bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flask culture system: Part 2
Authors: Ng Wenfa
Published: January 2018

The characteristics of the culture vessel determine, to a large extent, the type of growth medium suitable for use. For example, most growth media for high cell density cultivation are designed for expensive bioreactors operating either in continuous or fed-batch mode, where provision of additional nutrients and/or removal of metabolic waste products from the basal medium – comprising salts, buffer components and small amount of carbon and nitrogen sources - help increase biomass yield by maintaining culture conditions within the range conducive for growth. The inexpensive and ubiquitous shake flask, in contrast, is usually operated in batch mode and contains, at the outset, a comprehensive medium with all necessary nutrients for conversion into biomass and, also serves as a repository for secreted metabolites - some of which are detrimental for cell growth. Thus, designing medium for high cell density cultivation in shake-flask is an optimization process aiming to increase biomass formation while reducing toxic metabolite secretion. This preprint reports improvements to a previously reported semi-defined medium (Wenfa Ng, 2013, https://peerj.com/preprints/115v1) for high cell density aerobic cultivation of Escherichia coli DH5α (ATCC 53868) in shake flask. Specifically, by reducing the concentrations of glucose (from 6.0 to 4.0 g/L) and ammonium chloride (from 1.5 to 1.0 g/L), the following improvements were obtained: a shorter diauxic lag phase (3 versus 5 hours); a higher maximal optical density (12.0 versus 11.0) in a shorter total culture period (27 versus 48 hours), and smaller pH variation during cultivation (6.0 to 7.6 versus 5.5 to 7.8). Similar to the earlier study, glucose and yeast extract served as principal carbon sources in separate growth phases for E. coli in the improved formulated medium (FMimproved). Specifically, an OD600nm of 6.6 was attained after 9 hours of growth on glucose at 37 oC. Following a lag phase of 3 hours, growth resumed on yeast extract and the OD600nm reached 12.0 after 27 hours. The broth’s pH decreased from 7.1 to 6.0 during the first growth phase, whereupon it gradually rose to 7.6 at the end of culture. A smaller pH decrease along with higher biomass yield in the first growth phase suggested that the lower glucose concentration in FMimproved might have prevented overflow metabolism - and associated negative effects on growth - thus, resulting in a shorter diauxic lag phase and total culture period. Collectively, increase in cell yield, as well as decrease in total culture time and a shorter diauxic lag phase arise from a small reduction in glucose concentration - which suggested that an optimum exist, beyond which, occurrence of overflow metabolism would reduce cell yield and biomass formation.
Less is more stable: arguing for few names in turtle’s taxonomy
Authors: Romano Pedro S. R.
Published: January 2018

Background. Beyond the International Codes of Zoological (ICZN) and Botanical Nomenclature and the PhyloCode, there is an alternative taxonomic system for phylogenetic systematics proposed. This phylogenetic nomenclature suggests the elimination of suprageneric names and the use of negative indexes instead of it. This system of nomenclature has a basic principle to identify clades: the presence of nominal heterobathmy, which is analogous to Hennig's "heterobathmy of characters", but applied to taxa names. Here I argue for an extensive use of heterobathmy as basic criteria to determinate “good” nodes to identify higher level taxa names. Methods. I used a previews published dataset (doi:10.5061/dryad.f2h6r) and ran several searches for Most Parsimonious Trees (MPT) using different search algorithms and assumptions in TNT. After that, I compared the results of different searches, mapped the characters transformations, and calculate the Bremer supports. The results were then compared with the current taxonomy proposed for Pelomedusoides, with emphasis on Bothremydidae. Results. The remarkable divergences with the current taxonomy of Bothremydidae are: (1) Kurmademydini and Bothremydini need to be redefined; (2) Cearachelyini and Galianemys lack diagnostic characters and, therefore, are not monophyletic; and (3) Bothremydidae do not possess common diagnostic characters in all MPT, thus, lacks a well supported heterobathmy with its sister-group, Podocnemidinura (=Pan-Podocnemididae). Moreover, the Infrafamily Bothremydodda has Bremer support of 3. However, given that all bothremydids are extinct, it is impossible to define a panstem clade based on a crown group. The result is an unstable nomenclature with more names than necessary. Discussion. The use of heterobathmy is a center point in Hennig's argumentation for phylogenetic reconstruction. Indeed, it implies the zero length collapsing rule applied to cladistic reconstruction (which is the TNT default option). Nonetheless, ambiguous characters or several equal MPT can imply on phylogenetic reconstructions that lack a consistent heterobathmy (i.e.: a common diagnostic character in the ancestor eidophoront of a given node in all MPT; as is the case of Bothremydidae). A possible solution is to use the suffix “formes” to designate extinct lineages with stem-species when some nodes are not well supported in a given phylogeny. In the example presented here, it would consist on naming ICZN’s Bothremydodda as “Bothremydidae” (sensu stricto) and ICZN’s Bothremydidae (sensu lato, i.e.: including stem-Bothremydidae) as “Bothremydidiformes” and avoid naming each node of the consensus tree unless it has high Bremer support. By taking into account this delimitation criterion, we can propose a more stable and clean taxonomy.
Cranial ontogenetic variation in early saurischians and the role of heterochrony in the diversification of predatory dinosaurs
Authors: Foth Christian , Hedrick Brandon P , Ezcurra Martin D
Published: January 2018

Non-avian saurischian skulls underwent at least 165 million years of evolution and shapes varied from elongated skulls, such as in Coelophysis, to short and box-shaped skulls, such as in Camarasaurus. A number of factors have long been considered to drive skull shape, including phylogeny, dietary preferences and functional constraints. However, heterochrony is increasingly being recognized as a major factor in dinosaur evolution. In order to quantitatively analyse the impact of heterochrony on saurischian skull shape, we have analysed five ontogenetic trajectories using two-dimensional geometric morphometrics in a phylogenetic framework. This allowed for the evaluation of how heterochrony affected overall skull shape through both ontogenetic and phylogenetic trajectories and how it impacted modular changes within the skull. Using principal component analyses and multivariate regressions, it was possible to quantify different ontogenetic trajectories in light of heterochrony. The results recovered here indicate that taxa underwent a combination of local paedomorphosis and peramorphosis within the skull along individual ontogenies and phylogenies, but that either peramorphosis or paedomorphosis dominated when the skull was considered as a whole. We found that the hypothetical ancestor of Saurischia led to basal Sauropodomorpha mainly through paedomorphosis, and to Neotheropoda mainly through peramorphosis. Paedomorphosis then led from Orionides to Avetheropoda, indicating that the paedomorphic trend previously found in advanced coelurosaurs may extend back into the early evolution of Avetheropoda. Not only are changes in saurischian skull shape complex due to the large number of factors that affect shape, but heterochrony itself is complex, with a number of reversals throughout non-avian saurischian evolution. The sampling of ontogenetic trajectories is considerably lower than the sampling of adult species and the current study represents a first exploratory analysis. To better understand the impact of heterochrony on cranial evolution in saurischians, the data set we present must be expanded and complemented with further sampling from future fossil discoveries, especially of juvenile taxa.
Aggressiveness, reliable signaling and survival in a wild songbird
Authors: Akçay Çağlar , Campbell S. Elizabeth , Beecher Michael D.
Published: January 2018

The evolution and maintenance of honest or reliable signaling has been a major question in evolutionary biology. The question is especially puzzling for a particular class of signals used in aggressive interactions: threat signals. Here we report a study on song sparrows (Melospiza melodia) in which we assayed males with playbacks in their territories to quantify their aggressiveness and aggressive signaling levels and asked whether these affect their survival on territory. We found that the effect on survival of residual signaling (signaling above or below the level predicted by their aggressiveness) depended on aggression levels such that among males with low aggression, those with higher residual signaling scores had higher survival. The residual signaling did not have a strong effect among high aggression males. Aggressiveness by itself did not have an effect on survival. These results present a first step in understanding the fitness consequences of honest signaling in aggressive contexts.
Influence of occupational dysfunction on the psychological problem in healthcare workers: A study using structural equation modeling
Authors: Teraoka Mutsumi , Kyougoku Makoto
Published: January 2018

Purpose: This study identified the effect of occupational dysfunction on psychological factors of stress response, burnout syndrome, and depression in healthcare workers.

Method: Three cross sectional studies were conducted to assess the following relations: 1) occupational dysfunction on stress response (n = 468), 2) occupational dysfunction on burnout syndrome (n = 1142), and 3) occupational dysfunction on depression (n = 687). Personal characteristics were collected through a questionnaire (such as age, gender, and job category, opportunities for refreshment, time spent on leisure activities, and work relationships) as well as the Classification and Assessment of Occupational Dysfunction (CAOD). Furthermore, study 1 included the Stress Response Scale-18 (SRS-18), study 2 used the Japanese Burnout Scale (JBS), and study 3 employed the Center for Epidemiological Studies Depression Scale (CES-D). The Kolmogorov–Smirnov test, confirmatory factor analysis (CFA), exploratory factor analysis (EFA), and path analysis of structural equation modeling (SEM) analysis were used in all of the studies. EFA and CFA were used to measure structural validity of four assessments; CAOD, SRS-18, JBS, and CES-D. For examination of a potential covariate, we assessed the correlation of the total score of CAOD and personal factors in all studies. Moreover, direct and indirect effects of occupational dysfunction on stress response (Study 1), burnout syndrome (Study 2), and depression (Study 3) were also analyzed.

Results: CAOD had 16 items and 5 factors. SRS-18 had 18 items and 3 factors, JBS had 17 items and 3 factors, CES-D had 20 items and 4 factors. All studies found that there were significant correlations between the CAOD total score and the personal factor that included opportunities for refreshment, time spent on leisure activities, and work relationships (p<0.01). The causal sequence model results suggest that the classification of occupational dysfunction had positive causal effects on the stress response (RMSEA = 0.058, CFI = 0.951, and TLI = 0.947), burnout syndrome (RMSEA = 0.074, CFI = 0.922, and TLI = 0.915), and depression (RMSEA=0.059, CFI=0.926, TLI=0.920). Moreover, the positive effect of external covariates include opportunities for refreshment, time spent on leisure activities, and work relationships on occupational dysfunction.

Conclusion: The classification of occupational dysfunction indicated a possibility of increase in the stress response, burnout syndrome, and depression in healthcare workers. Furthermore, occupational dysfunction affected personal factors including opportunities for refreshment, time spent on leisure activities, and work relationships. Therefore, it is necessary to adopt occupational therapy strategies to prevent this problem.
A rapid assessment of logging effects on bird species in Kelantan forests areas, Malaysia
Authors: Ghasemi Saber
Published: January 2018

Kelantan Forest Areas (KFA) are known to be the major portion of Taman Negara National Park, and it has been identified as an Environmentally Sensitive Area (ESA) rank 1 under Malaysia’s National Physical Plan (NPP). Since access to the forest areas is often lacking and vital forest information are often inadequate, this study aims to find a baseline data for macro EIA of KFA. This study consists of rapid assessment of logging effects on bird species. Based on the study, Kelantan forests are divided into (1) lowland evergreen rain forest, (2) lower mountain rain forest and (3) upper mountain rain forest, using general vegetation forms. A total of 321 species of birds were recorded in KFA using data collection from related agencies, Mist-netting Method, Transect survey Method (Distance Sampling Method; Point Count Method) and Secondary data. Out of this number, 220, 49, 7 and 1 species were falls under totally protected, nearly threatened, vulnerable and critically endangered categories, respectively. Out of the total recorded species, a total of 155, 292 and 128 species were recorded in lowland evergreen rain forest reserves, lower mountain rain forest reserve and upper Kelantan mountain rain forest respectively. The blue-banded kingfisher Alcedo euryzonia in the list of Kelantan birds was fall under critically endangered status. A total of 83 species were observed commonly in 3 kinds of habitat, 20 species were recorded only in Kelantan lowland forest reserve, which species Jambu fruit-dove was fall under nearly threatened. Furthermore, a total of 5 species were recorded just in upper mountain Kelantan rain forest. This study considered that Kelantan forests could be one of the `megadiversity’ places in Malaysia, and effects of logging on wildlife species as well as birds were cleared.
A simple and general method for accounting for phylogenetic uncertainty via Rubin’s rules in comparative analysis
Authors: Nakagawa Shinichi , de Villemereuil Pierre
Published: January 2018

Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species’ trait evolution. These methods, however, usually assume that phylogenetic trees are known without error or uncertainty, but this assumption is most likely incorrect. So far, Markov chain Monte Carlo, MCMC-based Bayesian methods have successfully been deployed to account for such phylogenetic uncertainty in PCMs. Yet, the use of these methods seems to have been limited, probably due to difficulties in their implementation. Here, we propose an approach with which phylogenetic uncertainty is incorporated in a simple, readily implementable and reliable manner. Our approach uses Rubin’s rules, which are an integral part of a standard multiple imputation procedure, often employed to recover missing data. In our case, we see the true phylogenetic tree as a missing piece of data, and apply Rubin’s rules to amalgamate parameter estimates from a number of models using a set of phylogenetic trees (e.g. a Bayesian posterior distribution of phylogenetic trees). Using a simulation study, we demonstrate that our approach using Rubin’s rules performs better in accounting for phylogenetic uncertainty than alternative methods such as MCMC-based Bayesian and Akaike information criterion, AIC-based model averaging approaches; that is, on average, our approach has the best 95% confidence/credible interval coverage among all. A unique property of the multiple imputation procedure is that the index, named ‘relative efficiency’, could be used to quantify the number of trees required for incorporating phylogenetic uncertainty. Thus, by using the relative efficiency, we show the required tree number is surprisingly small (~50 trees) at least in our simulation. In addition to these advantages above, our approach could be combined seamlessly with PCMs that utilize multiple imputation to recover missing data. Given the ubiquity of missing data, it is likely that the use of the multiple imputation procedure with Rubin’s rules will be popular to deal with phylogenetic uncertainty as well as missing data in comparative data.
On the impact of sampling frequency on software energy measurements
Authors: Saborido Rubén , Arnaoudova Venera Venera , Beltrame Giovanni , Khomh Foutse , Antoniol Giuliano
Published: January 2018

Energy consumption is a major concern when developing and evolving mobile applications. The user wishes to access fast and powerful mobile applications, which is usually in contrast to optimized battery life and heat generation. The software engineering community have acknowledged the relevance of the problem and researchers are investigating ways to reduce energy consumption, for example by examining which library, device configuration, and applications parameters should be used to promote long battery life. We conjecture that these studies are at the border between hardware and software and we must be careful on how the energy consumption is measured and how the energy consumption is attributed to methods and libraries.To the best of our knowledge, no previous work investigates how much energy and power consumption is due to high frequency events missed when sampling at low frequencies such as 10 kHz and verified the error at the precision of method level. Low frequency sampling is a rough approximation that hinders the understanding of fine grain details: the real picture of energy consumption as well as the root causes are missed. This has profound implications on the choice of methods to evolve or components to replace.In this paper, we propose an approach for accurate measurements of the energy consumption of mobile applications. We apply the proposed approach to assess the energy consumption of 21 mobile, closed source, applications and four open source Android applications.We show that by sampling at 10 kHz one may expect a median error of 8%, however, such error may be as high as 50% for short fast executing methods. Finally, we revisit a previous approach that estimates the energy consumption of methods based on execution time and found that it can miss as much as 84% of the energy, with a median of 30%.
Is consciousness inherently unstable? An iterated data rate theorem model of high metabolic demand in neural tissues
Authors: Wallace Rodrick
Published: January 2018

Evolutionary process has selected for inherently unstable physiological systems in higher animals that can react swiftly to patterns of threat or affordance, for example blood pressure and the immune response. However, these require ongoing strict regulation: unregulated blood pressure is fatal, and immune cells can attack 'self' tissues. Consciousness, perhaps the most sophisticated rapid large-scale neural process, demands high rates of metabolic free energy to both operate and regulate the basic physiological machinery. Both the 'stream of consciousness' and the 'riverbanks' that confine it to useful realms are constructed and reconstructed moment-by-moment in response to highly dynamic internal and environmental circumstances. Using an information bottleneck method that links control and information theories, it is relatively easy to show that rapid response based on instability and its stabilization will always require high rates of metabolic free energy. In sum, neural structures in higher animals are highly 'coevolutionary', responding both to environmental signals and to signals from other physiological systems, and stabilizing coevolutionary cognitive structures is as difficult as programming them. Consciousness appears fundamentally unstable, and the necessary synergism between conscious action and its regulation underlies the ten-fold higher rate of metabolic energy consumption in human neural tissues. Implications for the etiology of certain psychiatric disorders are obvious.
Identifying Genetic Interactions Associated with Late-Onset Alzheimer’s Disease
Authors: Floudas Charalampos S , Um Nara , Kamboh M. Ilyas , Barmada Michael M , Visweswaran Shyam
Published: January 2018

Background Identifying genetic interactions in data obtained from genome-wide association studies (GWASs) can help in understanding the genetic basis of complex diseases. The large number of single nucleotide polymorphisms (SNPs) in GWASs however makes the identification of genetic interactions computationally challenging. We developed the Bayesian Combinatorial Method (BCM) that can identify pairs of SNPs that in combination have high statistical association with disease. Results We applied BCM to two late-onset Alzheimer’s disease (LOAD) GWAS datasets to identify SNP-SNP interactions between a set of known SNP associations and the dataset SNPs. For evaluation we compared our results with those from PLINK, an established method. Gene Ontology analysis of genes from the top 200 dataset SNPs for both GWAS datasets showed overrepresentation of LOAD-related terms. Four genes were common to both datasets: APOE and APOC1, which have well established associations with LOAD, and CAMK1D and FBXL13, not previously linked to LOAD but having evidence of involvement in LOAD. Supporting evidence was also found for additional genes from the top 30 dataset SNPs. Conclusion BCM performed well in identifying several SNPs having evidence of involvement in the pathogenesis of LOAD that would not have been identified by univariate analysis due to small main effect. These results provide support for applying BCM to identify potential genetic variants such as SNPs from high dimensional GWAS datasets.
The multiple origins of the H5N8 avian influenza sub-type
Authors: Dalby Andrew
Published: January 2018

A significant outbreak of H5N8 avian influenza began in early 2014 in Korea. H5N8 is a highly pathogenic avian influenza that is often fatal to chickens and other domestic poultry but which can be asymptomatic in ducks. The virus was also found in migratory birds in Europe and more recently in North America. This is the first time that an H5N8 outbreak has spread so widely and persisted for so long. Previous outbreaks have usually been short and geographically localised. In this study I present a phylogenetic analysis of all of the H5 hemagglutinin and N8 neuraminidase sequences to show that each of the H5N8 outbreaks has resulted from a different re-assortment event and that there have been at least 7 distinct origins of the viral sub-type since it was first characterised in a Turkey in Ireland in 1983.
External morphology of eyes and Nebenaugen of caridean decapods – ecological and systematic considerations
Authors: Johnson Magnus L , Dobson Nicola C , De Grave Sammy
Published: January 2018

Most caridean decapods have compound eyes of the reflecting superposition kind and some additionally possess an accessory eye-like organ of unknown function also referred to as the nebenauge. We examined 308 caridean genera to assess the general morphology of the eye, rostrum length, eye diameter and the presence or absence and, when present, the diameter of the nebenauge. We have attempted to relate these data to ecological and taxonomic considerations. We consider there to be 6 distinct eye types based on the margin between the eyestalk and cornea. The presence of nebenaugen appears to be generally linked to an active lifestyle, as evidenced by the fact that species that have nebenaugen tend to have larger eyes and are more likely to have a distinct rostrum. We suggest that the inconsistencies in its presence/absence under both systematic and ecological lenses may indicate that when present it has various roles relating to behavioural and physiological rhythms.
Red-winged blackbird aggression but not nest defense success is predicted by exposure to brood parasitism by brown-headed cowbirds
Authors: Yasukawa Ken , Lindsey-Robbins Josie , Henger Carol S. , Hauber Mark E.
Published: January 2018

The brown-headed cowbird (Molothrus ater) is an obligate brood parasite known to use over 200 host species. The red-winged blackbird (Agelaius phoeniceus) is a commonly used accepter host that incubates cowbird eggs and cares for cowbird nestlings and fledglings. This host species, however, may reduce the risk of parasitism with a frontloaded antiparasite strategy in which it attacks parasites that approach active host nests. To test this frontloaded parasite-defense hypothesis (FPDH), we presented taxidermic models of a female northern cardinal (Cardinalis cardinalis), which represents no threat to redwings, a male cowbird, which cannot lay a parasitic egg, and a female cowbird, together with species- and sex-specific vocalization playbacks for 5 min. We conducted these presentations at 25 active redwing nests at Newark Road Prairie in south-central Rock County, Wisconsin, USA, where 18% of redwing nests were parasitized by cowbirds in 2015. As predicted by the FPDH, the female cowbird mount elicited the most aggressive responses and the female cardinal mount the least aggressive, as measured by number of times more than one male redwing responded and number of times the male host attacked the mount, and by Principal Component analyses yielding redwing aggressive behavior and intimidation scores. Contrary to the predictions of FPDH regarding the success of nest defense behaviors, male redwings responding at naturally parasitized nests were significantly more likely to attack the mount than males with nests that were not parasitized. We also compared our results with those of a study using the same methods and conducted in New York State where cowbird parasitism was rare. Wisconsin redwings were more aggressive toward the female cowbird mount than redwings in New York State. Red-winged blackbirds appear to frontload their antiparasite defenses and the aggressiveness, but the apparent success of those defenses depends on individual and population-level experience with parasites.
Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution
Authors: Khang Tsung Fei , Soo Oi Yoon Michelle , Tan Wooi Boon , Lim Lee Hong Susan
Published: January 2018

Anchors are important attachment appendages that prevent the physical dislodging of a monogenean parasite from fish host gills. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies. We used a geometric morphometric approach to explore anchor shape variation in 13 Ligophorus (Monogenea:Ancyrocephalidae) species infecting two marine mugilid (Teleostei: Mugilidae) fish hosts (Moolgarda buchanani and Liza subviridis) in the waters off West Peninsular Malaysia. Molecular sequence data from three nuclear markers: 28S rRNA, 18S rRNA and ITS1, were used to infer a maximum likelihood phylogeny to enable visualization of shape evolution in phylomorphospace. For inferring patterns of size evolution in the phylogeny, we used a size measure based on the first principal component of all pairwise Euclidean distances between landmarks. Cluster heat map and principal component analysis showed that anchor shape variation had sufficient systematic information for delimiting 12 of the 13 species. Adams' multivariate K test indicated significant correlation between anchor shape and phylogeny (p-value = 0.0001). We also discovered that characters based on anchor shaft shape, the length between inner and outer root tips and the length between inner root tip and the dent point were more phylogenetically informative than inner and outer lengths, as indicated by a maximum parsimony tree that was better resolved and had major clades congruent with those of the molecular phylogenetic tree. Continuous character mapping of size onto the inferred molecular phylogeny and Rayleigh’s test for departure from directional uniformity in each species’s landmark relative to the ancestor indicated that species infecting M. buchanani generally evolved larger and more robust anchors, while those infecting L. subviridis generally evolved smaller and more delicate anchors. Nevertheless, phylogenetic regression of anchor shape against body size and anchor size showed significant correlation (p-value = 0.02) between anchor shape and size, suggesting morphometric constraints in anchor evolution. Finally, morphological integration analysis revealed tight integration between the root and point compartments within anchors, confirming that the anchor functions as a single, fully integrated module. The present work is supported by the development of integrative analytical tools in the form of a new R package – monogeneaGM. By lowering barriers to data integration and analysis , we aim to encourage the scientific community to collect and contribute morphometric and genetic data from other Ligophorus species, which are essential for developing Ligophorus as a model system for understanding association between patterns of anchor shape size evolution and biodiversity in the Monogenea.
Nanopublication beyond the Sciences
Authors: Golden Patrick , Shaw Ryan
Published: January 2018

The information expressed in humanistic datasets is inextricably tied to a wider discursive environment that is irreducible to complete formal representation. Humanities scholars must wrestle with this fact when they attempt to publish or consume structured data. The practice of “nanopublication”, which originated in the e-science domain, offers a way to maintain the connection between formal representations of humanistic data and its discursive basis. In this paper we describe nanopublication, its potential applicability to the humanities, and our experience curating humanities nanopublications in the PeriodO period gazetteer.
Perioperative morbidity and mortality of cardiothoracic surgery in patients with a do-not-resuscitate order
Authors: Maxwell Bryan G , Lobato Robert L. , Cason Molly B. , Wong Jim K.
Published: January 2018

Background: Do-not-resuscitate (DNR) orders are often active in patients with multiple comorbidities and a short natural life expectancy, but limited information exists as to how often these patients undergo high-risk operations and of the perioperative outcomes in this population. Methods: Using comprehensive inpatient administrative data from the Public Discharge Data file (years 2005 through 2010) of the California Office of Statewide Health Planning and Development, which includes a dedicated variable recording DNR status, we identified cohorts of DNR patients who underwent major cardiac or thoracic operations and compared them to age- and procedure-matched comparison cohorts. The primary study outcome was in-hospital mortality. Results: DNR status was not uncommon in cardiac (n=2,678, 1.1% of all admissions for cardiac surgery, age 71.6 ± 15.9 years) and thoracic (n=3,129, 3.7% of all admissions for thoracic surgery, age 73.8 ± 13.6 years) surgical patient populations. Relative to controls, patients who were DNR experienced significantly greater in-hospital mortality after cardiac (37.5% vs. 11.2%, p<0.0001) and thoracic (25.4% vs. 6.4%) operations. DNR status remained an independent predictor of in-hospital mortality on multivariate analysis after adjustment for baseline and comorbid conditions in both the cardiac (OR 4.78, 95% confidence interval 4.21-5.41, p<0.0001) and thoracic (OR 6.11, 95% confidence interval 5.37-6.94, p<0.0001) cohorts. Conclusions: DNR status is associated with worse outcomes of cardiothoracic surgery even when controlling for age, race, insurance status, and serious comorbid disease. DNR status appears to be a marker of substantial perioperative risk, and may warrant substantial consideration when framing discussions of surgical risk and benefit, resource utilization, and biomedical ethics surrounding end-of-life care.
FSOL - a workflow for the detection of patient subgroups and affected molecular features in high-throughput omics data
Authors: Ahrens Maike , Turewicz Michael , Marcus Katrin , Meyer Helmut E. , May Caroline , Eisenacher Martin , Rahnenführer Jörg
Published: January 2018

In personalized medicine, one major goal is the identification of yet unknown patient subgroups with specific gene or protein expression. Different subgroups can indicate different molecular subtypes of a disease. These subtypes might correlate with disease progression, prognosis or therapy response, and the subgroup-specific genes or proteins are potential drug targets. Using high-throughput molecular data, the aim is to characterize the patient subgroup by identifying both the set of samples that shows a distinct expression pattern as well as the set of features that are affected. We present the new workflow FSOL for the identification of patient subgroups from two sample comparisons (e.g. healthy vs. diseased). First, a pre-filtering based on the univariate score FisherSum (FS) is applied to assess subgroup-specific expression of the features. FS has been shown to outperform competing methods in several settings. Second, the selected features are compared regarding the samples that form the affected subgroup. This step uses the OrderedList (OL) method that was originally developed for the comparison of result lists from gene expression studies. We compare our workflow FSOL to a reference workflow based on biclustering using real world and simulated data. On a leukemia data set, a true biological subgroup can be detected with higher stability by FSOL. On simulated data, FSOL shows higher sensitivity and accuracy compared to biclustering especially for small to moderate differences. The exploratory approach FSOL may help in identifying yet unknown mechanisms in pathologic processes and may assist in the generation of new research hypotheses.
Disruption of de novo purine biosynthesis in Pseudomonas fluorescens Pf0-1 leads to reduced biofilm formation and a reduction in cell size of surface-attached but not planktonic cells
Authors: Yoshioka Shiro , Newell Peter D
Published: January 2018

Pseudomonas fluorescens Pf0-1 is one of the model organisms for biofilm research. Our previous transposon mutagenesis study suggested a requirement for the de novo purine nucleotide biosynthesis pathway for biofilm formation by this organism. This study was performed to verify that observation and investigate the basis for the defects in biofilm formation shown by purine biosynthesis mutants. Constructing deletion mutations in 8 genes in this pathway, we found that they all showed reductions in biofilm formation that could be partly or completely restored by nucleotide supplementation or genetic complementation. We demonstrated that, despite a reduction in biofilm formation, more viable mutant cells were recovered from the surface-attached population than from the planktonic phase under conditions of purine deprivation. Analyses using scanning electron microscopy revealed that the surface-attached mutant cells were 25~30% shorter in length than WT, which partly explains the reduced biomass in the mutant biofilms. The laser diffraction particle analyses confirmed this finding, and further indicated that the WT biofilm cells were smaller than their planktonic counterparts. The defects in biofilm formation and reductions in cell size shown by the mutants were fully recovered upon adenine or hypoxanthine supplementation, indicating that the purine shortages caused reductions in cell size. Our results are consistent with surface attachment serving as a survival strategy during nutrient deprivation, and indicate that changes in the cell size may be a natural response of P. fluorescens to growth on a surface. Finally, cell sizes in WT biofilms became slightly smaller in the presence of exogenous adenine than in its absence. Our findings suggest that purine nucleotides or related metabolites may influence the regulation of cell size in this bacterium.
Pharmacophagy in green lacewings (Neuroptera: Chrysopidae: Chrysopa spp.)?
Authors: Aldrich Jeffrey R , Chauhan Kamal , Zhang Qing-He
Published: January 2018

Green lacewings (Neuroptera: Chrysopidae) are voracious predators of aphids and other small, soft-bodied insects and mites. Earlier, we identified the first lacewing pheromone from field-collected males of the goldeneyed lacewing, Chrysopa oculata Say; (1R,2S,5R,8R)-iridodial is released from thousands of microscopic dermal glands on the abdominal sternum of males, along with comparable amounts of nonanal, nonanol and nonanoic acid. Iridodial-baited traps attract C. oculata and other Chrysopa spp. males into traps, while females come to the vicinity of, but do not usually enter baited traps. Despite their healthy appearance, normal fertility and usual amounts of C9 compounds, laboratory-reared C. oculata males do not produce iridodial. However, we observed that goldeneyed lacewing males caught alive in iridodial-baited traps sometimes try to eat the lure, and in Asia Chrysopa spp. males reportedly eat the native plant, Actinidia polygama (Siebold & Zucc.) Maxim. (Actinidiaceae) to obtain the iridoid, neomatatabiol. These observations prompted us to investigate why laboratory-reared Chrysopa green lacewings do not produce iridodial. Lacewing adult males fed various monoterpenes reduced carbonyls to alcohols and saturated double bonds, but did not convert these compounds to iridodial. Males fed the bicyclic iridoid aphid pheromone component, (4aS,7S,7aR)-nepetalactone, converted ~75% to dihydronepetalactone, but did not produce iridodial; however, wild C. oculata males collected in May often contained traces of dihydronepetalactone. On the other hand, adult males fed the second common aphid pheromone component, (1R,4aS,7S,7aR)-nepetalactol, converted this compound to iridodial. In California the peak late-season attraction of green lacewings to nepetalactol (the lactone is unattractive) occurs at least a month earlier than the peak in aphid oviparae (the pheromone producing morph of aphids), consistent with the hypothesis that Chrysopa males feed on oviparae to obtain nepetalactol as a precursor to iridodial. Adult males from laboratory-reared C. oculata larvae fed nepetalactol failed to produce iridodial, and wild C. oculata males collected early in the spring produce less iridodial than males collected later in the season. Therefore, we further hypothesize that Asian Chrysopa eat A. polygama to obtain iridoid precursors in order to make their pheromone, and that other iridoid-producing plants elsewhere in the world must be similarly usurped by male Chrysopa species to sequester pheromone precursors. Whether or not sequestration of iridodial precursors from oviparae and/or iridoid-containing plants is truly the explanation for lack of pheromone in laboratory-reared Chrysopa awaits further research .
A unifying theory for physiological transmembrane transport derived from thermodynamic principles
Authors: Herrera-Valdez Marco Arieli
Published: January 2018

Cellular homeostasis involves transmembrane molecular transport mediated by membrane-spanning proteins. Such proteins either carry the molecules across the membrane, or facilitate their diffusion. A generic formulation that describes transmembrane fluxes, derived from basic thermodynamic principles, and describing fluxes mediated by carrier proteins or by open channels using the same functional form is presented here. An alternative derivation from the Nernst-Planck equation that yields the same generic formulation can be obtained for the case of channel- mediated electrodiffusion. In general terms, the generic formulation is a product of an amplitude and a driving force. The amplitude models properties of the protein mediating the transport including basal rates of transport. The driving force term that depends non-linearly on the transmembrane concentrations of the molecules being transported, and possibly the transmembrane potential. The model applied for channel mediated currents is capable of displaying rectification. Further, an extension for channel gating derived en passage allows fitting of currents recorded in voltage-clamp without using powers for the gating variables. The generic formulation explicitly shows that the basal rate at which ions cross the membrane is the main macroscopic difference between currents mediated by carrier proteins and channels. Many functional forms that were not always derived from the same assumptions can be found in modelling studies of transmembrane transport, especially those studies focusing on the membrane potential of excitable cells. The derivations presented here unify the theory of biological transmembrane transport. Of particular interest, electrogenic transmembrane fluxes described with the general formulation can be converted to currents for the construction of models of membrane excitability; all based on the same assumptions and having the same functional form. The applicability of the generic derivations presented here is illustrated with models of excitability for neurones and pacemaker cardiocytes.
Hybrid HDFS: decreasing energy consumption and speeding up Hadoop using SSDs
Authors: Polato Ivanilton , Barbosa Denilson , Hindle Abram , Kon Fabio
Published: January 2018

Apache Hadoop has evolved significantly over the last years, with more than 60 releases bringing new features. By implementing the MapReduce programming paradigm and leveraging HDFS, its distributed file system, Hadoop has become a reliable and fault tolerant middleware for parallel and distributed computing over large datasets. Nevertheless, Hadoop may struggle under certain workloads, resulting in poor performance and high energy consumption. Users increasingly demand that high performance computing solutions being to address sustainability and limit power consumption. In this paper, we introduce HDFSH, a hybrid storage mechanism for HDFS, which uses a combination of Hard Disks and Solid-State Disks to achieve higher performance while saving power in Hadoop computations. HDFSH brings to middleware the best from HDs (affordable cost per GB and high storage capacity) and SSDs (high throughput and low energy consumption) in a configurable fashion, using dedicated storage zones for each storage device type. We implemented our mechanism as a block placement policy for HDFS, and assessed it over six recent releases of the Hadoop project, representing different designs of the Hadoop middleware. Results indicate that our approach increases overall job performance while decreasing the energy consumption under most hybrid configurations evaluated. Our results also showed that in many cases storing only part of the data in SSDs results in significant energy savings and execution speedups.
Cardiovascular manifestations of renovascular hypertension in diabetic mice
Authors: Kashyap Sonu , Engel Sean , Osman Mazen , Al-Saiegh Yousif , Wongjarupong Asarn , Grande Joseph P
Published: January 2018

Purpose. Type 2 diabetes is the leading cause of end stage renal disease in the United States. Atherosclerotic renal artery stenosis is commonly observed in diabetic patients and impacts the rate of renal and cardiovascular disease progression. We hypothesized that renal artery stenosis contributes to bilateral renal disease in diabetics. In our original study, we found that leptin-deficient diabetic (db/db) mice subjected to RAS developed severe and bilateral renal disease, with the contralateral (uncuffed) kidney showing features reminiscent of progressive diabetic nephropathy. In non-diabetic mice (WT), the cuffed kidney developed progressive atrophy, but the contralateral kidney showed minimal histopathologic alterations. In doing these studies, we observed increased sudden death in db/db mice with RAS, but not in WT mice with RAS. The objective of this study was to characterize the aortic and cardiac phenotype of db/db mice subjected to RAS. Methods. We developed a murine model of renal artery stenosis by placement of a polytetrafluoroethylene cuff on the right renal artery in db/db mice. We studied 109 WT and 95 db/db mice subjected to Renal artery stenosis (RAS) or sham surgery. Results. The mortality rate of db/db RAS mice was about 23.5%, whereas only 1.5% deaths were observed in WT RAS mice. Interestingly, 60% of mortality in the db/db mice occurred in the first two weeks following RAS surgery. Necropsy showed massive intrathoracic hemorrhage associated with aortic dissection. Aortas from db/db RAS mice showed more smooth muscle dropout, medial disruption, and hemorrhage than aortas from WT mice with RAS. Cardiac tissue from db/db RAS mice had more fibrosis than did cardiac tissue from WT RAS mice. Conclusions. Db/db mice subjected to RAS are prone to develop fatal aortic dissection, which is not observed in WT mice with RAS. The db/db RAS model provides the basis for future studies directed towards defining basic mechanisms underlying the interaction of hypertension and diabetes on the development of aortic lesions.
Smart traps for automatic remote monitoring of Rhynchophorus ferrugineus (Coleoptera: Curculionidae)
Authors: Potamitis Ilyas , Rigakis Iraklis
Published: January 2018

This work describes a novel solution to remote R. ferrugineus monitoring. Classical, plastic RPW traps containing aggregation pheromones for RPW are modified to include an optical sensor that senses adult pests falling in the trap. The counts of the pests are accumulated through the day and the counts are transmitted via the mobile phone network straight to a smartphone/tablet or internet address. The device is small and is attached internally in the trap carrying all necessary electronic equipment to allow optical detection, counting and transmission of counts through GSM. Smart RPW traps are expected to reduce the cost of monitoring and allow for reliable decision making as the wireless transmission is instantaneous thus allows the creations of real-time infestation maps. Our device has been tested extensively in real field delivering excellent detection results. We did not observe a single case that a RPW was not detected while being inside the trap and our trap delivers nearly zero rate false alarms.
Operationalizing Central Place Theory and Central Flow Theory with mobile phone data
Authors: Doran Derek , Fox Andrew
Published: January 2018

Central Place and Central Flow Theory are geographic principles explaining why and how cities develop across large regional spaces. Central Place Theory postulates that cities self-organize into a spatial hierarchy were small numbers of very large ‘Central Places’ support numerous surrounding and less developed ‘Low Places’, while ‘Middle Places’ develop at the periphery of where Central Places carry spatial influence. Central Flow Theory is a comple- mentary notion that explains the cooperative development of cities through joint information sharing. Both theories are often discussed, with multiple regional development and economic models built upon their tenents. However, it is very difficult to quantify the degree to which Central Place and Central Flow Theory explains the development and positions of cities in a region, particularly in developing countries where socioeconomic data is difficult to collect. To facilitate these measurements, this paper presents a way to operationalize Central Place and Central Flow Theory using mobile phone data collected across a region. It defines a set of mobile phone data attributes that are related to basic facets of the two theories, and demonstrates how their measurements speak to the degree to which the theories hold in the region the mobile phone data covers. The theory is then applied in a case study where promising locations for economic investment in a developing nation are identified.