bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding Designers Behavior in Parameter Design Activities
Authors: Alelyani Turki , Yang Ye , Grogan Paul T.
Published: November 2017

Successful design processes and tools are vital for the success of any design project, particularly when developing aerospace, automotive and other complex systems that can entail imposing design constraints to meet desired objectives. These constraints, coupled with a lack of uniform strategies to define, acquire and process the interaction between designers and tools, add new challenges to the design process. So appropriate processes and tools that allow problem designers to assist in framing and resolving complex design problems can extend the power of the individual working memory, according to previous research. This current research investigates the behavior of engineers working on a parameter design experiment. In the study, 30 subjects solved parameter design problems with both coupled and uncoupled variables. Results showed a relationship among designers’ actions and other features such as gender, recorded error, problem complexity, and performance. These findings can guide future research into engineering design and can inform ideas for better strategies for various aspects of parameter designing.
Developing and Comparing Alternative Design Optimization Formulations for a Vibration Absorber Example
Authors: Luan Siyao , Thurston Deborah L. , Arora Madhav , Allison James T.
Published: November 2017

In some cases, the level of effort required to formulate and solve an engineering design problem as a mathematical optimization problem is significant, and the potential improved design performance may not be worth the excessive effort. In this article we address the tradeoffs associated with formulation and modeling effort. Here we define three core elements (dimensions) of design formulations: design representation, comparison metrics, and predictive model. Each formulation dimension offers opportunities for the design engineer to balance the expected quality of the solution with the level of effort and time required to reach that solution. This paper demonstrates how using guidelines can be used to help create alternative formulations for the same underlying design problem, and then how the resulting solutions can be evaluated and compared. Using a vibration absorber design example, the guidelines are enumerated, explained, and used to compose six alternative optimization formulations, featuring different objective functions, decision variables, and constraints. The six alternative optimization formulations are subsequently solved, and their scores reflecting their complexity, computational time, and solution quality are quantified and compared. The results illustrate the unavoidable tradeoffs among these three attributes. The best formulation depends on the set of tradeoffs that are best in that situation.
Designing for Trust: Understanding the Role of Agent Gender and Location on User Perceptions of Trust in Home Automation
Authors: Damen Nicole B. , Toh Christine A.
Published: November 2017

The potential of smart home devices for improving the comfort, energy efficiency, and security of its residents has been noted by researchers and early adopters of these technologies. Despite these advantages and advances in home automation technology, their adoption has not been as widespread as anticipated by experts. Existing research has shown that the lack of trust in home devices is a significant deterrent to widespread adoption. There is little data on how this perceived trustworthiness of the system might be impacted by the location that the device operates in, and the perceived gender of the automated agent within the device. Therefore, this exploratory study addresses this knowledge gap by exploring the role of agent location (office / home) and gender of the agent’s voice (female / male) on perceptions of trustworthiness in a controlled laboratory setting with a simulated smart lock system. Preliminary results following quantitative and qualitative analysis of this pilot study show that users trust stereotype-congruent automated agents (male voice in office, female voice in home) more than stereotype-incongruent automated agents. These results shed light on users’ perceptions of trust with home automation devices, and provide directions for future research and development of trustworthy home automation devices.
Optimal Surrogate and Neural Network Modeling for Day-Ahead Forecasting of the Hourly Energy Consumption of University Buildings
Authors: Ghassemi Payam , Zhu Kaige , Chowdhury Souma
Published: November 2017

This paper presents the development and evaluation of Artificial Neural Networks (ANN) based models and optimally selected surrogate models to provide the day-ahead forecast of the hourly-averaged energy load of buildings, by relating it to eight weather parameters as well as the hour of the day. Although ANN and other surrogate models have been used to predict building energy loads in the past, there is a limited understanding of what type of model prescriptions impact their performance as well as how un-recorded impact factors (e.g., human behavior and building repair work) should be accounted for. Here, the recorded energy data of three university buildings, from 9/2013–12/2015, is cleaned and synchronized with the local weather data. The data is then classified into eight classes; weekends and weekdays of Fall/Winter/Spring/Summer semesters. Both Multi-Layer Perceptron (MLP) and Radial Basis Function (RBF) NNs are explored. Differing number of hidden layers and transfer function choices are also explored, leading to the choice of the hyperbolic-tangent-sigmoid transfer function and 60 hidden layers. Similarly, an automated surrogate modeling framework is used to select the best models from among a pool of Kriging, RBF, and SVR models. A baseline concept, that uses energy information from the previous day as an added input to the ANN, helps to account for otherwise unrecorded recent changes in the building behavior, leading to improvement in fidelity of up to 30%.
Agent-Based Modeling of Automobile Producer and Consumer Behavior to Support Design for Market Systems Analysis
Authors: Zadbood Amineh , Hoffenson Steven
Published: November 2017

Improving design for market systems analysis relies on understanding the motivations and interactions among producers and consumers. Producers should theoretically develop their strategies for designing new products based on consumer demand and the expected profits from their sales. In this study, an agent-based modeling approach is proposed to simulate consumer and producer behavior for use in market systems analysis, and it is demonstrated through a simplified automobile market. In the model, consumers make heterogeneous purchasing decisions based on product attributes, which provides the producers with insights into their preferences and how to improve upon these design attributes over time. Emergent behavior of the model shows that analyzing the behavior of consumers provides the opportunity for producers to compete which one another with different strategies to improve their designs by investing in technology improvements. This lays the foundation for future work that can model how different business and regulatory strategies, social structures, and policies influence consumer and producer behavior, which in turn influences economic, environmental, and social impacts.
Voice Recognition for STEM Education Using Robotics
Authors: Chen Shubo , Qian Binsen , Cheng Harry
Published: November 2017

In this paper, we provide a new voice recognition framework which allows K-12 students to write programs to solve problems using voice control. The framework contains the voice recognition module SPHINX which is based on an open source machine learning tool developed by Carnegie Mellon University and a wrapper function which is written in C/C++ interpreter Ch. The wrapper function allows students to interact the module in Ch. Along with Ch programming and robotic coursework, students will get the chance to learn the basic concept of machine learning and voice recognition technique. In order to bring students attention and interest in machine learning, various tasks have been designed for students to accomplish based on the framework. The framework is also flexible for them to explore other interesting projects.
Economic Driving Strategy for Commercial Vehicles in Mountainous Areas
Authors: Ping Xianyao , Tan Gangfeng , Liu Jialiang , Lu Zilin , Pang Yuxin , Wu Yahui , Zhou Renjie , Wang Chenyu , Zuo Lei
Published: November 2017

Steep and long slope is an obvious characteristic of mountainous highways. Unreasonable acceleration or deceleration of the vehicles on the slopes will increase the fuel consumption. Improving the performance of the engine or the transmission system has limited energy saving potential, and most fuel-efficient driving assistant systems don’t consider the road conditions. The main purpose of this paper is to introduce an economic driving strategy to optimize vehicle speed profile for commercial vehicles traveling in mountainous areas with consideration of future road conditions. Economic driving strategy based on the energy conservation principle can adapt to various vehicles due to its less dependence on the engine fuel consumption characteristics. The engine brake performance measurement based on the vehicle longitudinal dynamics is achieved by analyzing the vehicle state information during transportation, which reduces the test times in the laboratory or the proving ground. Economic driving strategy will plan optimal speed profiles for commercial vehicles with consideration of future road conditions before the vehicles reach the slopes. Economic driving strategy guides the drivers to adjust vehicle speed reasonably, distribute effectively braking distance of the engine brake and the friction brakes on the slopes. The engine output energy and the brake energy loss can be reduced for improving the vehicle energy utilization rate when the drivers follow economic driving guidance. Semi-physical simulations were carried out to validate the effectiveness of economic driving strategy. The simulation results showed that economic driving strategy could increases the fuel economy by 3.4% to 5.5% averagely compared with the drives without economic guidance. The transportation cost and the abrasions of the friction brakes will be effectively reduced when economic driving strategy is applied to advanced driving assistance systems.
Design Innovation: A Study of Integrated Practice
Authors: Camburn Bradley A. , Auernhammer Jan M. , Sng Karen Hui En , Mignone Paul J. , Arlitt Ryan M. , Perez K. Blake , Huang Zack , Basnet Subarna , Blessing Lucienne T. , Wood Kristin L.
Published: November 2017

Design is a ubiquitous human activity. Design is valued by individuals, teams, organizations, and cultures. There are patterns and recurrent phenomena across the diverse set of approaches to design and also variances. Designers can benefit from leveraging conceptual tools like process models, methods, and design principles to amplify design phenomena. There are many variant process models, methods, and principles for design. Likewise, usage of these conceptual tools differentiates in industrial contexts. We present an integrated process model, with exemplar methods and design principles that is synthesized from a review of several case studies in client based industrial design projects for product, service, and system development, professional education courses, and literature review. Concepts from several branches of design practice: (1) design thinking, (2) business design, (3) systems engineering, and (4) design engineering are integrated. A design process model, method set, and set of abstracted design principles are porposed.
Optimization of Hypoid Gear Design and Tooth Contact Analysis
Authors: Sun Shouli , Wang Shilong , Wang Yawen , Lim Teik C. , Zhou Baocang , Hu Zongyan
Published: November 2017

Hypoid gears are effectively used in cross axis power transmission systems. Design of hypoid gear parameters is complex and dependent on designers’ experiences. In this paper, an easy approach to design the parameters of hypoid gear to obtain the minimum of maximum principle normal contact stress and peak to peak transmission error is presented. An improved Particle Swarm Optimization (PSO) and Back Propagation (BP) algorithm is proposed to predict the stress and the transmission error if certain design parameters are given. The predictive accuracy is evaluated by Root Mean Square Error (RMSE) equation. The results show that the predictive accuracy is in reasonable agreement with the values calculated by the software [1]. Based on the prediction model, the optimization model for the design parameters of hypoid gear is established. This paper proposes a method to design a set of hypoid gears with minimum of maximum principle normal stress and peak to peak transmission error.
Enhancing Economic and Environmental Sustainability Benefits Across the Design and Manufacturing of Medical Devices: A Case Study of Ankle Foot Orthosis
Authors: Mirkouei Amin , Silwal Bishal , Ramiscal Lawrence
Published: November 2017

Government and societal interests in additive manufacturing have increased scrutiny on process analysis, cross-cutting sustainability, and integrated decision-making methods to address commercialization and sustainability challenges. One of the key challenges is the absence of standardized metrics to assess design parameters and manufacturing practices. The primary objective of this research is to create a knowledge-based multi-criteria decision-making framework for enhancing sustainability across the design and fabrication of medical devices. The motivation behind this study lies in the inherent limitations of the existing methods. The proposed framework herein improves the traditional approaches by integrating extensive sharing of information and feedback among all design and manufacturing steps, and consequently coupling the economic and environmental sustainability dimensions. The framework includes sets of qualitative (e.g., data processing and design analysis) and quantitative (e.g., build time and energy use analyses) methods to assess transforming the raw material into optimal and sustainable final products. As an application of this study, optimal and sustainable approaches for the developing and competitive market of Orthotic and Prosthetic, particularly Ankle Foot Orthosis (AFO), is examined. Decision makers, such as managers and manufacturers, will benefit from the integrated methods in the proposed framework. The results indicate the framework offers a promising approach to address existing sustainability challenges in the AFO industry.
Nonlinear Dynamics of a Slender Axially Graded Beam Embedded in a Viscoelastic Medium
Authors: Babilio Enrico
Published: November 2017

In the present contribution the nonlinear dynamics of beams under axial time-dependent excitation is studied. The beams, which are embedded in a linear viscoelastic medium, are assumed as axially graded in terms of material properties. The transversal motion equation is derived under two main hypotheses, namely the beams satisfy the requirements of Euler-Bernoulli theory and undergo moderately large deflections.
Contribution to the knowledge of the oribatid mite genus Lamellarea (Acari, Oribatida, Lamellareidae)
Authors: Ermilov Sergey G. , Hugo-coetzee Elizabeth A. , Khaustov Alexander A.
Published: November 2017

A new species of the genus Lamellarea (Oribatida, Lamellareidae) is described from nests of the termite Trinervitermes trinervoides (Sjöstedt) in the Franklin Game Reserve (Bloemfontein, South Africa). Lamellarea koki sp. nov. differs from all species of the genus by the following main morphological traits: lamellar cusps triangular, without anteromedial processes, separated; translamella long; rostrum with median indentation; several ridges located near tutoria. A revised generic diagnosis, an identification key to known species, and data on the distribution and ecology of Lamellarea are presented.
Oxidation sharpening of silicon tips in the atmospheric environment
Authors: Dey Ripon Kumar , Shen Jiashi , Cui Bo
Published: November 2017

Sharp tips are essential for high-resolution atomic force microscopy (AFM) imaging and high-performance electron emitters in vacuum microelectronic devices. Thermal oxidation at high temperature followed by oxide removal is widely used in the nanofabrication of sharp silicon AFM/emitter tips. This method relies on the fact that oxide grows slower on areas with a smaller radius of curvature. Thermal oxidation is commonly carried out in a dedicated oxidation furnace that is costly, and the tips or wafer of tips must be cleaned thoroughly using Radio Corporation of America (RCA) cleaning. Here, the authors report that oxidation sharpening can also be attained using a very low-cost generic box furnace in the atmospheric environment that does not require the tips to go through an RCA cleaning process. As is apparent, such cleaning is not convenient for millimeter-scale AFM probes. The minimum tip apex radius of 2.5 nm was obtained by oxidation at 950 °C in the atmospheric environment. The obvious application of this approach is the regeneration of sharp tips out of worn out and thus blunt AFM probes at very low cost.
Optical and electrical characterizations of graphene nanoplatelet coatings on low density polyethylene
Authors: Palomba Mariano , Longo Angela , Carotenuto Gianfranco , Coscia Ubaldo , Ambrosone Giuseppina , Rusciano Giulia , Nenna Giuseppe , Barucca Gianni , Longobardo Luigi
Published: November 2017

Coatings of graphene nanoplatelets (GNPs) were deposited on a low density polyethylene (LDPE) substrate by a micromechanical method based on rubbing graphite platelets against the surface of the polymer. Transmission electron microscopy measurements reveal that the coatings were composed of nanoplatelets containing 13–30 graphene layers. Thermal gravimetric analysis shows that the investigated GNP coatings on LDPE (GNP/LDPE) samples are thermally stable up to 250 °C. Optical spectra of these samples, compared to those of pristine LDPE in the ultraviolet-visible-near-infrared range, indicate an increase in both reflectance and absorptance. On the other hand, the coating is able to markedly improve the surface conductivity of the polymeric substrate, indeed in the case of electrical contacts in the coplanar configuration (1 cm long and spaced 1 mm), the resistance of LDPE is 1015 Ω, while that of GNP/LDPE is 670 Ω. Electrical measurements under white light illumination point out a decrease in the conductance and a linear behavior of the photoconductance as a function of the optical power density. GNP/LDPE materials can be used for their optical, electrical, thermal, and flexibility properties in large area plastic electronics and optoelectronics.
Cloning and Expression of Novel Aminoglycoside Phosphotransferase Genes from Campylobacter and Their Role in the Resistance to Six Aminoglycosides
Authors: Zhao S. , Mukherjee S. , Li C. , Jones S. B. , Young S. , McDermott P. F.
Published: November 2017

Nine
aph
genes, including
aph(2″)-Ib
,
aph(2″)-Ic
,
aph(2″)-Ig
,
aph(2″)-If
,
aph(2″)-If1
,
aph(2″)-If3
,
aph(2″)-Ih
,
aac(6′)-Ie
–
aph(2″)-Ia
, and
aac(6′)-Ie
–
aph(2″)-If2
, were previously identified in
Campylobacter
. To measure the contribution of these alleles to aminoglycoside resistance, we cloned nine genes into the pBluescript and expressed them in
Escherichia coli
DH5α. The nine
aph
expressed in
E. coli
showed various levels of resistance to gentamicin, kanamycin, and tobramycin. Three genes,
aac(6″)-Ie
–
aph(2″)-Ia
,
aph2″-If1
, and
aph2″-Ig
, showed increased MICs to amikacin, and five
aph
genes were transferrable.
Zika Virus Replication Is Substantially Inhibited by Novel Favipiravir and Interferon Alpha Combination Regimens
Authors: Pires de Mello Camilly P. , Tao Xun , Kim Tae Hwan , Bulitta Jürgen B. , Rodriquez Jaime L. , Pomeroy Justin J. , Brown Ashley N.
Published: November 2017

Zika virus (ZIKV) is a major public health concern due to its overwhelming spread into the Americas. Currently, there are neither licensed vaccines nor antiviral therapies available for the treatment of ZIKV. We aimed to identify and rationally optimize effective therapeutic regimens for ZIKV by evaluating the antiviral potentials of the approved broad-spectrum antiviral agents favipiravir (FAV), interferon alpha (IFN), and ribavirin (RBV) as single agents and in combinations. For these studies, Vero cells were infected with ZIKV in the presence of increasing concentrations of FAV, IFN, or/and RBV for 4 days. Supernatants were harvested daily, and the viral burden was quantified by a plaque assay on Vero cells. The time course of the viral burden during treatment
in vitro
was characterized by a novel translational, mechanism-based model, which was subsequently used to rationally optimize combination dosage regimens. The combination regimen of FAV plus IFN provided the greatest extent of viral inhibition without cytotoxicity, reducing the viral burden by 4.4 log
10
PFU/ml at concentrations of 250 μM FAV and 100 IU/ml IFN. Importantly, these concentrations are achievable in humans. The translational, mechanism-based model yielded unbiased and reasonably precise curve fits. Simulations with the model predicted that clinically relevant regimens of FAV plus IFN would markedly reduce viral burdens in humans, resulting in at least a 10,000-fold reduction in the amount of the virus during the first 4 days of treatment. These findings highlight the substantial promise of rationally optimized combination dosage regimens of FAV plus IFN, which should be further investigated to combat ZIKV.
Heat-Stable Antifungal Factor (HSAF) Biosynthesis in Lysobacter enzymogenes Is Controlled by the Interplay of Two Transcription Factors and a Diffusible Molecule
Authors: Su Zhenhe , Han Sen , Fu Zheng Qing , Qian Guoliang , Liu Fengquan
Published: November 2017

Lysobacter enzymogenes
is a Gram-negative, environmentally ubiquitous bacterium that produces a secondary metabolite, called heat-stable antifungal factor (HSAF), as an antifungal factor against plant and animal fungal pathogens. 4-Hydroxybenzoic acid (4-HBA) is a newly identified diffusible factor that regulates HSAF synthesis via
L. enzymogenes
LysR (LysR
Le
), an LysR-type transcription factor (TF). Here, to identify additional TFs within the 4-HBA regulatory pathway that control HSAF production, we reanalyzed the LenB2-based transcriptomic data, in which LenB2 is the enzyme responsible for 4-HBA production. This survey led to identification of three TFs (Le4806, Le4969, and Le3904). Of them, LarR (Le4806), a member of the MarR family proteins, was identified as a new TF that participated in the 4-HBA-dependent regulation of HSAF production. Our data show the following: (i) that LarR is a downstream component of the 4-HBA regulatory pathway controlling the HSAF level, while LysR
Le
is the receptor of 4-HBA; (ii) that 4-HBA and LysR
Le
have opposite regulatory effects on
larR
transcription whereby
larR
transcript is negatively modulated by 4-HBA while LysR
Le
, in contrast, exerts positive transcriptional regulation by directly binding to the
larR
promoter without being affected by 4-HBA
in vitro
; (iii) that LarR, similar to LysR
Le
, can bind to the promoter of the HSAF biosynthetic gene operon, leading to positive regulation of HSAF production; and (iv) that LarR and LysR
Le
cannot interact and instead control HSAF biosynthesis independently. These results outline a previously uncharacterized mechanism by which biosynthesis of the antibiotic HSAF in
L. enzymogenes
is modulated by the interplay of 4-HBA, a diffusible molecule, and two different TFs.

IMPORTANCE
Bacteria use diverse chemical signaling molecules to regulate a wide range of physiological and cellular processes. 4-HBA is an “old” chemical molecule that is produced by diverse bacterial species, but its regulatory function and working mechanism remain largely unknown. We previously found that 4-HBA in
L. enzymogenes
could serve as a diffusible factor regulating HSAF synthesis via LysR
Le
. Here, we further identified LarR, an MarR family protein, as a second TF that participates in the 4-HBA-dependent regulation of HSAF biosynthesis. Our results dissected how LarR acts as a protein linker to connect 4-HBA and HSAF synthesis, whereby LarR also has cross talk with LysR
Le
. Thus, our findings not only provide fundamental insight regarding how a diffusible molecule (4-HBA) adopts two different types of TFs for coordinating HSAF biosynthesis but also show the use of applied microbiology to increase the yield of the antibiotic HSAF by modification of the 4-HBA regulatory pathway in
L. enzymogenes
.
Draft Genome Sequences of Escherichia coli O113:H21 Strains Recovered from a Major Produce Production Region in California
Authors: Quiñones Beatriz , Yambao Jaszemyn C. , Lee Bertram G.
Published: November 2017

Shiga toxin-producing
Escherichia coli
is a foodborne and waterborne pathogen and is responsible for outbreaks of human gastroenteritis. This report documents the draft genome sequences of seven O113:H21 strains recovered from livestock, wildlife, and soil samples recovered from a major agricultural region for leafy greens in California, USA.
Complete Genome Sequence of Delftia acidovorans RAY209, a Plant Growth-Promoting Rhizobacterium for Canola and Soybean
Authors: Perry Benjamin J. , Bergsveinson Jordyn , Tambalo Dinah D. , Yost Christopher K. , Khan Nurul H. , Whiting Mike
Published: November 2017

Herein, we report the genome sequence of
Delftia acidovorans
strain RAY209, a plant growth-promoting rhizobacterium that is used in commercial inoculants for canola and soybean. The genome of RAY209 has a consensus of 6,528,879 bp and an estimated 5,721 coding sequences.
Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Acinetobacter pittii Strain ABC Isolated from Noonmati Refinery, Assam, India
Authors: Singh Arvind Kumar , Chettri Bobby , Ghosh Arpita , Chikara Surendra K. , Tripathi Timir
Published: November 2017

We report here the 3.84-Mb draft genome sequence of hydrocarbon-degrading
Acinetobacter pittii
strain ABC isolated from oil-contaminated soil in Guwahati, India. The genome sequence contains 3,602 coding sequences and a G+C content of 38.83%. This is the first report of the genome sequence of an
Acinetobacter pittii
from an oil-contaminated environment.
Orientia tsutsugamushi Modulates Endoplasmic Reticulum-Associated Degradation To Benefit Its Growth
Authors: Rodino Kyle G. , VieBrock Lauren , Evans Sean M. , Ge Hong , Richards Allen L. , Carlyon Jason A.
Published: November 2017

Orientia tsutsugamushi
, an obligate intracellular bacterium that is auxotrophic for the aromatic amino acids and histidine, causes scrub typhus, a potentially deadly infection that threatens 1 billion people.
O. tsutsugamushi
growth is minimal during the first 24 to 48 h of infection but its growth becomes logarithmic thereafter. How the pathogen modulates cellular functions to support its growth is poorly understood. The unfolded protein response (UPR) is a cytoprotective pathway that relieves endoplasmic reticulum (ER) stress by promoting ER-associated degradation (ERAD) of misfolded proteins. Here, we show that
O. tsutsugamushi
invokes the UPR in the first 48 h and benefits from ER stress in an amino acid-dependent manner.
O. tsutsugamushi
also impedes ERAD during this time period. By 72 h, ER stress is alleviated and ERAD proceeds unhindered. Sustained inhibition of ERAD using RNA interference results in an
O. tsutsugamushi
growth defect at 72 h that can be rescued by amino acid supplementation. Thus,
O. tsutsugamushi
temporally stalls ERAD until ERAD-derived amino acids are needed to support its growth. The
O. tsutsugamushi
effector Ank4 is linked to this phenomenon. Ank4 interacts with Bat3, a eukaryotic chaperone that is essential for ERAD, and is transiently expressed by
O. tsutsugamushi
during the infection period when it inhibits ERAD. Ectopically expressed Ank4 blocks ERAD to phenocopy
O. tsutsugamushi
infection. Our data reveal a novel mechanism by which an obligate intracellular bacterial pathogen modulates ERAD to satisfy its nutritional virulence requirements.
Candidalysin Drives Epithelial Signaling, Neutrophil Recruitment, and Immunopathology at the Vaginal Mucosa
Authors: Richardson Jonathan P. , Willems Hubertine M. E. , Moyes David L. , Shoaie Saeed , Barker Katherine S. , Tan Shir Lynn , Palmer Glen E. , Hube Bernhard , Naglik Julian R. , Peters Brian M.
Published: November 2017

Unlike other forms of candidiasis, vulvovaginal candidiasis, caused primarily by the fungal pathogen
Candida albicans
, is a disease of immunocompetent and otherwise healthy women. Despite its prevalence, the fungal factors responsible for initiating symptomatic infection remain poorly understood. One of the hallmarks of vaginal candidiasis is the robust recruitment of neutrophils to the site of infection, which seemingly do not clear the fungus, but rather exacerbate disease symptomatology. Candidalysin, a newly discovered peptide toxin secreted by
C. albicans
hyphae during invasion, drives epithelial damage, immune activation, and phagocyte attraction. Therefore, we hypothesized that Candidalysin is crucial for vulvovaginal candidiasis immunopathology. Anti-
Candida
immune responses are anatomical-site specific, as effective gastrointestinal, oral, and vaginal immunities are uniquely compartmentalized. Thus, we aimed to identify the immunopathologic role of Candidalysin and downstream signaling events at the vaginal mucosa. Microarray analysis of
C. albicans
-infected human vaginal epithelium
in vitro
revealed signaling pathways involved in epithelial damage responses, barrier repair, and leukocyte activation. Moreover, treatment of A431 vaginal epithelial cells with Candidalysin induced dose-dependent proinflammatory cytokine responses (including interleukin 1α [IL-1α], IL-1β, and IL-8), damage, and activation of c-Fos and mitogen-activated protein kinase (MAPK) signaling, consistent with fungal challenge. Mice intravaginally challenged with
C. albicans
strains deficient in Candidalysin exhibited no differences in colonization compared to isogenic controls. However, significant decreases in neutrophil recruitment, damage, and proinflammatory cytokine expression were observed with these strains. Our findings demonstrate that Candidalysin is a key hypha-associated virulence determinant responsible for the immunopathogenesis of
C. albicans
vaginitis.
Genome-Wide Screens Reveal New Gene Products That Influence Genetic Competence in Streptococcus mutans
Authors: Shields Robert C. , O'Brien Greg , Maricic Natalie , Kesterson Alexandria , Grace Megan , Hagen Stephen J. , Burne Robert A.
Published: November 2017

A network of genes and at least two peptide signaling molecules tightly control when
Streptococcus mutans
becomes competent to take up DNA from its environment. Widespread changes in the expression of genes occur when
S. mutans
is presented with competence signal peptides
in vitro
, including the increased production of the alternative sigma factor, ComX, which activates late competence genes. Still, the way that gene products that are regulated by competence peptides influence DNA uptake and cellular physiology are not well understood. Here, we developed and employed comprehensive transposon mutagenesis of the
S. mutans
genome, with a screen to identify mutants that aberrantly expressed
comX
, coupled with transposon sequencing (Tn-seq) to gain a more thorough understanding of the factors modulating
comX
expression and progression to the competent state. The screens effectively identified genes known to affect competence, e.g.,
comR
,
comS
,
comD
,
comE
,
cipB
,
clpX
,
rcrR
, and
ciaH
, but disclosed an additional 20 genes that were not previously competence associated. The competence phenotypes of mutants were characterized, including by fluorescence microscopy to determine at which stage the mutants were impaired for
comX
activation. Among the novel genes studied were those implicated in cell division, the sensing of cell envelope stress, cell envelope biogenesis, and RNA stability. Our results provide a platform for determining the specific chemical and physical cues that are required for genetic competence in
S. mutans
, while highlighting the effectiveness of using Tn-seq in
S. mutans
to discover and study novel biological processes.

IMPORTANCE
Streptococcus mutans
acquires DNA from its environment by becoming genetically competent, a physiologic state triggered by cell-cell communication using secreted peptides. Competence is important for acquiring novel genetic traits and has a strong influence on the expression of virulence-associated traits of
S. mutans
. Here, we used transposon mutagenesis and genomic technologies to identify novel genes involved in competence development. In addition to identifying genes previously known to be required for
comX
expression, 20 additional genes were identified and characterized. The findings create opportunities to diminish the pathogenic potential of
S. mutans
, while validating technologies that can rapidly advance our understanding of the physiology, biology, and genetics of
S. mutans
and related pathogens.
Insights into Biofilm Dispersal Regulation from the Crystal Structure of the PAS-GGDEF-EAL Region of RbdA from Pseudomonas aeruginosa
Authors: Liu Chong , Liew Chong Wai , Wong Yee Hwa , Tan Siok Thing , Poh Wee Han , Manimekalai Malathy S. S. , Rajan Sreekanth , Xin Lingyi , Liang Zhao-Xun , Grüber Gerhard , Rice Scott A. , Lescar Julien
Published: November 2017

RbdA is a positive
r
egulator of
b
iofilm
d
ispersal of
Pseudomonas aeruginosa
. Its cytoplasmic region (cRbdA) comprises an N-terminal Per-ARNT-Sim (PAS) domain followed by a diguanylate cyclase (GGDEF) domain and an EAL domain, whose phosphodiesterase activity is allosterically stimulated by GTP binding to the GGDEF domain. We report crystal structures of cRbdA and of two binary complexes: one with GTP/Mg
2+
bound to the GGDEF active site and one with the EAL domain bound to the c-di-GMP substrate. These structures unveil a 2-fold symmetric dimer stabilized by a closely packed N-terminal PAS domain and a noncanonical EAL dimer. The autoinhibitory switch is formed by an α-helix (S-helix) immediately N-terminal to the GGDEF domain that interacts with the EAL dimerization helix (α
6-E
) of the other EAL monomer and maintains the protein in a locked conformation. We propose that local conformational changes in cRbdA upon GTP binding lead to a structure with the PAS domain and S-helix shifted away from the GGDEF-EAL domains, as suggested by small-angle X-ray scattering (SAXS) experiments. Domain reorientation should be facilitated by the presence of an α-helical lever (H-helix) that tethers the GGDEF and EAL regions, allowing the EAL domain to rearrange into an active dimeric conformation.

IMPORTANCE
Biofilm formation by bacterial pathogens increases resistance to antibiotics. RbdA positively regulates biofilm dispersal of
Pseudomonas aeruginosa
. The crystal structures of the cytoplasmic region of the RbdA protein presented here reveal that two evolutionarily conserved helices play an important role in regulating the activity of RbdA, with implications for other GGDEF-EAL dual domains that are abundant in the proteomes of several bacterial pathogens. Thus, this work may assist in the development of small molecules that promote bacterial biofilm dispersal.
Role of microRNA-146a in regulation of fibrosis in orbital fibroblasts from patients with Graves’ orbitopathy
Authors: Jang Sun Young , Park Seong Jun , Chae Min Kyung , Lee Joon H , Lee Eun Jig , Yoon Jin Sook
Published: November 2017

Aim

To examine the role of microRNA-146a (miR-146a) in the regulation of fibrosis in an in vitro model of Graves’ orbitopathy (GO).

Methods

Orbital fat/connective tissues were harvested from patients with GO and non-GO for primary orbital fibroblast cultures. The effects of transforming growth factor-β (TGF-β), a potent cytokine that promotes fibrosis, on miR-146a expression were analysed in GO and non-GO orbital fibroblasts using quantitative real-time PCR. The effects of overexpressed miR-146a on TGF-β-induced fibrotic markers were examined in GO orbital fibroblasts by western blot analysis. Expression ofSma and Mad related family (Smad) 4/tumour necrosis factor receptor-associated factor 6 (TRAF6) after transfection of miR-146a mimics or inhibitors were examined.

Results

TGF-β induced an increase in miR-146a expression in orbital fibroblasts from patients with GO in a time-dependent and concentration-dependent manner. miR-146a mimics further decreased the production of TGF-β-induced fibronectin, collagen Iα and α-smooth muscle actin protein. The Smad4 and TRAF6 protein levels were significantly decreased by miR-146a mimics, compared with control mimics, and significantly increased on inhibition of miR-146a production compared with a control.

Conclusions

miR-146a plays a role as a negative regulator in the production of TGF-β-induced fibrotic markers. Thus, miR-146a may be involved in the regulation of fibrosis in orbital fibroblasts from patients with GO.
Heart rate variability: exploring age, sex & concussion symptoms in youth athletes
Authors: Paniccia Melissa , Lee Verweel , Taha Tim , Keightley Michelle , Thomas Scott , Reed Nick
Published: November 2017

Objective

(1) Explore the influence of age, sex on heart rate variability (HRV) in youth athletes; (2) Examine the relationship between baseline/pre-injury concussion symptom domains (physical, cognitive, emotional, fatigue) and HRV

Design

Cross-sectional.

Setting

Pre-injury/baseline data was obtained from youth athletes across various sports in the Greater Toronto Area.

Participants

Youth athletes between 13–18 years of age (N=294), in which females and males were equally represented across age groups. Inclusion criteria: between 13–18 years old, English speaking. Exclusion criteria: developmental and neurological diagnoses.

Intervention

Independent variables of interest included demographic factors such as age and sex as well as concussion symptoms. Concussion symptoms were measured using the Post Concussion Symptom Inventory and were stratified by physical, cognitive, fatigue and emotional domains.

Outcome measures

Heart rate variability, collected over 24 hours was the main outcome of interest and included time (e.g. SDNN, RMSSD) and frequency domain measures (e.g. HF, Total Power). Variables were logarithmically transformed to increase robustness of linear regression models.

Main results

Statistical threshold set at p ≤ 0.05. Significant age effects revealed that older participants displayed higher HRV compared to younger athletes. Significant interaction effect between concussion symptoms and sex on HRV. Cognitive and fatigue symptoms in healthy youth athletes had significant effect on HRV.

Conclusions

This study highlights the potential value of a novel neurophysiological indicator used in conjunction with the self-report of symptoms for clinical management. Prospective longitudinal research is needed to further explore the multi-faceted contextual influences of a youth athlete’s environment.

Competing interests

None.
Evaluation of the HS-1000 acoustic neuromonitoring device in the diagnosis and assessment of sports-induced concussion
Authors: Sills Allen , Lee Timothy , Kwiatkowski Tricia , Swanson Thomas , Weinberg Guy
Published: November 2017

Objective

To evaluate the correlation between data collected from the HS-1000 multi-modality brain monitoring device and standard neurological, psychomotor, and neuropsychological diagnostics in the assessment of acute sports-induced concussion.

Design

Prospective, open-label, non-randomised study.

Setting

Collegiate athletes were recruited at the Vanderbilt Sports Concussion Centre, Nashville, TN.

Participants

Sixty-four subjects across concussed (n1=14) and healthy control (n2=50) arms were consented.

Interventions and assessment of risk factors

Eligible subjects suffering recent concussion and age/gender-matched healthy controls were enrolled into the study. Participants in both groups were monitored for at least 15min per recording with the HS-1000. Concussed subjects were recorded 4 times relative to time of concussion injury: acute/baseline, 48 hr, 1 wk, 1 mo. Healthy control subjects were recorded at 2 time points: baseline, 2 wk.

Outcome measures

Standard clinical diagnostics and demographic information were collected from all study participants. As per current clinical standards and their assigned group, concussed subjects received Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT), Modified Balance Assessment Scale (mBESS), and total clinical symptom index scores. MathWorks MATLAB™ (Matrix Laboratory) engineering software was used to interpret signals and calculate sensitivity-specificity as a function of predictive accuracy with clinically confirmed concussion status.

Main results

Post-processing of HS-1000 signals identified concussed athletes with a sensitivity-specificity of 86.1% and 91%, respectively.

Conclusions

The HS-1000 demonstrated strong predictive accuracy compared with clinical diagnosis. Improved statistical power through greater sampling sizes and the development of a real-time diagnostic algorithm suggests this technology holds promise in the assessment and diagnosis of sports-induced concussion.

Competing interests

None.
Transcranial doppler ultrasound measures of neurovascular coupling are maintained following acute sport-related concussion
Authors: Smirl Jonathan D , Wright Alexander D , Bouliane Kevin , Bryk Kelsey , Donkelaar Paul van
Published: November 2017

Objective

To determinethe extentto which an acute sport-related concussion disrupts elevations in cerebral blood velocity (CBV) in the posterior cerebral artery (PCA) during visual tasks.

Design

Prospective Cohort.

Setting

Laboratory.

Participants

136 male contact-sport athletes (19.1±1.4 years) recruited, subset of 14 participants (19±1.4 years) sustained concussions.

Intervention

Transcranial Doppler ultrasound was used to index CBV in the PCA during a series of visual tasks. Participants closed their eyes (20 seconds), and when prompted, opened their eyes and completed a visual task (40 seconds). Testing was completed prior to the start of their athletic season (T0), and again (if concussed) at 72-hours (T1), 2-weeks (T2), and 1-month (T3) post-injury. The raw traces from each trial were averaged to enhance the signal-to-noise ratio of the outcome measurements. Independent variable tested was time (4 points).

Outcome measures

Eyes-closed CBV (cm/s), peak elevation in CBV (cm/s), relative change in CBV (%) and total activation during the first 30 seconds of the task (indexed via area under the curve-AUC)

Main results

RM-ANOVA indicated there were no time effects forany of the outcome metrics: Eyes-closed CBV (p=0.473), peak CBV (p=0.541),% CBV elevation (p=0.603) and AUC (p=0.972).

Conclusions

These negative findings are important, as they indicate the PCA is able to maintain nutrient delivery required for visual challenges. Thus, neurovascular coupling is maintained despite the reported impairments in indices of cerebral autoregulation in the same population.

Competing interests

None.
Utilisation of brain network activation in the concussed athlete a case series
Authors: Danan Ilan J , Williams Vernon B , Mandelbaum Bert R
Published: November 2017

Objective

While the approach to concussion and post-concussion syndrome management remains largely clinical, significant advancements have been made in identifying potential biomarkers to aid in the diagnosis and management of head injures. One such potential biomarker is Brain Network Activation (BNA) analysis. BNA is a multi-channel, EEG-ERP based platform that involves algorithmic analysis to provide a network map of cortical activity and quantitative data during specific tasks.

Design

Case Series.

Setting

Outpatient, clinic-based.

Participants

Three (3) athletes.

Outcome measures

Analysis of the subject’s BNA performance yieldsa BNA score,which reflects the degree of similarity between the performance of the subject and the normative data. BNA scores are further placed into one of three subcategories: Working Memory and Attention (Target Stimuli), Automatic Attention Orienting (Novel Stimuli), and Sensory (Frequent Stimuli). Each subject underwent a BNA analysis while symptomatic, followed by repeat analyses once subjects were identified as clinically asymptomatic.

Main results

In each of the three studies, there were improvements in BNA scores identified in one, or several, subcategories. More importantly, improvements in BNA scores directly correlated with clinical improvement in the post-concussive setting.

Conclusions

Approach to concussion management, in both the short-term and long-term setting, remains largely clinical. Current research seeks a more objective means of assessing not only potential structural abnormalities following a concussion, but also an improved means of assessing a patient’s neurocognitive status. BNA has proven to be an effective, supportive tool in allowing clinicians and patients to objectify one’s progress following a concussive injury.

Competing interests

None.
Clinical characteristics, referral patterns and time to recovery in youth and adults following a sport-related concussion (src)
Authors: MacGregor Katie , Atkins Christine , Blake Tracy , Ziel Micah , Schneider Kathryn
Published: November 2017

Objective

To describe the clinical characteristics, referral patterns and time to recovery in an acute sport-related concussion (SRC) clinic population.

Design

Prospective Case Series

Setting

Acute Sport Concussion Clinic (ASCC)

Participants

Patients aged 13-60 years seen within 4 weeks of SRC at the ASCC from September 2015–April 2016.

Outcome measures

Frequency, proportions, medians and interquartile ranges (IQR) were used to describe sex, age group, time from injury to assessment, referral sources, time to recovery (days), referrals to additional services, and attrition.

Results

ASCC assessments were requested by 111 patients a median of 9 days (IQR:4-17) post-concussion [33% female; 60 children [median age 15 years (IQR:14-16)], 51 adults [median age 31 years (IQR:21-42)]; attrition rate=10%]. Referral sources included: self-referral [n=94 (85%)], emergency department [n=9 (8%)], primary care physician [n=7 (5%)], and athletic therapist (n=1). Initial assessment occurred a median of 7 days (IQR:2-9) following the evaluation request. Patients underwent a standardised assessment including symptom scores, neurological, cervical spine and vestibulo-ocular screening a median of 17 days (IQR:9-25) post-concussion. There were 94 (85%) patients with clinical findings of cervical spine and/or vestibulo-ocular dysfunction. Treatment was received by 71/94 (76%) of patients with observed dysfunction. Medical clearance to return to play occurred a median of 30 days (IQR:21-107) post-concussion (n=51) .

Conclusions

A novel direct-access clinic specific to SRC assists in early triage, leading to expedited assessment, management and treatment in the early post-concussion period. Focused assessment assists in management and recovery with accelerated referral to appropriate services.

Competing interests

None.