bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibration of a Tapered Roller Bearing Excited by Localized Damage on a Rotating Cone Raceway
Authors: Li Desheng 
Published: November 2017

Localized damages such as spalls, dents and raised metal may develop on bearing raceways and roller bodies in operation for various reasons. They can excite bearings and adjacent mechanical structures into vibration. By measuring machine vibration, it is possible to detect potential bearing damage. However, to do so, it is critical to understand the bearing vibration characteristics that are excited by localized damages.
The vibration of a TRB (tapered roller bearing) excited by a localized damage on a rotating cone (inner ring) raceway was studied using a three-dimensional, non-linear vibration model. Bearing vibration responses were analyzed in three directions. The responses exhibited multiple BPFI (ball passing frequency, inner) harmonics. The spectral envelope is determined by the bearing’s dynamic properties. The vibration characteristics in the axial direction were discovered to be different from those in the radial directions. The reason behind that is revealed in this paper.
A Study of Rapid Tetrapod Running and Turning Dynamics Utilizing Inertial Measurement Units in Greyhound Sprinting
Authors: Hayati Hasti , Eager David , Jusufi Ardian , Brown Terry 
Published: November 2017

Understanding the biomechanics of rapid running locomotion plays an important role in comparative biomechanics and bio-inspired engineering and is an integral part of animal welfare.
However, this is not easily achieved using conventional methods of gait analysis: measuring ground reaction forces using a force plate, mainly on irregular granular terrain i.e. greyhounds in racing conditions or in animal’s natural habitats i.e. cheetahs in natural terrain. An alternative to measuring forces externally via force platforms embedded in track ways, we can attach inertial measurement units to agile quadrupeds to measure the effects of rapid running and turning.
Here we deployed an IMU equipped with a tri-axial accelerometer on sprinting greyhounds to analyze rapid locomotion behaviors like dynamic banking and turning in conditions equivalent to racing. High speed videography and paw print analysis of the entire race were used for calibration. The results are beneficial in locomotion analysis and welfare of greyhounds.
Theoretical and Experimental Study on Lip Seal Losses in Large High-Speed Rotors
Authors: Bhatia Narayan Jatinder , Missaglia Elia , Previati Giorgio , Mastinu Gianpiero , Ramakrishnan Kesavan , Gobbi Massimiliano 
Published: November 2017

This paper is devoted to the theoretical study of rubber-metal friction with particular reference to a lip seal for large high-speed rotor applications.
The paper, starting from previously published mathematical models related to friction estimations, presents a semi-analytical mathematical model to estimate friction loss induced by rubber lip seals. The sliding friction model is formulated on the basis of rubber and metal surface properties. Viscoelastic and hysteretic properties of the rubber are considered as function of temperature and excitation frequency. The metal surface profile is modelled as a superimposition of base ideal peak profiles.
Finally, the friction coefficient is modelled as a function of temperature, frequency and contact pressure. A preliminary validation of the model is achieved by comparing the estimated friction torque provided by the model with the friction torque measured on an actual rotor-stator system at different operating temperatures.
Evaluating Assembly Design Efficiency: A Comparison Between Lucas and Boothroyd-Dewhurst Methods
Authors: Dochibhatla Surya Venkata Sumanth , Bhattacharya Manas , Morkos Beshoy 
Published: November 2017

DFA principles are widely used to ease the assembly/manufacturing of a design in general. There are various methods which use the DFA principles to quantify design efficiency. The most commonly used industry approved methods are Lucas method and Boothroyd-Dewhurst method. Lucas and Boothroyd methods are both different approaches in DFA; the former is used to analyze product design without need for specific dimensions. On the other hand, to use the Boothroyd method, it is assumed that the designer already has all the dimensions of the part (parametric design). This paper focuses on answering the following research questions-
1. Are there any similarities between the Lucas method and Boothroyd-Dewhurst method?
2. Is there any similarity between the Efficiency index of Lucas method and Design efficiency of Boothroyd method?
3. Can the two methods be integrated and used as one method?
4. After integrating, can the method be coded as computer software?
The research questions will be validated by implementing the DFA methods on a stapler, table fan, and bottle opener. In this paper, the goal is to identify if Boothroyd and Lucas method can work together in product design phase; and if they could be used together, the authors propose a flowchart explaining the process. New DFA techniques are not being investigated/proposed. The Design efficiency of Stapler, Table fan, and Cork opener were 71.4%, 21.05%, and 50% respectively using Lucas method; The corresponding Feeding index was 2.12, 7.7, and 2.17 respectively, and Fitting index was 2.94, 11.25, and 6.93 respectively; And, 63%, 28.86% and 52.7% respectively using Boothroyd method. Design efficiency results indicate that Lucas method and Boothroyd-Dewhurst method are similar analysis and are equally important during the design phase. The above 2 methods can work in tandem with each other to provide insight into: “how many functional parts are there in a product?” and “how long it will take for it to assemble?”
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

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