bluuebunny/crossref_metadata_2025_split huggingface dataset:
Saccadic foraging reveals mechanisms of value-based decision-making in primate superior colliculus
Authors: Zhang Beizhen , Kan Janis Ying Ying , Dorris Michael Christopher 
Published: September 2019

AbstractMuch progress has been made in understanding the neural basis of value-based decision-making using two-alternative forced-choice tasks. A limitation of these tasks is that the value of each option is often confounded with other cognitive factors (e.g. attention/choice probability/motor preparation). To overcome this limitation, monkeys were trained to use gaze to forage among many visual targets of varying value while neurophysiology was conducted in the saccade control center superior colliculus (SC). Surprisingly, each target’s value was represented in the SC predominantly in an absolute manner, that is, irrespective of the value of other available items. After fixating a target, the next choice was quickly selected once neural activity rose to a provisional ‘selection level’. This selection level systematically decreased, not as individual targets were harvested, but only after a class of value items was completely depleted. Our results reveal the exquisite balance across SC activities that transform value to choice.
The response ofPseudomonas putidato a complex lignolysate
Authors: Park Mee-Rye , Chen Yan , Thompson Mitchell , Benites Veronica T. , Fong Bonnie , Petzold Christopher J. , Baidoo Edward E. K. , Gladden John M. , Adams Paul D. , Keasling Jay D. , Simmons Blake A. , Singer Steven W. 
Published: September 2019

AbstractThere is strong interest in the valorization of lignin derived from plant biomass to produce valuable products; however, the structural complexity of this biopolymer has been a major bottleneck to conversion. Chemical pretreatment liberates soluble fractions of lignin that may be upgraded by biological conversion. Here, ionic liquid pretreatment was employed to obtain soluble aromatic-rich fractions from sorghum, which were converted byPseudomonas putidaKT2440, a promising host for bioconversion of aromatics derived from lignin. Growth studies and mutational analysis demonstrated thatP. putidagrowth on these soluble lignin-derived fractions, referred to as lignolysate, was dependent on aromatic monomers derived from lignin (p-coumarate and ferulate), but other, unknown factors in the lignolysate contributed to growth. Proteomic and metabolomic analyses provided evidence that these unknown factors were amino acids and residual ionic liquid. Proteomic measurements indicated a coordinated response in which these substrates were catabolized simultaneously. A cholinium catabolic pathway was identified and deletion of five genes in the pathway abrogated the ability ofP. putidato grow on cholinium as a sole carbon source. This work demonstrates that lignolysates obtained through biomass pretreatment contain multiple substrates and conversion strategies for lignin-derived should take this complexity into account.ImportanceLignin is one of the most abundant biopolymers on Earth and is generated as a co-product in the processing of lignocellulosic biomass. Valorization of these residual lignin streams is a promising method to enhance the economic viability of modern lignocellulosic biorefineries. In this study we developed a process to couple chemical depolymerization of lignin and biological conversion usingPseudomonas putidaKT2440. Water-soluble and bioavailable lignolysate was obtained from sorghum and further characterized as a growth substrate forP. putida. Proteomic and metabolomic analyses demonstrated that P. putida metabolized other components of the lignolysate beyond monoaromatic compounds, which illuminates how microbes can process complex lignolysates obtained from plants. Understanding the underlying microbial responses in lignolysates will enable the design of rational strategies for lignin valorization.
Search as a simple take-the-best heuristic
Authors: Yahosseini Kyanoush Seyed , Moussaïd Mehdi 
Published: September 2019

AbstractHumans commonly engage in a variety of search behaviours, for example when looking for an object, a partner, information, or a solution to a complex problem. The success or failure of a search strategy crucially depends on the structure of the environment and the constraints it imposes on the individuals. Here we focus on environments in which individuals have to explore the solution space gradually and where their reward is determined by one unique solution they choose to exploit. This type of environment has been relatively overlooked in the past despite being relevant to numerous real-life situations, such as spatial search and various problem-solving tasks.By means of a dedicated experimental design, we show that the search behaviour of experimental participants can be well described by a simple heuristic model. Both in rich and poor solution spaces, a take-the-best procedure that ignores all but one cue at a time is capable of reproducing a diversity of observed behavioural patterns. Our approach, therefore, sheds lights on the possible cognitive mechanisms involved in human search.
Species-specific secretion of ESX-5 type VII substrates is determined by the linker 2 of EccC5
Authors: Bunduc C. M. , Ummels R. , Bitter W. , Houben E.N.G. 
Published: September 2019

AbstractType VII secretion systems (T7SSs) are used by mycobacteria to translocate a wide range of effector proteins across their diderm cell envelope. These systems, also known as ESX systems, have crucial roles for the viability and/or virulence of mycobacterial pathogens, including Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum. We previously observed species-specificity in the secretion of the PE_PGRS proteins by the ESX-5 system [1], in that the M. tuberculosis ESX-5 system was unable to fully complement an M. marinum esx-5 mutant. In this study, we established that the responsible factor for this is the central membrane ATPase EccC5, which has three nucleotide binding domains (NBDs). By creating chimeric M. marinum/M. tuberculosis EccC5 constructs, we observed that PE_PGRS secretion is mediated only in the presence of an EccC5 containing the cognate linker 2, irrespective of the origin of the EccC5 backbone. This region is responsible for linking the first two NBDs and for keeping the first NBD in an inhibited state. Notably, this region is disordered in a EccC crystal structure and is particularly extended in EccC proteins of the different ESX-5 systems. These results indicate that this region is involved in species-specific substrate recognition and might therefore be an additional substrate recognition site of EccC5.
GroundwaterElusimicrobiaare metabolically diverse compared to gut microbiomeElusimicrobiaand some have a novel nitrogenase paralog
Authors: Méheust Raphaël , Castelle Cindy J. , Carnevali Paula B. Matheus , Farag Ibrahim F. , He Christine , Chen Lin-Xing , Amano Yuki , Hug Laura A. , Banfield Jillian F. 
Published: September 2019

AbstractCurrently described members ofElusimicrobia, a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-livingElusimicrobiahave been detected in sediments, soils and groundwater, raising questions regarding their metabolic capacities and evolutionary relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, including 30 newly reconstructed genomes, from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater-associatedElusimicrobiaare predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds andRhodobacternitrogen fixation-dependent (Rnf-dependent) acetogenesis with hydrogen and carbon dioxide as the substrates. Genomes from two clades of groundwater-associatedElusimicrobiaoften encode a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. We identified similar genomic loci in genomes of bacteria from the Gracilibacteria phylum and theMyxococcalesorder and predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associatedElusimicrobiaclades nest phylogenetically within two free-living-associated clades. Thus, we propose an evolutionary trajectory in which someElusimicrobiaadapted to animal-associated lifestyles from free-living species via genome reduction.
A model for the regulation of the timing of cell division by the circadian clock in the cyanobacterium Synechococcus elongatus
Authors: Ho Po-Yi , Martins Bruno M.C. , Amir Ariel 
Published: September 2019

1SummaryCells of the cyanobacterium Synechococcus elongatus possess a circadian clock in the form of three core clock proteins (the Kai proteins) whose concentrations and phosphorylation states oscillate with daily periodicity under constant conditions [1]. The circadian clock regulates the cell cycle such that the timing of cell divisions is biased towards certain times during the circadian period [2, 3, 4, 5], but the mechanism underlying how the clock regulates division timing remains unclear. Here, we propose a mechanism in which a protein limiting for division accumulates at a rate proportional to cell volume growth and modulated by the clock. This “modulated rates” model, in which the clock signal is integrated over time to affect division timing, differs fundamentally from the previously proposed “gating” concept, in which the clock is assumed to suppress divisions during a specific time window [2, 3]. We found that while both models can capture the single-cell statistics of division timing in S. elongatus, only the modulated rates model robustly places divisions away from darkness during changes in the environment. Moreover, within the framework of the modulated rates model, existing experiments on S. elongatus are consistent with the simple mechanism that division timing is regulated by the accumulation of a division limiting protein in phase with genes whose activity peak at dusk.
Transcriptomic response ofNitrosomonas europaeatransitioned from ammonia- to oxygen-limited steady-state growth
Authors: Sedlacek Christopher J. , Giguere Andrew T. , Dobie Michael D. , Mellbye Brett L. , Ferrell Rebecca V , Woebken Dagmar , Sayavedra-Soto Luis A. , Bottomley Peter J. , Daims Holger , Wagner Michael , Pjevac Petra 
Published: September 2019

AbstractAmmonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacteriumNitrosomonas europaeais the best characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology ofN. europaea, e.g. by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation onN. europaeahave focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole genome transcriptomics to investigate the overall effect of oxygen limitation onN. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia to nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper containing cytochromecoxidases encoded byN. europaeawere upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement ofN. europaea’ssNOR with regards to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase inN. europaeaand other AOB.ImportanceNitrification is a ubiquitous, microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments increasing the eutrophication of downstream aquatic ecosystems and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their response to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here we investigate the physiology of the best characterized ammonia-oxidizing bacterium,Nitrosomonas europaea, growing under oxygen-limited conditions.
Genetic “General Intelligence,” Objectively Determined and Measured
Authors: de la Fuente Javier , Davies Gail , Grotzinger Andrew D. , Tucker-Drob Elliot M. , Deary Ian J. 
Published: September 2019

AbstractIt has been known for 125 years that, in humans, diverse cognitive traits are positively intercorrelated; this forms the basis for the general factor of intelligence (g). We directly test for a genetic basis for g using data from seven different cognitive tests (N = 11,263 to N = 331,679) and genome-wide autosomal single nucleotide polymorphisms. A genetic g factor accounts for 58.4% (SE = 4.8%) of the genetic variance in the cognitive traits, with trait-specific genetic factors accounting for the remaining 41.6%. We distill genetic loci broadly relevant for many cognitive traits (g) from loci associated with only individual cognitive traits. These results elucidate the etiological basis for a long-known yet poorly-understood phenomenon, revealing a fundamental dimension of genetic sharing across diverse cognitive traits.
Direct risk factors and cost performance of road projects in developing countries
Authors: Ogbu Chukwuemeka Patrick , Adindu Chinedu Chimdi 
Published: September 2019

Purpose
Globally, road projects are notorious for riskiness, which often results in cost overruns. In developing countries, these risks are amplified by economic instabilities and institutional failures. Majority of road projects in these countries are awarded to notedly inept indigenous contractors. Currently, research on the relationship between risks and cost performance of road projects has predominantly focussed on the client’s perspective. Effects of risks on contractors’ cost performance (profit) are inadequately investigated in literature. The purpose of this paper is to determine the relationship between direct risks and cost performance of road projects by indigenous contractors of developing countries from the contractors’ perspective.

Design/methodology/approach
The multivariate structural equation modelling technique was used to analyse purposively obtained data from indigenous contractors that recently completed road projects in Nigeria.

Findings
It was observed that a significant positive relationship exists between the aggregate project risk, i.e. project risk index of cost (PRIC) and cost performance of the projects. Significant positive relationships were also found to exist between identified cost risk centres and PRIC and between risk factors and cost risk centres. The risk centre site environment and location contributes the most to PRIC.

Research limitations/implications
Indigenous contractors of developing countries are to analyse the identified risk factors and centres prior to bidding for road projects and carefully manage them during project execution.

Originality/value
Future studies of risks in road project should aim to obtain project risk indices of costs for the projects.
Interaction of multiple cracks in a nonhomogeneous piezoelectric rectangular plane under an electromechanical loading
Authors: Kafaei Keyvan , Bagheri Rasul 
Published: September 2019

Purpose
In accord with the literature reviews, there is not a promising examination regarding the several straight and curved cracks interaction with arbitrary arrangement in the rectangular FGP plane. The purpose of this paper is to consider the effect of crack length, position of the point load, material non-homogeneity constant and also the arrangement of cracks on the resulting field intensity factors.

Design/methodology/approach
First of all, in order to obtain a set of Cauchy singular integral equations, both the dislocation method and the finite Fourier cosine transform technique are applied. Using the corresponding solution to these equations, the dislocation densities on the crack surfaces are then obtained. Considering the results, both the stress intensity factors (SIFs) and electric displacement intensity factors (EDIFs) for a vertical crack and the interaction between two straight and curved cracks, which have an arbitrary configuration, are determined.

Findings
The numerical examples are represented in order to illustrate the interesting mechanical and electrical coupling phenomena induced by multi-crack interactions. At the end, the effects of the material non-homogeneity constant, the crack length and the cracks arrangements on the SIFs and EDIFs are investigated.

Originality/value
The solutions are obtained in series expansion forms which may be considered as Green’s functions in an FGP rectangular plane possessing multiple cracks. The technique of Green’s function provides the ability to analyze multiple cracks having any smooth configuration.
MHD flow and heat transfer analysis of Newtonian and non-Newtonian nanofluids due to an inclined stretching surface
Authors: Nandeppanavar Mahantesh M. , Srinivasulu T. , Bandari Shanker 
Published: September 2019

Purpose
The purpose of this paper is to study the flow, heat and mass transfer of MHD Casson nanofluid due to an inclined stretching sheet using similarity transformation, the governing PDE’S equations of flow, heat and mass transfer are converted into ODE’S. The resulting non-linear ODE’S are solved numerically using an implicit finite difference method, which is known as Kellor-box method. The effects of various governing parameters on velocity, temperature and concentration are plotted for both Newtonian and non-Newtonian cases. The numerical values of skin friction, Nusselt number and Sherwood number are calculated and tabulated in various tables for different values of physical parameters. It is noticed that the effect of angle of inclination enhances the temperature and concentration profile whereas velocity decreases. The temperature decreases due to the increase in the parametric values of Pr and Gr due to thickening in the boundary layer.

Design/methodology/approach
Numerical method is applied to find the results.

Findings
Flow and heat transfer analysis w.r.t various flow and temperature are analyzed for different values of the physical parameters.

Research limitations/implications
The numerical values of skin friction, Nusselt number and Sherwood number are calculated and tabulated in various tables for different values of physical parameters.

Practical implications
The study of the boundary layer flow, heat and mass transfer is important due to its applications in industries and many manufacturing processes such as aerodynamic extrusion of plastic sheets and cooling of metallic sheets in a cooling bath.

Originality/value
Here in this paper the authors have investigated the MHD boundary layer flow of a Casson nanofluid over an inclined stretching sheet along with the Newtonian nanofluid as a limited.
Effects of rotation, voids and diffusion on characteristics of plane waves in a thermoelastic material
Authors: Singh Baljeet , Singla Himanshu 
Published: September 2019

Purpose
The purpose of this paper is to study the effects of rotation, voids and diffusion on characteristics of plane waves in a thermoelastic material.

Design/methodology/approach
Lord and Shulman generalization of linear thermoelasticity is used to study the plane waves in a rotating thermoelastic material with voids and diffusion. The thermoelastic solid is rotating with a uniform angular velocity. The problem is specialized in two dimensions to study wave propagation. The plane harmonic solutions of governing field equations in a plane are obtained.

Findings
A velocity equation is obtained which indicates the propagation of five coupled plane waves in the medium. Reflection of an incident plane wave from stress-free surface of a half-space is also considered to obtain the amplitude ratios of various reflected waves. A numerical example is considered to illustrate graphically the effects of rotation, frequency, void and diffusion parameters on speeds and amplitude ratios of plane waves.

Originality/value
The present problem covers the combined effects of rotation, voids and diffusion on characteristics of plane waves in linear thermoelastic material in the context of Lord and Shulman (1967) and Aouadi (2010) theories, which are not studied in literature yet.
Analysis of activation energy in quadratic convective flow of a micropolar fluid with chemical reaction and suction/injection effects
Authors: RamReddy C. , Naveen P. 
Published: September 2019

Purpose
The purpose of this paper is to analyze the combined effects of thermal radiation and activation energy with a chemical reaction on the quadratic convective flow of a micropolar fluid over an inclined plate. Convective thermal boundary condition and suction/injection effects are considered at the surface of an inclined plate.

Design/methodology/approach
The convection along with nonlinear Boussinesq approximation (i.e. quadratic convection or nonlinear convection) and usual boundary layer assumptions is employed in the mathematical formulation. Highly coupled nonlinear governing equations are tackled by a combined local non-similarity and successive linearization techniques.

Findings
The behavior of various pertinent parameters on the fluid flow characteristics is conferred through graphs and it reveals that the qualitative behaviors of velocity, temperature, skin friction and heat transfer rates of a micropolar fluid are similar for Biot number and radiation parameters. The suction/injection and activation energy parameters increase the concentration of the micropolar fluid within the boundary layer, while the chemical reaction parameter reduces the concentration in the same region. Further, this quadratic convection shows a strong influence on the fluid flow characteristics and then the impact of pertinent parameters is more prominent on the physical quantities, compared therewith results of the linear convection.

Practical implications
This kind of investigation is useful in the mechanism of combustion, aerosol technology, high-temperature polymeric mixtures and solar collectors which are operated at moderate to very high temperatures.

Originality/value
This attempt is a unique contribution to the establishment of both micropolar fluid and activation energy. This kind of study even in the absence of quadratic convection is not yet noted.