bluuebunny/crossref_metadata_2025 huggingface dataset:
An evolving computational platform for biological mass spectrometry: Work-flows, statistics and Data Mining with MASSyPup64
Authors: Winkler Robert
Published: January 2018

In biological mass spectrometry, crude instrumental data need to be converted into meaningful theoretical models. Several data processing and data evaluation steps are required to come to the final results. These operations are often difficult to reproduce, because of too specific computing platforms. This effect, known as ’workflow decay’, can be diminished by using a standardized informatic infrastructure. Thus, we compiled an integrated platform, which contains ready-to-use tools and workflows for mass spectrometry data analysis. Apart from general unit operations, such as peak picking and identification of proteins and metabolites, we put a strong emphasis on the statistical validation of results and Data Mining. MASSyPup64 includes e.g. the OpenMS/TOPPAS framework, the Trans-Proteomic-Pipeline programs, the ProteoWizard tools, X!Tandem, Comet and SpiderMass. The statistical computing language R is installed with packages for MS data analyses, such as XCMS/metaXCMS and MetabR. The R package Rattle provides a user-friendly access to multiple Data Mining methods. Further, we added the non-conventional spreadsheet program teapot for editing large data sets and a command line tool for transposing large matrices. Individual programs, console commands and modules can be integrated using the Workflow Management System (WMS) taverna. We explain the useful combination of the tools by practical examples: 1) A workflow for protein identification and validation, with subsequent Association Analysis of peptides, 2) Cluster analysis and Data Mining in targeted Metabolomics, and 3) Raw data processing, Data Mining and identification of metabolites in untargeted Metabolomics. Association Analyses reveal relationships between variables across different sample sets. We present its application for finding co-occurring peptides, which can be used for target proteomics, the discovery of alternative biomarkers and protein-protein interactions. Data Mining derived models displayed a higher robustness and accuracy for classifying sample groups in targeted Metabolomics than cluster analyses. Random Forest models do not only provide predictive models, which can be deployed for new data sets, but also the variable importance. We demonstrate that the later is especially useful for tracking down significant signals and affected pathways in untargeted Metabolomics. Thus, Random Forest modeling supports the unbiased search for relevant biological features in Metabolomics. Our results clearly manifest the importance of Data Mining methods to disclose non-obvious information in biological mass spectrometry . The application of a Workflow Management System and the integration of all required programs and data in a consistent platform makes the presented data analyses strategies reproducible for non-expert users. The simple remastering process and the Open Source licenses of MASSyPup64 (http://www. bioprocess.org/massypup/) enable the continuous improvement of the system.
The mind-writing pupil: A human-computer interface based on decoding of covert attention through pupillometry
Authors: Mathôt Sebastiaan , Melmi Jean-Baptiste , van der Linden Lotje , Van der Stigchel Stefan
Published: January 2018

We present a new human-computer interface that is based on decoding of attention through pupillometry. Our method builds on the recent finding that covert visual attention affects the pupillary light response: Your pupil constricts when you covertly (without looking at it) attend to a bright, compared to a dark, stimulus. In our method, participants covertly attend to one of several letters with oscillating brightness. Pupil size reflects the brightness of the selected letter, which allows us--with high accuracy and in real time--to determine which letter the participant intends to select. The performance of our method is comparable to the best covert-attention brain-computer interfaces to date, and has several advantages: no movement other than pupil-size change is required; no physical contact is required (i.e. no electrodes); it is easy to use; and it is reliable. Potential applications include: communication with totally locked-in patients, training of sustained attention, and ultra-secure password input.
A nomenclature for the standard linguistic description of the kinematics of networks
Authors: Pabico Jaderick P , Albacea Eliezer A
Published: January 2018

The rate of change \(\partial M/\partial t\) of some metric \(M\) measured as one of the kinematic properties of a network described by a graph \(G\) transitioning from \(G(V_{t}, E_{t})\) to \(G(V_{t+\partial t}, E_{t+\partial t})\) over time range \(\partial t\) has been described in the literature with linguistic descriptions that often provide ambiguity. For example, one rate of change \((\partial M/\partial t)_{1}\) has been described as ``dynamic'' and another \((\partial M/\partial t)_{2}\) as ``highly dynamic'' but \((\partial M/\partial t)_{1}>(\partial M/\partial t)_{2}\). We propose in this paper a nomenclature for the standard linguistic description of the kinematics of networks in the hope that description in the literature will be standardized and understood with the corresponding quantitative meaning. We termed a network as ``static'' when \(\partial M/\partial t=0\), as ``non-volatile'' when \(0<\partial M/\partial t\le 1\), and as ``volatile'' when \(\partial M/\partial t>1\). In the development of the linguistic nomenclature, we borrowed heavily from the standard used in signal theory to provide linguistic descriptions to various ranges for \(\partial M/\partial t>1\). We described the kinematics of example real-world networks where the proposed nomenclature was used: (1) The collaboration network of Filipino Computer Scientists; (2) The network created from friendship relations among Batangas and Laguna Facebook users; and (3) The network created from the followed-follower relations among the top ten globally influential Twitter users.
Fossils, footprints and fakes
Authors: Graham Mark R
Published: January 2018

The Natural History Museum has undertaken a series of annual field trips to Morocco for collections enhancement purposes. Specimens are collected directly from various locations and also obtained from local collectors and dealers, introduced to the group by trusted local contacts with whom the museum has built a relationship. The 2015 fieldtrip in late February/early March was very eventful, with sudden snowfall and floods encountered, hidden mountainside quarries visited, little publicised dinosaur trackways discovered and fossil fakery by skilled preparators witnessed at first hand!. This presentation highlights the scientific value and potential pitfalls of such collaborations.
Fibroblast growth factors as tissue repair and regeneration therapeutics
Authors: Nunes Quentin M , Li Yong , Sun Changye , Kinnunen Tarja K , Fernig David G
Published: January 2018

Cell communication is central to the integration of cell function required for the development and homeostasis of multicellular animals. Proteins are an important currency of cell communication, acting locally (auto-, juxta-, or paracrine) or systemically (endocrine). The fibroblast growth factor (FGF) family contributes to the regulation of virtually all aspects of development and organogenesis, and after birth to tissue maintenance, as well as particular aspects of organism physiology. In the West oncology has been the focus of translation of FGF research, whereas in China and to an extent Japan a major focus has been to use FGFs in repair and regeneration settings. These differences have their roots in research history and aims. The Chinese drive into biotechnology and the delivery of engineered clinical grade FGFs by a major Chinese research group were important enablers in this respect. The Chinese language clinical literature is not widely accessible. To put this into context, we provide the essential molecular and functional background to the FGF communication system covering FGF ligands, the heparan sulfate and Klotho co-receptors and FGF receptor (FGFR) tyrosine kinases. We then summarise a selection of case reports that demonstrate the efficacy of engineered recombinant FGF ligands in treating a wide range of conditions that require tissue repair / regeneration. Alongside the functional reasons why application of exogenous FGF ligands does not lead to cancers are described. Together, this highlights that the FGF ligands represent a major opportunity for clinical translation, that has been largely overlooked in the West.
Bayesian characterization of uncertainty in species interaction strengths
Authors: Wolf Christopher , Novak Mark , Gitelman Alix I.
Published: January 2018

Considerable effort has been devoted to the empirical estimation of species interaction strengths. This effort has focused primarily on statistical significance testing and on obtaining point estimates of parameters that contribute to interaction strength magnitude, leaving characterizations of estimation uncertainty and distinctions between the deterministic and stochastic contributions to variation largely unconsidered. Here we consider a means of quantifying interaction strength uncertainty by formulating an observational method for estimating per capita attack rates as a Bayesian statistical model. This formulation permits the explicit incorporation of multiple sources of uncertainty. In doing so we highlight the informative nature of several so-called non-informative prior choices in modeling the sparse data typical of predator feeding surveys and provide evidence for the superior performance of a new neutral prior choice. A case study application shows that while Bayesian point estimates may be made to correspond with those obtained by frequentist approaches, estimation uncertainty as described by the 95% intervals is more biologically realistic using the Bayesian method in that the lower bounds of the Bayesian posterior intervals for the attack rates do not include zero when the occurrence of a given predator-prey interaction is in fact observed. This contrasts with bootstrap confidence intervals that often do contain zero in such cases. The Bayesian approach provides a straightforward, probabilistic characterization of interaction strength uncertainty. In doing so it provides a framework for considering both the deterministic and stochastic drivers of species interactions and their impact on food web dynamics.
Emotion detection from natural walking
Authors: Cui Liqing , Li Shun , Zhu Tingshao
Published: January 2018

Emotion identification, which aims to determine a person's affective state automatically, has immense potential value in many areas, such as action tendency, health care, psychological detection and human-computer (robot) interaction. In this paper, we provide a novel method for identifying emotion from natural walking. After obtaining the three-axis acceleration data of wrist and ankle recorded by smartphone, we run a moving average filter with different window size w, then cut actual data into slices. 114 features are extracted from each slice, and principal component analysis(PCA) is used for feature selection. We train SVM, Decision Tree, Multilayerperception, Random Tree and Random Forest classification models, and compare the accuracy of emotion identification using different datasets (wrist vs. ankle) in different models. Results show that acceleration data from ankle has better performance in emotion identification than wrist. Among different models, SVM has the highest accuracy, 90:31% when differ anger from neutral, 89:76% when differ happy from neutral, and 87:10% when differ anger from happy. The model for identifying anger/neutral/happy yields the best accuracy of 85%-78%-78%. The results show that we could identify peoples emotional states through the gait of walking with high accuracy.
Request type prediction for Web robot and Internet of Things traffic
Authors: Doran Derek , Rude Nathan
Published: January 2018

The volume of Web robot traffic seen by Web servers and clouds continue to increase with the popularity of Internet of Things (IoT) devices. Such traffic exhibits decidedly different statistical and resource request patterns compared to humans. However, the optimizations ensuring high levels of Web systems and cloud performance requires traffic to exhibit the statistical and behavioral patterns of humans, not robots. This necessitates the design of novel Web system optimizations to handle Web robot traffic effectively. Caches are a basic component of high performing Web systems, but their effectiveness relies on accurate resource request prediction. In this paper, we explore a suite of classifiers for the resource request type prediction problem for robot traffic. Our analysis reveals: (i) a striking difference in the request patterns of robots across multiple servers from the same domain; and (ii) that Elman neural networks hold promise to predict request types despite these differences.
Relationship between small-scale catch-per-unit-effort and abundance in New Zealand abalone (pāua, Haliotis iris) fisheries
Authors: Abraham Edward R , Neubauer Philipp
Published: January 2018

Catch-per-unit-effort (CPUE) is commonly used as an index of abundance in fishery stock assessments, but CPUE may be misleading, as a number of global fishery collapses have been attributed to a hyper-stable CPUE. In abalone (Halitidae family) fisheries, CPUE at large spatial scales may be hyper-stable because of aggregating behaviour and serial-depletion, whereby fishers sequentially fish areas with no corresponding decline in CPUE. Obtaining detailed spatial information in abalone fisheries might mitigate this problem, allowing CPUE to be used more confidently in these fisheries. Here, we report on the use of newly-developed high-resolution Global Positioning System (GPS) data loggers in New Zealand's blacklip abalone (pāua, Haliotis iris) fisheries. Using these data loggers, we tested, via a fish-down experiment, if CPUE is a reliable indicator of abundance at a small spatial scale and over a period of months. In the experiment, hyper-stability at small spatial scales occurred at high abundance, but CPUE reflected the estimated depletion level at the end of experimental fishing. This experiment suggests that the GPS data loggers provide a promising avenue to track CPUE at a small spatial scale, and to assess spatial resource use in New Zealand's pāua fisheries.
Testing the grouper biocontrol hypothesis: A response to Mumby et al. 2013
Authors: Bruno John F , Valdivia Abel , Hackerott Serena , Cox Courtney E , Green Stephaine , Côté Isabelle , Akins Lad , Layman Craig , Precht William
Published: January 2018

Biotic resistance is the idea that native species negatively affect the invasion success of introduced species. We tested the hypothesis that native grouper are controlling the abundance of exotic lionfish on Caribbean coral reefs by assessing the relationship between the density and biomass of lionfish and native predators at 71 reefs in three biogeographic regions. Our results indicated that: (a) the abundance of lionfish and large grouper are not negatively related, and (b) lionfish abundance is controlled by a number of physical site characteristics, and possibly by culling. Taken together, our results suggest that managers cannot rely on native grouper populations to control the lionfish invasion. Mumby et al. (2013) objected to several aspects of our analysis and conclusions. Here we address their criticisms and argue that our original conclusions are valid.
Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads
Authors: Ye Chengxi , Ma Sam
Published: January 2018

Motivation: The third generation sequencing (3GS) technology generates long sequences of thousands of bases. However, its error rates are estimated in the range of 15-40%, much higher than the previous generation (approximately 1%). Fundamental tasks such as genome assembly and variant calling require us to obtain high quality sequences from these long erroneous sequences. Results: In this paper we describe a versatile and efficient linear complexity consensus algorithm Sparc that builds a sparse k-mer graph using a collection of sequences from the same genomic region. The heaviest path approximates the most likely genome sequence (consensus) and is sought through a sparsity-induced reweighted graph. Experiments show that our algorithm can efficiently provide high-quality consensus sequences with error rate <0.5% using both PacBio and Oxford Nanopore sequencing technologies. Compared with the existing approaches, Sparc calculates the consensus with higher accuracy, uses 80% less memory, and is 5x faster, approximately. Availability: The source code is available for download at http://sourceforge.net/p/sparc-consensus/code/ and a testing dataset is available: https://www.dropbox.com/sh/trng8vdaeqywx1e/AAASJesLVAJZcbORkU9f4LuBa?dl=0 (Please copy the link to a browser to access if directly clicking the link fails)
Agricolae - Ten years of an open source statistical tool for experiments in breeding, agriculture and biology
Authors: De Mendiburu Felipe , Simon Reinhard
Published: January 2018

Plant breeders and educators working with the International Potato Center (CIP) needed freely available statistical tools. In response, we created first a set of scripts for specific tasks using the open source statistical software R. Based on this we eventually compiled the R package agricolae as it covered a niche. Here we describe for the first time its main functions in the form of an article. We also review its reception using download statistics, citation data, and feedback from a user survey. We highlight usage in our extended network of collaborators. The package has found applications beyond agriculture in fields like aquaculture, ecology, biodiversity, conservation biology and cancer research. In summary, the package agricolae is a well established statistical toolbox based on R with a broad range of applications in design and analyses of experiments also in the wider biological community .
The loss of foundation species revisited
Authors: Degrassi Allyson , Brantley Steven T , Levine Carrie R. , Miller Robert , Mohan Jacqueline , Record Sydne , Ellison Aaron M
Published: January 2018

Ecologists and environmental scientists often prioritize research efforts with conservation importance. Dominant, widespread, or locally abundant species at low risk of extinction receive relatively little attention unless they are invasive. Native foundation species create habitats and environmental conditions that support many associated species and modulate local-scale ecosystem processes, but the generally high local or regional abundance of foundation species may lead to less research about them. We used citation analysis (2005-2014) to examine research following from a suggestion to identify and study foundation species while they were still common and not threatened. We explored the use and expanding definition of the foundation species concept, as well as the trajectory and ecological focus of research on foundation species throughout the world in 378 papers published in this nine-year span. Contemporary authors who cite key papers defining a foundation species pay little attention to its actual definition and species studied in this context rarely were identified as foundation species. Although functions and roles of foundation species, such as creating unique microclimates or supporting dependent species, are being studied, less research is focused on identifying them before they are threatened or lost from the ecosystem that they otherwise define. Invasive species were identified as the most common threat to foundation species. Our citation analysis and synthesis provides a new conceptual framework linking identification of and research about foundation species with their functional roles and our ability to manage emerging threats to them.
Eocene tarpons from the North Sea region, Denmark and UK
Authors: Leal Maria E. C. , Schultz Bo P. , Madsen Henrik , Villa Chiara , Lynnerup Niels , Rosenkrants Niels Jørgen , Veje Ulrich , Bonde Niels
Published: January 2018

There are very few tarpons (family Megalopidae) and other elopiforms (fam. Elopidae) recorded in the Tertiary. The records are mainly from the Eocene, and more abundant in the ‘North Sea Region’ in Early Eocene, as for instance the large Danish forms. They are also found in late Early Eocene in London Clay, in Late Eocene in Caucasia, and in Miocene of SE-Asia, although none were described from the famous Bolca fauna (early Mid Eocene). However, there is a large, still undescribed ‘tarpon-like’ fish in the Bolca Museum (obs. MECL & NB 2014). There are even fewer described from the long Cretaceous period, 4-5? genera, including the large Paraelops from Romualdo Formation, Araripe Basin, NE-Brazil, and a large undescribed megalopid from Tlayua, Pueblo, Mexico, both ‘Mid Cretaceous’. The oldest elopiforms are from Late Jurassic Solnhofen Limestone. The large Danish ‘tarpons’ come from ‘cementstones’ in Fur Formation (earliest Eocene, ca. 55 m.y.), and here we report an almost complete specimen which is ca. 110 cm long; however, big isolated scales found in this formation indicate fishes at least twice as big (comparable in size with the living Tarpon atlanticus - over 2½ m). This specimen has a heavy skull lacking the lower jaw, and is preserved in 3-D. It was split in the midline and acid prepared, being then CT-scanned in Aarhus and reconstructed in the Laboratory of Biological Anthropology, Copenhagen University to attempt precise, detailed comparisons with modern skulls and with the 3-D skulls preserved in concretions from the London Clay.
Comparison of three clustering approaches for detecting novel environmental microbial diversity
Authors: Forster Dominik , Dunthorn Micah , Stoeck Thorsten , Mahé Frédéric
Published: January 2018

Discovery of novel diversity in high-throughput sequencing (HTS) studies is a central task in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on novel diversity discovery, we clustered an environmental marine protist HTS dataset of protist reads together with accessions from the taxonomically curated PR2 reference database using three de novo approaches: sequence similarity networks, USEARCH, and Swarm. The novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as novel by USEARCH and Swarm were actually highly similar to reference accessions. Using graph theory we found additional novel diversity within OTUs that would have gone unnoticed without further using their underlying network topologies. Our results suggest that novel diversity inferred from clustering approaches requires further validation, whereas graph theory provides a powerful tool for microbial ecology and the analyses of environmental HTS datasets.
Replacement of native by non-native animal communities assisted by human introduction and management on Isla Victoria, Nahuel Huapi National Park
Authors: Martin-Albarracin Valeria L , Nuñez Martin A , Amico Guillermo C
Published: January 2018

One of the possible consequences of biological invasions is the decrease of native species abundances or their replacement by non-native species. In Andean Patagonia, southern Argentina and Chile, many non-native animals have been introduced and are currently spreading. On Isla Victoria, Nahuel Huapi National Park, many non-native vertebrates were introduced ca. 1937. Records indicate that several native vertebrates were present before these species were introduced. We hypothesize that seven decades after the introduction of non-native species and without appropriate management to maintain native diversity, non-native vertebrates have displaced native species -given the known invasiveness and impacts of some of the introduced species-. We conducted direct censuses in linear transects 500m long (n=10) in parallel with camera-trapping (1253 camera-days) surveys in two regions of the island with different levels of disturbance: high (n=4) and low (n= 6) to study the community of terrestrial mammals and birds and the relative abundances of native and non-native species. Results show that currently non-native species are dominant across all environments; 60.4% of census records and 99.7% of camera trapping records are of non-native animals. We detected no native large mammals; the assemblage of large vertebrates consisted of five non-native mammals and one non-native bird. Native species detected were one small mammal and one small bird. Species with a highest trapping rate were red and fallow deer, wild boar, silver pheasant (the four species non-native) and chucao (a native bird). These results suggest that native species are being displaced by non-natives and are currently in very low numbers.
On fearfulness and patterns of bird urbanisation in an Australian metropolis
Authors: Conole Lawrence E
Published: January 2018

I have utilised an assemblage of 91 bird species, their urban tolerance status objectively classified, with data on bird flight initiation distance (FID), to test questions of the importance of birds’ fearfulness of humans in determining urban tolerance or intolerance in the metropolis of Melbourne, Australia. While several studies have shown that mean FID for bird species (mFID) differs between rural and urban populations of bird species, stronger predictive ability is shown by variability in FID (cvFID) in modelling urban invasiveness. I test two hypotheses. Firstly, that mFID will be shorter in urban exploiter bird species than urban adapters and avoiders. Secondly that cvFID is positively correlated with bird incidence at the landscape scale in Melbourne. Relatively weak explanatory power of cvFID found in this study suggest that environmental and behavioural factors acting in concert better explain the urban tolerance of bird species and assemblages, rather than fearfulness alone.
Recognition of emotions using Kinects
Authors: Li Shun , Cui Liqing , Zhu Changye , Zhao Nan , Li Baobin , Zhu Tingshao
Published: January 2018

Emotion recognition can improve the quality of patient care, product development and human-machine interaction.Psychological studies indicate that emotional state can be expressed in the way people walk,and the human gait can be used to reveal a person's emotional state.This paper proposes a novel method to do emotion recognition by using Microsoft Kinect to record gait patterns and train machine learning algorithms for emotion recognition. 59 subjects are recruited, and their gait patterns are recorded by two Kinect cameras.Joint selection, coordinate system transformation, sliding window gauss filtering,differential operation, and data segmentation are used for data preprocessing.We run Fourier transformation to extract features from the gait patterns and utilize Principal Component Analysis(PCA) for feature selection. By using NaiveBayes, RandomForests, LibSVM and SMO classifiers, the accuracy of recognition between natural and angry emotions can reach 80%,and the accuracy of recognition between natural and happy emotions can reach above 70%.The result indicates that Kinect can be used in the recognition of emotions with fairly well performance.
Role of heparan sulfate in mediating CXCL8-induced endothelial cell migration
Authors: Yan Zhiping , Liu Jingxia , Xie Linshen , Liu Xiaoheng , Zeng Ye
Published: January 2018

Several positively charged epitopes on the surface of CXCL8 involved in the binding of the major components of endothelial glycocalyx, sulfated glycosaminoglycans (GAGs).In the present study, we aimed to test the hypothesis that the surface GAGs — heparan sulfate (HS) is a crucial prerequisite for enhancement of endothelial cell migration by CXCL8, and to explore its underlying mechanism by detecting the changes in expression of Rho-GTPases and in the organization of actin cytoskeleton after enzymatic removal of HS on human umbilical vein endothelial cells (HUVECs) by using heparinase III.Our results revealed that the reduction of wound area by CXCL8 was greatly attenuated by removal of HS. The upregulations of Rho-GTPases, including Cdc42, Rac1, and RhoA by CXCL8 were suppressed by removal of HS . The polymerization and polarization of actin cytoskeleton, and the increasing of stress fibers by CXCL8 were also abolished by heparinase III. Taken together, our results demonstrated an essential role of HS in mediating CXCL8-induced endothelial cell migration, and highlighted the biological relevance of the CXCL8 and GAGs interactions in endothelial cell migration.
Essential design modeling for scientific software development
Authors: Ahmed Zeeshan
Published: January 2018

Software design and its engineering is essential for bioinformatics software impact. We propose a new approach ‘Butterfly’, for the betterment of modeling of scientific software solutions by targeting key developmental points: intuitive, graphical user interface design, stable methodical implementation and comprehensive output presentation. The focus of research was to address following three key points: 1) differences and different challenges required to change from traditional to scientific software engineering, 2) scientific software solution development needs feedback and control loops following basic engineering principles for implementation and 3) software design with new approach which helps in developing and implementing a comprehensive scientific software solution. We validated the approach by comparing old and new bioinformatics software solutions. Moreover, we have successfully applied our approach in the design and engineering of different well applied and published Bioinformatics and Neuroinformatics tools including DroLIGHT, LS-MIDA, Isotopo, Ant-App-DB, GenomeVX and Lipid-Pro.
Are attractive male crickets better able to pay the costs of an immune challenge?
Authors: Kelly Clint D , Telemeco Melissa , Toth Amy L , Bartholomay Lyric C
Published: January 2018

Reproduction and immunity are fitness-related traits that trade-off with each other. Parasite-mediated theories of sexual selection suggest, however, that higher-quality males should suffer smaller costs to reproduction-related traits and behaviours (e.g. sexual display) from an immune challenge because these males possess more resources with which to deal with the challenge. We used Gryllus texensis field crickets to test the prediction that attractive males should better maintain the performance of a fitness-related traits (e.g. calling effort) in the face of an immune challenge compared with unattractive males. We found no support for our original predictions. However, that immune activation causes attractive males to significantly increase their calling effort compared with unattractive males suggests that these males might terminally invest in order to compensate for decreased future reproduction.
Identification and typing of Salmonella for public health surveillance using whole genome sequencing
Authors: Ashton Philip M , Nair Satheesh , Peters Tansy , Bale Janet , Powell David G , Painset Anaïs , Tewolde Rediat , Jenkins Claire , Dallman Timothy J , DePinna Elizabeth M , Grant Kathie A ,   Salmonella Whole Genome Sequencing Implementation Group
Published: January 2018

In April 2015, Public Health England implemented whole genome sequencing (WGS) as a routine typing tool for public health surveillance of Salmonella, adopting a multilocus sequence typing (MLST) approach as a replacement for traditional serotyping. The WGS derived sequence type (ST) was compared to the phenotypic serotype for 6887 isolates of S. enterica subspecies I, and of these, 6616 (96%) were concordant. Of the 4% (n=271) of isolates of subspecies I exhibiting a mismatch, 119 were due to a process error in the laboratory, 26 were likely caused by the serotype designation in the MLST database being incorrect and 126 occurred when two different serovars belonged to the same ST. The population structure of S. enterica subspecies II-IV differs markedly from that of subspecies I and, based on current data, defining the serovar from the clonal complex may be less appropriate for the classification of this group. Novel sequence types that were not present in the MLST database were identified in 8.6% of the total number of samples tested (including S. enterica subspecies I-IV and S. bongori) and these 654 isolates belonged to 326 novel STs. For S. enterica subspecies I, WGS MLST derived serotyping is a high throughput, accurate, robust, reliable typing method, well suited to routine public health surveillance. The combined output of ST and serovar supports the maintenance of traditional serovar nomenclature while providing additional insight on the true phylogenetic relationship between isolates.
Potential bias in the indirect methods for extracting summary statistics in literature-based meta-analyses: an empirical evaluation
Authors: Abdallah Dima Y
Published: January 2018

Background: In literature-based meta-analyses of cancer prognostic studies, methods for extracting summary statistics from published reports have been extensively employed. However, no assessment of the magnitude of bias produced by these methods or comparison of their influence on fixed vs. random effects models have been published previously. Therefore, the purpose of this study is to empirically assess the degree of bias produced by the methods used for extracting summary statistics and examine potential effects on fixed and random effects models. Methods: Using published data from cancer prognostic studies, systematic differences between reported statistics and those obtained indirectly using log-rank test p-values and total number of events were tested using paired t tests and the log-rank test of survival-agreement plots. The degree of disagreement between estimates was quantified using an information-based disagreement measure, which was also used to examine levels of disagreement between expressions obtained from fixed and random effects models. Results: Thirty-four studies provided a total of 65 estimates of lnHR and its variance. There was a significant difference between the means of the indirect lnHRs and the reported values (mean difference = -0.272, t = -4.652, p-value <0.0001), as well as between the means of the two estimates of variances (mean difference = -0.115, t = -4.5556, p-value <0.0001). Survival agreement plots illustrated a bias towards under-estimation by the indirect method for both lnHR (log-rank p-value = 0.031) and its variance (log-rank p-value = 0.0432). The magnitude of disagreement between estimates of lnHR based on the information-based measure was 0.298 (95% CI: 0.234 – 0.361) and, for the variances it was 0.406 (95% CI: 0.339 – 0.470). As the disagreement between variances was higher than that between lnHR estimates, this increased the level of disagreement between lnHRs weighted by the inverse of their variances in fixed effect models. In addition, results indicated that random effects meta-analyses could be more prone to bias than fixed effects meta-analyses as, in addition to bias in estimates of lnHRs and their variances, levels of disagreement as high as 0.487 (95% CI: 0.416 – 0.552) and 0.568 (95% CI: 0.496 – 0.635) were produced due to between-studies variance calculations. Conclusions: Extracting summary statistics from published studies could introduce bias in literature-based meta-analyses and undermine the validity of the evidence. These findings emphasise the importance of reporting sufficient statistical information in research articles and warrant further research into the influence of potential bias on random effects models.
Computerized methods for collecting confidence ratings: Task influences on patterns of responding
Authors: DeSoto K. Andrew
Published: January 2018

Retrospective confidence ratings and other judgments frequently are collected in computer-based psychology studies, but little research has investigated whether the method with which these ratings are collected influences the resulting data. To explore whether different confidence rating entry methods elicit different responses, 96 subjects were tested in a recognition memory paradigm. To rate confidence in recognition decisions from 0 - 100, half of the subjects used the numeric keypad on the keyboard to respond whereas the other half used an on-screen slider. Notably, whereas subjects using the numeric keypad frequently chose to enter confidence ratings divisible by 5 and 10, subjects using the slider showed no such preference but instead were more likely to accept the slider default value (i.e., 50) for each trial. The method with which confidence ratings are collected may have unintended consequences on confidence rating data and their interpretation.
Ketamine modulates subgenual cingulate connectivity with the memory-related neural circuit – a mechanism of relevance to resistant depression?
Authors: Wong Jing J , O'Daly Owen , Mehta Mitul A , Stone James M
Published: January 2018

Background: Ketamine has been reported to have efficacy as an antidepressant in several studies of treatment-resistant depression. In this study, we investigate whether an acute administration of ketamine leads to reductions in the functional connectivity of subgenual anterior cingulate cortex (sgACC) with other brain regions. Methods: Thirteen right-handed healthy male subjects underwent a 15 minute resting state fMRI with an infusion of intravenous ketamine (target blood level=150ng/ml) starting at 5 minutes. We used a seed region centred on the sgACC and assessed functional connectivity before and during ketamine administration. Results: Before ketamine administration, positive coupling with the sgACC seed region was observed in a large cluster encompassing the anterior cingulate and negative coupling was observed with the anterior cerebellum. Following ketamine administration, sgACC coupling decreased with the brainstem, hippocampus, parahippocampal gyrus, retrosplenial cortex, and thalamus. Discussion: Ketamine reduced functional connectivity of the sgACC with brain regions implicated in emotion, memory and mind wandering. It is possible the therapeutic effects of ketamine may be mediated via this mechanism, although further work is required to test this hypothesis.
A comparison between risk assessments methods: assessing five species of cloud forest rodents in Mexico
Authors: Ramirez Rafael S , Quintero Esther
Published: January 2018

Background. Red Lists have been traditionally used as the instruments to guide conservation strategies to avoid extinctions. There is little objection to the idea that categorizing species according to their risk of extinction is a good way to prioritize and implement conservation actions; however, there is little consensus in the best way to do this categorization, and different countries have developed different methods according to their specific needs. The scope of this paper is to contrast the Mexican Risk of Extinction Assessment Method (MER) and the one used by the IUCN Red List, and test how simple, objective and transparent are them. Methods. In order to compare the we performed a search within IUCN´s data base to find species ranked as critically endangered which have not been assessed by the MER. We picked 5 species from the rodent genus Habromys and performed a literature review to assess them through the MER guidelines; we then compared the outcomes with UICN Red List. Results. The five assessed species of cloud forest rodents yield equivalent results through both the MER and IUCN assessments; however, the information asked for by the MER was scant for all the species, and we argue that the results of the assessments are thus not entirely objectives. Moreover, we found that the MER is not a simple method to use due to ambiguities of the criteria. Discussion. The aim of risk assessments is to clearly define the conservation status of a given species, displayed in a simple, transparent, objective, way, which can be relevant in terms of scope and impact on conservation actions. Unfortunately the MER does not fulfil all these requirements, potentially compromising conservation actions. As a result, we propose that it is time reevaluate the current version of the Mexican Risk of Extinction Assessment Method.
Ground control point requirements for structure-from-motion derived topography in low-slope coastal environments
Authors: Goldstein Evan B , Oliver Amber R , deVries Elsemarie , Moore Laura J , Jass Theo
Published: January 2018

Vegetated coastal dunes grow as a result of feedbacks between vegetation and sand transport. Observing the coevolution of vegetation and the sand surface is therefore critical for unraveling the dynamics of coastal dune growth. Capturing synchronous topography and photography at high spatial resolution and high temporal frequency using traditional techniques (airplane-based aerial photography, LiDAR) is expensive and time-consuming. Structure-from-Motion combined with Multiview-Stereo, a photogrammetry workflow that uses low-cost, consumer-grade equipment, is an economical alternative to traditional collection methods. This workflow still requires the definition of ground control points (GCPs) — locations with known coordinates — to develop accurate digital surface models. In this contribution we address how the number of GCPs used impacts the accuracy of digital surface models. We flew a 9-foot single-line delta kite attached to a consumer-grade camera to photograph the beach and dune of Hog Island, VA, a site that contains 178 high precision GCPs over an area of ~0.025 km2 (as part of an ongoing field experiment). We then processed the 318 photographs using Agisoft Photoscan and compared the elevation accuracy of digital surface models rendered using SfM, with varying GCPs, to points surveyed by a total station. Our results suggest that there is ‘diminishing returns’ when greater than 10 GCPs are used. Results from this study can be used to inform future Structure-from-Motion studies using UAVs or kites in flat, low-sloping coastal environments.
Structure and stability of recombinant bovine odorant-binding protein: I. Design and analysis of monomeric mutants
Authors: Stepanenko Olga V , Roginskii Denis O , Stepanenko Olesya V , Kuznetsova Irina M , Uversky Vladimir N , Turoverov Konstantin K
Published: January 2018

Bovine odorant-binding protein (bOBP) differs from other lipocalins by lacking the conserved disulfide bond and being able to form the domain-swapped dimers. To identify structural features responsible for the formation of the bOBP unique dimeric structure and to understand the role of the domain swapping on maintaining the native structure of the protein, structural properties of the recombinant wild type bOBP and its mutant that cannot dimerize via the domain swapping were analyzed. We also looked at the effect of the disulfide bond by designing a monomeric bOBPs with restored disulfide bond which is conserved in other lipocalins. Finally, to understand which features in the microenvironment of the bOBP tryptophan residues play a role in the defining peculiarities of the intrinsic fluorescence of this protein we designed and investigated single-tryptophan mutants of the monomeric bOBP. Our analysis revealed that the insertion of the glycine after the residue 121 of the bOBP prevents domain swapping and generates a stable monomeric protein bOBP-Gly121+. We also show that the restored disulfide bond in the GCC-bOBP mutant leads to the noticeable stabilization of the monomeric structure. Structural and functional analysis revealed that none of the amino acid substitutions introduced to the bOBP affected functional activity of the protein and that the ligand binding leads to the formation of a more compact and stable state of the recombinant bOBP and its mutant monomeric forms. Finally, analysis of the single-tryptophan mutants of the monomeric bOBP gave us a unique possibility to find peculiarities of the microenvironment of tryptophan residues which were not previously described.
Antibiotic-resistant Neisseria gonorrhoeae spread faster with more treatment, not more sexual partners
Authors: Fingerhuth Stephanie M , Bonhoeffer Sebastian , Low Nicola , Althaus Christian L
Published: January 2018

The sexually transmitted bacterium Neisseria gonorrhoeae has developed resistance to all antibiotic classes that have been used for treatment and strains resistant to multiple antibiotic classes have evolved. In many countries, there is only one antibiotic remaining for empirical N. gonorrhoeae treatment and antibiotic management to counteract resistance spread is urgently needed. Understanding dynamics and drivers of resistance spread can provide rationales for antibiotic management. In our study, we first used antibiotic resistance surveillance data to estimate the rates at which antibiotic-resistant N. gonorrhoeae spread in two host populations, heterosexual men (HetM) and men who have sex with men (MSM). We found higher rates of spread for MSM (0.86 to 2.38 y−1, mean doubling time: 6 months) compared to HetM (0.24 to 0.86 y−1, mean doubling time: 16 months). We then developed a dynamic transmission model to reproduce the observed dynamics of N. gonorrhoeae transmission in populations of heterosexual men and women (HMW) and MSM. We parameterized the model using sexual behavior data and calibrated it to N. gonorrhoeae prevalence and incidence data. In the model, antibiotic-resistant N. gonorrhoeae spread with a median rate of 0.88 y−1 in HMW and 3.12 y−1 in MSM. These rates correspond to median doubling times of 9 (HMW) and 3 (MSM) months. The model shows the difference in the host population’s treatment rate rather than the difference in the number of sexual partners explains the differential spread of resistance. As higher treatment rates result in faster spread of antibiotic resistance, treatment recommendations for N. gonorrhoeae should carefully balance prevention of infection and avoidance of resistance spread.
Cross-platform normalization of microarray and RNA-seq data for machine learning applications
Authors: Thompson Jeffrey A , Tan Jie , Greene Casey S
Published: January 2018

Large, publicly available gene expression datasets are often analyzed with the aid of machine learning algorithms. Although RNA-seq is increasingly the technology of choice, a wealth of expression data already exist in the form of microarray data. If machine learning models built from legacy data can be applied to RNA-seq data, larger, more diverse training datasets can be created and validation can be performed on newly generated data. We developed Training Distribution Matching (TDM), which transforms RNA-seq data for use with models constructed from legacy platforms. We evaluated TDM, as well as quantile normalization and a simple log2 transformation, on both simulated and biological datasets of gene expression. Our evaluation included both supervised and unsupervised machine learning approaches. We found that TDM exhibited consistently strong performance across settings and that quantile normalization also performed well in many circumstances. We also provide a TDM package for the R programming language.