bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Recursive Body-Body Formulation for Reducing the Computational Cost of Pairwise Coulomb Force Computation for Modeling and Simulation of Biopolymers, Using a Multibody Approach to Model Reduction
Authors: Laflin Jeremy , Anderson Kurt 
Published: February 2014

This work presents a method for recursively assembling tensor-like quantities that parameterize the charge distribution of rigid bodies, which result from model reduction of biopolymeric systems using an articulated multibody approach. This is done with the goal of reducing the computational cost associated with the pairwise force determination encountered in molecular dynamics simulations. To achieve a linear computational cost complexity of the force determination, with respect to the number of bodies in the system (N), a recursive assembly and disassembly (evaluation) sweep is proposed. This work proposes assembling these tensor quantities (pseudo-inertia tensors), which are associated with the body’s charge distribution, with a method that uses the standard parallel axis theorem to shift these tensors to a common point so they may be summed.
This work presents a preliminary numerical example that examines the accuracy of the force and moment computation using a pseudo-inertia tensor resulting after one level of recursive assembly. The Coulomb force and associated moment on a target body due to the assembled body is computed. The test problem approximates a system that is highly negatively or positively charged. The orientation of the bodies that are assembled is varied, along with the distance between the assembly and the target body. The preliminary results presented herein suggest that this is a viable method of efficiently representing the charge distribution of an assembly. The numerical example presented determines the Coulomb force and the associated moment, as a function of distance and the pseudo-inertia tensor. However, the approximation can be used for any force that is of the form 1/rs, where s is any power.
Ceramic Matrix Composite Materials by Design Using Robust Variable Fidelity Optimization
Authors: Khadke Kunal R. , An Weigang , Tovar Andrés 
Published: February 2014

Ceramic matrix composites (CMC) have been widely studied to tailor desired properties at high temperatures. However, research applications involving design tool development for multi-phase material design are at an early stage of development. While numerical CMC modeling provides significant insight on the material performance, the computational cost of the numerical simulations and the type of variables involved in these models are a hindrance for the effective application of design methods. This technical challenge heightens with the need of considering the uncertainty of material processing and service. For this reason, few design researchers have addressed the design paradox that accompanies the rapid design space expansion in CMC material design.
The objective of this research is to establish a tractable approach for CMC design considering uncertainty. Traditionally, surrogate models of statistical data are incorporated in the design strategy. An alternative to surrogate modeling is the use of lower fidelity models, which captures some of the physics of the problem and avoids the generation of uncertainty quantification. A variable fidelity optimization (VFO) management framework is incorporated in this research. In the proposed VFO method, a high-fidelity, cohesive, finely meshed finite-element model guides the coarsely meshed, low-fidelity model towards the optimal material design. Uncertainty in CMC material processing (multiphase nucleation and growth) is quantified using a stochastic material microstructural lattice model. The lattice model is verified with laboratory processed microstructures.
Dimension reduction for reduction of the number of random variables under consideration. Linear data transformation and principal component analysis (PCA) is traditionally used in dimension reduction. However, nonlinear dimension reduction techniques are better handle complex nonlinear data. This work incorporates Maximum Variance Unfolding (MVU) that preserves global properties of the original data in the low-dimensional representation.
The proposed methodology is applied to the optimal distribution of the matrix and the disperse phases in the composite structure. Results are demonstrated in the design of silicon carbide (SiC) fibers in a silicon-nitride (Si3N4) matrix for maximum fracture energy. The results provide a reference for SiC-Si3N4 nanocomposite.
A Novel Combinatorial Algorithm for Determining the Generic/Topological Mobility of Planar and Spherical Mechanisms
Authors: Shai Offer , Müller Andreas 
Published: February 2014

Structural mobility criteria, such as the well-known Chebychev-Kutzbach-Grübler (CKG) formula, give the correct generic mobility of a linkage (possibly of a certain class, e.g. planar, spherical, spatial) provided that it is not topologically overconstrained. As a matter of fact all known structural mobility criteria are prone to topological redundancies.
In this paper a combinatorial algorithm is introduced that determines the correct generic/topological mobility of any planar and spherical mechanism. The algorithm also yields a set of independent links that can be used as input, as well as the redundantly constrained sub-linkages. A mathematical proof of the algorithm and the underlying mathematical concept is presented. The proposed method relies on an established algorithm developed within combinatorial rigidity theory, called pebble game, originally developed for checking the rigidity/immobility of constraint graphs. A novel theorem is introduced and later proved in the paper which in turn enables applying the algorithm to any holonomic planar or spherical mechanism with higher and lower kinematic pairs and multiple joints. A further important result of applying this algorithm is that it gives rise to a decomposition into Assur graphs, which is briefly discussed in this paper.
Decision Making Tool in Life Cycle Assessment for Packaging Sustainability
Authors: Qi Huihui , Lee Euihark , Gea Hae Chang 
Published: February 2014

The Life Cycle Assessment (LCA) is a method to measure the environmental impact of a product’s life stages from the cradle to the grave, and is widely used for packaging sustainability. Although many successful applications using LCA have been reported, the current state of LCA tools still has many limitations. For example, it is difficult to select the best design among the LCA results of design sets. Moreover, the LCA tool cannot implement a decision maker’s preference into the process easily.
To overcome these limitations, we developed a decision making tool using LCA for packaging sustainability. First, Pareto Active Set Selection (PASS) method is proposed to find Pareto Front of packaging options. Additionally, Design Preference Function (DPF) is introduced to implement the designer’s preference for selecting the best packaging options. Case studies are presented to demonstrate this decision making tool.
Reconstructing Humans’ Hand Motion: Preliminary Results and Applications in the Design of Mechanical Fingers for Anthropomorphic Tasks
Authors: Ghosh Shramana , Moon Hyosang , Robson Nina P. 
Published: February 2014

This paper reports the development of a low-cost sensor-based glove device using commercially available components that can be used to obtain position, velocity and acceleration data for individual fingers of the hand. Optical tracking of the human hand and finger motion is a challenging task due to the large number of degrees of freedom (DOFs) packed in a relatively small space. We propose methods to simplify the hand motion capture by utilizing accelerometers and adopting a reduced marker protocol.
The preliminary results show that the use of relative position, velocity and acceleration homogeneous transformations enable us in getting improved finger motion data with respect to those obtained from a Vicon system. This data is directly related to contact and curvature constraints between the fingers and the grasped object. Once obtained from the glove, the higher derivative specifications are used in formulating the synthesis task for the design of robotic fingers.
The CasKR Two-Component System Is Required for the Growth of Mesophilic and Psychrotolerant Bacillus cereus Strains at Low Temperatures
Authors: Diomandé Sara Esther , Chamot Stéphanie , Antolinos Vera , Vasai Florian , Guinebretière Marie-Hélène , Bornard Isabelle , Nguyen-the Christophe , Broussolle Véronique , Brillard Julien 
Published: February 2014

ABSTRACT

The different strains of
Bacillus cereus
can grow at temperatures covering a very diverse range. Some
B. cereus
strains can grow in chilled food and consequently cause food poisoning. We have identified a new sensor/regulator mechanism involved in low-temperature
B. cereus
growth. Construction of a mutant of this two-component system enabled us to show that this system, called CasKR, is required for growth at the minimal temperature (
T
min
). CasKR was also involved in optimal cold growth above
T
min
and in cell survival below
T
min
. Microscopic observation showed that CasKR plays a key role in cell shape during cold growth. Introducing the
casKR
genes in a Δ
casKR
mutant restored its ability to grow at
T
min
. Although it was first identified in the ATCC 14579 model strain, this mechanism has been conserved in most strains of the
B. cereus
group. We show that the role of CasKR in cold growth is similar in other
B. cereus sensu lato
strains with different growth temperature ranges, including psychrotolerant strains.
Deciphering the Regulon of Streptomyces coelicolor AbrC3, a Positive Response Regulator of Antibiotic Production
Authors: Rico Sergio , Santamaría Ramón I. , Yepes Ana , Rodríguez Héctor , Laing Emma , Bucca Giselda , Smith Colin P. , Díaz Margarita 
Published: February 2014

ABSTRACT

The atypical two-component system (TCS) AbrC1/C2/C3 (encoded by
SCO4598
,
SCO4597
, and
SCO4596
), comprising two histidine kinases (HKs) and a response regulator (RR), is crucial for antibiotic production in
Streptomyces coelicolor
and for morphological differentiation under certain nutritional conditions. In this study, we demonstrate that deletion of the RR-encoding gene,
abrC3
(
SCO4596
), results in a dramatic decrease in actinorhodin (ACT) and undecylprodiginine (RED) production and delays morphological development. In contrast, the overexpression of
abrC3
in the parent strain leads to a 33% increase in ACT production in liquid medium. Transcriptomic analysis and chromatin immunoprecipitation with microarray technology (ChIP-chip) analysis of the Δ
abrC3
mutant and the parent strain revealed that AbrC3 directly controls ACT production by binding to the
actII-ORF4
promoter region; this was independently verified by
in vitro
DNA-binding assays. This binding is dependent on the sequence 5′-GAASGSGRMS-3′. In contrast, the regulation of RED production is not due to direct binding of AbrC3 to either the
redZ
or
redD
promoter region. This study also revealed other members of the AbrC3 regulon: AbrC3 is a positive autoregulator which also binds to the promoter regions of
SCO0736
,
bdtA
(
SCO3328
),
absR1
(
SCO6992
), and
SCO6809
. The direct targets share the 10-base consensus binding sequence and may be responsible for some of the phenotypes of the Δ
abrC3
mutant. The identification of the AbrC3 regulon as part of the complex regulatory network governing antibiotic production widens our knowledge regarding TCS involvement in control of antibiotic synthesis and may contribute to the rational design of new hyperproducer host strains through genetic manipulation of such systems.
Lactose-Inducible System for Metabolic Engineering of Clostridium ljungdahlii
Authors: Banerjee Areen , Leang Ching , Ueki Toshiyuki , Nevin Kelly P. , Lovley Derek R. 
Published: February 2014

ABSTRACT

The development of tools for genetic manipulation of
Clostridium ljungdahlii
has increased its attractiveness as a chassis for autotrophic production of organic commodities and biofuels from syngas and microbial electrosynthesis and established it as a model organism for the study of the basic physiology of acetogenesis. In an attempt to expand the genetic toolbox for
C. ljungdahlii
, the possibility of adapting a lactose-inducible system for gene expression, previously reported for
Clostridium perfringens
, was investigated. The plasmid pAH2, originally developed for
C. perfringens
with a
gusA
reporter gene, functioned as an effective lactose-inducible system in
C. ljungdahlii
. Lactose induction of
C. ljungdahlii
containing pB1, in which the gene for the aldehyde/alcohol dehydrogenase AdhE1 was downstream of the lactose-inducible promoter, increased expression of
adhE1
30-fold over the wild-type level, increasing ethanol production 1.5-fold, with a corresponding decrease in acetate production. Lactose-inducible expression of
adhE1
in a strain in which
adhE1
and the
adhE1
homolog
adhE2
had been deleted from the chromosome restored ethanol production to levels comparable to those in the wild-type strain. Inducing expression of
adhE2
similarly failed to restore ethanol production, suggesting that
adhE1
is the homolog responsible for ethanol production. Lactose-inducible expression of the four heterologous genes necessary to convert acetyl coenzyme A (acetyl-CoA) to acetone diverted ca. 60% of carbon flow to acetone production during growth on fructose, and 25% of carbon flow went to acetone when carbon monoxide was the electron donor. These studies demonstrate that the lactose-inducible system described here will be useful for redirecting carbon and electron flow for the biosynthesis of products more valuable than acetate. Furthermore, this tool should aid in optimizing microbial electrosynthesis and for basic studies on the physiology of acetogenesis.
Removal of Pharmaceuticals and Personal Care Products during Water Recycling: Microbial Community Structure and Effects of Substrate Concentration
Authors: Onesios-Barry Kathryn M. , Berry David , Proescher Jody B. , Sivakumar I. K. Ashok , Bouwer Edward J. 
Published: February 2014

ABSTRACT

Many pharmaceuticals and personal care products (PPCPs) have been shown to be biotransformed in water treatment systems. However, little research exists on the effect of initial PPCP concentration on PPCP biotransformation or on the microbial communities treating impacted water. In this study, biological PPCP removal at various concentrations was assessed using laboratory columns inoculated with wastewater treatment plant effluent. Pyrosequencing was used to examine microbial communities in the columns and in soil from a soil aquifer treatment (SAT; a method of water treatment prior to reuse) site. Laboratory columns were supplied with different concentrations (0.25, 10, 100, or 1,000 μg liter
−1
) of each of 15 PPCPs. Five PPCPs (4-isopropyl-3-methylphenol [biosol],
p
-chloro-
m
-xylenol, gemfibrozil, ketoprofen, and phenytoin) were not removed at any tested concentrations. Two PPCPs (naproxen and triclosan) exhibited removals independent of PPCP concentration. PPCP removal efficiencies were dependent on initial concentrations for biphenylol,
p
-chloro-
m
-cresol, chlorophene, diclofenac, 5-fluorouracil, ibuprofen, and valproic acid, showing that PPCP concentration can affect biotransformation. Biofilms from sand samples collected from the 0.25- and 10-μg liter
−1
PPCP columns were pyrosequenced along with SAT soil samples collected on three consecutive days of a wetting and drying cycle to enable comparison of these two communities exposed to PPCPs. SAT communities were similar to column communities in taxonomy and phylotype composition, and both were found to contain close relatives of known PPCP degraders. The efficiency of biological removal of PPCPs was found to be dependent on the concentration at which the contamination occurs for some, but not all, PPCPs.
Characterization of an Allylic/Benzyl Alcohol Dehydrogenase from Yokenella sp. Strain WZY002, an Organism Potentially Useful for the Synthesis of α,β-Unsaturated Alcohols from Allylic Aldehydes and Ketones
Authors: Ying Xiangxian , Wang Yifang , Xiong Bin , Wu Tingting , Xie Liping , Yu Meilan , Wang Zhao 
Published: February 2014

ABSTRACT

A novel whole-cell biocatalyst with high allylic alcohol-oxidizing activities was screened and identified as
Yokenella
sp. WZY002, which chemoselectively reduced the C=O bond of allylic aldehydes/ketones to the corresponding α,β-unsaturated alcohols at 30°C and pH 8.0. The strain also had the capacity of stereoselectively reducing aromatic ketones to (
S
)-enantioselective alcohols. The enzyme responsible for the predominant allylic/benzyl alcohol dehydrogenase activity was purified to homogeneity and designated YsADH (alcohol dehydrogenase from
Yokenella
sp.), which had a calculated subunit molecular mass of 36,411 Da. The gene encoding YsADH was subsequently expressed in
Escherichia coli
, and the purified recombinant YsADH protein was characterized. The enzyme strictly required NADP(H) as a coenzyme and was putatively zinc dependent. The optimal pH and temperature for crotonaldehyde reduction were pH 6.5 and 65°C, whereas those for crotyl alcohol oxidation were pH 8.0 and 55°C. The enzyme showed moderate thermostability, with a half-life of 6.2 h at 55°C. It was robust in the presence of organic solvents and retained 87.5% of the initial activity after 24 h of incubation with 20% (vol/vol) dimethyl sulfoxide. The enzyme preferentially catalyzed allylic/benzyl aldehydes as the substrate in the reduction of aldehydes/ketones and yielded the highest activity of 427 U mg
−1
for benzaldehyde reduction, while the alcohol oxidation reaction demonstrated the maximum activity of 79.9 U mg
−1
using crotyl alcohol as the substrate. Moreover, kinetic parameters of the enzyme showed lower

K
m

values and higher catalytic efficiency for crotonaldehyde/benzaldehyde and NADPH than for crotyl alcohol/benzyl alcohol and NADP
+
, suggesting the nature of being an aldehyde reductase.
Low-Molecular-Weight Metabolites Secreted by Paenibacillus larvae as Potential Virulence Factors of American Foulbrood
Authors: Schild Hedwig-Annabell , Fuchs Sebastian W. , Bode Helge B. , Grünewald Bernd 
Published: February 2014

ABSTRACT

The spore-forming bacterium
Paenibacillus larvae
causes a severe and highly infective bee disease, American foulbrood (AFB). Despite the large economic losses induced by AFB, the virulence factors produced by
P. larvae
are as yet unknown. To identify such virulence factors, we experimentally infected young, susceptible larvae of the honeybee,
Apis mellifera carnica
, with different
P. larvae
isolates. Honeybee larvae were reared
in vitro
in 24-well plates in the laboratory after isolation from the brood comb. We identified genotype-specific differences in the etiopathology of AFB between the tested isolates of
P. larvae
, which were revealed by differences in the median lethal times. Furthermore, we confirmed that extracts of
P. larvae
cultures contain low-molecular-weight compounds, which are toxic to honeybee larvae. Our data indicate that
P. larvae
secretes metabolites into the medium with a potent honeybee toxic activity pointing to a novel pathogenic factor(s) of
P. larvae
. Genome mining of
P. larvae
subsp.
larvae
BRL-230010 led to the identification of several biosynthesis gene clusters putatively involved in natural product biosynthesis, highlighting the potential of
P. larvae
to produce such compounds.
The Stringent Response Modulates 4-Hydroxy-2-Alkylquinoline Biosynthesis and Quorum-Sensing Hierarchy in Pseudomonas aeruginosa
Authors: Schafhauser James , Lepine Francois , McKay Geoffrey , Ahlgren Heather G. , Khakimova Malika , Nguyen Dao 
Published: February 2014

ABSTRACT

As a ubiquitous environmental organism and an important human pathogen,
Pseudomonas aeruginosa
readily adapts and responds to a wide range of conditions and habitats. The intricate regulatory networks that link quorum sensing and other global regulators allow
P. aeruginosa
to coordinate its gene expression and cell signaling in response to different growth conditions and stressors. Upon nutrient transitions and starvation, as well as other environmental stresses, the stringent response is activated, mediated by the signal (p)ppGpp.
P. aeruginosa
produces a family of molecules called HAQ (4-hydroxy-2-alkylquinolines), some of which exhibit antibacterial and quorum-sensing signaling functions and regulate virulence genes. In this study, we report that (p)ppGpp negatively regulates HAQ biosynthesis: in a (p)ppGpp-null (ΔSR) mutant, HHQ (4-hydroxyl-2-heptylquinoline) and PQS (3,4-dihydroxy-2-heptylquinoline) levels are increased due to upregulated
pqsA
and
pqsR
expression and reduced repression by the
rhl
system. We also found that (p)ppGpp is required for full expression of both
rhl
and
las
AHL (acyl-homoserine lactone) quorum-sensing systems, since the ΔSR mutant has reduced
rhlI
,
rhlR
,
lasI
, and
lasR
expression, butanoyl-homoserine lactone (C
4
-HSL) and 3-oxo-dodecanoyl-homoserine lactone (3-oxo-C
12
-HSL) levels, and rhamnolipid and elastase production. Furthermore, (p)ppGpp significantly modulates the AHL and PQS quorum-sensing hierarchy, as the
las
system no longer has a dominant effect on HAQ biosynthesis when the stringent response is inactivated.
Identification of an
O
-Acyltransferase Gene (
oacB
) That Mediates 3- and 4-O-Acetylation of Rhamnose III in Shigella flexneri O Antigens
Authors: Wang Jianping , Knirel Yuriy A. , Lan Ruiting , Senchenkova Sof'ya N. , Luo Xia , Perepelov Andrei V. , Wang Yiting , Shashkov Alexander S. , Xu Jianguo , Sun Qiangzheng 
Published: February 2014

ABSTRACT

O antigen (O polysaccharide) is an important and highly variable cell component present on the surface of cells which defines the serospecificity of Gram-negative bacteria. Most O antigens of
Shigella flexneri
, a cause of shigellosis, share a backbone composed of →2)-α-
l
-Rha
p
III
-(1→2)-α-
l
-Rha
p
II
-(1→3)-α-
l
-Rha
p
I
-(1→3)-β-
d
-Glc
p
NAc-(1→ repeats, which can be modified by adding various substituents, giving rise to 19 serotypes. The known modifications include glucosylation on various sugar residues, O-acetylation on Rha
I
, and phosphorylation with phosphoethanolamine on Rha
II
or/and Rha
III
. Recently, two new O-antigen modifications, namely, O-acetylation at position 3 or 4 of Rha
III
and position 6 of GlcNAc, have been identified in several
S. flexneri
serotypes. In this work, the genetic basis for the 3/4-O-acetylation on Rha
III
was elucidated. Bioinformatic analysis of the genome of
S. flexneri
serotype 2a strain Sf301, which carries 3/4-O-acetylation on Rha
III
, revealed an O-acyltransferase gene designated
oacB
. Genetic studies combined with O-antigen structure analysis demonstrated that this gene is responsible for the 3/4-O-acetylation in serotypes 1a, 1b, 2a, 5a, and Y but not serotype 6, which has a different O-antigen backbone structure. The
oacB
gene is carried by a transposon-like structure located in the
proA-adrA
region on the chromosome, which represents a novel mechanism of mobilization of O-antigen modification factors in
S. flexneri
. These findings enhance our knowledge of
S. flexneri
O-antigen modifications and shed light on the origin of new O-antigen variants.