Filtering Options Research Articles

The effectiveness of steroid injection in treatment of plantar fasciitis: A systematic review and meta-analysis of controlled-randomized trials

Plantar fasciitis is very troublesome in clinical fields. Although steroid injection has been a widely used treatment option in musculoskeletal disorders, there have been arguments about the effectiveness in plantar fasciitis. This study is to determine the effectiveness of steroid injection in the treatment of plantar fasciitis. Meta-analysis was conducted using searching engines such as Google Scholar, PubMed, CINAHL, Embase and manual searching which were searched to December 2017. The following key search terms were used; plantar fasciopathy fasciitis in google scholar, “fasciitis, plantar”[Mesh] with two filter options “Randomized Controlled Trial” and “human” in PubMed, plantar fasciopathy fasciitis in CINAHL, plantar AND fasciopathy AND (“fasciitis” OR “fasciitis”/exp OR fasciitis) in Embase. Two articles were also found using manual searching. Total 35 articles were found and duplicates were removed. Two reviewers reviewed and selected the articles, which has randomized controlled design and eligible data. Four articles were determined to be relevant, meeting inclusion and exclusion criteria. We found that the overall standardized mean differences of pain outcome between steroid injection and other treatments or sham was −0.57 (95% confidence interval: −0.83 to −0.30), with low heterogeneity ( P = 0.52, I 2 = 0%) at 1 month, but −0.33 (95% confidence interval: −0.76 to 0.10, P = 0.13, I 2 = 50%) at 3 month. It suggested evidence of the effectiveness of short-term steroid injection, compared with autologous blood injection or other conservative treatment, but limited evidence of long-term effectiveness and functional improvement. Although steroid injection in treating plantar fasciitis has been arguing, there is evidence of the effectiveness of steroid injection in relieving pain for 1 month. But further study is needed to determine long-term effectiveness of steroid injection.

Abstract 2288: Assessing patient trial readiness for precision cancer medicine clinical trials through computational trial matching and rule-based logic applied to genomic and clinical data

Abstract More than 1,100 phase I treatment trials are registered with clinicaltrials.cancer.gov. Patient identification and recruitment to these trials is particularly challenging due to the vast molecular data now available for patients and the increasingly complex nature of the molecular eligibility criteria. Additionally, Phase I trial staff often manage a portfolio of dozens of trials, making patient identification, recruitment, screening, and enrollment an arduous task. To address the need for better and more efficient patient identification, we have developed MatchMiner, a novel open source computational platform for matching patient-specific genomic profiles to precision cancer medicine clinical trials, and a pre-screening tool that includes options for filtering and sorting patients based on clinical data elements. MatchMiner excels at identifying patients who are eligible for clinical trials based on genomic, cancer type, age, and gender criteria, but the great majority of patients are not currently ready for a trial. The pre-screening tool allows for the integration of additional clinical data, including genomic testing date, appointments, treatment plan history, and radiology scan impression text, in order to provide an assessment of ‘trial readiness'. To integrate these tools into the clinical workflow, we have implemented a weekly MatchMiner Tumor Board Review process, where together with the DFCI Early-Phase Drug Development Center (EDDC) physicians and staff, a thorough assessment of potential patient-trial matches is performed. Currently we have scaled this initiative to include 18 genomically-driven trials. Each week, ~9000 patient-trial matches are computed across all open trials, which are then computationally filtered to a list of ~300 patient-trial matches utilizing rules-based logic applied to our clinical data sources. The MatchMiner team then performs a manual review of pre-filtered matches based on additional requirements, such as evidence of progression in the radiology scan text impressions. The final list of ~10-20 patients is reviewed with the EDDC, and patients deemed to be ‘trial ready' are flagged. E-mail notifications are then sent out to the patient's oncologist, alerting them to a potential genomically-driven clinical trial opportunity. The combination of computational patient-trial match identification and rules-based computational pre-filtering based on additional clinical data has allowed us to screen thousands of patients per week, which would not be possible otherwise. To evaluate the success of this initiative, we are tracking patient consults and trial enrollments, and capturing feedback on workflow integration and utilization. Additionally, efforts to further automate trial readiness measurements to minimize the need for manual review are ongoing. Citation Format: Catherine Del Vecchio Fitz, Khanh Do, James Lindsay, Suzanne Hector-Barry, Zachary Zwiesler, Priti Kumari, Tali Mazor, Tamba Monrose, Adem Albayrak, John Methot, Michael Hassett, Geoffrey Shapiro, Ethan Cerami. Assessing patient trial readiness for precision cancer medicine clinical trials through computational trial matching and rule-based logic applied to genomic and clinical data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2288.

Abstract 3281: PDX Finder: An open and global catalogue of patient tumor-derived xenograft models

Abstract Patient-derived tumor xenograft (PDX) mouse models have emerged as an important oncology research platform to study tumor evolution, drug response and for tailoring chemotherapeutic approaches to individual patients. PDX models are produced and made available in repositories managed by small academic labs, large research consortia and contract research organizations. Because of the distributed and heterogeneous nature of PDX repositories, finding relevant models of interest to investigators is a challenge. To address this issue, The Jackson Laboratory and EMBL-EBI have co-developed the PDX Finder, a comprehensive open global catalogue of PDX models and their associated data across resources. In support this initiative, we coordinated the community initiative to develop the PDX models Minimal Information standard (PDX-MI) that defines the minimal information necessary for describing key elements of a PDX model including the clinical attributes of a patient's tumor, methods of implantation, host strain, and quality assurance methods used for model validation†. PDX-MI serves as the basis for PDX Finder's comprehensive search and attribute filtering options (e.g., tumor histology, molecular variant, drug response). Within PDX Finder, model attributes are harmonized and integrated into a cohesive ontological data model that supports consistent searching across the originating resources. From PDX Finder, direct links to these resources are provided to allow users to contact the relevant institution for model acquisition and further collaboration. PDX Finder is formally collaborating with several worldwide consortia including PDXnet and EurOPDX to increase “findability” of PDX models and to advance cancer research and drug discovery. PDX Finder is currently displaying over 1200 PDX models for a wide variety of cancers and is actively recruiting more models. The community is invited to explore and provide feedback on our portal as we build this rich resource at : www.pdxfinder.org. † Meehan et al, 2017. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. Cancer Res. 2017 Nov 1;77(21):e62-e66. Citation Format: Nathalie A. Conte, Terrence F. Meehan, Dale A. Begley, Debbie M. Krupke, Csaba Halmagyi, Jeremy C. Mason, Abayomi Mosaku, Steven B. Neuhauser, Helen Parkinson, Carol J. Bult. PDX Finder: An open and global catalogue of patient tumor-derived xenograft models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3281.

Life cycle assessment and environmental profile evaluations of high volumetric efficiency capacitors

High volumetric efficiency capacitors are found in all smart electronic devices, providing important applications within circuits, including flexible filter options, power storage and sensing, decoupling and circuit smoothing functions. Multilayer ceramic capacitors (MLCCs) hold the major market share but tantalum electrolytic capacitors (TECs) provide a viable alternative if higher breakdown strengths are required. The reduced costs, smaller dimensions suitable for space-constrained electronic circuits, exceptional high-frequency characteristics, higher reliability, ripple control and longevity, however, are driving the market to replace TECs with MLCCs wherever possible. To date, no current research regarding the transition from TECS to MLCCs has been conducted from an entirely environmental viewpoint. This article identifies, quantifies, ranks and compares the environmental impacts of the MLCC and TEC supply chains using an integrated hybrid life cycle assessment framework. Three recovery methods: incineration; hydrometallurgy and pyrometallurgy are considered in the overall impact assessment. Electrical energy consumption during fabrication alongside the use of nickel paste are the major environmental hotspot for MLCCs. The high proportion of tantalum in TECs results in an overall greater environmental impact in comparison with MLCCs, due to intensive extraction, processing and purification requirements of tantalum. Of the three recovery methods, the hydrometallurgy process offers the least environmental impact for both MLCCs and TECs. Overall, the current work shows that while the industry led transition from TECs to MLCCs offers both an operational and functional edge, it is also an environmentally intelligent move. Intervention options that can further drive down the environmental impacts of MLCCs are also proposed such as a reduction in the reliance of MLCCs on rare earth elements and Cu external electrodes in some designs and material recovery.

Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies

BackgroundSingle nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Methods of SNP discovery have been a matter of debate for their potential of introducing ascertainment bias, and genetic diversity results obtained from the SNP genotype data can be misleading. We used a total of 42 chicken populations where both individual genotyped array data and pool whole genome resequencing (WGS) data were available. We compared allele frequency distributions and genetic diversity measures (expected heterozygosity (He), fixation index (FST) values, genetic distances and principal components analysis (PCA)) between the two data types. With the array data, we applied different filtering options (SNPs polymorphic in samples of two Gallus gallus wild populations, linkage disequilibrium (LD) based pruning and minor allele frequency (MAF) filtering, and combinations thereof) to assess their potential to mitigate the ascertainment bias.ResultsRare SNPs were underrepresented in the array data. Array data consistently overestimated He compared to WGS data, however, with a similar ranking of the breeds, as demonstrated by Spearman’s rank correlations ranging between 0.956 and 0.985. LD based pruning resulted in a reduced overestimation of He compared to the other filters and slightly improved the relationship with the WGS results. The raw array data and those with polymorphic SNPs in the wild samples underestimated pairwise FST values between breeds which had low FST (<0.15) in the WGS, and overestimated this parameter for high WGS FST (>0.15). LD based pruned data underestimated FST in a consistent manner. The genetic distance matrix from LD pruned data was more closely related to that of WGS than the other array versions. PCA was rather robust in all array versions, since the population structure on the PCA plot was generally well captured in comparison to the WGS data.ConclusionsAmong the tested filtering strategies, LD based pruning was found to account for the effects of ascertainment bias in the relatively best way, producing results which are most comparable to those obtained from WGS data and therefore is recommended for practical use.

Formalization of the process of the strategic adaptation of the manufacturing company to integration of complex-technical systems in the supply chain

The experience of functioning supply chains both in Ukraine and abroad convincingly proves the importance of a high level of synchronization of actions of all its participants. The formation of a successful model for managing these integrated structures underscores, at the same time, the exceptional importance of strategic harmonization of the goals of the chain and its participants. Despite the existence of a huge heritage of works devoted to the strategic aspects of the operation of such structures, research aimed at strategic adaptation of an individual participant to integration into the supply chain is clearly not enough. A consequence of the lack of a methodology for adapting an enterprise's strategy to integration into the supply chain is not only a lack of understanding by Ukrainian entrepreneurs of the potential benefits and threats of such integration, but also hostile to it.Thanks to the use of known strategic analysis tools such as SCOC and SWOT analysis, a scheme for identifying the motives for integrating a manufacturing enterprise into the supply chain of complex technical systems is proposed, which allows the enterprise to decide on the timeliness or, conversely, the relevance of such initiative.Taking into account the prioritization of the application of the project approach to the formation of the integration strategy of the supply chain, this allows to identify the impact of this strategy on the business strategy. In particular, for a manufacturing enterprise, this is considered within the framework of such strategic benchmarks as «efficiency» and «elasticity». In combination with the formation of corresponding sets of characteristic landmarks for each type of functional strategies, the formalization of the process of strategic adaptation of a separate manufacturing enterprise of complex technical systems to integration into the supply chain becomes possible in the context of the strategic goal set by the project. The practical value of such formalization lies in simplifying the decision-making process associated with the need to harmonize them with decisions of a higher level. And also with the choice of alternative options for filtering out those that contradict the main goal of the supply chain.

Denali, Tulip, and Option Inferior Vena Cava Filter Retrieval: A Single Center Experience.

To compare the technical success of filter retrieval in Denali, Tulip, and Option inferior vena cava filters. A retrospective analysis of Denali, Gunther Tulip, and Option IVC filters was conducted. Retrieval failure rates, fluoroscopy time, sedation time, use of advanced retrieval techniques, and filter-related complications that led to retrieval failure were recorded. There were 107 Denali, 43 Option, and 39 Tulip filters deployed and removed with average dwell times of 93.5, 86.0, and 131days, respectively. Retrieval failure rates were 0.9% for Denali, 11.6% for Option, and 5.1% for Tulip filters (Denali vs. Option p=0.018; Denali vs. Tulip p=0.159; Tulip vs. Option p=0.045). Median fluoroscopy time for filter retrieval was 3.2min for the Denali filter, 6.75min for the Option filter, and 4.95min for the Tulip filter (Denali vs. Option p<0.01; Denali vs. Tulip p<0.01; Tulip vs. Option p=0.67). Advanced retrieval techniques were used in 0.9% of Denali filters, 21.1% in Option filters, and 10.8% in Tulip filters (Denali vs. Option p<0.01; Denali vs. Tulip p<0.01; Tulip vs. Option p<0.01). Filter retrieval failure rates were significantly higher for the Option filter when compared to both the Denali and Tulip filters. Retrieval of the Denali filter required significantly less amount of fluoroscopy time and use of advanced retrieval techniques when compared to both the Option and Tulip filters. The findings of this study indicate easier retrieval of the Denali and Tulip IVC filters when compared to the Option filter.

FAPEC, a versatile and efficient data compressor for space missions

ABSTRACTFully Adaptive Prediction Error Coder (FAPEC) is a data compressor which offers good compression ratios even when data is severely affected by noise and outliers. This, combined with its high computing performance, makes it suitable for space applications. It is based on a variety of pre-processing stages followed by an outlier-resilient adaptive entropy coder. Sample sizes of 8–24 bits are supported. Pre-processing stages range from simple delta algorithms (with interleaving, lossy, and filtering options) to more complex discrete wavelet transform and Hierarchical Pixel Averaging image algorithms (with or without losses, for single or multiple bands). A quick prediction-based lossless multi-band algorithm is also available, as well as lightweight dictionary-like pattern recognition. Thus, one can have functionalities equivalent to those of Consultative Committee for Space Data Systems (CCSDS) 121.0, 122.x, and 123.x in a single system, as well as some features not supported yet by any recommendation. Here, we describe the main features of FAPEC and the results obtained on a variety of data, comparing compression ratios and speeds against CCSDS standards.

Arabic-English Parallel Corpus: A New Resource for Translation Training and Language Teaching

Parallel corpora can be defined as collections of aligned, translated texts of two or more languages. They play a major role in translation and contrastive studies, and are also becoming popular in translation training and language teaching, with the advent of the data-driven learning (DDL) approach. Despite their significance, however, Arabic seems to lack a satisfactory general-use parallel corpus resource. The literature describes few Arabic–English parallel corpora, and these few are usually inaccurate and/or expensive. Some are small in size, while others are restricted in terms of genre, failing to meet the requirements of many academics and researchers. This paper describes an ongoing project at the College of Languages and Translation, King Saud University, to compile a 10-million-word Arabic–English parallel corpus to be used as a resource for translation training and language teaching. The bidirectional corpus can be used to compare translated and source language and identify differences. The corpus has been manually verified at different stages, including translation, text segmentation, alignment, and file preparation; it is available as full-text in XML format and through a user-friendly web interface that provides a concordancer to support bilingual search queries and several filtering options.

Kmer-SSR: a fast and exhaustive SSR search algorithm.

MotivationOne of the main challenges with bioinformatics software is that the size and complexity of datasets necessitate trading speed for accuracy, or completeness. To combat this problem of computational complexity, a plethora of heuristic algorithms have arisen that report a ‘good enough’ solution to biological questions. However, in instances such as Simple Sequence Repeats (SSRs), a ‘good enough’ solution may not accurately portray results in population genetics, phylogenetics and forensics, which require accurate SSRs to calculate intra- and inter-species interactions.ResultsWe present Kmer-SSR, which finds all SSRs faster than most heuristic SSR identification algorithms in a parallelized, easy-to-use manner. The exhaustive Kmer-SSR option has 100% precision and 100% recall and accurately identifies every SSR of any specified length. To identify more biologically pertinent SSRs, we also developed several filters that allow users to easily view a subset of SSRs based on user input. Kmer-SSR, coupled with the filter options, accurately and intuitively identifies SSRs quickly and in a more user-friendly manner than any other SSR identification algorithm.Availability and implementationThe source code is freely available on GitHub at https://github.com/ridgelab/Kmer-SSR.

An Accuracy Assessment of Derived Digital Elevation Models from Terrestrial Laser Scanning in a Sub-Tropical Forested Environment

Forest structure attributes produced from terrestrial laser scanning (TLS) rely on normalisation of the point cloud values from sensor coordinates to height above ground. One method to do this is through the derivation of an accurate and repeatable digital elevation model (DEM) from the TLS point cloud that is used to adjust the height. The primary aim of this paper was to test a number of TLS scan configurations, filtering options and output DEM grid resolutions (from 0.02 m to 1.0 m) to define a best practice method for DEM generation in sub-tropical forest environments. The generated DEMs were compared to both total station (TS) spot heights and a 1-m DEM generated from airborne laser scanning (ALS) to assess accuracy. The comparison to TS spot heights found that a DEM produced using the minimum elevation (minimum Z value) from a point cloud derived from a single scan had mean errors &gt;1 m for DEM grid resolutions &lt;0.2 m at a 25-m plot radius. At a 1-m grid resolution, the mean error was 0.19 m. The addition of a filtering approach that combined a median filter with a progressive morphological filter and a global percentile filter was able to reduce mean error of the 0.02-m grid resolution DEM to 0.31 m at a 25-m plot radius using all returns. Using multiple scan positions to derive the DEM reduced the mean error for all DEM methods. Our results suggest that a simple minimum Z filtering DEM method using a single scan at the grid resolution of 1 m can produce mean errors &lt;0.2 m, but for a small grid resolution, such as 0.02 m, a more complex filtering approach and multiple scan positions are required to reduced mean errors. The additional validation data provided by the 1-m ALS DEM showed that when using the combined filtering method on a point cloud derived from a single scan at the plot centre, errors between 0.1 and 0.5 m occurred in the TLS DEM for all tested grid resolutions at a plot radius of 25 m. These findings present a protocol for DEM production from TLS data at a range of grid resolutions and provide an overview of factors affecting DEMs produced from single and multiple TLS scan positions.

Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders.

Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis. This tool offers a user-friendly interface, and leads clinicians through simple steps by limiting the number of candidates to achieve a final diagnosis of a medical genetics case. A useful innovation is the “1-click” method, which enables listing all the relevant variants in genes present at OMIM for perusal by clinicians. Mendel,MD was experimentally validated using clinical cases from the literature and was tested by students at the Universidade Federal de Minas Gerais, at GENE–Núcleo de Genética Médica in Brazil and at the Children’s University Hospital in Dublin, Ireland. We show in this article how it can simplify and increase the speed of identifying the culprit mutation in each of the clinical cases that were received for further investigation. Mendel,MD proved to be a reliable web-based tool, being open-source and time efficient for identifying the culprit mutation in different clinical cases of patients with Mendelian Disorders. It is also freely accessible for academic users on the following URL: https://mendelmd.org.

Mobile Application Development for Smart Tourist Guide

The development of internet technologies and smartphones have changed the behavior of people in everyday life interact with one another. Society is becoming more easily in requesting and obtaining information through mobile devices. Surakarta is an autonomous region with the status of a town under the Central Java province that has many interesting attractions area for foreign tourists as well as locals. By 2015 the number of tourists visiting the city of Surakarta as much as 4.2 million people. Some tourists still difficulty in getting information on the location of tourist attractions in the city of Surakarta. This research is used to help travelers in monetizing location information tours in the city of Surakarta. This research method using KNN algorithm, K-means and collaborative filtering. Distance between data user’s needs with a purpose will be collected in a category with KNN algorithm and data will be grouped based on the cluster with the nearest mean. Then choose the nearest one and filter options and recommend options are left with major users. The results of the research were obtained that travelers easy and quick in getting the location information in the tourist city of Surakarta. So taste our satisfaction to travelers and may increase the number of tourists visiting the city of Surakarta.

LIVIVO \u2013 the Vertical Search Engine for Life Sciences

The explosive growth of literature and data in the life sciences challenges researchers to keep track of current advancements in their disciplines. Novel approaches in the life science like the One Health paradigm require integrated methodologies in order to link and connect heterogeneous information from databases and literature resources. Current publications in the life sciences are increasingly characterized by the employment of trans-disciplinary methodologies comprising molecular and cell biology, genetics, genomic, epigenomic, transcriptional and proteomic high throughput technologies with data from humans, plants, and animals. The literature search engine LIVIVO empowers retrieval functionality by incorporating various literature resources from medicine, health, environment, agriculture and nutrition. LIVIVO is developed in-house by ZB MED – Information Centre for Life Sciences. It provides a user-friendly and usability-tested search interface with a corpus of 55 Million citations derived from 50 databases. Standardized application programming interfaces are available for data export and high throughput retrieval. The search functions allow for semantic retrieval with filtering options based on life science entities. The service oriented architecture of LIVIVO uses four different implementation layers to deliver search services. A Knowledge Environment is developed by ZB MED to deal with the heterogeneity of data as an integrative approach to model, store, and link semantic concepts within literature resources and databases. Future work will focus on the exploitation of life science ontologies and on the employment of NLP technologies in order to improve query expansion, filters in faceted search, and concept based relevancy rankings in LIVIVO.

Arabic-English Parallel Corpus: A New Resource for Translation Training and Language Teaching

Parallel corpora can be defined as collections of aligned, translated texts of two or more languages. They play a major role in translation and contrastive studies, and are also becoming popular in translation training and language teaching, with the advent of the data-driven learning (DDL) approach. Despite their significance, however, Arabic seems to lack a satisfactory general-use parallel corpus resource. The literature describes few Arabic–English parallel corpora, and these few are usually inaccurate and/or expensive. Some are small in size, while others are restricted in terms of genre, failing to meet the requirements of many academics and researchers. This paper describes an ongoing project at the College of Languages and Translation, King Saud University, to compile a 10-million-word Arabic–English parallel corpus to be used as a resource for translation training and language teaching. The bidirectional corpus can be used to compare translated and source language and identify differences. The corpus has been manually verified at different stages, including translation, text segmentation, alignment, and file preparation; it is available as full-text in XML format and through a user-friendly web interface that provides a concordancer to support bilingual search queries and several filtering options.

ESAP plus: a web-based server for EST-SSR marker development.

BackgroundSimple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases.ResultsA web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can download all the results through the web interface.ConclusionsESAP Plus is a comprehensive and convenient web-based bioinformatic tool for SSR marker development. ESAP Plus offers all necessary EST-SSR development processes with various adjustable options that users can easily use to identify SSR markers from a large EST collection. With familiar web interface, users can upload the raw EST using the data submission page and visualize/download the corresponding EST-SSR information from within ESAP Plus. ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3328-4) contains supplementary material, which is available to authorized users.

A benchmark testing ground for integrating homology modeling and protein docking.

Protein docking procedures carry out the task of predicting the structure of a protein-protein complex starting from the known structures of the individual protein components. More often than not, however, the structure of one or both components is not known, but can be derived by homology modeling on the basis of known structures of related proteins deposited in the Protein Data Bank (PDB). Thus, the problem is to develop methods that optimally integrate homology modeling and docking with the goal of predicting the structure of a complex directly from the amino acid sequences of its component proteins. One possibility is to use the best available homology modeling and docking methods. However, the models built for the individual subunits often differ to a significant degree from the bound conformation in the complex, often much more so than the differences observed between free and bound structures of the same protein, and therefore additional conformational adjustments, both at the backbone and side chain levels need to be modeled to achieve an accurate docking prediction. In particular, even homology models of overall good accuracy frequently include localized errors that unfavorably impact docking results. The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations. Here we present a benchmark dataset that should help to explore and solve combined modeling and docking problems. This dataset comprises a subset of the experimentally solved 'target' complexes from the widely used Docking Benchmark from the Weng Lab (excluding antibody-antigen complexes). This subset is extended to include the structures from the PDB related to those of the individual components of each complex, and hence represent potential templates for investigating and benchmarking integrated homology modeling and docking approaches. Template sets can be dynamically customized by specifying ranges in sequence similarity and in PDB release dates, or using other filtering options, such as excluding sets of specific structures from the template list. Multiple sequence alignments, as well as structural alignments of the templates to their corresponding subunits in the target are also provided. The resource is accessible online or can be downloaded at http://cluspro.org/benchmark, and is updated on a weekly basis in synchrony with new PDB releases. Proteins 2016; 85:10-16. © 2016 Wiley Periodicals, Inc.

COMODI: an ontology to characterise differences in versions of computational models in biology.

BackgroundOpen model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to different model versions. Taken together, the underlying changes reflect a model’s provenance and thus can give valuable insights into the studied biology. Currently, however, changes cannot be semantically interpreted. To improve this situation, we developed an ontology of terms describing changes in models. The ontology can be used by scientists and within software to characterise model updates at the level of single changes. When studying or reusing a model, these annotations help with determining the relevance of a change in a given context.MethodsWe manually studied changes in selected models from BioModels and the Physiome Model Repository. Using the BiVeS tool for difference detection, we then performed an automatic analysis of changes in all models published in these repositories. The resulting set of concepts led us to define candidate terms for the ontology. In a final step, we aggregated and classified these terms and built the first version of the ontology.ResultsWe present COMODI, an ontology needed because COmputational MOdels DIffer. It empowers users and software to describe changes in a model on the semantic level. COMODI also enables software to implement user-specific filter options for the display of model changes. Finally, COMODI is a step towards predicting how a change in a model influences the simulation results.ConclusionCOMODI, coupled with our algorithm for difference detection, ensures the transparency of a model’s evolution, and it enhances the traceability of updates and error corrections. COMODI is encoded in OWL. It is openly available at http://comodi.sems.uni-rostock.de/.Electronic supplementary materialThe online version of this article (doi:10.1186/s13326-016-0080-2) contains supplementary material, which is available to authorized users.Electronic supplementary materialThe online version of this article (doi:10.1186/s13326-016-0080-2) contains supplementary material, which is available to authorized users.

NemaCount: quantification of nematode chemotaxis behavior in a browser.

Nematodes such as Caenorhabditis elegans offer a very effective and tractable system to probe the underlying mechanisms of diverse sensory behaviors. Numerous platforms exist for quantifying nematode behavior and often require separate dependencies or software. Here I describe a novel and simple tool called NemaCount that provides a versatile solution for the quantification of nematode chemotaxis behavior. The ease of installation and user-friendly interface makes NemaCount a practical tool for measuring diverse behaviors and image features of nematodes such as C. elegans. The main advantage of NemaCount is that it operates from within a modern browser such as Google Chrome or Apple Safari. Any features that change in total number, size, shape, or angular distance between control and experimental preparations are suited to NemaCount for image analysis, while commonly used chemotaxis assays can be quantified, and statistically analyzed using a suite of functions from within NemaCount. NemaCount also offers image filtering options that allow the user to improve object detection and measurements. NemaCount was validated by examining nematode chemotaxis behavior; angular distances of locomotory tracks in C. elegans; and body lengths of Heterorhabditis bacteriophora nematodes. Apart from a modern browser, no additional software is required to operate NemaCount, making NemaCount a cheap, simple option for the analysis of nematode images and chemotaxis behavior.

Using others’ experiences. Cancer patients’ expectations and navigation of a website providing narratives on prostate, breast and colorectal cancer

ObjectiveTo understand what cancer patients expect and may learn from other patients’ experiences, as analyzed and sorted for presentation on a website called krankheitserfahrungen.de (meaning “illness experiences”). MethodsMixed methods approach including log file analyses, survey data analyses and thematic analysis of focus group discussions. ResultsUsers highly valued the wide range of patient experiences presented. The academic leadership of krankheitserfahrungen.de made them trust the information quality. Reading, watching and listening to other cancer patients’ experiences gave users a feeling of hope and confidence. Searching for persons with similar experiences was a major way of navigating the website. ConclusionPatient narratives as presented on krankheitserfahrungen.de provide a helpful resource, supporting cancer patients’ engagement with their disease. Having access to such research-informed accounts of everyday cancer experiences was seen as a great contribution to existing available patient information. Practice implicationsWhen health information websites include experiences, they should adhere to quality standards of qualitative research and encompass a wide range, so that users are able to find patients similar to themselves. Filter options are a helpful tool. A mix of written text and videos is beneficial, as users have different preferences. The inclusion of patient photographs and video interviews facilitates authenticity and closeness.