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Alex R Hardisty, Finn Bacall, Niall Beard, Maria-Paula Balcázar-Vargas, Bachir Balech, Zoltán Barcza, Sarah J Bourlat, Renato De Giovanni, Yde de Jong, Francesca De Leo, Laura Dobor, Giacinto Donvito, Donal Fellows, Antonio Fernandez Guerra, Nuno Ferreira, Yuliya Fetyukova, Bruno Fosso, Jonathan Giddy, Carole Goble, Anton Güntsch, Robert Haines, Vera Hernández Ernst, Hannes Hettling, Dóra Hidy, Ferenc Horváth, Dóra Ittzés, Péter Ittzés, Andrew Jones, Renzo Kottmann, Robert Kulawik, Sonja Leidenberger, Päivi Lyytikäinen-Saarenmaa, Cherian Mathew, Norman Morrison, Aleksandra Nenadic, Abraham Nieva de la Hidalga, Matthias Obst, Gerard Oostermeijer, Elisabeth Paymal, Graziano Pesole, Salvatore Pinto, Axel Poigné, Francisco Quevedo Fernandez, Monica Santamaria, Hannu Saarenmaa, Gergely Sipos, Karl-Heinz Sylla, Marko Tähtinen, Saverio Vicario, Rutger Aldo Vos, Alan R Williams, Pelin Yilmaz
BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science...
October 20, 2016: BMC Ecology
David Shaw, Denie Georgieva, Bernadette Haase, Dale Gardiner, Penney Lewis, Nichon Jansen, Tineke Wind, Undine Samuel, Maryon McDonald, Rutger Ploeg
Millions of people want to donate their organs after they die for transplantation, and many of them have registered their wish to do so or told their family and friends about their decision. For most of them, however, this wish is unlikely to be fulfilled, as only a small number of deaths (1% in the United Kingdom) occur in circumstances where the opportunity to donate organs is possible. Even for those who do die in the 'right' way and have recorded their wishes or live in a jurisdiction with a 'presumed consent' system, donation often does not go ahead because of another issue: their families refuse to allow donation to proceed...
October 19, 2016: Transplantation
Rutger J Maas, Jeroen K Deegens, Bart Smeets, Marcus J Moeller, Jack F Wetzels
Minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) are the key histological findings in patients with idiopathic nephrotic syndrome (INS). Although MCD and idiopathic FSGS are often considered to represent separate entities based on differences in their presenting characteristics, histology and outcomes, little evidence exists for this separation. We propose that MCD and idiopathic FSGS are different manifestations of the same progressive disease. The gradual development of FSGS in patients with non-remitting or relapsing INS has been well documented...
October 17, 2016: Nature Reviews. Nephrology
Najaf Amin, Nadezhda M Belonogova, Olivera Jovanova, Rutger W W Brouwer, Jeroen G J van Rooij, Mirjam C G N van den Hout, Gulnara R Svishcheva, Robert Kraaij, Irina V Zorkoltseva, Anatoly V Kirichenko, Albert Hofman, André G Uitterlinden, Wilfred F J van IJcken, Henning Tiemeier, Tatiana I Axenovich, Cornelia M van Duijn
BACKGROUND: Despite high heritability, little success was achieved in mapping genetic determinants of depression-related traits by means of genome-wide association studies. METHODS: To identify genes associated with depressive symptomology, we performed a gene-based association analysis of nonsynonymous variation captured using exome-sequencing and exome-chip genotyping in a genetically isolated population from the Netherlands (n = 1999). Finally, we reproduced our significant findings in an independent population-based cohort (n = 1604)...
August 11, 2016: Biological Psychiatry
Jan Pieter Marchal, Heleen Maurice-Stam, Bregje A Houtzager, Susanne L Rutgers van Rozenburg-Marres, Kim J Oostrom, Martha A Grootenhuis, A S Paul van Trotsenburg
BACKGROUND: We analysed developmental outcomes from a clinical trial early in life and its follow-up at 10.7 years in 123 children with Down syndrome. AIMS: To determine 1) strengths and weaknesses in adaptive functioning and motor skills at 10.7 years, and 2) prognostic value of early-life characteristics (early developmental outcomes, parental and child characteristics, and comorbidity) for later intelligence, adaptive functioning and motor skills. METHODS AND PROCEDURES: We used standardized assessments of mental and motor development at ages 6, 12 and 24 months, and of intelligence, adaptive functioning and motor skills at 10...
October 13, 2016: Research in Developmental Disabilities
Daniel P Russo, Marlene T Kim, Wenyi Wang, Daniel Pinolini, Sunil Shende, Judy Strickland, Thomas Hartung, Hao Zhu
: We have developed a public Chemical In vitro - In vivo Profiling (CIIPro) portal, which can automatically extract in vitro biological data from public resources (i.e. PubChem) for user-supplied compounds. For compounds with in vivo target activity data (e.g. animal toxicity testing results), the integrated cheminformatics algorithm will optimize the extracted biological data using in vitro - in vivo correlations. The resulting in vitro biological data for target compounds can be used for read-across risk assessment of target compounds...
October 14, 2016: Bioinformatics
Rutger Bennet, Margareta Eriksson
AIM: This study described the epidemiology and clinical features of childhood tuberculosis (TB) in Stockholm over a 45-year period, when there was a resurge of tuberculosis concomitant with increased immigration. METHODS: We describe 220 children up to the age of 16 years with active TB, seen at the Astrid Lindgren Children's Hospital from 1971-2015. The study period was divided into three 15-year periods. RESULTS: Cases increased from 10 children in 1971-1985 to 76 in 1986-2000 and 134 in 2001-2015, with overall incidence increasing from <1 to four per 100,000...
October 14, 2016: Acta Paediatrica
Marloes Visser, Jeroen F van der Heijden, Jasper J van der Smagt, Pieter A Doevendans, Arthur A Wilde, Peter Loh, Rutger J Hassink
BACKGROUND: Idiopathic ventricular fibrillation (IVF) is a rare cause of sudden cardiac arrest. Limited data are available on the long-term outcome of IVF patients. METHODS AND RESULTS: In this retrospective cohort study, 107 consecutive patients with an initial diagnosis of IVF were analyzed (age at index event 40.4 years, 60% male). Missing diagnostic data were acquired during follow-up, including genetic testing, to exclude underlying disease. A specific diagnosis was revealed in 22 of 107 patients (21%) during a median follow-up of 10...
October 2016: Circulation. Arrhythmia and Electrophysiology
Marie Skogs, Charlotte Stadler, Rutger Schutten, Martin Hjelmare, Christian Gnann, Lars Björk, Ina Poser, Anthony A Hyman, Mathias Uhlén, Emma K Lundberg
Antibodies are indispensible research tools, yet the scientific community has not adopted standardized procedures to validate their specificity. Here we present a strategy to systematically validate antibodies for immunofluorescence applications using gene tagging. We have assessed the on- and off-target binding capabilities of 197 antibodies using 108 cell lines expressing EGFP tagged target proteins at endogenous levels. Furthermore, we assessed batch-to-batch effects for 35 target proteins showing that both the on- and off-target binding patterns vary significantly between antibody batches and that the proposed strategy serves as a reliable procedure for ensuring reproducibility upon production of new antibody batches...
October 11, 2016: Journal of Proteome Research
Karin V Greco, Lydia Francis, Honglei Huang, Rutger Ploeg, Aldo R Boccaccini, Tahera Ansari
As biocompatible matrices, porcine dermal scaffolds have limited application in tissue engineering due to rapid degradation following implantation. This study compared the physical, chemical, and biomechanical changes that occurred when genipin and quercetin were used to crosslink dermal scaffolds and to determine whether quercetin could be used as an alternative to genipin. Physicochemical changes in the collagen were assessed using spectroscopic methods (XRD and NMR analysis). Crosslinking reaction was evaluated by quantification of amino acids and the degree of this reaction by ninhydrin assay...
October 7, 2016: Journal of Tissue Engineering and Regenerative Medicine
Johanna M Meulepas, Anne M J B Smets, Rutger A J Nievelstein, Patrycja Gradowska, Jonathan Verbeke, Herma C Holscher, Matthieu J C M Rutten, Mariëtte Kieft, Cécile M Ronckers, Michael Hauptmann
OBJECTIVE: To evaluate trends and patterns in CT usage among children (aged 0-17 years) in The Netherlands during the period 1990-2012. METHODS: Lists of electronically archived paediatric CT scans were requested from the Radiology Information Systems (RIS) of Dutch hospitals which reported >10 paediatric CT scans annually in a survey conducted in 2010. Data included patient identification, birth date, gender, scan date and body part scanned. For non-participating hospitals and for years prior to electronic archiving in some participating hospitals, data were imputed by calendar year and hospital type (academic, general with <500 beds, general with ≥ 500 beds)...
October 5, 2016: European Radiology
Maria Kaisar, Leon F A van Dullemen, Marie-Laëtitia Thézénas, M Zeeshan Akhtar, Honglei Huang, Sandrine Rendel, Philip D Charles, Roman Fischer, Rutger J Ploeg, Benedikt M Kessler
BACKGROUND: The successful application of-omics technologies in the discovery of novel biomarkers and targets of therapeutic interventions is facilitated by large collections of well curated clinical samples stored in bio banks. Mining the plasma proteome holds promise to improve our understanding of disease mechanisms and may represent a source of biomarkers. However, a major confounding factor for defining disease-specific proteomic signatures in plasma is the variation in handling and processing of clinical samples leading to protein degradation...
2016: Clinical Proteomics
Cas Teunissen, Nick Clappers, Wil Kassenberg, Rutger J Hassink, Jeroen F van der Heijden, Peter Loh
AIMS: Adenosine testing can reveal dormant pulmonary vein (PV) conduction after PV antrum isolation (PVAI). However, the optimal timing for adenosine administration is unknown. We hypothesized that adenosine testing immediately after PVAI reliably reveals PV reconnection and thereby eliminates the need for an observation period. METHODS: Fifty patients underwent PVAI. Immediately after isolation of a PV pair, adenosine was administered. Both PV pairs were separately tested...
October 4, 2016: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
Vanja Rozenblat, Deborah Ong, Matthew Fuller-Tyszkiewicz, Kirsti Akkermann, David Collier, Rutger C M E Engels, Fernando Fernandez-Aranda, Jaanus Harro, Judith R Homberg, Andreas Karwautz, Evelyn Kiive, Kelly L Klump, Christine L Larson, Sarah E Racine, Jodie Richardson, Howard Steiger, Scott F Stoltenberg, Tatjana van Strien, Gudrun Wagner, Janet Treasure, Isabel Krug
OBJECTIVES: To summarize and synthesize the growing gene x environment (GxE) research investigating the promoter region of the serotonin transporter gene (5-HTTLPR) in the eating disorders (ED) field, and overcome the common limitation of low sample size, by undertaking a systematic review followed by a secondary data meta-analysis of studies identified by the review. METHOD: A systematic review of articles using PsycINFO, PubMed, and EMBASE was undertaken to identify studies investigating the interaction between 5-HTTLPR and an environmental or psychological factor, with an ED-related outcome variable...
September 24, 2016: Journal of Psychiatric Research
Qiu-Ling Liu, Li Xue, Wei-Wei Wu, Xin He, Kai-Yan Liu, Hu Zhao, De-Jian Lu
In this study, a panel of 13 STR loci locate on chromosome 3, 4, and 17 (D3S2402, D3S2452, D3S1766, D3S4554, D3S2388, D3S3051, D3S3053, D4S2404, D4S2364, AC001348A, AC001348B, D17S975, and D17S1294) were assessed for pairwise kinship analysis. Map distances between these STR loci ranged from 0.07 cM to 97.03 cM. The population genetic study of Chinese Han population showed that linkage disequilibrium exists in two clusters of closely linked markers (D4S2404-D4S2364 and D17S975-D17S1294), in which the recombination fractions were 0...
October 4, 2016: Electrophoresis
R Tuli, A Osipov, J K Rutgers, D Dhall, J Naziri, S Chopra, Q Li, A E Hendifar, N N Nissen
No abstract text is available yet for this article.
October 1, 2016: International Journal of Radiation Oncology, Biology, Physics
Babs G Sibinga Mulder, J Sven D Mieog, Henricus J M Handgraaf, Arantza Farina Sarasqueta, Hans F A Vasen, Thomas P Potjer, Rutger-Jan Swijnenburg, Saskia A C Luelmo, Shirin Feshtali, Akin Inderson, Alexander L Vahrmeijer, Bert A Bonsing, Tom van Wezel, Hans Morreau
To improve the diagnostic value of fine-needle aspiration (FNA)-derived material, we perform targeted next-generation sequencing (NGS) in patients with a suspect lesion of the pancreas. The NGS analysis can lead to a change in the treatment plan or supports inconclusive or uncertain cytology results. We describe the advantages of NGS using one particular patient with a recurrent pancreatic lesion 7 years after resection of a pancreatic ductal adenocarcinoma (PDAC). Our NGS analysis revealed the presence of a presumed second primary cancer in the pancreatic remnant, which led to a change in treatment: resection with curative intend instead of palliation...
September 26, 2016: Journal of Clinical Pathology
Emma J Groen, Lotte E Elshof, Lindy L Visser, Emiel J Th Rutgers, Hillegonda A O Winter-Warnars, Esther H Lips, Jelle Wesseling
With the widespread adoption of population-based breast cancer screening, ductal carcinoma in situ (DCIS) has come to represent 20-25% of all breast neoplastic lesions diagnosed. Current treatment aims at preventing invasive breast cancer, but the majority of DCIS lesions will never progress to invasive disease. Still, DCIS is treated by surgical excision, followed by radiotherapy as part of breast conserving treatment, and/or endocrine therapy. This implies over-treatment of the majority of DCIS, as less than 1% of DCIS patients will go on to develop invasive breast cancer annually...
September 23, 2016: Breast: Official Journal of the European Society of Mastology
Joeva J Barrow, Eduardo Balsa, Francisco Verdeguer, Clint D J Tavares, Meghan S Soustek, Louis R Hollingsworth, Mark Jedrychowski, Rutger Vogel, Joao A Paulo, Jan Smeitink, Steve P Gygi, John Doench, David E Root, Pere Puigserver
Mitochondrial diseases comprise a heterogeneous group of genetically inherited disorders that cause failures in energetic and metabolic function. Boosting residual oxidative phosphorylation (OXPHOS) activity can partially correct these failures. Herein, using a high-throughput chemical screen, we identified the bromodomain inhibitor I-BET 525762A as one of the top hits that increases COX5a protein levels in complex I (CI) mutant cybrid cells. In parallel, bromodomain-containing protein 4 (BRD4), a target of I-BET 525762A, was identified using a genome-wide CRISPR screen to search for genes whose loss of function rescues death of CI-impaired cybrids grown under conditions requiring OXPHOS activity for survival...
October 6, 2016: Molecular Cell
Dorothea Evers, Jaap Jan Zwaginga, Janneke Tijmensen, Rutger A Middelburg, Masja de Haas, Karen M K de Vooght, Daan van de Kerkhof, Otto Visser, Nathalie C V Péquériaux, Francisca Hudig, Johanna G van der Bom
Red cell alloimmunization may induce severe hemolytic side effects. Identification of risk modifying conditions will help tailor preventative strategies. This study aims to quantify the associations of hematological malignancies and solid cancers with red cell alloimmunization in patients receiving red cell transfusions. We performed a nested multicenter case-control study in a source population of 24,063 patients receiving their first and subsequent red cell transfusions during an eight year follow-up period...
September 15, 2016: Haematologica
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