bluuebunny/crossref_metadata_2025 huggingface dataset:
Histology and Cytopathology Capacity in the Public Health Sector in Kenya
Authors: Brand Nathan R. , Wolf Nicholas , Flanigan John , Njoroge Richard , Karagu Alfred
Published: December 2017

Purpose

Histology and cytopathology services are necessary for cancer diagnosis and treatment. However, the current capacity of Kenya’s pathology laboratories is unknown. A national survey was conducted among public sector pathology laboratories to assess their capacity to perform histology, fine-needle aspiration, and bone marrow aspiration.

Methods

Between April and June 2017, we identified all public hospitals that provide pathology services in Kenya. In total, two national and 13 county referral hospitals met the inclusion criteria and were sent a standardized, pretested, self-administered questionnaire.

Results

A total of 11 hospitals (73%) completed the survey. The reported total caseload of histology, fine-needle aspiration, and bone marrow aspiration for 2016 was 26,472. All of the facilities staffed a pathologist and were providing cancer-related diagnostic services. Nine (82%) of the hospitals maintain a register of diagnosed cancer cases, but only one (11%) of those uses an electronic system. Six (55%) of the surveyed hospitals were able to perform histology with a median turnaround time of 14 days. Six (55%) laboratories regularly referred some specimens elsewhere for interpretation, but three of these centers relied on patients for transportation of the specimen to the referral institution. No laboratories were accredited by an external organization; however, 10 (91%) of the laboratories were working toward achieving accreditation, but only for clinical pathology services.

Conclusion

This study describes the current status of histology and cytopathology capacity in Kenya’s public sector hospitals. It provides useful baseline information needed by the Ministry of Health to develop necessary capacity building and referral-strengthening interventions. A high proportion of hospitals are working to achieve accreditation points toward their commitment to providing quality services to the Kenyan public.
Πρόλογος. Από τον πολιτικό σχολιασμό στην Πολιτική Επιστήμη
Authors: Κιτρομηλίδης Πασχάλης Μ.
Published: December 2017

Δεν διατίθεται περίληψη / no abstract available
New and interesting lichen records from the Ural Mountains, Russia
Authors: Paukov Alexander G. , Gagarina Lyudmila V. , Frolov Ivan V.
Published: December 2017

Ten species of lichenized ascomycetes are reported from the Urals. Aspicilia spermatomanes, Fuscidea praeruptorum, Lepra excludens, L. monogona, Metamelanea caesiella and Pertusaria amarescens are new to Russia while Bryobilimbia ahlesii, Lecanora orosthea, L. rouxii and Tephromela grumosa are new for the Urals. Our records considerably extend the ranges or fill gaps in the formerly disjunctive distributions of these species. The morphology, secondary chemistry and ecology of the species are discussed.
New findings of rare aphyllophoroid fungi from the Murmansk Region, eastern Fennoscandia (North-West Russia)
Authors: Khimich Yuliia R. , Isaeva Ludmila G. , Borovichev Eugene A.
Published: December 2017

The present paper provides new information on the distribution of three rare aphyllophoroid fungi (Haploporus odorus (Sommerf.) Bondartsev & Singer, Skeletocutis lilacina A. David & Jean Keller, Trametes trogii Berk.) in East Fennoscandia. Their distributions and ecological features are discussed.
New records of lichens and allied fungi from the Leningrad Region, Russia. VIII
Authors: Himelbrant Dmitry E. , Stepanchikova Irina S. , Motiejūnaitė Jurga , Gerasimova Julia V. , Kuznetsova Ekaterina S. , Dyomina Aleksandra V. , Tsurykau Andrey G.
Published: December 2017

Thirteen species and one variety of lichens, nine lichenicolous and two saprobic fungi are reported for the first time for St. Petersburg, the whole Leningrad Region or its western or eastern parts. The lichens Bacidina brandii, B. neosquamulosa, Porina leptalea, Rinodina aspersa and the lichenicolous fungus Scutula dedicata are reported for the first time for Russia, lichenicolous fungus Lichenoconium aeruginosum – for European Russia, the lichen Tetramelas chloroleucus, lichenicolous fungi Lichenoconium pyxidatae and Tremella cetrariicola are new for the North-Western European Russia. The most interesting records are briefly discussed.
Hans-Voldemar Trass 02.05.1928–14.02.2017 in memoriam
Authors: Martin Jüri , Martin Ljudmilla
Published: December 2017

Glimpses of memories of his students.
ТАЙГА КАК МАРКЕР РЕГИОНАЛЬНОЙ ИДЕНТИЧНОСТИ В ПРОЗЕ А.М. БОНДАРЕНКО
Authors: Zyryanova Ol’ga Nikolaevna , Bakhor Tamara Andreevna , Mazurova Nadezhda Alekseevna
Published: December 2017

Цель. Статья посвящена проявлению региональной идентичности в прозе писателей Красноярского края. Объектом рассмотрения стали повести, роман и рассказы А.М. Бондаренко, посвященные малой родине, предметом – образ тайги как важнейший маркер региональной идентичности.Методология и методы проведения работы. Основу исследования образуют герменевтический, структурно-семантический, сравнительно-сопоставительный методы.Результаты. В статье показано, что тайга как маркер региональной идентичности в прозе А.М. Бондаренко, с одной стороны, соответствует общепринятому представлению о Сибири, актуализируя дихотомию «свой – чужой», с другой – ее семантика определена спецификой местного региона.Область применения результатов. Материалы статьи могут быть использованы в образовательном процессе при чтении спецкурсов по региональной литературе.
Assessment for Urban Environmental Status Based on Nuclear Approximation
Authors: Бельская Екатерина , Belskaya Ekaterina , Медведев А. , Medvedev A. , Михов Е. , Mihov E. , Тасейко О. , Taseyko O.
Published: December 2017

In the work has been demonstrated the importance of the process of revealing and forecasting for existing ecological problems related to urban environment (on the example of Krasnoyarsk city). Have been considered the main sources of atmospheric air pollution. Has been argued the need for building the model for urban environment’s ecological state assessment in the context of new type of models (named H-models). In the construction of mathematical models for ecological problems solution the correct definition of variables essentially acting on considered environment’s ecological status is playing an important part. A novel way for determining of the most informative variables has been proposed. Based on presented by the authors approach to the modeling has been developed a nonparametric model for formaldehyde space distribution along city’s territory using data of atmospheric air state monitoring network. Modeling velocity allows use this method in the real-time.
Safety Analysis for Traffic of Vehicles in Potash Mine Workings
Authors: Котельников В. , Kotelnikov V. , Грозовский Г. , Grozovskiy G. , Сидорчук В. , Sidorchuk V. , Грот В. , Grot V. , Бром А. , Brom A.
Published: December 2017

The analysis of motor vehicles’ traffic conditions affecting their safety in mine workings has been carried out. The probabilities and risk level of accidents for various combinations of influencing factors have been determined for a typical potash mine. Has been evaluated the signal control impact on the traffic safety. Based on performed estimations has been made a conclusion that a signal control in potash mines only slightly reduces the possibility of accidents, so it’s unlikely that the signal control is economically justifiable.
Can zinc protect cells from the cytotoxic effects of cobalt ions and nanoparticles derived from metal-on-metal joint arthroplasties?
Authors: Liu Y. , Zhu H. , Hong H. , Wang W. , Liu F.
Published: December 2017

Objectives

Recently, high failure rates of metal-on-metal (MOM) hip implants have raised concerns of cobalt toxicity. Adverse reactions occur to cobalt nanoparticles (CoNPs) and cobalt ions (Co2+) during wear of MOM hip implants, but the toxic mechanism is not clear.

Methods

To evaluate the protective effect of zinc ions (Zn2+), Balb/3T3 mouse fibroblast cells were pretreated with 50 μM Zn2+for four hours. The cells were then exposed to different concentrations of CoNPs and Co2+for four hours, 24 hours and 48 hours. The cell viabilities, reactive oxygen species (ROS) levels, and inflammatory cytokines were measured.

Results

CoNPs and Co2+can induce the increase of ROS and inflammatory cytokines, such as tumour necrosis factor α (TNF-α), interleukin-1β (IL-1β) and interleukin-6 (IL-6). However, Zn pretreatment can significantly prevent cytotoxicity induced by CoNPs and Co2+, decrease ROS production, and decrease levels of inflammatory cytokines in Balb/3T3 mouse fibroblast cells.

Conclusion

These results suggest that Zn pretreatment can provide protection against inflammation and cytotoxicity induced by CoNPs and Co2+in Balb/3T3 cells. Cite this article: Y. Liu, H. Zhu, H. Hong, W. Wang, F. Liu. Can zinc protect cells from the cytotoxic effects of cobalt ions and nanoparticles derived from metal-on-metal joint arthroplasties? Bone Joint Res 2017;6:649–655. DOI: 10.1302/2046-3758.612.BJR-2016-0137.R2.
Hiperrealitas dalam Pemasaran Langsung Kerupuk Purnama oleh Tunanetra
Authors: Novelia Novelia
Published: December 2017

This study examines hyperreality in direct marketing process of Kerupuk Purnama conducted by the blind. The hyperreality phenomenon is explained through four stages of imaging based on Jean Baudrillard’s theory. The data were collected through in-depth interviews and observation of the principal informants chosen purposively, four blind sellers of Kerupuk Purnama, as well as interviews with the secondary informants, two ordinary people who had experience in buying the related product. The results showed the happening of hyperreality in direct marketing of Kerupuk Purnama done by the blind. Consumers do not buy the product essence, but the sign that they care about the seller who is considered weaker. The study provides a theoretical contribution to Richard Perloff's interpersonal persuasion technique that persuasion should not start with initial offering but also can be done with praises and warnings of the norm at the end of the process to lure the persuasion targets' addiction.[Penelitian ini mengkaji hiperrealitas dalam proses pemasaran langsung produk Kerupuk Purnama yang dilakukan oleh penyandang tunanetra. Fenomena hiperrealitas dijelaskan melalui empat tahapan pencitraan sesuai teori yang dikemukakan Jean Baudrillard. Pengumpulan data dilaksanakan dengan metode wawancara mendalam dan observasi terhadap informan utama yang dipilih secara purposive, yaitu empat tunanetra penjual Kerupuk Purnama, serta wawancara terhadap informan pendukung, yaitu dua orang masyarakat umum yang memiliki pengalaman membeli produk terkait. Hasil penelitian menunjukkan terjadinya hiperrealitas dalam proses pemasaran langsung Kerupuk Purnama yang dilakukan oleh penyandang tunanetra. Konsumen tidak membeli esensi produk, namun tanda bahwa ia peduli terhadap penjualnya yang dianggap lebih lemah. Penelitian memberikan sumbangan teoritis terhadap teknik persuasi interpersonal Richard Perloff, bahwa teknik persuasi tidak harus dimulai dengan penawaran di awal proses, namun dapat dilakukan dengan pujian dan peringatan terhadap norma di akhir proses untuk memancing adiksi pihak terpersuasi.]
Sartre’s Case for Nonthetic Consciousness: The Ground of the Cartesian Cogito’s Certainty and the Methodological Basis for Phenomenological Ontology
Authors: Sommerlatte Curtis
Published: December 2017

Sartre’s phenomenological view of consciousness gives primacy to the thesis that all consciousness is nonthetically aware of itself, i. e. pre-reflectively aware of itself but not as an object. Few commentators, however, have explained Sartre’s grounds for holding this thesis, despite his view that the thesis’s truth underwrites the certainty of the Cartesian cogito and thereby the method of Sartre’s own phenomenological ontology. I document three lines of support for the thesis, the most promising of which consists in a proof by cases. Namely, Sartre’s texts contain the argument that the existence of nonthetic consciousness is the only satisfactory explanation of the Cartesian cogito’s certainty. The paper concludes with an examination of whether and how nonthetic consciousness can serve as a foundation for Sartre’s method of phenomenological ontology.
Zu neuen elephantinischen Zeugnissen für die Umlage des Steueraufkommens von Flüchtlingen
Authors: Reiter Fabian
Published: December 2017

Several recent editions of receipts from Elephantine for the substitute tax caused by tax-payers who have fled their homes allow new conclusions regarding the development of the tax-rate. The article also contains critical observations on the readings and dates of some of the receipts.
House Price Models for Banking and Insurance Applications: The Impact of Property Characteristics
Authors: Shao Adam W. , Hanewald Katja , Michael Sherris and
Published: December 2017

House price indices are needed to assess house price risk in households’ portfolio allocation decisions and in many housing-related financial products such as reverse mortgages, mortgage insurance and real estate derivatives. This paper first introduces nine widely-used house price models to the insurance, risk management and actuarial literature and provides new evidence on the relative performance of these models. We then show how portfolio-level house price indices for properties with specific physical and locational characteristics can be constructed for these different models. All analyses are based on a large dataset of individual property transactions in Sydney, Australia, for the period 1971-2011. The unrestricted hedonic model and a hybrid hedonic repeat-sales model provide a good model fit and reliable portfolio-level house price indices. Our results are important for banks, insurers and investors that have exposure to house price risks.
Development of a new biochip array for APOE4 classification from plasma samples using immunoassay-based methods
Authors: Badrnya Sigrun , Doherty Tara , Richardson Ciaran , McConnell Robert I. , Lamont John V. , Veitinger Michael , FitzGerald Stephen P. , Zellner Maria , Umlauf Ellen
Published: December 2017

Background:

Apolipoprotein E (APOE) is a key player in lipid transport and metabolism and exists in three common isoforms: APOE2, APOE3 and APOE4. The presence of the E4 allelic variant is recognized as a major genetic risk factor for dementia and other chronic (neuro)degenerative diseases. The availability of a validated assay for rapid and reliable APOE4 classification is therefore advantageous.

Methods:

Biochip array technology (BAT) was successfully applied to identify directly the APOE4 status from plasma within 3 h, through simultaneous immunoassay-based detection of both specific APOE4 and total APOE levels.

Results:

Samples (n=432) were first genotyped by polymerase chain reaction (PCR), and thereafter, using BAT, the corresponding plasma was identified as null, heterozygous or homozygous for the E4 allele by calculating the ratio of APOE4 to total APOE protein. Two centers based in Austria and Ireland correctly classified 170 and 262 samples, respectively, and achieved 100% sensitivity and specificity.

Conclusions:

This chemiluminescent biochip-based sandwich immunoarray provides a novel platform to detect rapidly and accurately an individual’s APOE4 status directly from plasma. The E4 genotype of individuals has been shown previously to affect presymptomatic risk, prognosis and treatment response for a variety of diseases, including Alzheimer’s disease. The biochip’s potential for being incorporated in quantitative protein biomarker arrays capable of analyzing disease stages makes it a superior alternative to PCR-based APOE genotyping and may deliver additional protein-specific information on a variety of diseases in the future.
Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae
Authors: Song Yu , Yao Xin , Liu Bing , Tan Yunhong , Corlett Richard T.
Published: December 2017

Alseodaphne is a genus of timber trees (ca. 40 spp.) belonging to the Persea group of the Lauraceae. It is widely distributed in tropical Asia, but is often confused with Dehaasia and Nothaphoebe, and the systematics of the genus is unclear. Here, the complete chloroplast genome sequences of A. semecarpifolia will be reported, the type species of Alseodaphne, and two China-endemic species, A. gracilis and A. huanglianshanensis. The three plastomes were 153 051 bp, 153 099 bp and 153 070 bp, respectively. Comparative genomic analyses indicate that the three Alseodaphne plastomes have similar genome size and those are very different with previously published plastomes of Lauraceae in length. The length difference is directly caused by inverted repeats expansion/contraction. Four highly variable loci including psbD-trnM, ndhF-rpl32, rpl32-trnL and ycf1 among the three Alseodaphne species were identified as useful plastid candidate barcodes for Alseodaphne and Lauraceae species. Phylogenetic analyses based on 12 complete plastomes of Lauraceae species confirm a monophyletic Persea group comprising species of Alseodaphne, Phoebe, Persea and Machilus.
Scrimber board (SB) manufacturing by a new method and characterization of SB’s mechanical properties and dimensional stability
Authors: Zhang Yamei , Huang Xian’ai , Zhang Yahui , Yu Yanglun , Yu Wenji
Published: December 2017

A novel process has been developed for manufacturing poplar wood scrimber boards (SBs), in the course of which thick veneers are produced first and then the oriented wood fiber mats (OWFMs) are fabricated in a pilot scale fluffing machine. A low molecular weight phenol-formaldehyde (PF) resin is applied for gluing and the cold-prepressing of the mats is followed by hot-curing between 120 and 130°C for 12 h. The mechanical properties and dimensional stability of the SBOWFMs were measured. The new process resulted in significantly better mechanical properties of SBOWFMs compared with those of raw wood and other poplar wood-based composites. All data including the dimensional stability of SBOWFMs increased with increasing density.
Dependence of Poisson’s ratio and Young’s modulus on microfibril angle (MFA) in wood
Authors: Ando Kosei , Mizutani Mayu , Toba Keisuke , Yamamoto Hiroyuki
Published: December 2017

Microfibril angle (MFA) is a major structural variable that describes the fine structure of the cell wall in wood. In this study, the relationships between the MFA of the S2 layer and the Poisson’s ratios and Young’s moduli (modulus of elasticity, MOE) of five wood species (agathis, larch, Japanese cedar, Japanese cypress and ginkgo) were determined by analyzing both their normal and compression woods. It was found that both the longitudinal MOE (MOEL) and MOE of the cell-wall substance (MOEW) decreased with increasing MFA, while the peaks values of Poisson’s ratio (νLT) were obtained at MFAs of ≈25°. In particular, at MFAs lower than 25°, theνLTincreased with increasing MFA, and the opposite relationship was observed at MFA values exceeding 25°. This trend is in good agreement with the estimates obtained based on the theory of orthotropic elasticity with the underlying assumption that the orthotropic elasticity of materials is MFA-dependent. Hence, the MFA parameter incorporated into the orthotropic elasticity theory is useful for determination of the Poisson’s ratio.
Visual Understanding of Metabolic Pathways Across Organisms Using Layout in Two and a Half Dimensions
Authors: Brandes Ulrik , Dwyer Tim , Schreiber Falk
Published: December 2017

We propose a method for visualizing a set of related metabolic pathways across organisms using 2 1/2 dimensional graph visualization. Interdependent, twodimensional layouts of each pathway are stacked on top of each other so that biologists get a full picture of subtle and significant differences among the pathways. The (dis)similarities between pathways are expressed by the Hamming distances of the underlying graphs which are used to compute a stacking order for the pathways. Layouts are determined by a global layout of the union of all pathway graphs using a variant of the proven Sugiyama approach for layered graph drawing. Our variant layout approach allows edges to cross if they appear in different graphs.
Statistical Embedding in Complex Biosystems
Authors: Capobianco Enrico
Published: December 2017

Complex high-dimensional systems represent an important area of interdisciplinary research in systems biology. Gene expression values obtained by microarray data represent a good example, owing to their various features that depend on biological network dynamics. This work emphasizes the role of blind source separation for dealing with dimensionality reduction and feature selection, and their useful combination with fuzzy rules, embedding principles and entropic measures. In particular, entropy and embedding are useful tools for controlling the robustness and stability of the decomposition of a system with larger than intrinsic dimensionality. As a result, the convergence to a small intrinsic dimensionality occurs by the means of least dependent components, seen as a minimal number of salient features.
A First Step towards Learning which uORFs Regulate Gene Expression
Authors:   Selpi, Bryant Christopher H. , Kemp Graham J.L. , Cvijovic Marija
Published: December 2017

We have taken a first step towards learning which upstream Open Reading Frames (uORFs) regulate gene expression (i.e., which uORFs are functional) in the yeast Saccharomyces cerevisiae. We do this by integrating data from several resources and combining a bioinformatics tool, ORF Finder, with a machine learning technique, inductive logic programming (ILP). Here, we report the challenge of using ILP as part of this integrative system, in order to automatically generate a model that identifies functional uORFs. Our method makes searching for novel functional uORFs more efficient than random sampling. An attempt has been made to predict novel functional uORFs using our method. Some preliminary evidence that our model may be biologically meaningful is presented.
Multi-model inference of network properties from incomplete data
Authors: Stumpf Michael P. H. , Thorne Thomas
Published: December 2017

It has previously been shown that subnets differ from global networks from which they are sampled for all but a very limited number of theoretical network models. These differences are of qualitative as well as quantitative nature, and the properties of subnets may be very different from the corresponding properties in the true, unobserved network. Here we propose a novel approach which allows us to infer aspects of the true network from incomplete network data in a multi-model inference framework. We develop the basic theoretical framework, including procedures for assessing confidence intervals of our estimates and evaluate the performance of this approach in simulation studies and against subnets drawn from the presently available PIN network data in Saccaromyces cerevisiae. We then illustrate the potential power of this new approach by estimating the number of interactions that will be detectable with present experimental approaches in sfour eukaryotic species, inlcuding humans. Encouragingly, where independent datasets are available we obtain consistent estimates from different partial protein interaction networks. We conclude with a discussion of the scope of this approaches and areas for further research
A Graphical Notation to Describe the Logical Interactions of Biological Pathways
Authors: Moodie Stuart L. , Sorokin Anatoly , Goryanin Igor , Ghazal Peter
Published: December 2017

The modelling of biological intra-cellular pathways requires the systematic capture and representation of interactions between components that are biologically correct and computationally rigorous. The challenge is two fold, to verify and extend our understanding of such pathways by comparing in silico models to experiments; and to ensure that such models are understandable by biologists and for checking biological validity. In this report we present a graphical notation, the Edinburgh Pathway Notation (EPN), which satisfies the central biologically driven requirements while providing a strict formal framework for analysis. The EPN emphasises the use of a logical representation of pathways, which is particularly suited to pathways were some mechanisms are not known in detail.
Functional diversity within protein superfamilies
Authors: Casbon James , Saqi Mansoor
Published: December 2017

Structural genomics projects are leading to the discovery of relationships between proteins that would not have been anticipated from consideration of sequence alone. However the assignment of function via structure remains difficult as some structures are compatible with a variety of functions. In this study we explore the relationships between structural diversity and functional diversity within distantly related members of SCOP superfamilies. We use the Gene Ontology functional classification scheme and Greens path entropy to measure functional diversity. We observe a negative correlation between the functional entropy of a superfamily and the size of the conserved core.
The ABC (Analysing Biomolecular Contacts)-database
Authors: Walter Peter , Ansari Sam , Helms Volkhard
Published: December 2017

As protein-protein interactions are one of the basic mechanisms in most cellular processes, it is desirable to understand the molecular details of protein-protein contacts and ultimately be able to predict which proteins interact. Interface areas on a protein surface that are involved in protein interactions exhibit certain characteristics. Therefore, several attempts were made to distinguish protein interactions from each other and to categorize them. One way of classification are the groups of transient and permanent interactions. Previously two of the authors analysed several properties for transient complexes such as the amino acid and secondary structure element composition and pairing preferences. Certainly, interfaces can be characterized by many more possible attributes and this is a subject of intense ongoing research. Although several freely available online databases exist that illuminate various aspects of protein-protein interactions, we decided to construct a new database collecting all desired interface features allowing for facile selection of subsets of complexes. As database-server we applied MySQL and the program logic was written in JAVA. Furthermore several class extensions and tools such as JMOL were included to visualize the interfaces and JfreeChart for the representation of diagrams and statistics. The contact data is automatically generated from standard PDB files by a tcl/tk-script running through the molecular visualization package VMD. Currently the database contains 536 interfaces extracted from 479 PDB files and it can be queried by various types of parameters. Here, we describe the database design and demonstrate its usefulness with a number of selected features.

Availability: The ABC-database can be accessed on http://service.bioinformatik.unisaarland.de/abc.
Flexible web-based integration of distributed large-scale human protein interaction maps
Authors: Chaurasia Gautam , Iqbal Yasir , Hänig Christian , Herzel Hanspeter , Wanker Erich E. , Futschik Matthias E.
Published: December 2017

Protein-protein interactions constitute the backbone of many molecular processes. This has motivated the recent construction of several large-scale human protein-protein interaction maps [1-10]. Although these maps clearly offer a wealth of information, their use is challenging: complexity, rapid growth, and fragmentation of interaction data hamper their usability. To overcome these hurdles, we have developed a publicly accessible database termed UniHI (Unified Human Interactome) for integration of human protein-protein interaction data. This database is designed to provide biomedical researchers a common platform for exploring previously disconnected human interaction maps. UniHI offers researchers flexible integrated tools for accessing comprehensive information about the human interactome. Several features included in the UniHI allow users to perform various types of network-oriented and functional analysis. At present, UniHI contains over 160,000 distinct interactions between 17,000 unique proteins from ten major interaction maps derived by both computational and experimental approaches [1-10]. Here we describe the details of the implementation and maintenance of UniHI and discuss the challenges that have to be addressed for a successful integration of interaction data.
Duplicate detection of 2D-NMR Spectra
Authors: Hinneburg Alexander , Egert Björn , Porzel Andrea
Published: December 2017

2D-Nuclear magnetic resonance (NMR) spectra are used in the (structural) analysis of small molecules. In contrast to 1D-NMR spectra, 2D-NMR spectra correlate the chemical shifts of 1H and 13C at the same time. A spectrum consists of several peaks in a two--dimensional space. The most important information of a peak is the location of its center, which captures the bonding relationships of hydrogen and carbon atoms. A spectrum contains much information about the chemical structure of a product, but in most cases the structure cannot be read off in a simple and straightforward manner. Structure elucidation involves a considerable amount (manual) efforts.

Using high-field NMR spectrometers, many 2D-NMR spectra can be recorded in short time. So the common situation is that a lab or company has a repository of 2D-NMR spectra, partially annotated with the structural information. For the remaining spectra the structure in unknown. In case two research labs are collaborating, the repositories will be merged and annotations shared.

We reduce that problem to the task of finding duplicates in a given set of 2D-NMR spectra. Therefore, we propose a simple but robust definition of 2D-NMR duplicates, which allows for small measurement errors. We give a quadratic algorithm for the problem, which can be implemented in SQL. Further, we analyze a more abstract class of heuristics, which are based on selecting particular peaks. Such a heuristic works as a filter step on the pairs of possible duplicates and allows false positives. We compare all methods with respect to their run time. Finally we discuss the effectiveness of the duplicate definition on real data.
MetHouse: Raw and Preprocessed Mass Spectrometry Data
Authors: Gaida Antje , Neumann Steffen
Published: December 2017

We are developing a vendor-independent archive and on top of that a data warehouse for mass spectrometry metabolomics data. The archive schema resembles the communitydeveloped object model, the Java implementation of the model classes, and an editor (for both mzData XML files and the database) have been generated using the Eclipse Modeling Framework. Persistence is handled by the JDO2 -compliant framework JPOX. The main content of the Data Warehouse are the results of the signal processing and peak-picking tasks, carried out using the XCMS package from Bioconductor, putative identification and mass decomposition are added to the warehouse afterwards.

We present the system architecture, current content, performance observations and describe the analysis tools on top of the warehouse.

Availability: http://msbi.ipb-halle.de/
A Reliable and Distributed LIMS for Efficient Management of the Microarray Experiment Environment
Authors: Jin Hee-Jeong , Lee Jeong-Won , Cho Hwan-Gue
Published: December 2017

A microarray is a principal technology in molecular biology. It generates thousands of expressions of genotypes at once. Typically, a microarray experiment contains many kinds of information, such as gene names, sequences, expression profiles, scanned images, and annotation. So, the organization and analysis of vast amounts of data are required. Microarray LIMS (Laboratory Information Management System) provides data management, search, and basic analysis. Recently, microarray joint researches, such as the skeletal system disease and anti-cancer medicine have been widely conducted. This research requires data sharing among laboratories within the joint research group. In this paper, we introduce a web based microarray LIMS, SMILE (Small and solid MIcroarray Lims for Experimenters), especially for shared data management. The data sharing function of SMILE is based on Friend-to-Friend (F2F), which is based on anonymous P2P (Peer-to-Peer), in which people connect directly with their “friends”. It only allows its friends to exchange data directly using IP addresses or digital signatures you trust. In SMILE, there are two types of friends: “service provider”, which provides data, and “client”, which is provided with data. So, the service provider provides shared data only to its clients. SMILE provides useful functions for microarray experiments, such as variant data management, image analysis, normalization, system management, project schedule management, and shared data management. Moreover, it connections with two systems: ArrayMall for analyzing microarray images and GENAW for constructing a genetic network. SMILE is available on http://neobio.cs.pusan.ac.kr:8080/smile.
IMS2 – An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath
Authors: Baumbach Jan , Bunkowski Alexander , Lange Sita , Oberwahrenbrock Timm , Kleinbölting Nils , Rahmann Sven , Baumbach Jörg Ingo
Published: December 2017

IMS2 is an Integrated Medical Software system for the analysis of Ion Mobility Spectrometry (IMS) data. It assists medical staff with the following IMS data processing steps: acquisition, visualization, classification, and annotation. IMS2 provides data analysis and interpretation features on the one hand, and also helps to improve the classification by increasing the number of the pre-classified datasets on the other hand. It is designed to facilitate early detection of lung cancer, one of the most common cancer types with one million deaths each year around the world.

After reviewing the IMS technology, we first describe the software architecture of IMS2 and then the integrated classification module, including necessary pre-processing steps and different classification methods. The Lung Hospital Hemer (Germany) provided IMS data of 35 patients suffering from lung cancer and 72 samples of healthy persons. IMS2 correctly classifies 99% of the samples, evaluated using 10-fold cross-validation.
GeneBrowser: an approach for integration and functional classification of genomic data
Authors: Arrais Joel , Santos Bruno , Fernandes João , Carreto Laura , Santos Manuel A.S. , Oliveira José Luis
Published: December 2017

The achievements coming from genome analysis depend greatly on the quality of computational and processing methods. Tools for functional mRNA profiling and for gene information integration have become essential to this task. We have developed GeneBrowser as a novel approach that combines the advantages of mRNA profiling tools, at genome-scale experiments, with the features provided by data integration systems. For a given set of genes, GeneBrowser integrates bibliography information with functional annotations, using Gene Ontology, Entrez Gene, KEGG Orthology and KEGG Pathways. The result is a comprehensive and easy to use web application that helps researchers to extract knowledge from large data sets and to speed up the discovery process.

Availability: GeneBrowser is freely available at http://bioinformatics.ua.pt/genebrowser
Converting Biomolecular Modelling Data Based on an XML Representation
Authors: Sun Yudong , McKeever Steve
Published: December 2017

Biomolecular modelling has provided computational simulation based methods for investigating biological processes from quantum chemical to cellular levels. Modelling such microscopic processes requires atomic description of a biological system and conducts in fine timesteps. Consequently the simulations are extremely computationally demanding. To tackle this limitation, different biomolecular models have to be integrated in order to achieve high-performance simulations. The integration of diverse biomolecular models needs to convert molecular data between different data representations of different models. This data conversion is often non-trivial, requires extensive human input and is inevitably error prone. In this paper we present an automated data conversion method for biomolecular simulations between molecular dynamics and quantum mechanics/molecular mechanics models. Our approach is developed around an XML data representation called BioSimML (Biomolecular Simulation Markup Language). BioSimML provides a domain specific data representation for biomolecular modelling which can effciently support data interoperability between different biomolecular simulation models and data formats.
Widespread existence of uncorrelated probe intensities from within the same probeset on Affymetrix GeneChips
Authors: Sanchez-Graillet Olivia , Rowsell Joanna , Langdon William B. , Stalteri Maria , Arteaga-Salas Jose M. , Upton Graham J. G. , Harrison Andrew P.
Published: December 2017

We have developed a computational pipeline to analyse large surveys of A ymetrix GeneChips, for example NCBI’s Gene Expression Omnibus. GEO samples data for many organisms, tissues and phenotypes. Because of this experimental diversity, any observed correlations between probe intensities can be associated either with biology that is robust, such as common co-expression, or with systematic biases associated with the GeneChip technology.

Our bioinformatics pipeline integrates the mapping of probes to exons, quality control checks on each GeneChip which identifies flaws in hybridization quality, and the mining of correlations in intensities between groups of probes. The output from our pipeline has enabled us to identify systematic biases in GeneChip data. We are also able to use the pipeline as a discovery tool for biology.

We have discovered that in the majority of cases, A ymetrix probesets on Human GeneChips do not measure one unique block of transcription. Instead we see numerous examples of outlier probes. Our study has also identified that in a number of probesets the mismatch probes are an informative diagnostic of expression, rather than providing a measure of background contamination. We report evidence for systematic biases in GeneChip technology associated with probe-probe interactions. We also see signatures associated with post-transcriptional processing of RNA, such as alternative polyadenylation.
Integrative Systems Biology Visualization with MAYDAY
Authors: Symonsy Stephan , Zipplies Christian , Battke Florian , Nieselt Kay
Published: December 2017

Visualization is pivotal for gaining insight in systems biology data. As the size and complexity of datasets and supplemental information increases, an efficient, integrated framework for general and specialized views is necessary. MAYDAY is an application for analysis and visualization of general ‘omics’ data. It follows a trifold approach for data visualization, consisting of flexible data preprocessing, highly customizable data perspective plots for general purpose visualization and systems based plots. Here, we introduce two new systems biology visualization tools for MAYDAY. Efficiently implemented genomic viewers allow the display of variables associated with genomic locations. Multiple variables can be viewed using our new track-based ChromeTracks tool. A functional perspective is provided by visualizing metabolic pathways either in KEGG or BioPax format. Multiple options of displaying pathway components are available, including Systems Biology Graphical Notation (SBGN) glyphs. Furthermore, pathways can be viewed together with gene expression data either as heatmaps or profiles.

We apply our tools to two ‘omics’ datasets of Pseudomonas aeruginosa. The general analysis and visualization tools of MAYDAY as well as our ChromeTracks viewer are applied to a transcriptome dataset. We furthermore integrate this dataset with a metabolome dataset and compare the activity of amino acid degradation pathways between these two datasets, by visually enhancing the pathway diagrams produced by MAYDAY.
The LAILAPS Search Engine: A Feature Model for Relevance Ranking in Life Science Databases
Authors: Lange Matthias , Spies Karl , Colmsee Christian , Flemming Steffen , Klapperstück Matthias , Scholz Uwe
Published: December 2017

Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking.

In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable.

The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries.

Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.de
An integrative approach to modeling biological networks
Authors: Memišević Vesna , Milenković Tijana , Pržulj Nataša
Published: December 2017

Networks are used to model real-world phenomena in various domains, including systems biology. Since proteins carry out biological processes by interacting with other proteins, it is expected that cellular functions are reflected in the structure of protein-protein interaction (PPI) networks. Similarly, the topology of residue interaction graphs (RIGs) that model proteins’ 3-dimensional structure might provide insights into protein folding, stability, and function. An important step towards understanding these networks is finding an adequate network model, since models can be exploited algorithmically as well as used for predicting missing data. Evaluating the fit of a model network to the data is a formidable challenge, since network comparisons are computationally infeasible and thus have to rely on heuristics, or “network properties.” We show that it is difficult to assess the reliability of the fit of a model using any network property alone. Thus, we present an integrative approach that feeds a variety of network properties into five machine learning classifiers to predict the best-fitting network model for PPI networks and RIGs. We confirm that geometric random graphs (GEO) are the best-fitting model for RIGs. Since GEO networks model spatial relationships between objects and are thus expected to replicate well the underlying structure of spatially packed residues in a protein, the good fit of GEO to RIGs validates our approach. Additionally, we apply our approach to PPI networks and confirm that the structure of merged data sets containing both binary and co-complex data that are of high coverage and confidence is also consistent with the structure of GEO, while the structure of less complete and lower confidence data is not. Since PPI data are noisy, we test the robustness of the five classifiers to noise and show that their robustness levels differ. We demonstrate that none of the classifiers predicts noisy scale-free (SF) networks as GEO, whereas noisy GEOs can be classified as SF. Thus, it is unlikely that our approach would predict a real-world network as GEO if it had a noisy SF structure. However, it could classify the data as SF if it had a noisy GEO structure. Therefore, the structure of the PPI networks is the most consistent with the structure of a noisy GEO.
ExPlanes: Exploring Planes in Triplet Data
Authors: Schwenk Bruno , Selbig Joachim , Ben-Zion Yehuda , Holschneider Matthias
Published: December 2017

Many methods for the analysis of gene expression-, protein- or metabolite-data focus on the investigation of binary relationships, while the underlying biological processes creating this data may generate relations of higher than bivariate complexity. We give a novel method ExPlanes that helps to explore certain types of ternary relationships in a statistically robust, Bayesian framework. To arrive at an characterization of the data structure contained in triplet data we investigate 2-dimensional planes being the only linear structures that cannot be inferred from projections of the data. The key part of our methodology is the definition of a robust, Bayesian plane posterior under the assumption of an invariant prior and a Gaussian error model. A numerical representation of the plane posterior can be explored interactively. Beyond this purely Bayesian approach we can use the plane posterior to construct a family of posterior-based test statistics that allow testing the data for different plane related hypotheses. To demonstrate practicability we queried triplets of metabolic data from a plant crossing experiment for the presence of plane-, line- and point-structures by using posterior-based test statistics and were able to show their distinctiveness.
Complementarity of network and sequence information in homologous proteins
Authors: Memišević Vesna , Milenković Tijana , Pržulj Nataša
Published: December 2017

Traditional approaches for homology detection rely on finding sufficient similarities between protein sequences. Motivated by studies demonstrating that from non-sequence based sources of biological information, such as the secondary or tertiary molecular structure, we can extract certain types of biological knowledge when sequence-based approaches fail, we hypothesize that protein-protein interaction (PPI) network topology and protein sequence might give insights into different slices of biological information. Since proteins aggregate to perform a function instead of acting in isolation, analyzing complex wirings around a protein in a PPI network could give deeper insights into the protein’s role in the inner working of the cell than analyzing sequences of individual genes. Hence, we believe that one could lose much information by focusing on sequence information alone.

We examine whether the information about homologous proteins captured by PPI network topology differs and to what extent from the information captured by their sequences. We measure how similar the topology around homologous proteins in a PPI network is and show that such proteins have statistically significantly higher network similarity than nonhomologous proteins. We compare these network similarity trends of homologous proteins with the trends in their sequence identity and find that network similarities uncover almost as much homology as sequence identities. Although none of the two methods, network topology and sequence identity, seems to capture homology information in its entirety, we demonstrate that the two might give insights into somewhat different types of biological information, as the overlap of the homology information that they uncover is relatively low. Therefore, we conclude that similarities of proteins’ topological neighborhoods in a PPI network could be used as a complementary method to sequence-based approaches for identifying homologs, as well as for analyzing evolutionary distance and functional divergence of homologous proteins.