bluuebunny/crossref_metadata_2025 huggingface dataset:
Toxicity of differently sized and coated silver nanoparticles to the bacterium Pseudomonas putida
Authors: Matzke Marianne , Jurkschat Kerstin , Backhaus Thomas
Published: January 2018

Aim of this study was to describe the toxicity of a set of different commercially available silver nanoparticles (AgNPs) to the gram-negative bacterium Pseudomonas putida (growth inhibition assay, ISO 10712) in order to contribute to their environmental hazard and risk assessment. Different AgNP sizes and coatings were selected in order to analyze whether those characteristics are determinants of nanoparticle toxicity. Silver nitrate was tested for comparison. In general Pseudomonas putida reacted very sensitive towards the exposure to silver, with an EC 05 value of 0.043 µ g L-1 for AgNO 3 and between 0.13 and 3.41 µ g L-1 for the different AgNPs (EC 50 values 0.16 µ g L-1 for AgNO3, resp. between 0.25 and 13.5 µ g L-1 for AgNPs). As the ionic form of silver is clearly the most toxic, an environmental hazard assessment for microorganisms based on total silver concentration and the assumption that AgNPs dissolve is sufficiently protective. Neither specific coatings nor certain sizes could be linked to increasing or decreasing toxicity. The characterization of particle behavior as well as the total and dissolved silver content in the medium during the exposures was not possible due to the high sensitivity of Pseudomonas (test concentrations were below detection limits), indicating the need for further development in the analytical domain. Monitored silver concentrations in the aquatic environment span six orders of magnitude (0.1 – 120000 ng L-1 ), which falls into the span of observed EC 05 values and might hence indicate a risk to environmental bacteria.
Aeolian mass flux characterization: uncertainties from a wind-tunnel perspective and implications for field studies
Authors: Poortinga Ate , Keijsers Joep GS , Maroulis Jerry , Visser Saskia M.
Published: January 2018

Aeolian sediment traps are widely used to estimate the total volume of wind-driven sediment transport, but also to study the vertical mass distribution of a saltating sand cloud. The reliability of sediment flux estimations from this data are dependent upon the specific configuration of the measurement compartments and the analysis approach used. In this study, we analyse the uncertainty of these measurements by investigating the vertical cumulative probability distribution and relative sediment flux derived from both wind-tunnel and field studies. Three existing datasets were used in combination with a newly acquired meteorological dataset, which was collected in combination with sediment fluxes from six different events, using three customized catchers at one of the beaches of Ameland in the north of The Netherlands. Fast-temporal data collected in a wind-tunnel shows that eq has a scattered pattern between impact and fluid threshold, but increases linearly with shear velocities above the fluid threshold. For finer sediment fractions, a larger portion of the sediment was transported closer to the surface compared to coarser sediment fractions. It was also shown that errors originating from the the distribution of the sampling compartments, specifically the location of the lowest sediment trap relative to the surface, can be identified using the relative sediment flux. In the field, surface conditions such as surface moisture, surface crusts or frozen surfaces have a more pronounced, but localized effect, than shear velocity. Uncertainty in aeolian mass flux estimates can be reduced by placing multiple compartments in closer proximity to the surface.
Disjoint combinations profiling (DCP): a new method for the prediction of antibody CDR conformation from sequence.
Authors: Nikoloudis Dimitris , Pitts Jim E. , Saldanha José W.
Published: January 2018

The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in antibody variable regions. It relies on canonical templates which detail allowed residues at key positions in the variable region framework or in the CDR itself for 5 of the 6 CDRs. While no templates have as yet been defined for the hypervariable CDR-H3, instead, reliable sequence rules have been devised for predicting the base of the CDR-H3 loop. Here a new method termed Disjoint Combinations Profiling (DCP) is presented, which contributes a considerable advance in the prediction of CDR conformations. This novel method is explained and compared with canonical templates and sequence rules in a 3-way blind prediction. DCP achieved 93% accuracy over 951 blind predictions and showed an improvement in cumulative accuracy compared to predictions with canonical templates or sequence-rules. In addition to its overall improvement in prediction accuracy, it is suggested that DCP is open to better implementations in the future and that it can improve as more antibody structures are deposited in the databank. In contrast, it is argued that canonical templates and sequence rules may have reached their peak.
Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior
Authors: Balakrishnan Christopher N , Mukai Motoko , Gonser Rusty A , Wingfield John C , London Sarah E , Tuttle Elaina M , Clayton David F
Published: January 2018

Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel’s white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, 80% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with transcript assembly N50s ranging from 2,557 to 4,072. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as a primary determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.
Out of control mortality matters: the effect of perceived uncontrollable mortality risk on a health-related decision
Authors: Pepper Gillian V , Nettle Daniel
Published: January 2018

Prior evidence from the public health literature suggests that both control beliefs and perceived threats to life are important for health behaviour. Our previously presented theoretical model generated the more specific hypothesis that uncontrollable, but not controllable, personal mortality risk should alter the payoff from investment in health protection behaviours. We carried out three experiments to test whether altering the perceived controllability of mortality risk would affect a health-related decision. Experiment 1 demonstrated that a mortality prime could be used to alter a health-related decision: the choice between a healthier food reward (fruit) and an unhealthy alternative (chocolate). Experiment 2 demonstrated that it is the controllability of the mortality risk being primed that generates the effect, rather than mortality risk per se. Experiment 3 showed that the effect could be seen in a surreptitious experiment that was not explicitly health related. Our results suggest that perceptions about the controllability of mortality risk may be an important factor in people’s health-related decisions. Thus, techniques for adjusting perceptions about mortality risk could be important tools for use in health interventions. More importantly, tackling those sources of mortality that people perceive to be uncontrollable could have a dual purpose. Making neighbourhoods and workplaces safer would have the primary benefit of reducing uncontrollable mortality risk, which could lead to a secondary benefit from improved health behaviours.
Adeno-associated virus Type 2 Rep proteins mediate integration of lentiviral vectors
Authors: McAlister Victor J , Craig Anthony T , Owens Roland A
Published: January 2018

Aims: Adeno-associated virus type 2 (AAV2) is a naturally defective human parvovirus that is being developed as a gene therapy vector. In dividing cells, AAV2 DNA persists by integration into the host chromosomes. AAV2 is unique among mammalian viruses in its ability to integrate preferentially into a particular locus within human chromosome 19, designated AAVS1(also known as Mbs 85). The AAV2 Rep68 and Rep78 proteins mediate this integration. Recent data suggest that Rep68 and Rep78 can mediate integration of non-AAV2 DNA with free ends. To test this hypothesis, we targeted insertion of different lentiviral vectors to AAVS1.

Methods: Cells were co-infected with wild-type AAV2, and integrase-proficient or integrase-deficient lentivirus vectors. A highly specific PCR-based assay was used to detect lentivirus integration at AAVS1. Similar experiments were performed using lentiviral vectors containing the AAV2 rep gene.

Results: All lentiviral vectors tested integrated at AAVS1, if the rep gene was present either within the lentiviral vector or supplied in trans. All that was required for integration at AAVS1 was the amino acid sequence shared between Rep68 and Rep78. The results were similar with integrase-proficient or integrase-deficient lentiviral vectors.

Conclusions: The inclusion of the rep gene with lentiviral vectors may produce more predictable integration patterns.
Fish mislabelling in France: substitution rates and retail types
Authors: Bénard-Capelle Julien , Guillonneau Victoire , Nouvian Claire , Fournier Nicolas , Le Loët Karine , Dettai Agnès
Published: January 2018

The development of citizen science has brought together scientific expertise and volunteer involvement to answer both scientific and societal questions. In this study, a consortium of citizens, journalist, scientists and non governmental organisations reports the first measure of the market-wide rate of fish mislabelling in France.We collected in fishmonger shops, supermarkets and restaurants and sequenced 390 samples of fish either in fillets or prepared meals, which is the largest dataset assembled to date in an European country.The overall substitution rate is one of the lowest observed for comparable surveys with large sampling in Europe. Remarkably, we detected no case of species mislabelling among the frozen fillets or in industrially prepared meals. We also investigated most of the mislabelling cases detected directly from the sellers. A number of them admitted that the substitution took place at the end of the supply chain.The rate of mislabelling does not differ between species (3.7 %, ci 2.2-6.4%), except for bluefin tuna. Despite a very small sample size (n=6), this species stands in sharp contrast with the low substitution rate observed for the other species (rate between 36 and 99%). This study shows that even in countries where species substitution rate is low, citizen science can enhance the management of natural resources and provide important insights for regulation policies.
Psychometric properties of the Children's Revised Impact of Events Scale (CRIES) with Bangladeshi children and adolescents
Authors: Deeba Farah , Rapee Ronald M , Prvan Tania
Published: January 2018

Identification of possible cases suffering post-traumatic stress disorder (PTSD) is important, especially in developing countries where traumatic events are typically prevalent. The Children’s Revised Impact of Events Scale is a reliable and valid measure that has two brief versions (13 items and 8 items) to assess reactions to traumatic events among young people. The current study evaluated the psychometric properties of both versions of the CRIES in a sample of 1342 children and adolescents aged 9-17 years (M=12.3 years, SD=2.12) recruited from six districts of Bangladesh. A sub-group of 135 children from four schools was re-tested on the measures within 3.5 weeks. Confirmatory factor analysis supported factor structures similar to those found in other studies for both versions of the CRIES. Multiple group confirmatory factor analysis showed gender and age-group differences within the sample, supporting established age and gender differences in prevalence of PTSD symptoms. Analyses also indicated moderate to excellent internal consistency and test-retest reliability and clear discriminant and convergent validity. These data support use of both the CRIES-13 and CRIES-8 to provide quick and psychometrically sound assessment of symptoms of PTSD among children and adolescents from Bangla-speaking communities.
Global broadcast and attention can be highly punctuated in fuzzy cognitive systems
Authors: Wallace Rodrick
Published: January 2018

Previous theoretical work on consciousness and other punctuated global broadcasts associated with attention states has focused on the evolutionary exaptation of the inevitable crosstalk between related sets of unconscious cognitive modules (UCM). This has invoked a groupoid treatment of the equivalence class structure arising from information sources 'dual', in a formal sense, to the UCM, via a standard spontaneous symmetry breaking/lifting methodology abducted from statistical physics, and through an index theorem approach based on an Onsager-like stochastic differential equations model. Surprisingly, similar arguments can be applied to the formally 'fuzzy' generalizations that are likely to better fit actual biological complexities.
SKIMMR: Facilitating knowledge discovery in life sciences by machine-aided skim reading
Authors: Novacek Vit , Burns Gully APC
Published: January 2018

Background: Unlike full reading, 'skim-reading' involves the process of looking quickly over information in an attempt to cover more material whilst still being able to retain a superficial view of the underlying content. Within this work, we specifically emulate this natural human activity by providing a dynamic graph-based view of entities automatically extracted from text. For the extraction, we use shallow parsing, co-occurrence analysis and semantic similarity computation techniques. Our main motivation is to assist biomedical researchers and clinicians in coping with increasingly large amounts of potentially relevant articles in life sciences.

Methods: To construct the high-level network overview of articles, we extract weighted binary statements from the text. We consider two types of these statements, co-occurrence and similarity, both organised in the same distributional representation (i.e., in a vector-space model). For the co-occurrence weights, we use point-wise mutual information that indicates the degree of non-random association between two co-occurring entities. For computing the similarity statement weights, we use cosine distance based on the relevant co-occurrence vectors. These statements are used to build fuzzy indices of terms, statements and provenance article identifiers, which support fuzzy querying and subsequent result ranking. These indexing and querying processes are then used top construct a graph-based interface for searching and browsing entity networks extracted from articles, as well as articles relevant to the networks being browsed.

Results: We provide a web-based prototype (called `SKIMMR') that generates a network of inter-related entities from a set of documents which a user may explore through our interface. When a particular area of the entity network looks interesting to a user, the tool displays the documents that are most relevant to those entities of interest currently shown in the network. We present this as a methodology for browsing a collection of research articles. To illustrate the practical applicability of SKIMMR, we present examples of its use in the domains of Spinal Muscular Atrophy and Parkinson's Disease. Last but not least, we describe a methodology for automated experimental evaluation of SKIMMR instances. The method uses formal comparison of the graphs generated by our tool to relevant gold standards based on manually curated PubMed, TREC challenge and MeSH data. The results of experiments performed on three different instances of SKIMMR show that the presented method for machine-aided skim reading outperforms state of the art tools like PubMed regarding focused browsing and informativeness of the browsing context.

Conclusions: In preliminary trials, users find new, interesting and non-trivial facts with SKIMMR. Our evaluation showed a high potential of the presented work for facilitating knowledge discovery in life sciences.
Metaproduct Prototype on the basis of Runningpad
Authors: Daumer Martin , Burger Patrick
Published: January 2018

Imagine a world where everything from products to people, spaces and services is connected and together operates as a living network. ‘Meta Products’ is the next generation of ’living’ products, services and spaces referring to the potential of the Internet of Things to reach everywhere and to be embodied in everything. In the current transition period we are living in, we are building new aspirations that demand increasingly clever ways to use the potentially endless amounts of information we can track, sense, measure, share and produce via the constantly improving omnipresent technologies. So we are bringing information-fuelled products and services that will be around us as a network whenever we need them. The result of finding these increasingly clever ways to use information is what we call Meta-Products.
Women are underrepresented on the editorial boards of journals in environmental biology and natural resource management
Authors: Cho Alyssa , Johnson Shelly A , Schuman Carrie , Adler Jennifer , Gonzalez Oscar , Graves Sarah J , Huebner Jana , Marchant D Blaine , Rifai Sami , Skinner Irina , Bruna Emilio M
Published: January 2018

Despite women earning similar numbers of graduate degrees as men in STEM disciplines, they are underrepresented in upper level positions in both academia and industry. Editorial board memberships are an important example of such positions; membership is both a professional honor in recognition of achievement and an opportunity for professional advancement. We surveyed 10 highly regarded journals in environmental biology, natural resource management, and plant sciences to quantify the number of women on their editorial boards and in positions of editorial leadership from 1985-2013. We found that during this time period, only 16% of editorial board members were women, with more pronounced disparities in positions of editorial leadership (i.e., Associate Editors, Editors-in-Chief). Although the trend was towards improvement over time, there was surprising variation between journals. We argue editorial boards should strive for gender parity to increase the number of women afforded the opportunities and benefits that accompany membership, as well as increase the number of role models and mentors for early-career scientists and students.
Equilibrium switching in nonlinear interaction networks with concurrent antagonism
Authors: Rabajante Jomar
Published: January 2018

In this paper, we examine a nonlinear concurrent decision-making model (CDM) of interaction networks that involve more than two antagonistic components (e.g., proteins, species, communities, mental choices). The model assumes sigmoid kinetics where every component stimulates itself but represses all others. We are able to prove general dynamical properties of the CDM (e.g., location and stability of steady states) for any dimension of the state space even if the reciprocal antagonism between two components is asymmetric. There are cases where asymmetric interaction generates oscillatory behavior. Some parameters can serve as biological regulators for inducing steady state switching by leading a temporal state to escape an undesired equilibrium. Increasing the maximal growth rate and decreasing the decay rate can expand the basin of attraction of a steady state with the desired component having the dominant value. We further show that perpetually adding an external stimulus can shutdown multi-stability of the system that increases the robustness of the system against stochastic noise.
Error estimates for the analysis of differential expression from RNA-seq count data
Authors: Burden Conrad , Qureshi Sumaira , Wilson Susan R
Published: January 2018

A number of algorithms exist for analysing RNA-sequencing data to infer profiles of differential gene expression. Problems inherent in building algorithms around statistical models of over dispersed count data are formidable and frequently lead to non-uniform p-value distributions for null-hypothesis data and to inaccurate estimates of false discovery rates (FDRs). This can lead to an inaccurate measure of significance and loss of power to detect differential expression. We use synthetic and real biological data to assess the ability of several available R packages to accurately estimate FDRs. The packages surveyed are based on statistical models of overdispersed Poisson data and include edgeR, DESeq, DESeq2, PoissonSeq and QuasiSeq. Also tested is an add-on package to edgeR and DESeq which we introduce called Polyfit. Polyfit aims to address the problem of a non-uniform null p-value distribution for two-class datasets by adapting the Storey-Tibshirani procedure. We find the best performing package in the sense that it achieves a low FDR which is accurately estimated over the full range of p-values to be the QLSpline implementation of QuasiSeq. This finding holds provided the number of biological replicates in each condition is at least 4. The next best performing packages are edgeR and DESeq. When the number of biological replicates is sufficiently high, and within a range accessible to multiplexed experimental designs, the Polyfit extension improves the performance edgeR (for ≤ \le 10 replicates per condition) or DESeq (for ≤ \le 6 replicates per condition) in our tests with synthetic data.
Consistent, comprehensive and computationally efficient OTU definitions
Authors: Rideout Jai Ram , He Yan , Navas-Molina Jose Antonio , Walters William A , Ursell Luke K , Gibbons Sean M , Chase John H , McDonald Daniel , Gonzalez Antonio , Robbins-Pianka Adam , Clemente Jose C , Gilbert Jack , Huse Susan M , Zhou Hong-Wei , Knight Rob , Caporaso J Gregory
Published: January 2018

We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because parts of our algorithm can be run in parallel, it makes open-reference OTU picking tractable on massive amplicon sequence data sets. We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by “legacy” open-reference OTU picking, where less of the process can be parallelized, through comparisons on three well-studied datasets. We therefore recommend that subsampled open-reference OTU picking always be applied in favor of “legacy” open-reference OTU picking. An implementation of this algorithm is provided in the popular QIIME software package. Finally, we present a comparison of parameter settings in QIIME’s OTU picking workflows and make recommendations on settings for these free parameters.
Bayesian estimation of predator diet composition from fatty acids and stable isotopes
Authors: Neubauer Philipp , Jensen Olaf P
Published: January 2018

Quantitative analysis of stable isotopes (SI) and, more recently, fatty acid profiles (FAP) are useful and complementary tools for estimating the relative contribution of different prey items in the diet of a predator. The combination of these two approaches, however, has thus far been limited and qualitative. We propose a mixing model for FAP that follows the Bayesian machinery employed in state-of-the-art mixing models for SI. This framework provides both point estimates and probability distributions for individual and population level diet proportions. Where fat content and conversion coefficients are available, they can be used to improve diet estimates. This model can be explicitly integrated with analogous models for SI to increase resolution and clarify predator-prey relationships. We apply our model to simulated data and an experimental dataset that allows us to illustrate modeling strategies and demonstrate model performance. Our methods are provided as an open source software package for the statistical computing environment R.
Effects of Deuterium Oxide on Cell Cycle and Vesicle Speed in RBL-2H3 Cells
Authors: Kalkur Roshni S , Ballast Andrew , Triplett Ashley R , Spendier Kathrin
Published: January 2018

For the first time we show the effects of deuterium oxide on the cell cycle and vesicle transport in rat basophilic leukemia (RBL-2H3) cells. RBL-2H3 cultured with 15 moles/L deuterium oxide were observed to halt near the G2-M-phase of the cell cycle. Experimental observations also showed an increase in vesicle speed. This increase in vesicle speed was not observed in cultures treated with a microtubule-destabilizing drug suggesting that deuterium oxide affects microtubule-dependent vesicle transport.
Oxygen transport and release of adenosine triphosphate in micro-channels and arterioles in the human microcirculation
Authors: Moschandreou Terry
Published: January 2018

The governing nonlinear equations for oxygen transport and ATP concentration in a microfluidic channel and tube are solved in a novel way with the aid of Maple and COMSOL Multiphysics simulation software. Considering a model which assumes a larger plasma velocity near the wall of a channel/tube in comparison to RBC velocity near the centerline we obtain results showing clearly that there is a significant decrease in oxygen tension in the vicinity of an oxygen permeable membrane placed midway on the upper channel/tube wall and to the right side of it in the downstream field. The purpose of the membrane is to cause a rapid change in oxygen saturation as RBC’s flow through channel/tube. To the right of the membrane downstream the greatest amount of ATP is released. It is shown that for smaller arterioles there is an optimal size for which greater amounts of ATP can be released. Finally the corresponding time-dependent oxygen transport problem for plug flow in a channel, which has not been simulated in previous models in the literature, is analyzed and different starting times are shown for ATP release at different points in the channel. The FE modelling is very accurate: The time evolution problem is modelled and solved in it`s entirety with exact parameters used in the literature for blood flow and oxygen transport in the microcirculation. A comparison is made between the steady state and time dependent solutions in order to validate the results. The implications of the time dependent model for biological systems such as the human microcirculation requires exact information on release of energy as ATP is released from blood cells and the present work is important in providing this information. In particular, the time varying problem for ATP concentration and it’s temporal dynamics, as calculated in this paper is crucial in determining the ADP/ATP concentration pair which is an oscillating pair in the biochemical oscillations that occur in glycolysis in anaerobic yeast cultures.
Genetic profiling of the isoprenoid and sterol biosynthesis pathways of Trypanosoma cruzi
Authors: Cosentino Raul O , Diosque Patricio , Agüero Fernán
Published: January 2018

Background. Sterols such as cholesterol, are important components of cellular membranes. But unlike mammalian cells, the main sterols found in the membranes of trypanosomes and fungi are ergosterol, and other 24-methyl sterols, which are required for growth and viability. In spite of this strict requirement, this group of organisms have evolved different strategies to produce and/or obtain sterols. Trypanosoma cruzi is the causative agent of Chagas Disease. In this parasite, one of the few validated targets for chemotherapeutic intervention is the sterol biosynthesis pathway. In this work we present a study of the genetic diversity observed in genes of the isoprenoid and sterol biosynthesis pathways in T. cruzi, and a comparative analysis of the diversity found in other trypanosomatids.

Methodology/Principal Findings. Using a number of bioinformatic strategies, we first completed a number of holes in the pathway by identifying the sequences of genes that were missing and/or were truncated in the draft T. cruzi genome. Based on this analysis we identified a non-orthologous homolog of the yeast ERG25 gene (sterol methyl oxidase, SMO) and propose that the orthologs of ERG25 have been lost in trypanosomes (but not in leishmanias). Next, starting from a set of 16 T. cruzi strains representative of six major evolutionary lineages, we have amplified and sequenced ~ 24Kbp from 18 genes of the pathway, and identified a total of 975 SNPs or fixed differences, of which 28% represent nonsynonymous changes. We observed different patterns of accumulation of nucleotide changes for different genes of the pathway, from genes with a density of substitutions ranging from those close to the average (~2.5/100 bp) to some showing a high number of changes (11.4/100 bp, for a putative lathosterol oxidase gene). The majority of genes are under apparent purifying selection. However, two genes (TcPMK, TcSMO-like) have a ratio of nonsynonymous to synonymous changes that is close to neutrality. None of the nonsynonymous changes identified affect a catalytic or a ligand binding site residue. However, after mapping these changes on top of available structural data, we identified a number of changes that are in the close vicinity (7 Angstrom) of key residues, and that could therefore be functionally important. A comparative analysis of the corresponding T. brucei and Leishmania genes, obtained from available complete genomes highlights a high degree of conservation of the pathway, but with differences in the genes that are under apparent purifying selection in each case.

Conclusions/Significance. We have identified a number of genes of the sterol biosynthesis pathway that were missing from the T. cruzi genome assembly. Also, we have identified unequal apparent selection acting on these genes, which may provide essential information for the future of drug development studies focused on this pathway.
Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression
Authors: Polka Jessica , Silver Pamela A
Published: January 2018

Bacterial from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical.

Here we show that B. subtilis, an organism which typically does not respond to media compression, can be induced to do so with two simple and synergistically perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases cell length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells.

These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a genetically tractable chassis for engineering compression sensitive organisms in the future. Second, the sensitivity of colony morphology to media compression in Bacillus is a physical rather than biological phenomenon dependent on a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof.
Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression
Authors: Polka Jessica , Silver Pamela A
Published: January 2018

Bacterial from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical.

Here we show that B. subtilis, an organism which typically does not respond to media compression, can be induced to do so with two simple and synergistic perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases cell length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells.

These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a genetically tractable chassis for engineering compression sensitive organisms in the future. Second, the sensitivity of colony morphology to media compression in Bacillus is a physical rather than biological phenomenon dependent on a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof.
Psycho-social determinants of antenatal anxiety and depression in Pakistan: Is social support a mediator?
Authors: Waqas Ahmed , Raza Nahal , Wajid Lodhi Haneen , Muhammad Zerwah , Jamal Mehak , Suleman Abdul Rehman AR
Published: January 2018

Introduction: Pregnancy is generally viewed as a time of fulfillment and joy, however, for many women, it can be a stressful event. In South Asia, it is associated with cultural stigmas revolving around gender discrimination, abnormal births and genetic abnormalities. It is also associated with several psychiatric problems in women, most notably, depression and anxiety. Methodology: This cross sectional study was undertaken in four teaching hospitals in Lahore from February, 2014 to June, 2014. 500 Pregnant women presenting at the outdoors of obstetrics and gynecology department were interviewed. The questionnaire consisted of three sections: Demographics, Hospital anxiety and depression scale and social provision scale. Data was analyzed in SPSS v.20. Descriptive statistics were analyzed for demographics. Pearson Chi Square, Bivariate Correlations and Partial Correlations were run to analyze associations of independent variables with scores on HAD scale and SPS. Results: There were a total of 500 respondents. Mean age of respondents was 27.41 years (5.65). Anxiety levels of participants were categorized as Normal 145 (29%), borderline 110 (22%) and anxious 245 (49%). Depression levels were categorized as 218 (43.6%) normal, 123 (24.6%) borderline, and 159 (31.8%) depressed. Inferential analysis revealed that higher scores on HAD scale were significantly associated with lower scores on SPS, rural background, history of harassment, abortion, C-sections and unplanned pregnancies (P < .05). Social support also mediated the relationship between total numbers of children, gender of previous offspring and scores on HAD and SPS scales. Women reporting higher numbers of female children were significantly associated with higher scores on HAD scale and lower on SPS scale. Whereas increasing number of male progeny were associated with low scores on these scales (P < .05). Conclusion: Keeping in context the predominantly patriarchal socio-cultural setting, the predictors of antenatal anxiety and depression in Pakistan may differ from those of the developed countries. Rural women and working women showed higher levels of antenatal anxiety and depression, which contradicts studies from western countries. Our study revealed higher number of female progeny was associated with higher levels of depression and anxiety while male progeny had a protective influence. We, therefore, suggest that interventions designed to reduce antenatal anxiety and depression should take these unique factors, operating in developing countries and patriarchal societies, into account in their design and implementation.
Psycho-social determinants of antenatal anxiety and depression in Pakistan: Is social support a mediator?
Authors: Waqas Ahmed , Raza Nahal , Wajid Lodhi Haneen , Muhammad Zerwah , Jamal Mehak , Suleman Abdul Rehman AR
Published: January 2018

Introduction: Pregnancy is generally viewed as a time of fulfillment and joy, however, for many women, it can be a stressful event. In South Asia, it is associated with cultural stigmas revolving around gender discrimination, abnormal births and genetic abnormalities. It is also associated with several psychiatric problems in women, most notably, depression and anxiety.

Methodology: This cross sectional study was undertaken in four teaching hospitals in Lahore from February, 2014 to June, 2014. 500 Pregnant women presenting at the outdoors of obstetrics and gynecology department were interviewed. The questionnaire consisted of three sections: Demographics, Hospital anxiety and depression scale and social provision scale. Data was analyzed in SPSS v.20. Descriptive statistics were analyzed for demographics. Pearson Chi Square, Bivariate Correlations and linear regression were run to analyze associations of independent variables with scores on HAD scale and SPS.

Results: There were a total of 500 respondents. Mean age of respondents was 27.41 years (5.65). Anxiety levels of participants were categorized as Normal 145 (29%), borderline 110 (22%) and anxious 245 (49%). Depression levels were categorized as 218 (43.6%) normal, 123 (24.6%) borderline, and 159 (31.8%) depressed. Inferential analysis revealed that higher scores on HAD scale were significantly associated with lower scores on social provisions scale (SPS), rural background, history of harassment, abortion, C-sections and unplanned pregnancies (P < .05).

Social support also mediated the relationship between gender of previous offspring and scores on HAD scale. Women reporting higher numbers of female children were significantly associated with higher scores on HAD scale and lower on SPS scale. Whereas increasing number of male progeny were associated with low scores on depression subscale (P < .05).

Conclusion: Keeping in context the predominantly patriarchal socio-cultural setting, the predictors of antenatal anxiety and depression in Pakistan may differ from those of the developed countries. Rural women and working women showed higher levels of antenatal anxiety and depression, which contradicts studies from western countries. Our study revealed higher number of female progeny was associated with higher levels of depression and anxiety while male progeny had a protective influence. We, therefore, suggest that interventions designed to reduce antenatal anxiety and depression should take these unique factors, operating in developing countries and patriarchal societies, into account in their design and implementation.
Non invasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches
Authors: Asakura Taiga , Sakata Kenji , Yoshida Seiji , Date Yasuhiro , Kikuchi Jun
Published: January 2018

An NMR-based metabolomic approach in aquatic ecosystems is valuable for studying the environmental effects of pharmaceuticals and other chemicals on fish. This technique has also contributed to new information in numerous research areas, such as basic physiology and development, disease, and water pollution. We evaluated the microbial diversity in various fish species collected from Japan’s coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fish-microbial symbiotic ecosystems in laboratory-scale experiments. Intestinal bacteria of fish in their natural environment were characterized (using 16S rRNA genes) for trophic level using pyrosequencing and noninvasive sampling procedures developed to study the metabolism of intestinal symbiotic ecosystems in fish reared in their environment. Metabolites in feces were compared, and intestinal contents and feed were annotated based on HSQC and TOCSY using SpinAssign and network analysis. Feces were characterized by species and varied greatly depending on the feeding types. In addition, feces samples demonstrated a response to changes in the time series of feeding. The potential of this approach as a non-invasive inspection technique in aquaculture is suggested.
Morphometric analysis of feedforward pathways from the primary somatosensory area (S1) of rats
Authors: de Sá Andrea Lima , Castro Corrêa Vânia , Pacheco Bahia Carlomagno , Dias Ivanira , Gomes Leal Walace , Pinho André Luís Santos , Houzel Jean-Christophe , Picanço Diniz Cristovam Wanderley , Pereira Antonio
Published: January 2018

In this report, we used biotinylated dextran amine to anterogradely label individual axons projecting from primary somatosensory cortex (S1) to four cortical areas in rats, namely the secondary somatosensory (S2), the parietal ventral (PV), the perirhinal (PR), and the contralateral S1 (S1c). A major goal was to determine whether axon terminals could be classified on the basis of morphological criteria, such as the shape and density of boutons, and the shape and size of individual terminal arbors. Evidence from reconstruction of isolated axon terminal fragments (n=111) supported a degree of morphological heterogeneity. In particular, morphological parameters associated with the complexity of terminal arbors and the proportion of beaded, en passant boutons (Bp) vs. stalked boutons terminaux (Bt) were found to differ significantly. Two broad groups could be established following a discriminant function analysis across axon fragments. Both groups occurred in all four target areas, possibly consistent with a commonality of presynaptic processing of tactile information in these areas. However, more work is needed to investigate synaptic function at the single bouton level and see how this might be associated with emerging properties in the postsynaptic targets.
Collective cognitive epidemiology: Introducing subjective parameters into disease spread models
Authors: Akundi Aditya , Zarei Milad , Smith Eric D
Published: January 2018

Modern instances of disease emergence have shown that human subjective reactions to a novel disease can be as important as the objective reality of the disease spread. Therefore, this work introduces human cognitive heuristics and biases into epidemiological modeling. Human subjective perception and reaction to the presence of the disease is represented in the difference between the objective and subjective probability of contagion. It is assumed that humans within a disease spread situation will have either limited or full information about the objective probability of contagion. From this information, humans subjectively react, forming a subjective assessment of probability of contagion. Although the translation from the objective to subjective probability of contagion is rooted in a biological basis, the translation has been adequately determined by previous research in Prospect theory as developed by Daniel Kahneman and Amos Tversky. The formulation of Lotka-Volterra epidemiology models with parameters for perceived probability of contagion was followed by numerical experimentation and sensitivity analysis that determined values of parameters that create cyclic population behavior, whether growing or dampened, as well as acyclic behavior. The results show that the model is capable of capturing stable as well as unstable behavior, and is able to model key epidemiological disease behaviors and states, such as epidemic and endemic conditions.
Selective comparability and physiological studies of lactic acid bacteria protease and Calotropis procera (linn) extracts
Authors: Akinkugbe Abiodun O , Onilude Abiodun A
Published: January 2018

The West African soft cheese (wara) is traditionally produced using latex extracts of the leaves of Calotropis procera. Even though no death has been apparently traced to it, the extract is said to be poisonous causing death by paralysis of the heart. This project, therefore, aims at obtaining an alternative (in this case lactic acid bacteria protease) to the latex extract of C. procera in order to rule out possible poisoning effect. The physiological characteristics of such alternative protease was studied and compared to that of the extracts from C. procera. Seven lactic acid bacteria species were isolated from samples of the West African soft cheese (wara) obtained from local retailers. They were identified as Streptococcus lactis , Streptococcus pyogenes, Lactobacillus acidophilus, Lactobacillus brevis, Leuconostoc mesenteroides, Lactococcus lactis and Streptococcus faecalis. The isolates were subjected to growth and protease production studies. Optimization of protease production was carried out on three selected isolates - Streptococcus lactis, Lactobacillus acidophilus and Lactococcus lactis. Enzymes obtained were further characterized and separated using molecular exclusion procedures. Results obtained were compared to those of different extracts of C. procera. It was observed that Streptococcus lactis had the highest (4.25 units/ml) protease production at 28°C after 72 hours with peptone and casein as nitrogen sources in the presence of glucose as carbon source. The ethanolic extract of Calotropis procera had the highest protease activity (12.60 units/ml) at 5% substrate concentration. Lactococcus lactis and C. procera extracts were inhibited (0.00 units/ml) at 0.2M and 0.3M concentrations EDTA respectively thus suggesting the presence of a metallic protease. Na2+ ion was seen to enhance protease activity in all the extracts. Comparative results show that Streptococcus lactis protease had a Km of 0.42 mg/ml for casein at a Vmax of 2.0; Lactobacillus acidophilus protease had a Km of 0.77 mg/ml for casein at a Vmax of 2.50; Lactococcus lactis protease had a Km of 3.3 mg/ml for casein at a Vmax of 0.87; The crude extract of Calotropis procera had a Km of 5.0 mg/ml for casein at a Vmax of 1.54; the ethanolic extract of C. procera had a Km of 2.44 mg/ml for casein at a Vmax of 8.77 while the methanolic extract of C. procera had a Km of 5.0 mg/ml for casein at a Vmax of 4.17. In conclusion, the lactic acid bacteria protease from Streptococcus lactis was found to fare better physiologically, while the protease from the ethanolic extract of C. procera faired better amongst the plant extracts.