bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-monotonicity of Fano factor in a stochastic model for protein expression with sequesterisation at decoy binding sites
Authors: Hojcka Michal , Bokes Pavol 
Published: November 2017

We present a stochastic model motivatedВ by gene expression which incorporates unspecific interactionsВ between proteins and binding sites. WeВ focus on characterizing the distribution of free (i.e.В unbound) protein molecules in a cell. Although itВ cannot be expressed in a closed form, we presentВ three different approaches to obtain it: stochastic simulationВ algorithms, system of ODEs and quasi-steadystateВ solution. Additionally we use a large-system-sizeВ scaling to derive statistical measures of approximateВ distribution of the amount of free protein, such as theВ Fano factor. Intriguingly, we report that while in the absence of or in the excess of decoy binding sites theВ Fano factor is equal to one (suggestive of PoissonianВ fluctuations), in the intermediate regimes of moderateВ levels of binding sites the Fano factor is greater thanВ one (suggestive of super-Poissonian fluctuations). WeВ support and illustrate all of our results with numericalВ simulations.
Design and Testing of a Prosthetic Foot Prototype With Interchangeable Custom Rotational Springs to Adjust Ankle Stiffness for Evaluating Lower Leg Trajectory Error, an Optimization Metric for Prosthetic Feet
Authors: Prost Victor , Olesnavage Kathryn M. , Winter Amos G. 
Published: November 2017

A prosthetic foot prototype intended for evaluating a novel design objective for passive prosthetic feet, the Lower Leg Trajectory Error (LLTE), is presented. This metric enables the optimization of prosthetic feet by modeling the trajectory of the lower leg segment throughout a step for a given prosthetic foot and selecting design variables to minimize the error between this trajectory and target physiological lower leg kinematics. Thus far, previous work on the LLTE has mainly focused on optimizing conceptual foot architectures. To further study this metric, extensive clinical testing on prototypes optimized using this method has to be performed. Initial prototypes replicating the LLTE-optimal designs in previous work were optimized and built, but at 1.3 to 2.1 kg they proved too heavy and bulky to be considered for testing. A new, fully-characterized foot design reducing the weight of the final prototype while enabling ankle stiffness to be varied is presented and optimized for LLTE.
The novel merits of this foot are that it can replicate a similar quasi-stiffness and range of motion of a physiological ankle, and be tested with variable ankle stiffnesses to test their effect on LLTE. The foot consists of a rotational ankle joint with interchangeable U-shaped constant stiffness springs ranging from 1.5 Nm/deg to 16 Nm/deg, a rigid structure extending 0.093 m from the ankle-knee axis, and a cantilever beam forefoot with a bending stiffness of 16 Nm2. The prototype was built using machined acetal resin for the rigid structure, custom nylon springs for the ankle, and a nylon beam forefoot. In preliminary testing, this design performed as predicted and its modularity allowed us to rapidly change the springs to vary the ankle stiffness of the foot. Qualitative feedback from preliminary testing showed that this design is ready to be used in larger-scale studies. In future work, extensive clinical studies with testing different ankle stiffnesses will be conducted to validate the optimization method using the LLTE as a design objective.
Determination of Resistance Factor for Tortuous Paths in Drip Emitters
Authors: Narain Jaya , Winter Amos 
Published: November 2017

Drip irrigation has the potential to decrease water consumption and increase crop yields and profit. Globally, drip irrigation has had low adoption rates. There are several major barriers to adoption, including the cost of the system and its energy consumption. Mathematical models describing the behavior of drip emitters can provide insights on the performance of drip systems. The models and procedures developed in this paper can be used as a tool for the design of improved drip irrigation systems.
This paper presents a method of combining a CFD model that characterizes flow through the tortuous paths of emitters with an analytical model describing pressure-compensating behavior. The CFD model detailed in this paper was verified for three commercially available emitter designs. The model fell within acceptable variation bounds when compared to experimental data. The results of CFD analysis are represented in a resistance factor that can be used in a hybrid analytical-computational model. This method requires significantly less processing than using computational models alone.
Future work on this topic will detail an analytical model that accurately predicts the behavior of inline PC drip emitters of varying geometries and an optimization of the geometry to lower activation pressure and material costs. Analytical models to predict the flow behavior of a range of tortuous path designs given a prescribed geometry will also be developed.
Emergent Behavior Characterization of an Ant-Inspired, Multiple-Pheromone-Driven Robot Swarm
Authors: Schroeder Adam M. , Mohamed Marwan H. , Trease Brian P. 
Published: November 2017

Inspired by chemotactic phenomena observed in ants where individual ants can distinguish their own pheromone from others in their colony, a novel control paradigm for a robot swarm is introduced where each agent deposits an agent-specific, diffusive and evaporative pheromone. Agent’s are repulsed by the pheromone and execute a biased random walk from high-concentration to low-concentration areas. The biased random walk is Lévy flight which causes ‘anomalous diffusion’ by the agents. The ratio of an agent’s sensitivity to its own pheromone compared to other ant’s pheromones, called ‘vanity’, is varied and swarm behavior is characterized using general metrics, e.g. mean squared displacement, and application-specific metrics.
It was found that varying the agent vanity resulted in smooth trends in the general behavior metrics, but bifurcations appeared in the application-specific, area coverage metrics. This control scheme is also compared to a scheme that uses a global, common pheromone.
Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization
Authors: Orellana Luis H. , Chee-Sanford Joanne C. , Sanford Robert A. , Löffler Frank E. , Konstantinidis Konstantinos T. 
Published: November 2017

ABSTRACT

The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for a better understanding of nutrient cycling. Here, we analyzed 20 short-read metagenomes collected at four time points during 1 year from two depths (0 to 5 and 20 to 30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty loam) with similar cropping histories. Although the microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural aquatic ecosystems. For example, among the 69 population genomes assembled from the metagenomes, 75% showed a less than 2-fold change in abundance between any two sampling points. Interestingly, six deep-branching
Thaumarchaeota
and three complete ammonia oxidizer (comammox)
Nitrospira
populations increased up to 5-fold in abundance upon the addition of N fertilizer. These results indicated that indigenous archaeal ammonia oxidizers may respond faster (are more copiotrophic) to N fertilization than previously thought. None of 29 recovered putative denitrifier genomes encoded the complete denitrification pathway, suggesting that denitrification is carried out by a collection of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations in agricultural soils that should facilitate future monitoring efforts and N-related studies.

IMPORTANCE
Even though the impact of agricultural management on the microbial community structure has been recognized, an understanding of the dynamics of individual microbial populations and what functions each population carries are limited. Yet, this information is important for a better understanding of nutrient cycling, with potentially important implications for preserving nitrogen in soils and sustainability. Here, we show that reconstructed metagenome-assembled genomes (MAGs) are relatively stable in their abundance and functional gene content year round, and seasonal nitrogen fertilization has selected for novel
Thaumarchaeota
and comammox
Nitrospira
nitrifiers that are potentially less oligotrophic than their marine counterparts previously studied.
Enhancing the Thermostability of Rhizomucor miehei Lipase with a Limited Screening Library by Rational-Design Point Mutations and Disulfide Bonds
Authors: Li Guanlin , Fang Xingrong , Su Feng , Chen Yuan , Xu Li , Yan Yunjun 
Published: November 2017

ABSTRACT

Rhizomucor miehei
lipase (RML), as a kind of eukaryotic protein catalyst, plays an important role in the food, organic chemical, and biofuel industries. However, RML retains its catalytic activity below 50°C, which limits its industrial applications at higher temperatures. Soluble expression of this eukaryotic protein in
Escherichia coli
not only helps to screen for thermostable mutants quickly but also provides the opportunity to develop rapid and effective ways to enhance the thermal stability of eukaryotic proteins. Therefore, in this study, RML was engineered using multiple computational design methods, followed by filtration via conservation analysis and functional region assessment. We successfully obtained a limited screening library (only 36 candidates) to validate thermostable single point mutants, among which 24 of the candidates showed higher thermostability and 13 point mutations resulted in an apparent melting temperature (

T

m

app

) of at least 1°C higher. Furthermore, both of the two disulfide bonds predicted from four rational-design algorithms were further introduced and found to stabilize RML. The most stable mutant, with T18K/T22I/E230I/S56C-N63C/V189C-D238C mutations, exhibited a 14.3°C-higher

T

m

app

and a 12.5-fold increase in half-life at 70°C. The catalytic efficiency of the engineered lipase was 39% higher than that of the wild type. The results demonstrate that rationally designed point mutations and disulfide bonds can effectively reduce the number of screened clones to enhance the thermostability of RML.

IMPORTANCE
R. miehei
lipase, whose structure is well established, can be widely applied in diverse chemical processes. Soluble expression of
R. miehei
lipase in
E. coli
provides an opportunity to explore efficient methods for enhancing eukaryotic protein thermostability. This study highlights a strategy that combines computational algorithms to predict single point mutations and disulfide bonds in RML without losing catalytic activity. Through this strategy, an RML variant with greatly enhanced thermostability was obtained. This study provides a competitive alternative for wild-type RML in practical applications and further a rapid and effective strategy for thermostability engineering.
Genome Sequences of Acholeplasma laidlawii Strains Differing in Sensitivity to Ciprofloxacin
Authors: Medvedeva Elena S. , Siniagina Maria N. , Malanin Sergey Y. , Boulygina Eugenia A. , Malygina Tatyana Y. , Baranova Natalia B. , Mouzykantov Alexey A. , Davydova Marina N. , Chernova Olga A. , Chernov Vladislav M. 
Published: November 2017

ABSTRACT

Acholeplasma laidlawii
is a well-suited model for study of the molecular basis of the adaptation of mollicutes to environmental conditions. Here we present the whole-genome sequences of four strains of
A. laidlawii
with differential sensitivity to ciprofloxacin.
Draft Genome Sequences of the Black Rock Fungus
Knufia petricola
and Its Spontaneous Nonmelanized Mutant
Authors: Tesei Donatella , Tafer Hakim , Poyntner Caroline , Piñar Guadalupe , Lopandic Ksenija , Sterflinger Katja 
Published: November 2017

ABSTRACT

The fungal genus
Knufia
mostly comprises extremotolerant species from environmental sources, especially rock surfaces. The draft genome sequence of the rock fungus
Knufia petricola
presented here is the first whole-genome sequence of the only species among black fungi known to have a nonmelanized spontaneous mutant.
A history of multiple concussions does not confer long-term impairments to dynamic cerebral autoregulation
Authors: Wright Alexander D , Smirl Jonathan D , Fraser Sarah K , Bryk Kelsey , Donkelaar Paul van 
Published: November 2017

ObjectiveTo examine the effects of concussion history on an index of cerebral autoregulation in a healthy athlete population.DesignRetrospective Cohort.SettingLaboratory.Participants136 male contact sport athletes (19.1±1.4 years, 66 football, 70 hockey) were recruited; 39 presented with 0 previous concussions, 16 with 3+ previous concussions; exclusion criteria included history of concussion within 6 months.InterventionParticipants completed baseline testing prior to the athletic season. Squat-stand manoeuvres at 0.05 and 0.10 Hz were used to enhance blood pressure (BP) variation. BP and cerebral blood velocity (CBV) in the middle cerebral artery were indexed non-invasively via finger photoplethysmography and transcranial Doppler ultrasound, respectively. Independent variables included sport (2) and concussion history (2).OutcomesTransfer function analysis point estimates at 0.05 and 0.10 Hz characterised the coherence (correlation), phase (synchronisation), and gain (amplitude buffer) between BP and CBV waveforms during the squat-stand manoeuvres.ResultsThese findings suggest that, despite reductions in 0.10 Hz phase lead being reported acutely after concussion, multiple concussions do not appear to induce long-term impairments in dynamic cerebral autoregulation metrics. This is an important revelation as it indicates that the cerebrovasculature is able to adequately recover following the acutely diminished buffering capacity associated with a concussive injuryConclusionsThese findings suggest that, despite reductions in 0.10 Hz phase lead being reported acutely after concussion, multiple concussions do not appear to induce long-term impairments in dynamic cerebral autoregulation metrics. This is an important revelation as it indicates that the cerebrovasculature is able to adequately recover following the acutely diminished buffering capacity associated with a concussive injuryCompeting interestsNone.
Brains with sporadic Creutzfeldt-Jakob disease and copathology showed a prolonged end-stage of disease
Authors: Miguelez-Rodriguez Aitzol , Santos-Juanes Jorge , Vicente-Etxenausia Ikerne , Perez de Heredia-Goñi Katty , Garcia Beatriz , Quiros Luis M , Lorente-Gea Laura , Guerra-Merino Isabel , Aguirre Jose J , Fernandez-Vega Ivan 
Published: November 2017

AimsTo investigate the expression of major proteins related to primary neurodegenerative diseases and their prognostic significance in brains with Creutzfeldt-Jakob disease (CJD).Materials and methodsThirty consecutive cases of confirmed CJD during the period 2010–2015 at Basque Brain bank were retrospectively reviewed. Moreover, major neurodegenerative-associated proteins (phosphorylated Tau, 4R tau, 3R tau, alpha-synuclein, TDP43, amyloid beta) were tested. Clinical data were reviewed. Cases were divided according to the presence or absence of copathology. Survival curves were also determined.ResultsCopathology was significantly associated with survival in brains with CJD (4.2±1.2 vs 9.2±1.9; P=0.019) and in brains with MM1/MV1 CJD (2.1±1.0 vs 6.7±2.8; P=0.012). Besides, the presence of more than one major neurodegenerative-associated protein was significantly associated with survival (4.2±1.2 vs 10.7±2.6; P=0.017). Thus, univariate analyses further pointed out variables significantly associated with better survival: copathology in CJD (HR=0.430; P=0.033); more than one neurodegenerative-associated protein in CJD (HR=0.369; P=0.036) and copathology in MM1/MV1 CJD (HR=0.525; P=0.032).ConclusionThe existence of copathology significantly prolongs survival in patients with rapidly progressive dementia due to CJD. The study of major neurodegenerative-associated proteins in brains with CJD could allow us to further understand the molecular mechanisms behind prion diseases.
United Nations Global Compact: an ‘Inroad’ into the UN and reputation boost for the tobacco industry
Authors: van der Eijk Yvette , McDaniel Patricia A , Glantz Stanton A , Bialous Stella A 
Published: November 2017

BackgroundThe United Nations Global Compact (UNGC), a UN initiative to engage corporations in supporting the UN’s mission, sets out principles that companies should follow for more ethical business practices. Since its inception in 2000, at least 13 tobacco companies, subsidiaries and tobacco industry affiliates joined the UNGC. In a September 2017 integrity review, the UNGC Board excluded from UNGC participation companies who derive revenue from tobacco production or manufacturing.ObjectiveTo determine, from the tobacco industry’s perspective, tobacco companies’ motives for joining the UNGC.MethodTobacco industry documents search using the Truth Tobacco Industry Documents Library, and search of published reports and documents on the tobacco industry and the UNGC.ResultsTobacco companies sought to join the UNGC for two reasons: (1) to improve their reputation, in keeping with other corporate social responsibility efforts; (2) to gain proximity to UN agencies and weaken the WHO’s influence, part of an overall strategy to undermine the WHO Framework Convention on Tobacco Control.ConclusionsExcluding tobacco manufacturers from UNGC participation is an important step to limit the tobacco industry’s ability to influence the UN and promote its image and, by extension, its deadly products. It is important to monitor enforcement of this policy and resist the engagement of tobacco industry front groups, such as industry-funded foundations, with the UNGC.
Chapter 6 Material properties and geohazards
Authors: Culshaw M. G. , Entwisle D. C. , Giles D. P. , Berry T. , Collings A. , Banks V. J. , Donnelly L. J. 
Published: November 2017

Abstract
In engineering terms, all materials deposited as a result of glacial and periglacial processes are transported soils. Many of these deposits have engineering characteristics that differ from those of water-lain sediments. In the UK, the most extensive glacial and periglacial deposits are tills. Previously, engineering geologists have classified them geotechnically as lodgement, melt-out, flow and deformation tills, or as variants of these. However, in this book tills have been reclassified as: subglacial traction till, glaciotectonite and supraglacial mass-flow diamicton/glaciogenic debris-flow deposits (see Chapter 4, Sections 4.1–4.3). Because this classification is new, it is not possible to relate geotechnical properties and characteristics to the subdivisions of the new classification. Consequently, the domain/stratigraphic classification, recently developed by the British Geological Survey and others, has been used and their geotechnical properties and characteristics are discussed on this basis. The geotechnical properties and characteristics of the other main glacial and periglacial deposits are also discussed. For some of these (e.g. glaciolacustrine deposits, quick clays and loess), geohazards relating to the lithology and/or fabric of the deposit are discussed along with their properties. Other geohazards that do not relate to lithology and/or fabric are discussed separately as either local or regional geohazards. In some cases (e.g. glaciofluvial sands and gravels), the geotechnical properties and behaviour are similar to sediments deposited under different climatic conditions; these deposits are therefore not discussed at length. Similarly, some of the local geohazards that are found associated with glacial and periglacial deposits relate to current climatic conditions and are not discussed here. Examples include landsliding and highly compressible organic soils (peats).
Chapter 8 Design and construction considerations
Authors: Winter M. G. , Troughton V. , Bayliss R. , Golightly C. , Spasic-Gril L. , Hobbs P. R. N. , Privett K. D. 
Published: November 2017

Abstract
Relict glacial and periglacial environments are widespread, and the deposits that they are associated with mean it is inevitable that the design and construction of many projects will be influenced by their presence and nature. Tills and other glaciogenic deposits prove to be particularly challenging in this context for reasons that include: the spatial variability of the nature of the deposits; the wide range of particle sizes often included within a given soil, including large-sized particles; spatial variation in soil type and properties; variation in depth to rockhead and variable degrees of weathering and alteration; the presence of groundwater, that is misinterpreted as perched water, as well as sub-artesian and artesian conditions; the presence of solution features and fissures, partly or completely infilled with soft or loose material; and the presence of (often shallow) shear surfaces at residual strength. In this chapter, some of the more common problems and associated solutions associated with earthworks and man-made slopes, tunnels and underground structures, dams and reservoirs, foundations, and offshore engineering and installations are reviewed. It is important that great care is taken in addressing the influences of variability, complexity and uncertainty inherent in glacial/periglacial soil formations at all stages of the construction process, from feasibility to end-of-project activities, such as preparation of the as-built drawings.