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Structural equation modeling and partial least squares elucidate cortical substrates of trail making test performance

Timothy Herron, John Wyma, , & David Woods
We deconstructed adult completion times on three computerized trail-making tests (TMT) to examine the correlations of isolated ability subcomponents with several MRI cortical anatomy quantities. The three TMT tests had a hierarchical design and all required item selection with the mouse. A click-the-dots test was used to estimate the speed and precision of mouse control. Trails A (TrA) was used to estimate the efficiency of sequencing and visual search. Finally, Trails B (TrB) was used...

Implementing a cervical cancer screening and treatment programme; lessons learned from Zimbabwe

Anna Sellberg, Jakob Arhem, Rebecca Harrison, Musa Hamdam, Charles Ssonko & Debbie Price
The aims of this project were to approximate rates of cancerous and pre-cancerous lesions and to determine the effectiveness of the programme.It was found that there is a high prevalence of cervical cancer among HIV positive women. Also staff training had a decisive impact on capacity to identify lesions.

A practical approach for monitoring the effectiveness of seasonal malaria chemoprevention in Niger

Alena Koscalova, Etienne Gignoux, , Andrew Azman, Esther Sterk & Michel Quere
Objectives of this research project are: estimating seasonal malaria chemoprevention (SMC) effectiveness in Magaria district, Niger, globally and per each SMC round. Also we will evaluate how SMC effectiveness changes in time elapsed since the last SMC distribution.The method used proved practical to evaluate SMC. SMC is effective in Niger, but protective effects seems to wane through the distribution rounds.

Fear conditioned visual information gains preferential access to consciousness

Surya Gayet, Chris Paffen, Artem Belopolsky, Jan Theeuwes & Stefan Van Der Stigchel
The present study aimed at investigating whether fear conditioned visual information gains preferential access to consciousness. We used visual stimuli with no intrinsic relevance (colored rings) and associated one of them with aversive stimulation (electric pulses) following a fear conditioning procedure. Participants were then informed that they would not receive any more electric pulses. We subsequently measured the duration that these stimuli remained invisible under continuous flash suppression, a method derived from binocular rivalry. This...

Utilization of grinting grass (Cynodon dactylon) weeds in Indonesia as an anti-diabetic botanical medicine

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Grinting grass (Cynodon dactylon): traditionally used to medicate dibetes, the compounds of grinting grass are saponin, sterol, alkaloid and flavonoid, which is known to have antidiabetic activity. NPF-GG has high antidiabetic potential along with hypoglycemic effect and increasing cell quantity of Langerhans pankreatic islet.

Post traumatic stress reactions in Ebola patient survivors in Sierra Leone

Malcolm Hugo, Hilde Declerck, Gabriel Fitzpatrick, Nathalie Severy, Osman BM Gbabai, Tom Decroo, Rafael Van Den Bergh & Michel Van Herp
The aim of this study was to investigate the psychological reactions in Ebola Virus Disease (EVD) survivors following their discharge from the MSF Ebola Treatment Center (ETC) in Sierra Leone.<br /> <br /> Survivors have experienced a potentially traumatizing experience as inpatients. They have faced a life threatening event, have witnessed significant suffering and death (often their own family) and most have been hospitalized for a significant length of time (median length of stay 12.5...

Survey on ICP, target CPP and MAP measurement level in patients with severe acute brain injury in different ICUs

Marie Van Laer, Koen Deschilder & Willem Stockman
Since most patients with acute brain injury are treated head-up 30-45°, there can be a height difference of up to 15 cm between the heart and the ear canal. This causes a difference between “mathematical” CPP and “true” CPP of up to 11 mmHg depending on the zero reference level used and the body length of the patient. We conducted a survey to analyse the current practice on CPP targets and zero reference levels in...

Low concordance of differential DNA methylation analysis methods

Helen McCormick, Peter Hickey, Eleni Giannoulatou, Jennifer Cropley & Catherine Suter
DNA methylation is one of the most widely used markers for the study of epigenetic contributions to phenotypic variation and disease. There are several methods for analyzing genome-wide DNA methylation data in common use, but there has been no rigorous evaluation of their performance. We have performed a systematic assessment and comparison of three packages: MethySig, methylKit and DSS, using an empirical dataset of 12 reduced representation bisulphite sequencing libraries (6 test, 6 control). Surprisingly,...

Pathogen identification by the 23S rRNA

Allan Cézar De Azevedo Martins
Some pathogenic agents are classified in risk groups (A, B or C) accordingly to its outbreak spread and priority in a Bioterrorist act. Quickness and accuracy in pathogens identification are essential to a response. Our aim is identify v-regions which could be used to identify pathogens in species level using 23S rRNA sequences. We performed a multiple alignment of the sequences and identified 37 variable regions. V6, V27, V29, V30 and V34 variable regions present...

Structural basis of the effect of Systemic Lupus Erythematosus-Associated mutations in NCF2 on the activity of NADPH oxidase

Miriam Eisenstein, Chaim O. Jacob, Raphael Zidovetzki & Don Armstrong
Systemic Lupus Erythematosus (SLE) is a multisystem autoimmune disorder associated with mutations in multiple genes, including NCF2. We found that mutation H389Q in NCF2 is a SLE risk factor in North Americans of European or Hispanic descent and mutation R395W is independently associated with SLE in Hispanics. Both mutations are within the PB1 domain of NCF2, which binds the PB1 domain of NCF4. NCF1, NCF2 and NCF4 are the cytosolic subunits of NADPH oxidase, a...

The Rostlab Metaproteome Analysis Pipeline (RMAP)

Jonas Rädle, , Diana Iacob & Burkhard Rost

Meeting the global thirst for bioinformatics training

Teresa Attwood, Michelle Brazas, Fran Lewitter, Vicky Schneider &
Around the world, the demand for bioinformatics training is increasing, year-on-year. To meet this demand, GOBLET – the Global Organisation for Bioinformatics Learning, Education & Training – has engaged in numerous training programs and initiatives. This poster presents some of GOBLET's recent world-wide enterprises, sharing lessons learned along the way, and discussing the impact they have had on further outreach efforts.

GenomeRNAi: A phenotype database for large-scale RNAi screens

Esther Schmidt, Oliver Pelz, Svetlana Buhlmann, Hannah Fleckenstein, Johanna Mehl & Michael Boutros
RNA interference (RNAi) represents a popular approach for the systematic perturbation of gene expression. Large-scale screening experiments can be performed, employing a wide variety of biological assays, resulting in the observation of loss-of-function phenotypes across many fields in biology. These phenotypes constitute a rich source of functional gene annotation.

The GenomeRNAi database is a repository for RNAi phenotype and reagent data, aiming to provide a platform for data mining and comparisons. Data is extracted from...

Building text-mining framework for biological-event extraction using deep learning

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The scientific literature is a rich resource for information retrieval on the biological knowledge. Nevertheless, the unstructured textual data in the research articles makes it difficult to access the information with computer-aided systems. Text-mining is one of the solution that can transform unstructured information in the text into database content, and most of the approaches are based on the machine learning models. Since these approaches require high-dimensional features, the performance of the model is heavily...

It is not just about giving the drugs: Medication Adherence Clubs (MACs) for HIV and Non-Communicable Disease (NCD) patients in an informal setting in Kibera, Kenya

Emily Venables, Kelly Khabala, Jeffrey Edwards, Helga Ritter, Tony Reid, Joseph Kibachio, William Etienne, & Helen Bygrave
13 million people are currently on lifelong antiretroviral therapy (ART). Adaptation of ART delivery models could lead to treatment of larger numbers of stable patients. These adaptations include longer drug refills and collecting drugs in clinic-based clubs or the community.This is an innovative model, acceptable to patients and health-care workers. MACs provide large numbers of stable HIV &amp; NCD patients with drug refills: retention will need to be assessed next. MACs also provide peer support,...

Mass drug administration in the Ebola epidemic in Sierra Leone and Liberia

John Pringle, Anna Kuehne, Michel Janssens, Yves Houedakor, Amanda Tiffany, Estrella Lasry, , , Jas Mantero, Carolina Nanclares, , Mathieu Bichet, Olimpia De La Rosa, Samuel Smith & Oliver Pratt
MSF did two mass drug administrations of 3-day courses of artesunate-amodiaquine (ASAQ) as both treatment and chemoprevention for malaria in Freetown, Sierra Leone and Monrovia, Liberia in collaboration with the ministries of health.We expect that the intervention significantly reduced the number of febrile patients in the targeted communities and in the holding centers, resulting in a likely decreased risk of transmission of Ebola to malaria patients; and a reduction of &ldquo;non Ebola&rdquo; pressure on the...

Patient characteristics and risk of mortality in the MSF Ebola Management Centres during the West African Ebola outbreak: a multicentric study

Francesco Grandesso
The Ebola virus disease (EVD) outbreak, ongoing in West Africa since March 2014, is the largest in history. A major activity of MSF has been providing patient care in Ebola Management Centres (EMCs). MSF EMCs were set up progressively in the three most affected countries: two in Guinea in March, two in Liberia in August, and four in Sierra Leone between June and December. We present a retrospective analysis of the main characteristics of patients...

Artesunate-amodiaquine is associated with reduced Ebola mortality

Etienne Gignoux, Andrew S Azman, Martin De Smet, Philippe Azuma, Josephus Bolongei, Moses Massaquoi, Dorian Job, Amanda Tiffany, Roberta Petrucci, Esther Sterk, Julien Potet, Motoi Suzuki, Andreas Kurth, Angela Cannas, Anne Bocquin, Thomas Strecker, Christopher Logue, Thomas Pottage, Constanze Yue, , Micaela Serafini &
Malaria treatment is recommended for all suspected cases of Ebola virus disease (EVD), either presumptively or based on malaria diagnosis. In Foya Ebola Management Centre (EMC), Lofa County, Liberia, the first-line anti-malarial, artemether-lumefantrine (AL), ran out for a 2-week period in August 2014. During this stock rupture, patients received artesunate-amodiaquine (ASAQ); amodiaquine is known to have anti-Ebola virus activity <i>in vitro</i>. We analysed routine programme data with the aim of determining the effect of malaria...

BioSolr – building better search for bioinformatics

Tony Burdett
BioSolr aims to significantly advance the state of the art with regard to indexing and querying biomedical data with freely available open source software.

The video of this presentation is available on the BOSC YouTube channel: view video.

Systematic exploration of guide-tree topology effects for small protein alignments

Fabian Sievers, Graham Hughes & Des Higgins
Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree construction schemes are based on pair-wise distances amongst unaligned sequences. Others try to emulate an underlying evolutionary tree and involve various iteration methods.

In vivo whole-cell recording of neocortical neurons during cortical spreading depression

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We use in vivo whole-cell electrophysiology to understand cellular and synaptic mechanisms post-spreading depolarization. Our findings provide the first in vivo whole-cell phenotype of cortical spreading depression. We show that spontaneous synaptic activity at the single-cell level is drastically reduced after the depolarization and intrinsic membrane properties are affected to a lesser extent.

Investigating intra-tumour heterogeneity in prostate cancer using structural variation

Marek Cmero, Niall Corcoran, Christopher Hovens, Ke Yuan, Florian Markowetz, &
Many approaches have arisen for inferring the evolutionary dynamics of tumour cell populations from point-mutation and copy-number data. However, there are currently no methods that incorporate structural variants (SVs). We present a method, SVClone, for inferring the subclonal make-up of tumour samples using large-scale genomic rearrangements obtained from whole-genome sequencing data. This approach is particularly useful for cancers driven by structural variation, such as prostate cancer.

Sequencing analysis of fHbp, porA, nhbA and nadA genes from serogroup W strains

Emma Ispasanie, Gerd Pluschke, Abraham Hodgson, Ali Sie, & Oliver Koeberling
The genes encode fHbp v.2, ID 22 or 23, PorA subtype P1.5,2, NHBA allele 17 and NadA allele 3 with and without insertion sequence IS1301. DNA sequences were translated into protein sequences and sequence queries were performed using the database on http://pubmlst.org/neisseria.

Supplementary file S1

Johannes M. Dijkstra & David B. Alexander
Alignment of PMEPA1-NKILA promoter region sequences of representative animals and deduced PMEPA1 amino acid sequences for the species compared in.

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