bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel approach reveals that HLA class 1 single antigen bead-signatures provide a means of high-accuracy pre-transplant risk assessment of acute cellular rejection
Authors: Wittenbrink Nicole , Herrmann Sabrina , Blazquez-Navarro Arturo , Gulberti Alessandro , Bauer Chris , Lindberg Eric , Reinke Petra , Sawitzki Birgit , Thomusch Oliver , Hugo Christian , Babel Nina , Seitz Harald , Or-Guil Michal
Published: October 2018

Acute cellular rejection (ACR) is associated with complications after kidney transplantation, such as graft dysfunction and graft loss. Early risk assessment is therefore critical for the improvement of transplantation outcomes. In this work, we retrospectively analyzed a pre-transplant HLA antigen bead assay data set that was acquired by the e:KID consortium as part of a systems medicine approach. The data set included single antigen bead (SAB) reactivity profiles of 52 low-risk graft recipients (negative complement dependent cytotoxicity crossmatch, PRA<30%) who showed detectable pre-transplant anti-HLA 1 antibodies. To assess whether the reactivity profiles provide a means for ACR risk assessment, we established a novel approach which differs from standard approaches in two aspects: the use of quantitative continuous data and the use of a multiparameter classification method. Remarkably, it achieved significant prediction of the 38 graft recipients who experienced ACR with a balanced accuracy of 82.7% (sensitivity=76.5%, specificity= 88.9%). The resultant classifier achieved one of the highest prediction accuracies in the literature for pre-transplant risk assessment of ACR. Importantly, it can facilitate risk assessment in non-sensitized patients who lack donor-specific antibodies. As the classifier is based on continuous data and includes weak signals, our results emphasize that not only strong but also weak binding interactions of antibodies and HLA 1 antigens contain predictive information.
Automatic Human-like Mining and Constructing Reliable Genetic Association Database with Deep Reinforcement Learning
Authors: Wang Haohan , Liu Xiang , Tao Yifeng , Ye Wenting , Jin Qiao , Cohen William W. , Xing Eric P.
Published: October 2018

The increasing amount of scientific literature in biological and biomedical science research has created a challenge in the continuous and reliable curation of the latest knowledge discovered, and automatic biomedical text-mining has been one of the answers to this chal-lenge. In this paper, we aim to further improve the reliability of biomedical text-mining by training the system to directly simulate the human behaviors such as querying the PubMed, selecting articles from queried results, and reading selected articles for knowledge. We take advantage of the efficiency of biomedical text-mining, the flexibility of deep reinforcement learning, and the massive amount of knowledge collected in UMLS into an integrative arti-ficial intelligent reader that can automatically identify the authentic articles and effectively acquire the knowledge conveyed in the articles. We construct a system, whose current pri-mary task is to build the genetic association database between genes and complex traits of the human. Our contributions in this paper are three-fold: 1) We propose to improve the reliability of text-mining by building a system that can directly simulate the behavior of a researcher, and we develop corresponding methods, such as Bi-directional LSTM for text mining and Deep Q-Network for organizing behaviors. 2) We demonstrate the effec-tiveness of our system with an example in constructing a genetic association database. 3) We release our implementation as a generic framework for researchers in the community to conveniently construct other databases.
A hierarchical watershed model of fluid intelligence in childhood and adolescence
Authors: Fuhrmann D. , Simpson-Kent I. L. , Bathelt J. ,   the CALM team, Kievit R. A.
Published: October 2018

Fluid intelligence is the capacity to solve novel problems in the absence of task-specific knowledge, and is highly predictive of outcomes like educational attainment and psychopathology. Here, we modelled the neurocognitive architecture of fluid intelligence in two cohorts: CALM (N= 551, aged 5 - 17 years) and NKI-RS (N= 335, aged 6 - 17 years). We used multivariate Structural Equation Modelling to test a preregistered watershed model of fluid intelligence. This model predicts that white matter contributes to intermediate cognitive phenotypes, like working memory and processing speed, which, in turn, contribute to fluid intelligence. We found that this model performed well for both samples and explained large amounts of variance in fluid intelligence (R2CALM= 51.2%,R2NKI-RS= 78.3%). The relationship between cognitive abilities and white matter differed with age, showing a dip in strength around ages 7 - 12 years. This age-effect may reflect a reorganization of the neurocognitive architecture around pre- and early puberty. Overall, these findings highlight that intelligence is part of a complex hierarchical system of partially independent effects.
Fetal bovine serum-triggered Titan cell formation and growth inhibition are unique to theCryptococcusspecies complex
Authors: Dylag Mariusz , Colon-Reyes Rodney , Kozubowski Lukasz
Published: October 2018

In the genusCryptococcus,C. neoformansandC. gattiistand out by the number of virulence factors that allowed those fungi to achieve evolutionary success as pathogens. Among the factors contributing to cryptococcosis is a peculiar morphological transition to form giant (Titan) cells. Formation of Titans has been describedin vitro. However, it remains unclear whether non-C. neoformans/non-C. gattiispecies are capable of titanisation. Based on a survey of several basidiomycetous yeasts, we propose that titanisation is unique toC. neoformansandC. gattii. In addition, we find that underin vitroconditions that induce titanisation, fetal bovine serum (FBS) possesses activity that inhibits growth ofC. gattiiand killsC. neoformansif incubation is conducted in the absence of 5% CO2. Moreover, lowering of pH or addition of an antioxidant, rescues growth in the presence of FBS and allows titanisation even in the absence of 5% CO2. Strikingly, acapsular mutants,cap10Δ andcap59Δ, show complete or partial reduction of titanisation, respectively and a partial resistance to growth inhibition imposed by the FBS. Our data implicate titanisation as a unique feature ofC. neoformansandC. gattiiand provide novel insights about the nature of this unusual morphological transition.
Study on the Difference of Prokaryotic Flora Structure on the Surface of Micro-nano Coating with Different Antifouling Property
Authors: Gu Qingze , Zhang Aihan , Yan Zhengyu , Guo Changlu , Zhang Zhizhou
Published: October 2018

Low surface energy composite antifouling coatings prepared from carbon nanotubes (CNTs) and polydimethylsiloxane (PDMS) have good values for investigation of biofouling-related biological questions on marine biofilm. In order to deeply study the mechanism of antifouling on the surface of CNTs-PDMS coatings, it is necessary to investigate the structure of the microbial flora in the early biofilm on the coating surface. In the present study, the specific aim of this study was to investigate the structure differences of prokaryotic flora in biofilm samples at the early stage of biofouling through 16S rDNA based high-throughput DNA sequencing. By annotating high-throughput DNA sequencing results, this study identified dominant prokaryotic phyla and genera in biofilms of CNTs-PDMS coatings and identified significant differences in microbial composition and its dynamics among different coatings. Though the analysis of the Shannon index, Simpson index, Chao1 index and ACE index, coatings with better antifouling properties and antifouling properties have significant differences in community diversity and abundance, indicating different antifouling properties can affect the type and content of biofilm communities. According to the canonical correspondence analysis (CCA), time and temperature are more related to microbial community distribution, while the diameter and length of nanomaterials are less correlated. Through this study, the differences in microbial composition and content of prokaryotic communities, differences in diversity and abundance of sample communities, the differences between multiple samples and the correlation with important environmental factors were preliminarily analyzed, which laid a decent foundation for further research on the mechanism of anti-fouling on the surface of CNTs and PDMS coatings.
The dynamics of spawning acts by a semelparous fish and its associated energetic costs
Authors: Tentelier Cédric , Bouchard Colin , Bernardin Anaïs , Tauzin Amandine , Aymes Jean-Christophe , Lange Frédéric , Recapet Charlotte , Rives Jacques
Published: October 2018

Abstract

During the reproductive season, animals have to manage both their energetic budget and gamete stock. In particular, for semelparous capital breeders with determinate fecundity and no parental care other than gametic investment, the depletion of energetic stock must match the depletion of gametic stock, so that individuals get exhausted just after their last egg is laid and fertilized. Although these budgets are managed continuously, monitoring the dynamics of mating acts and energy expenditure at a fine temporal scale in the wild is challenging.

This study aimed to quantify the individual dynamics of spawning acts and the concomitant energy expenditure of female Allis shad (Alosa alosa) throughout their mating season.

Using eight individual-borne accelerometers for one month, we collected tri-axial acceleration, temperature, and pressure data that we analysed to i) detect the timing of spawning acts, ii) estimate energy expenditure from tail beat frequency and water temperature, and iii) monitor changes in body roundness from the position of the dorsally-mounted tag relative to the vertical plane.

Female shad had a higher probability to spawn during warmer nights, and their spawning acts were synchronized (both individually and inter-individually) within each active night. They experienced warmer temperature, remained deeper, swan more slowly and spent less energy during daytime than night time. Over one month of spawning, they performed on average 15.75 spawning acts, spent on average 6 277 kJ and died with a significant portion of residual oocytes. The acceleration-based indicator of body roundness was correlated to condition coefficient measured at capture, and globally decreased through the spawning season, although the indicator was noisy and was not correlated to changes in estimated energy expenditure.

Despite significant individual variability, our results indicate that female shad exhausted their energetic stock faster than their egg stock. Water warming will increase the rate of energy expenditure, which might increase the risk that shad die with a large stock of unspent eggs. Although perfectible, the three complementary analyses of acceleration data are promising for in situ monitoring of energy expenditure related to specific behaviour.
Conditional approach as cooperation in predator inspection: a role for serotonin?
Authors: Nogueira Pimentel Ana Flávia , dos Santos Carvalho Tamires , Lima Fernando , Lima-Maximino Monica , Soares Marta Candeias , Maximino Caio
Published: October 2018

In guppies (Poecilia reticulata), a small number of individuals break away from a shoal and approach a potential predator, a behavior termed “predator inspection”. These animals often employ a “conditional approach” strategy, in which an individual approaches the predator in the first move and subsequently approaches it only if a second individual swims even with it during inspection. This strategy is analogous to the “tit-for-tat” strategy of the Prisoner’s Dilemma, suggesting that it could be used to study cooperation. Serotonin is thought to mediate cooperative behavior in other fish species. Exposure to the animated image of a predator in a tank that contained a parallel mirror – mimicking an equally cooperating conspecific – promoted inspection and decreased refuge use, but increased freezing, suggesting that conditional approach is also associated with fear. To understand whether serotonin participates in conditional approach in guppies, we treated animals with either vehicle (Cortland’s salt solution), fluoxetine (2.5 mg/kg) or metergoline (1 mg/kg), and tested then in a predator inspection paradigm. Fluoxetine increased the time the animal spent inspecting the predator image, while metergoline decreased it. Fluoxetine also decreased time spent avoiding the predator and increased freezing, while metergoline decreased freezing. These results suggest that phasic increases in serotonin levels promote conditional approach, suggesting a role for this neurotransmitter in cooperation.

Preprint: https://doi.org/10.1101/436345; Data and scripts: https://github.com/lanec-unifesspa/TFT
A complex symbiosis involving within species variation in the response ofDictyosteliumamoebae toBurkholderiabacteria
Authors: Shu Longfei , Brock Debra A. , Geista Katherine S. , Miller Jacob W. , Queller David C. , Strassmann Joan E. , DiSalvo Susanne
Published: October 2018

Recent symbioses, particularly facultative ones, are well suited for unravelling the evolutionary give and take between partners. Here we look at variation in wild-collected samples of the social amoebaDictyostelium discoideumand their relationships with bacterial symbionts,Burkholderia hayleyellaandBurkholderia agricolaris. Only about a third of field-collected amoebae carry a symbiont. We cured and cross-infectedD. discoideumhosts with different symbiont association histories and then compared the responses of the amoebae to each symbiont type. Before curing, field-collected clones did not vary significantly in overall fitness, but infected hosts produced morphologically different multicellular structures. After curing and re-infecting, host fitness declined overall. However, naturalB. hayleyellahosts suffered fewer fitness costs when re-infected withB. hayleyella,indicating that they have evolved mechanisms to tolerate their naturally acquired symbiont. Exploring relationships between endosymbionts and hosts that vary within species may also reveal much about disease dynamics.
Measuring the Importance of Vertices in the Weighted Human Disease Network
Authors: Almasi Seyed Mehrzad , Hu Ting
Published: October 2018

Many human genetic disorders and diseases are known to be related to each other through frequently observed co-occurrences. Studying the correlations among multiple diseases provides an important avenue to better understand the common genetic background of diseases and to help develop new drugs that can treat multiple diseases. Meanwhile, network science has seen increasing applications on modeling complex biological systems, and can be a powerful tool to elucidate the correlations of multiple human diseases. In this article, known disease-gene associations were represented using a weighted bipartite network. We extracted a weighted human diseases network from such a bipartite network to show the correlations of diseases. Subsequently, we proposed a new centrality measurement for the weighted human disease network in order to quantify the importance of diseases. Using our centrality measurement to quantify the importance of vertices in the weighted human disease network, we were able to find a set of most central diseases. By investigating the 30 top diseases and their most correlated neighbors in the network, we identified disease linkages including known disease pairs and novel findings. Our research helps better understand the common genetic origin of human diseases and suggests top diseases that likely induce other related diseases.
Diffusion Acceleration with Gaussian process Estimated Reconstruction (DAGER)
Authors: Wu Wenchuan , Koopmans Peter J , Andersson Jesper , Miller Karla L
Published: October 2018

Purpose

Image acceleration provides multiple benefits to diffusion MRI (dMRI), with in-plane acceleration reducing distortion and slice-wise acceleration increasing the number of directions that can be acquired in a given scan time. However, as acceleration factors increase, the reconstruction problem becomes ill-conditioned, particularly when using both in-plane acceleration and simultaneous multi-slice (SMS) imaging. In this work, we develop a novel reconstruction method for in-vivo MRI acquisition that provides acceleration beyond what conventional techniques can achieve.

Theory and Methods

We propose to constrain the reconstruction in the spatial (k) domain by incorporating information from the angular (q) domain. This approach exploits smoothness of the signal in q-space using Gaussian processes, as has previously been exploited in post-reconstruction analysis. We demonstrate in-plane acceleration exceeding the theoretical parallel imaging limits, and SMS combined with in-plane acceleration at a total factor of 12. This reconstruction is cast within a Bayesian framework that incorporates estimation of smoothness hyper-parameters, with no need for manual tuning.

Results

Simulations and in vivo results demonstrate superior performance of the proposed method compared with conventional parallel imaging methods. These improvements are achieved without loss of spatial or angular resolution and require only a minor modification to standard pulse sequences.

Conclusion

The proposed method provides improvements over existing methods for diffusion acceleration, particularly for high SMS acceleration with in-plane undersampling.
The SIRAH force field 2.0: Altius, Fortius, Citius
Authors: Machado Matías R. , Barrera Exequiel E. , Klein Florencia , Sóñora Martín , Silva Steffano , Pantano Sergio
Published: October 2018

A new version of the coarse-grained (CG) SIRAH force field for proteins has been developed. Modifications to bonded and non-bonded interactions on the existing molecular topologies significantly ameliorate the structural description and flexibility of a non-redundant set of proteins. The SIRAH 2.0 force field has also been ported to the popular simulation package AMBER, which along with the former implementation in GROMACS expands significantly the potential range of users and performance of this CG force field on CPU/GPU codes.

As a non-trivial example of application, we undertook the structural and dynamical analysis of the most abundant and conserved calcium-binding protein, namely, Calmodulin (CaM). CaM is constituted by two calcium-binding motifs called EF-hands, which in presence of Calcium specifically recognize a cognate peptide by embracing it. CG simulations of CaM bound to four Calcium ions in the presence or absence of a binding peptide (holo and apo forms, respectively), resulted in good and stable ion coordination. The simulation of the holo form starting from an experimental structure sampled near-native conformations, retrieving quasi-atomistic precision. Removing the binding peptide enabled the EF-hands to perform large reciprocal movements, comparable to those observed in NMR structures. On the other hand, the isolated peptide starting from the helical conformation experienced spontaneous unfolding, in agreement with previous experimental data. However, repositioning the peptide in the neighborhood of one EF-hand not only prevented the peptide unfolding but also drove CaM to a fully bound conformation with both EF-hands embracing the cognate peptide, resembling the experimental holo structure.

Therefore, SIRAH 2.0 showed the capacity to handle a number of structurally and dynamically challenging situations including metal ion coordination, unbiased conformational sampling, and specific protein-peptide recognition.

TOC.
Down syndrome fibroblasts exhibit diminished autophagic clearance and endosomal dysfunction after serum starvation
Authors: Aivazidis Stefanos , Jain Abhilasha , Anderson Colin C. , Orlicky David J. , Rauniyar Abhishek K. , Fritz Kristofer S. , Harris Peter S. , Siegel David , Maclean Kenneth N. , Roede James R.
Published: October 2018

Down syndrome (DS) is a genetic disorder caused by trisomy of chromosome 21 (Tri21). This unbalanced karyotype has the ability to produce proteotoxic stress and dysfunction of the proteostasis network (PN), which are mechanistically associated with several comorbidities found in the DS phenotype. Autophagy is the cellular process responsible for bulk protein degradation and its impairment could negatively impact protein quality control. Based on our previous observations of PN disruption in DS, we investigated possible dysfunction of the autophagic machinery in human DS fibroblasts. Both euploid (CTL) and DS fibroblasts induced autophagy successfully through serum starvation (SS), as evidenced by increased LC3-II abundance in CTL and DS. However, DS cells displayed evidence of autophagolysosome (AL) accumulation and impaired clearance of autophagosome cargo, e.g. accumulation of p62 and NBR1. Similar observations were also present in DS cells from multiple differentiation stages, implicating impeded autophagic degradation as a possible early pathologic mechanism in DS. Lysosomal pH and cathepsin B proteolytic activity were found to not differ in CTL and DS fibroblasts after SS, indicating that lysosomal dysfunction did not appear to contribute to unsuccessful autophagic clearance. Based on these results, we hypothesized that possible interference of the endosomal system with autophagy results in autophagosome fusion with endosomal vesicles and negatively impacts degradation. Consistent with this hypothesis, we observed increased abundance of the recycling endosome marker, Rab11, after SS in DS fibroblasts. Further, colocalization of autophagosome markers with resident proteins of early endosomes, late endosomes and recycling endosomes (Rab11) further support our hypothesis. In summary, our work is consistent with impairment of autophagic flux and general PN dysfunction as candidate mechanisms for pathology in DS.
Evolved phenological cueing strategies show variable responses to climate change
Authors: Edwards Collin B. , Yang Louie
Published: October 2018

Several studies have documented a global pattern of phenological advancement that is consistent with ongoing climate change. However, the magnitude of these phenological shifts is highly variable across taxa and locations. This variability of phenological responses has been difficult to explain mechanistically. To examine how the evolution of multi-trait cueing strategies could produce variable responses to climate change, we constructed a model in which organisms evolve strategies that integrate multiple environmental cues to inform anticipatory phenological decisions. We simulated the evolution of phenological cueing strategies in multiple environments, using historic climate data from 78 locations in North America and Hawaii to capture features of climatic correlation structures in the real world. Organisms in our model evolved diverse strategies that were spatially autocorrelated across locations on a continental scale, showing that similar strategies tend to evolve in similar climates. Within locations, organisms often evolved a wide range of strategies that showed similar response phenotypes and fitness outcomes under historical conditions. However, these strategies responded differently to novel climatic conditions, with variable fitness consequences. Our model shows how the evolution of phenological cueing strategies can explain observed variation in phenological shifts and unexpected responses to climate change.
WITER: A powerful method for the estimation of cancer-driver genes using a weighted iterative regression accurately modelling background mutation rate
Authors: Jiang Lin , Zheng Jingjing , Him Kwan Johnny Sheung , Dai Sheng , Li Cong , Li Mulin Jun , Yu Bolan , TO Ka Fai , Sham Pak Chung , Zhu Yonghong , Li Miaoxin
Published: October 2018

Genomic identification of driver mutations and genes in cancer cells are critical for precision medicine. Due to difficulty in modeling distribution of background mutations, existing statistical methods are often underpowered to discriminate driver genes from passenger genes. Here we propose a novel statistical approach, weighted iterative zero-truncated negative-binomial regression (WITER), to detect cancer-driver genes showing an excess of somatic mutations. By solving the problem of inaccurately modeling background mutations, this approach works even in small or moderate samples. Compared to alternative methods, it detected more significant and cancer-consensus genes in all tested cancers. Applying this approach, we estimated 178 driver genes in 26 different cancers types. In silico validation confirmed 90.5% of predicted genes as likely known drivers and 7 genes unique for individual cancers as likely new drivers. The technical advances of WITER enable the detection of driver genes in TCGA datasets as small as 30 subjects, rescuing more genes missed by alternative tools.
Integrative Network and Brain Expression Analysis reveals Mechanistic Modules in Ataxia
Authors: Eidhof Ilse , Warrenburg Bart P van de , Schenck Annette
Published: October 2018

Background

Genetic forms of ataxia are a heterogenous group of degenerative diseases of the cerebellum. Many causative genes have been identified, but a systematic investigation of these genes to understand ataxia pathophysiology has not been performed.

Methods

A manually curated catalogue of 71 genes involved in disorders with progressive ataxias as a major clinical feature was subjected to an integrated gene ontology (GO), protein network, and brain gene expression profiling analysis.

Results

We found that ataxia genes operate in networks with significantly enriched protein connectivity, demonstrating coherence on a global level, independent of inheritance mode. Moreover, elevated expression specifically in the cerebellum predisposes to ataxia. Genes expressed in this pattern are significantly overrepresented among ataxia genes and are enriched for ion homeostasis/synaptic functions. The majority of ataxia genes, however, does not show elevated cerebellar expression that could account for region-specific degeneration. For these, we identified defective cellular stress responses as a major common biological theme, suggesting that the defense pathways against stress are more critical to maintain cerebellar integrity than integrity of other brain regions. Approximately half of the ataxia genes, mostly part of the stress module, show higher expression at embryonic stages, which argues for a developmental predisposition.

Conclusion

Genetic defects in ataxia predominantly affect neuronal homeostasis, to which the cerebellum appears to be excessively susceptible. Based on the identified modules, it is conceivable to propose common therapeutic interventions that target deregulated calcium and ROS levels, or mechanisms that can decrease the harmful downstream effects of these deleterious insults.
Optimised DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol
Authors: Cruaud Astrid , Nidelet Sabine , Arnal Pierre , Weber Audrey , Fusu Lucian , Gumovsky Alex , Huber John , Polaszek Andrew , Rasplus Jean-Yves
Published: October 2018

Enriching subsets of the genome prior to sequencing allows focusing effort on regions that are relevant to answer specific questions. As experimental design can be adapted to sequence many samples simultaneously, using such approach also contributes to reduce cost. In the field of ecology and evolution, target enrichment is increasingly used for genotyping of plant and animal species or to better understand the evolutionary history of important lineages through the inference of statistically robust phylogenies. Limitations to routine target enrichment by research laboratories are both the complexity of current protocols and low input DNA quantity. Thus, working with tiny organisms such as micro-arthropods can be challenging. Here, we propose easy to set up optimisations for DNA extraction and library preparation prior to target enrichment. Prepared libraries were used to capture 1432 Ultra-Conserved Elements (UCEs) from microhymenoptera (Chalcidoidea), which are among the tiniest insects on Earth and the most commercialized worldwide for biological control purposes. Results show no correlation between input DNA quantities (1.8-250ng, 0.4 ng with an extra whole genome amplification step) and the number of sequenced UCEs. Phylogenetic inferences highlight the potential of UCEs to solve relationships within the families of chalcid wasps, which has not been achieved so far. The protocol (library preparation + target enrichment), allows processing 96 specimens in five working days, by a single person, without requiring the use of expensive robotic molecular biology platforms, which could help to generalize the use of target enrichment for minute specimens.
Cerebral blood flow measured with diffusing wave spectroscopy during anesthesia
Authors: Belau Markus , Scheffer Wolfgang , Maret Georg
Published: October 2018

The adequate perfusion of the brain is of utmost importance where already short periods of hypoperfusion may lead to permanent damage. In order to increase patient safety the cerebral blood flow should be monitored in clinical settings during situations, such as anesthesia, where the perfusion might be disturbed. The cerebral blood flow is however not monitored on a routine basis during anesthesia. Diffusing wave spectroscopy is a relative novel optical method that non-invasively measures changes in cerebral blood flow. Here we report changes in cerebral blood flow associated with a delayed cardiac output, a change in isoflurane concentration and body temperature observed during general anesthesia with isoflurane in pigeons.
Robust Algorithms for Capturing Population Dynamics and Transport in Oceanic Variables along Drifter Trajectories using Linear Dynamical Systems with Latent Variables
Authors: Yan Yan , Jebara Tony , Abernathey Ryan , Goes Joaquim , Gomes Helga
Published: October 2018

The blooms ofNoctilucain the Gulf of Oman and the Arabian Sea have been intensifying in recent years posing a threat to regional fisheries and the long-term health of an ecosystem supporting a coastal population of nearly 120 million people. We present the results of a microscopic data analysis to investigate the onset and patterns of theNoctiluca(mixotrophic dinoflagellateNoctiluca scintillans) blooms, which form annually during the winter monsoon in the Gulf of Oman and in the Arabian Sea. Our approach combines methods in physical and biological oceanography with machine learning techniques. In particular, we present a robust algorithm, the variable-length Linear Dynamic Systems (vLDS) model, that extracts the causal factors and latent dynamics at the microscopic population-level along each individual drifter trajectory, and demonstrate its effectiveness by using it to test and confirm previously benchmarked macroscopic scientific hypotheses. The test results provide microscopic statistical evidence to support and recheck the macroscopic physical and biological Oceanography hypotheses on theNoctilucablooms; it also helps identify complementary microscopic dynamics that might not be visible or discoverable at the macroscopic scale. The vLDS model also exhibits a generalization capability (inherited from a machine learning methodology) to investigate important causal factors and hidden dynamics associated with ocean biogeochemical processes and phenomena at the population-level.
Topological Scoring of Protein Interaction Networks
Authors: Sardiu Mihaela E. , Gilmore Joshua M. , Groppe Brad D. , Dutta Arnob , Florens Laurence , Washburn Michael P.
Published: October 2018

It remains a significant challenge to define individual protein associations within networks where an individual protein can directly interact with other proteins and/or be part of large complexes, which contain functional modules. Here we demonstrate the topological scoring (TopS) algorithm for the analysis of quantitative proteomic analyses of affinity purifications. Data is analyzed in a parallel fashion where a bait protein is scored in an individual affinity purification by aggregating information from the entire dataset. A broad range of scores is obtained which indicate the enrichment of an individual protein in every bait protein analyzed. TopS was applied to interaction networks derived from human DNA repair proteins and yeast chromatin remodeling complexes. TopS captured direct protein interactions and modules within complexes. TopS is a rapid method for the efficient and informative computational analysis of datasets, is complementary to existing analysis pipelines, and provides new insights into protein interaction networks.
Unwarping GISAXS data
Authors: Liu Jiliang , Yager Kevin G.
Published: October 2018

Grazing-incidence small-angle X-ray scattering (GISAXS) is a powerful technique for measuring the nanostructure of coatings and thin films. However, GISAXS data are plagued by distortions that complicate data analysis. The detector image is a warped representation of reciprocal space because of refraction, and overlapping scattering patterns appear because of reflection. A method is presented to unwarp GISAXS data, recovering an estimate of the true undistorted scattering pattern. The method consists of first generating a guess for the structure of the reciprocal-space scattering by solving for a mutually consistent prediction from the transmission and reflection sub-components. This initial guess is then iteratively refined by fitting experimental GISAXS images at multiple incident angles, using the distorted-wave Born approximation (DWBA) to convert between reciprocal space and detector space. This method converges to a high-quality reconstruction for the undistorted scattering, as validated by comparing with grazing-transmission scattering data. This new method for unwarping GISAXS images will broaden the applicability of grazing-incidence techniques, allowing experimenters to inspect undistorted visualizations of their data and allowing a broader range of analysis methods to be applied to GI data.
Nonlinear time-optimal trajectory planning for varying-rope-length overhead cranes
Authors: Wu Yiming , Sun Ning , Chen He , Zhang Jianyi , Fang Yongchun
Published: October 2018

Purpose

From practical perspectives and to improve the working efficiency, trolley transportation and payload hoisting/lowering should be simultaneously controlled. Moreover, in practical crane applications, the transportation time is an important criterion for improving transportation efficiency. Based on these requirements, this paper aims to solve positioning and antiswing control problems and shorten the transportation time for underactuated varying-rope-length overhead cranes.

Design/methodology/approach

By choosing trolley acceleration and varying-rope-length acceleration as system inputs, the crane system dynamic model is converted into an equivalent model without linearizing/approximating. Then, based on the converted model and system state constraints, a time-optimal problem is formulated. Further, the original problem is converted into an optimization problem with algebraic constraints which can be conveniently solved. Finally, by solving the optimization problem, the optimal trajectories of system states, including displacements, velocities and accelerations, are obtained.

Findings

This paper first provides a nonlinear time-optimal trajectory planner for varying-rope-length overhead cranes, which achieves accurate and fast trolley positioning and eliminates payload residual swings. Meanwhile, all system states satisfy the given constraints during the entire process. Hardware experimental results show that the proposed time-optimal planner is effective and has better performance compared with existing methods.

Originality/value

This paper proposes a time-optimal trajectory planner for overhead crane systems with hoisting/lowering motion. The proposed planner achieves fast trolley positioning and eliminates payload residual swing with all the system states being constrained within given scopes. The planner is presented based on the original nonlinear system dynamics without linearization/approximation.
Flight path optimization with application to in-flight replanning to changing destinations
Authors: Babel Luitpold
Published: October 2018

Purpose

The purpose of this paper is to present a new approach for finding a minimum-length trajectory for an autonomous unmanned air vehicle or a long-range missile from a release point with specified release conditions to a destination with specified approach conditions. The trajectory has to avoid obstacles and no-fly zones and must take into account the kinematic constraints of the air vehicle.

Design/methodology/approach

A discrete routing model is proposed that represents the airspace by a sophisticated network. The problem is then solved by applying standard shortest-path algorithms.

Findings

In contrast to the most widely used grids, the generated networks allow arbitrary flight directions and turn angles, as well as maneuvers of different strengths, thus fully exploiting the flight capabilities of the aircraft. Moreover, the networks are resolution-independent and provide high flexibility by the option to adapt density.

Practical implications

As an application, a concept for in-flight replanning of flight paths to changing destinations is proposed. All computationally intensive tasks are performed in a pre-flight planning prior to the launch of the mission. The in-flight planning is based entirely on precalculated data, which are stored in the onboard computer of the air vehicle. In particular, no path finding algorithms with high or unpredictable running time and uncertain outcome have to be applied during flight.

Originality/value

The paper presents a new network-based algorithm for flight path optimization that overcomes weaknesses of grid-based approaches and allows high-quality solutions. The method can be applied for quick in-flight replanning of flight paths.
Paradigms in business process management specifications: a critical overview
Authors: Chountalas Panos T. , Lagodimos Athanasios G.
Published: October 2018

Purpose

Despite its popularity, business process management (BPM) is not unequivocally defined, but obtains different forms with varying specifications. This paper presents a critical overview of BPM, as it appears within four dominant management paradigms: total quality management, standardized management systems, business process reengineering and Six Sigma. The purpose of this paper is to explore BPM specifications and compare the BPM implementation potential under each paradigm.

Design/methodology/approach

This is based on the analysis of a large number of highly cited scholarly publications. In order to identify the nature of BPM within each paradigm, a common framework for comparison is first established and then, for each paradigm, BPM is analyzed according to the main parameters of this framework.

Findings

Many differences among various BPM forms are paradigm driven. So, the approach adopted by each paradigm (i.e. individual-process or systemic approach) affects the scope and role of BPM. The principles of each paradigm directly affect the attributes assigned to BPM. Despite of important differences, the structure of BPM within all paradigms conforms to the stages of the classical BPM lifecycle. However, each paradigm assigns different weights to each stage and also displays different levels of BPM implementability.

Originality/value

The paper presents a first systematic comparison of BPM specifications for the dominant management paradigms primarily deployed. It thus explains why many attributes originating from the paradigms have crept into the general BPM specifications. This work can be considered as a step toward defining the core attributes of a paradigm-independent BPM model, thus enhancing its application scope as an invaluable management tool.
Manufacturing strategy, organizational slack, and the formation of interfirm linkages
Authors: Lu Lin-Hua , Huang Yi-Fen
Published: October 2018

Purpose

This study aims to examine what types of interfirm linkages a firm enters in relation to its manufacturing strategy. The authors further aim to determine whether heterogeneous resources have different moderating effects on the relationship between a firm’s manufacturing strategy and interfirm linkages.

Design/methodology/approach

The sample consists of survey and archival data on 80 publicly listed electronics firms from the semiconductor and optoelectronics industries in Taiwan. Because the dependent variable, interfirm linkage, is a binary term, the authors apply logistic regression in our study.

Findings

This paper provides empirical insight into how a firm’s manufacturing strategy affects its probability to engage in specific types of interfirm linkages. The authors find that when a firm pursues an efficiency (flexibility) strategy, it will tend to engage in marketing (technical) interfirm linkages. In addition, absorbed slack strengthens the fit between manufacturing strategy and interfirm linkage type more than unabsorbed slack does.

Research limitations/implications

Because the sample is drawn from the Taiwanese semiconductor and optoelectronic industries, the authors encourage scholars to examine the generalizability of the findings. Future studies can furthermore adopt in-depth interviews to facilitate a better understanding of decision-makers’ considerations when entering interfirm linkages.

Originality/value

This study extends resource dependence theory across a firm’s boundary and applies the resource-based view to resource heterogeneity. The findings advance the understanding of the relationships between strategic orientation, slack resources and interfirm linkage choices. The authors show that it is important that firms consider strategic fit when they create linkages outside their existing boundaries.
Adept smart meters using homomorphic encryption based on factor problem over groups
Authors: Valisireddy Jalaja , G.S.G.N Anjaneyulu
Published: October 2018

Purpose

The purpose of this paper is to replace electronic meters with smart meters. Smart meters will provide high resolution real-time end-user power consumption data for utilities to better monitor and control the system, which is used for end users to better manage their energy usage and bills. By using smart meters, we can reduce the errors and also minimize human intervention in processing information in an efficient way. So that time will be reduced for organization functionalities and accuracy will be increase.

Design/methodology/approach

The authors propose a new cryptosystem based on factor problem over non commutative groups. They tried to use this cryptosystem in the field of electricity. They extend and transform this projected cryptosystem to design expert smart meters based on homomorphic encryption with factor problem.

Findings

In these smart meters, a monitoring system is integrated that preserves customer’s privacy by homomorphically accumulating the consumption of all n members of a specific domain.

Originality/value

This expert smart meter system has a proficient linear O(n) communication cost and is proven to protect customer's privacy even in the presence of a corrupted substation and some malicious smart meters.
Preparation and tribological properties of Ag nanoparticles/reduced graphene oxide nanocomposites
Authors: Xu Leihua , Zhang Yong , Zhang Dekun , Leng Mei
Published: October 2018

Purpose

This paper aims to report the tribological behavior of Ag nanoparticles/reduced graphene oxide nanocomposites (Ag/RGO NCs) and Ag nanoparticles (Ag NPs) as a green additive in oil with different concentration and under different friction conditions.

Design/methodology/approach

The Ag/RGO NCs and Ag NPs were both synthesized in a chemical reduction method. The diameter of silver nanoparticles implanted between RGO sheets was about 25 nm and that of silver sol was 70 nm. The morphology and structure of Ag/RGO NC were characterized by TEM, XRD and FTIR. The tribological properties of Ag/RGO NCs and Ag NPs as lubricant oil additive were evaluated by measuring the friction coefficients and wear of the surface in different condition which were tested on UMT-II.

Findings

The results indicated that both the additives improved the friction-reduced and anti-wear properties of paraffin oil, and Ag/RGO NCs has better tribological performance than Ag NPs. The excellent tribological properties were attributed to the special structure of Ag/RGO NC and the formation of tribofilm reducing the friction and wear on the shearing surfaces.

Research limitations/implications

It is relatively difficult to observe the morphology of the lubricant film formed on the friction surface and to analyze the chemical composition at different depths of the lubricant film.

Originality/value

It is the first time for Ag/RGO NCs to be applied to improve the friction-reduced and anti-wear properties of lubricant oil as additive.
Empirical studies of collaborative information seeking: a review of methodological issues
Authors: Hertzum Morten , Hansen Preben
Published: October 2018

Purpose

Information seeking is often performed in collaborative contexts. The research into such collaborative information seeking (CIS) has been proceeding since the 1990s but lacks methodological discussions. The purpose of this paper is to analyze and discuss methodological issues in existing CIS studies.

Design/methodology/approach

The authors systematically review 69 empirical CIS studies.

Findings

The review shows that the most common methods of data collection are lab experiments (43 percent), observation (19 percent) and surveys (16 percent), that the most common methods of data analysis are description (33 percent), statistical testing (29 percent) and content analysis (19 percent) and that CIS studies involve a fairly even mix of novice, intermediate and specialist participants. However, the authors also find that CIS research is dominated by exploratory studies, leaves it largely unexplored in what ways the findings of a study may be specific to the particular study setting, appears to assign primacy to precision at the expense of generalizability, struggles with investigating how CIS activities extend over time and provides data about behavior to a larger extent than about reasons, experiences and especially outcomes.

Research limitations/implications

The major implication of this review is its identification of the need for a shared model to which individual CIS studies can contribute in a cumulative manner. To support the development of such a model, the authors discuss a model of the core CIS process and a model of the factors that trigger CIS.

Originality/value

This study assesses the current state of CIS research, provides guidance for future CIS studies and aims to inspire further methodological discussion.