC or MPO. Plates were blocked with 1 % bovine serum albumin, and incubated with supernatants. Plates were washed with phosphate buffered saline pH 7.4 with 0.05 % Tween 20. Bound factors were detected with biotin coupled detection antibodies. Biotin coupled antibodies were bound with streptavidin horseradish peroxidase (HRP), or goat-anti-human antibodies with rabbit-anti-goat HRP . Detection was performed with SuperSignal West Pico Chemiluminescent substrate, and read with a luminometer. The intra-assay variation coefficient was 10 %. Levels of hsTnI were measured using the All samples (Singaporean and Dutch) were randomly distributed across the plates for all analyses.Figures are presented as means with standard deviations for normally distributed variables or medians with interquartile ranges for non-normally distributed variables. Baseline characteristics were compared among the ethnic groups using ANOVA for normally distributed variables, Kruskal-Wallis tests for non-normally distributed data and chi-square tests for categorical data.We evaluated inter-ethnic differences in biomarker levels, adjusted for baseline differences in age, sex, body mass index, diabetes, hypertension, dyslipidaemia, smoking, indication for procedure, severity of CAD, antiplatelet medication use, beta blocker use, calcium antagonist use, renin-angiotensin-aldosterone system medication use and statin use. Using ANCOVA, adjusted biomarker levels were calculated for each ethnic group. Biomarker levels were positively skewed and therefore log-transformed for analysis when used as the dependent variable. The presented adjusted biomarker level means are antilogs . Biomarker levels were compared among the ethnic groups through Tukey post-hoc testing, thus adjusting for multiple testing.Also, we tested for interactions between ethnicity and biomarker levels for the SYNTAX score in univariable and multivariable regression models. Direct comparison of biomarker coefficients between ethnicities was performed by testing an interaction term of biomarker level with ethnicity; Caucasian ethnicity was the reference group. A conservative p-value of 0.05 for the interaction terms was deemed significant.Next, using receiver operating characteristic (ROC) analysis, we compared the optimal cut-off biomarker values by ethnicity, defined as the biomarker level at which sensitivity + specificity for a high SYNTAX score was largest. Also, areas under curves were calculated for association with a high SYNTAX score for each biomarker in each ethnic group . The outAll analyses were performed using the R software package . A two-tp < 0.001). Among Indian and Malay patients, diabetes  and dyslipidaemia  were strikingly more common than in Caucasians . The prevalence of current smokers was highest among Indians (42.9 %).Marked baseline differences were observed among the ethnic groups Table . Indian p < 0.001). Stable CAD was slightly less common among Indians and Malays . Unstable angina or non-ST-elevated myocardial infarction was more frequently observed in all three Asian groups than in Caucasians . Also, triple-vessel disease was more often diagnosed in the Asian ethnic groups than in Caucasians .The indication for angiography differed among the ethnic groups (p < 0.001). Coronary artery bypass graft (CABG) surgery was performed most often in Malays .Percutaneous coronary intervention (PCI) was performed more often on Caucasians than in the other ethnic groups, in whom a conservative strategy was more frequently opted for . MPO levels were higher in Caucasians than in Indians , hsTnI levels were higher in Malays than in Caucasians and Indians  and hsTnI levels were higher in Chinese than in Caucasians . High-sensitivity CRP levels and CysC levels  did not differ among the ethnic groups.When adjusted for baseline characteristics, certain differences in biomarker levels remained statistically significant. Post-hoc testing revealed that multivariable-adjusted NTproBNP levels were significantly higher in Malays than in Chinese and Caucasians , indicating a steeper increase in SYNTAX score with every 100-unit increase of NTproBNP in Malays than in Caucasians. Also, we found a significantly higher beta, in both the univariable  and the multivariable  model, for MPO levels in Malays than in Caucasians, indicating that with a 10-unit increase of MPO, the SYNTAX score increases more steeply in Malays than in Caucasians. For hsTnI levels (per 100-unit increase) we found a lower beta for Malays than for Caucasians ; however, this difference was abolished when adjusting for baseline differences.We tested interactions of ethnicity with biomarker levels for SYNTAX score . This indicates that especially in Indians and Malays, lower levels of hsTnI concur with more severe CAD.We observed inter-ethnic differences in biomarkers related to CAD. Also, the optimal cut-off levels at which these biomarkers offered discrimination of severe CAD varied substantially between ethnicities.Differences in NTproBNP levels in the general population have mainly been reported between Blacks and Caucasians, with lower levels reported for Blacks . In our High-sensitivity CRP levels are known to differ markedly among the ethnic groups in the general population with very low levels reported for Chinese and Japanese people , 25. In In our study we found no inter-ethnic differences in CysC levels among CAD patients whilst inter-ethnic differences have been described in the general population, with lower levels in Blacks than in Whites . To our MPO levels have been reported to be related to coronary atherosclerosis in Blacks, but not in Whites or Hispanics , demonstA striking difference was found for hsTnI levels, which were much higher in Malays (multivariably adjusted) than in Caucasians. Population levels have been reported to be comparable among Chinese, Indians and Malays in a Malaysian study , thus thCut-off levels of hsTnI for high SYNTAX score were much higher in Caucasians than in the other ethnic groups, indicating that cardiomyocyte damage is greater in Caucasians than in the other ethnic groups at a SYNTAX score of 18 points. One of the explanations for this feature could be preconditioning occurring in more severe, unstable CAD resulting in resilient myocardium releasing less troponin upon prolonged ischaemia . The CauIn summary, our results suggest that inter-ethnic differences in biomarker levels exist and that the association of these biomarkers with the extent of disease differs by ethnicity. Prior to implementation of biomarkers into clinical practice, their performance should be evaluated in an ethnicity-specific manner .Biomarker levels in our study were measured in arterial blood; these levels may differ from venous levels. However, Martin et al. showed that arterial and venous levels of hsCRP and NTproBNP did not differ . Also, ln = 3 in the Indian ethnic group). Follow-up data on other adverse cardiovascular events were unfortunately not available.Although follow-up data for all-cause death were available, an ethnicity-specific mortality analysis was not possible due to small numbers of fatalities in certain ethnic groups (e.g. We have adjusted our results for baseline differences among the ethnic groups as much as possible. However, profound differences were observed at baseline, which might not have been completely abolished after adjustment. In larger multi-ethnic cohorts propensity-matched  analysisIn a patient group undergoing coronary angiography we found inter-ethnic differences in levels of biomarkers, related to CAD. These differences persisted after correcting for baseline differences among ethnicities. Furthermore, certain biomarkers displayed inter-ethnic differences in the relationship of biomarkers to severity of CAD, with cut-off values from ROC analyses varying over a five-fold range between ethnicities.Future research should focus on ethnicity-specific cut-off values of established CAD biomarkers.


Previous studies used a text-fading procedure as a training tool with the goal to increase silent reading fluency . In recently published studies, this procedure resulted in lasting reading enhancements for adult and adolescent research samples. However, studies working with children reported mixed results. While reading rate improvements were observable for Dutch reading children in a text-fading training study, reading fluency improvements in standardized reading tests post-training attributable to the fading manipulation were not detectable. These results raise the question of whether text-fading training is not effective for children or whether research design issues have concealed possible transfer effects. Hence, the present study sought to investigate possible transfer effects resulting from a text-fading based reading training program, using a modified research design. Over a period of 3 weeks, two groups of German third-graders read sentences either with an adaptive text-fading procedure or at their self-paced reading rate. A standardized test measuring reading fluency at the word, sentence, and text level was conducted pre- and post-training. Text level reading fluency improved for both groups equally. Post-training gains at the word level were found for the text-fading group, however, no significant interaction between groups was revealed for word reading fluency. Sentence level reading fluency gains were found for the text-fading group, which significantly differed from the group of children reading at their self-paced reading routine. These findings provide evidence for the efficacy of text-fading as a training method for sentence reading fluency improvement also for children. Efficient learning demands the ability to read texts at appropriate levels of accuracy and speed  and instructed to read passages together using different strategies  from three different classes of the same school participated in the study. The school was located in a rural region of the Rhine-Main area, mainly populated by middle to high-income families. Two children were identified as outliers and later excluded from analysis, because they reached the maximum scores in both the pre- and post-test, leaving no room for improvement. Hence, 22 children were considered for data analysis . All children were native speakers of German. Parental informed and written consent was obtained for each child. Ethical approval was received from the local ethical review board .Twenty-four German third-graders , the other group was trained at their individual self-paced reading rate without text-fading . In an initial assessment session, participants of both groups read 30 sentences at their own self-paced reading rate.The study followed a pre-post-test design (standardized reading test measurements before and after training) with participating children assigned to one of two training groups. One group was trained with a text-fading procedure  used for the subsequent text-fading training. During each of the following eight training sessions all participants read 40 sentences, depending on the group, either with a text-fading procedure (text-fading group) or without text-fading (self-paced group). Therefore, the total number of items read over the nine sessions amounted to 350 items. All sessions were distributed over a period of 3 weeks (three sessions per week) and lasted approximately 30 min each.crα = 0.97, crα = 0.93, and crα = 0.92 at the word, sentence and text reading level, respectively.Two parallel versions of a standardized reading test  are provided and were used for statistical analyses.The test was administered as paper-pencil test in a classroom setting. All subtests consist of more items than third-graders usually accomplish in the given time frame . The two children, who finished with all items correct, were therefore considered as outliers in this study.A pool of 350 training items adequate for third grade readers was created, each comprising a sentence (7–21 words long) and a corresponding multiple-choice question with four answer options. To prompt attentive reading sentences, questions and multiple-choice answers contained different wording and included reasonable distractors , and children were instructed to click on the correct answer. Once they had clicked another continue button, the next trial started; feedback was not provided. The average reading rate in milliseconds per character  was calculated for all correctly answered trials. After the children received instructions at the first and second session by a trained examiner, they proceeded to work independently and quietly. The examiner was present during all sessions and supervised the course of events. For the eight training sessions, the procedure differed for the two training groups.Participants were trained in a group setting (maximum nine children simultaneously) in an extra room provided by the school. Training items were presented left-justified in black letters  against a light gray background on 15.4-inch laptops running Breznitz' original Reading Acceleration Program , kept constant , or decelerated by 2% . Text-fading rates in milliseconds per character as well as reading comprehension performance were recorded throughout each training session. All children started the next training session at the fading rate they had reached at the end of the preceding training session. Example movies illustrating the text fading procedure are provided in the Supplementary Material.continue button, which then triggered the appearance of the multiple-choice question. Children's reading rate in milliseconds per character and reading comprehension was measured for each trial.The self-paced group read the same training items in the same order and responded to the same multiple-choice questions as participants of the text-fading group; however, the text-fading manipulation was not applied. Instead, the presented sentences remained on the screen until the child clicked the U-tests for independent samples did not reveal any differences for word reading, U = 53.5, for sentence reading, U = 53.5, or for text reading, U = 52.0, between the two training groups in pre-tests. Furthermore, mean z-scores around zero for all three subtests . Tests were separately conducted for each Group (text-fading vs. self-paced). While word reading fluency improved for the text-fading group, F = 8.92, p = 0.007. However, no significant interactions were found for word, F = 1.13, p = 0.301, and text reading fluency F = 0.67, p = 0.424.These separately conducted analyses suggest an interaction of the factors Time and Group, however, they do not reveal interaction effects. Non-parametric procedures that allow the estimation of interaction effects are still not widely used. However, in order to test for interaction effects we opted for presenting the results of the aligned-rank transform procedure (ART) developed in 1994 by Higgins and Tashtoush  and compared text-fading to self-paced reading training. But most importantly, in contrast to a previous study with Dutch children (Snellings et al., The question remains why differential transfer effects were only observed for sentence reading fluency. Obviously, participants were trained in sentence reading; it is therefore not surprising that effects were strongest at this level. Results at the word level showed a significant improvement for the text-fading group and no effect for the self-paced group in the Wilcoxon signed-rank test; the ART, however, did not find a significant interaction effect. Hence, the findings on the word level have to be interpreted with caution. It can be argued that the text-fading group improved on the word level since fast word recognition represents the basis for fast sentence reading. Nevertheless, future research studies will have to clarify whether differential effects with significant interactions between groups can also be revealed on the word reading level.Text reading was not explicitly trained in this study. However, both groups improved equally and did not differ statistically as no interaction effect was revealed for text reading fluency. As outlined earlier, text reading requires a large variety of skills and is therefore highly challenging for beginning readers. Compared to single word reading, which primarily demands proficient decoding (Klauda and Guthrie, Certainly, there are several limitations. The small sample size and the relatively small number of training trials are limiting the statistical power of this study. A larger sample size would have provided more robust data and might have allowed the differentiation of subsamples with varying reading proficiency levels. Furthermore, as outlined in a recent meta-analysis comparing reading training approaches (Galuschka et al., Nonetheless, the present study followed the National Reading Panel's  demand tAlthough it was neither in the scope nor the aim of the current study to investigate the underlying cognitive factors responsible for the observed training gains, it would be desirable to know the active principle of text-fading training. The investigation of possible underlying factors might allow for a more targeted assignment of children in need to this specific approach. Even though some theoretical assumptions have been made, such as for instance a reduction of working memory load, suppression of phonological recoding or improved attention allocation (Breznitz, In summary, we were able to detect differential transfer effects on sentence reading fluency as a result of text-fading training. Text-fading based reading training therefore seems to represent an effective, ecologically valid, and economically attractive training approach for improving silent sentence reading fluency not only in adults, but also in children. However, further research will have to investigate the training's applicability for different reading proficiency levels and age groups, as well as for its effectiveness on word and text reading level. Furthermore, text-fading training should be compared to established reading training programs to estimate its efficacy, and underlying cognitive factors as well as reading strategy behavior possibly accountable for improvements should be investigated in detail.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.