bluuebunny/crossref_metadata_2025 huggingface dataset:
Deer herbivory reduces web-building spider abundance by simplifying forest vegetation structure
Authors: Roberson Elizabeth J , Chips Michael J , Carson Walter P , Rooney Thomas P
Published: January 2018

Indirect ecological effects are a common feature of ecological systems, arising when one species affects interactions among two or more other species. We examined how browsing by white-tailed deer (Odocoileus virginianus) indirectly affected the abundance and composition of a web-building spider guild through their effects on the structure of the ground and shrub layers of northern hardwood forests. We examined paired plots consisting of deer-free and control plots in the Allegheny Plateau region Pennsylvania and Northern Highlands region of Wisconsin. We recorded the abundance of seven types of webs, each corresponding to a family of web-building spiders. We quantified vegetation structure and habitat suitability for the spiders by computing a web scaffold availability index (WSAI) at 0.5 m and 1.0 m above the ground. At Northern Highlands sites, we recorded prey availability. Spider webs were twice as abundant in deer-free plots compared to control plots, while WSAI was 7-12 times greater in deer-free plots. Prey availability was lower in deer-free plots. With the exception of funnel web-builders, all spider web types were significantly more abundant in deer-free plots. Both deer exclusion and the geographic region of plots were significant predictors of spider community structure. In closed canopy forests with high browsing pressure, the low density of tree saplings and shrubs provides few locations for web-building spiders to anchor webs. Recruitment of these spiders may become coupled with forest disturbance events that increase tree and shrub recruitment. By modifying habitat structure, deer appear to indirectly modify arthropod food web interactions. As deer populations have increased in eastern North America over the past several decades, the effects of deer on web-building spiders may be widespread.
Mapping irrigated areas using multi-sensor remote sensing data in a Mediterranean environment
Authors: Nino Pasquale , Vanino Silvia , Lupia Flavio , Pulighe Giuseppe , De Michele Carlo , D'Urso Guido
Published: January 2018

Water managers need map of irrigated areas (defined as the identification of their location and their areal extent) to plan a rational use of water under limited availability and to prevent the unauthorized withdrawals. Many authors have shown that the Earth Observation techniques are an effective tool for mapping irrigated areas worldwide at different spatial scales (global/regional/and local). This study presents a methodology for mapping irrigated areas in semi-arid environment based on Earth Observation techniques and by fully exploiting datasets freely available processed by open source software and tools. Data acquired with the Landsat 8 Operational Land Imager (OLI) and the new Sentinel 2A MultiSpectral Instrument (MSI) sensors were integrated to obtain cloud free dense time series allowing to monitor the vegetation development throughout the growing seasons. Irrigated areas were identified by analysing the growing patterns under water deficit conditions from NDVI values under the assumption that, in arid and semi-arid environment (like the Mediterranean Region), high trend of vegetation growth are compatible only with irrigation. The method was applied in the Cixerri Consortium Irrigation District located in South of Sardinia (Italy).
A template-based approach to the modification of binding properties of globular proteins II: Rationale and proposed approach.
Authors: Jeff-Eke Imadol V
Published: January 2018

We present a rationale and proposed approach to the modification and development of bind sites using their respective cognate ligands as template. This is in support of a plausible “instructive” role for the ligand and therefore its involvement in determination of the structure and properties of bind sites. We emphasize the relationship between substrate and active site as an example of the relationship between ligand and bind sites, respectively. This is based on the assumption that there are shared features between all ligand:bind site complexes. Therefore, principles that apply to a specific complex can be applied, in general, to other protein-based complexes. We define ligand-associated probability bias as the difference between the probability of finding activity-determining conformations (ADCs) in the presence- and absence of ligands. For cognate ligands, the given bias is in favor of these ADCs. Thus, bind sites are more likely to assume ADCs when their cognate ligands are present. We relate such probability bias to structural reorganization, disorganization, and preorganization events. We then propose a means of deriving an [apparent] preorganized bind site structure by way of reorganization events that occur with cognate ligand. Finally, we propose a means of deriving an [actual] preorganized bind site structure by way of reorganization events that occur with cognate ligand, albeit during the folding process. The assumption is that the role of the ligand in derivation of such [actual] preorganized bind site structures is an instructive role, and is in support of the Haurowitz-Pauling hypothesis.
Structured unit testable templated code for efficient code review process
Authors: Patwardhan Amol S
Published: January 2018

Background: Modern software development teams are distributed across onsite and off-shore locations. Each team has developers with varying experience levels and English communication skills. In such a diverse development environment it is important to maintain the software quality, coding standards, timely delivery of features and bug fixes. It is also important to reduce testing effort, minimize side effects such as change in functionality, user experience or application performance. Code reviews are intended to control code quality. Unfortunately, many projects lack enforcement of processes and standards because of approaching deadlines, live production issues and lack of resource availability.

Objective: This study examines a novel structured, unit testable templated code method to enforce code review standards with an intent to reduce coding effort, minimize revisions and eliminate functional and performance side effects on the system. The proposed method would also result in unit-testable code that can also be easily rolled back and increase team productivity.

Method: The baseline for traditional code review processes using metrics such as code review duration, bug regression rate, revision count was measured. These metrics were then compared with results from the proposed code review process that used structured unit testable templated code. The performance on 2 large enterprise level applications spanning over 2 years and 9 feature and maintenance release cycles was evaluated.

Results: The structured unit testable templated code method resulted in a decrease in total code review time, revision count and coding effort. It also decreased the number of live production issues caused by code churn or side effects of bug fix when compared to traditional code review process.

Conclusion: The study confirmed that the structured unit testable templated code results in improved code review efficiency. It also increased code quality and provided a robust tool to enforce coding standards in a cross-continent software maintenance team environment. It also relieved core resources from code review effort so that they could concentrate more on newer feature development.
Sex ratio elasticity influences the selection of sex ratio strategy
Authors: Wang Yaqiang , Wang Ruiwu , Li Yaotang , Ma Zhanshan (Sam)
Published: January 2018

There are three sex ratio strategies (SRS) in nature—male-biased sex ratio, female-biased sex ratio and, equal sex ratio depending on the proportion of male offspring being greater than, less than, or equal to ½. The problem was already noted in Darwin’s (1859) “Origin of Species,” and it was R. A. Fisher (1930) who first explained why most species in nature display a sex ratio of ½. Consequent SRS theories such as Hamilton’s (1967) local mate competition (LMC) and Clark’s (1978) local resource competition (LRC) separately explained the observed deviations from the seemingly universal 1:1 ratio. However, to the best of our knowledge, there is not yet a unified theory that accounts for the mechanisms of the three SRS. Here, we introduce the price elasticity theory in economics to define sex ratio elasticity (SRE), and present an analytical model that derives three SRSs based on the following assumption: simultaneously existing competitions for both resources and mates influence the level of SRE in both sexes differently. Consequently, it is the difference (between two sexes) in the level of their sex ratio elasticity that leads to three different SRS. Our analytical results demonstrate that the elasticity-based model not only reveals a highly plausible mechanism that explains the evolution of SRS in nature, but also offers a novel framework for unifying two major classical theories (i.e., LMC & LRC) in the field of SRS research.
Genome-wide identification and characterization of WRKY gene family in Salix suchowensis
Authors: Bi Changwei , Xu Yiqing , Ye Qiaolin , Yin Tongming , Ye Ning
Published: January 2018

WRKY proteins are the plant-specific zinc finger transcription factors. They can specifically interact with the W-box ([C/T]TGAC[T/C]), which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to the present studies, plentiful WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow. With the whole genome sequencing in Salix suchowensis, we have the opportunity to conduct the genome-wide research for willow WRKY gene family. In this study, we identified 85 WRKY genes in the willow genome and renamed them from SsWRKY1 to SsWRKY85 on the basis of their specific distributions on chromosomes. Due to their diverse structural features, the 85 willow WRKY genes could be further classified into three main groups (group I - III), with five subgroups (IIa - IIe) in group II. With the multiple sequence alignment and the manual search, we found three variations of the WRKYGQK heptapeptide: WRKYGRK, WKKYGQK and WRKYGKK, and four variations of the normal zinc finger motif, which might execute some new biological functions. In addition, the SsWRKY genes from the same subgroup share the similar exon–intron structures and conserved motif domains. Further studies of SsWRKY genes revealed that segmental duplication events played the prominent roles in the expansion of SsWRKY genes. Distinct expression profiles of SsWRKY genes with RNA sequencing data revealed that diverse expression patterns among five tissues, including tender roots, young leaves, vegetative buds, non-lignified stems and barks. With the analyses of WRKY gene family in willow, it is not only beneficial to complete the functional and annotation information of WRKY genes family in woody plants, but also provide important references to investigate the expansion and evolution of this gene family in flowering plants.
Food availability and flight routes for migratory birds: a GIS approach
Authors: Tattoni Clara , Soardi Erica , Zatelli Paolo , Ciolli Marco
Published: January 2018

Bird migration is a wide studied phenomenon but still many factors that influence migratory flows remain unknown or poorly understood. Food availability en route is particularly important for many species and can affect their migration success, pattern and timing but this relationship have not often been addressed at wide scale due to the lack of spatial models of food availability on the terrain.The aim of this work is to fill this gap with a GIS-database approach that links together spatial and non-spatial information in order to map and measure food availability in the different periods of the year in the SE Alps, an important node of European migratory routes. We created a unique database that contains information on the presence and periods of fruitification of 52 wild plants carriyng berries and a series of original cartographic themes. With this approach we were able to identify various flyways and compare them with known stopover sites, ringing stations and food availability using a mix of techniques of statistical geostatistical and interpretation of ecological data.
Examining the context of health promoting schools: a translational approach to characterization and measurement of school ethos to support health and wellbeing
Authors: Penney Tarra L , McIsaac Jessie-Lee D , Storey Kate E , Kontak Julia C , Ata Nicole , Kuhle Stefan , Kirk Sara FL
Published: January 2018

Background: Health promoting schools (HPS) is hypothesized to influence student health and wellbeing by promoting a ‘school ethos’ that shapes the physical environment, social relations, organisational structure, policies and practices within the school. This complex set of conceptual dimensions makes school ethos challenging to measure as an important context for the implementation of HPS. The purpose of this research was to develop and explore a comprehensive measure of health promoting school ethos (HPSE) for the evaluation of HPS implementation, student health and well-being. Methods: We used a multi-method, iterative process to identify relevant HPSE concepts through triangulation of conceptual literature, existing tools and the tacit knowledge of school stakeholders. The HPSE measurement tool was administered to 18 elementary schools through a principal and teacher survey and an environmental assessment, followed by the development of a total and dimensional HPSE scores for each school. Testing for internal consistency of items was used to examine theorised concepts and sub-scores across HPSE dimensions, and total scores are summarised. Results: HPSE included eight conceptual dimensions with internal consistency ranging from α = 0.60 to a = 0.87. Total HPSE scores across schools (N = 18) ranged from 1 to 8 (Mean = 3.94, SD = 2.1), with 28% to 65% of schools reporting ‘high’ on respective HPSE dimensions. Conclusions: The HPSE tool holds potential for the conceptualization of critical components of school context as it relates to HPS. Schools included a heterogeneous mixture of health supportive school ethos, particularly among sub-dimensions.
Diversity and natural history of birds in green urban areas of the city of Quito, Ecuador (America)
Authors: Cisneros-Heredia Diego F , Montenegro Eliana
Published: January 2018

The diversity and ecology of urban bird communities have been extensively studied in Neartic and Paleartic areas, however, little is known about urban Neotropical areas. Quito, capital city of Ecuador, is located on a highland valley in the megadiverse tropical Andes. Founded in 1534, Quito did not increase significantly its urban area until the late 19th century, growing at an accelerated and unplanned rate during the 20th century. More than 100 species were known to inhabit in Quito at the end of the 19th century. Currently, most authors estimated that no more than 40 species occur in Quito, although no systematic bird studies have been conducted. Our research is a first approach to the avifauna of Quito, surveying the diversity living in green urban areas within the city borders. We used two field methodologies, i.e. line transects and point counts, to survey 16 green urban areas over 12 months. We recorded 65 species of birds, belonging to 20 families and 9 orders. Three species were the most common and frequent: Eared Dove Zenaida auriculata, Rufous-collared Sparrow Zonotrichia capensis, and Great Thrush Turdus fuscater, being omnivores and granivores adapted to anthropic habitats with low ecological complexity. Six species were equally common but not as frequent: American Kestrel Falco sparverius, Sparkling Violetear Colibri coruscans, Black-tailed Trainbearer Lesbia victoriae, Brown-bellied Swallow Oreochelidon murina, Black Flowerpiercer Diglossa humeralis, and Cinereous Conebill Conirostrum cinereum, being nectarivores or small predators. All other species were either uncommon or rare, mainly insectivores and frugivores that prefer wildlife habitats with mid/high ecological complexity, and restricted to large urban parks with patches of native vegetation. We found a negative correlation between human impact and bird richness in all studied areas. These data provide important information to encourage better urban practices and to promote conservation and recovery of Quito’s native wildlife.
Data Fusion for cleavage target prediction
Authors: Marini Simone , Demartini Andrea , Vitali Francesca , Bellazzi Riccardo , Akutsu Tatsuya
Published: January 2018

Motivation: Protein cleavage is a pivotal process in cell metabolism. It is involved, among other processes, in cell differentiation and cycle control, stress and immune response, removal of abnormally folded proteins and cell death. Proteases (i.e. protein responsible for cleavage) account for ~2% of all gene products. As consequence, wrongly regulated proteolytic activity may result in diseases. The problem of predicting cleavage targets have been addressed by a number of algorithms. Traditional prediction models tackle the cleavage target machinery encoding directly related information to the outcome class (e.g. by extracting sequence patterns or frequency matrices). We are aware, however, that a huge amount of indirectly-related information is available in public data sets. Peptidases and targets are both proteins, and share similarities as well as non-cleavage interactions in knowledge bases; they are both encoded by genes, and gene interactions are also in databases. Our proposed Data Fusion algorithm leverages on these secondary information sources to infer novel peptidase targets.

Methods: Our approach is based on tri-factorization. The multiplicity of data are fused by inferring a joint model, and without altering their original structure, i.e. data are explicitly represented in the form of a relational block matrix R. Diagonal blocks of R are set to 0, while other blocks are sparse matrices, populated with the relations harvested from the various data sources. R elements are constrained into the range [0, 1], where 0s represent negative or unknown relationships, while 1s are interpreted as certain relationships. We considered three elements in our matrix, namely peptidases, targets and genes. From MEROPS we obtained 657 human peptidases affecting 3460 targets and forming 8931 pairs. From their mapping on Uniprot, 3833 genes coding for pepidases or targets were retained. This information was used to populate the peptidase-target, peptidase-gene and target-gene R blocks. During the data fusion process, each R block is decomposed into three sub-matrices, characterized by low dimensions (if compared to the original R block size). There is no clear consensus about a technique to define these dimensions, and we proceeded by choosing a rank for a given block based on the number of known interactions. Once the dimensions are set, the three sub-matrices are used to reconstruct a user-defined target block Rt. R decomposition is obtained through an iterative process, where constraint matrices play an important role. Constraint matrices are populated with the associations relating objects of the same type. In our application we utilized five constraints: one gene-gene interaction matrix from BIOGrid; two target-target and protease-protease interaction matrices from STRING (0.7 as combined score threshold); two target-target and protease-protease...

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Towards an integrated interactive database for the search of stratification biomarkers in Alkaptonuria
Authors: Cicaloni Vittoria , Zugarini Andrea , Rossi Alberto , Zazzeri Matteo , Santucci Annalisa , Bernini Andrea , Spiga Ottavia
Published: January 2018

MOTIVATION Alkaptonuria (AKU) is a rare and genetic disease which causes discoloration of bone (a process called ‘ochronosis’) and induces early-onset osteoarthritis. AKU data have not been organized yet and the disease has no approved biomarkers. The ability to collect, integrate and analyze relevant data streams is the core for developing a “Precision Medicine Ecosystem” AKU-dedicated in which biological resources are shared between researchers, clinicians and patients. Computational modeling can be a useful guide to generate an exhaustive and dynamic picture of the individual and to identify the molecular interactions between biomarkers on which progressive diseases are based.

METHODS It has been built a new integrated interactive database thanks to MySQL, the most frequently chosen for use in web applications. In addition, data are statistically analyzed by R software (www.r-project.org) based on Pearson’s correlation coefficient andPvalue. For a biological interpretation of statistic results, Stitch (Kuhn M. et al, 2007) and KEGG (Kanehisa M. et al, 2000) are used.

RESULTS For Precision Medicine (PM) application to AKU, the collection of as much data as possible Alkaptonuria affected patients has been needed in order to organize them in an interactive and integrated database and to find a data-processing system for AKU biomarkers discovery. The database is an effective tool for registered researchers, clinicians and patients who could both easily access all the current information, as well as being able to insert new data, refreshing or replacing previous entries. Data are divided into different sections: genetic, proteic, biochemical, histopathologic and clinical. As far as data analysis is concerned, it has been developed an algorithm to build up a refreshable correlation matrix based on Pearson’s correlation coefficient andPvalue which allows the monitoring of renewable correlations between the most recent data inserted. Together with the mathematical and statistical interpretation, a biological explanation of the results is needed in order to investigate on AKU biomarkers. This dynamic tool could be useful for biomarkers investigation also in other osteoarticular diseases and it is a good starting point for the creation of data management and analysis model appropriate for PM. Through the use of AKU-dedicated database and this innovative analytic approach, it has been possible to become aware of the failure of biomarkers clinically used and to improve the detenction of more exploitable prognostic biomarkers for a more reliable AKU patients clinical monitoring.
Algorithms for the compression of genomic big data
Authors: Prezza Nicola , Policriti Alberto
Published: January 2018

Motivations. Building the Burrows-Wheeler transform (BWT) and computing the Lempel-Ziv parsing (LZ77) of huge collections of genomes is becoming an important task in bioinformatic analyses as these datasets often need to be compressed and indexed prior to analysis. Given that the sizes of such datasets often exceed RAM capacity of common machines however, standard algorithms cannot be used to solve this problem as they require a working space at least linear in the input size. One way to solve this problem is to exploit the intrinsic compressibility of such datasets: two genomes from the same species share most of their information (often more than 99%), so families of genomes can be considerably compressed. A solution to the above problem could therefore be that of designing algorithms working in compressed working space, i.e. algorithms that stream the input from disk and require in RAM a space that is proportional to the size of the compressed text.

Methods. In this work we present algorithms and data structures to compress and index text in compressed working space. These results build upon compressed dynamic data structures, a sub-field of compressed data structures research that is lately receiving a lot of attention. We focus on two measures of compressibility: the empirical entropy H of the text and the number r of equal-letter runs in the BWT of the text. We show how to build the BWT and LZ77 using only O(Hn) and (rlog n) working space, n being the size of the collection. For the case of repetitive text collections (such as sets of genomes from the same species), this considerably improves the working space required by state-of-the art algorithms in the literature. The algorthms and data structures here discussed have all been implemented in a public C++ library, available at github.com/nicolaprezza/DYNAMIC. The library includes dynamic gap-encoded bitvectors, run-length encoded (RLE) strings, and RLE FM-indexes.

Results. We conclude with an overview of the experimental results that we obtained running our algorithms on highly repetitive genomic datasets. As expected, our solutions require only a small fraction of the working space used by solutions working in non-compressed space, making it feasible to compute BWT and LZ77 of huge collections of genomes even on desktop computers with small amounts of RAM available. As a downside of using complex dynamic data structures however, running times are still not practical so improvements such as parallelization may be needed in order to make these solutions fully practical.
Differential proteomics analysis of oligodendrogliomas and astrocytomas using iTRAQ quantification
Authors: Lin Shide , Li Jingzhe , Wang Peng , Zang Yujie , Feng Fan , Zhao TingBao
Published: January 2018

Background: Astrocytomas and oligodendrogliomas are two types of primary Central nervous system (CNS) tumors. Because of the cytoarchitectural variability and lacking of accurate differential diagnosis biomarkers, distinguishing between these neoplasms remains a challenge. Method: In this study, we utilized the tumor tissue proteome to distinguish the astrocytomas and oligodendrogliomas. The protein samples from astrocytomas and oligodendrogliomas tumor tissues were analyzed by 2DLC/MS/MS and isobaric tags for relative and absolute quantitation (iTRAQ) quantification. The differential proteins were analyzed by IPA software, and three identified differential proteins were validated by Western Blot. Results: A total of 2189 proteins were identified, including 150 upregulated and 103 downregulated in astrogliomas compared to oligodendrogliomas. By bioinformatics analysis, compared to oligodendrogliomas, the astrocytomas is more likely tend to cell proliferation, migration and the tumor angiogenesis, indicating astrocytomas was more malignant than the oligodendrogliomas. Pathway analysis showed that members of Rho Family GTPases were remarkably changed between astrocytomas and oligodendrogliomas. Two member of Rho family of GTPases, Cell division control protein 42 homolog (CDC42) and Transforming protein RhoA (RHOA) were over-expressed in astrocytomas and oligodendrogliomas, respectively. Discussion: Above data indicated that the differential proteome could be useful to distinguish between astrocytomas and oligodendrogliomas, especially the Rho family of GTPases. Differential proteome could partially reflect the pathological characteristics of these two diseases.
Structural states of a RNA aptamer, molecular dynamics simulation study
Authors: Autiero Ida , Vitagliano Luigi , Improta Roberto , Ruvo Menotti -
Published: January 2018

Motivation

RNA, which adopts a wide range of secondary structures is involved in several kind of chemical interactions and shows a notable structural plasticity. Due to remarkable chemical properties and an important physiological role of RNAs, there is a growing interest in development of RNA-based drugs and ligands of clinical relevance. However, RNAs structural and dynamic features as well as the main RNA-protein recognition effects remain largely unaddressed. We have studied the conformational behaviour and the dynamic of two different structural arrangements of an aptamer binding the bacillus anthracis ribosomal protein S8. This RNA aptamer has experimentally shown two different topologies in free state and in protein-bound state, although sequences differ for just few residues beyond the common internal loop. The role of the interacting protein on the RNA folding, stabilizing or inducing a particular conformation will be discussed.

Methods

Three molecular dynamic simulations of 300 ns each have been performed starting from three distinct aptamer structures: i) the aptamer free-state, using a representative model of a NMR ensemble of structures (pdb 2lun); ii) a similar aptamer bound to its target protein (4pdb) iii); an aptamer model built using the sequence of the RNA in the free state but with the structural arrangement of the bound-state to investigate a possible influence of the sequence on the RNA folding. All the systems under investigations were solvated in a truncated octahedral water box using explicit water models, with a least a 1.1 Å distance to the border, using Na+ counter-ions to neutralize. 6 steps of heating simulation from 50 K to 300K were carried out before to perform the final MD run of 300 ns in NPT conditions without restrains. The trajectories were analysed using the GROMACS utilities and X3DNA program.

Results

Our data show that both bound-state RNA arrangements are structurally stable, holding all the main interactions since the beginning of the simulations. The free-state RNA is the system with the largest flexibility, reaching an equilibrium after 40 ns of simulation. Although the NMR structure appears less rigid, during the total run it never matches the arrangement of the bound state. Definitely, within our time scale, a convergence of the free state with the bound-state trajectories has never been observed and the two different arrangements show differences in flexibility. Preliminary data suggest a significantly different behaviour of the free- and bound-state structures supporting a preminent role of the interacting partner protein on the RNA overall folding to induce a particular stable structural arrangement.
A computational study to identify potential inhibitors for human chymase from natural and/or biogenic sources
Authors: Dubey Amit , Marabotti Anna , Ramteke Pramod W , Facchiano Angelo
Published: January 2018

Motivation. The human chymase (EC 3.4.21.39) is a hydrolase abundant in secretory granules of mast cells, responsible for the synthesis of angiotensin II from its precursor. Moreover, it is also responsible for the conversion of transforming growth factor-β (TGF-β) and matrix metalloproteinase (MMP)-9 precursors to their active forms. Since a link between heart failure and chymase has been proved, specific chymase inhibitors are actively searched to develop new therapeutic treatments for cardiovascular diseases, considering also that chymase has no enzymatic activity in normal tissues. Therefore, specific chymase inhibitors may have no effects on any other target in healthy states. The use of natural products has been an integral part of the treatment of different diseases throughout the world since past centuries. Many plants with potential therapeutic activity were widely used as natural medicines with negligible undesired effects. Therefore, the search for new active compounds from natural sources is gaining interest in the scientific community, and the application of novel approaches to an old science could result in the discovery of valuable compounds useful to develop innovative drugs. We present here our search for novel inhibitors of chymase enzyme from natural sources or inspired by nature, using a computational approach that allowed us to screen databases of compounds and to predict which molecules can be able to bind to chymase with a good affinity and selectivity against other serine proteases. Methods. The crystal structure of human chymase complexed to a known inhibitor, available in the Protein Data Bank (PDB code 1T31), was selected for the development of ten structure-based pharmacophore models, using the protocol available in Discovery Studio. After a validation step, the best pharmacophore was used to screen a special subset of ZINC database (ZINC Biogenic compounds) containing more than 120,000 nature-inspired compounds. After identification of the best potential compounds matching the pharmacophore features, and further filtering strategies, few potential ZINC compounds were selected for further steps. In parallel, selected compounds from plants were identified as potential candidates, also on the basis of their correspondence to the pharmacophore features obtained in the previous step. The 3D structures of all these selected compounds, as well as those of the known co-crystallized chymase inhibitor and of other known inhibitors used as reference molecules, were retrieved from ZINC and/or PubChem databases and were docked in the active site of human chymase. Their predicted binding affinities and their interactions with the enzyme were then compared. Finally, all these molecules were docked into the active sites of other human serine proteases (kallikrein, elastase and tryptase), whose 3D structures were selected ...

Abstract truncated at 3,000 characters - the full version is available in the pdf file
Big Data for disease prevention and precision medicine
Authors: Moscatelli Marco , Gnocchi Matteo , Manconi Andrea , Milanesi Luciano
Published: January 2018

Motivation

Nowadays, advances in technology has arisen in a huge amount of data in both biomedical research and healthcare systems. This growing amount of data gives rise to the need for new research methods and analysis techniques. Analysis of these data offers new opportunities to define novel diagnostic processes. Therefore, a greater integration between healthcare and biomedical data is essential to devise novel predictive models in the field of biomedical diagnosis. In this context, the digitalization of clinical exams and medical records is becoming essential to collect heterogeneous information. Analysis of these data by means of big data technologies will allow a more in depth understanding of the mechanisms leading to diseases, and contextually it will facilitate the development of novel diagnostics and personalized therapeutics. The recent application of big data technologies in the medical fields will offer new opportunities to integrate enormous amount of medical and clinical information from population studies. Therefore, it is essential to devise new strategies aimed at storing and accessing the data in a standardized way. Moreover, it is important to provide suitable methods to manage these heterogeneous data.

Methods

In this work, we present a new information technology infrastructure devised to efficiently manage huge amounts of heterogeneous data for disease prevention and precision medicine. A test set based on data produced by a clinical and diagnostic laboratory has been built to set up the infrastructure. When working with clinical data is essential to ensure the confidentiality of sensitive patient data. Therefore, the set up phase has been carried out using "anonymous data". To this end, specific techniques have been adopted with the aim to ensure a high level of privacy in the correlation of the medical records with important secondary information (e.g., date of birth, place of residence). It should be noted that the rigidity of relational databases does not lend to the nature of these data. In our opinion, better results can be obtained using non-relational (NoSQL) databases. Starting from these considerations, the infrastructure has been developed on a NoSQL database with the aim to combine scalability and flexibility performances. In particular, MongoDB [1] has been used as it fits better to manage different types of data on large scale. In doing so, the infrastructure is able to provide an optimized management of huge amounts of heterogeneous data, while ensuring high speed of analysis.

Results

The presented infrastructure exploits big data technologies in order to overcome the limitations of relational databases when working with large and heterogeneous data. The infrastructure implements a set of interface procedures aimed at preparing the metadata for importing data in a NOSQL DB.

Abstract truncated at 3,000 characters - the full version is available in the pdf file
A qualitative view of the HIV epidemic in coastal Ecuador
Authors: Beckman Adam L , Wilson Magdelana M , Prabhu Vishaal , Soekoe Nicola , Mata Humberto , Grau Lauretta E
Published: January 2018

In 2013 approximately 37,000 people were living with HIV in Ecuador (prevalence 0.4%), representing a generalized epidemic where most new infections arise from sexual interactions in the general population. Studies that examine attitudes towards people living with HIV (PLWH), individual risk perception of acquiring HIV amongst Ecuadorians, and the ways in which levels of risk perception may affect risk behaviors are lacking. This qualitative study aimed to fill this gap in the literature by investigating these issues in the rural, coastal community of Manglaralto, Ecuador, which has among the highest incidence of HIV in Ecuador. We conducted interviews with 15 patients at Manglaralto Hospital. Analysis of interview transcripts revealed widespread negative attitudes towards PLWH, prevalent risk behaviors such as multiple sex partners and lack of condom use, and low individual risk-perception of contracting HIV. These findings underscore the need for increased efforts to prevent further growth of the HIV epidemic in Ecuador.
Optimizing the use of a sensor resource for opponent polarization coding
Authors: Heras Francisco J. H. , Laughlin Simon B
Published: January 2018

Flies use specialized photoreceptors R7 and R8 in the dorsal rim area (DRA) to detect skylight polarization. R7 and R8 form a tiered waveguide (rhabdom) with R7 on top, filtering light delivered to R8. We examine how the division of a given resource, rhabdom length, between R7 and R8 affects their ability to code polarization angle. We model optical absorption to show how the length fractions allotted to R7 and R8 determine the rates at which they transduce photons, and correct these rates for transduction unit saturation. The rates give polarization signal and photon noise in R7, and in R8. Their signals are combined in an opponent unit, intrinsic noise added, and the unit’s output analysed to extract two measures of coding ability, number of discriminable polarization angles and mutual information. A very long R7 maximizes opponent signal amplitude, but codes inefficiently due to photon noise in the very short R8. Discriminability and mutual information are optimized by maximizing signal to noise ratio, SNR. At lower light levels approximately equal lengths of R7 and R8 are optimal because photon noise dominates. At higher light levels intrinsic noise comes to dominate and a shorter R8 is optimum. The optimum R8 length fractions falls to one third. This intensity dependent range of optimal length fractions corresponds to the range observed in different fly species and is not affected by transduction unit saturation. We conclude that a limited resource, rhabdom length, can be divided between two polarization sensors, R7 and R8, to optimize opponent coding. We also find that coding ability increases sub-linearly with total rhabdom length, according to the law of diminishing returns. Consequently the specialized shorter central rhabdom in the DRA codes polarization twice as efficiently with respect to rhabdom length than the longer rhabdom used in the rest of the eye.
Ancient science networks in action: the collaboration between J.G. Hidalgo and H. Crosse, and the creation of ‘Moluscos del Viaje al Pacifico, Univalvos terrestres’
Authors: Breure Abraham S H , Backhuys Wim
Published: January 2018

The material collected during a Spanish, multi-year expedition to the Neotropics in the 1860s was described by J.G. Hidalgo in the ‘Moluscos del Viaje al Pacifico’. Correspondence between Hidalgo and H. Crosse reveals how part of the material collected by the ‘Comisión Cientifíca del Pacífico' was identified by Crosse, some of it published as new species in his Journal de Conchyliologie. This correspondence further reveals how the obstacles to publish the results of the expedition were overcome, and sheds light on the actual publication date of the different parts. A reconstruction of the contacts of Hidalgo shows how diversified the network of the malacologist was.
Recent developments of the cell line integrated molecular authentication database
Authors: Romano Paolo D , Visconti Paola , Parodi Barbara
Published: January 2018

Cross-contamination of human and animal cell lines is a frequent event. For this reason, the results obtained with the same cell lines by different research groups are often not fully comparable, this leading to main reproducibility issues. The short tandem repeat (STR) profile has been proposed as a molecular method for cell line authentication. STR profile standard data sets for human cell lines were proposed by some of the leading cell banks worldwide which also have made the results of STR profiling of their cell lines available on-line. We have built the Cell Line Integrated Molecular Authentication Database (CLIMA) as a reference portal where authentication data are made available to the scientific community. This system, although already largely utilized by researchers from all over the world, presented some limitations and only included a limited amount of STR profiles. Here, we present its most recent developments: the inclusion of additional cell banks and profiles and the availability of a new identification tool.
Optimization of 16S amplicon analysis using mock communities: implications for estimating community diversity
Authors: Krohn Andrew , Stevens Bo , Robbins-Pianka Adam , Belus Matthew , Allan Gerard J , Gehring Catherine
Published: January 2018

The diversity of complex microbial communities can be rapidly assessed by high-throughput DNA sequencing of marker gene (e.g., 16S) PCR amplicon pools, often yielding many thousands of DNA sequences per sample. However, analysis of such community amplicon sequencing data requires multiple computational steps which affect the outcome of a final data set. Here we use mock communities to describe the effects of parameter adjustments for raw sequence quality filtering, picking operational taxonomic units (OTUs), taxonomic assignment, and OTU table filtering as implemented in the popular microbial ecology analysis package, QIIME 1.9.1. We demonstrate a workflow optimization based upon this exploration, which we also apply to environmental samples. We found that quality filtering of raw data and filtering of OTU tables had large effects on observed OTU diversity. While all taxonomy assignment programs performed with similar accuracy, an appropriate choice of similarity threshold for defining OTUs depended on the method used for OTU picking. Our “default” analysis in QIIME overestimated mock community OTU diversity by at least a factor of ten. Our optimized analysis correctly characterized mock community taxonomic composition and improved the OTU diversity estimate, reducing overestimation to a factor of about two. Though observed relative abundances of mock community member taxa were approximately correct, most were still represented by multiple OTUs. Low-frequency OTUs conspecific to constituent mock community taxa were characterized by multiple substitution and indel errors and the presence of a low-quality base call resulting in sequence truncation during quality filtering. Low-quality base calls were observed at “G” positions most of the time, and were also associated with a preceding “TTT” trinucleotide motif. Environmental diversity estimates were reduced by about 40% from 2508 to 1533 OTUs when comparing output from the default and optimized workflows. We attribute this reduction in observed diversity to the removal of erroneous sequences from the data set. Our results indicate that both strict quality filtering of raw sequencing data and careful filtering of raw OTU tables are important steps for accurately estimating microbial community diversity.
Adulteration of herbal products: Bamboo tea authentication
Authors: Horn Thomas , Häser Annette
Published: January 2018

Background. Names for ”substances” used in food products are rarely precise. The term bamboo (Bambusoideae, Poaceae) comprises over 1600 distinct species of which only few are well established sources for food products on the European market (i.e. bamboo sprouts).

Methods. We analysed bamboo species and tea products containing an exotic ingredient (bamboo leaves) using anatomical leaf characters and DNA sequence data. Our primary concern was to determine the taxonomic origin of bamboo leaves to establish a baseline for EU legislation, to introduce a simple PCR based test to distinguish bamboo from other Poaceae leaf components and to assess the diagnostic potential of DNA Barcoding markers to resolve taxonomic entities within the bamboo subfamily and tribes.

Results. Based on anatomical and DNA data we can pinpoint the taxonomic origin of genuine bamboo leaves used in commercial products to the genera Phyllostachys and Pseudosasa from the temperate ”woody” bamboo tribe (Arundinarieae). We detected adulteration by carnation in 4 of 8 tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women.
Learning protein folding and evolution with a snake puzzle
Authors: Nido Gonzalo S , Bachschmid-Romano Ludovica , Bastolla Ugo , Pascual-García Alberto
Published: January 2018

We propose here a working unit for teaching basic concepts of protein folding and evolution centred around the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master course at the Universidad Autónoma de Madrid (Spain), the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Overlap. It also allows a simple representation of misfolded conformations and their free energy. These concepts, in particular protein structure comparison and the stability of the native state with respect to unfolded and misfolded conformations, will motivate evolutionary questions. We address these questions by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.